U.S. patent application number 15/164828 was filed with the patent office on 2017-05-18 for bacteria engineered to treat diseases associated with hyperammonemia.
This patent application is currently assigned to Synlogic, Inc.. The applicant listed for this patent is Synlogic, Inc.. Invention is credited to Dean Falb, Vincent M. Isabella, Jonathan W. Kotula, Suman Machinani, Paul F. Miller.
Application Number | 20170137789 15/164828 |
Document ID | / |
Family ID | 57276642 |
Filed Date | 2017-05-18 |
United States Patent
Application |
20170137789 |
Kind Code |
A9 |
Falb; Dean ; et al. |
May 18, 2017 |
Bacteria Engineered to Treat Diseases Associated with
Hyperammonemia
Abstract
Genetically engineered bacteria, pharmaceutical compositions
thereof, and methods of modulating and treating disorders
associated with hyperammonemia are disclosed.
Inventors: |
Falb; Dean; (Sherborn,
MA) ; Isabella; Vincent M.; (Cambridge, MA) ;
Kotula; Jonathan W.; (Somerville, MA) ; Miller; Paul
F.; (Salem, CT) ; Machinani; Suman;
(Cambridge, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Synlogic, Inc. |
Cambridge |
MA |
US |
|
|
Assignee: |
Synlogic, Inc.
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20160333326 A1 |
November 17, 2016 |
|
|
Family ID: |
57276642 |
Appl. No.: |
15/164828 |
Filed: |
May 25, 2016 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
PCT/US2016/020530 |
Mar 2, 2016 |
|
|
|
15164828 |
|
|
|
|
14960333 |
Dec 4, 2015 |
9487764 |
|
|
PCT/US2016/020530 |
|
|
|
|
62291468 |
Feb 4, 2016 |
|
|
|
62256048 |
Nov 16, 2015 |
|
|
|
62248805 |
Oct 30, 2015 |
|
|
|
62184770 |
Jun 25, 2015 |
|
|
|
62263329 |
Dec 4, 2015 |
|
|
|
62256039 |
Nov 16, 2015 |
|
|
|
62256041 |
Nov 16, 2015 |
|
|
|
62184811 |
Jun 25, 2015 |
|
|
|
62183935 |
Jun 24, 2015 |
|
|
|
62173706 |
Jun 10, 2015 |
|
|
|
62173710 |
Jun 10, 2015 |
|
|
|
62150508 |
Apr 21, 2015 |
|
|
|
62103513 |
Jan 14, 2015 |
|
|
|
62087854 |
Dec 5, 2014 |
|
|
|
62293749 |
Feb 10, 2016 |
|
|
|
62277654 |
Jan 12, 2016 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 14/245 20130101;
C12N 9/1029 20130101; Y02A 50/473 20180101; C12N 15/52 20130101;
A61K 35/741 20130101; C12Y 203/01001 20130101; A61K 35/74 20130101;
C12R 1/19 20130101; C12P 7/52 20130101; C12N 15/70 20130101 |
International
Class: |
C12N 9/10 20060101
C12N009/10; A61K 35/74 20060101 A61K035/74 |
Claims
1. A bacterium comprising a gene sequence encoding an arginine
feedback resistant N-acetylglutamate synthetase (ArgA.sup.fbr),
wherein the ArgA.sup.fbr has reduced arginine feedback inhibition
as compared to a wild-type N-acetylglutamate synthetase from the
same bacterial subtype under the same conditions, wherein the gene
sequence encoding the ArgA.sup.fbr is present in the bacterial
chromosome and is operably linked in the chromosome to a promoter
that is induced under low-oxygen or anaerobic conditions; wherein
the bacterium has been modified to lack a functional ArgR; and
wherein the bacterium is an auxotroph in a gene that is
complemented when the bacterium is present in a mammalian gut.
2. The bacterium of claim 1, wherein the bacterium is a thyA
auxotroph.
3. The bacterium of claim 1, wherein the bacterium comprises an
antibiotic resistance gene.
4. The bacterium of claim 3, wherein the antibiotic resistance gene
is selected from a kanamycin resistance gene, a chloramphenicol
resistance gene, and a rifaximin resistance gene.
5. The bacterium of claim 2, wherein the bacterium comprises an
antibiotic resistance gene.
6. The bacterium of claim 1, wherein the bacterium contains a DNA
sequence having at least 90% homology to SEQ ID NO: 38.
7. The bacterium of claim 6, wherein the bacterium contains a DNA
sequence comprising SEQ ID NO: 38.
8. The bacterium of claim 3, wherein the bacterium contains a DNA
sequence having at least 90% homology to SEQ ID NO: 37.
9. The bacterium of claim 8, wherein the bacterium contains a DNA
sequence comprising SEQ ID NO: 37.
10.-12. (canceled)
13. The bacterium of claim 1, wherein the promoter that is induced
under low-oxygen or anaerobic conditions is an FNR promoter
selected from nirB1, nirB2, nirB3, ydfZ, fnrS1, and fnrS2.
14. The bacterium of claim 13, wherein the FNR promoter is
fnrS1.
15. (canceled)
16. The bacterium of claim 15, wherein the fnrS1 promoter comprises
SEQ ID NO: 113.
17. The bacterium of claim 1, wherein the arginine feedback
resistant N-acetylglutamate synthetase gene has a DNA sequence
selected from: a) SEQ ID NO: 30, b) a DNA sequence that, but for
the redundancy of the genetic code, encodes the same polypeptide as
encoded by SEQ ID NO: 30, c) a DNA sequence that encodes the
polypeptide of SEQ ID NO: 31, and d) a DNA sequence that encodes a
polypeptide having 95% homology with the polypeptide of SEQ ID NO:
31.
18. The bacterium of claim 1, wherein the bacterium is selected
from the group consisting of Bacteroides, Bifidobacterium,
Clostridium, Escherichia, Lactobacillus, and Lactococcus.
19. The bacterium of claim 1, wherein the bacterium is Escherichia
coli strain Nissle.
20. A pharmaceutical composition comprising the bacterium of claim
1 and a pharmaceutically acceptable carrier.
21. The pharmaceutical composition of claim 20, wherein the
pharmaceutical composition is formulated for oral
administration.
22. The bacterium of claim 1, wherein the bacterium comprises gene
sequence encoding a biosynthetic pathway for producing
butyrate.
23. The bacterium of claim 22, wherein the gene sequence encoding
the biosynthetic pathway is operably linked to a promoter that is
induced under low-oxygen or anaerobic conditions.
24. The bacterium of claim 23, wherein the promoter that is
operably linked to the gene sequence encoding ArgA.sup.fbr and the
promoter that is operably linked to the gene sequence encoding the
biosynthetic pathway is an FNR promoter.
Description
BACKGROUND
[0001] This application is a continuation-in-part of U.S.
application Ser. No. 14/960,333, filed Dec. 4, 2015; a
continuation-in-part of PCT Application No. PCT/US2016/020530,
filed Mar. 2, 2016; and claims the benefit of U.S. Provisional
Application No. 62/173,710, filed Jun. 10, 2015; U.S. Provisional
Application No. 62/173,706, filed Jun. 10, 2015; U.S. Provisional
Application No. 62/183,935, filed Jun. 24, 2015; U.S. Provisional
Application No. 62/184,811, filed Jun. 25, 2015; U.S. Provisional
Application No. 62/184,770, filed Jun. 25, 2015; U.S. Provisional
Application No. 62/248,805, filed Oct. 30, 2015; U.S. Provisional
Application No. 62/256,041, filed Nov. 16, 2015; U.S. Provisional
Application No. 62/256,039, filed Nov. 16, 2015; U.S. Provisional
Application No. 62/256,048, filed Nov. 16, 2015; U.S. Provisional
Application No. 62/263,329, filed Dec. 4, 2015; U.S. Provisional
Application No. 62/291,468, filed Feb. 4, 2016; U.S. Provisional
Application No. 62/277,654, filed Jan. 12, 2016; U.S. Provisional
Application No. 62/150,508, filed Apr. 21, 2015; U.S. Provisional
Application No. 62/103,513, filed Jan. 14, 2015; U.S. Provisional
Application No. 62/087,854, filed Dec. 5, 2014; and U.S.
Provisional Application No. 62/293,749, filed Feb. 10, 2016; which
are incorporated herein by reference in their entirety to provide
continuity of disclosure.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Jun. 23, 2016, is named 12671_0006-01000_SL.txt and is 252,583
bytes in size.
[0003] Ammonia is highly toxic and generated during metabolism in
all organs (Walker, 2012). In mammals, the healthy liver protects
the body from ammonia by converting ammonia to non-toxic molecules,
e.g., urea or glutamine, and preventing excess amounts of ammonia
from entering the systemic circulation. Hyperammonemia is
characterized by the decreased detoxification and/or increased
production of ammonia. In mammals, the urea cycle detoxifies
ammonia by enzymatically converting ammonia into urea, which is
then removed in the urine. Decreased ammonia detoxification may be
caused by urea cycle disorders (UCDs) in which urea cycle enzymes
are defective, such as argininosuccinic aciduria, arginase
deficiency, carbamoylphosphate synthetase deficiency,
citrullinemia, N-acetylglutamate synthetase deficiency, and
ornithine transcarbamylase deficiency (Haberle et al., 2012). The
National Urea Cycle Disorders Foundation estimates that the
prevalence of UCDs is 1 in 8,500 births. In addition, several
non-UCD disorders, such as hepatic encephalopathy, portosystemic
shunting, and organic acid disorders, can also cause
hyperammonemia. Hyperammonemia can produce neurological
manifestations, e.g., seizures, ataxia, stroke-like lesions, coma,
psychosis, vision loss, acute encephalopathy, cerebral edema, as
well as vomiting, respiratory alkalosis, hypothermia, or death
(Haberle et al., 2012; Haberle et al., 2013).
[0004] Ammonia is also a source of nitrogen for amino acids, which
are synthesized by various biosynthesis pathways. For example,
arginine biosynthesis converts glutamate, which comprises one
nitrogen atom, to arginine, which comprises four nitrogen atoms.
Intermediate metabolites formed in the arginine biosynthesis
pathway, such as citrulline, also incorporate nitrogen. Thus,
enhancement of arginine biosynthesis may be used to incorporate
excess nitrogen in the body into non-toxic molecules in order to
modulate or treat conditions associated with hyperammonemia.
Likewise, histidine biosynthesis, methionine biosynthesis, lysine
biosynthesis, asparagine biosynthesis, glutamine biosynthesis, and
tryptophan biosynthesis are also capable of incorporating excess
nitrogen, and enhancement of those pathways may be used to modulate
or treat conditions associated with hyperammonemia.
[0005] Current therapies for hyperammonemia and UCDs aim to reduce
ammonia excess, but are widely regarded as suboptimal (Nagamani et
al., 2012; Hoffmann et al., 2013; Torres-Vega et al., 2014). Most
UCD patients require substantially modified diets consisting of
protein restriction. However, a low-protein diet must be carefully
monitored; when protein intake is too restrictive, the body breaks
down muscle and consequently produces ammonia. In addition, many
patients require supplementation with ammonia scavenging drugs,
such as sodium phenylbutyrate, sodium benzoate, and glycerol
phenylbutyrate, and one or more of these drugs must be administered
three to four times per day (Leonard, 2006; Diaz et al., 2013).
Side effects of these drugs include nausea, vomiting, irritability,
anorexia, and menstrual disturbance in females (Leonard, 2006). In
children, the delivery of food and medication may require a
gastrostomy tube surgically implanted in the stomach or a
nasogastric tube manually inserted through the nose into the
stomach. When these treatment options fail, a liver transplant may
be required (National Urea Cycle Disorders Foundation). Thus, there
is significant unmet need for effective, reliable, and/or long-term
treatment for disorders associated with hyperammonemia, including
urea cycle disorders.
[0006] The liver plays a central role in amino acid metabolism and
protein synthesis and breakdown, as well as in several
detoxification processes, notably those of end-products of
intestinal metabolism, like ammonia. Liver dysfunction, resulting
in hyperammonemia, may cause hepatic encephalopathy (HE), which
disorder encompasses a spectrum of potentially reversible
neuropsychiatric abnormalities observed in patients with liver
dysfunction (after exclusion of unrelated neurologic and/or
metabolic abnormalities). In HE, severe liver failure (e.g.,
cirrhosis) and/or portosystemic shunting of blood around the liver
permit elevated arterial levels of ammonia to permeate the
blood-brain barrier (Williams, 2006), resulting in altered brain
function.
[0007] Ammonia accumulation in the brain leads to cognitive and
motor disturbances, reduced cerebral perfusion, as well as
oxidative stress-mediated injury to astrocytes, the brain cells
capable of metabolizing ammonia. There is evidence to suggest that
excess ammonia in the brain disrupts neurotransmission by altering
levels of the predominant inhibitory neurotransmitter,
.gamma.-aminobutyric acid (GABA) (Ahboucha and Butterworth, 2004).
Elevated cerebral manganese concentrations and manganese deposition
have also been reported in the basal ganglia of cirrhosis patients,
and are suspected to contribute to the clinical presentation of HE
(Cash et al., 2010; Rivera-Mancia et al., 2012). General
neurological manifestations of hyperammonemia include seizures,
ataxia, stroke-like lesions, Parkinsonian symptoms (such as
tremors), coma, psychosis, vision loss, acute encephalopathy,
cerebral edema, as well as vomiting, respiratory alkalosis,
hypothermia, or death (Haberle et al., 2012; Haberle et al.,
2013).
[0008] Ammonia dysmetabolism cannot solely explain all the
neurological changes that are seen in patients with HE. Sepsis is a
well-known precipitating factor for HE. The systemic inflammatory
response syndrome (SIRS) results from the release and circulation
of proinflammatory cytokines and mediators. In patients with
cirrhosis, SIRS may exacerbate the symptoms of HE, both in patients
with minimal and overt HE in a process likely mediated by tumor
necrosis factor (TNF) and interleukin-6 (IL6). Notably, enhanced
production of reactive nitrogen species (RNS) and reactive oxygen
species (ROS) occurs in cultured astrocytes that are exposed to
ammonia, inflammatory cytokines, hyponatremia or
benzodiazepines.
[0009] Hyperammonemia is also a prominent feature of Huntington's
disease, an autosomal dominant disorder characterized by
intranuclear/cytoplasmic aggregates and cell death in the brain
(Chen et al., 2015; Chiang et al., 2007). In fact, hyperammonemia
is a feature of several other disorders, as discussed herein, all
of which can be treated by reducing the levels of ammonia.
[0010] Current therapies for hepatic encephalopathy, Huntington's
disease, and other diseases and disorders associated with excess
ammonia levels, are insufficient (Cash et al., 2010; Cordoba and
Minguez, 2008; Shannon and Fraint, 2015). In Huntington's disease,
the side effects of antipsychotic drugs (e.g., haloperidol,
risperidone, quetiapine) and drugs administered to suppress
involuntary movements (e.g., tetrabenazine, amantadine,
levetiracetam, clonazepam) may worsen muscle rigidity and cognitive
decline in patients (Mayo Clinic). Antibiotics directed to
urease-producing bacteria were shown to have severe secondary
effects, such as nephrotoxicity, especially if administered for
long periods (Blanc et al., 1992; Berk and Chalmers, 1970). Protein
restriction is also no longer a mainstay therapy, as it can favor
protein degradation and poor nutritional status, and has been
associated with increased mortality (Kondrup and Muller, 1997;
Vaqero et al., 2003). Protein restriction is only appropriate for
one third of cirrhotic patients with HE (Nguyen and Morgan, 2014).
Thus, there is significant unmet need for effective, reliable,
and/or long-term treatment for hepatic encephalopathy and
Huntington's disease.
SUMMARY
[0011] The disclosure provides genetically engineered bacteria that
are capable of reducing excess ammonia and converting ammonia
and/or nitrogen into alternate byproducts. In certain embodiments,
the genetically engineered bacteria reduce excess ammonia and
convert ammonia and/or nitrogen into alternate byproducts. In
certain embodiments, the genetically engineered bacteria are
non-pathogenic and may be introduced into the gut in order to
reduce toxic ammonia. As much as 70% of excess ammonia in a
hyperammonemic patient accumulates in the gastrointestinal tract.
Another aspect of the invention provides methods for selecting or
targeting genetically engineered bacteria based on increased levels
of ammonia and/or nitrogen consumption, or production of a
non-toxic byproduct, e.g., arginine or citrulline. The invention
also provides pharmaceutical compositions comprising the
genetically engineered bacteria, and methods of modulating and
treating disorders associated with hyperammonemia, e.g., urea cycle
disorders and hepatic encephalopathy.
[0012] The disclosure also provides genetically engineered bacteria
that are capable of reducing excess ammonia and other deleterious
molecules, e.g., GABA, manganese. In certain embodiments, the
genetically engineered bacteria reduce excess ammonia and convert
ammonia and/or nitrogen into alternate byproducts. In certain
embodiments, the genetically engineered bacteria are non-pathogenic
and may be introduced into the gut in order to reduce toxic
ammonia. In certain embodiments, the genetically engineered
bacteria are capable of reducing excess ammonia and other
deleterious molecules, e.g., GABA, manganese, and are also capable
of producing one or more gut barrier enhancer molecules, e.g., one
or more short chain fatty acid(s), such as butyrate. Another aspect
of the disclosure provides methods for selecting or targeting
genetically engineered bacteria based on increased levels of
ammonia and/or nitrogen consumption, or production of a non-toxic
byproduct, e.g., arginine or citrulline. The invention also
provides pharmaceutical compositions comprising the genetically
engineered bacteria, and methods of modulating and treating
disorders associated with excess ammonia, including, for example,
hepatic encephalopathy and Huntington's disease.
[0013] In some embodiments, the genetically engineered bacteria
comprise one or more gene(s) or gene cassette(s) or circuit(s),
containing one or more native or non-native component(s), which
mediate one or more mechanisms of action. Additionally, one or more
endogenous genes or regulatory regions within the bacterial
chromosome may be mutated or deleted. The genetically engineered
bacteria harbor these genes or gene cassettes or circuits on a
plasmid or, alternatively, the genes/gene cassettes have been
inserted into the chromosome at certain regions, where they do not
interfere with essential gene expression.
[0014] These gene(s)/gene cassette(s) may be under the control of
constitutive or inducible promoters. Exemplary inducible promoters
described herein include oxygen level-dependent promoters (e.g.,
FNR-inducible promoter), promoters induced by HE-specific molecules
or metabolites indicative of liver damage (e.g., bilirubin),
promoters induced by inflammation or an inflammatory response (RNS,
ROS promoters), and promoters induced by a metabolite that may or
may not be naturally present (e.g., can be exogenously added) in
the gut, e.g., arabinose and tetracycline.
[0015] In addition, the engineered bacteria may further comprise
one or more of more of the following: (1) one or more auxotrophies,
such as any auxotrophies known in the art and provided herein,
e.g., thyA auxotrophy, (2) one or more kill switch circuits, such
as any of the kill-switches described herein or otherwise known in
the art, (3) one or more antibiotic resistance circuits, (4) one or
more transporters for importing biological molecules or substrates,
such any of the transporters described herein or otherwise known in
the art, (5) one or more secretion circuits, such as any of the
secretion circuits described herein and otherwise known in the art,
and (6) combinations of one or more of such additional
circuits.
BRIEF DESCRIPTION OF THE FIGURES
[0016] FIGS. 1A and 1B depict the state of the arginine regulon in
one embodiment of an ArgR deletion bacterium of the invention under
non-inducing (FIG. 1A) and inducing (FIG. 1B) conditions. FIG. 1A
depicts relatively low arginine production under aerobic conditions
due to arginine ("Arg" in oval) interacting with ArgA (squiggle )
to inhibit (indicated by "X") ArgA activity, while oxygen (O.sub.2)
prevents (indicated by "X") FNR (dotted boxed FNR) from dimerizing
and activating the FNR promoter (grey FNR box) and the argA.sup.fbr
gene under its control. FIG. 1B depicts up-regulated arginine
production under anaerobic conditions due to FNR dimerizing (two
dotted boxed FNRs) and inducing FNR promoter (grey FNR
box)-mediated expression of ArgA.sup.fbr (squiggle above
argA.sup.fbr), which is resistant to inhibition by arginine. This
overcomes (curved arrow) the inhibition of the wild-type ArgA
caused by arginine ("Arg" in oval) interacting with ArgA (squiggle
above box depicting argA). Each gene in the arginine regulon is
depicted by a rectangle containing the name of the gene. Each arrow
adjacent to one or a cluster of rectangles depict the promoter
responsible for driving transcription, in the direction of the
arrow, of such gene(s). Heavier lines adjacent one or a series of
rectangles depict ArgR binding sites, which are not utilized
because of the ArgR deletion in this bacterium. Arrows above each
rectangle depict the expression product of each gene.
[0017] FIGS. 2A and 2B depict an alternate exemplary embodiment of
the present invention. FIG. 2A depicts the embodiment under aerobic
conditions where, in the presence of oxygen, the FNR proteins (FNR
boxes) remain as monomers and are unable to bind to and activate
the FNR promoter ("FNR") which drives expression of the arginine
feedback resistant argA.sup.fbr gene. The wild-type ArgA protein is
functional, but is susceptible to negative feedback inhibition by
binding to arginine, thus keeping arginine levels at or below
normal. All of the arginine repressor (ArgR) binding sites in the
promoter regions of each arginine biosynthesis gene (argA, argE,
argC, argB, argH, argD, argI, argG, carA, and carB) have been
mutated (black bars; black "X") to reduce or eliminate binding to
ArgR. FIG. 2B depicts the same embodiment under anaerobic
conditions where, in the absence of oxygen the FNR protein (FNR
boxes) dimerizes and binds to and activates the FNR promoter
("FNR"). This drives expression of the arginine feedback resistant
argA.sup.fbr gene (black squiggle ()=argA.sup.fbr gene expression
product), which is resistant to feedback inhibition by arginine
("Arg" in ovals). All of the arginine repressor (ArgR) binding
sites in the promoter regions of each arginine biosynthetic gene
(argA, argE, argC, argB, argH, argD, argI, argG, carA, and carB)
have been mutated (black bars) to reduce or eliminate binding to
ArgR (black "X"), thus preventing inhibition by an arginine-ArgR
complex. This allows high level production of arginine.
[0018] FIG. 3 depicts another embodiment of the invention. In this
embodiment, a construct comprising an ArgR binding site (black bar)
in a promoter driving expression of the Tet repressor (TetR) from
the tetR gene is linked to a second promoter comprising a TetR
binding site (black bar between TetR and X) that drives expression
of gene X. Under low arginine concentrations, TetR is expressed and
inhibits the expression of gene X. At high arginine concentrations,
ArgR associates with arginine and binds to the ArgR binding site,
thereby inhibiting expression of TetR from the tetR gene. This, in
turn, removes the inhibition by TetR allowing gene X expression
(black squiggle ()).
[0019] FIG. 4 depicts another embodiment of the invention. In this
embodiment, a construct comprising an ArgR binding site (black bar)
in a promoter driving expression of the Tet repressor (TetR) from
the tetR gene is linked to a second promoter comprising a TetR
binding site (black bar bound to TetR oval) that drives expression
of green fluorescent protein ("GFP"). Under low arginine
concentrations, TetR is expressed and inhibits the expression of
GFP. At high arginine concentrations, ArgR associates with arginine
and binds to the ArgR binding site, thereby inhibiting expression
of TetR from the tetR gene. This, in turn, removes the inhibition
by TetR allowing GFP expression. By mutating a host containing this
construct, high arginine producers can be selected on the basis of
GFP expression using fluorescence-activated cell sorting
("FACS").
[0020] FIG. 5 depicts another embodiment of the invention. In this
embodiment, a construct comprising an ArgR binding site (black bar
bound by the ArgR-Arg complex) in a promoter driving expression of
the Tet repressor (not shown) from the tetR gene is linked to a
second promoter comprising a TetR binding site (black bar) that
drives expression of an auxotrophic protein necessary for host
survival ("AUX"). Under high arginine concentrations, the
ArgR-arginine complex binds to the ArgR binding site, thereby
inhibiting expression of TetR from the tetR gene. This, in turn,
allows expression of AUX, allowing the host to survive. Under low
arginine concentrations, TetR is expressed from the tetR gene and
inhibits the expression of AUX, thus killing the host. The
construct in FIG. 5 enforces high arginine ("Arg") production by
making it necessary for host cell survival through its control of
AUX expression.
[0021] FIG. 6 depicts a schematic diagram of the argA.sup.fbr gene
under the control of an exemplary FNR promoter (fnrS) fused to a
strong ribosome binding site.
[0022] FIG. 7 depicts another schematic diagram of the argA.sup.fbr
gene under the control of an exemplary FNR promoter (nirB) fused to
a strong ribosome binding site. Other regulatory elements may also
be present.
[0023] FIG. 8 depicts a schematic diagram of the argA.sup.fbr gene
under the control of an exemplary FNR promoter (nirB) fused to a
weak ribosome binding site.
[0024] FIGS. 9A and 9B depict exemplary embodiments of a
FNR-responsive promoter fused to a CRP binding site. FIG. 9A
depicts a map of the FNR-CRP promoter region, with restriction
sites shown in bold. FIG. 9B depicts a schematic diagram of the
argA.sup.fbr gene under the control of an exemplary FNR promoter
(nirB promoter), fused to both a CRP binding site and a ribosome
binding site. Other regulatory elements may also be present.
[0025] FIGS. 10A and 10B depict alternate exemplary embodiments of
a FNR-responsive promoter fused to a CRP binding site. FIG. 10A
depicts a map of the FNR-CRP promoter region, with restriction
shown in bold. FIG. 10B depicts a schematic diagram of the
argA.sup.fbr gene under the control of an exemplary FNR promoter
(fnrS promoter), fused to both a CRP binding site and a ribosome
binding site.
[0026] FIG. 11 depicts an exemplary embodiment of a constitutively
expressed argG construct in E. coli Nissle. The constitutive
promoter is BBa_J23100, boxed in gray. Restriction sites for use in
cloning are in bold.
[0027] FIG. 12 depicts a map of the wild-type argG operon E. coli
Nissle, and a constitutively expressing mutant thereof. ARG boxes
are present in the wild-type operon, but absent from the mutant.
ArgG is constitutively expressed under the control of the
BBa_J23100 promoter.
[0028] FIG. 13 depicts a schematic diagram of an exemplary BAD
promoter-driven argA.sup.fbr construct. In this embodiment, the
argA.sup.fbr gene is inserted between the araC and araD genes.
ArgA.sup.fbr is flanked by a ribosome binding site, a FRT site, and
one or more transcription terminator sequences.
[0029] FIG. 14 depicts an exemplary embodiment of an engineered
bacterial strain deleted for the argR gene and expressing the
feedback-resistant argA.sup.fbr gene. In some embodiments, this
strain further comprises one or more auxotrophic modifications on
the chromosome. This strain is useful for the consumption of
ammonia and the production of arginine.
[0030] FIG. 15 depicts an exemplary embodiment of an engineered
bacterial strain deleted for the argR and argG genes, and
expressing the feedback-resistant argA.sup.fbr gene. In some
embodiments, this strain further comprises one or more auxotrophic
modifications on the chromosome. This strain is useful for the
consumption of ammonia and the production of citrulline.
[0031] FIG. 16 depicts an exemplary embodiment of an engineered
bacterial strain which lacks ArgR binding sites and expresses the
feedback-resistant argA.sup.fbr gene. In some embodiments, this
strain further comprises one or more auxotrophic modifications on
the chromosome. This strain is useful for the consumption of
ammonia and the production of arginine.
[0032] FIG. 17 depicts an exemplary embodiment of an engineered
bacterial strain which lacks ArgR binding sites in all of the
arginine biosynthesis operons except for argG, and expresses the
feedback-resistant argA.sup.fbr gene. In some embodiments, this
strain further comprises one or more auxotrophic modifications on
the chromosome. This strain is useful for the consumption of
ammonia and the production of citrulline.
[0033] FIG. 18 depicts a map of exemplary integration sites within
the E. coli 1917 Nissle chromosome. These sites indicate regions
where circuit components may be inserted into the chromosome
without interfering with essential gene expression. Backslashes (/)
are used to show that the insertion will occur between divergently
or convergently expressed genes. Insertions within biosynthetic
genes, such as thyA, can be useful for creating nutrient
auxotrophies. In some embodiments, an individual circuit component
is inserted into more than one of the indicated sites. The malE/K
site is circled. In some embodiments of the disclosure, FNR-ArgAfbr
is inserted at the malEK locus.
[0034] FIG. 19 depicts three bacterial strains which constitutively
express red fluorescent protein (RFP). In strains 1-3, the rfp gene
has been inserted into different sites within the bacterial
chromosome, and results in varying degrees of brightness under
fluorescent light. Unmodified E. coli Nissle (strain 4) is
non-fluorescent.
[0035] FIG. 20 depicts the gene organization of exemplary contructs
of the disclosure. Non-limiting examples of strains comprising such
a construct include SYN-UCD301 and SYN-UCD302. SYN-UCD301 comprises
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, Wild type ThyA, and Chloramphenicol resistance.
[0036] FIG. 21 depicts the gene organization of an exemplary
construct of the disclosure. Non-limiting examples of strains
comprising such a construct include SYN-UCD303, SYN-UCD306,
SYN-UCD307, and SYN-UCD309. For example, SYN-UCD303 comprises
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and kanamycin resistance.
[0037] FIG. 22 depicts the gene organization of exemplary
constructs of the disclosure. Non-limiting examples of strains
comprising such a construct include SYN-UCD304, SYN-UCD305,
SYN-UCD308, and SYN-UCD310. For example, SYN-UCD304 comprises
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, wild type ThyA, and no antibiotic resistance.
SYN-UCD305 comprises .DELTA.ArgR, PfnrS-ArgAfbr integrated into the
chromosome at the malEK locus, .DELTA.ThyA, and no antibiotic
resistance.
[0038] FIG. 23 depicts a bar graph of in vitro arginine levels
produced by streptomycin-resistant control Nissle (SYN-UCD103),
SYN-UCD201, SYN-UCD202, and SYN-UCD203 under inducing (+ATC) and
non-inducing (-ATC) conditions. SYN-UCD201 comprises .DELTA.ArgR
and no argA.sup.fbr. SYN-UCD202 comprises .DELTA.ArgR and
tetracycline-inducible argA.sup.fbr on a high-copy plasmid.
SYN-UCD203 comprises .DELTA.ArgR and tetracycline-driven
argA.sup.fbr on a low-copy plasmid.
[0039] FIG. 24 depicts a bar graph of in vitro levels of arginine
and citrulline produced by streptomycin-resistant control Nissle
(SYN-UCD103), SYN-UCD104, SYN-UCD204, and SYN-UCD105 under inducing
conditions. SYN-UCD104 comprises wild-type ArgR,
tetracycline-inducible argA.sup.fbr on a low-copy plasmid,
tetracycline-inducible argG, and mutations in each ARG box for each
arginine biosynthesis operon except for argG. SYN-UCD204 comprises
.DELTA.ArgR and argA.sup.fbr expressed under the control of a
tetracycline-inducible promoter on a low-copy plasmid. SYN-UCD105
comprises wild-type ArgR, tetracycline-inducible argA.sup.fbr on a
low-copy plasmid, constitutively expressed argG (BBa_J23100
constitutive promoter), and mutations in each ARG box for each
arginine biosynthesis operon except for argG.
[0040] FIG. 25 depicts a bar graph of in vitro arginine levels
produced by streptomycin-resistant Nissle (SYN-UCD103), SYN-UCD205,
and SYN-UCD204 under inducing (+ATC) and non-inducing (-ATC)
conditions, in the presence (+O.sub.2) or absence (-O.sub.2) of
oxygen. SYN-UCD103 is a control Nissle construct. SYN-UCD205
comprises .DELTA.ArgR and argA.sup.fbr expressed under the control
of a FNR-inducible promoter on a low-copy plasmid. SYN204 comprises
.DELTA.ArgR and argA.sup.fbr expressed under the control of a
tetracycline-inducible promoter on a low-copy plasmid.
[0041] FIG. 26 depicts a bar graph of in vitro ammonia levels in
culture media from SYN-UCD101, SYN-UCD102, and blank controls at
baseline, two hours, and four hours. Both SYN-UCD101 and SYN-UCD102
are capable of consuming ammonia in vitro. SYN-UCD101 comprises
wild type ArgR, and wild type ThyA, and no ArgAFbr; SYN-UCD102
comprises wild type ArgR, tetracycline-inducible argAfbr on a low
copy plasmid, and wild type ThyA.
[0042] FIG. 27 depicts a bar graph of in vitro ammonia levels in
culture media from SYN-UCD202, SYN-UCD203, and blank controls at
baseline, two hours, and four hours. Both SYN-UCD202 and SYN-UCD203
are capable of consuming ammonia in vitro. SYN-UCD202 and
SYN-UCD203 both comprise .DELTA.ArgR, tetracycline-inducible
argAfbr on a high-copy plasmid or low copy plasmid, respectively,
Amp resistance, and wild type ThyA.
[0043] FIGS. 28A, 28B, and 28C depict bar graphs of ammonia levels
in hyperammonemic TAA mice. FIG. 28A depicts a bar graph of ammonia
levels in hyperammonemic mice treated with unmodified control
Nissle or SYN-UCD202, a genetically engineered strain in which the
Arg repressor gene is deleted and the argA.sup.fbr gene is under
the control of a tetracycline-inducible promoter on a high-copy
plasmid. A total of 96 mice were tested, and the error bars
represent standard error. Blood ammonia (BA) levels in mice treated
with SYN-UCD202 are lower than ammonia levels in mice treated with
unmodified control Nissle at day 4 and day 5 (Nissle, BA=220 mM;
SYN-UCD202, BA=105 mM; BA.sub.Nissle-BA.sub.SYN-UCD202=115 mM;
average blood volume=1.5 mL. FIG. 28B depicts a bar graph showing
in vivo efficacy (ammonia consumption) of SYN-UCD204 in the TAA
mouse model, relative to streptomycin-resistant control Nissle
(SYN-UCD103) and vehicle-only controls. FIG. 28C depicts a bar
graph of the percent change in blood ammonia concentration between
24-48 hours post-TAA treatment.
[0044] FIG. 29 depicts a bar graph of ammonia levels in
hyperammonemic spf.sup.ash mice. Fifty-six spf.sup.ash mice were
separated into four groups. Group 1 was fed normal chow, and groups
2-4 were fed 70% protein chow following an initial blood draw.
Groups were gavaged twice daily, with water, streptomycin-resistant
Nissle control (SYN-UCD103), or SYN-UCD204, and blood was drawn 4
hours following the first gavage. SYN-UCD204, comprising
.DELTA.ArgR and argA.sup.fbr expressed under the control of a
tetracycline-inducible promoter on a low-copy plasmid,
significantly reduced blood ammonia to levels below the
hyperammonemia threshold.
[0045] FIG. 30 depicts a bar graph of ammonia levels in
hyperammonemic spf.sup.ash mice on a high protein diet. Mice were
treated with SYN-UCD204 (comprising .DELTA.ArgR, PfnrS-ArgAfbr on a
low-copy plasmid and wild type ThyA), SYN-UCD206 (comprising
.DELTA.ArgR, PfnrS-ArgAfbr on a low-copy plasmid and .DELTA.ThyA)
or water, then switched to high protein chow after 2 days. As seen
in FIG. 30, at 48 hours after switch to high protein chow ammonia
levels were reduced to a similar extent in both SYN-UCD205 and
SYN-UCD206, indicating that ThyA auxotrophy does not have a
significant effect on efficacy.
[0046] FIGS. 31A and 31B depict bar graphs of ammonia levels in the
media at various time points post anaerobic induction. FIG. 31A
depicts a bar graph of the levels of arginine production of
SYN-UCD205, SYN-UCD206, and SYN-UCD301 measured at 0, 30, 60, and
120 minutes. FIG. 31B depicts a bar graph of the levels of arginine
production of SYN-UCD204 (comprising .DELTA.ArgR, PfnrS-ArgAfbr on
a low-copy plasmid and wild type ThyA), SYN-UCD301, SYN-UCD302, and
SYN-UCD303 (all three of which comprise an integrated FNR-ArgAfbr
construct; SYN UCD301 comprises .DELTA.ArgR, and wtThyA; SYN 303
comprises .DELTA.ArgR, and .DELTA.ThyA). Results indicate that
chromosomal integration of FNR ArgA fbr results in similar levels
of arginine production as seen with the low copy plasmid strains
expressing the same construct.
[0047] FIGS. 32A and 32B depicts a bar graph of ammonia levels and
a survival curve for hyperammonemic spf.sup.ash mice on a normal
(NC) or high protein (HP) diet. Two strains with an integrated copy
of FNR-ArgAfbr, one with (SYN-UCD303) and one without a ThyA
deletion (SYN-UCD301) were compared. FIG. 32A depicts a bar graph
of ammonia levels in hyperammonemic spf.sup.ash mice on a normal
(NC) or high protein (HP) diet. Ammonia levels of spf-ash mice in a
high protein diet were reduced in the SYN-UCD301 and SYN-UCD303
groups as compared to the H2O high protein diet control group. The
observed reduction in ammonia levels was similar in both SYN-UCD301
and SYN-UCD303, indicating that ThyA auxotrophy does not have a
significant effect on efficacy of SYN-UCD303. FIG. 32B depicts a
survival curve of hyperammonemic spf.sup.ash mice on a normal (NC)
or high protein (HP) diet and shows that SYN-UCD301 and SYN-UCD303
displayed prolonged survival as compared to controls.
[0048] FIG. 33 depicts a graph of bood ammonia levels in an
hyperammonemic spf.sup.ash mice on a normal (NC) or high protein
(HP) diet. For SYN-UCD303, doses of 1.times.10.sup.7,
1.times.10.sup.8, 1.times.10.sup.9, and 1.times.10.sup.10 cells
were administered daily over a time course of 12 days. Blood
ammonia levels were measured on day 5. Both doses of
1.times.10.sup.8 and 1.times.10.sup.9 were sufficient to result in
a significant reduction of blood ammonia levels in this model.
SYN-UCD303 comprises .DELTA.ArgR, PfnrS-ArgAfbr integrated into the
chromosome at the malEK locus, .DELTA.ThyA, and Kanamycin
resistance.
[0049] FIG. 34 depicts a graph of Nissle residence in vivo.
Streptomycin-resistant Nissle was administered to mice via oral
gavage without antibiotic pre-treatment. Fecal pellets from six
total mice were monitored post-administration to determine the
amount of administered Nissle still residing within the mouse
gastrointestinal tract. The bars represent the number of bacteria
administered to the mice. The line represents the number of Nissle
recovered from the fecal samples each day for 10 consecutive
days.
[0050] FIGS. 35A, 35B, and 35C depict bar graphs of bacterial
residence in various compartments of the intestinal tract at 1, 4,
8, 12, 24, and 30 hours post gavage. Mice were treated with
approximately 10.sup.9 CFU, and at each timepoint, animals (n=4)
were euthanized, and intestine, cecum, and colon were removed. The
small intestine was cut into three sections, and the large
intestine and colon each into two sections. Intestinal effluents
gathered and CFUs in each compartment were determined by serial
dilution plating. FIG. 35A depicts a bar graph of residence over
time for SYN-UCD103 (streptomycin resistant Nissle). FIG. 35B
depicts a bar graph residence over time for SYN-UCD106, comprising
.DELTA.ArgR and .DELTA.ThyA and no ArgAfbr. FIG. 35C depicts a bar
graph showing residence over time for SYN-UCD303, comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, and .DELTA.ThyA.
[0051] FIGS. 36A, 36B, and 36C depict bar graphs of viable
bacterial cells and arginine production. Cells were either
incubated with 70% isopropanol or phosphate buffered saline (PBS)
as a control for 1 hour with shaking. After treatment, the cells
were mixed at specific ratios in M9 media supplemented with 0.5%
glucose and 3 mM thymidine and incubated with shaking at 37 C for 2
hours. As seen in FIGS. 36A and 36B, a greater ratio of isopropanol
treated cells to untreated in a culture results in fewer CFUs as
determined by plating, and lower levels of arginine production.
Arginine production relative to amount of bacteria present remained
constant across the various cultures (FIG. 36C). These results
indicate that only viable bacteria are contributing to arginine
production.
[0052] FIG. 37. Depicts the number of bacteria quantified in fecal
samples collected in a non-human primate toxicity study.
Pharmacokinetics and pharmacodynamics resulting from administration
of SYN-UCD107 (a kanamycin resistant Nissle) and SYN-UCD303
(comprising .DELTA.ArgR, PfnrS-ArgAfbr integrated into the
chromosome at the malEK locus, .DELTA.ThyA, and Kanamycin
resistance) was compared over 50 days. Results indicate that under
these dosing conditions, similar amounts of bacteria were recovered
with the auxotroph SYN-UCD303 as control kanamycin resistant Nissle
in the feces. Similar results have been observed in mice.
[0053] FIG. 38 depicts an exemplary synthetic genetic circuit for
treating hepatic encephalopathy and other disorders characterized
by hyperammonemia. In the ammonia conversion circuit, ammonia is
taken up by a bacterium (e.g., E. coli Nissle), converted to
glutamate, and glutamate is subsequently metabolized to arginine.
Arginine ultimately exits the bacterial cell.
[0054] FIG. 39 depicts one embodiment of the invention. In this
embodiment, the genetically engineered bacteria comprise four
exemplary circuits for the treatment of hepatic encephalopathy. In
one circuit, ammonia is taken up by the bacterium, converted to
glutamate, and glutamate is subsequently metabolized to arginine.
Arginine ultimately exits the bacterial cell. In a second circuit,
the GABA membrane transport protein (GabP) is expressed by the gabP
gene, and facilitates GABA transport into the cell. In a third
circuit, the bacterial manganese transport protein (MntH) is
expressed by the mntH gene, and facilitates manganese transport
into the cell. In a fourth circuit, expression of a butyrate gene
cassette results in the production of butyrate, and release of this
gut barrier enhancer molecule outside of the cell. In some
embodiments, all four circuits are each under the control of the
same inducible promoter. In other embodiments, the four circuits
may be under the control of different inducible promoters.
Exemplary inducible promoters include oxygen level-dependent
promoters (e.g., FNR-inducible promoter), promoters induced by
HE-specific molecules or metabolites indicative of liver damage
(e.g., bilirubin), promoters induced by inflammation or an
inflammatory response, and promoters induced by a metabolite that
may or may not be naturally present (e.g., can be exogenously
added) in the gut, e.g., arabinose.
[0055] FIG. 40 depicts one embodiment of the invention. In this
embodiment, the genetically engineered bacteria comprise two
exemplary circuits for the treatment of hepatic encephalopathy. In
one circuit, ammonia is taken up by the bacterium, converted to
glutamate, and glutamate is subsequently metabolized to arginine.
Arginine ultimately exits the bacterial cell. In a second circuit,
the GABA membrane transport protein (GabP) is expressed by the gabP
gene, and facilitates GABA transport into the cell. In some
embodiments, both circuits are under the control of the same
inducible promoter. In other embodiments, the two circuits may each
be under the control of a different inducible promoter. Exemplary
inducible promoters include oxygen level-dependent promoters (e.g.,
FNR-inducible promoter), promoters induced by HE-specific molecules
or metabolites indicative of liver damage (e.g., bilirubin),
promoters induced by inflammation or an inflammatory response, and
promoters induced by a metabolite that may or may not be naturally
present (e.g., can be exogenously added) in the gut, e.g.,
arabinose. In other embodiments, the genetically engineered
bacteria may further comprise an additional circuit for reducing
the level of GABA, e.g., a circuit for metabolizing (catabolizing)
GABA.
[0056] FIGS. 41A and 41B depict the catabolism of GABA following
uptake into genetically engineered bacteria comprising synthetic
genetic circuits. In FIG. 41A, upon entry into the cell, GABA is
converted to succinyl semialdehyde by GABA .alpha.-ketoglutarate
transaminase (GSST). Succinate-semialdehyde dehydrogenase (SSDH)
then catalyzes the second and only other specific step in GABA
catabolism, the oxidation of succinyl semialdehyde to succinate.
Ultimately, succinate becomes a substrate for the citric acid (TCA)
cycle. GOT (glutamate oxaloacetate transaminase) converts
alpha-ketoglutarate to glutamate. In certain embodiments, the
genetically engineered bacteria of the disclosure comprise a GABA
consuming circuit including, but not limited to, one or more of
GSST, SSDH, and GOT. FIG. 41B depicts a schematic representation of
the GABA utilization pathway in E. coli Nissle.
[0057] FIG. 42 depicts one embodiment of the invention. In this
embodiment, the genetically engineered bacteria comprise two
exemplary circuits for the treatment of hepatic encephalopathy. In
one circuit, ammonia is taken up by the bacterium, converted to
glutamate, and glutamate is subsequently metabolized to arginine.
Arginine ultimately exits the bacterial cell. In a second circuit,
the bacterial manganese transport protein (MntH) is expressed by
the mntH gene, and facilitates manganese transport into the cell.
In some embodiments, both circuits are under the control of the
same inducible promoter. In other embodiments, the two circuits may
each be under the control of different inducible promoter.
Exemplary inducible promoters include oxygen level-dependent
promoters (e.g., FNR-inducible promoter), promoters induced by
HE-specific molecules or metabolites indicative of liver damage
(e.g., bilirubin), promoters induced by inflammation or an
inflammatory response, and promoters induced by a metabolite that
may or may not be naturally present (e.g., can be exogenously
added) in the gut, e.g., arabinose.
[0058] FIG. 43 depicts one embodiment of the invention. In this
embodiment, the genetically engineered bacteria comprise two
exemplary circuits for the treatment of hepatic encephalopathy. In
one circuit, ammonia is taken up by the bacterium, converted to
glutamate, and glutamate is subsequently metabolized to arginine.
Arginine ultimately exits the bacterial cell. In a second circuit,
expression of a butyrate gene cassette results in the production of
butyrate, and release of this gut barrier enhancer molecule outside
of the cell. In some embodiments, both circuits are under the
control of the same inducible promoter. In other embodiments, the
two circuits may each be under the control of different inducible
promoter. Exemplary inducible promoters include oxygen
level-dependent promoters (e.g., FNR-inducible promoter), promoters
induced by HE-specific molecules or metabolites indicative of liver
damage (e.g., bilirubin), promoters induced by inflammation or an
inflammatory response, and promoters induced by a metabolite that
may or may not be naturally present (e.g., can be exogenously
added) in the gut, e.g., arabinose. One or more of the butyrate
cassettes described herein may be expressed by the genetically
engineered bacteria comprising an arginine (and/or citrulline)
producing circuit.
[0059] FIG. 44 depicts an exemplary schematic of the E. coli 1917
Nissle chromosome comprising multiple mechanisms of action
(MoAs).
[0060] FIG. 45 depicts an exemplary schematic of the E. coli 1917
Nissle chromosome comprising multiple MoAs. In some embodiments, an
ammonia conversion circuit, a butyrate production circuit, a GABA
transport and/or a GABA metabolic circuit, and a manganese
transport circuit are inserted at four or more different
chromosomal insertion sites
[0061] FIGS. 46A and 46B depict an exemplary schematic of the E.
coli 1917 Nissle chromosome comprising multiple MoAs. In FIG. 46A,
an ammonia conversion circuit, a butyrate production circuit, and a
GABA transport and/or GABA metabolic circuit are inserted at three
different chromosomal insertion sites. In FIG. 46B, an ammonia
conversion circuit, a GABA transport and/or GABA metabolic circuit,
and a manganese transport circuit are inserted at three or more
different chromosomal insertion sites.
[0062] FIGS. 47A and 47B depict an exemplary schematic of the E.
coli 1917 Nissle chromosome comprising multiple MoAs. In FIG. 47A,
an ammonia conversion circuit, and a manganese transport circuit
are inserted at two different chromosomal insertion sites. In FIG.
47B, an ammonia conversion circuit, and a GABA transport and/or
GABA metabolic circuit are inserted at two or more different
chromosomal insertion sites.
[0063] FIG. 48A depicts a metabolic pathway for butyrate production
FIGS. 48B and 48C depict two schematics of two different butyrate
producing circuits (found in SYN-UCD503 and SYN-UCD504), both under
the control of a tetracycline inducible promoter. FIG. 48D depicts
a schematic of a third butyrate gene cassette (found in SYN-UCD505)
under the control of a tetracycline inducible promoter. SYN-UCD503
comprises a bdc2 butyrate cassette under control of tet promoter on
a plasmid. A "bdc2 cassette" or "bdc2 butyrate cassette" refres to
a butyrate producing cassette that comprises at least the following
genes: bcd2, etfB3, etfA3, hbd, crt2, pbt, and buk genes.
SYN-UCD504 comprises a ter butyrate cassette (ter gene replaces the
bcd2, etfB3, and etfA3 genes) under control of tet promoter on a
plasmid. A "ter cassette" or "ter butyrate cassette" refers to a
butyrate producing cassete that comprises at least the following
genes: ter, thiA1, hbd, crt2, pbt, buk. SYN-UCD505 comprises a tesB
butyrate cassette (ter gene is present and tesB gene replaces the
pbt gene and the buk gene) under control of tet promoter on a
plasmid. A "tes or tesB cassette or "tes or tesB butyrate cassette"
refers to a butyrate producing cassette that comprises at least
ter, thiA1, hbd, crt2, and tesB genes. An alternative butyrate
cassette of the disclosure comprises at least bcd2, etfB3, etfA3,
thiA1, hbd, crt2, and tesB genes. In some embodiments, the tes or
tesB cassette is under control of an inducible promoter other than
tetracycline. Exemplary inducible promoters which may control the
expression of the tesB cassette include oxygen level-dependent
promoters (e.g., FNR-inducible promoter), promoters induced by
HE-specific molecules or metabolites indicative of liver damage
(e.g., bilirubin), promoters induced by inflammation or an
inflammatory response (RNS, ROS promoters), and promoters induced
by a metabolite that may or may not be naturally present (e.g., can
be exogenously added) in the gut, e.g., arabinose and
tetracycline.
[0064] FIGS. 49A-F depict the gene organization of exemplary
engineered bacteria of the disclosure and their induction under
anaerobic or inflammatory conditions for the production of
butyrate. FIGS. 49A and 49B depict the gene organization of an
exemplary recombinant bacterium of the invention and its induction
under low-oxygen conditions. FIG. 49A depicts relatively low
butyrate production under aerobic conditions in which oxygen (02)
prevents (indicated by "X") FNR (grey boxed "FNR") from dimerizing
and activating the FNR-responsive promoter ("FNR promoter").
Therefore, none of the butyrate biosynthesis enzymes (bcd2, etfB3,
etfA3, thiA1, hbd, crt2, pbt, and buk; black boxes) is expressed.
FIG. 49B depicts increased butyrate production under low-oxygen
conditions due to FNR dimerizing (two grey boxed "FNR" s), binding
to the FNR-responsive promoter, and inducing expression of the
butyrate biosynthesis enzymes, which leads to the production of
butyrate. FIGS. 49C and 49D depict the gene organization of an
exemplary recombinant bacterium of the invention and its
derepression in the presence of nitric oxide (NO). In FIG. 49C, in
the absence of NO, the NsrR transcription factor (gray circle,
"NsrR") binds to and represses a corresponding regulatory region.
Therefore, none of the butyrate biosynthesis enzymes (bcd2, etfB3,
etfA3, thiA1, hbd, crt2, pbt, buk; black boxes) is expressed. In
FIG. 49D, in the presence of NO, the NsrR transcription factor
interacts with NO, and no longer binds to or represses the
regulatory sequence. This leads to expression of the butyrate
biosynthesis enzymes (indicated by gray arrows and black squiggles)
and ultimately to the production of butyrate. FIGS. 49E and F
depict the gene organization of an exemplary recombinant bacterium
of the invention and its induction in the presence of H2O2. In FIG.
49E, in the absence of H2O2, the OxyR transcription factor (gray
circle, "OxyR") binds to, but does not induce, the oxyS promoter.
Therefore, none of the butyrate biosynthesis enzymes (bcd2, etfB3,
etfA3, thiA1, hbd, crt2, pbt, buk; black boxes) is expressed. In
FIG. 49F, in the presence of H2O2, the OxyR transcription factor
interacts with H2O2 and is then capable of inducing the oxyS
promoter. This leads to expression of the butyrate biosynthesis
enzymes (indicated by gray arrows and black squiggles) and
ultimately to the production of butyrate.
[0065] FIGS. 50A-F depict the gene organization of exemplary
recombinant bacteria of the disclosure and their induction under
anaerobic or inflammatory conditions for the production of
butyrate. FIGS. 50A and 50B depict the gene organization of an
exemplary recombinant bacterium of the invention and its induction
under low-oxygen conditions. FIG. 50A depicts relatively low
butyrate production under aerobic conditions in which oxygen
(O.sub.2) prevents (indicated by "X") FNR (grey boxed "FNR") from
dimerizing and activating the FNR-responsive promoter ("FNR
promoter"). Therefore, none of the butyrate biosynthesis enzymes
(ter, thiA1, hbd, crt2, pbt, and buk; black boxes) is expressed.
FIG. 50B depicts increased butyrate production under low-oxygen
conditions due to FNR dimerizing (two grey boxed "FNR" s), binding
to the FNR-responsive promoter, and inducing expression of the
butyrate biosynthesis enzymes, which leads to the production of
butyrate. FIGS. 50C and 50D depict the gene organization of another
exemplary recombinant bacterium of the invention and its
derepression in the presence of NO. In FIG. 50C, in the absence of
NO, the NsrR transcription factor (gray circle, "NsrR") binds to
and represses a corresponding regulatory region. Therefore, none of
the butyrate biosynthesis enzymes (ter, thiA1, hbd, crt2, pbt, buk;
black boxes) is expressed. In FIG. 50D, in the presence of NO, the
NsrR transcription factor interacts with NO, and no longer binds to
or represses the regulatory sequence. This leads to expression of
the butyrate biosynthesis enzymes (indicated by gray arrows and
black squiggles) and ultimately to the production of butyrate.
FIGS. 50E and 50F depict the gene organization of another exemplary
recombinant bacterium of the invention and its induction in the
presence of H.sub.2O.sub.2. In FIG. 50E, in the absence of
H.sub.2O.sub.2, the OxyR transcription factor (gray circle, "OxyR")
binds to, but does not induce, the oxyS promoter. Therefore, none
of the butyrate biosynthesis enzymes (ter, thiA1, hbd, crt2, pbt,
buk; black boxes) is expressed. In FIG. 50F, in the presence of
H.sub.2O.sub.2, the OxyR transcription factor interacts with
H.sub.2O.sub.2 and is then capable of inducing the oxyS promoter.
This leads to expression of the butyrate biosynthesis enzymes
(indicated by gray arrows and black squiggles) and ultimately to
the production of butyrate.
[0066] FIGS. 51A and 51B depict a graph of butyrate production
using the circuits (SYN-UCD-503, SYN-UCD-504, SYN-UCD-505) shown in
FIGS. 48B-D. Cells were grown in M9 minimal media containing 0.2%
glucose and induced with ATC at early log phase. As seen in FIG.
51A, similar amounts of butyrate were produced for each construct
under aerobic vs anaerobic conditions. The ter strain produces more
butyrate overall. SYN-UCD503 comprises pLogic031 (bdc2 butyrate
cassette under control of tet promoter on a plasmid) and SYN-UCD504
comprises pLogic046 (ter butyrate cassette under control of tet
promoter on a plasmid). FIG. 51B depicts butyrate production of
SYN-UCD504 (pLogic046 (ter butyrate cassette under control of tet
promoter on a plasmid)) and SYN-UCD505 (a Nissle strain comprising
plasmid pLOGIC046-delta pbt.buk/tesB+, an ATC-inducible
ter-comprising butyrate construct with a deletion in the pbt-buk
genes and their replacement with the tesB gene). The tesB construct
results in greater butyrate production.
[0067] FIG. 52 depicts a graph of butyrate production using
different butyrate-producing circuits comprising a nuoB gene
deletion. Strains depicted are SYN-UCD503, SYN-UCD504, SYN-UCD510
(SYN-UCD510 is the same as SYN-UCD503 except that it further
comprises a nuoB deletion), and SYN-UCD511 (SYN-UCD511 is the same
as SYN-UCD504 except that it further comprises a nuoB deletion).
The NuoB gene deletion results in greater levels of butyrate
production as compared to a wild-type parent control in butyrate
producing strains. NuoB is a main protein complex involved in the
oxidation of NADH during respiratory growth. In some embodiments,
preventing the coupling of NADH oxidation to electron transport
increases the amount of NADH being used to support butyrate
production.
[0068] FIG. 53A depicts a schematic of a butyrate producing circuit
under the control of an FNR promoter. FIG. 53B depicts a bar graph
of anaerobic induction of butyrate production. FNR-responsive
promoters were fused to butyrate cassettes containing either the
bcd or ter circuits. Transformed cells were grown in LB to early
log and placed in anaerobic chamber for 4 hours to induce
expression of butyrate genes. Cells were washed and resuspended in
minimal media w/ 0.5% glucose and incubated microaerobically to
monitor butyrate production over time. SYN-UCD501 led to
significant butyrate production under anaerobic conditions. FIG.
53C depicts SYN-UCD501 in the presence and absence of glucose and
oxygen in vitro. SYN-UCD501 comprises pSC101 PydfZ-ter butyrate
plasmid; SYN-UCD500 comprises pSC101 PydfZ-bcd butyrate plasmid;
SYN-UCD506 comprises pSC101 nirB-bcd butyrate plasmid. FIG. 53D
depicts levels of mouse lipocalin 2 and calprotectin quantified by
ELISA using the fecal samples in an in vivo model of HE. SYN-UCD501
reduces inflammation and/or protects gut barrier function as
compared to control SYN-UCD103.
[0069] FIGS. 54A and 54B depict bar graphs showing in vitro
arginine (FIG. 54A) and butyrate (FIG. 54B) production for (1)
butyrate producing strain; (2) arginine producing strain (ammonia
consuming strain), and (3) strain that produces butyrate and also
consumes ammonia. SYN-UCD501 (butyrate producing strain comprising
Logic156 (pSC101 PydfZ-ter butyrate plasmid; amp resistance)), and
SYN-UCD305 (arginine producing/ammonia consuming strain comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, and .DELTA.ThyA, with no antibiotic resistance), and
SYN-UCD601 (butyrate producing and arginine producing/ammonia
consuming strain comprising .DELTA.ArgR, PfnrS-ArgAfbr integrated
into the chromosome at the malEK locus, .DELTA.ThyA, and Logic156
(pSC101 PydfZ-ter butyrate plasmid; amp resistance)). The data show
that SYN-UCD601 is able to produce similar levels of arginine as
SYN-UCD305 and similar levels of butyrate as SYN-UCD501 in
vitro.
[0070] FIGS. 55A and 55B depict the gene organization of an
exemplary engineered bacterium of the invention and its induction
under low-oxygen conditions for the production of propionate. FIG.
55A depicts relatively low propionate production under aerobic
conditions in which oxygen (O.sub.2) prevents (indicated by "X")
FNR (grey boxed "FNR") from dimerizing and activating the
FNR-responsive promoter ("FNR promoter"). Therefore, none of the
propionate biosynthesis enzymes (pct, lcdA, lcdB, lcdC, etfA, acre,
acrC; black boxes) are expressed. FIG. 55B depicts increased
propionate production under low-oxygen conditions due to FNR
dimerizing (two grey boxed "FNR" s), binding to the FNR-responsive
promoter, and inducing expression of the propionate biosynthesis
enzymes, which leads to the production of propionate.
[0071] FIG. 56 depicts an exemplary propionate biosynthesis gene
cassette.
[0072] FIGS. 57A, 57B and 57C depict the gene organization of an
exemplary engineered bacterium and its induction under low-oxygen
conditions for the production of propionate. FIG. 57A depicts
relatively low propionate production under aerobic conditions in
which oxygen (O.sub.2) prevents (indicated by "X") FNR (grey boxed
"FNR") from dimerizing and activating the FNR-responsive promoter
("FNR promoter"). Therefore, none of the propionate biosynthesis
enzymes (thrA, thrB, thrC, ilvA, aceE, aceF, lpd; black boxes) are
expressed. FIG. 57B depicts increased propionate production under
low-oxygen conditions due to FNR dimerizing (two grey boxed "FNR"
s), binding to the FNR-responsive promoter, and inducing expression
of the propionate biosynthesis enzymes, which leads to the
production of propionate. FIG. 57C depicts an exemplary propionate
biosynthesis gene cassette.
[0073] FIGS. 58A and 58B depict the gene organization of an
exemplary engineered bacterium of the invention and its induction
under low-oxygen conditions for the production of propionate. FIG.
58A depicts relatively low propionate production under aerobic
conditions in which oxygen (O.sub.2) prevents (indicated by "X")
FNR (grey boxed "FNR") from dimerizing and activating the
FNR-responsive promoter ("FNR promoter"). Therefore, none of the
propionate biosynthesis enzymes (thrA, thrB, thrC, ilvA, aceE,
aceF, lpd, tesB; black boxes) are expressed. FIG. 58B depicts
increased propionate production under low-oxygen conditions due to
FNR dimerizing (two grey boxed "FNR" s), binding to the
FNR-responsive promoter, and inducing expression of the propionate
biosynthesis enzymes, which leads to the production of
propionate.
[0074] FIG. 59 depicts an exemplary propionate biosynthesis gene
cassette.
[0075] FIGS. 60A and 60B depict diagrams of exemplary constructs
which may be used to produce a positive feedback auxotroph and
select for high arginine production. FIG. 60A depicts a map of the
astC promoter driving expression of thyA. FIG. 60B depicts a
schematic diagram of the thyA gene under the control of an astC
promoter. The regulatory region comprises binding sites for CRP,
ArgR, and RNA polymerase (RNAP), and may also comprise additional
regulatory elements.
[0076] FIG. 61 depicts another exemplary embodiment of an
engineered bacterial strain to target urea cycle disorder (UCD),
via the conversion of ammonia to desired products, such as
citrulline or arginine. The strain is deleted for the argR gene and
expressing the feedback-resistant argAfbr gene. In some
embodiments, this strain further comprises one or more auxotrophic
modifications on the chromosome. The synthetic biotic engineered to
target urea cycle disorder (UCD) also has the kill-switch
embodiment described in FIG. 65. In this example, the Int
recombinase and the Kid-Kis toxin-antitoxin system are used in a
recombinant bacterial cell for treating UCD. The recombinant
bacterial cell is engineered to consume excess ammonia to produce
beneficial byproducts to improve patient outcomes. The recombinant
bacterial cell also comprises a highly controllable kill switch to
ensure safety. In response to a low oxygen environment (e.g., such
as that found in the gut), the FNR promoter induces expression of
the Int recombinase and also induces expression of the Kis
anti-toxin. The Int recombinase causes the Kid toxin gene to flip
into an activated conformation, but the presence of the accumulated
Kis anti-toxin suppresses the activity of the expressed Kid toxin.
In the presence of oxygen (e.g., outside the gut), expression of
the anti-toxin is turned off. Since the toxin is constitutively
expressed, it continues to accumulate and kills the bacterial
cell.
[0077] FIG. 62 depicts one non-limiting embodiment of the
disclosure, where an exogenous environmental condition or one or
more environmental signals activates expression of a heterologous
gene and at least one recombinase from an inducible promoter or
inducible promoters. The recombinase then flips a toxin gene into
an activated conformation, and the natural kinetics of the
recombinase create a time delay in expression of the toxin,
allowing the heterologous gene to be fully expressed. Once the
toxin is expressed, it kills the cell.
[0078] FIG. 63 depicts another non-limiting embodiment of the
disclosure, where an exogenous environmental condition or one or
more environmental signals activates expression of a heterologous
gene, an anti-toxin, and at least one recombinase from an inducible
promoter or inducible promoters. The recombinase then flips a toxin
gene into an activated conformation, but the presence of the
accumulated anti-toxin suppresses the activity of the toxin. Once
the exogenous environmental condition or cue(s) is no longer
present, expression of the anti-toxin is turned off. The toxin is
constitutively expressed, continues to accumulate, and kills the
bacterial cell.
[0079] FIG. 64 depicts another non-limiting embodiment of the
disclosure, where an exogenous environmental condition or one or
more environmental signals activates expression of a heterologous
gene and at least one recombinase from an inducible promoter or
inducible promoters. The recombinase then flips at least one
excision enzyme into an activated conformation. The at least one
excision enzyme then excises one or more essential genes, leading
to senescence, and eventual cell death. The natural kinetics of the
recombinase and excision genes cause a time delay, the kinetics of
which can be altered and optimized depending on the number and
choice of essential genes to be excised, allowing cell death to
occur within a matter of hours or days. The presence of multiple
nested recombinases can be used to further control the timing of
cell death.
[0080] FIG. 65 depicts a schematic of an activation-based kill
switch, in which R is any inducible promoter, e.g., a
FNR-responsive promoter. When the therapeutic is induced, the
anti-toxin and recombinases are turned on, which results in the
toxin being `flipped` to the ON position after 4-6 hours, which
results in a build-up of anti-toxin before the toxin is expressed.
In absence of the inducing signal, only toxin is made and the cell
dies.
[0081] Hyperammonemia can also contribute to other pathologies.
FIG. 66A depicts another non-limiting embodiment of the disclosure,
wherein the expression of a heterologous gene is activated by an
exogenous environmental signal. In the absence of arabinose, the
AraC transcription factor adopts a conformation that represses
transcription. In the presence of arabinose, the AraC transcription
factor undergoes a conformational change that allows it to bind to
and activate the ParaBAD promoter (P.sub.araBAD), which induces
expression of the Tet repressor (TetR) and an anti-toxin. The
anti-toxin builds up in the recombinant bacterial cell, while TetR
prevents expression of a toxin (which is under the control of a
promoter having a TetR binding site). However, when arabinose is
not present, both the anti-toxin and TetR are not expressed. Since
TetR is not present to repress expression of the toxin, the toxin
is expressed and kills the cell. FIG. 66A also depicts another
non-limiting embodiment of the disclosure, wherein the expression
of an essential gene not found in the recombinant bacteria is
activated by an exogenous environmental signal. In the absence of
arabinose, the AraC transcription factor adopts a conformation that
represses transcription of the essential gene under the control of
the araBAD promoter and the bacterial cell cannot survive. In the
presence of arabinose, the AraC transcription factor undergoes a
conformational change that allows it to bind to and activate the
araBAD promoter, which induces expression of the essential gene and
maintains viability of the bacterial cell. FIG. 66B depicts a
non-limiting embodiment of the disclosure, where an anti-toxin is
expressed from a constitutive promoter, and expression of a
heterologous gene is activated by an exogenous environmental
signal. In the absence of arabinose, the AraC transcription factor
adopts a conformation that represses transcription. In the presence
of arabinose, the AraC transcription factor undergoes a
conformational change that allows it to bind to and activate the
araBAD promoter, which induces expression of TetR, thus preventing
expression of a toxin. However, when arabinose is not present, TetR
is not expressed, and the toxin is expressed, eventually overcoming
the anti-toxin and killing the cell. The constitutive promoter
regulating expression of the anti-toxin should be a weaker promoter
than the promoter driving expression of the toxin. The araC gene is
under the control of a constitutive promoter in this circuit. FIG.
66C depicts another non-limiting embodiment of the disclosure,
wherein the expression of a heterologous gene is activated by an
exogenous environmental signal. In the absence of arabinose, the
AraC transcription factor adopts a conformation that represses
transcription. In the presence of arabinose, the AraC transcription
factor undergoes a conformational change that allows it to bind to
and activate the araBAD promoter, which induces expression of the
Tet repressor (TetR) and an anti-toxin. The anti-toxin builds up in
the recombinant bacterial cell, while TetR prevents expression of a
toxin (which is under the control of a promoter having a TetR
binding site). However, when arabinose is not present, both the
anti-toxin and TetR are not expressed. Since TetR is not present to
repress expression of the toxin, the toxin is expressed and kills
the cell. The araC gene is either under the control of a
constitutive promoter or an inducible promoter (e.g., AraC
promoter) in this circuit.
[0082] FIG. 67 depicts the use of GeneGuards as an engineered
safety component. All engineered DNA is present on a plasmid which
can be conditionally destroyed. See, e.g., Wright et al.,
"GeneGuard: A Modular Plasmid System Designed for Biosafety," ACS
Synthetic Biology (2015) 4: 307-316.
[0083] FIG. 68 depicts a one non-limiting embodiment of the
disclosure, which comprises a plasmid stability system with a
plasmid that produces both a short-lived anti-toxin and a
long-lived toxin. When the cell loses the plasmid, the anti-toxin
is no longer produced, and the toxin kills the cell. In one
embodiment, the genetically engineered bacteria produce an equal
amount of a Hok toxin and a short-lived Sok antitoxin. In the upper
panel, the cell produces equal amounts of toxin and anti-toxin and
is stable. In the center panel, the cell loses the plasmid and
anti-toxin begins to decay. In the lower panel, the anti-toxin
decays completely, and the cell dies.
[0084] FIG. 69 depicts a schematic of a secretion system based on
the flagellar type III secretion in which an incomplete flagellum
is used to secrete a therapeutic peptide of interest (star) by
recombinantly fusing the peptide to an N-terminal flagellar
secretion signal of a native flagellar component so that the
intracellularly expressed chimeric peptide can be mobilized across
the inner and outer membranes into the surrounding host
environment.
[0085] FIG. 70 depicts a schematic of a type V secretion system for
the extracellular production of recombinant proteins in which a
therapeutic peptide (star) can be fused to an N-terminal secretion
signal, a linker and the beta-domain of an autotransporter. In this
system, the N-terminal signal sequence directs the protein to the
SecA-YEG machinery which moves the protein across the inner
membrane into the periplasm, followed by subsequent cleavage of the
signal sequence. The beta-domain is recruited to the Bam complex
where the beta-domain is folded and inserted into the outer
membrane as a beta-barrel structure. The therapeutic peptide is
then thread through the hollow pore of the beta-barrel structure
ahead of the linker sequence. The therapeutic peptide is freed from
the linker system by an autocatalytic cleavage or by targeting of a
membrane-associated peptidase (scissors) to a complementary
protease cut site in the linker.
[0086] FIG. 71 depicts a schematic of a type I secretion system,
which translocates a passenger peptide directly from the cytoplasm
to the extracellular space using HlyB (an ATP-binding cassette
transporter); HlyD (a membrane fusion protein); and TolC (an outer
membrane protein) which form a channel through both the inner and
outer membranes. The secretion signal-containing C-terminal portion
of HlyA is fused to the C-terminal portion of a therapeutic peptide
(star) to mediate secretion of this peptide.
[0087] FIG. 72 depicts a schematic of the outer and inner membranes
of a gram-negative bacterium, and several deletion targets for
generating a leaky or destabilized outer membrane, thereby
facilitating the translocation of a therapeutic polypeptides to the
extracellular space, e.g., therapeutic polypeptides of eukaryotic
origin containing disulphide bonds. Deactivating mutations of one
or more genes encoding a protein that tethers the outer membrane to
the peptidoglycan skeleton, e.g., lpp, ompC, ompA, ompF, tolA,
tolB, paI, and/or one or more genes encoding a periplasmic
protease, e.g., degS, degP, nlpI, generates a leaky phenotype.
Combinations of mutations may synergistically enhance the leaky
phenotype.
[0088] FIG. 73 depicts a modified type 3 secretion system (T3SS) to
allow the bacteria to inject secreted therapeutic proteins into the
gut lumen. An inducible promoter (small arrow, top), e.g. a
FNR-inducible promoter, drives expression of the T3 secretion
system gene cassette (3 large arrows, top) that produces the
apparatus that secretes tagged peptides out of the cell. An
inducible promoter (small arrow, bottom), e.g. a FNR-inducible
promoter, drives expression of a regulatory factor, e.g. T7
polymerase, that then activates the expression of the tagged
therapeutic peptide (hexagons).
[0089] FIG. 74 depicts an exemplary L-homoserine and L-methionine
biosynthesis pathway. Circles indicate genes repressed by MetJ, and
deletion of metJ leads to constitutive expression of these genes
and activation of the pathway.
[0090] FIG. 75 depicts an exemplary histidine biosynthesis
pathway.
[0091] FIG. 76 depicts an exemplary lysine biosynthesis
pathway.
[0092] FIG. 77 depicts an exemplary asparagine biosynthesis
pathway.
[0093] FIG. 78 depicts an exemplary glutamine biosynthesis
pathway.
[0094] FIG. 79 depicts an exemplary tryptophan biosynthesis
pathway.
[0095] FIG. 80 depicts a schematic of non-limiting processes for
designing and producing the genetically engineered bacteria of the
present disclosure. The step of "defining" comprises 1.
Identification of diverse candidate approaches based on microbial
physiology and disease biology; 2. Use of bioinformatics to
determine candidate metabolic pathways; the use of prospective
tools to determine performance targets required of optimized
engineered synthetic biotics. The step of "designing" comprises the
use of 1. Cutting-edge DNA assembly to enable combinatorial testing
of pathway organization; 2. Mathematical models to predict pathway
efficiency; 3. Internal stable of proprietary switches and parts to
permit control and tuning of engineered circuits. The step of
"Builing" comprises 1. Building core structures "chassies" 2.
Stably integrating engineered circuits into optimal chromosomal
locations for efficient expression; 3. Employing unique functional
assays to assess genetic circuit fidelity and activity. The step of
"integrating" comprises 1. Use of chromosomal markers, which enable
monitoring of synthetic biotic localization and transit times in
animal models; 2. Leveraging expert microbiome network and
bioinformatics support to expand understanding of how specific
disease states affect GI microbial flora and the behaviors of
synthetic biotics in that environment; 3. Activating process
development research and optimization in-house during the discovery
phase, enabling rapid and seamless transition of development
candidates to pre-clinical progression; Drawing upon extensive
experience in specialized disease animal model refinement, which
supports prudent, high quality testing of candidate synthetic
biotics.
[0096] FIGS. 81A, B, C, D, and E depict a schematic of non-limiting
manufacturing processes for upstream and downstream production of
the genetically engineered bacteria of the present disclosure. FIG.
81A depicts the parameters for starter culture 1 (SC1): loop
full--glycerol stock, duration overnight, temperature 37.degree.
C., shaking at 250 rpm. FIG. 81B depicts the parameters for starter
culture 2 (SC2): 1/100 dilution from SC1, duration 1.5 hours,
temperature 37.degree. C., shaking at 250 rpm. FIG. 81C depicts the
parameters for the production bioreactor: inoculum--SC2,
temperature 37.degree. C., pH set point 7.00, pH dead band 0.05,
dissolved oxygen set point 50%, dissolved oxygen cascade
agitation/gas FLO, agitation limits 300-1200 rpm, gas FLO limits
0.5-20 standard liters per minute, duration 24 hours. FIG. 81D
depicts the parameters for harvest: centrifugation at speed 4000
rpm and duration 30 minutes, wash 1.times.10% glycerol/PBS,
centrifugation, re-suspension 10% glycerol/PBS. FIG. 81E depicts
the parameters for vial fill/storage: 1-2 mL aliquots, -80.degree.
C.
[0097] FIGS. 82A-C depict ATC (FIG. 82A) or nitric oxide-inducible
(FIG. 82B) reporter constructs. These constructs, when induced by
their cognate inducer, lead to expression of GFP. Nissle cells
harboring plasmids with either the control, ATC-inducible
P.sub.tet-GFP reporter construct or the nitric oxide inducible
P.sub.nsrR-GFP reporter construct induced across a range of
concentrations. Promoter activity is expressed as relative
florescence units. FIG. 82C depicts a schematic of the
constructs.
[0098] FIG. 83 depicts a dot blot of bacteria harboring a plasmid
expressing NsrR under control of a constitutive promoter and the
reporter gene gfp (green fluorescent protein) under control of an
NsrR-inducible promoter. DSS-treated mice serve as exemplary models
for HE. As in HE subjects, the guts of mice are damaged by
supplementing drinking water with 2-3% dextran sodium sulfate
(DSS). Chemiluminescent is shown for NsrR-regulated promoters
induced in DSS-treated mice.
[0099] FIG. 84 depicts butyrate production by genetically
engineered Nissle comprising the pLogic031-nsrR-norB-butyrate
construct (SYN-UCD507) or the pLogic046-nsrR-norB-butyrate
construct (SYN-UCD508), which produce more butyrate as compared to
wild-type Nissle.
DESCRIPTION OF EMBODIMENTS
[0100] The invention includes genetically engineered bacteria,
pharmaceutical compositions thereof, and methods of modulating or
treating disorders associated with hyperammonemia, e.g., urea cycle
disorders, hepatic encephalopathy and other disorders associated
with excess ammonia or elevated ammonia levels. The genetically
engineered bacteria are capable of reducing excess ammonia,
particularly under certain environmental conditions, such as those
in the mammalian gut. In some embodiments, the genetically
engineered bacteria reduce excess ammonia by incorporating excess
nitrogen in the body into non-toxic molecules, e.g., arginine,
citrulline, methionine, histidine, lysine, asparagine, glutamine,
or tryptophan. In some embodiments, the genetically engineered
bacteria reduce excess ammonia and also reduce one or more other
toxic substances, e.g., GABA and/or manganese. In some embodiments,
the genetically engineered bacteria reduce excess ammonia and also
reduce GABA levels, e.g., by importing GABA and/or by metabolizing
GABA. In some embodiments, the genetically engineered bacteria
reduce excess ammonia and also reduce manganese levels, e.g., by
importing manganese. The genetically engineered bacteria may
additionally produce one or molecules that improve gut barrier
function or otherwise alleviate a symptom of a disorder associated
with elevated ammonia (e.g., UCDs, HE, etc). Thus, in any of the
described embodiments, the genetically engineered bacteria may also
produce one or molecules that improve gut barrier function or
otherwise alleviate a symptom of a disorder associated with
elevated ammonia. In some embodiments, the genetically engineered
bacteria produce a short chain fatty acid, e.g., butyrate,
propionate, and/or acetate. In some embodiments, the engineered
bacteria reduce excess ammonia and produce one or molecules that
improve gut barrier function or otherwise alleviate a symptom of a
disorder associated with elevated ammonia, e.g., produce a short
chain fatty acid, such as butyrate, propionate, and/or acetate. In
some embodiments, the engineered bacteria reduce excess ammonia,
reduce one or more other toxic substances, e.g., GABA and/or
manganese, and produce one or molecules that improve gut barrier
function or alleviate a symptom of a disorder associated with
elevated ammonia, e.g., produce a short chain fatty acid, such as
butyrate, propionate, and/or acetate. In some embodiments, the
genetically engineered bacteria reduce excess ammonia, reduce GABA
levels, e.g., by importing GABA and/or by metabolizing GABA, and
produce one or molecules that improve gut barrier function or
alleviate a symptom of a disorder associated with elevated ammonia,
e.g., produce a short chain fatty acid, such as butyrate,
propionate, and/or acetate. In some embodiments, the genetically
engineered bacteria reduce excess ammonia, reduce manganese levels,
e.g., by importing manganese, and produce one or molecules that
improve gut barrier function or alleviate a symptom of a disorder
associated with elevated ammonia, e.g., produce a short chain fatty
acid, such as butyrate, propionate, and/or acetate.
[0101] In any of the described embodiments, the engineered bacteria
may further comprise one or more of more of the following: (1) one
or more auxotrophies, such as any auxotrophies known in the art and
provided herein, e.g., thyA auxotrophy, (2) one or more kill switch
circuits, such as any of the kill-switches described herein or
otherwise known in the art, (3) one or more antibiotic resistance
circuits, (4) one or more transporters for importing biological
molecules or substrates, such any of the transporters described
herein or otherwise known in the art, (5) one or more secretion
circuits, such as any of the secretion circuits described herein
and otherwise known in the art, and (6) combinations of one or more
of such additional circuits.
[0102] In some embodiments, any one or more of the payload or
therapeutic circuits (e.g., ammonia consuming, GABA reducing,
manganese reducing, short chain fatty acid producing circuits)
and/or any one or more of the additional circuits (e.g.,
auxotrophies, kill switch circuits, antibiotic resistance circuits,
transporters, and secretion circuits) may be regulated by a
constitutive promoter. In some embodiments, any one or more of the
payload or therapeutic circuits (e.g., ammonia consuming, GABA
reducing, manganese reducing, short chain fatty acid producing
circuits) and/or any one or more of the additional circuits (e.g.,
auxotrophies, kill switch circuits, antibiotic resistance circuits,
transporters, and secretion circuits) may be regulated by a
tissue-specific promoter. In some embodiments, any one or more of
the payload or therapeutic circuits (e.g., ammonia consuming, GABA
reducing, manganese reducing, short chain fatty acid producing
circuits) and/or any one or more of the additional circuits (e.g.,
auxotrophies, kill switch circuits, antibiotic resistance circuits,
transporters, and secretion circuits) may be regulated by an
inducible promoter. In some embodiments, any one or more of the
payload or therapeutic circuits (e.g., ammonia consuming, GABA
reducing, manganese reducing, short chain fatty acid producing
circuits) and/or any one or more of the additional circuits (e.g.,
auxotrophies, kill switch circuits, antibiotic resistance circuits,
transporters, and secretion circuits) may be regulated by an
inducible promoter that is responsive to environmental conditions,
factors, or cues, e.g., environmental conditions, factors, or cues
found in the mammalian gut. Exemplary inducible promoters include
oxygen level-dependent promoters (e.g., FNR-inducible promoter),
promoters induced by HE-specific molecules or metabolites
indicative of liver damage (e.g., bilirubin), promoters induced by
inflammation or an inflammatory response (RNS, ROS promoters), and
promoters induced by a metabolite that may or may not be naturally
present (e.g., can be exogenously added) in the gut, e.g.,
arabinose and tetracycline.
[0103] In some embodiments, any one or more of the payload or
therapeutic circuits (e.g., ammonia consuming, GABA reducing,
manganese reducing, short chain fatty acid producing circuits)
and/or any one or more of the additional circuits (e.g.,
auxotrophies, kill switch circuits, antibiotic resistance circuits,
transporters, and secretion circuits) may be present on one or more
low copy or high copy plasmids. In some embodiments, any one or
more of the payload or therapeutic circuits (e.g., ammonia
consuming, GABA reducing, manganese reducing, short chain fatty
acid producing circuits) and/or any one or more of the additional
circuits (e.g., auxotrophies, kill switch circuits, antibiotic
resistance circuits, transporters, and secretion circuits) may be
integrated into the bacterial chromosome. In order that the
disclosure may be more readily understood, certain terms are first
defined. These definitions should be read in light of the remainder
of the disclosure and as understood by a person of ordinary skill
in the art. Unless defined otherwise, all technical and scientific
terms used herein have the same meaning as commonly understood by a
person of ordinary skill in the art. Additional definitions are set
forth throughout the detailed description.
[0104] "Hyperammonemia," "hyperammonemic," or "excess ammonia" is
used to refer to increased concentrations of ammonia in the body.
Hyperammonemia is caused by decreased detoxification and/or
increased production of ammonia. Decreased detoxification may
result from urea cycle disorders (UCDs), such as argininosuccinic
aciduria, arginase deficiency, carbamoylphosphate synthetase
deficiency, citrullinemia, N-acetylglutamate synthetase deficiency,
and ornithine transcarbamylase deficiency; or from bypass of the
liver, e.g., open ductus hepaticus; and/or deficiencies in
glutamine synthetase (Hoffman et al., 2013; Haberle et al., 2013).
Decreased detoxification may also result from liver disorders such
as hepatic encephalopathy, acute liver failure, or chronic liver
failure; and neurodegenerative disorders such as Huntington's
disease (Chen et al., 2015; Chiang et al., 2007). Increased
production of ammonia may result from infections, drugs, neurogenic
bladder, and intestinal bacterial overgrowth (Haberle et al.,
2013). Other disorders and conditions associated with
hyperammonemia include, but are not limited to, liver disorders
such as hepatic encephalopathy, acute liver failure, or chronic
liver failure; organic acid disorders; isovaleric aciduria;
3-methylcrotonylglycinuria; methylmalonic acidemia; propionic
aciduria; fatty acid oxidation defects; carnitine cycle defects;
carnitine deficiency; .beta.-oxidation deficiency; lysinuric
protein intolerance; pyrroline-5-carboxylate synthetase deficiency;
pyruvate carboxylase deficiency; ornithine aminotransferase
deficiency; carbonic anhydrase deficiency;
hyperinsulinism-hyperammonemia syndrome; mitochondrial disorders;
valproate therapy; asparaginase therapy; total parenteral
nutrition; cystoscopy with glycine-containing solutions;
post-lung/bone marrow transplantation; portosystemic shunting;
urinary tract infections; ureter dilation; multiple myeloma; and
chemotherapy (Hoffman et al., 2013; Haberle et al., 2013; Pham et
al., 2013; Lazier et al., 2014). In healthy subjects, plasma
ammonia concentrations are typically less than about 50 .mu.mol/L
(Leonard, 2006). In some embodiments, a diagnostic signal of
hyperammonemia is a plasma ammonia concentration of at least about
50 .mu.mol/L, at least about 80 .mu.mol/L, at least about 150
.mu.mol/L, at least about 180 .mu.mol/L, or at least about 200
.mu.mol/L (Leonard, 2006; Hoffman et al., 2013; Haberle et al.,
2013).
[0105] "Ammonia" is used to refer to gaseous ammonia (NH.sub.3),
ionic ammonia (NH.sub.4.sup.+), or a mixture thereof. In bodily
fluids, gaseous ammonia and ionic ammonium exist in
equilibrium:
NH.sub.3+H.sup.+NH.sub.4.sup.+
[0106] Some clinical laboratory tests analyze total ammonia
(NH.sub.3+NH.sub.4.sup.+) (Walker, 2012). In any embodiment of the
invention, unless otherwise indicated, "ammonia" may refer to
gaseous ammonia, ionic ammonia, and/or total ammonia.
[0107] "Detoxification" of ammonia is used to refer to the process
or processes, natural or synthetic, by which toxic ammonia is
removed and/or converted into one or more non-toxic molecules,
including but not limited to: arginine, citrulline, methionine,
histidine, lysine, asparagine, glutamine, tryptophan, or urea. The
urea cycle, for example, enzymatically converts ammonia into urea
for removal from the body in the urine. Because ammonia is a source
of nitrogen for many amino acids, which are synthesized via
numerous biochemical pathways, enhancement of one or more of those
amino acid biosynthesis pathways may be used to incorporate excess
nitrogen into non-toxic molecules. For example, arginine
biosynthesis converts glutamate, which comprises one nitrogen atom,
to arginine, which comprises four nitrogen atoms, thereby
incorporating excess nitrogen into non-toxic molecules. In humans,
arginine is not reabsorbed from the large intestine, and as a
result, excess arginine in the large intestine is not considered to
be harmful. Likewise, citrulline is not reabsorbed from the large
intestine, and as a result, excess citrulline in the large
intestine is not considered to be harmful. Arginine biosynthesis
may also be modified to produce citrulline as an end product;
citrulline comprises three nitrogen atoms and thus the modified
pathway is also capable of incorporating excess nitrogen into
non-toxic molecules.
[0108] "Arginine regulon," "arginine biosynthesis regulon," and
"arg regulon" are used interchangeably to refer to the collection
of operons in a given bacterial species that comprise the genes
encoding the enzymes responsible for converting glutamate to
arginine and/or intermediate metabolites, e.g., citrulline, in the
arginine biosynthesis pathway. The arginine regulon also comprises
operators, promoters, ARG boxes, and/or regulatory regions
associated with those operons. The arginine regulon includes, but
is not limited to, the operons encoding the arginine biosynthesis
enzymes N-acetylglutamate synthetase, N-acetylglutamate kinase,
N-acetylglutamylphosphate reductase, acetylornithine am
inotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase,
carbamoylphosphate synthase, operators thereof, promoters thereof,
ARG boxes thereof, and/or regulatory regions thereof. In some
embodiments, the arginine regulon comprises an operon encoding
ornithine acetyltransferase and associated operators, promoters,
ARG boxes, and/or regulatory regions, either in addition to or in
lieu of N-acetylglutamate synthetase and/or N-acetylornithinase. In
some embodiments, one or more operons or genes of the arginine
regulon may be present on a plasmid in the bacterium. In some
embodiments, a bacterium may comprise multiple copies of any gene
or operon in the arginine regulon, wherein one or more copies may
be mutated or otherwise altered as described herein.
[0109] One gene may encode one enzyme, e.g., N-acetylglutamate
synthetase (argA). Two or more genes may encode distinct subunits
of one enzyme, e.g., subunit A and subunit B of carbamoylphosphate
synthase (carA and carB). In some bacteria, two or more genes may
each independently encode the same enzyme, e.g., ornithine
transcarbamylase (argF and argI). In some bacteria, the arginine
regulon includes, but is not limited to, argA, encoding
N-acetylglutamate synthetase; argB, encoding N-acetylglutamate
kinase; argC, encoding N-acetylglutamylphosphate reductase; argD,
encoding acetylornithine aminotransferase; argE, encoding
N-acetylornithinase; argG, encoding argininosuccinate synthase;
argH, encoding argininosuccinate lyase; one or both of argF and
argI, each of which independently encodes ornithine
transcarbamylase; carA, encoding the small subunit of
carbamoylphosphate synthase; carB, encoding the large subunit of
carbamoylphosphate synthase; operons thereof; operators thereof;
promoters thereof; ARG boxes thereof; and/or regulatory regions
thereof. In some embodiments, the arginine regulon comprises argJ,
encoding ornithine acetyltransferase (either in addition to or in
lieu of N-acetylglutamate synthetase and/or N-acetylornithinase),
operons thereof, operators thereof, promoters thereof, ARG boxes
thereof, and/or regulatory regions thereof.
[0110] "Arginine operon," "arginine biosynthesis operon," and "arg
operon" are used interchangeably to refer to a cluster of one or
more of the genes encoding arginine biosynthesis enzymes under the
control of a shared regulatory region comprising at least one
promoter and at least one ARG box. In some embodiments, the one or
more genes are co-transcribed and/or co-translated. Any combination
of the genes encoding the enzymes responsible for arginine
biosynthesis may be organized, naturally or synthetically, into an
operon. For example, in B. subtilis, the genes encoding
N-acetylglutamylphosphate reductase, N-acetylglutamate kinase,
N-acetylornithinase, N-acetylglutamate kinase, acetylornithine am
inotransferase, carbamoylphosphate synthase, and ornithine
transcarbamylase are organized in a single operon,
argCAEBD-carAB-argF (see, e.g., Table 2), under the control of a
shared regulatory region comprising a promoter and ARG boxes. In E.
coli K12 and Nissle, the genes encoding N-acetylornithinase,
N-acetylglutamylphosphate reductase, N-acetylglutamate kinase, and
argininosuccinate lyase are organized in two bipolar operons,
argECBH. The operons encoding the enzymes responsible for arginine
biosynthesis may be distributed at different loci across the
chromosome. In unmodified bacteria, each operon may be repressed by
arginine via ArgR. In some embodiments, arginine and/or
intermediate byproduct production may be altered in the genetically
engineered bacteria of the invention by modifying the expression of
the enzymes encoded by the arginine biosynthesis operons as
provided herein. Each arginine operon may be present on a plasmid
or bacterial chromosome. In addition, multiple copies of any
arginine operon, or a gene or regulatory region within an arginine
operon, may be present in the bacterium, wherein one or more copies
of the operon or gene or regulatory region may be mutated or
otherwise altered as described herein. In some embodiments, the
genetically engineered bacteria are engineered to comprise multiple
copies of the same product (e.g., operon or gene or regulatory
region) to enhance copy number or to comprise multiple different
components of an operon performing multiple different
functions.
[0111] "ARG box consensus sequence" refers to an ARG box nucleic
acid sequence, the nucleic acids of which are known to occur with
high frequency in one or more of the regulatory regions of argR,
argA, argB, argC, argD, argE, argF, argG, argH, argI, argJ, carA,
and/or carB. As described above, each arg operon comprises a
regulatory region comprising at least one 18-nucleotide imperfect
palindromic sequence, called an ARG box, that overlaps with the
promoter and to which the repressor protein binds (Tian et al.,
1992). The nucleotide sequences of the ARG boxes may vary for each
operon, and the consensus ARG box sequence is A/T nTGAAT A/T A/T
T/A T/A ATTCAn T/A (SEQ ID NO: 120) (Maas, 1994). The arginine
repressor binds to one or more ARG boxes to actively inhibit the
transcription of the arginine biosynthesis enzyme(s) that are
operably linked to that one or more ARG boxes.
[0112] "Mutant arginine regulon" or "mutated arginine regulon" is
used to refer to an arginine regulon comprising one or more nucleic
acid mutations that reduce or eliminate arginine-mediated
repression of each of the operons that encode the enzymes
responsible for converting glutamate to arginine and/or an
intermediate byproduct, e.g., citrulline, in the arginine
biosynthesis pathway, such that the mutant arginine regulon
produces more arginine and/or intermediate byproduct than an
unmodified regulon from the same bacterial subtype under the same
conditions. In some embodiments, the genetically engineered
bacteria comprise an arginine feedback resistant N-acetylglutamate
synthase mutant, e.g., argA.sup.fbr, and a mutant arginine regulon
comprising one or more nucleic acid mutations in at least one ARG
box for one or more of the operons that encode the arginine
biosynthesis enzymes N-acetylglutamate kinase,
N-acetylglutamylphosphate reductase, acetylornithine
aminotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase, and
carbamoylphosphate synthase, thereby derepressing the regulon and
enhancing arginine and/or intermediate byproduct biosynthesis. In
some embodiments, the genetically engineered bacteria comprise a
mutant arginine repressor comprising one or more nucleic acid
mutations such that arginine repressor function is decreased or
inactive, or the genetically engineered bacteria do not have an
arginine repressor (e.g., the arginine repressor gene has been
deleted), resulting in derepression of the regulon and enhancement
of arginine and/or intermediate byproduct biosynthesis. In some
embodiments, the genetically engineered bacteria comprise an
arginine feedback resistant N-acetylglutamate synthase mutant,
e.g., argA.sup.fbr, a mutant arginine regulon comprising one or
more nucleic acid mutations in at least one ARG box for each of the
operons that encode the arginine biosynthesis enzymes, and/or a
mutant or deleted arginine repressor. In some embodiments, the
genetically engineered bacteria comprise an arginine feedback
resistant N-acetylglutamate synthase mutant, e.g., argA.sup.fbr and
a mutant arginine regulon comprising one or more nucleic acid
mutations in at least one ARG box for each of the operons that
encode the arginine biosynthesis enzymes. In some embodiments, the
genetically engineered bacteria comprise an arginine feedback
resistant N-acetylglutamate synthase mutant, e.g., argA.sup.fbr and
a mutant or deleted arginine repressor. In some embodiments, the
mutant arginine regulon comprises an operon encoding wild-type
N-acetylglutamate synthetase and one or more nucleic acid mutations
in at least one ARG box for said operon. In some embodiments, the
mutant arginine regulon comprises an operon encoding wild-type
N-acetylglutamate synthetase and mutant or deleted arginine
repressor. In some embodiments, the mutant arginine regulon
comprises an operon encoding ornithine acetyltransferase (either in
addition to or in lieu of N-acetylglutamate synthetase and/or
N-acetylornithinase) and one or more nucleic acid mutations in at
least one ARG box for said operon.
[0113] The ARG boxes overlap with the promoter in the regulatory
region of each arginine biosynthesis operon. In the mutant arginine
regulon, the regulatory region of one or more arginine biosynthesis
operons is sufficiently mutated to disrupt the palindromic ARG box
sequence and reduce ArgR binding, but still comprises sufficiently
high homology to the promoter of the non-mutant regulatory region
to be recognized as the native operon-specific promoter. The operon
comprises at least one nucleic acid mutation in at least one ARG
box such that ArgR binding to the ARG box and to the regulatory
region of the operon is reduced or eliminated. In some embodiments,
bases that are protected from DNA methylation and bases that are
protected from hydroxyl radical attack during ArgR binding are the
primary targets for mutations to disrupt ArgR binding (see, e.g.,
Table 3). The promoter of the mutated regulatory region retains
sufficiently high homology to the promoter of the non-mutant
regulatory region such that RNA polymerase binds to it with
sufficient affinity to promote transcription of the operably linked
arginine biosynthesis enzyme(s). In some embodiments, the G/C:A/T
ratio of the promoter of the mutant differs by no more than 10%
from the G/C:A/T ratio of the wild-type promoter.
[0114] In some embodiments, more than one ARG box may be present in
a single operon. In one aspect of these embodiments, at least one
of the ARG boxes in an operon is altered to produce the requisite
reduced ArgR binding to the regulatory region of the operon. In an
alternate aspect of these embodiments, each of the ARG boxes in an
operon is altered to produce the requisite reduced ArgR binding to
the regulatory region of the operon.
[0115] "Reduced" ArgR binding is used to refer to a reduction in
repressor binding to an ARG box in an operon or a reduction in the
total repressor binding to the regulatory region of said operon, as
compared to repressor binding to an unmodified ARG box and
regulatory region in bacteria of the same subtype under the same
conditions. In some embodiments, ArgR binding to a mutant ARG box
and regulatory region of an operon is at least about 50% lower, at
least about 60% lower, at least about 70% lower, at least about 80%
lower, at least about 90% lower, or at least about 95% lower than
ArgR binding to an unmodified ARG box and regulatory region in
bacteria of the same subtype under the same conditions. In some
embodiments, reduced ArgR binding to a mutant ARG box and
regulatory region results in at least about 1.5-fold, at least
about 2-fold, at least about 10-fold, at least about 15-fold, at
least about 20-fold, at least about 30-fold, at least about
50-fold, at least about 100-fold, at least about 200-fold, at least
about 300-fold, at least about 400-fold, at least about 500-fold,
at least about 600-fold, at least about 700-fold, at least about
800-fold, at least about 900-fold, at least about 1,000-fold, or at
least about 1,500-fold increased mRNA expression of the one or more
genes in the operon.
[0116] "ArgR" or "arginine repressor" is used to refer to a protein
that is capable of suppressing arginine biosynthesis by regulating
the transcription of arginine biosynthesis genes in the arginine
regulon. When expression of the gene that encodes for the arginine
repressor protein ("argR") is increased in a wild-type bacterium,
arginine biosynthesis is decreased. When expression of argR is
decreased in a wild-type bacterium, or if argR is deleted or
mutated to inactivate arginine repressor function, arginine
biosynthesis is increased.
[0117] Bacteria that "lack any functional ArgR" and "ArgR deletion
bacteria" are used to refer to bacteria in which each arginine
repressor has significantly reduced or eliminated activity as
compared to unmodified arginine repressor from bacteria of the same
subtype under the same conditions. Reduced or eliminated arginine
repressor activity can result in, for example, increased
transcription of the arginine biosynthesis genes and/or increased
concentrations of arginine and/or intermediate byproducts, e.g.,
citrulline. Bacteria in which arginine repressor activity is
reduced or eliminated can be generated by modifying the bacterial
argR gene or by modifying the transcription of the argR gene. For
example, the chromosomal argR gene can be deleted, can be mutated,
or the argR gene can be replaced with an argR gene that does not
exhibit wild-type repressor activity.
[0118] "Operably linked" refers a nucleic acid sequence, e.g., a
gene encoding feedback resistant ArgA, that is joined to a
regulatory region sequence in a manner which allows expression of
the nucleic acid sequence, e.g., acts in cis.
A regulatory region is a nucleic acid that can direct transcription
of a gene of interest and may comprise promoter sequences, enhancer
sequences, response elements, protein recognition sites, inducible
elements, promoter control elements, protein binding sequences, 5'
and 3' untranslated regions, transcriptional start sites,
termination sequences, polyadenylation sequences, and introns.
[0119] An "inducible promoter" refers to a regulatory region that
is operably linked to one or more genes, wherein expression of the
gene(s) is increased in the presence of an inducer of said
regulatory region. In some embodiments, the genetically engineered
bacteria of the invention comprise an oxygen level-dependent
promoter induced by low-oxygen, microaerobic, or anaerobic
conditions. In some embodiments, the genetically engineered
bacteria comprise a promoter induced by a molecule or metabolite,
for example, a tissue-specific molecule or metabolite or a molecule
or metabolite indicative of liver damage. In some embodiments, the
metabolites may be gut specific. In some embodiments, the
metabolite may be associated with hepatic encephalopathy, e.g.,
bilirubin. Non-limiting examples of molecules or metabolites
include, e.g., bilirubin, aspartate aminotransferase, alanine
aminotransferase, blood coagulation factors II, VII, IX, and X,
alkaline phosphatase, gamma glutamyl transferase, hepatitis
antigens and antibodies, alpha fetoprotein, anti-mitochondrial,
smooth muscle, and anti-nuclear antibodies, iron, transferrin,
ferritin, copper, ceruloplasmin, ammonia, and manganese in their
blood and intestines. Promoters that respond to one of these
molecules or their metabolites may be used in the genetically
engineered bacteria provided herein. In some embodiments, the
genetically engineered bacteria comprise a promoter induced by
inflammation or an inflammatory response, e.g., RNS or ROS
promoter. In some embodiments, the genetically engineered bacteria
comprise a promoter induced by a metabolite that may or may not be
naturally present (e.g., can be exogenously added) in the gut,
e.g., arabinose and tetracycline.
[0120] "Exogenous environmental condition(s)" refer to setting(s)
or circumstance(s) under which the promoter described herein is
induced. The phrase "exogenous environmental conditions" is meant
to refer to the environmental conditions external to the engineered
micororganism, but endogenous or native to the host subject
environment. Thus, "exogenous" and "endogenous" may be used
interchangeably to refer to environmental conditions in which the
environmental conditions are endogenous to a mammalian body, but
external or exogenous to an intact microorganism cell. In some
embodiments, the exogenous environmental conditions are specific to
the gut of a mammal. In some embodiments, the exogenous
environmental conditions are specific to the upper gastrointestinal
tract of a mammal. In some embodiments, the exogenous environmental
conditions are specific to the lower gastrointestinal tract of a
mammal. In some embodiments, the exogenous environmental conditions
are specific to the small intestine of a mammal. In some
embodiments, exogenous environmental conditions refer to the
presence of molecules or metabolites that are specific to the
mammalian gut in a healthy or disease state (e.g., HE). In some
embodiments, the exogenous environmental conditions are low-oxygen,
microaerobic, or anaerobic conditions, such as the environment of
the mammalian gut. In some embodiments, exogenous environmental
conditions are molecules or metabolites that are specific to the
mammalian gut, e.g., propionate. In some embodiments, the exogenous
environmental condition is a tissue-specific or disease-specific
metabolite or molecule(s). In some embodiments, the exogenous
environmental condition is a low-pH environment. In some
embodiments, the genetically engineered microorganism of the
disclosure comprises a pH-dependent promoter. In some embodiments,
the genetically engineered microorganism of the diclosure comprise
an oxygen level-dependent promoter. In some aspects, bacteria have
evolved transcription factors that are capable of sensing oxygen
levels. Different signaling pathways may be triggered by different
oxygen levels and occur with different kinetics.
[0121] An "oxygen level-dependent promoter" or "oxygen
level-dependent regulatory region" refers to a nucleic acid
sequence to which one or more oxygen level-sensing transcription
factors is capable of binding, wherein the binding and/or
activation of the corresponding transcription factor activates
downstream gene expression.
[0122] Examples of oxygen level-dependent transcription factors
include, but are not limited to, FNR, ANR, and DNR. Corresponding
FNR-responsive promoters, ANR-responsive promoters, and
DNR-responsive promoters are known in the art (see, e.g.,
Castiglione et al., 2009; Eiglmeier et al., 1989; Galimand et al.,
1991; Hasegawa et al., 1998; Hoeren et al., 1993; Salmon et al.,
2003), and non-limiting examples are shown in Table 1.
[0123] In a non-limiting example, a promoter (PfnrS) was derived
from the E. coli Nissle fumarate and nitrate reductase gene S
(fnrS) that is known to be highly expressed under conditions of low
or no environmental oxygen (Durand and Storz, 2010; Boysen et al,
2010). The PfnrS promoter is activated under anaerobic conditions
by the global transcriptional regulator FNR that is naturally found
in Nissle. Under anaerobic conditions, FNR forms a dimer and binds
to specific sequences in the promoters of specific genes under its
control, thereby activating their expression. However, under
aerobic conditions, oxygen reacts with iron-sulfur clusters in FNR
dimers and converts them to an inactive form. In this way, the
PfnrS inducible promoter is adopted to modulate the expression of
proteins or RNA. PfnrS is used interchangeably in this application
as FNRS, fnrs, FNR, P-FNRS promoter and other such related
designations to indicate the promoter PfnrS.
TABLE-US-00001 TABLE 1 Examples of transcription factors and
responsive genes and regulatory regions Exemplary responsive genes,
Transcription promoters, and/or regulatory Factor regions: FNR
nirB, ydfZ, pdhR, focA, ndH, hlyE, narK, narX, narG, yfiD, tdcD ANR
arcDABC DNR norb, norC
[0124] "Gut barrier function enhancer molecules" include, but are
not limited to, short-chain fatty acids, butyrate, propionate,
acetate, GLP-2, IL-10, IL-27, TGF-.beta.1, TGF-.beta.2,
N-acylphosphatidylethanolamines (NAPEs), elafin (also called
peptidase inhibitor 3 and SKALP), trefoil factor, melatonin, PGD2,
kynurenic acid, and kynurenine. A gut barrier function enhancer
molecule may be encoded by a single gene, e.g., elafin is encoded
by the PI3 gene. Alternatively, a gut barrier function enhancer
molecule may be synthesized by a biosynthetic pathway requiring
multiple genes, e.g., butyrate. These molecules may also be
referred to as therapeutic molecules.
[0125] As used herein, a "gene cassette" or "operon" encoding a
biosynthetic pathway refers to the two or more genes that are
required to produce a gut barrier function enhancer molecule, e.g.,
butyrate, propionate. In addition to encoding a set of genes
capable of producing said molecule, the gene cassette or operon may
also comprise additional transcription and translation elements,
e.g., a ribosome binding site.
[0126] A "butyrogenic gene cassette," "butyrate biosynthesis gene
cassette," and "butyrate operon" are used interchangeably to refer
to a set of genes capable of producing butyrate in a biosynthetic
pathway. Unmodified bacteria that are capable of producing butyrate
via an endogenous butyrate biosynthesis pathway include, but are
not limited to, Clostridium, Peptoclostridium, Fusobacterium,
Butyrivibrio, Eubacterium, and Treponema, and these endogenous
butyrate biosynthesis pathways may be a source of genes for the
genetically engineered bacteria of the invention. The genetically
engineered bacteria of the invention may comprise butyrate
biosynthesis genes from a different species, strain, or substrain
of bacteria, or a combination of butyrate biosynthesis genes from
different species, strains, and/or substrains of bacteria. A
butyrogenic gene cassette may comprise, for example, the eight
genes of the butyrate production pathway from Peptoclostridium
difficile (also called Clostridium difficile): bcd2, etfB3, etfA3,
thiA1, hbd, crt2, pbt, and buk, which encode butyryl-CoA
dehydrogenase subunit, electron transfer flavoprotein subunit beta,
electron transfer flavoprotein subunit alpha, acetyl-CoA
C-acetyltransferase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase,
phosphate butyryltransferase, and butyrate kinase, respectively
(Aboulnaga et al., 2013). One or more of the butyrate biosynthesis
genes may be functionally replaced or modified. Peptoclostridium
difficile strain 630 and strain 1296 are both capable of producing
butyrate, but comprise different nucleic acid sequences for etfA3,
thiA1, hbd, crt2, pbt, and buk. A butyrogenic gene cassette may
comprise bcd2, etfB3, etfA3, and thiA1 from Peptoclostridium
difficile strain 630, and hbd, crt2, pbt, and buk from
Peptoclostridium difficile strain 1296. Alternatively, a single
gene from Treponema denticola (ter, encoding trans-2-enoynl-CoA
reductase) is capable of functionally replacing all three of the
bcd2, etfB3, and etfA3 genes from Peptoclostridium difficile. Thus,
a butyrogenic gene cassette may comprise thiA1, hbd, crt2, pbt, and
buk from Peptoclostridium difficile and ter from Treponema
denticola. The butyrogenic gene cassette may comprise genes for the
aerobic biosynthesis of butyrate and/or genes for the anaerobic or
microaerobic biosynthesis of butyrate.
[0127] Likewise, a "propionate gene cassette" or "propionate
operon" refers to a set of genes capable of producing propionate in
a biosynthetic pathway. Unmodified bacteria that are capable of
producing propionate via an endogenous propionate biosynthesis
pathway include, but are not limited to, Clostridium propionicum,
Megasphaera elsdenii, and Prevotella ruminicola, and these
endogenous propionate biosynthesis pathways may be a source of
genes for the genetically engineered bacteria of the invention. The
genetically engineered bacteria of the invention may comprise
propionate biosynthesis genes from a different species, strain, or
substrain of bacteria, or a combination of propionate biosynthesis
genes from different species, strains, and/or substrains of
bacteria. In some embodiments, the propionate gene cassette
comprises acrylate pathway propionate biosynthesis genes, e.g.,
pct, lcdA, lcdB, lcdC, etfA, acre, and acrC, which encode
propionate CoA-transferase, lactoyl-CoA dehydratase A, lactoyl-CoA
dehydratase B, lactoyl-CoA dehydratase C, electron transfer
flavoprotein subunit A, acryloyl-CoA reductase B, and acryloyl-CoA
reductase C, respectively (Hetzel et al., 2003, Selmer et al.,
2002). In alternate embodiments, the propionate gene cassette
comprises pyruvate pathway propionate biosynthesis genes (see,
e.g., Tseng and Prather, 2012), e.g., thrA.sup.fbr, thrB, thrC,
ilvA.sup.fbr, aceE, aceF, and lpd, which encode homoserine
dehydrogenase 1, homoserine kinase, L-threonine synthase,
L-threonine dehydratase, pyruvate dehydrogenase, dihydrolipoamide
acetyltransferase, and dihydrolipoyl dehydrogenase, respectively.
In some embodiments, the propionate gene cassette further comprises
tesB, which encodes acyl-CoA thioesterase. The propionate gene
cassette may comprise genes for the aerobic biosynthesis of
propionate and/or genes for the anaerobic or microaerobic
biosynthesis of propionate. One or more of the propionate
biosynthesis genes may be functionally replaced or modified, e.g.,
codon optimized.
[0128] An "acetate gene cassette" or "acetate operon" refers to a
set of genes capable of producing acetate in a biosynthetic
pathway. Bacteria "synthesize acetate from a number of carbon and
energy sources," including a variety of substrates such as
cellulose, lignin, and inorganic gases, and utilize different
biosynthetic mechanisms and genes, which are known in the art
(Ragsdale et al., 2008). Unmodified bacteria that are capable of
producing acetate via an endogenous acetate biosynthesis pathway
may be a source of acetate biosynthesis genes for the genetically
engineered bacteria of the invention. The genetically engineered
bacteria of the invention may comprise acetate biosynthesis genes
from a different species, strain, or substrain of bacteria, or a
combination of acetate biosynthesis genes from different species,
strains, and/or substrains of bacteria. Escherichia coli are
capable of consuming glucose and oxygen to produce acetate and
carbon dioxide during aerobic growth (Kleman et al., 1994). Several
bacteria, such as Acetitomaculum, Acetoanaerobium, Acetohalobium,
Acetonema, Balutia, Butyribacterium, Clostridium, Moorella,
Oxobacter, Sporomusa, and Thermoacetogenium, are acetogenic
anaerobes that are capable of converting CO or CO.sub.2+H.sub.2
into acetate, e.g., using the Wood-Ljungdahl pathway
(Schiel-Bengelsdorf et al., 2012). Genes in the Wood-Ljungdahl
pathway for various bacterial species are known in the art. The
acetate gene cassette may comprise genes for the aerobic
biosynthesis of acetate and/or genes for the anaerobic or
microaerobic biosynthesis of acetate. One or more of the acetate
biosynthesis genes may be functionally replaced or modified.
[0129] "GABA" and ".gamma.-aminobutyric acid" are used to refer to
the predominant inhibitory neurotransmitter
(C.sub.4H.sub.9NO.sub.2) in the mammalian central nervous system.
In humans, GABA is also directly responsible for regulating muscle
tone. GABA is capable of activating the GABA.sub.A receptor, which
is part of a ligand-gated ion channel complex, as well as the
GABA.sub.B metabotropic G protein-coupled receptor. Neurons that
produce GABA are known as "GABAergic" neurons, and activation of
GABA receptors is described as GABAergic tone (i.e., increased
activation of GABA receptors refers to increased GABAergic
tone).
[0130] "GABA transporter" and "GabP" are used to refer to a
membrane transport protein that is capable of transporting GABA
into bacterial cells (see, e.g., Li et al., 2001). In Escherichia
coli, the gabP gene encodes a high-affinity GABA permease
responsible for GABA transport (Li et al., 2001). In some
embodiments, the GABA transporter is encoded by a gabP gene derived
from a bacterial species, including but not limited to, Bacillus
subtilis and Escherichia coli. These endogenous GABA transporter
genes may be a source of genes for the genetically engineered
bacteria of the invention. Any suitable gene(s) encoding a GABA
transporter may be used.
[0131] "Manganese" refers to a chemical element with the symbol
"Mn" and atomic number 25. In biological systems, manganese is an
essential trace metal and plays an important role in
enzyme-mediated catalysis, but can also have deleterious effects.
Cells maintain manganese under tight homeostatic control in order
to avoid toxicity. Some disorders associated with hyperammonemia
may also be characterized by elevated levels of manganese;
manganese may contribute to disease pathogenesis (e.g., hepatic
encephalopathy) (Rivera-Mancia et al., 2012).
[0132] "Manganese transporter" and "MntH" refer to a membrane
transport protein that is capable of transporting manganese into
bacterial cells (see, e.g., Jensen and Jensen, 2014). In
Escherichia coli, the mntH gene encodes a proton-stimulated,
divalent metal cation uptake system involved in manganese transport
(Porcheron et al., 2013). In some embodiments, the manganese
transporter is encoded by a mntH gene derived from a bacterial
species, including but not limited to, Salmonella typhimurium,
Shigella flexneri, Yersinia pestis, and Escherichia coli. These
endogenous manganese transporter genes may be a source of genes for
the genetically engineered bacteria of the invention. Any suitable
gene(s) encoding a manganese transporter may be used.
[0133] As used herein, a "non-native" nucleic acid sequence refers
to a nucleic acid sequence not normally present in a bacterium,
e.g., an extra copy of an endogenous sequence, or a heterologous
sequence such as a sequence from a different species, strain, or
substrain of bacteria, or a sequence that is modified and/or
mutated as compared to the unmodified sequence from bacteria of the
same subtype. In some embodiments, the non-native nucleic acid
sequence is a synthetic, non-naturally occurring sequence (see,
e.g., Purcell et al., 2013). The non-native nucleic acid sequence
may be a regulatory region, a promoter, a gene, and/or one or more
genes in gene cassette. In some embodiments, "non-native" refers to
two or more nucleic acid sequences that are not found in the same
relationship to each other in nature. The non-native nucleic acid
sequence, e.g., gene or gene cassette, may be present on a plasmid
or bacterial chromosome. In some embodiments, the genetically
engineered bacteria of the invention comprise a gene cassette that
is operably linked to a directly or indirectly inducible promoter
that is not associated with said gene cassette in nature, e.g., a
FNR-responsive promoter operably linked to a butyrogenic gene
cassette, or an arginine production cassette. In addition, multiple
copies of the gene, gene cassette, or regulatory region may be
present in the bacterium, wherein one or more copies may be mutated
or otherwise altered as described herein. In some embodiments, the
genetically engineered bacteria are engineered to comprise multiple
copies of the same non-native nucleic acid sequence, e.g., gene,
gene cassette, or regulatory region, in order to enhance copy
number or to comprise multiple different components of a gene
cassette performing multiple different functions.
[0134] "Constitutive promoter" refers to a promoter that is capable
of facilitating continuous transcription of a coding sequence or
gene under its control and/or to which it is operably linked.
Constitutive promoters and variants are well known in the art and
include, but are not limited to, BBa_J23100, a constitutive
Escherichia coli .sigma..sup.S promoter (e.g., an osmY promoter
(International Genetically Engineered Machine (iGEM) Registry of
Standard Biological Parts Name BBa_J45992; BBa_J45993)), a
constitutive Escherichia coli .sigma..sup.32 promoter (e.g., htpG
heat shock promoter (BBa_J45504)), a constitutive Escherichia coli
.sigma..sup.70 promoter (e.g., lacq promoter (BBa_J54200;
BBa_J56015), E. coli CreABCD phosphate sensing operon promoter
(BBa_J64951), GlnRS promoter (BBa_K088007), lacZ promoter
(BBa_K119000; BBa_K119001); M13K07 gene I promoter (BBa_M13101);
M13K07 gene II promoter (BBa_M13102), M13K07 gene III promoter
(BBa_M13103), M13K07 gene IV promoter (BBa_M13104), M13K07 gene V
promoter (BBa_M13105), M13K07 gene VI promoter (BBa_M13106), M13K07
gene VIII promoter (BBa_M13108), M13110 (BBa_M13110)), a
constitutive Bacillus subtilis .sigma..sup.A promoter (e.g.,
promoter veg (BBa_K143013), promoter 43 (BBa_K143013), P.sub.liaG
(BBa_K823000), P.sub.lepA (BBa_K823002), P.sub.veg (BBa_K823003)),
a constitutive Bacillus subtilis .sigma..sup.B promoter (e.g.,
promoter ctc (BBa_K143010), promoter gsiB (BBa_K143011)), a
Salmonella promoter (e.g., Pspv2 from Salmonella (BBa_K112706),
Pspv from Salmonella (BBa_K112707)), a bacteriophage T7 promoter
(e.g., T7 promoter (BBa_1712074; BBa_1719005; BBa_J34814;
BBa_J64997; BBa_K113010; BBa_K113011; BBa_K113012; BBa_R0085;
BBa_R0180; BBa_R0181; BBa_R0182; BBa_R0183; BBa_Z0251; BBa_Z0252;
BBa_Z0253)), a bacteriophage SP6 promoter (e.g., SP6 promoter
(BBa_J64998)), and functional fragments thereof.
[0135] As used herein, genetically engineered bacteria that
"overproduce" arginine or an intermediate byproduct, e.g.,
citrulline, refer to bacteria that comprise a mutant arginine
regulon. For example, the engineered bacteria may comprise a
feedback resistant form of ArgA, and when the arginine feedback
resistant ArgA is expressed, are capable of producing more arginine
and/or intermediate byproduct than unmodified bacteria of the same
subtype under the same conditions. The genetically engineered
bacteria may alternatively or further comprise a mutant arginine
regulon comprising one or more nucleic acid mutations in at least
one ARG box for each of the operons that encode the arginine
biosynthesis enzymes. The genetically engineered bacteria may
alternatively or further comprise a mutant or deleted arginine
repressor. In some embodiments, the genetically engineered bacteria
produce at least about 1.5-fold, at least about 2-fold, at least
about 10-fold, at least about 15-fold, at least about 20-fold, at
least about 30-fold, at least about 50-fold, at least about
100-fold, at least about 200-fold, at least about 300-fold, at
least about 400-fold, at least about 500-fold, at least about
600-fold, at least about 700-fold, at least about 800-fold, at
least about 900-fold, at least about 1,000-fold, or at least about
1,500-fold more arginine than unmodified bacteria of the same
subtype under the same conditions. In some embodiments, the
genetically engineered bacteria produce at least about 1.5-fold, at
least about 2-fold, at least about 10-fold, at least about 15-fold,
at least about 20-fold, at least about 30-fold, at least about
50-fold, at least about 100-fold, at least about 200-fold, at least
about 300-fold, at least about 400-fold, at least about 500-fold,
at least about 600-fold, at least about 700-fold, at least about
800-fold, at least about 900-fold, at least about 1,000-fold, or at
least about 1,500-fold more citrulline or other intermediate
byproduct than unmodified bacteria of the same subtype under the
same conditions. In some embodiments, the mRNA transcript levels of
one or more of the arginine biosynthesis genes in the genetically
engineered bacteria are at least about 1.5-fold, at least about
2-fold, at least about 10-fold, at least about 15-fold, at least
about 20-fold, at least about 30-fold, at least about 50-fold, at
least about 100-fold, at least about 200-fold, at least about
300-fold, at least about 400-fold, at least about 500-fold, at
least about 600-fold, at least about 700-fold, at least about
800-fold, at least about 900-fold, at least about 1,000-fold, or at
least about 1,500-fold higher than the mRNA transcript levels in
unmodified bacteria of the same subtype under the same conditions.
In certain embodiments, the unmodified bacteria will not have
detectable levels of arginine, intermediate byproduct, and/or
transcription of the gene(s) in such operons. However, protein
and/or transcription levels of arginine and/or intermediate
byproduct will be detectable in the corresponding genetically
engineered bacterium having the mutant arginine regulon.
Transcription levels may be detected by directly measuring mRNA
levels of the genes. Methods of measuring arginine and/or
intermediate byproduct levels, as well as the levels of transcript
expressed from the arginine biosynthesis genes, are known in the
art. Arginine and citrulline, for example, may be measured by mass
spectrometry.
[0136] "Gut" refers to the organs, glands, tracts, and systems that
are responsible for the transfer and digestion of food, absorption
of nutrients, and excretion of waste. In humans, the gut comprises
the gastrointestinal tract, which starts at the mouth and ends at
the anus, and additionally comprises the esophagus, stomach, small
intestine, and large intestine. The gut also comprises accessory
organs and glands, such as the spleen, liver, gallbladder, and
pancreas. The upper gastrointestinal tract comprises the esophagus,
stomach, and duodenum of the small intestine. The lower
gastrointestinal tract comprises the remainder of the small
intestine, i.e., the jejunum and ileum, and all of the large
intestine, i.e., the cecum, colon, rectum, and anal canal. Bacteria
can be found throughout the gut, e.g., in the gastrointestinal
tract, and particularly in the intestines.
[0137] As used herein, the term "gene sequence" is meant to refer
to a genetic sequence, e.g., a nucleic acid sequence. The gene
sequence or genetic sequence is meant to include a complete gene
sequence or a partial gene sequence. The gene sequence or genetic
sequence is meant to include sequence that encodes a protein or
polypeptide and is also menat to include genetic sequence that does
not encode a protein or polypeptide, e.g., a regulatory sequence,
leader sequence, signal sequence, or other non-protein coding
sequence.
[0138] "Microorganism" refers to an organism or microbe of
microscopic, submicroscopic, or ultramicroscopic size that
typically consists of a single cell. Examples of microrganisms
include bacteria, viruses, parasites, fungi, certain algae, and
protozoa. In some aspects, the microorganism is engineered
("engineered microorganism") to produce one or more therapeutic
molecules. In certain aspects, the microorganism is engineered to
import and/or catabolize certain toxic metabolites, substrates, or
other compounds from its environment, e.g., the gut. In certain
aspects, the microorganism is engineered to synthesize certain
beneficial metabolites, molecules, or other compounds (synthetic or
naturally occurring) and release them into its environment. In
certain embodiments, the engineered microorganism is an engineered
bacterium. In certain embodiments, the engineered microorganism is
an engineered virus.
[0139] "Non-pathogenic bacteria" refer to bacteria that are not
capable of causing disease or harmful responses in a host. In some
embodiments, non-pathogenic bacteria are commensal bacteria.
Examples of non-pathogenic bacteria include, but are not limited to
Bacillus, Bacteroides, Bifidobacterium, Brevibacteria, Clostridium,
Enterococcus, Escherichia coli, Lactobacillus, Lactococcus,
Saccharomyces, and Staphylococcus, e.g., Bacillus coagulans,
Bacillus subtilis, Bacteroides fragilis, Bacteroides subtilis,
Bacteroides thetaiotaomicron, Bifidobacterium bifidum,
Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium
longum, Clostridium butyricum, Enterococcus faecium, Lactobacillus
acidophilus, Lactobacillus bulgaricus, Lactobacillus casei,
Lactobacillus johnsonii, Lactobacillus paracasei, Lactobacillus
plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus,
Lactococcus lactis, and Saccharomyces boulardii (Sonnenborn et al.,
2009; Dinleyici et al., 2014; U.S. Pat. No. 6,835,376; U.S. Pat.
No. 6,203,797; U.S. Pat. No. 5,589,168; U.S. Pat. No. 7,731,976).
Naturally pathogenic bacteria may be genetically engineered to
provide reduce or eliminate pathogenicity.
[0140] As used herein, "payload" refers to one or more
polynucleotides and/or polypeptides of interest to be produced by a
genetically engineered microorganism, such as a bacteria or a
virus. In some embodiments, the payload is encoded by a gene or
multiple genes or an operon. In some embodiments, the one or more
genes and/or operon(s) comprising the payload are endogenous to the
microorganism. In some embodiments, the one or more elements of the
payload is derived from a different microorganism and/or organism.
In some embodiments, the payload is a therapeutic payload. In some
embodiments, the payload is encoded by genes for the biosynthesis
of a molecule. In some embodiments, the payload is encoded by genes
for the metabolism, catabolism, or degradation of a molecule. In
some embodiments, the payload is encoded by genes for the
importation of a molecule. In some embodiments, the payload is
encoded by genes for the exportation of a molecule. In some
embodiments, the payload is a regulatory molecule(s), e.g., a
transcriptional regulator such as FNR. In some embodiments, the
payload comprises a regulatory element, such as a promoter or a
repressor. In some embodiments, the payload comprises an inducible
promoter, such as from FNRS. In some embodiments the payload
comprises a repressor element, such as a kill switch. In alternate
embodiments, the payload is produced by a biosynthetic or
biochemical pathway, wherein the biosynthetic or biochemical
pathway may optionally be endogenous to the microorganism. In some
embodiments, the genetically engineered microorganism comprises two
or more payloads. Non-limiting examples of payload(s) include one
or more of the following: (1) ArgAfbr, (2) mutated Arg Boxes, (3)
mutated ArgR, (4) mutated ArgG, (5) butyrate biosynthetic cassette,
(6) proprionate biosynthetic cassette, (7) acetate biosynthetic
cassette; (8) GABA-metabolizing cassette, (9) GABA-transporter,
(10) Mn-transporter. Other exemplary payloads include GLP-2, IL-10,
IL-27, TGF-.beta.1, TGF-.beta.2, elafin (also known as peptidase
inhibitor 3 or SKALP), trefoil factor, melatonin, PGD.sub.2,
kynurenic acid, and kynurenine. Other exemplary payloads include
mutated sequence(s) that result in an auxotrophy, e.g., thyA
auxotrophy, kill switch circuit, antibiotic resistance circuits,
transporter sequence for importing biological molecules or
substrates, secretion circuit.
[0141] "Probiotic" is used to refer to live, non-pathogenic
microorganisms, e.g., bacteria, which can confer health benefits to
a host organism that contains an appropriate amount of the
microorganism. In some embodiments, the host organism is a mammal.
In some embodiments, the host organism is a human. Some species,
strains, and/or subtypes of non-pathogenic bacteria are currently
recognized as probiotic bacteria. Examples of probiotic bacteria
include, but are not limited to, Bifidobacteria, Escherichia coli,
Lactobacillus, and Saccharomyces, e.g., Bifidobacterium bifidum,
Enterococcus faecium, Escherichia coli strain Nissle, Lactobacillus
acidophilus, Lactobacillus bulgaricus, Lactobacillus paracasei,
Lactobacillus plantarum, and Saccharomyces boulardii (Dinleyici et
al., 2014; U.S. Pat. No. 5,589,168; U.S. Pat. No. 6,203,797; U.S.
Pat. No. 6,835,376). The probiotic may be a variant or a mutant
strain of bacterium (Arthur et al., 2012; Cuevas-Ramos et al.,
2010; Olier et al., 2012; Nougayrede et al., 2006). Non-pathogenic
bacteria may be genetically engineered to enhance or improve
desired biological properties, e.g., survivability. Non-pathogenic
bacteria may be genetically engineered to provide probiotic
properties. Probiotic bacteria may be genetically engineered to
enhance or improve probiotic properties.
[0142] As used herein, "stably maintained" or "stable" bacterium is
used to refer to a bacterial host cell carrying non-native genetic
material, e.g., a feedback resistant argA gene, mutant arginine
repressor, and/or other mutant arginine regulon that is
incorporated into the host genome or propagated on a
self-replicating extra-chromosomal plasmid, such that the
non-native genetic material is retained, expressed, and propagated.
The stable bacterium is capable of survival and/or growth in vitro,
e.g., in medium, and/or in vivo, e.g., in the gut. For example, the
stable bacterium may be a genetically engineered bacterium
comprising an argA.sup.fbr gene, in which the plasmid or chromosome
carrying the argA.sup.fbr gene is stably maintained in the
bacterium, such that argA.sup.fbr can be expressed in the
bacterium, and the bacterium is capable of survival and/or growth
in vitro and/or in vivo.
[0143] As used herein, the terms "modulate" and "treat" and their
cognates refer to an amelioration of a disease, disorder, and/or
condition, or at least one discernible symptom thereof. In another
embodiment, "modulate" and "treat" refer to an amelioration of at
least one measurable physical parameter, not necessarily
discernible by the patient. In another embodiment, "modulate" and
"treat" refer to inhibiting the progression of a disease, disorder,
and/or condition, either physically (e.g., stabilization of a
discernible symptom), physiologically (e.g., stabilization of a
physical parameter), or both. In another embodiment, "modulate" and
"treat" refer to slowing the progression or reversing the
progression of a disease, disorder, and/or condition. As used
herein, "prevent" and its cognates refer to delaying the onset or
reducing the risk of acquiring a given disease, disorder and/or
condition or a symptom associated with such disease, disorder,
and/or condition.
[0144] Those in need of treatment may include individuals already
having a particular medical disorder, as well as those at risk of
having, or who may ultimately acquire the disorder. The need for
treatment is assessed, for example, by the presence of one or more
risk factors associated with the development of a disorder, the
presence or progression of a disorder, or likely receptiveness to
treatment of a subject having the disorder. Primary hyperammonemia
is caused by UCDs, which are autosomal recessive or X-linked inborn
errors of metabolism for which there are no known cures.
Hyperammonemia can also be secondary to other disruptions of the
urea cycle, e.g., toxic metabolites, infections, and/or substrate
deficiencies. Hyperammonemia can also contribute to other
pathologies. For example, Huntington's disease is an autosomal
dominant disorder for which there are no known cures. Urea cycle
abnormalities characterized by hyperammonemia, high blood
citrulline, and suppression of urea cycle enzymes may contribute to
the pathology of Huntington's disease, an autosomal dominant
disorder for which there are no known cures. Treating
hyperammonemia may encompass reducing or eliminating excess ammonia
and/or associated symptoms, and does not necessarily encompass the
elimination of the underlying hyperammonemia-associated
disorder.
[0145] As used herein a "pharmaceutical composition" refers to a
preparation of genetically engineered bacteria of the invention
with other components such as a physiologically suitable carrier
and/or excipient.
[0146] The phrases "physiologically acceptable carrier" and
"pharmaceutically acceptable carrier" which may be used
interchangeably refer to a carrier or a diluent that does not cause
significant irritation to an organism and does not abrogate the
biological activity and properties of the administered bacterial
compound. An adjuvant is included under these phrases.
[0147] The term "excipient" refers to an inert substance added to a
pharmaceutical composition to further facilitate administration of
an active ingredient. Examples include, but are not limited to,
calcium bicarbonate, calcium phosphate, various sugars and types of
starch, cellulose derivatives, gelatin, vegetable oils,
polyethylene glycols, and surfactants, including, for example,
polysorbate 20.
[0148] The terms "therapeutically effective dose" and
"therapeutically effective amount" are used to refer to an amount
of a compound that results in prevention, delay of onset of
symptoms, or amelioration of symptoms of a condition, e.g.,
hyperammonemia. A therapeutically effective amount may, for
example, be sufficient to treat, prevent, reduce the severity,
delay the onset, and/or reduce the risk of occurrence of one or
more symptoms of a disorder associated with elevated ammonia
concentrations. A therapeutically effective amount, as well as a
therapeutically effective frequency of administration, can be
determined by methods known in the art and discussed below.
[0149] As used herein, the term "polypeptide" includes
"polypeptide" as well as "polypeptides," and refers to a molecule
composed of amino acid monomers linearly linked by amide bonds
(i.e., peptide bonds). The term "polypeptide" refers to any chain
or chains of two or more amino acids, and does not refer to a
specific length of the product. Thus, "peptides," "dipeptides,"
"tripeptides, "oligopeptides," "protein," "amino acid chain," or
any other term used to refer to a chain or chains of two or more
amino acids, are included within the definition of "polypeptide,"
and the term "polypeptide" may be used instead of, or
interchangeably with any of these terms. The term "polypeptide" is
also intended to refer to the products of post-expression
modifications of the polypeptide, including but not limited to
glycosylation, acetylation, phosphorylation, amidation,
derivatization, proteolytic cleavage, or modification by
non-naturally occurring amino acids. A polypeptide may be derived
from a natural biological source or produced by recombinant
technology. In other embodiments, the polypeptide is produced by
the genetically engineered bacteria or virus of the current
invention. A polypeptide of the invention may be of a size of about
3 or more, 5 or more, 10 or more, 20 or more, 25 or more, 50 or
more, 75 or more, 100 or more, 200 or more, 500 or more, 1,000 or
more, or 2,000 or more amino acids. Polypeptides may have a defined
three-dimensional structure, although they do not necessarily have
such structure. Polypeptides with a defined three-dimensional
structure are referred to as folded, and polypeptides, which do not
possess a defined three-dimensional structure, but rather can adopt
a large number of different conformations, are referred to as
unfolded. The term "peptide" or "polypeptide" may refer to an amino
acid sequence that corresponds to a protein or a portion of a
protein or may refer to an amino acid sequence that corresponds
with non-protein sequence, e.g., a sequence selected from a
regulatory peptide sequence, leader peptide sequence, signal
peptide sequence, linker peptide sequence, and other peptide
sequence.
[0150] An "isolated" polypeptide or a fragment, variant, or
derivative thereof refers to a polypeptide that is not in its
natural milieu. No particular level of purification is required.
Recombinantly produced polypeptides and proteins expressed in host
cells, including but not limited to bacterial or mammalian cells,
are considered isolated for purposed of the invention, as are
native or recombinant polypeptides which have been separated,
fractionated, or partially or substantially purified by any
suitable technique. Recombinant peptides, polypeptides or proteins
refer to peptides, polypeptides or proteins produced by recombinant
DNA techniques, i.e. produced from cells, microbial or mammalian,
transformed by an exogenous recombinant DNA expression construct
encoding the polypeptide. Proteins or peptides expressed in most
bacterial cultures will typically be free of glycan. Fragments,
derivatives, analogs or variants of the foregoing polypeptides, and
any combination thereof are also included as polypeptides. The
terms "fragment," "variant," "derivative" and "analog" include
polypeptides having an amino acid sequence sufficiently similar to
the amino acid sequence of the original peptide and include any
polypeptides, which retain at least one or more properties of the
corresponding original polypeptide. Fragments of polypeptides of
the present invention include proteolytic fragments, as well as
deletion fragments. Fragments also include specific antibody or
bioactive fragments or immunologically active fragments derived
from any polypeptides described herein. Variants may occur
naturally or be non-naturally occurring. Non-naturally occurring
variants may be produced using mutagenesis methods known in the
art. Variant polypeptides may comprise conservative or
non-conservative amino acid substitutions, deletions or
additions.
[0151] Polypeptides also include fusion proteins. As used herein,
the term "variant" includes a fusion protein, which comprises a
sequence of the original peptide or sufficiently similar to the
original peptide. As used herein, the term "fusion protein" refers
to a chimeric protein comprising amino acid sequences of two or
more different proteins. Typically, fusion proteins result from
well known in vitro recombination techniques. Fusion proteins may
have a similar structural function (but not necessarily to the same
extent), and/or similar regulatory function (but not necessarily to
the same extent), and/or similar biochemical function (but not
necessarily to the same extent) and/or immunological activity (but
not necessarily to the same extent) as the individual original
proteins which are the components of the fusion proteins.
"Derivatives" include but are not limited to peptides, which
contain one or more naturally occurring amino acid derivatives of
the twenty standard amino acids. "Similarity" between two peptides
is determined by comparing the amino acid sequence of one peptide
to the sequence of a second peptide. An amino acid of one peptide
is similar to the corresponding amino acid of a second peptide if
it is identical or a conservative amino acid substitution.
Conservative substitutions include those described in Dayhoff, M.
O., ed., The Atlas of Protein Sequence and Structure 5, National
Biomedical Research Foundation, Washington, D.C. (1978), and in
Argos, EMBO J. 8 (1989), 779-785. For example, amino acids
belonging to one of the following groups represent conservative
changes or substitutions: -Ala, Pro, Gly, Gln, Asn, Ser, Thr; -Cys,
Ser, Tyr, Thr; -Val, Ile, Leu, Met, Ala, Phe; -Lys, Arg, His; -Phe,
Tyr, Trp, His; and -Asp, Glu.
[0152] As used herein, the term "sufficiently similar" means a
first amino acid sequence that contains a sufficient or minimum
number of identical or equivalent amino acid residues relative to a
second amino acid sequence such that the first and second amino
acid sequences have a common structural domain and/or common
functional activity. For example, amino acid sequences that
comprise a common structural domain that is at least about 45%, at
least about 50%, at least about 55%, at least about 60%, at least
about 65%, at least about 70%, at least about 75%, at least about
80%, at least about 85%, at least about 90%, at least about 91%, at
least about 92%, at least about 93%, at least about 94%, at least
about 95%, at least about 96%, at least about 97%, at least about
98%, at least about 99%, or at least about 100%, identical are
defined herein as sufficiently similar. Preferably, variants will
be sufficiently similar to the amino acid sequence of the peptides
of the invention. Such variants generally retain the functional
activity of the peptides of the present invention. Variants include
peptides that differ in amino acid sequence from the native and wt
peptide, respectively, by way of one or more amino acid
deletion(s), addition(s), and/or substitution(s). These may be
naturally occurring variants as well as artificially designed
ones.
[0153] As used herein the term "linker", "linker peptide" or
"peptide linkers" or "linker" refers to synthetic or non-native or
non-naturally-occurring amino acid sequences that connect or link
two polypeptide sequences, e.g., that link two polypeptide domains.
As used herein the term "synthetic" refers to amino acid sequences
that are not naturally occurring. Exemplary linkers are described
herein. Additional exemplary linkers are provided in US
20140079701, the contents of which are herein incorporated by
reference in its entirety.
[0154] As used herein the term "codon-optimized sequence" refers to
a sequence, which was modified from an existing coding sequence, or
designed, for example, to improve translation in an expression host
cell or organism of a transcript RNA molecule transcribed from the
coding sequence, or to improve transcription of a coding sequence.
Codon optimization includes, but is not limited to, processes
including selecting codons for the coding sequence to suit the
codon preference of the expression host organism.
[0155] Many organisms display a bias or preference for use of
particular codons to code for insertion of a particular amino acid
in a growing polypeptide chain. Codon preference or codon bias,
differences in codon usage between organisms, is allowed by the
degeneracy of the genetic code, and is well documented among many
organisms. Codon bias often correlates with the efficiency of
translation of messenger RNA (mRNA), which is in turn believed to
be dependent on, inter alia, the properties of the codons being
translated and the availability of particular transfer RNA (tRNA)
molecules. The predominance of selected tRNAs in a cell is
generally a reflection of the codons used most frequently in
peptide synthesis. Accordingly, genes can be tailored for optimal
gene expression in a given organism based on codon
optimization.
[0156] As used herein, the terms "secretion system" or "secretion
protein" refers to a native or non-native secretion mechanism
capable of secreting or exporting the protein of interest or
therapeutic protein from the microbial, e.g., bacterial cytoplasm.
The secretion system may comprise a single protein or may comprise
two or more proteins assembled in a complex e.g. HlyBD.
Non-limiting examples of secretion systems for gram negative
bacteria include the modified type III flagellar, type I (e.g.,
hemolysin secretion system), type II, type IV, type V, type VI, and
type VII secretion systems, resistance-nodulation-division (RN D)
multi-drug efflux pumps, various single membrane secretion systems.
Non-liming examples of secretion systems for gram positive bacteria
include Sec and TAT secretion systems. In some embodiments, the the
protein(s) of interest or therapeutic protein(s) include a
"secretion tag" of either RNA or peptide origin to direct the
protein(s) of interest or therapeutic protein(s) to specific
secretion systems. In some embodiments, the secretion system is
able to remove this tag before secreting the protein(s) of interest
or therapeutic protein(s) from the engineered bacteria. For
example, in Type V auto-secretion-mediated secretion the N-terminal
peptide secretion tag is removed upon translocation of the
"passenger" peptide from the cytoplasm into the periplasmic
compartment by the native Sec system. Further, once the
auto-secretor is translocated across the outer membrane the
C-terminal secretion tag can be removed by either an autocatalytic
or protease-catalyzed e.g., OmpT cleavage thereby releasing the
protein(s) of interest or therapeutic protein(s) into the
extracellular milieu.
[0157] As used herein, the term "transporter" is meant to refer to
a mechanism, e.g., protein or proteins, for importing a molecule,
e.g., amino acid, toxin, metabolite, substrate, etc. into the
microorganism from the extracellular milieu.
[0158] The articles "a" and "an," as used herein, should be
understood to mean "at least one," unless clearly indicated to the
contrary.
[0159] The phrase "and/or," when used between elements in a list,
is intended to mean either (1) that only a single listed element is
present, or (2) that more than one element of the list is present.
For example, "A, B, and/or C" indicates that the selection may be A
alone; B alone; C alone; A and B; A and C; B and C; or A, B, and C.
The phrase "and/or" may be used interchangeably with "at least one
of" or "one or more of" the elements in a list.
[0160] Bacteria
[0161] The genetically engineered bacteria disclosed herein are
capable of reducing excess ammonia and converting ammonia and/or
nitrogen into alternate byproducts. In some embodiments, the
genetically engineered bacteria are naturally non-pathogenic
bacteria. In some embodiments, the genetically engineered bacteria
are commensal bacteria. In some embodiments, the genetically
engineered bacteria are probiotic bacteria. In some embodiments,
the genetically engineered bacteria are naturally pathogenic
bacteria that are modified or mutated to reduce or eliminate
pathogenicity. Exemplary bacteria include, but are not limited to
Bacillus, Bacteroides, Bifidobacterium, Brevibacteria, Clostridium,
Enterococcus, Escherichia coli, Lactobacillus, Lactococcus,
Saccharomyces, and Staphylococcus, e.g., Bacillus coagulans,
Bacillus subtilis, Bacteroides fragilis, Bacteroides subtilis,
Bacteroides thetaiotaomicron, Bifidobacterium bifidum,
Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium
longum, Clostridium butyricum, Enterococcus faecium, Lactobacillus
acidophilus, Lactobacillus bulgaricus, Lactobacillus casei,
Lactobacillus johnsonii, Lactobacillus paracasei, Lactobacillus
plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus,
Lactococcus lactis, and Saccharomyces boulardii. In certain
embodiments, the genetically engineered bacteria are selected from
the group consisting of Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides subtilis, Bifidobacterium bifidum,
Bifidobacterium infantis, Bifidobacterium lactis, Clostridium
butyricum, Escherichia coli Nissle, Lactobacillus acidophilus,
Lactobacillus plantarum, Lactobacillus reuteri, and Lactococcus
lactis.
[0162] In some embodiments, the genetically engineered bacteria are
Escherichia coli strain Nissle 1917 (E. coli Nissle), a
Gram-negative bacterium of the Enterobacteriaceae family that has
evolved into one of the best characterized probiotics (Ukena et
al., 2007). The strain is characterized by its complete
harmlessness (Schultz, 2008), and has GRAS (generally recognized as
safe) status (Reister et al., 2014, emphasis added). Genomic
sequencing confirmed that E. coli Nissle lacks prominent virulence
factors (e.g., E. coli .alpha.-hemolysin, P-fimbrial adhesins)
(Schultz, 2008). In addition, it has been shown that E. coli Nissle
does not carry pathogenic adhesion factors, does not produce any
enterotoxins or cytotoxins, is not invasive, and not uropathogenic
(Sonnenborn et al., 2009). As early as in 1917, E. coli Nissle was
packaged into medicinal capsules, called Mutaflor, for therapeutic
use. E. coli Nissle has since been used to treat ulcerative colitis
in humans in vivo (Rembacken et al., 1999), to treat inflammatory
bowel disease, Crohn's disease, and pouchitis in humans in vivo
(Schultz, 2008), and to inhibit enteroinvasive Salmonella,
Legionella, Yersinia, and Shigella in vitro (Altenhoefer et al.,
2004). It is commonly accepted that E. coli Nissle's therapeutic
efficacy and safety have convincingly been proven (Ukena et al.,
2007).
[0163] One of ordinary skill in the art would appreciate that the
genetic modifications disclosed herein may be modified and adapted
for other species, strains, and subtypes of bacteria. It is known,
for example, that arginine-mediated regulation is remarkably well
conserved in very divergent bacteria, i.e., Gram-negative bacteria,
such as E. coli, Salmonella enterica serovar Typhimurium,
Thermotoga, and Moritella profunda, and Gram-positive bacteria,
such as B. subtilis, Geobacillus stearothermophilus, and
Streptomyces clavuligerus, as well as other bacteria (Nicoloff et
al., 2004). Furthermore, the arginine repressor is universally
conserved in bacterial genomes and that its recognition signal (the
ARG box), a weak palindrome, is also conserved between genomes
(Makarova et al., 2001).
[0164] Unmodified E. coli Nissle and the genetically engineered
bacteria of the invention may be destroyed, e.g., by defense
factors in the gut or blood serum (Sonnenborn et al., 2009). The
residence time of bacteria in vivo can be determined using the
methods described herein. In some embodiments, the residence time
is calculated for a human subject. A non-limiting example using a
streptomycin-resistant E. coli Nissle comprising a wild-type ArgR
and a wild-type arginine regulon is provided herein. In some
embodiments, residence time in vivo is calculated for the
genetically engineered bacteria of the invention.
[0165] Reduction of Excess Ammonia
[0166] Arginine Biosynthesis Pathway
[0167] In bacteria such as Escherichia coli (E. coli), the arginine
biosynthesis pathway is capable of converting glutamate to arginine
in an eight-step enzymatic process involving the enzymes
N-acetylglutamate synthetase, N-acetylglutamate kinase,
N-acetylglutamate phosphate reductase, acetylornithine
aminotransferase, N-acetylornithinase, carbamoylphosphate synthase,
ornithine transcarbamylase, argininosuccinate synthase, and
argininosuccinate lyase (Cunin et al., 1986). The first five steps
involve N-acetylation to generate an ornithine precursor. In the
sixth step, ornithine transcarbamylase (also known as ornithine
carbamoyltransferase) catalyzes the formation of citrulline. The
final two steps involve carbamoylphosphate utilization to generate
arginine from citrulline.
[0168] In some bacteria, e.g., Bacillus stearothermophilus and
Neisseria gonorrhoeae, the first and fifth steps in arginine
biosynthesis may be catalyzed by the bifunctional enzyme ornithine
acetyltransferase. This bifunctionality was initially identified
when ornithine acetyltransferase (argJ) was shown to complement
both N-acetylglutamate synthetase (argA) and N-acetylornithinase
(argE) auxotrophic gene mutations in E. coli (Mountain et al.,
1984; Crabeel et al., 1997).
[0169] ArgA encodes N-acetylglutamate synthetase, argB encodes
N-acetylglutamate kinase, argC encodes N-acetylglutamylphosphate
reductase, argD encodes acetylornithine aminotransferase, argE
encodes N-acetylornithinase, argF encodes ornithine
transcarbamylase, argI also encodes ornithine transcarbamylase,
argG encodes argininosuccinate synthase, argH encodes
argininosuccinate lyase, and argJ encodes ornithine
acetyltransferase. CarA encodes the small A subunit of
carbamoylphosphate synthase having glutaminase activity, and carB
encodes the large B subunit of carbamoylphosphate synthase that
catalyzes carbamoylphosphate synthesis from ammonia. Different
combinations of one or more of these arginine biosynthesis genes
(i.e., argA, argB, argC, argD, argE, argF, argG, argH, argI, argJ,
carA, and care) may be organized, naturally or synthetically, into
one or more operons, and such organization may vary between
bacterial species, strains, and subtypes (see, e.g., Table 2). The
regulatory region of each operon contains at least one ARG box, and
the number of ARG boxes per regulatory region may vary between
operons and bacteria.
[0170] All of the genes encoding these enzymes are subject to
repression by arginine via its interaction with ArgR to form a
complex that binds to the regulatory region of each gene and
inhibits transcription. N-acetylglutamate synthetase is also
subject to allosteric feedback inhibition at the protein level by
arginine alone (Tuchman et al., 1997; Caldara et al., 2006; Caldara
et al., 2008; Caldovic et al., 2010).
[0171] The genes that regulate arginine biosynthesis in bacteria
are scattered across the chromosome and organized into multiple
operons that are controlled by a single repressor, which Maas and
Clark (1964) termed a "regulon." Each operon is regulated by a
regulatory region comprising at least one 18-nucleotide imperfect
palindromic sequence, called an ARG box, that overlaps with the
promoter and to which the repressor protein binds (Tian et al.,
1992; Tian et al., 1994). The argR gene encodes the repressor
protein, which binds to one or more ARG boxes (Lim et al., 1987).
Arginine functions as a corepressor that activates the arginine
repressor. The ARG boxes that regulate each operon may be
non-identical, and the consensus ARG box sequence is A/T nTGAAT A/T
A/T T/A T/A ATTCAn T/A (SEQ ID NO: 120) (Maas, 1994). In addition,
the regulatory region of argR contains two promoters, one of which
overlaps with two ARG boxes and is autoregulated.
[0172] In some embodiments, the genetically engineered bacteria
comprise a mutant arginine regulon and produce more arginine and/or
an intermediate byproduct, e.g., citrulline, than unmodified
bacteria of the same subtype under the same conditions. The mutant
arginine regulon comprises one or more nucleic acid mutations that
reduce or prevent arginine-mediated repression--via ArgR binding to
ARG boxes and/or arginine binding to N-acetylglutamate
synthetase--of one or more of the operons that encode the enzymes
responsible for converting glutamate to arginine in the arginine
biosynthesis pathway, thereby enhancing arginine and/or
intermediate byproduct biosynthesis.
[0173] In alternate embodiments, the bacteria are genetically
engineered to consume excess ammonia via another metabolic pathway,
e.g., a histidine biosynthesis pathway, a methionine biosynthesis
pathway, a lysine biosynthesis pathway, an asparagine biosynthesis
pathway, a glutamine biosynthesis pathway, and a tryptophan
biosynthesis pathway. As used herein, "an ammonia conversion
circuit" refers to a metabolic pathway by which excess ammonia may
be consumed and/or reduced.
[0174] Histidine Biosynthesis Pathway
[0175] Histidine biosynthesis, for example, is carried out by eight
genes located within a single operon in E. coli. Three of the eight
genes of the operon (hisD, hisB, and hisI) encode bifunctional
enzymes, and two (hisH and hisF) encode polypeptide chains which
together form one enzyme to catalyze a single step, for a total of
10 enzymatic reactions (Alifano et al., 1996). The product of the
hisG gene, ATP phosphoribosyltransferase, is inhibited at the
protein level by histidine. In some embodiments, the genetically
engineered bacteria of the invention comprise a feedback-resistant
hisG. Bacteria may be mutagenized and/or screened for
feedback-resistant hisG mutants using techniques known in the art.
Bacteria engineered to comprise a feedback-resistant hisG would
have elevated levels of histidine production, thus increasing
ammonia consumption and reducing hyperammonemia. Alternatively, one
or more genes required for histidine biosynthesis could be placed
under the control of an inducible promoter, such as a FNR-inducible
promoter, and allow for increased production of rate-limiting
enzymes. Any other suitable modification(s) to the histidine
biosynthesis pathway may be used to increase ammonia
consumption.
[0176] Methionine Biosynthesis Pathway
[0177] The bacterial methionine regulon controls the three-step
synthesis of methionine from homoserine (i.e., acylation,
sulfurylation, and methylation). The metJ gene encodes a regulatory
protein that, when combined with methionine or a derivative
thereof, causes repression of genes within the methionine regulon
at the transcriptional level (Saint-Girons et al., 1984; Shoeman et
al., 1985). In some embodiments, the genetically engineered
bacteria of the invention comprise deleted, disrupted, or mutated
metJ. Bacteria engineered to delete, disrupt, or mutate metJ would
have elevated levels of methionine production, thus increasing
ammonia consumption and reducing hyperammonemia. Any other suitable
modification(s) to the methionine biosynthesis pathway may be used
to increase ammonia consumption.
[0178] Lysine Biosynthesis Pathway
[0179] Microorganisms synthesize lysine by one of two pathways. The
diaminopimelate (DAP) pathway is used to synthesize lysine from
aspartate and pyruvate (Dogovski et al., 2012), and the aminoadipic
acid pathway is used to synthesize lysine from alpha-ketoglutarate
and acetyl coenzyme A. The dihydrodipicolinate synthase (DHDPS)
enzyme catalyzes the first step of the DAP pathway, and is subject
to feedback inhibition by lysine (Liu et al., 2010; Reboul et al.,
2012). In some embodiments, the genetically engineered bacteria of
the invention comprise a feedback-resistant DHDPS. Bacteria
engineered to comprise a feedback-resistant DHDPS would have
elevated levels of histidine production, thus increasing ammonia
consumption and reducing hyperammonemia. Alternatively, lysine
production could be optimized by placing one or more genes required
for lysine biosynthesis under the control of an inducible promoter,
such as a FNR-inducible promoter. Any other suitable
modification(s) to the lysine biosynthesis pathway may be used to
increase ammonia consumption.
[0180] Asparagine Biosynthesis Pathway
[0181] Asparagine is synthesized directly from oxaloacetate and
aspartic acid via the oxaloacetate transaminase and asparagine
synthetase enzymes, respectively. In the second step of this
pathway, either L-glutamine or ammonia serves as the amino group
donor. In some embodiments, the genetically engineered bacteria of
the invention overproduce asparagine as compared to unmodified
bacteria of the same subtype under the same conditions, thereby
consuming excess ammonia and reducing hyperammonemia.
Alternatively, asparagine synthesis may be optimized by placing one
or both of these genes under the control of an inducible promoter,
such as a FNR-inducible promoter. Any other suitable
modification(s) to the asparagine biosynthesis pathway may be used
to increase ammonia consumption.
[0182] Glutamine Biosynthesis Pathway
[0183] The synthesis of glutamine and glutamate from ammonia and
oxoglutarate is tightly regulated by three enzymes. Glutamate
dehydrogenase catalyzes the reductive amination of oxoglutarate to
yield glutamate in a single step. Glutamine synthetase catalyzes
the ATP-dependent condensation of glutamate and ammonia to form
glutamine (Lodeiro et al., 2008). Glutamine synthetase also acts
with glutamine-oxoglutarate amino transferase (also known as
glutamate synthase) in a cyclic reaction to produce glutamate from
glutamine and oxoglutarate. In some embodiments, the genetically
engineered bacteria of the invention express glutamine synthetase
at elevated levels as compared to unmodified bacteria of the same
subtype under the same conditions. Bacteria engineered to have
increased expression of glutamine synthetase would have elevated
levels of glutamine production, thus increasing ammonia consumption
and reducing hyperammonemia. Alternatively, expression of glutamate
dehydrogenase and/or glutamine-oxoglutarate amino transferase could
be modified to favor the consumption of ammonia. Since the
production of glutamine synthetase is regulated at the
transcriptional level by nitrogen (Feng et al., 1992; van Heeswijk
et al., 2013), placing the glutamine synthetase gene under the
control of different inducible promoter, such as a FNR-inducible
promoter, may also be used to improve glutamine production. Any
other suitable modification(s) to the glutamine and glutamate
biosynthesis pathway may be used to increase ammonia
consumption.
[0184] Tryptophan Biosynthesis Pathway
[0185] In most bacteria, the genes required for the synthesis of
tryptophan from a chorismate precursor are organized as a single
transcriptional unit, the trp operon. The trp operon is under the
control of a single promoter that is inhibited by the tryptophan
repressor (TrpR) when high levels of tryptophan are present.
Transcription of the trp operon may also be terminated in the
presence of high levels of charged tryptophan tRNA. In some
embodiments, the genetically engineered bacteria of the invention
comprise a deleted, disrupted, or mutated trpR gene. The deletion,
disruption, or mutation of the trpR gene, and consequent
inactivation of TrpR function, would result in elevated levels of
both tryptophan production and ammonia consumption. Alternatively,
one or more enzymes required for tryptophan biosynthesis could be
placed under the control of an inducible promoter, such as a
FNR-inducible promoter. Any other suitable modification(s) to the
tryptophan biosynthesis pathway may be used to increase ammonia
consumption.
[0186] Engineered Bacteria Comprising a Mutant Arginine Regulon
[0187] In some embodiments, the genetically engineered bacteria
comprise an arginine biosynthesis pathway and are capable of
reducing excess ammonia. In a more specific aspect, the genetically
engineered bacteria comprise a mutant arginine regulon in which one
or more operons encoding arginine biosynthesis enzyme(s) is
derepressed to produce more arginine or an intermediate byproduct,
e.g., citrulline, than unmodified bacteria of the same subtype
under the same conditions. In some embodiments, the genetically
engineered bacteria overproduce arginine. In some embodiments, the
genetically engineered bacteria overproduce citrulline; this may be
additionally beneficial, because citrulline is currently used as a
therapeutic for particular urea cycle disorders (National Urea
Cycle Disorders Foundation). In some embodiments, the genetically
engineered bacteria overproduce an alternate intermediate byproduct
in the arginine biosynthesis pathway, such as any of the
intermediates described herein. In some embodiments, the
genetically engineered bacterium consumes excess ammonia by
producing more arginine, citrulline, and/or other intermediate
byproduct than an unmodified bacterium of the same bacterial
subtype under the same conditions. Enhancement of arginine and/or
intermediate byproduct biosynthesis may be used to incorporate
excess nitrogen in the body into non-toxic molecules in order to
treat conditions associated with hyperammonemia, including urea
cycle disorders and hepatic encephalopathy.
[0188] One of skill in the art would appreciate that the
organization of arginine biosynthesis genes within an operon varies
across species, strains, and subtypes of bacteria, e.g., bipolar
argECBH in E. coli K12, argCAEBD-carAB-argF in B. subtilis, and
bipolar carAB-argCJBDF in L. plantarum. Non-limiting examples of
operon organization from different bacteria are shown in Table 2
(in some instances, the genes are putative and/or identified by
sequence homology to known sequences in Escherichia coli; in some
instances, not all of the genes in the arginine regulon are known
and/or shown below). In certain instances, the arginine
biosynthesis enzymes vary across species, strains, and subtypes of
bacteria.
TABLE-US-00002 TABLE 2 Examples of arg operon organization Bacteria
Operon organization Escherichia coli argA bipolar argD argI argG
carAB Nissle argECBH Bacteroides argRGCD argF argB argE carAB
Clostridium argR argGH argI Bacillus subtilis argGH
argCAEBD-carAB-argF Bacillus subtilis argGH argCJBD-carAB-argF
Lactobacillus plantarum argGH bipolar carAB-argCJBDF Lactococcus
argE carA carB argGH argFBDJC
[0189] Each operon is regulated by a regulatory region comprising
at least one promoter and at least one ARG box, which control
repression and expression of the arginine biosynthesis genes in
said operon.
[0190] In some embodiments, the genetically engineered bacteria of
the invention comprise an arginine regulon comprising one or more
nucleic acid mutations that reduce or eliminate arginine-mediated
repression of one or more of the operons that encode the enzymes
responsible for converting glutamate to arginine and/or an
intermediate byproduct in the arginine biosynthesis pathway.
Reducing or eliminating arginine-mediated repression may be
achieved by reducing or eliminating ArgR repressor binding (e.g.,
by mutating or deleting the arginine repressor or by mutating at
least one ARG box for each of the operons that encode the arginine
biosynthesis enzymes) and/or arginine binding to N-acetylglutamate
synthetase (e.g., by mutating the N-acetylglutamate synthetase to
produce an arginine feedback resistant N-acetylglutamate synthase
mutant, e.g., argA.sup.fbr).
[0191] ARG Box
[0192] In some embodiments, the genetically engineered bacteria
comprise a mutant arginine regulon comprising one or more nucleic
acid mutations in at least one ARG box for one or more of the
operons that encode the arginine biosynthesis enzymes
N-acetylglutamate kinase, N-acetylglutamylphosphate reductase,
acetylornithine aminotransferase, N-acetylornithinase, ornithine
transcarbamylase, argininosuccinate synthase, argininosuccinate
lyase, and carbamoylphosphate synthase, thereby derepressing the
regulon and enhancing arginine and/or intermediate byproduct
biosynthesis. In some embodiments, the genetically engineered
bacteria comprise a mutant arginine repressor comprising one or
more nucleic acid mutations such that arginine repressor function
is decreased or inactive, or the genetically engineered bacteria do
not have an arginine repressor (e.g., the arginine repressor gene
has been deleted), resulting in derepression of the regulon and
enhancement of arginine and/or intermediate byproduct biosynthesis.
In either of these embodiments, the genetically engineered bacteria
may further comprise an arginine feedback resistant
N-acetylglutamate synthase mutant, e.g., argA.sup.fbr. Thus, in
some embodiments, the genetically engineered bacteria comprise a
mutant arginine regulon comprising one or more nucleic acid
mutations in at least one ARG box for one or more of the operons
that encode the arginine biosynthesis enzymes and an arginine
feedback resistant N-acetylglutamate synthase mutant, e.g.,
argA.sup.fbr. In some embodiments, the genetically engineered
bacteria comprise a mutant or deleted arginine repressor and an
arginine feedback resistant N-acetylglutamate synthase mutant,
e.g., argA.sup.fbr. In some embodiments, the genetically engineered
bacteria comprise an arginine feedback resistant N-acetylglutamate
synthase mutant, e.g., argA.sup.fbr, a mutant arginine regulon
comprising one or more nucleic acid mutations in at least one ARG
box for each of the operons that encode the arginine biosynthesis
enzymes, and/or a mutant or deleted arginine repressor.
[0193] In some embodiments, the genetically engineered bacteria
encode an arginine feedback resistant N-acetylglutamate synthase
and further comprise a mutant arginine regulon comprising one or
more nucleic acid mutations in each ARG box for one or more of the
operons that encode N-acetylglutamate kinase,
N-acetylglutamylphosphate reductase, acetylornithine
aminotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase,
carbamoylphosphate synthase, and wild-type N-acetylglutamate
synthetase, such that ArgR binding is reduced or eliminated,
thereby derepressing the regulon and enhancing arginine and/or
intermediate byproduct biosynthesis.
[0194] In some embodiments, the ARG boxes for the operon encoding
argininosuccinate synthase (argG) maintain the ability to bind to
ArgR, thereby driving citrulline biosynthesis. For example, the
regulatory region of the operon encoding argininosuccinate synthase
(argG) may be a constitutive, thereby driving arginine
biosynthesis. In alternate embodiments, the regulatory region of
one or more alternate operons may be constitutive. In certain
bacteria, however, genes encoding multiple enzymes may be organized
in bipolar operons or under the control of a shared regulatory
region; in these instances, the regulatory regions may need to be
deconvoluted in order to engineer constitutively active regulatory
regions. For example, in E. coli K12 and Nissle, argE and argCBH
are organized in two bipolar operons, argECBH, and those regulatory
regions may be deconvoluted in order to generate constitutive
versions of argE and/or argCBH.
[0195] In some embodiments, all ARG boxes in one or more operons
that comprise an arginine biosynthesis gene are mutated to reduce
or eliminate ArgR binding. In some embodiments, all ARG boxes in
one or more operons that encode an arginine biosynthesis enzyme are
mutated to reduce or eliminate ArgR binding. In some embodiments,
all ARG boxes in each operon that comprises an arginine
biosynthesis gene are mutated to reduce or eliminate ArgR binding.
In some embodiments, all ARG boxes in each operon that encodes an
arginine biosynthesis enzyme are mutated to reduce or eliminate
ArgR binding.
[0196] In some embodiments, the genetically engineered bacteria
encode an arginine feedback resistant N-acetylglutamate synthase,
argininosuccinate synthase driven by a ArgR-repressible regulatory
region, and further comprise a mutant arginine regulon comprising
one or more nucleic acid mutations in each ARG box for each of the
operons that encode N-acetylglutamate kinase,
N-acetylglutamylphosphate reductase, acetylornithine am
inotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase,
carbamoylphosphate synthase, and optionally, wild-type
N-acetylglutamate synthetase, such that ArgR binding is reduced or
eliminated, thereby derepressing the regulon and enhancing
citrulline biosynthesis. In some embodiments, the genetically
engineered bacteria capable of producing citrulline is particularly
advantageous, because citrulline further serves as a
therapeutically effective supplement for the treatment of certain
urea cycle disorders (National Urea Cycle Disorders
Foundation).
[0197] In some embodiments, the genetically engineered bacteria
encode an arginine feedback resistant N-acetylglutamate synthase,
argininosuccinate synthase driven by a constitutive promoter, and
further comprise a mutant arginine regulon comprising one or more
nucleic acid mutations in each ARG box for each of the operons that
encode N-acetylglutamate kinase, N-acetylglutamylphosphate
reductase, acetylornithine am inotransferase, N-acetylornithinase,
ornithine transcarbamylase, argininosuccinate lyase,
carbamoylphosphate synthase, and optionally, wild-type
N-acetylglutamate synthetase, such that ArgR binding is reduced or
eliminated, thereby derepressing the regulon and enhancing arginine
biosynthesis.
[0198] In some embodiments, the genetically engineered bacteria
comprise a mutant arginine regulon and a feedback resistant ArgA,
and when the arginine feedback resistant ArgA is expressed, are
capable of producing more arginine and/or an intermediate byproduct
than unmodified bacteria of the same subtype under the same
conditions. In any of these embodiments, the mutant arginine
regulon and/or a feedback resistant ArgA may be integrated into the
bacterial chromosome at one or more integration sites or may be
present on one or more plasmids.
[0199] Arginine Repressor Binding Sites (ARG Boxes)
[0200] In some embodiments, the genetically engineered bacteria
additionally comprise a mutant arginine regulon comprising one or
more nucleic acid mutations in at least one ARG box for one or more
of the operons that encode the arginine biosynthesis enzymes
N-acetylglutamate kinase, N-acetylglutamylphosphate reductase,
acetylornithine am inotransferase, N-acetylornithinase, ornithine
transcarbamylase, argininosuccinate synthase, argininosuccinate
lyase, and carbamoylphosphate synthase, such that the arginine
regulon is derepressed and biosynthesis of arginine and/or an
intermediate byproduct, e.g., citrulline, is enhanced.
[0201] In some embodiments, the mutant arginine regulon comprises
an operon encoding ornithine acetyltransferase and one or more
nucleic acid mutations in at least one ARG box for said operon. The
one or more nucleic acid mutations results in the disruption of the
palindromic ARG box sequence, such that ArgR binding to that ARG
box and to the regulatory region of the operon is reduced or
eliminated, as compared to ArgR binding to an unmodified ARG box
and regulatory region in bacteria of the same subtype under the
same conditions. In some embodiments, nucleic acids that are
protected from DNA methylation and hydroxyl radical attack during
ArgR binding are the primary targets for mutations to disrupt ArgR
binding. In some embodiments, the mutant arginine regulon comprises
at least three nucleic acid mutations in one or more ARG boxes for
each of the operons that encode the arginine biosynthesis enzymes
described above. The ARG box overlaps with the promoter, and in the
mutant arginine regulon, the G/C:A/T ratio of the mutant promoter
region differs by no more than 10% from the G/C:A/T ratio of the
wild-type promoter region (Table 3). The promoter retains
sufficiently high homology to the non-mutant promoter such that RNA
polymerase binds with sufficient affinity to promote
transcription.
[0202] The wild-type genomic sequences comprising ARG boxes and
mutants thereof for each arginine biosynthesis operon in E. coli
Nissle are shown in Table 3. For exemplary wild-type sequences, the
ARG boxes are indicated in italics, and the start codon of each
gene is . The RNA polymerase binding sites are underlined (Cunin,
1983; Maas, 1994). In some embodiments, the underlined sequences
are not altered. Bases that are protected from DNA methylation
during ArgR binding are , and bases that are protected from
hydroxyl radical attack during ArgR binding are bolded (Charlier et
al., 1992). The and bolded bases are the primary targets for
mutations to disrupt ArgR binding.
TABLE-US-00003 TABLE 3 Regulatory region Sequence argA WT
##STR00001## (SEQ ID NO: 1) ##STR00002## argA mutant
gcaaaaaaacactttaaaaacttaataatt (SEQ ID NO: 2)
tcctttaatcacttaaagaggtgtaccgtg argI WT ##STR00003## (SEQ ID NO: 3)
##STR00004## ##STR00005## argl mutant
agacttgcaaacttatacttatccatatag (SEQ ID NO: 4)
attttgttttaatttgttaaggcgttagcc acaggagggatctatg argCBH WT
TCATTGTTGACACACCTCTGGTCATGATAG (SEQ ID NO: 5) ##STR00006##
##STR00007## CACCAGCCGTAAGGTGAATGTTTTACGTTT
AACCTGGCAACCAGACATAAGAAGGTGAAT ##STR00008## argCBH mutant
tcattgttgacacacctctggtcatgatag (SEQ ID NO: 6)
tatcaaacttcatgggatatttatctttaa aaatacttgaacgttgagcgtaataaaacc
caccagccgtaaggtgaatgttttacgttt aacctggcaaccagacataagaaggtgaat
agccccgatg argE WT CATCGGGGCTATTCACCTTCTTATGTCTGG (SEQ ID NO: 7)
TTGCCAGGTTAAACGTAAAACATTCACCTT ACGGCTGGTGGGTTTTATTACGCTCAACGT
##STR00009## AATATTGATACTATCATGACCAGAGGTGTG ##STR00010## argE
mutant catcggggctattcaccttcttatgtctgg (SEQ ID NO: 8)
ttgccaggttaaacgtaaaacattcacctt acggctggtgggttttattacgctcaacgt
tcaagtatttttaaagataaatatcccatg aagtttgatactatcatgaccagaggtgtg
tcaacaatga carAB WT AGCAGATTTGCATTGATTTACGTCATCATT (SEQ ID NO: 9)
##STR00011## ##STR00012## carAB mutant
agcagatttgcattgatttacgtcatcatt (SEQ ID NO: 10)
gtcttttaatatcttaataactggagtgac gtttctctggagggtgttttg argD WT
##STR00013## (SEQ ID NO: 11) ##STR00014##
TTATGCGTAACAGGGTGATCATGAGATG argD mutant
tttctgattgccattcagtctttttttact (SEQ ID NO: 12)
tatattttgtctttataatcttatatttat ttatgcgtaacagggtgatcatgagatg argG WT
##STR00015## (SEQ ID NO: 13) TTCATTTGTTGAATACTTTTACCTTCTCCT
GCTTTCCCTTAAGCGCATTATTTTACAAAA AACACACTAAACTCTTCCTGTCTCCGATAA
##STR00016## ##STR00017## GGCTCATCATCAGTTAATTAAGCAGGGTGT
##STR00018## argG mutant ctaatcaccttaatgaatcttcagttcact (SEQ ID NO:
14) ttcatttgttgaatacttttaccttctcct gctttcccttaagcgcattattttacaaaa
aacacactaaactcttcctgtctccgataa aagatgatcttatgaaaacctttttatttc
ttataaaaatcttgtgaaagcagaaatcca ggctcatcatcagttaattaagcagggtgt
tattttatg argG mutant cctgaaacgtggcaaattctactcgttttg (SEQ ID NO:
15) ggtaaaaaatgcaaatactgctgggatttg gtgtaccgagacgggacgtaaaatctgcag
gcattatagtgatccacgccacattttgtc aacgtttattgctaatcattgacggctagc
tcagtcctaggtacagtgctagcACCCGTT TTTTTGGGCTAGAAATAATTTTGTTTAACT
TTAAGAAGGAGATATACATACCC
[0203] In some embodiments, more than one ARG box may be present in
a single operon. In one aspect of these embodiments, at least one
of the ARG boxes in an operon is mutated to produce the requisite
reduced ArgR binding to the regulatory region of the operon. In an
alternate aspect of these embodiments, each of the ARG boxes in an
operon is mutated to produce the requisite reduced ArgR binding to
the regulatory region of the operon. One of skill in the art would
appreciate that the number of ARG boxes per regulatory region may
vary across bacteria, and the nucleotide sequences of the ARG boxes
may vary for each operon. For example, the carAB operon in E. coli
Nissle comprises two ARG boxes, and one or both ARG box sequences
may be mutated. The argG operon in E. coli Nissle comprises three
ARG boxes, and one, two, or three ARG box sequences may be mutated,
disrupted, or deleted. In some embodiments, all three ARG box
sequences are mutated, disrupted, or deleted, and a constitutive
promoter, e.g., BBa_J23100, is inserted in the regulatory region of
the argG operon. One of skill in the art would appreciate that the
number of ARG boxes per regulatory region may vary across bacteria,
and the nucleotide sequences of the ARG boxes may vary for each
operon.
[0204] An exemplary embodiment of a constitutively expressed argG
construct in E. coli Nissle is depicted in Table 4. Table 4 depicts
the wild-type genomic sequence of the regulatory region and 5'
portion of the argG gene in E. coli Nissle, and a constitutive
mutant thereof. The promoter region of each sequence is underlined,
and a 5' portion of the argG gene is . In the wild-type sequence,
ArgR binding sites are in uppercase and underlined. In the mutant
sequence, the 5' untranslated region is in uppercase and
underlined. Bacteria expressing argG under the control of the
constitutive promoter are capable of producing arginine. Bacteria
expressing argG under the control of the wild-type,
ArgR-repressible promoter are capable of producing citrulline. A
map of the wild-type argG operon E. coli Nissle and a
constitutively expressing mutant thereof is shown in FIG. 12.
TABLE-US-00004 TABLE 4 Wild-type
gtgatccacgccacattttgtcaacgtttattgctaatcaCGTG argG
AATGAATATCCAGTtcactttcatttgttgaatacttttacctt (SEQ ID NO: 16)
ctcctgctttcccttaagcgcattattttacaaaaaacacacta
aactcttcctgtctccgataaaagatgATTAAATGAAAACTCAT
TtatTTTGCATAAAAATTCAGTgaaagcagaaatccaggctcat ##STR00019##
##STR00020## ##STR00021## ##STR00022## ##STR00023## ##STR00024##
##STR00025## ##STR00026## ##STR00027## ##STR00028## ##STR00029##
##STR00030## ##STR00031## ##STR00032## ##STR00033## ##STR00034##
##STR00035## ##STR00036## ##STR00037## ##STR00038## Constitutive
ttgacggctagctcagtcctaggtacagtgctagcACCCGTTTT argG
TTTGGGCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATA (SEQ ID NO: 17)
##STR00039## ##STR00040## ##STR00041## ##STR00042## ##STR00043##
##STR00044## ##STR00045## ##STR00046## ##STR00047## ##STR00048##
##STR00049## ##STR00050## ##STR00051## ##STR00052## ##STR00053##
##STR00054##
[0205] In some embodiments, the ArgR binding affinity to a mutant
ARG box or regulatory region of an operon is at least about 50%
lower, at least about 60% lower, at least about 70% lower, at least
about 80% lower, at least about 90% lower, or at least about 95%
lower than the ArgR binding affinity to an unmodified ARG box and
regulatory region in bacteria of the same subtype under the same
conditions. In some embodiments, the reduced ArgR binding to a
mutant ARG box and regulatory region increases mRNA expression of
the gene(s) in the associated operon by at least about 1.5-fold, at
least about 2-fold, at least about 10-fold, at least about 15-fold,
at least about 20-fold, at least about 30-fold, at least about
50-fold, at least about 100-fold, at least about 200-fold, at least
about 300-fold, at least about 400-fold, at least about 500-fold,
at least about 600-fold, at least about 700-fold, at least about
800-fold, at least about 900-fold, at least about 1,000-fold, or at
least about 1,500-fold.
[0206] In some embodiments, quantitative PCR (qPCR) is used to
amplify, detect, and/or quantify mRNA expression levels of the
arginine biosynthesis genes. Primers specific for arginine
biosynthesis genes, e.g., argA, argB, argC, argD, argE, argF, argG,
argH, argI, argJ, carA, and care, may be designed and used to
detect mRNA in a sample according to methods known in the art
(Fraga et al., 2008). In some embodiments, a fluorophore is added
to a sample reaction mixture that may contain arg mRNA, and a
thermal cycler is used to illuminate the sample reaction mixture
with a specific wavelength of light and detect the subsequent
emission by the fluorophore. The reaction mixture is heated and
cooled to predetermined temperatures for predetermined time
periods. In certain embodiments, the heating and cooling is
repeated for a predetermined number of cycles. In some embodiments,
the reaction mixture is heated and cooled to 90-100.degree. C.,
60-70.degree. C., and 30-50.degree. C. for a predetermined number
of cycles. In a certain embodiment, the reaction mixture is heated
and cooled to 93-97.degree. C., 55-65.degree. C., and 35-45.degree.
C. for a predetermined number of cycles. In some embodiments, the
accumulating amplicon is quantified after each cycle of the qPCR.
The number of cycles at which fluorescence exceeds the threshold is
the threshold cycle (C.sub.T). At least one C.sub.T result for each
sample is generated, and the C.sub.T result(s) may be used to
determine mRNA expression levels of the arginine biosynthesis
genes.
[0207] In some embodiments, the genetically engineered bacteria
comprising one or more nucleic acid mutations in at least one ARG
box for one or more of the operons that encode the arginine
biosynthesis enzymes N-acetylglutamate kinase,
N-acetylglutamylphosphate reductase, acetylornithine
aminotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase, and
carbamoylphosphate synthase additionally comprise an arginine
feedback resistant N-acetylglutamate synthase mutant, e.g.,
argA.sup.fbr.
[0208] In some embodiments, the genetically engineered bacteria
comprise a feedback resistant form of ArgA, as well as one or more
nucleic acid mutations in each ARG box of one or more of the
operons that encode the arginine biosynthesis enzymes
N-acetylglutamate kinase, N-acetylglutamylphosphate reductase,
acetylornithine aminotransferase, N-acetylornithinase, ornithine
transcarbamylase, argininosuccinate synthase, argininosuccinate
lyase, ornithine acetyltransferase, and carbamoylphosphate
synthase.
[0209] In some embodiments, the genetically engineered bacteria
comprise a feedback resistant form of ArgA, argininosuccinate
synthase driven by a ArgR-repressible regulatory region, as well as
one or more nucleic acid mutations in each ARG box of each of the
operons that encode the arginine biosynthesis enzymes
N-acetylglutamate kinase, N-acetylglutamylphosphate reductase,
acetylornithine aminotransferase, N-acetylornithinase, ornithine
transcarbamylase, argininosuccinate lyase, ornithine
acetyltransferase, and carbamoylphosphate synthase. In these
embodiments, the bacteria are capable of producing citrulline.
[0210] In some embodiments, the genetically engineered bacteria
comprise a feedback resistant form of ArgA, argininosuccinate
synthase expressed from a constitutive promoter, as well as one or
more nucleic acid mutations in each ARG box of each of the operons
that encode the arginine biosynthesis enzymes N-acetylglutamate
kinase, N-acetylglutamylphosphate reductase, acetylornithine
aminotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase, ornithine
acetyltransferase, and carbamoylphosphate synthase. In these
embodiments, the bacteria are capable of producing arginine.
[0211] Table 3 shows examples of mutant constructs in which one or
more nucleic acid mutations reduce or eliminate arginine-mediated
repression of each of the arginine operons. The mutant constructs
comprise feedback resistant form of ArgA driven by an oxygen
level-dependent promoter, e.g., a FNR promoter. Each mutant
arginine regulon comprises one or more nucleic acid mutations in at
least one ARG box for one or more of the operons that encode
N-acetylglutamate kinase, N-acetylglutamylphosphate reductase,
acetylornithine aminotransferase, N-acetylornithinase, ornithine
transcarbamylase, argininosuccinate synthase, argininosuccinate
lyase, carbamoylphosphate synthase, and wild-type N-acetylglutamate
synthetase, such that ArgR binding is reduced or eliminated,
thereby enhancing arginine and/or intermediate byproduct
biosynthesis. Non-limiting examples of mutant arginine regulon
constructs are shown in Table 5.
TABLE-US-00005 TABLE 5 Examples of ARG Box mutant constructs
Exemplary constructs (* indicates constitutive): Mutant construct
comprises: Construct 1 Construct 2 Construct 3 Construct 4
Construct 5 Construct 6 Arginine feedback resistant
N-acetylglutamate synthetase driven by an oxygen level- dependent
promoter Wild-type N-acetylglutamate synthetase Mutation(s)
Wild-type in at least N-acetylglutamate one ARG box synthetase for
the operon N-acetylglutamate encoding: kinase
N-acetylglutamylphosphate reductase acetylornithine
aminotransferase N-acetylornithinase ornithine transcarbamylase
argininosuccinate * * * synthase argininosuccinate lyase ornithine
acetyltransferase carbamoylphosphate synthase
[0212] The mutations may be present on a plasmid or chromosome. In
some embodiments, the arginine regulon is regulated by a single
repressor protein. In particular species, strains, and/or subtypes
of bacteria, it has been proposed that the arginine regulon may be
regulated by two putative repressors (Nicoloff et al., 2004). Thus,
in certain embodiments, the arginine regulon of the invention is
regulated by more than one repressor protein.
[0213] In certain embodiments, the mutant arginine regulon is
expressed in one species, strain, or subtype of genetically
engineered bacteria. In alternate embodiments, the mutant arginine
regulon is expressed in two or more species, strains, and/or
subtypes of genetically engineered bacteria.
[0214] Arginine Repressor (ArgR)
[0215] The genetically engineered bacteria of the invention
comprise an arginine regulon comprising one or more nucleic acid
mutations that reduce or eliminate arginine-mediated repression of
one or more of the operons that encode the enzymes responsible for
converting glutamate to arginine and/or an intermediate byproduct
in the arginine biosynthesis pathway. In some embodiments, the
reduction or elimination of arginine-mediated repression may be
achieved by reducing or eliminating ArgR repressor binding, e.g.,
by mutating at least one ARG box for one or more of the operons
that encode the arginine biosynthesis enzymes (as discussed above)
or by mutating or deleting the arginine repressor (discussed here)
and/or by reducing or eliminating arginine binding to
N-acetylglutamate synthetase (e.g., by mutating the
N-acetylglutamate synthetase to produce an arginine feedback
resistant N-acetylglutamate synthase mutant, e.g.,
argA.sup.fbr).
[0216] Thus, in some embodiments, the genetically engineered
bacteria lack a functional ArgR repressor and therefore ArgR
repressor-mediated transcriptional repression of each of the
arginine biosynthesis operons is reduced or eliminated. In some
embodiments, the engineered bacteria comprise a mutant arginine
repressor comprising one or more nucleic acid mutations such that
arginine repressor function is decreased or inactive. In some
embodiments, the genetically engineered bacteria do not have an
arginine repressor (e.g., the arginine repressor gene has been
deleted), resulting in derepression of the regulon and enhancement
of arginine and/or intermediate byproduct biosynthesis. In some
embodiments, each copy of a functional argR gene normally present
in a corresponding wild-type bacterium is independently deleted or
rendered inactive by one or more nucleotide deletions, insertions,
or substitutions. In some embodiments, each copy of the functional
argR gene normally present in a corresponding wild-type bacterium
is deleted.
[0217] In some embodiments, the arginine regulon is regulated by a
single repressor protein. In particular species, strains, and/or
subtypes of bacteria, it has been proposed that the arginine
regulon may be regulated by two distinct putative repressors
(Nicoloff et al., 2004). Thus, in certain embodiments, two distinct
ArgR proteins each comprising a different amino acid sequence are
mutated or deleted in the genetically engineered bacteria.
[0218] In some embodiments, the genetically modified bacteria
comprising a mutant or deleted arginine repressor additionally
comprise an arginine feedback resistant N-acetylglutamate synthase
mutant, e.g., argA.sup.fbr. In some embodiments, the genetically
engineered bacteria comprise a feedback resistant form of ArgA,
lack any functional arginine repressor, and are capable of
producing arginine. In certain embodiments, the genetically
engineered bacteria further lack functional ArgG and are capable of
producing citrulline. In some embodiments, the argR gene is deleted
in the genetically engineered bacteria. In some embodiments, the
argR gene is mutated to inactivate ArgR function. In some
embodiments, the argG gene is deleted in the genetically engineered
bacteria. In some embodiments, the argG gene is mutated to
inactivate ArgR function. In some embodiments, the genetically
engineered bacteria comprise argA.sup.fbr and deleted ArgR. In some
embodiments, the genetically engineered bacteria comprise
argA.sup.fbr, deleted ArgR, and deleted argG. In some embodiments,
the deleted ArgR and/or the deleted argG is deleted from the
bacterial genome and the argA.sup.fbr is present in a plasmid. In
some embodiments, the deleted ArgR and/or the deleted argG is
deleted from the bacterial genome and the argA.sup.fbr is
chromosomally integrated. In one specific embodiment, the
genetically modified bacteria comprise chromosomally integrated
argA.sup.fbr, deleted genomic ArgR, and deleted genomic argG. In
another specific embodiment, the genetically modified bacteria
comprise argA.sup.fbr present on a plasmid, deleted genomic ArgR,
and deleted genomic argG. In any of the embodiments in which argG
is deleted, citrulline rather than arginine is produced
[0219] In some embodiments, under conditions where a feedback
resistant form of ArgA is expressed, the genetically engineered
bacteria of the invention produce at least about 1.5-fold, at least
about 2-fold, at least about 10-fold, at least about 15-fold, at
least about 20-fold, at least about 30-fold, at least about
50-fold, at least about 100-fold, at least about 200-fold, at least
about 300-fold, at least about 400-fold, at least about 500-fold,
at least about 600-fold, at least about 700-fold, at least about
800-fold, at least about 900-fold, at least about 1,000-fold, or at
least about 1,500-fold more arginine, citrulline, other
intermediate byproduct, and/or transcript of the gene(s) in the
operon as compared to unmodified bacteria of the same subtype under
the same conditions.
[0220] In some embodiments, quantitative PCR (qPCR) is used to
amplify, detect, and/or quantify mRNA expression levels of the
arginine biosynthesis genes. Primers specific for arginine
biosynthesis genes, e.g., argA, argB, argC, argD, argE, argF, argG,
argH, argI, argJ, carA, and care, may be designed and used to
detect mRNA in a sample according to methods known in the art
(Fraga et al., 2008). In some embodiments, a fluorophore is added
to a sample reaction mixture that may contain arg mRNA, and a
thermal cycler is used to illuminate the sample reaction mixture
with a specific wavelength of light and detect the subsequent
emission by the fluorophore. The reaction mixture is heated and
cooled to predetermined temperatures for predetermined time
periods. In certain embodiments, the heating and cooling is
repeated for a predetermined number of cycles. In some embodiments,
the reaction mixture is heated and cooled to 90-100.degree. C.,
60-70.degree. C., and 30-50.degree. C. for a predetermined number
of cycles. In a certain embodiment, the reaction mixture is heated
and cooled to 93-97.degree. C., 55-65.degree. C., and 35-45.degree.
C. for a predetermined number of cycles. In some embodiments, the
accumulating amplicon is quantified after each cycle of the qPCR.
The number of cycles at which fluorescence exceeds the threshold is
the threshold cycle (C.sub.T). At least one C.sub.T result for each
sample is generated, and the C.sub.T result(s) may be used to
determine mRNA expression levels of the arginine biosynthesis
genes.
[0221] In any of these embodiments in which the ArgR is mutated,
the mutant ArgR and/or a feedback resistant ArgA may be integrated
into the bacterial chromosome at one or more integration sites or
may be present on one or more plasmids.
[0222] Feedback Resistant N-Acetylglutamate Synthetase
[0223] In some embodiments, the genetically engineered bacteria
comprise an arginine feedback resistant N-acetylglutamate synthase
mutant, e.g., argA.sup.fbr. In some embodiments, the genetically
engineered bacteria comprise a mutant arginine regulon comprising
an arginine feedback resistant ArgA, and when the arginine feedback
resistant ArgA is expressed, are capable of producing more arginine
and/or an intermediate byproduct than unmodified bacteria of the
same subtype under the same conditions. The arginine feedback
resistant N-acetylglutamate synthetase protein (argA.sup.fbr) is
significantly less sensitive to L-arginine than the enzyme from the
feedback sensitive parent strain (see, e.g., Eckhardt et al., 1975;
Rajagopal et al., 1998). The feedback resistant argA gene can be
present on a plasmid or chromosome. In some embodiments, expression
from the plasmid may be useful for increasing argA.sup.fbr
expression. In some embodiments, expression from the chromosome may
be useful for increasing stability of argA.sup.fbr expression.
[0224] In some embodiments, any of the described mutant sequences
involved in the arginine biosynthetic pathway (e.g., ArgR,
argA.sup.fbr, Arg Box sequence) are integrated into the bacterial
chromosome at one or more integration sites. For example, one or
more copies of the sequence encoding the arginine feedback
resistant N-acetylglutamate synthase may be integrated into the
bacterial chromosome. Having multiple copies of the arginine
feedback resistant N-acetylglutamate synthase integrated into the
chromosome allows for greater production of the N-acetylglutamate
synthase and also permits fine-tuning of the level of expression.
Alternatively, different circuits described herein, such as any of
the transporter or kill-switch circuits, in addition to the
arginine feedback resistant N-acetylglutamate synthase could be
integrated into the bacterial chromosome at one or more different
integration sites to perform multiple different functions. Multiple
distinct feedback resistant N-acetylglutamate synthetase proteins
are known in the art and may be combined in the genetically
engineered bacteria. In some embodiments, the argA.sup.fbr gene is
expressed under the control of a constitutive promoter. In some
embodiments, the argA.sup.fbr gene is expressed under the control
of a promoter that is induced by exogenous environmental
conditions. In some embodiments, the exogenous environmental
conditions are specific to the gut of a mammal. In some
embodiments, exogenous environmental conditions are molecules or
metabolites that are specific to the mammalian gut in a healthy or
disease state, e.g., propionate. In some embodiments, the exogenous
environmental conditions are low-oxygen or anaerobic conditions,
such as the environment of the mammalian gut.
[0225] Bacteria have evolved transcription factors that are capable
of sensing oxygen levels. Different signaling pathways may be
triggered by different oxygen levels and occur with different
kinetics. An oxygen level-dependent promoter is a nucleic acid
sequence to which one or more oxygen level-sensing transcription
factors is capable of binding, wherein the binding and/or
activation of the corresponding transcription factor activates
downstream gene expression. In one embodiment, the argA.sup.fbr
gene is under control of an oxygen level-dependent promoter. In a
more specific aspect, the argA.sup.fbr gene is under control of an
oxygen level-dependent promoter that is activated under low-oxygen
or anaerobic environments, such as the environment of the mammalian
gut.
[0226] In certain embodiments, the genetically engineered bacteria
comprise argA.sup.fbr expressed under the control of the fumarate
and nitrate reductase regulator (FNR) promoter. In E. coli, FNR is
a major transcriptional activator that controls the switch from
aerobic to anaerobic metabolism (Unden et al., 1997). In the
anaerobic state, FNR dimerizes into an active DNA binding protein
that activates hundreds of genes responsible for adapting to
anaerobic growth. In the aerobic state, FNR is prevented from
dimerizing by oxygen and is inactive. In alternate embodiments, the
genetically engineered bacteria comprise argA.sup.fbr expressed
under the control of an alternate oxygen level-dependent promoter,
e.g., an anaerobic regulation of arginine deiminiase and nitrate
reduction ANR promoter (Ray et al., 1997), a dissimilatory nitrate
respiration regulator DNR promoter (Trunk et al., 2010). In these
embodiments, the arginine biosynthesis pathway is particularly
activated in a low-oxygen or anaerobic environment, such as in the
gut.
[0227] In P. aeruginosa, the anaerobic regulation of arginine
deiminiase and nitrate reduction (ANR) transcriptional regulator is
"required for the expression of physiological functions which are
inducible under oxygen-limiting or anaerobic conditions" (Winteler
et al., 1996; Sawers 1991). P. aeruginosa ANR is homologous with E.
coli FNR, and "the consensus FNR site (TTGAT----ATCAA) (SEQ ID NO:
121) was recognized efficiently by ANR and FNR'' (Winteler et al.,
1996). Like FNR, in the anaerobic state, ANR activates numerous
genes responsible for adapting to anaerobic growth. In the aerobic
state, ANR is inactive. Pseudomonas fluorescens, Pseudomonas
putida, Pseudomonas syringae, and Pseudomonas mendocina all have
functional analogs of ANR (Zimmermann et al., 1991). Promoters that
are regulated by ANR are known in the art, e.g., the promoter of
the arcDABC operon (see, e.g., Hasegawa et al., 1998).
[0228] The FNR family also includes the dissimilatory nitrate
respiration regulator (DNR) (Arai et al., 1995), a transcriptional
regulator that is required in conjunction with ANR for "anaerobic
nitrate respiration of Pseudomonas aeruginosa" (Hasegawa et al.,
1998). For certain genes, the FNR-binding motifs "are probably
recognized only by DNR" (Hasegawa et al., 1998). Any suitable
transcriptional regulator that is controlled by exogenous
environmental conditions and corresponding regulatory region may be
used. Non-limiting examples include ArcA/B, ResD/E, NreA/B/C, and
AirSR, and others are known in the art.
[0229] FNR promoter sequences are known in the art, and any
suitable FNR promoter sequence(s) may be used in the genetically
engineered bacteria of the invention. Any suitable FNR promoter(s)
may be combined with any suitable argA.sup.fbr (e.g., the exemplary
argA.sup.fbr sequence shown in Table 7). Non-limiting FNR promoter
sequences are provided in Table 6. Table 6 depicts the nucleic acid
sequences of exemplary regulatory region sequences comprising a
FNR-responsive promoter sequence. Underlined sequences are
predicted ribosome binding sites, and bolded sequences are
restriction sites used for cloning. In some embodiments, the
genetically engineered bacteria of the invention comprise one or
more of: SEQ ID NO: 18, SEQ ID NO: 19, nirB1 promoter (SEQ ID NO:
20), nirB2 promoter (SEQ ID NO: 21), nirB3 promoter (SEQ ID NO:
22), ydfZ promoter (SEQ ID NO: 23), nirB promoter fused to a strong
ribosome binding site (SEQ ID NO: 24), ydfZ promoter fused to a
strong ribosome binding site (SEQ ID NO: 25), fnrS, an
anaerobically induced small RNA gene (fnrS1 promoter SEQ ID NO: 26
or fnrS2 promoter SEQ ID NO: 27), nirB promoter fused to a crp
binding site (SEQ ID NO: 28), and fnrS fused to a crp binding site
(SEQ ID NO: 29).
[0230] In some embodiments, genetically engineered bacteria
comprise a nucleic acid sequence that is at least about 80%, at
least about 85%, at least about 90%, at least about 95%, or at
least about 99% homologous to the DNA sequence of SEQ ID NO: 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29, or a functional
fragment thereof.
TABLE-US-00006 TABLE 6 FNR- responsive regulatory region
12345678901234567890123456789012345678901234567890 SEQ ID NO:
ATCCCCATCACTCTTGATGGAGATCAATTCCCCAAGCTGCTAGAGCGTTA 18
CCTTGCCCTTAAACATTAGCAATGTCGATTTATCAGAGGGCCGACAGGCT
CCCACAGGAGAAAACCG SEQ ID NO:
CTCTTGATCGTTATCAATTCCCACGCTGTTTCAGAGCGTTACCTTGCCCT 19
TAAACATTAGCAATGTCGATTTATCAGAGGGCCGACAGGCTCCCACAGGA GAAAACCG nirB1
GTCAGCATAACACCCTGACCTCTCATTAATTGTTCATGCCGGGCGGCACT SEQ ID NO:
ATCGTCGTCCGGCCTTTTCCTCTCTTACTCTGCTACGTACATCTATTTCT 20
ATAAATCCGTTCAATTTGTCTGTTTTTTGCACAAACATGAAATATCAGAC
AATTCCGTGACTTAAGAAAATTTATACAAATCAGCAATATACCCCTTAAG
GAGTATATAAAGGTGAATTTGATTTACATCAATAAGCGGGGTTGCTGAAT
CGTTAAGGTAGGCGGTAATAGAAAAGAAATCGAGGCAAAA nirB2
CGGCCCGATCGTTGAACATAGCGGTCCGCAGGCGGCACTGCTTACAGCAA SEQ ID NO:
ACGGTCTGTACGCTGTCGTCTTTGTGATGTGCTTCCTGTTAGGTTTCGTC 21
AGCCGTCACCGTCAGCATAACACCCTGACCTCTCATTAATTGCTCATGCC
GGACGGCACTATCGTCGTCCGGCCTTTTCCTCTCTTCCCCCGCTACGTGC
ATCTATTTCTATAAACCCGCTCATTTTGTCTATTTTTTGCACAAACATGA
AATATCAGACAATTCCGTGACTTAAGAAAATTTATACAAATCAGCAATAT
ACCCATTAAGGAGTATATAAAGGTGAATTTGATTTACATCAATAAGCGGG
GTTGCTGAATCGTTAAGGTAGGCGGTAATAGAAAAGAAATCGAGGCAAAA
atgtttgtttaactttaagaaggagatatacat nirB3
GTCAGCATAACACCCTGACCTCTCATTAATTGCTCATGCCGGACGGCACT SEQ ID NO:
ATCGTCGTCCGGCCTTTTCCTCTCTTCCCCCGCTACGTGCATCTATTTCT 22
ATAAACCCGCTCATTTTGTCTATTTTTTGCACAAACATGAAATATCAGAC
AATTCCGTGACTTAAGAAAATTTATACAAATCAGCAATATACCCATTAAG
GAGTATATAAAGGTGAATTTGATTTACATCAATAAGCGGGGTTGCTGAAT
CGTTAAGGTAGGCGGTAATAGAAAAGAAATCGAGGCAAAA ydfZ
ATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGACTTATGGC SEQ ID NO:
TCATGCATGCATCAAAAAAGATGTGAGCTTGATCAAAAACAAAAAATATT 23
TCACTCGACAGGAGTATTTATATTGCGCCCGTTACGTGGGCTTCGACTGT
AAATCAGAAAGGAGAAAACACCT nirB + RBS
GTCAGCATAACACCCTGACCTCTCATTAATTGTTCATGCCGGGCGGCACT SEQ ID NO:
ATCGTCGTCCGGCCTTTTCCTCTCTTACTCTGCTACGTACATCTATTTCT 24
ATAAATCCGTTCAATTTGTCTGTTTTTTGCACAAACATGAAATATCAGAC
AATTCCGTGACTTAAGAAAATTTATACAAATCAGCAATATACCCCTTAAG
GAGTATATAAAGGTGAATTTGATTTACATCAATAAGCGGGGTTGCTGAAT
CGTTAAGGATCCCTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATA TACAT ydfZ + RBS
CATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGACTTATGG SEQ ID NO:
CTCATGCATGCATCAAAAAAGATGTGAGCTTGATCAAAAACAAAAAATAT 25
TTCACTCGACAGGAGTATTTATATTGCGCCCGGATCCCTCTAGAAATAAT
TTTGTTTAACTTTAAGAAGGAGATATACAT fnrS1
AGTTGTTCTTATTGGTGGTGTTGCTTTATGGTTGCATCGTAGTAAATGGT SEQ ID NO:
TGTAACAAAAGCAATTTTTCCGGCTGTCTGTATACAAAAACGCCGTAAAG 26
TTTGAGCGAAGTCAATAAACTCTCTACCCATTCAGGGCAATATCTCTCTT
GGATCCCTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACAT fnrS2
AGTTGTTCTTATTGGTGGTGTTGCTTTATGGTTGCATCGTAGTAAATGGT SEQ ID NO:
TGTAACAAAAGCAATTTTTCCGGCTGTCTGTATACAAAAACGCCGCAAAG 27
TTTGAGCGAAGTCAATAAACTCTCTACCCATTCAGGGCAATATCTCTCTT
GGATCCAAAGTGAACTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGA TATACAT nirB +
crp TCGTCTTTGTGATGTGCTTCCTGTTAGGTTTCGTCAGCCGTCACCGTCAG SEQ ID NO:
CATAACACCCTGACCTCTCATTAATTGCTCATGCCGGACGGCACTATCGT 28
CGTCCGGCCTTTTCCTCTCTTCCCCCGCTACGTGCATCTATTTCTATAAA
CCCGCTCATTTTGTCTATTTTTTGCACAAACATGAAATATCAGACAATTC
CGTGACTTAAGAAAATTTATACAAATCAGCAATATACCCATTAAGGAGTA
TATAAAGGTGAATTTGATTTACATCAATAAGCGGGGTTGCTGAATCGTTA
AGGTAGaaatgtgatctagttcacatttGCGGTAATAGAAAAGAAATCGA
GGCAAAAatgtttgtttaactttaagaaggagatatacat fnrS + crp
AGTTGTTCTTATTGGTGGTGTTGCTTTATGGTTGCATCGTAGTAAATGGT SEQ ID NO:
TGTAACAAAAGCAATTTTTCCGGCTGTCTGTATACAAAAACGCCGCAAAG 29
TTTGAGCGAAGTCAATAAACTCTCTACCCATTCAGGGCAATATCTCTCaa
atgtgatctagttcacattttttgtttaactttaagaaggagatatacat
[0231] In other embodiments, argA.sup.fbr is expressed under the
control of an oxygen level-dependent promoter fused to a binding
site for a transcriptional activator, e.g., CRP. CRP (cyclic AMP
receptor protein or catabolite activator protein or CAP) plays a
major regulatory role in bacteria by repressing genes responsible
for the uptake, metabolism and assimilation of less favorable
carbon sources when rapidly metabolizable carbohydrates, such as
glucose, are present (Wu et al., 2015). This preference for glucose
has been termed glucose repression, as well as carbon catabolite
repression (Deutscher, 2008; Gorke and Stulke, 2008). In some
embodiments, argA.sup.fbr expression is controlled by an oxygen
level-dependent promoter fused to a CRP binding site. In some
embodiments, argA.sup.fbr expression is controlled by a FNR
promoter fused to a CRP binding site. In these embodiments, cyclic
AMP binds to CRP when no glucose is present in the environment.
This binding causes a conformational change in CRP, and allows CRP
to bind tightly to its binding site. CRP binding then activates
transcription of the argA.sup.fbr gene by recruiting RNA polymerase
to the FNR promoter via direct protein-protein interactions. In the
presence of glucose, cyclic AMP does not bind to CRP and
argA.sup.fbr gene transcription is repressed. In some embodiments,
an oxygen level-dependent promoter (e.g., a FNR promoter) fused to
a binding site for a transcriptional activator is used to ensure
that argA.sup.fbr is not expressed under anaerobic conditions when
sufficient amounts of glucose are present, e.g., by adding glucose
to growth media in vitro.
[0232] In some embodiments, argA.sup.fbr is expressed under the
control of an inducible promoter that is responsive to specific
molecules or metabolites in the environment, e.g., the mammalian
gut. For example, the short-chain fatty acid propionate is a major
microbial fermentation metabolite localized to the gut (Hosseini et
al., 2011). In one embodiment, argA.sup.fbr gene expression is
under the control of a propionate-inducible promoter. In a more
specific embodiment, argA.sup.fbr gene expression is under the
control of a propionate-inducible promoter that is activated by the
presence of propionate in the mammalian gut. Any molecule or
metabolite found in the mammalian gut, in a healthy and/or disease
state, may be used to induce argA.sup.fbr expression. Non-limiting
examples include propionate, bilirubin, aspartate aminotransferase,
alanine aminotransferase, blood coagulation factors II, VII, IX,
and X, alkaline phosphatase, gamma glutamyl transferase, hepatitis
antigens and antibodies, alpha fetoprotein, anti-mitochondrial,
smooth muscle, and anti-nuclear antibodies, iron, transferrin,
ferritin, copper, ceruloplasmin, ammonia, and manganese. In
alternate embodiments, argA.sup.fbr gene expression is under the
control of a P araBAD promoter, which is activated in the presence
of the sugar arabinose (see, e.g., FIG. 13).
[0233] Subjects with hepatic encephalopathy (HE) and other liver
disease or disorders have chronic liver damage that results in high
ammonia levels in their blood and intestines. In addition to
ammonia, these patients also have elevated levels of bilirubin,
aspartate aminotransferase, alanine aminotransferase, blood
coagulation factors II, VII, IX, and X, alkaline phosphatase, gamma
glutamyl transferase, hepatitis antigens and antibodies, alpha
fetoprotein, anti-mitochondrial, smooth muscle, and anti-nuclear
antibodies, iron, transferrin, ferritin, copper, ceruloplasmin,
ammonia, and manganese in their blood and intestines. Promoters
that respond to one of these HE-related molecules or their
metabolites may be used in the genetically engineered bacteria to
induce expression of argA.sup.fbr in the gut. These promoters would
not be expected to be induced in non-HE patients.
[0234] In some embodiments, the argA.sup.fbr gene is expressed
under the control of a promoter that is induced by exposure to
tetracycline. In some embodiments, the argA.sup.fbr gene is
expressed under the control of a promoter that is induced by
exposure to inflammation or an imflammatory response (e.g., RNS or
ROS promoters). In some embodiments, the argA.sup.fbr gene is
expressed under the control of a promoter that is induced by
exposure to a metabolite such as arabinose (e.g., AraBAD
promoter).
[0235] In some embodiments, gene expression is further optimized by
methods known in the art, e.g., by optimizing ribosomal binding
sites, manipulating transcriptional regulators, and/or increasing
mRNA stability. The nucleic acid sequence of an exemplary
argA.sup.fbr sequence is shown in Table 7. The polypeptide sequence
of an exemplary argA.sup.fbr sequence is shown in Table 8.
TABLE-US-00007 TABLE 7 Nucleotide sequence of exemplary
argA.sup.fbr sequence (SEQ ID NO: 30)
ATGGTAAAGGAACGTAAAACCGAGTTGGTCGAGGGATTCCGCCATTCGGT
TCCCTGTATCAATACCCACCGGGGAAAAACGTTTGTCATCATGCTCGGCG
GTGAAGCCATTGAGCATGAGAATTTCTCCAGTATCGTTAATGATATCGGG
TTGTTGCACAGCCTCGGCATCCGTCTGGTGGTGGTCTATGGCGCACGTCC
GCAGATCGACGCAAATCTGGCTGCGCATCACCACGAACCGCTGTATCACA
AGAATATACGTGTGACCGACGCCAAAACACTGGAACTGGTGAAGCAGGCT
GCGGGAACATTGCAACTGGATATTACTGCTCGCCTGTCGATGAGTCTCAA
TAACACGCCGCTGCAGGGCGCGCATATCAACGTCGTCAGTGGCAATTTTA
TTATTGCCCAGCCGCTGGGCGTCGATGACGGCGTGGATTACTGCCATAGC
GGGCGTATCCGGCGGATTGATGAAGACGCGATCCATCGTCAACTGGACAG
CGGTGCAATAGTGCTAATGGGGCCGGTCGCTGTTTCAGTCACTGGCGAGA
GCTTTAACCTGACCTCGGAAGAGATTGCCACTCAACTGGCCATCAAACTG
AAAGCTGAAAAGATGATTGGTTTTTGCTCTTCCCAGGGCGTCACTAATGA
CGACGGTGATATTGTCTCCGAACTTTTCCCTAACGAAGCGCAAGCGCGGG
TAGAAGCCCAGGAAGAGAAAGGCGATTACAACTCCGGTACGGTGCGCTTT
TTGCGTGGCGCAGTGAAAGCCTGCCGCAGCGGCGTGCGTCGCTGTCATTT
AATCAGTTATCAGGAAGATGGCGCGCTGTTGCAAGAGTTGTTCTCACGCG
ACGGTATCGGTACGCAGATTGTGATGGAAAGCGCCGAGCAGATTCGTCGC
GCAACAATCAACGATATTGGCGGTATTCTGGAGTTGATTCGCCCACTGGA
GCAGCAAGGTATTCTGGTACGCCGTTCTCGCGAGCAGCTGGAGATGGAAA
TCGACAAATTCACCATTATTCAGCGCGATAACACGACTATTGCCTGCGCC
GCGCTCTATCCGTTCCCGGAAGAGAAGATTGGGGAAATGGCCTGTGTGGC
AGTTCACCCGGATTACCGCAGTTCATCAAGGGGTGAAGTTCTGCTGGAAC
GCATTGCCGCTCAGGCTAAGCAGAGCGGCTTAAGCAAATTGTTTGTGCTG
ACCACGCGCAGTATTCACTGGTTCCAGGAACGTGGATTTACCCCAGTGGA
TATTGATTTACTGCCCGAGAGCAAAAAGCAGTTGTACAACTACCAGCGTA
AATCCAAAGTGTTGATGGCGGATTTAGGGTAA
TABLE-US-00008 TABLE 8 Polypeptide sequence of exemplary
argA.sup.fbr sequence (SEQ ID NO: 31)
MVKERKTELVEGFRHSVPCINTHRGKTFVIMLGGEAIEHENFSSIVNDIG
LLHSLGIRLVVVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQA
AGTLQLDITARLSMSLNNTPLQGAHINVVSGNFIIAQPLGVDDGVDYCHS
GRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGESFNLTSEEIATQLAIKL
KAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYNSGTVRF
LRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR
ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACA
ALYPFPEEKIGEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVL
TTRSIHWFQERGFTPVDIDLLPESKKQLYNYQRKSKVLMADLG Bold underline: mutated
amino acid resulting feedback resistance. (mutation is Y19C)
[0236] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 30 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 30 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 30 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 30 or a functional
fragment thereof.
[0237] In some embodiments, the genetically engineered bacteria
encode a polypeptide sequence of SEQ ID NO: 31 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria encode a polypeptide sequence encodes a polypeptide, which
contains one or more conservative amino acid substutions relative
to SEQ ID NO: 31 or a functional fragment thereof. In some
embodiments, genetically engineered bacteria encode a polypeptide
sequence that is at least about 80%, at least about 85%, at least
about 90%, at least about 95%, or at least about 99% homologous to
the DNA sequence of SEQ ID NO: 31 or a functional fragment
thereof.
[0238] In some embodiments, arginine feedback inhibition of
N-acetylglutamate synthetase is reduced by at least about 50%, at
least about 60%, at least about 70%, at least about 80%, at least
about 90%, or at least about 95% in the genetically engineered
bacteria when the arginine feedback resistant N-acetylglutamate
synthetase is active, as compared to a wild-type N-acetylglutamate
synthetase from bacteria of the same subtype under the same
conditions.
[0239] In some embodiments, the genetically engineered bacteria
comprise a stably maintained plasmid or chromosome carrying the
argA.sup.fbr gene, such that argA.sup.fbr can be expressed in the
host cell, and the host cell is capable of survival and/or growth
in vitro, e.g., in medium, and/or in vivo, e.g., in the gut. In
some embodiments, a bacterium may comprise multiple copies of the
feedback resistant argA gene. In some embodiments, the feedback
resistant argA gene is expressed on a low-copy plasmid. In some
embodiments, the low-copy plasmid may be useful for increasing
stability of expression. In some embodiments, the low-copy plasmid
may be useful for decreasing leaky expression under non-inducing
conditions. In some embodiments, the feedback resistant argA gene
is expressed on a high-copy plasmid. In some embodiments, the
high-copy plasmid may be useful for increasing argA.sup.fbr
expression. In some embodiments, the feedback resistant argA gene
is expressed on a chromosome.
[0240] In some embodiments, the bacteria are genetically engineered
to include multiple mechanisms of action (MOAs), e.g., circuits
producing multiple copies of the same product or circuits
performing multiple different functions. Examples of insertion
sites include, but are not limited to, malE/K, insB/I, araC/BAD,
lacZ, dapA, cea, and other shown in FIG. 18. For example, the
genetically engineered bacteria may include four copies of
argA.sup.fbr inserted at four different insertion sites, e.g.,
malE/K, insB/I, araC/BAD, and lacZ. Alternatively, the genetically
engineered bacteria may include three copies of argA.sup.fbr
inserted at three different insertion sites, e.g., malE/K, insB/I,
and lacZ, and three mutant arginine regulons, e.g., two producing
citrulline and one producing arginine, inserted at three different
insertion sites dapA, cea, and araC/BAD.
[0241] In some embodiments, the plasmid or chromosome also
comprises wild-type ArgR binding sites, e.g., ARG boxes. In some
instances, the presence and/or build-up of functional ArgR may
result in off-target binding at sites other than the ARG boxes,
which may cause off-target changes in gene expression. A plasmid or
chromosome that further comprises functional ARG boxes may be used
to reduce or eliminate off-target ArgR binding, i.e., by acting as
an ArgR sink. In some embodiments, the plasmid or chromosome does
not comprise functional ArgR binding sites, e.g., the plasmid or
chromosome comprises modified ARG boxes or does not comprise ARG
boxes.
[0242] In some embodiments, the feedback resistant argA gene is
present on a plasmid and operably linked to a promoter that is
induced under low-oxygen or anaerobic conditions. In some
embodiments, the feedback resistant argA gene is present in the
chromosome and operably linked to a promoter that is induced under
low-oxygen or anaerobic conditions. In some embodiments, the
feedback resistant argA gene is present on a plasmid and operably
linked to a promoter that is induced by molecules or metabolites
that are specific to the mammalian gut. In some embodiments, the
feedback resistant argA gene is present on a chromosome and
operably linked to a promoter that is induced by molecules or
metabolites that are specific to the mammalian gut. In some
embodiments, the feedback resistant argA gene is present on a
chromosome and operably linked to a promoter that is induced by
exposure to tetracycline. In some embodiments, the feedback
resistant argA gene is present on a plasmid and operably linked to
a promoter that is induced by exposure to tetracycline.
[0243] In some embodiments, the genetically engineered bacteria
comprise a variant or mutated oxygen level-dependent
transcriptional regulator, e.g., FNR, ANR, or DNR, in addition to
the corresponding oxygen level-dependent promoter. The variant or
mutated oxygen level-dependent transcriptional regulator increases
the transcription of operably linked genes in a low-oxygen or
anaerobic environment. In some embodiments, the corresponding
wild-type transcriptional regulator retains wild-type activity. In
alternate embodiments, the corresponding wild-type transcriptional
regulator is deleted or mutated to reduce or eliminate wild-type
activity. In certain embodiments, the mutant oxygen level-dependent
transcriptional regulator is a FNR protein comprising amino acid
substitutions that enhance dimerization and FNR activity (see,
e.g., Moore et al., 2006).
[0244] In some embodiments, the genetically engineered bacteria
comprise an oxygen level-dependent transcriptional regulator from a
different bacterial species that reduces and/or consumes ammonia in
low-oxygen or anaerobic environments. In certain embodiments, the
mutant oxygen level-dependent transcriptional regulator is a FNR
protein from N. gonorrhoeae (see, e.g., Isabella et al., 2011). In
some embodiments, the corresponding wild-type transcriptional
regulator is left intact and retains wild-type activity. In
alternate embodiments, the corresponding wild-type transcriptional
regulator is deleted or mutated to reduce or eliminate wild-type
activity.
[0245] In some embodiments, the genetically engineered bacteria
comprise argA.sup.fbr expressed under the control of an oxygen
level-dependent promoter, e.g., a FNR promoter, as well as
wild-type argA expressed under the control of a mutant regulatory
region comprising one or more ARG box mutations as discussed above.
In certain embodiments, the genetically engineered bacteria
comprise argA.sup.fbr expressed under the control of an oxygen
level-dependent promoter, e.g., a FNR promoter and do not comprise
wild-type argA. In still other embodiments, the mutant arginine
regulon comprises argA.sup.fbr expressed under the control of an
oxygen level-dependent promoter, e.g., a FNR promoter, and further
comprises wild-type argA without any ARG box mutations.
[0246] In some embodiments, the genetically engineered bacteria
express argA.sup.fbr from a plasmid and/or chromosome. In some
embodiments, the argA.sup.fbr gene is expressed under the control
of a constitutive promoter. In some embodiments, the argA.sup.fbr
gene is expressed under the control of an inducible promoter. In
one embodiment, argA.sup.fbr is expressed under the control of an
oxygen level-dependent promoter that is activated under low-oxygen
or anaerobic environments, e.g., a FNR promoter. The nucleic acid
sequence of an exemplary FNR promoter-driven argA.sup.fbr sequence
is shown in Table 9. The FNR promoter sequence is bolded and the
argA.sup.fbr sequence is . The nucleic acid sequence of a FNR
promoter-driven argA.sup.fbr plasmid is shown in Table 10, with the
FNR promoter sequence bolded and argA.sup.fbr sequence . Table 11
shows the nucleic acid sequence of an exemplary pSC101 plasmid. Any
suitable FNR promoter(s) may be combined with any suitable
feedback-resistant ArgA. Non-limiting FNR promoter sequences are
provided in Table 6. In some embodiments, the genetically
engineered bacteria of the invention comprise one or more of: SEQ
ID NO: 16, SEQ ID NO: 17, nirB1 promoter (SEQ ID NO: 18), nirB2
promoter (SEQ ID NO: 19), nirB3 promoter (SEQ ID NO: 20), ydfZ
promoter (SEQ ID NO: 21), nirB promoter fused to a strong ribosome
binding site (SEQ ID NO: 22), ydfZ promoter fused to a strong
ribosome binding site (SEQ ID NO: 23), fnrS, an anaerobically
induced small RNA gene (fnrS1 promoter SEQ ID NO: 24 or fnrS2
promoter SEQ ID NO: 25), nirB promoter fused to a crp binding site
(SEQ ID NO: 26), and fnrS fused to a crp binding site (SEQ ID NO:
27). Table 12 depicts the nucleic acid sequence of an exemplary
fnrS promoter-driven argA.sup.fbr sequence. The FNR promoter
sequence is bolded, the ribosome binding site is , and the
argA.sup.fbr sequence is .
[0247] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 32 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 32. In some embodiments, genetically engineered bacteria
comprise a nucleic acid sequence that is at least about 80%, at
least about 85%, at least about 90%, at least about 95%, or at
least about 99% homologous to the DNA sequence of SEQ ID NO: 32, or
a nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 32.
[0248] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 33 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 33. In some embodiments, genetically engineered bacteria
comprise a nucleic acid sequence that is at least about 80%, at
least about 85%, at least about 90%, at least about 95%, or at
least about 99% homologous to the DNA sequence of SEQ ID NO: 33, or
a nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 33.
[0249] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 35 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 35. In some embodiments, genetically engineered bacteria
comprise a nucleic acid sequence that is at least about 80%, at
least about 85%, at least about 90%, at least about 95%, or at
least about 99% homologous to the DNA sequence of SEQ ID NO: 35, or
a nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 35.
TABLE-US-00009 TABLE 9 Exemplary FNR promoter-driven argA.sup.fbr
sequence (SEQ ID NO: 32)
AGTTGTTCTTATTGGTGGTGTTGCTTTATGGTTGCATCGTAGTAAATGGTTGTAACAA
AAGCAATTTTTCCGGCTGTCTGTATACAAAAACGCCGCAAAGTTTGAGCGAAGTCAAT
AAACTCTCTACCCATTCAGGGCAATATCTCTCTTggatccaaagtgaactctagaaat
##STR00055## ##STR00056## ##STR00057## ##STR00058## ##STR00059##
##STR00060## ##STR00061## ##STR00062## ##STR00063## ##STR00064##
##STR00065## ##STR00066## ##STR00067## ##STR00068## ##STR00069##
##STR00070## ##STR00071## ##STR00072## ##STR00073## ##STR00074##
##STR00075## ##STR00076## ##STR00077## ##STR00078##
TABLE-US-00010 TABLE 10 Exemplary sequence of FNR promoter-driven
argA.sup.fbr plasmid (SEQ ID NO: 33)
GTAAAACGACGGCCAGTGAATTCGAGCTCGGTACCATCCCCATCACTCTTGATGGAGATCAA
TTCCCCAAGCTGCTAGAGCGTTACCTTGCCCTTAAACATTAGCAATGTCGATTTATCAGAGG
##STR00079## ##STR00080## ##STR00081## ##STR00082## ##STR00083##
##STR00084## ##STR00085## ##STR00086## ##STR00087## ##STR00088##
##STR00089## ##STR00090## ##STR00091## ##STR00092## ##STR00093##
##STR00094## ##STR00095## ##STR00096## ##STR00097## ##STR00098##
##STR00099## ##STR00100##
AATAAAAATACAATAATTTCGAATAATCATGCAAAGCTTGGCGTAATCATGGTCATAGCTGT
TTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATGTAC
GGGTTTTGCTGCCCGCAAACGGGCTGTTCTGGTGTTGCTAGTTTGTTATCAGAATCGCAGAT
CCGGCTTCAGGTTTGCCGGCTGAAAGCGCTATTTCTTCCAGAATTGCCATGATTTTTTCCCC
ACGGGAGGCGTCACTGGCTCCCGTGTTGTCGGCAGCTTTGATTCGATAAGCAGCATCGCCTG
TTTCAGGCTGTCTATGTGTGACTGTTGAGCTGTAACAAGTTGTCTCAGGTGTTCAATTTCAT
GTTCTAGTTGCTTTGTTTTACTGGTTTCACCTGTTCTATTAGGTGTTACATGCTGTTCATCT
GTTACATTGTCGATCTGTTCATGGTGAACAGCTTTAAATGCACCAAAAACTCGTAAAAGCTC
TGATGTATCTATCTTTTTTACACCGTTTTCATCTGTGCATATGGACAGTTTTCCCTTTGATA
TCTAACGGTGAACAGTTGTTCTACTTTTGTTTGTTAGTCTTGATGCTTCACTGATAGATACA
AGAGCCATAAGAACCTCAGATCCTTCCGTATTTAGCCAGTATGTTCTCTAGTGTGGTTCGTT
GTTTTTGCGTGAGCCATGAGAACGAACCATTGAGATCATGCTTACTTTGCATGTCACTCAAA
AATTTTGCCTCAAAACTGGTGAGCTGAATTTTTGCAGTTAAAGCATCGTGTAGTGTTTTTCT
TAGTCCGTTACGTAGGTAGGAATCTGATGTAATGGTTGTTGGTATTTTGTCACCATTCATTT
TTATCTGGTTGTTCTCAAGTTCGGTTACGAGATCCATTTGTCTATCTAGTTCAACTTGGAAA
ATCAACGTATCAGTCGGGCGGCCTCGCTTATCAACCACCAATTTCATATTGCTGTAAGTGTT
TAAATCTTTACTTATTGGTTTCAAAACCCATTGGTTAAGCCTTTTAAACTCATGGTAGTTAT
TTTCAAGCATTAACATGAACTTAAATTCATCAAGGCTAATCTCTATATTTGCCTTGTGAGTT
TTCTTTTGTGTTAGTTCTTTTAATAACCACTCATAAATCCTCATAGAGTATTTGTTTTCAAA
AGACTTAACATGTTCCAGATTATATTTTATGAATTTTTTTAACTGGAAAAGATAAGGCAATA
TCTCTTCACTAAAAACTAATTCTAATTTTTCGCTTGAGAACTTGGCATAGTTTGTCCACTGG
AAAATCTCAAAGCCTTTAACCAAAGGATTCCTGATTTCCACAGTTCTCGTCATCAGCTCTCT
GGTTGCTTTAGCTAATACACCATAAGCATTTTCCCTACTGATGTTCATCATCTGAGCGTATT
GGTTATAAGTGAACGATACCGTCCGTTCTTTCCTTGTAGGGTTTTCAATCGTGGGGTTGAGT
AGTGCCACACAGCATAAAATTAGCTTGGTTTCATGCTCCGTTAAGTCATAGCGACTAATCGC
TAGTTCATTTGCTTTGAAAACAACTAATTCAGACATACATCTCAATTGGTCTAGGTGATTTT
AATCACTATACCAATTGAGATGGGCTAGTCAATGATAATTACTAGTCCTTTTCCTTTGAGTT
GTGGGTATCTGTAAATTCTGCTAGACCTTTGCTGGAAAACTTGTAAATTCTGCTAGACCCTC
TGTAAATTCCGCTAGACCTTTGTGTGTTTTTTTTGTTTATATTCAAGTGGTTATAATTTATA
GAATAAAGAAAGAATAAAAAAAGATAAAAAGAATAGATCCCAGCCCTGTGTATAACTCACTA
CTTTAGTCAGTTCCGCAGTATTACAAAAGGATGTCGCAAACGCTGTTTGCTCCTCTACAAAA
CAGACCTTAAAACCCTAAAGGCTTAAGTAGCACCCTCGCAAGCTCGGGCAAATCGCTGAATA
TTCCTTTTGTCTCCGACCATCAGGCACCTGAGTCGCTGTCTTTTTCGTGACATTCAGTTCGC
TGCGCTCACGGCTCTGGCAGTGAATGGGGGTAAATGGCACTACAGGCGCCTTTTATGGATTC
ATGCAAGGAAACTACCCATAATACAAGAAAAGCCCGTCACGGGCTTCTCAGGGCGTTTTATG
GCGGGTCTGCTATGTGGTGCTATCTGACTTTTTGCTGTTCAGCAGTTCCTGCCCTCTGATTT
TCCAGTCTGACCACTTCGGATTATCCCGTGACAGGTCATTCAGACTGGCTAATGCACCCAGT
AAGGCAGCGGTATCATCAACAGGCTTACCCGTCTTACTGTCTTTTCTACGGGGTCTGACGCT
CAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCAC
CTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTT
GGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGT
TCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATC
TGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAA
TAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATC
CAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAA
CGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCA
GCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTT
AGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGT
TATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTG
GTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCG
GCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAA
ACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAAC
CCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCA
AAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACT
CATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGAT
ACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAA
GTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTAT
CACGAGGCCCTTTCGTCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGC
TCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGC
GCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGT
ACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCA
TCAGGCGCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCT
TCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCC
AGGGTTTTCCCAGTCACGACGTT
TABLE-US-00011 TABLE 11 Nucleic acid sequence of pSC101 plasmid
(SEQ ID NO: 34) ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTATTGCGTTG
CGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTA
ATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTT
CCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGA
GCGGTATCAGCTCACTCAAAGGCGGTAGTACGGGTTTTGCTGCCCGCAAA
CGGGCTGTTCTGGTGTTGCTAGTTTGTTATCAGAATCGCAGATCCGGCTT
CAGGTTTGCCGGCTGAAAGCGCTATTTCTTCCAGAATTGCCATGATTTTT
TCCCCACGGGAGGCGTCACTGGCTCCCGTGTTGTCGGCAGCTTTGATTCG
ATAAGCAGCATCGCCTGTTTCAGGCTGTCTATGTGTGACTGTTGAGCTGT
AACAAGTTGTCTCAGGTGTTCAATTTCATGTTCTAGTTGCTTTGTTTTAC
TGGTTTCACCTGTTCTATTAGGTGTTACATGCTGTTCATCTGTTACATTG
TCGATCTGTTCATGGTGAACAGCTTTAAATGCACCAAAAACTCGTAAAAG
CTCTGATGTATCTATCTTTTTTACACCGTTTTCATCTGTGCATATGGACA
GTTTTCCCTTTGATATCTAACGGTGAACAGTTGTTCTACTTTTGTTTGTT
AGTCTTGATGCTTCACTGATAGATACAAGAGCCATAAGAACCTCAGATCC
TTCCGTATTTAGCCAGTATGTTCTCTAGTGTGGTTCGTTGTTTTTGCGTG
AGCCATGAGAACGAACCATTGAGATCATGCTTACTTTGCATGTCACTCAA
AAATTTTGCCTCAAAACTGGTGAGCTGAATTTTTGCAGTTAAAGCATCGT
GTAGTGTTTTTCTTAGTCCGTTACGTAGGTAGGAATCTGATGTAATGGTT
GTTGGTATTTTGTCACCATTCATTTTTATCTGGTTGTTCTCAAGTTCGGT
TACGAGATCCATTTGTCTATCTAGTTCAACTTGGAAAATCAACGTATCAG
TCGGGCGGCCTCGCTTATCAACCACCAATTTCATATTGCTGTAAGTGTTT
AAATCTTTACTTATTGGTTTCAAAACCCATTGGTTAAGCCTTTTAAACTC
ATGGTAGTTATTTTCAAGCATTAACATGAACTTAAATTCATCAAGGCTAA
TCTCTATATTTGCCTTGTGAGTTTTCTTTTGTGTTAGTTCTTTTAATAAC
CACTCATAAATCCTCATAGAGTATTTGTTTTCAAAAGACTTAACATGTTC
CAGATTATATTTTATGAATTTTTTTAACTGGAAAAGATAAGGCAATATCT
CTTCACTAAAAACTAATTCTAATTTTTCGCTTGAGAACTTGGCATAGTTT
GTCCACTGGAAAATCTCAAAGCCTTTAACCAAAGGATTCCTGATTTCCAC
AGTTCTCGTCATCAGCTCTCTGGTTGCTTTAGCTAATACACCATAAGCAT
TTTCCCTACTGATGTTCATCATCTGAGCGTATTGGTTATAAGTGAACGAT
ACCGTCCGTTCTTTCCTTGTAGGGTTTTCAATCGTGGGGTTGAGTAGTGC
CACACAGCATAAAATTAGCTTGGTTTCATGCTCCGTTAAGTCATAGCGAC
TAATCGCTAGTTCATTTGCTTTGAAAACAACTAATTCAGACATACATCTC
AATTGGTCTAGGTGATTTTAATCACTATACCAATTGAGATGGGCTAGTCA
ATGATAATTACTAGTCCTTTTCCTTTGAGTTGTGGGTATCTGTAAATTCT
GCTAGACCTTTGCTGGAAAACTTGTAAATTCTGCTAGACCCTCTGTAAAT
TCCGCTAGACCTTTGTGTGTTTTTTTTGTTTATATTCAAGTGGTTATAAT
TTATAGAATAAAGAAAGAATAAAAAAAGATAAAAAGAATAGATCCCAGCC
CTGTGTATAACTCACTACTTTAGTCAGTTCCGCAGTATTACAAAAGGATG
TCGCAAACGCTGTTTGCTCCTCTACAAAACAGACCTTAAAACCCTAAAGG
CTTAAGTAGCACCCTCGCAAGCTCGGGCAAATCGCTGAATATTCCTTTTG
TCTCCGACCATCAGGCACCTGAGTCGCTGTCTTTTTCGTGACATTCAGTT
CGCTGCGCTCACGGCTCTGGCAGTGAATGGGGGTAAATGGCACTACAGGC
GCCTTTTATGGATTCATGCAAGGAAACTACCCATAATACAAGAAAAGCCC
GTCACGGGCTTCTCAGGGCGTTTTATGGCGGGTCTGCTATGTGGTGCTAT
CTGACTTTTTGCTGTTCAGCAGTTCCTGCCCTCTGATTTTCCAGTCTGAC
CACTTCGGATTATCCCGTGACAGGTCATTCAGACTGGCTAATGCACCCAG
TAAGGCAGCGGTATCATCAACAGGCTTACCCGTCTTACTGTCTTTTCTAC
GGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCA
TGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGA
AGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTA
CCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTT
CATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAG
GGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTC
ACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGC
GCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGT
TGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGT
TGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGG
CTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCC
ATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAG
AAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATA
ATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAG
TACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTC
TTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAA
AAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATC
TTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTG
ATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAG
GAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGA
ATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTA
TTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAA
TAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAA
ACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCC
CTTTCGTCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGC
AGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGA
CAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCT
TAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGT
GTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCAT
TCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTC
TTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCG
TABLE-US-00012 Table 12 Nucleotide sequence of exemplary fnrS
promoter-driven argA.sup.fbr pSC101 plasmid (SEQ ID NO: 35)
##STR00101## ##STR00102## ##STR00103## ##STR00104## ##STR00105##
##STR00106## ##STR00107## ##STR00108## ##STR00109## ##STR00110##
##STR00111## ##STR00112## ##STR00113## ##STR00114## ##STR00115##
##STR00116## ##STR00117## ##STR00118## ##STR00119## ##STR00120##
##STR00121## ##STR00122## ##STR00123## ##STR00124## ##STR00125##
GTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAG
TGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCG
CTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGG
CGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGG
CTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAGTACGGGTTTTGCTGCCCGCAAACGGGC
TGTTCTGGTGTTGCTAGTTTGTTATCAGAATCGCAGATCCGGCTTCAGGTTTGCCGGCTGAAAG
CGCTATTTCTTCCAGAATTGCCATGATTTTTTCCCCACGGGAGGCGTCACTGGCTCCCGTGTTG
TCGGCAGCTTTGATTCGATAAGCAGCATCGCCTGTTTCAGGCTGTCTATGTGTGACTGTTGAGC
TGTAACAAGTTGTCTCAGGTGTTCAATTTCATGTTCTAGTTGCTTTGTTTTACTGGTTTCACCT
GTTCTATTAGGTGTTACATGCTGTTCATCTGTTACATTGTCGATCTGTTCATGGTGAACAGCTT
TAAATGCACCAAAAACTCGTAAAAGCTCTGATGTATCTATCTTTTTTACACCGTTTTCATCTGT
GCATATGGACAGTTTTCCCTTTGATATCTAACGGTGAACAGTTGTTCTACTTTTGTTTGTTAGT
CTTGATGCTTCACTGATAGATACAAGAGCCATAAGAACCTCAGATCCTTCCGTATTTAGCCAGT
ATGTTCTCTAGTGTGGTTCGTTGTTTTTGCGTGAGCCATGAGAACGAACCATTGAGATCATGCT
TACTTTGCATGTCACTCAAAAATTTTGCCTCAAAACTGGTGAGCTGAATTTTTGCAGTTAAAGC
ATCGTGTAGTGTTTTTCTTAGTCCGTTACGTAGGTAGGAATCTGATGTAATGGTTGTTGGTATT
TTGTCACCATTCATTTTTATCTGGTTGTTCTCAAGTTCGGTTACGAGATCCATTTGTCTATCTA
GTTCAACTTGGAAAATCAACGTATCAGTCGGGCGGCCTCGCTTATCAACCACCAATTTCATATT
GCTGTAAGTGTTTAAATCTTTACTTATTGGTTTCAAAACCCATTGGTTAAGCCTTTTAAACTCA
TGGTAGTTATTTTCAAGCATTAACATGAACTTAAATTCATCAAGGCTAATCTCTATATTTGCCT
TGTGAGTTTTCTTTTGTGTTAGTTCTTTTAATAACCACTCATAAATCCTCATAGAGTATTTGTT
TTCAAAAGACTTAACATGTTCCAGATTATATTTTATGAATTTTTTTAACTGGAAAAGATAAGGC
AATATCTCTTCACTAAAAACTAATTCTAATTTTTCGCTTGAGAACTTGGCATAGTTTGTCCACT
GGAAAATCTCAAAGCCTTTAACCAAAGGATTCCTGATTTCCACAGTTCTCGTCATCAGCTCTCT
GGTTGCTTTAGCTAATACACCATAAGCATTTTCCCTACTGATGTTCATCATCTGAGCGTATTGG
TTATAAGTGAACGATACCGTCCGTTCTTTCCTTGTAGGGTTTTCAATCGTGGGGTTGAGTAGTG
CCACACAGCATAAAATTAGCTTGGTTTCATGCTCCGTTAAGTCATAGCGACTAATCGCTAGTTC
ATTTGCTTTGAAAACAACTAATTCAGACATACATCTCAATTGGTCTAGGTGATTTTAATCACTA
TACCAATTGAGATGGGCTAGTCAATGATAATTACTAGTCCTTTTCCTTTGAGTTGTGGGTATCT
GTAAATTCTGCTAGACCTTTGCTGGAAAACTTGTAAATTCTGCTAGACCCTCTGTAAATTCCGC
TAGACCTTTGTGTGTTTTTTTTGTTTATATTCAAGTGGTTATAATTTATAGAATAAAGAAAGAA
TAAAAAAAGATAAAAAGAATAGATCCCAGCCCTGTGTATAACTCACTACTTTAGTCAGTTCCGC
AGTATTACAAAAGGATGTCGCAAACGCTGTTTGCTCCTCTACAAAACAGACCTTAAAACCCTAA
AGGCTTAAGTAGCACCCTCGCAAGCTCGGGCAAATCGCTGAATATTCCTTTTGTCTCCGACCAT
CAGGCACCTGAGTCGCTGTCTTTTTCGTGACATTCAGTTCGCTGCGCTCACGGCTCTGGCAGTG
AATGGGGGTAAATGGCACTACAGGCGCCTTTTATGGATTCATGCAAGGAAACTACCCATAATAC
AAGAAAAGCCCGTCACGGGCTTCTCAGGGCGTTTTATGGCGGGTCTGCTATGTGGTGCTATCTG
ACTTTTTGCTGTTCAGCAGTTCCTGCCCTCTGATTTTCCAGTCTGACCACTTCGGATTATCCCG
TGACAGGTCATTCAGACTGGCTAATGCACCCAGTAAGGCAGCGGTATCATCAACAGGCTTACCC
GTCTTACTGTCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTT
GGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAA
TCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCAC
CTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAAC
TACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCA
CCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTG
CAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCC
AGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTT
GGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGT
GCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTT
ATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTT
TCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCT
CTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCAT
TGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATG
TAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAG
CAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACT
CATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATAC
ATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGC
CACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAG
GCCCTTTCGTCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAG
ACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGG
GTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCA
CCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCATTCG
CCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGC
TGGCGAAAGGGGGATGTGCTGCAAGGCG
[0250] In some embodiments, the genetically engineered bacteria
comprise argA.sup.fbr integrated into the chromosome. In some
embodiments, the integrated fbrArgA is under the control of the
fnrS promoter. In some embodiments, an antibiotic resistance
cassette is also present at the same site. In some embodiments, no
antibiotic resistance cassette is present. In some embodiments, the
antibiotic resistance is chloramphenicol. In some embodiments, the
antibiotic resistance is kanamycin. In some embodiments, the
genetically engineered bacteria comprising argA.sup.fbr integrated
into the chromosome is a thyA auxotroph. In some embodiments, the
genetically engineered bacteria comprise argA.sup.fbr integrated
into the chromosome and also comprise an ArgR mutation or have ArgR
deleted. In one specific embodiment, the genetically engineered
bacteria comprise argA.sup.fbr under the control of the fnrS
promoter and integrated into the chromosome, comprise an ArgR
mutation or have ArgR deleted, and comprise a thyA auxotrophy. In
another specific embodiment, the genetically engineered bacteria
comprise argA.sup.fbr under the control of the fnrS promoter and
integrated into the chromosome, comprise an ArgR mutation or have
ArgR deleted, comprise a thyA auxotrophy, and comprise an
antibiotic resistance cassette. In another specific embodiment, the
genetically engineered bacteria comprise argAfbr under the control
of the fnrS promoter and integrated into the chromosome, comprise
an ArgR mutation or have ArgR deleted, comprise a thyA auxotrophy,
and comprise a kanamycin resistance cassette. In one specific
embodiment, the genetically engineered bacteria is SYN-UCD305. In
another specific embodiment, the genetically engineered bacteria is
SYN_UCD303.
[0251] Table 13 shows non-limiting examples of FNRS-fbrArgA
constructs which are integrated into the chromosome.
[0252] SEQ ID NO: 36 comprises FNRS-fbrArgA and chloramphenicol
resistance, e.g., as comprised in SYN-UCD301, SYN-UCD302. SEQ ID
NO: 37 comprises FNRS-fbrArgA and kanamycin resistance, e.g., as
comprised in SYN-UCD303, SYN-UCD306, SYN-UCD307, and SYN-UCD309.
SEQ ID NO: 38 FNRS-fbrArgA and no antibiotic resistance, e.g., as
comprised in SYN-UCD305 SYN-UCD304, SYN-UCD308, SYNUCD310.
TABLE-US-00013 SEQ ID Description Sequence NO FNRS-fbrArgA
ctacgccccatcgttgctttgtgtgatctctgttacaga SEQ ID and
attggcggtaatgtggagatgcgcacataaaatcgccat NO: 36 chloramphenicol
gatttttgcaagcaacatcacgaaattccttacatgacc resistance,
tcggtttagttcacaggacgtcccatggctcgagCATGC e.g., SYN-
GAGAGTAGGGAACTGCCAGGCATCAAATAAAAtGAAAGG UCD301, SYN-
CTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTT UCD302; a
TGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGG schematic of
GAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGT the
GGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAA construct is
TTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGT depicted in
GGCCAGTGCCAAGCTTGCATGCAGATTGCAGCATTACAC FIG. 20;
GTCTTGAGCGATTGTGTAGGCTGGAGCTGCTTC UPPERCASE underlined:
ATTTAAATGGCGCGCCTTACGCCCCGCCCTGCCACT CmR gene;
CATCGCAGTACTGTTGTATTCATTAAGCATCTGCCGACA UPPERCASE
TGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCC italics: CmR
AGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTG promoter;
CCCATGGTGAAAACGGGGGCGAAGAAGTTGTCCATATTG UPPERCASE
GCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGA italic and
TTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTA underlined:
GGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCT fnrS
TGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGG promoter;
TATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCA UPPERCASE
TGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATC bold:
ACCAGCTCACCGTCTTTCATTGCCATACGTAATTCCGGA ArgAfbr;
TGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCC UPPERCASE
GGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAA bold
AAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTA underline:
CATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTA terminator
CGATGCCATTGGGATATATCAACGGTGGTATATCCAGTG sequence;
ATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAAT UPPERCASE
CTCGACAACTCAAAAAATACGCCCGGTAGTGATCTTATT italic bold:
TCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCA frt sites
ACGTCTCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCCG
GTATCAACAGGGACACCAGGATTTATTTATTCTGCGAAG TGATCTTCCGTCACAGGTAGGCGCGCC
AGGA GGATATTCATATGGACCATGGCTAATTCCCAGGTACCAG
TTGTTCTTATTGGTGGTGTTGCTTTATGGTTGCATCGTA
GTAAATGGTTGTAACAAAAGCAATTTTTCCGGCTGTCTG
TATACAAAAACGCCGTAAAGTTTGAGCGAAGTCAATAAA
CTCTCTACCCATTCAGGGCAATATCTCTCTTGGATCCaa
agtgaactctagaaataattttgtttaactttaagaagg
agatatacatATGGTAAAGGAACGTAAAACCGAGTTGGT
CGAGGGATTCCGCCATTCGGTTCCCTGTATCAATACCCA
CCGGGGAAAAACGTTTGTCATCATGCTCGGCGGTGAAGC
CATTGAGCATGAGAATTTCTCCAGTATCGTTAATGATAT
CGGGTTGTTGCACAGCCTCGGCATCCGTCTGGTGGTGGT
CTATGGCGCACGTCCGCAGATCGACGCAAATCTGGCTGC
GCATCACCACGAACCGCTGTATCACAAGAATATACGTGT
GACCGACGCCAAAACACTGGAACTGGTGAAGCAGGCTGC
GGGAACATTGCAACTGGATATTACTGCTCGCCTGTCGAT
GAGTCTCAATAACACGCCGCTGCAGGGCGCGCATATCAA
CGTCGTCAGTGGCAATTTTATTATTGCCCAGCCGCTGGG
CGTCGATGACGGCGTGGATTACTGCCATAGCGGGCGTAT
CCGGCGGATTGATGAAGACGCGATCCATCGTCAACTGGA
CAGCGGTGCAATAGTGCTAATGGGGCCGGTCGCTGTTTC
AGTCACTGGCGAGAGCTTTAACCTGACCTCGGAAGAGAT
TGCCACTCAACTGGCCATCAAACTGAAAGCTGAAAAGAT
GATTGGTTTTTGCTCTTCCCAGGGCGTCACTAATGACGA
CGGTGATATTGTCTCCGAACTTTTCCCTAACGAAGCGCA
AGCGCGGGTAGAAGCCCAGGAAGAGAAAGGCGATTACAA
CTCCGGTACGGTGCGCTTTTTGCGTGGCGCAGTGAAAGC
CTGCCGCAGCGGCGTGCGTCGCTGTCATTTAATCAGTTA
TCAGGAAGATGGCGCGCTGTTGCAAGAGTTGTTCTCACG
CGACGGTATCGGTACGCAGATTGTGATGGAAAGCGCCGA
GCAGATTCGTCGCGCAACAATCAACGATATTGGCGGTAT
TCTGGAGTTGATTCGCCCACTGGAGCAGCAAGGTATTCT
GGTACGCCGTTCTCGCGAGCAGCTGGAGATGGAAATCGA
CAAATTCACCATTATTCAGCGCGATAACACGACTATTGC
CTGCGCCGCGCTCTATCCGTTCCCGGAAGAGAAGATTGG
GGAAATGGCCTGTGTGGCAGTTCACCCGGATTACCGCAG
TTCATCAAGGGGTGAAGTTCTGCTGGAACGCATTGCCGC
TCAGGCTAAGCAGAGCGGCTTAAGCAAATTGTTTGTGCT
GACCACGCGCAGTATTCACTGGTTCCAGGAACGTGGATT
TACCCCAGTGGATATTGATTTACTGCCCGAGAGCAAAAA
GCAGTTGTACAACTACCAGCGTAAATCCAAAGTGTTGAT
GGCGGATTTAGGGTAAgtcgacgcatgcatcgataagcc
gcgttctcatcctcccgcctcctcccccataaaaaagcc
agggggtggaggatttaagccatctcctgatgac FNRS-fbrArgA
ctacgccccatcgttgctttgtgtgatctctgttacaga SEQ ID and
attggcggtaatgtggagatgcgcacataaaatcgccat NO: 37 kanamycin
gatttttgcaagcaacatcacgaaattccttacatgacc resistance,
tcggtttagttcacaggacgtcccatggctcgagCATGC e.g., SYN-
GAGAGTAGGGAACTGCCAGGCATCAAATAAAATGAAAGG UCD303, SYN-
CTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTT UCD306, SYN-
TGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGG UCD307, and
GAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGT SYN-UCD309;
GGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAA a schematic
TTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGT of the
GGCCAGTGCCAAGCTTGCATGCAGATTGCAGCATTACAC construct is
GTCTTGAGCGATTGTGTAGGCTGGAGCTGCTTC depicted in FIG. 21
aagatcccctcacgctgccgcaagcactcagggcgc Lowercase
aagggctgctaaaggaagcggaacacgtagaaagccagt underlined:
ccgcagaaacggtgctgaccccggatgaatgtcagctac KanR
tgggctatctggacaagggaaaacgcaagcgcaaagaga promoter;
aagcaggtagcttgcagtgggcttacatggcgatagcta lowercase
gactgggcggttttatggacagcaagcgaaccggaattg italic: KanR
ccagctggggcgccctctggtaaggttgggaagccctgc gene;
aaagtaaactggatggctttcttgccgccaaggatctga UPPERCASE
tggcgcaggggatcaagatctgatcaagagacaggatga underlined:
ggatcgtttcgcatgattgaacaagatggattgcacgca fnrS
ggttctccggccgcttgggtggagaggctattcggctat promoter;
gactgggcacaacagacaatcggctgctctgatgccgcc UPPERCASE
gtgttccggctgtcagcgcaggggcgcccggttcttttt bold:
gtcaagaccgacctgtccggtgccctgaatgaactgcag ArgAfbr
gacgaggcagcgcggctatcgtggctggccacgacgggc UPPERCASE
gttccttgcgcagctgtgctcgacgttgtcactgaagcg bold
ggaagggactggctgctattgggcgaagtgccggggcag underline:
gatctcctgtcatctcaccttgctcctgccgagaaagta terminator
tccatcatggctgatgcaatgcggcggctgcatacgctt sequence;
gatccggctacctgcccattcgaccaccaagcgaaacat UPPERCASE
cgcatcgagcgagcacgtactcggatggaagccggtctt italic bold:
gtcgatcaggatgatctggacgaagagcatcaggggctc frt sites
gcgccagccgaactgttcgccaggctcaaggcgcgcatg
cccgacggcgaggatctcgtcgtgacccatggcgatgcc
tgcttgccgaatatcatggtggaaaatggccgcttttct
ggattcatcgactgtggccggctgggtgtggcggaccgc
tatcaggacatagcgttggctacccgtgatattgctgaa
gagcttggcggcgaatgggctgaccgcttcctcgtgctt
tacggtatcgccgctcccgattcgcagcgcatcgccttc
tatcgccttcttgacgagttcttctgagcgggactctgg
ggttcgaaatgaccgaccaagcgacgcccaacctgccat
cacgagatttcgattccaccgccgccttctatgaaaggt
tgggcttcggaatcgttttccgggacgccggctggatga
tcctccagcgcggggatctcatgctggagttcttcgccc accccagcttcaaaagcgctct
AGGAGGATA TTCATATGGACCATGGCTAATTCCCAGATATGGTACCAG
TTGTTCTTATTGGTGGTGTTGCTTTATGGTTGCATCGTA
GTAAATGGTTGTAACAAAAGCAATTTTTCCGGCTGTCTG
TATACAAAAACGCCGTAAAGTTTGAGCGAAGTCAATAAA
CTCTCTACCCATTCAGGGCAATATCTCTCTTGGATCCaa
agtgaactctagaaataattttgtttaactttaagaagg
agatatacatATGGTAAAGGAACGTAAAACCGAGTTGGT
CGAGGGATTCCGCCATTCGGTTCCCTGTATCAATACCCA
CCGGGGAAAAACGTTTGTCATCATGCTCGGCGGTGAAGC
CATTGAGCATGAGAATTTCTCCAGTATCGTTAATGATAT
CGGGTTGTTGCACAGCCTCGGCATCCGTCTGGTGGTGGT
CTATGGCGCACGTCCGCAGATCGACGCAAATCTGGCTGC
GCATCACCACGAACCGCTGTATCACAAGAATATACGTGT
GACCGACGCCAAAACACTGGAACTGGTGAAGCAGGCTGC
GGGAACATTGCAACTGGATATTACTGCTCGCCTGTCGAT
GAGTCTCAATAACACGCCGCTGCAGGGCGCGCATATCAA
CGTCGTCAGTGGCAATTTTATTATTGCCCAGCCGCTGGG
CGTCGATGACGGCGTGGATTACTGCCATAGCGGGCGTAT
CCGGCGGATTGATGAAGACGCGATCCATCGTCAACTGGA
CAGCGGTGCAATAGTGCTAATGGGGCCGGTCGCTGTTTC
AGTCACTGGCGAGAGCTTTAACCTGACCTCGGAAGAGAT
TGCCACTCAACTGGCCATCAAACTGAAAGCTGAAAAGAT
GATTGGTTTTTGCTCTTCCCAGGGCGTCACTAATGACGA
CGGTGATATTGTCTCCGAACTTTTCCCTAACGAAGCGCA
AGCGCGGGTAGAAGCCCAGGAAGAGAAAGGCGATTACAA
CTCCGGTACGGTGCGCTTTTTGCGTGGCGCAGTGAAAGC
CTGCCGCAGCGGCGTGCGTCGCTGTCATTTAATCAGTTA
TCAGGAAGATGGCGCGCTGTTGCAAGAGTTGTTCTCACG
CGACGGTATCGGTACGCAGATTGTGATGGAAAGCGCCGA
GCAGATTCGTCGCGCAACAATCAACGATATTGGCGGTAT
TCTGGAGTTGATTCGCCCACTGGAGCAGCAAGGTATTCT
GGTACGCCGTTCTCGCGAGCAGCTGGAGATGGAAATCGA
CAAATTCACCATTATTCAGCGCGATAACACGACTATTGC
CTGCGCCGCGCTCTATCCGTTCCCGGAAGAGAAGATTGG
GGAAATGGCCTGTGTGGCAGTTCACCCGGATTACCGCAG
TTCATCAAGGGGTGAAGTTCTGCTGGAACGCATTGCCGC
TCAGGCTAAGCAGAGCGGCTTAAGCAAATTGTTTGTGCT
GACCACGCGCAGTATTCACTGGTTCCAGGAACGTGGATT
TACCCCAGTGGATATTGATTTACTGCCCGAGAGCAAAAA
GCAGTTGTACAACTACCAGCGTAAATCCAAAGTGTTGAT
GGCGGATTTAGGGTAAgtcgacgcatgcatcgataagcc
gcgttctcatcctcccgcctcctcccccataaaaaagcc
agggggtggaggatttaagccatctcctgatgac FNRS-fbrArgA
ctacgccccatcgttgctttgtgtgatctctgttacaga SEQ ID and no
attggcggtaatgtggagatgcgcacataaaatcgccat NO: 38 antibiotic
gatttttgcaagcaacatcacgaaattccttacatgacc resistance,
tcggtttagttcacaggacgtcccatggctcgagCATGC e.g., SYN-
GAGAGTAGGGAACTGCCAGGCATCAAATAAAATGAAAGG UCD305 SYN-
CTCAGTCGAAAGACTGGGCCTTTCGTTTTATCT UCD304, SYN-
GTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATC UCD308,
CGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCG SYNUCD310; a
GAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGC schematic of
TCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTT the
TTGCGTGGCCAGTGCCAAGCTTGCATGCAGATTGCAGCA construct is
TTACACGTCTTGAGCGATTGTGTAGGCTGGAGCTGCTTC depicted in FIG. 22;
AGGAGGATATTCATATGGACCATGGCTAATT UPPERCASE
CCCAGGTACCAGTTGTTCTTATTGGTGGTGTTGCTTTAT underline:
GGTTGCATCGTAGTAAATGGTTGTAACAAAAGCAATTTT fnrS
TCCGGCTGTCTGTATACAAAAACGCCGTAAAGTTTGAGC promoter;
GAAGTCAATAAACTCTCTACCCATTCAGGGCAATATCTC UPPERCASE
TCTTGGATCCaaagtgaactctagaaataattttgttta bold:
actttaagaaggagatatacatATGGTAAAGGAACGTAA ArgAfbr;
AACCGAGTTGGTCGAGGGATTCCGCCATTCGGTTCCCTG UPPERCASE
TATCAATACCCACCGGGGAAAAACGTTTGTCATCATGCT bold
CGGCGGTGAAGCCATTGAGCATGAGAATTTCTCCAGTAT underline:
CGTTAATGATATCGGGTTGTTGCACAGCCTCGGCATCCG terminator
TCTGGTGGTGGTCTATGGCGCACGTCCGCAGATCGACGC sequence;
AAATCTGGCTGCGCATCACCACGAACCGCTGTATCACAA UPPERCASE
GAATATACGTGTGACCGACGCCAAAACACTGGAACTGGT italic bold:
GAAGCAGGCTGCGGGAACATTGCAACTGGATATTACTGC frt sites
TCGCCTGTCGATGAGTCTCAATAACACGCCGCTGCAGGG
CGCGCATATCAACGTCGTCAGTGGCAATTTTATTATTGC
CCAGCCGCTGGGCGTCGATGACGGCGTGGATTACTGCCA
TAGCGGGCGTATCCGGCGGATTGATGAAGACGCGATCCA
TCGTCAACTGGACAGCGGTGCAATAGTGCTAATGGGGCC
GGTCGCTGTTTCAGTCACTGGCGAGAGCTTTAACCTGAC
CTCGGAAGAGATTGCCACTCAACTGGCCATCAAACTGAA
AGCTGAAAAGATGATTGGTTTTTGCTCTTCCCAGGGCGT
CACTAATGACGACGGTGATATTGTCTCCGAACTTTTCCC
TAACGAAGCGCAAGCGCGGGTAGAAGCCCAGGAAGAGAA
AGGCGATTACAACTCCGGTACGGTGCGCTTTTTGCGTGG
CGCAGTGAAAGCCTGCCGCAGCGGCGTGCGTCGCTGTCA
TTTAATCAGTTATCAGGAAGATGGCGCGCTGTTGCAAGA
GTTGTTCTCACGCGACGGTATCGGTACGCAGATTGTGAT
GGAAAGCGCCGAGCAGATTCGTCGCGCAACAATCAACGA
TATTGGCGGTATTCTGGAGTTGATTCGCCCACTGGAGCA
GCAAGGTATTCTGGTACGCCGTTCTCGCGAGCAGCTGGA
GATGGAAATCGACAAATTCACCATTATTCAGCGCGATAA
CACGACTATTGCCTGCGCCGCGCTCTATCCGTTCCCGGA
AGAGAAGATTGGGGAAATGGCCTGTGTGGCAGTTCACCC
GGATTACCGCAGTTCATCAAGGGGTGAAGTTCTGCTGGA
ACGCATTGCCGCTCAGGCTAAGCAGAGCGGCTTAAGCAA
ATTGTTTGTGCTGACCACGCGCAGTATTCACTGGTTCCA
GGAACGTGGATTTACCCCAGTGGATATTGATTTACTGCC
CGAGAGCAAAAAGCAGTTGTACAACTACCAGCGTAAATC
CAAAGTGTTGATGGCGGATTTAGGGTAAgtcgacgcatg
catcgataagccgcgttctcatcctcccgcctcctcccc
cataaaaaagccagggggtggaggatttaagccatctcc tgatgac
[0253] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 36 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 36 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 36 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 37 or a functional
fragment thereof.
[0254] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 37 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 37 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 37 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 37 or a functional
fragment thereof.
[0255] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 38 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 38 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 38 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 38 or a functional
fragment thereof.
[0256] Arginine Catabolism
[0257] An important consideration in practicing the invention is to
ensure that ammonia is not overproduced as a byproduct of arginine
and/or citrulline catabolism. In the final enzymatic step of the
urea cycle, arginase catalyzes the hydrolytic cleavage of arginine
into ornithine and urea (Cunin et al., 1986). Urease, which may be
produced by gut bacteria, catalyzes the cleavage of urea into
carbon dioxide and ammonia (Summerskill, 1966; Aoyagi et al., 1966;
Cunin et al., 1986). Thus, urease activity may generate ammonia
that can be toxic for human tissue (Konieczna et al., 2012). In
some bacteria, including E. coli Nissle, the gene arcD encodes an
arginine/ornithine antiporter, which may also liberate ammonia
(Vander Wauven et al., 1984; Gamper et al., 1991; Meng et al.,
1992).
[0258] AstA is an enzyme involved in the conversion of arginine to
succinate, which liberates ammonia. SpeA is an enzyme involved in
the conversion of arginine to agmatine, which can be further
catabolized to produce ammonia. Thus, in some instances, it may be
advantageous to prevent the breakdown of arginine. In some
embodiments, the genetically engineered bacteria comprising a
mutant arginine regulon additionally includes mutations that reduce
or eliminate arginine catabolism, thereby reducing or eliminating
further ammonia production. In some embodiments, the genetically
engineered bacteria also comprise mutations that reduce or
eliminate ArcD activity. In certain embodiments, ArcD is deleted.
In some embodiments, the genetically engineered bacteria also
comprise mutations that reduce or eliminate AstA activity. In
certain embodiments, AstA is deleted. In some embodiments, the
genetically engineered bacteria also comprise mutations that reduce
or eliminate SpeA activity. In certain embodiments, SpeA is
deleted. In some embodiments, the genetically engineered bacteria
also comprise mutations that reduce or eliminate arginase activity.
In certain embodiments, arginase is deleted. In some embodiments,
the genetically engineered bacteria also comprise mutations that
reduce or eliminate urease activity. In certain embodiments, urease
is deleted. In some embodiments, one or more other genes involved
in arginine catabolism are mutated or deleted.
[0259] Other Hyperammonemia Disorders
[0260] Hepatic encephalopathy (HE) is characterized by
neurocognitive changes in patients and biochemical derangements
have been implicated in pathogenesis. Specifically, elevated
ammonia levels are suspected to partly contribute to disease
pathophysiology. In addition to hyperammonemia, elevated levels of
cerebral GABA and manganese levels have been noted and suspected to
contribute to clinical presentation.
[0261] In some embodiments, the disclosure provides genetically
engineered microorganisms, e.g., bacteria and virus, pharmaceutical
compositions thereof, and methods of modulating or treating
diseases or disorders associated with hyperammonemia, e.g., hepatic
encephalopathy and Huntington's disease. The genetically engineered
bacteria are capable of reducing excess ammonia in a mammal. In
some embodiments, the genetically engineered bacteria reduce excess
ammonia by incorporating excess nitrogen in the body into non-toxic
molecules, e.g., arginine, citrulline, methionine, histidine,
lysine, asparagine, glutamine, or tryptophan. In some embodiments,
the genetically engineered bacteria further comprise one or more
circuits (genetic sequence) to reduce the levels of other toxic or
deleterious molecule(s), e.g., GABA, manganese. In some
embodiments, the genetically engineered bacteria further comprise
one or more circuits to produce a gut barrier enhancer molecule,
e.g., a short chain fatty acid such as butyrate, propionate, and
acetate. This disclosure also provides compositions and therapeutic
methods for reducing excess ammonia and other deleterious
molecules, e.g., GABA and manganese. In certain aspects, the
disclosure provides genetically engineered bacteria that are
capable of reducing excess ammonia and other deleterious molecules.
In certain embodiments, the disclosure provides genetically
engineered bacteria that are capable of reducing excess ammonia and
other deleterious molecules and further producing one or more
therapeutic molecules, such as a gut barrier function enhancer
molecule, e.g., butyrate. In some embodiments, the disclosure
provides genetically engineered bacteria comprising one or more
circuits for reducing excess ammonia in which the circuits are
under the control of an inducible promoter. In some embodiments,
the disclosure provides genetically engineered bacteria comprising
one or more circuits for reducing excess ammonia and one or more
circuits for reducing other deleterious molecules in which one or
more of the circuits are under the control of an inducible
promoter. In some embodiments, the disclosure provides genetically
engineered bacteria comprising one or more circuits for reducing
excess ammonia and one or more circuits for reducing other
deleterious molecules and further producing one or more therapeutic
molecules, such as a gut barrier function enhancer molecule, e.g.,
butyrate in which one or more of the circuits and/or therapeutic
molecule(s) are under the control of an inducible promoter. In
certain aspects, the compositions and methods disclosed herein may
be used for treating a disease or disorder associated with excess
ammonia, for example, hepatic encephalopathy or Huntington's
disease, and/or one or more symptoms associated with disease or
disorder associated with excess ammonia, such as hepatic
encephalopathy or Huntington's disease.
[0262] GABA Transport and Metabolism
[0263] .gamma.-Aminobutyric acid (GABA) is the predominant
inhibitory neurotransmitter in the mammalian central nervous
system. In humans, GABA activates the post-synaptic GABA.sub.A
receptor, which is part of a ligand-gated chloride-specific ion
channel complex. Activation of this complex on a post-synaptic
neuron allows chloride ions to enter the neuron and exert an
inhibitory effect. Alterations of such GABAergic neurotransmission
have been implicated in the pathophysiology of several neurological
disorders, including epilepsy (Jones-Davis and MacDonald, 2003),
Huntington's disease (Krogsgaard-Larsen, 1992), and hepatic
encephalopathy (Jones and Basile, 1997).
[0264] Neurons in the brain that are modulated by GABA are said to
be under inhibitory GABAergic tone. This inhibitory tone prevents
neuronal firing until a sufficiently potent stimulatory stimulus is
received, or until the inhibitory tone is otherwise released.
Increased GABAergic tone in hepatic encephalopathy was initially
described in the early 1980s, based on a report of similar visual
response patterns in rabbits with galactosamine-induced liver
failure and rabbits treated with allosteric modulators of the
GABA.sub.A receptor (e.g., pentobarbital, diazepam) (Jones and
Basile, 1997). Clinical improvements in HE patients treated with a
highly selective benzodiazapene antagonist at the GABA.sub.A
receptor, flumazenil, further confirmed these observations (Banksy
et al., 1985; Scollo-Lavizzari and Steinmann, 1985). Increased
GABAergic tone in HE has since been proposed as a consequence of
one or more of the following: (1) increased GABA concentrations in
the brain, (2) altered integrity of the GABA.sub.A receptor, and/or
(3) increased concentrations of endogenous modulators of the
GABA.sub.A receptor (Ahboucha and Butterworth, 2004).
[0265] GABA uptake in E. coli is driven by membrane potential and
facilitated by the membrane transport protein, GabP (Li et al.,
2001). GabP is a member of the amino acid/polymaine/organocation
(APC) transporter superfamily, one of the two largest families of
secondary active transporters (Jack et al., 2000). GabP protein,
encoded by the gabP gene, consists of 466 amino acids and 12
transmembrane alpha-helices, wherein both N- and C-termini face the
cytosol (Hu and King, 1998a). The GabP residue sequence also
includes a consensus amphipathic region (CAR), which is conserved
between members of the APC family from bacteria to mammals (Hu and
King, 1998b). Upon entry into the cell, GABA is converted to
succinyl semialdehyde (SSA) by GABA .alpha.-ketoglutarate
transaminase (GSST). Succinate-semialdehyde dehydrogenase (SSDH)
then catalyzes the second and only other specific step in GABA
catabolism, the oxidation of succinyl semialdehyde to succinate
(Dover and Halpern, 1972). Ultimately, succinate becomes a
substrate for the citric acid (TCA) cycle.
[0266] In some embodiments, the bacteria are genetically engineered
to consume excess ammonia via a metabolic pathway, e.g., an
arginine biosynthesis pathway, a histidine biosynthesis pathway, a
methionine biosynthesis pathway, a lysine biosynthesis pathway, an
asparagine biosynthesis pathway, a glutamine biosynthesis pathway,
or a tryptophan biosynthesis pathway as described herein (an
"ammonia conversion circuit"). In some embodiments, the genetically
engineered bacteria comprise an arginine biosynthesis pathway and
are capable of reducing excess ammonia. In some embodiments, the
ammonia conversion circuit is under the control of an inducible
promoter. In some embodiments, the ammonia conversion circuit is
under the control of an oxygen level-dependent promoter, e.g., an
FNR-inducible promoter. In some embodiments, the ammonia conversion
circuit is under the control of a promoter induced by a molecule or
metabolite associated with hepatic encephalopathy, e.g., bilirubin,
aspartate aminotransferase, alanine aminotransferase, transferase,
hepatitis antigens and antibodies, alpha fetoprotein,
anti-mitochondrial, smooth muscle, and anti-nuclear antibodies,
iron, transferrin, ferritin, copper, ceruloplasm in, ammonia, or
manganese
[0267] In some embodiments, the genetically engineered bacteria
comprising an ammonia conversion circuit further comprise one or
more circuits for producing one or more GABA membrane transport
protein(s), e.g., GabP, and are capable of transporting GABA into
the cell (a "GABA transport circuit") (FIG. 41).
[0268] In some embodiments, the genetically engineered bacteria
comprising an ammonia conversion circuit further comprise one or
more circuits for producing one or more GABA catabolism enzyme(s),
e.g., GSST, SSDH, and/or COT (a "GABA metabolic circuit") (FIG.
49). In some embodiments, the genetically engineered bacteria
comprising an ammonia conversion circuit further comprise one or
more circuits for producing one or more GABA membrane transport
protein(s), e.g., GabP, and one or more circuits for producing one
or more GABA catabolism enzyme(s), e.g., GSST, SSDH, and/or COT (a
"GABA metabolic circuit") (FIG. 41).
[0269] In a more specific aspect, the genetically engineered
bacteria comprise an ammonia conversion circuit, a GABA transport
circuit, and a GABA metabolic circuit. In some embodiments, the
ammonia conversion circuit, GABA transport circuit, and GABA
metabolic circuit are under the control of the same promoter. In
alternate embodiments, the ammonia conversion circuit, GABA
transport circuit, and GABA metabolic circuit are under the control
of different promoters. Exemplary promoters include any of the
promoters disclosed herein. For example, in some embodiments, the
genetically engineered bacteria of the invention comprise an oxygen
level-dependent promoter induced by low-oxygen, microaerobic, or
anaerobic conditions. In some embodiments, the genetically
engineered bacteria comprise a promoter induced by a molecule or
metabolite, for example, a tissue-specific molecule or metabolite
or a molecule or metabolite indicative of liver damage.
Non-limiting examples of molecules or metabolites include, e.g.,
bilirubin, aspartate aminotransferase, alanine aminotransferase,
blood coagulation factors II, VII, IX, and X, alkaline phosphatase,
gamma glutamyl transferase, hepatitis antigens and antibodies,
alpha fetoprotein, anti-mitochondrial, smooth muscle, and
anti-nuclear antibodies, iron, transferrin, ferritin, copper,
ceruloplasmin, ammonia, and manganese in their blood and
intestines. In some embodiments, the genetically engineered
bacteria comprise a promoter induced by inflammation or an
inflammatory response, e.g., RNS or ROS promoter. In some
embodiments, the genetically engineered bacteria comprise a
promoter induced by a metabolite that may or may not be naturally
present (e.g., can be exogenously added) in the gut, e.g.,
arabinose and tetracycline.
[0270] The amino acid sequence of an exemplary GabP transporter is
shown in Table 42. In some embodiments, the genetically engineered
bacteria comprise the amino acid sequence of SEQ ID NO: 105 or a
functional fragment thereof. In some embodiments, the genetically
engineered bacteria comprise a nucleic acid sequence that, but for
the redundancy of the genetic code, encodes the same polypeptide as
SEQ ID NO: 105 or a functional fragment thereof. In some
embodiments, genetically engineered bacteria comprise an amino acid
sequence that is at least about 80%, at least about 85%, at least
about 90%, at least about 95%, or at least about 99% homologous to
the amino acid sequence of SEQ ID NO: 105 or a functional fragment
thereof, or a nucleic acid sequence that, but for the redundancy of
the genetic code, encodes the same polypeptide as SEQ ID NO: 105 or
a functional fragment thereof.
[0271] A non-limiting example of a polynucleotide sequence is shown
in Table 43 (SEQ ID NO: 106).
[0272] Manganese Transport
[0273] Manganese is a biologically important trace metal and is
required for the survival of most living organisms. In mammals,
manganese is excreted in the bile, but its disposal is affected by
the impaired flow of bile from the liver to the duodenum (i.e.,
cholestasis) that accompanies liver failure. Similar to ammonia,
elevated concentrations of manganese play a role in the development
of hepatic encephalopathy (Rivera-Mancia et al., 2012). Astrocytes
in the brain which detoxify ammonia in a reaction catalyzed by
glutamine synthetase, require manganese as a cofactor and thus have
a tendency to accumulate this metal (Aschner et al., 1999). In
vitro studies have demonstrated that manganese can result in the
inhibition of glutamate transport (Hazell and Norenberg, 1996),
abnormalities in astrocyte morphology (Hazell et al., 2006), and
increased cell volume (Rama Rao et al., 2007). Manganese and
ammonia have also been shown to act synergistically in the
pathogenesis of hepatic encephalopathy (Jayakumar et al.,
2004).
[0274] Metal ion homeostasis in prokaryotic cells, which lack
internal compartmentalization, is maintained by the tight
regulation of metal ion flux across in cytoplasmic membrane (Jensen
and Jensen, 2014). Manganese uptake in bacteria predominantly
involves two major types of transporters: proton-dependent
Nramp-related transporters, and/or ATP-dependent ABC transporters.
The Nramp (Natural resistance-associated macrophage protein)
transporter family was first described in plants, animals, and
yeasts (Cellier et al., 1996), but MntH has since been
characterized in several bacterial species (Porcheron et al.,
2013). Selectivity of the Nramp1 transporter for manganese has been
shown in metal accumulation studies, wherein overexpression of
Staphylococcus aureus mntH resulted in increased levels of
cell-associated manganese, but no accumulation of calcium, copper,
iron, magnesium, or zinc (Horsburgh et al., 2002). Additionally,
Bacillus subtilis strains comprising a mutation in the mntH gene
exhibited impaired growth in metal-free medium that was rescued by
the addition of manganese (Que and Helmann, 2000). The amino acid
sequence of an exemplary MntH transporter is shown in Table 44. In
some embodiments, the genetically engineered bacteria comprise the
amino acid sequence of SEQ ID NO: 107 or a functional fragment
thereof. In some embodiments, the genetically engineered bacteria
comprise a nucleic acid sequence that, but for the redundancy of
the genetic code, encodes the same polypeptide as SEQ ID NO: 36 or
a functional fragment thereof. In some embodiments, genetically
engineered bacteria comprise an amino acid sequence that is at
least about 80%, at least about 85%, at least about 90%, at least
about 95%, or at least about 99% homologous to the amino acid
sequence of SEQ ID NO: 107 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 107 or a
functional fragment thereof. A non-limiting example of a
polynucleotide sequence is shown in Table 45 (SEQ ID NO: 108).
[0275] High-affinity manganese uptake may also be mediated by ABC
(ATP-binding cassette) transporters. Members of this transporter
superfamily utilize the hydrolysis of ATP to fuel the import or
export of diverse substrates, ranging from ions to macromolecules,
and are well characterized for their role in multi-drug resistance
in both prokaryotic and eukaryotic cells. Non-limiting examples of
bacterial ABC transporters involved in manganese import include
MntABCD (Bacillus subtilis, Staphylococcus aureus), SitABCD
(Salmonella typhimurium, Shigella flexneri), PsaABCD (Streptococcus
pneumoniae), and YfeABCD (Yersinia pestis) (Bearden and Perry,
1999; Kehres et al., 2002; McAllister et al., 2004; Zhou et al.,
1999). The MntABCD transporter complex consists of three subunits,
wherein MntC and MntD are integral membrane proteins that comprise
the permease subunit mediate cation transport, MntB is the ATPase,
and MntA binds and delivers manganese to the permease submit. Other
ABC transporter operons, such as sitABCD, psaABCD, and yfeABCD,
exhibit similar subunit organization and function (Higgins, 1992;
Rees et al., 2009).
[0276] In some embodiments, the genetically engineered bacteria
comprising an ammonia conversion circuit further comprise one or
more circuits for producing a manganese membrane transport protein,
e.g., MntH, and are capable of transporting manganese ions into the
cell (a "manganese transport circuit") (FIG. 42).
[0277] In some embodiments, the genetically engineered bacteria
comprise an ammonia conversion circuit, a manganese transport
circuit, and a GABA metabolic circuit. In some embodiments, the
genetically engineered bacteria comprise an ammonia conversion
circuit, a manganese transport circuit, and a GABA transport
circuit. In some embodiments, the genetically engineered bacteria
comprise an ammonia conversion circuit, a manganese transport
circuit, a GABA transport circuit, and a GABA metabolic circuit. In
some embodiments, the circuits are under the control of the same
promoter. In alternate embodiments, the circuits are under the
control of different promoters. In some embodiments, the
genetically engineered bacteria of the invention comprise an oxygen
level-dependent promoter induced by low-oxygen, microaerobic, or
anaerobic conditions. In some embodiments, the genetically
engineered bacteria comprise a promoter induced by a molecule or
metabolite, for example, a tissue-specific molecule or metabolite
or a molecule or metabolite indicative of liver damage.
Non-limiting examples of molecules or metabolites include, e.g.,
bilirubin, aspartate aminotransferase, alanine aminotransferase,
blood coagulation factors II, VII, IX, and X, alkaline phosphatase,
gamma glutamyl transferase, hepatitis antigens and antibodies,
alpha fetoprotein, anti-mitochondrial, smooth muscle, and
anti-nuclear antibodies, iron, transferrin, ferritin, copper,
ceruloplasmin, ammonia, and manganese in their blood and
intestines. In some embodiments, the genetically engineered
bacteria comprise a promoter induced by inflammation or an
inflammatory response, e.g., RNS or ROS promoter. In some
embodiments, the genetically engineered bacteria comprise a
promoter induced by a metabolite that may or may not be naturally
present (e.g., can be exogenously added) in the gut, e.g.,
arabinose and tetracycline.
[0278] Production of Butyrate and Other Gut Barrier Function
Enhancer Molecules
[0279] In some embodiments, the genetically engineered bacteria of
the invention further comprise a gene encoding a gut barrier
function enhancer molecule, or a gene cassette encoding a
biosynthetic pathway capable of producing a gut barrier function
enhancer molecule. In some embodiments, the molecule is selected
from the group consisting of a short-chain fatty acid, butyrate,
propionate, acetate, GLP-2, IL-10, IL-27, TGF-.beta.1, TGF-.beta.2,
elafin (also known as peptidase inhibitor 3 or SKALP), trefoil
factor, melatonin, PGD.sub.2, kynurenic acid, and kynurenine.
[0280] In some embodiments, the genetically engineered bacteria of
the invention express a gut barrier function enhancer molecule that
is encoded by a single gene, e.g., the molecule is elafin and
encoded by the PI3 gene. In alternate embodiments, the genetically
engineered bacteria of the invention encode a gut barrier function
enhancer molecule, e.g., butyrate or propionate, that is
synthesized by a biosynthetic pathway requiring multiple genes.
[0281] The gene or gene cassette may be expressed on a high-copy
plasmid, a low-copy plasmid, or a chromosome. In some embodiments,
expression from the plasmid may be useful for increasing expression
of the gut barrier function enhancer molecule. In some embodiments,
expression from the chromosome may be useful for increasing
stability of expression of the gut barrier function enhancer
molecule. In some embodiments, the gene or gene cassette for
producing the gut barrier function enhancer molecule is integrated
into the bacterial chromosome at one or more integration sites in
the genetically engineered bacteria. For example, one or more
copies of the butyrate biosynthesis gene cassette may be integrated
into the bacterial chromosome. In some embodiments, the gene or
gene cassette for producing the gut barrier function enhancer
molecule is expressed from a plasmid in the genetically engineered
bacteria. In some embodiments, the gene or gene cassette for
producing the gut barrier function enhancer molecule is inserted
into the bacterial genome at one or more of the following insertion
sites in E. coli Nissle: malE/K, araC/BAD, lacZ, thyA, malP/T. Any
suitable insertion site may be used (see, e.g., FIG. 18). The
insertion site may be anywhere in the genome, e.g., in a gene
required for survival and/or growth, such as thyA (to create an
auxotroph); in an active area of the genome, such as near the site
of genome replication; and/or in between divergent promoters in
order to reduce the risk of unintended transcription, such as
between AraB and AraC of the arabinose operon.
[0282] In some embodiments, the genetically engineered bacteria of
the invention comprise a butyrogenic gene cassette and are capable
of producing butyrate. The genetically engineered bacteria may
include any suitable set of butyrogenic genes (see, e.g., Table
14). Unmodified bacteria comprising butyrate biosynthesis genes are
known and include, but are not limited to, Peptoclostridium,
Clostridium, Fusobacterium, Butyrivibrio, Eubacterium, and
Treponema, and these endogenous butyrate biosynthesis pathways may
be a source of genes for the genetically engineered bacteria of the
invention. In some embodiments, the genetically engineered bacteria
of the invention comprise butyrate biosynthesis genes from a
different species, strain, or substrain of bacteria. In some
embodiments, the genetically engineered bacteria comprise the eight
genes of the butyrate biosynthesis pathway from Peptoclostridium
difficile, e.g., Peptoclostridium difficile strain 630: bcd2,
etfB3, etfA3, thiA1, hbd, crt2, pbt, and buk (Aboulnaga et al.,
2013), and are capable of producing butyrate in low-oxygen
conditions, in the presence of HE-specific molecules or
metabolites, in the presence of molecules or metabolites associated
with liver damage, inflammation or an inflammatory response, or in
the presence of some other metabolite such as arabinose.
Peptoclostridium difficile strain 630 and strain 1296 are both
capable of producing butyrate, but comprise different nucleic acid
sequences for etfA3, thiA1, hbd, crt2, pbt, and buk. In some
embodiments, the genetically engineered bacteria comprise a
combination of butyrogenic genes from different species, strains,
and/or substrains of bacteria, and are capable of producing
butyrate in low-oxygen conditions or in the presence of HE-specific
molecules or metabolites. For example, in some embodiments, the
genetically engineered bacteria comprise bcd2, etfB3, etfA3, and
thiA1 from Peptoclostridium difficile strain 630, and hbd, crt2,
pbt, and buk from Peptoclostridium difficile strain 1296. In some
embodiments, the genetically engineered bacteria are capable of
expressing the butyrate biosynthesis cassette and producing
butyrate in low-oxygen conditions or in the presence of HE-specific
molecules or metabolites. The genes may be codon-optimized, and
translational and transcriptional elements may be added. Table 14
depicts the nucleic acid sequences of exemplary genes in butyrate
biosynthesis gene cassettes. In some embodiments, genetically
engineered bacteria comprise a nucleic acid sequence that is at
least about 80%, at least about 85%, at least about 90%, at least
about 95%, or at least about 99% homologous to the DNA sequence of
SEQ ID NO: 39, 40, 41, 42, 43, 44, 45, 46, 47, or 48 a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise the nucleic acid sequence of SEQ ID NO: 39, 40,
41, 42, 43, 44, 45, 46, 47, or 48, or a functional fragment
thereof.
TABLE-US-00014 TABLE 14 Description Sequence bcd2
ATGGATTTAAATTCTAAAAAATATCAGATGCTTAAAGAGCTATATGTAAG (SEQ ID NO:
CTTCGCTGAAAATGAAGTTAAACCTTTAGCAACAGAACTTGATGAAGAAG 39)
AAAGATTTCCTTATGAAACAGTGGAAAAAATGGCAAAAGCAGGAATGATG
GGTATACCATATCCAAAAGAATATGGTGGAGAAGGTGGAGACACTGTAGG
ATATATAATGGCAGTTGAAGAATTGTCTAGAGTTTGTGGTACTACAGGAG
TTATATTATCAGCTCATACATCTCTTGGCTCATGGCCTATATATCAATAT
GGTAATGAAGAACAAAAACAAAAATTCTTAAGACCACTAGCAAGTGGAGA
AAAATTAGGAGCATTTGGTCTTACTGAGCCTAATGCTGGTACAGATGCGT
CTGGCCAACAAACAACTGCTGTTTTAGACGGGGATGAATACATACTTAAT
GGCTCAAAAATATTTATAACAAACGCAATAGCTGGTGACATATATGTAGT
AATGGCAATGACTGATAAATCTAAGGGGAACAAAGGAATATCAGCATTTA
TAGTTGAAAAAGGAACTCCTGGGTTTAGCTTTGGAGTTAAAGAAAAGAAA
ATGGGTATAAGAGGTTCAGCTACGAGTGAATTAATATTTGAGGATTGCAG
AATACCTAAAGAAAATTTACTTGGAAAAGAAGGTCAAGGATTTAAGATAG
CAATGTCTACTCTTGATGGTGGTAGAATTGGTATAGCTGCACAAGCTTTA
GGTTTAGCACAAGGTGCTCTTGATGAAACTGTTAAATATGTAAAAGAAAG
AGTACAATTTGGTAGACCATTATCAAAATTCCAAAATACACAATTCCAAT
TAGCTGATATGGAAGTTAAGGTACAAGCGGCTAGACACCTTGTATATCAA
GCAGCTATAAATAAAGACTTAGGAAAACCTTATGGAGTAGAAGCAGCAAT
GGCAAAATTATTTGCAGCTGAAACAGCTATGGAAGTTACTACAAAAGCTG
TACAACTTCATGGAGGATATGGATACACTCGTGACTATCCAGTAGAAAGA
ATGATGAGAGATGCTAAGATAACTGAAATATATGAAGGAACTAGTGAAGT
TCAAAGAATGGTTATTTCAGGAAAACTATTAAAATAG etfB3
ATGAATATAGTCGTTTGTATAAAACAAGTTCCAGATACAACAGAAGTTAA (SEQ ID NO:
ACTAGATCCTAATACAGGTACTTTAATTAGAGATGGAGTACCAAGTATAA 40)
TAAACCCTGATGATAAAGCAGGTTTAGAAGAAGCTATAAAATTAAAAGAA
GAAATGGGTGCTCATGTAACTGTTATAACAATGGGACCTCCTCAAGCAGA
TATGGCTTTAAAAGAAGCTTTAGCAATGGGTGCAGATAGAGGTATATTAT
TAACAGATAGAGCATTTGCGGGTGCTGATACTTGGGCAACTTCATCAGCA
TTAGCAGGAGCATTAAAAAATATAGATTTTGATATTATAATAGCTGGAAG
ACAGGCGATAGATGGAGATACTGCACAAGTTGGACCTCAAATAGCTGAAC
ATTTAAATCTTCCATCAATAACATATGCTGAAGAAATAAAAACTGAAGGT
GAATATGTATTAGTAAAAAGACAATTTGAAGATTGTTGCCATGACTTAAA
AGTTAAAATGCCATGCCTTATAACAACTCTTAAAGATATGAACACACCAA
GATACATGAAAGTTGGAAGAATATATGATGCTTTCGAAAATGATGTAGTA
GAAACATGGACTGTAAAAGATATAGAAGTTGACCCTTCTAATTTAGGTCT
TAAAGGTTCTCCAACTAGTGTATTTAAATCATTTACAAAATCAGTTAAAC
CAGCTGGTACAATATACAATGAAGATGCGAAAACATCAGCTGGAATTATC
ATAGATAAATTAAAAGAGAAGTATATCATATAA etfA3
ATGGGTAACGTTTTAGTAGTAATAGAACAAAGAGAAAATGTAATTCAAAC (SEQ ID NO:
TGTTTCTTTAGAATTACTAGGAAAGGCTACAGAAATAGCAAAAGATTATG 41)
ATACAAAAGTTTCTGCATTACTTTTAGGTAGTAAGGTAGAAGGTTTAATA
GATACATTAGCACACTATGGTGCAGATGAGGTAATAGTAGTAGATGATGA
AGCTTTAGCAGTGTATACAACTGAACCATATACAAAAGCAGCTTATGAAG
CAATAAAAGCAGCTGACCCTATAGTTGTATTATTTGGTGCAACTTCAATA
GGTAGAGATTTAGCGCCTAGAGTTTCTGCTAGAATACATACAGGTCTTAC
TGCTGACTGTACAGGTCTTGCAGTAGCTGAAGATACAAAATTATTATTAA
TGACAAGACCTGCCTTTGGTGGAAATATAATGGCAACAATAGTTTGTAAA
GATTTCAGACCTCAAATGTCTACAGTTAGACCAGGGGTTATGAAGAAAAA
TGAACCTGATGAAACTAAAGAAGCTGTAATTAACCGTTTCAAGGTAGAAT
TTAATGATGCTGATAAATTAGTTCAAGTTGTACAAGTAATAAAAGAAGCT
AAAAAACAAGTTAAAATAGAAGATGCTAAGATATTAGTTTCTGCTGGACG
TGGAATGGGTGGAAAAGAAAACTTAGACATACTTTATGAATTAGCTGAAA
TTATAGGTGGAGAAGTTTCTGGTTCTCGTGCCACTATAGATGCAGGTTGG
TTAGATAAAGCAAGACAAGTTGGTCAAACTGGTAAAACTGTAAGACCAGA
CCTTTATATAGCATGTGGTATATCTGGAGCAATACAACATATAGCTGGTA
TGGAAGATGCTGAGTTTATAGTTGCTATAAATAAAAATCCAGAAGCTCCA
ATATTTAAATATGCTGATGTTGGTATAGTTGGAGATGTTCATAAAGTGCT
TCCAGAACTTATCAGTCAGTTAAGTGTTGCAAAAGAAAAAGGTGAAGTTT TAGCTAACTAA
thiA1 ATGAGAGAAGTAGTAATTGCCAGTGCAGCTAGAACAGCAGTAGGAAGTTT (SEQ ID
NO: TGGAGGAGCATTTAAATCAGTTTCAGCGGTAGAGTTAGGGGTAACAGCAG 42)
CTAAAGAAGCTATAAAAAGAGCTAACATAACTCCAGATATGATAGATGAA
TCTCTTTTAGGGGGAGTACTTACAGCAGGTCTTGGACAAAATATAGCAAG
ACAAATAGCATTAGGAGCAGGAATACCAGTAGAAAAACCAGCTATGACTA
TAAATATAGTTTGTGGTTCTGGATTAAGATCTGTTTCAATGGCATCTCAA
CTTATAGCATTAGGTGATGCTGATATAATGTTAGTTGGTGGAGCTGAAAA
CATGAGTATGTCTCCTTATTTAGTACCAAGTGCGAGATATGGTGCAAGAA
TGGGTGATGCTGCTTTTGTTGATTCAATGATAAAAGATGGATTATCAGAC
ATATTTAATAACTATCACATGGGTATTACTGCTGAAAACATAGCAGAGCA
ATGGAATATAACTAGAGAAGAACAAGATGAATTAGCTCTTGCAAGTCAAA
ATAAAGCTGAAAAAGCTCAAGCTGAAGGAAAATTTGATGAAGAAATAGTT
CCTGTTGTTATAAAAGGAAGAAAAGGTGACACTGTAGTAGATAAAGATGA
ATATATTAAGCCTGGCACTACAATGGAGAAACTTGCTAAGTTAAGACCTG
CATTTAAAAAAGATGGAACAGTTACTGCTGGTAATGCATCAGGAATAAAT
GATGGTGCTGCTATGTTAGTAGTAATGGCTAAAGAAAAAGCTGAAGAACT
AGGAATAGAGCCTCTTGCAACTATAGTTTCTTATGGAACAGCTGGTGTTG
ACCCTAAAATAATGGGATATGGACCAGTTCCAGCAACTAAAAAAGCTTTA
GAAGCTGCTAATATGACTATTGAAGATATAGATTTAGTTGAAGCTAATGA
GGCATTTGCTGCCCAATCTGTAGCTGTAATAAGAGACTTAAATATAGATA
TGAATAAAGTTAATGTTAATGGTGGAGCAATAGCTATAGGACATCCAATA
GGATGCTCAGGAGCAAGAATACTTACTACACTTTTATATGAAATGAAGAG
AAGAGATGCTAAAACTGGTCTTGCTACACTTTGTATAGGCGGTGGAATGG
GAACTACTTTAATAGTTAAGAGATAG hbd
ATGAAATTAGCTGTAATAGGTAGTGGAACTATGGGAAGTGGTATTGTACA (SEQ ID NO:
AACTTTTGCAAGTTGTGGACATGATGTATGTTTAAAGAGTAGAACTCAAG 43)
GTGCTATAGATAAATGTTTAGCTTTATTAGATAAAAATTTAACTAAGTTA
GTTACTAAGGGAAAAATGGATGAAGCTACAAAAGCAGAAATATTAAGTCA
TGTTAGTTCAACTACTAATTATGAAGATTTAAAAGATATGGATTTAATAA
TAGAAGCATCTGTAGAAGACATGAATATAAAGAAAGATGTTTTCAAGTTA
CTAGATGAATTATGTAAAGAAGATACTATCTTGGCAACAAATACTTCATC
ATTATCTATAACAGAAATAGCTTCTTCTACTAAGCGCCCAGATAAAGTTA
TAGGAATGCATTTCTTTAATCCAGTTCCTATGATGAAATTAGTTGAAGTT
ATAAGTGGTCAGTTAACATCAAAAGTTACTTTTGATACAGTATTTGAATT
ATCTAAGAGTATCAATAAAGTACCAGTAGATGTATCTGAATCTCCTGGAT
TTGTAGTAAATAGAATACTTATACCTATGATAAATGAAGCTGTTGGTATA
TATGCAGATGGTGTTGCAAGTAAAGAAGAAATAGATGAAGCTATGAAATT
AGGAGCAAACCATCCAATGGGACCACTAGCATTAGGTGATTTAATCGGAT
TAGATGTTGTTTTAGCTATAATGAACGTTTTATATACTGAATTTGGAGAT
ACTAAATATAGACCTCATCCACTTTTAGCTAAAATGGTTAGAGCTAATCA
ATTAGGAAGAAAAACTAAGATAGGATTCTATGATTATAATAAATAA crt2
ATGAGTACAAGTGATGTTAAAGTTTATGAGAATGTAGCTGTTGAAGTAGA (SEQ ID NO:
TGGAAATATATGTACAGTGAAAATGAATAGACCTAAAGCCCTTAATGCAA 44)
TAAATTCAAAGACTTTAGAAGAACTTTATGAAGTATTTGTAGATATTAAT
AATGATGAAACTATTGATGTTGTAATATTGACAGGGGAAGGAAAGGCATT
TGTAGCTGGAGCAGATATTGCATACATGAAAGATTTAGATGCTGTAGCTG
CTAAAGATTTTAGTATCTTAGGAGCAAAAGCTTTTGGAGAAATAGAAAAT
AGTAAAAAAGTAGTGATAGCTGCTGTAAACGGATTTGCTTTAGGTGGAGG
ATGTGAACTTGCAATGGCATGTGATATAAGAATTGCATCTGCTAAAGCTA
AATTTGGTCAGCCAGAAGTAACTCTTGGAATAACTCCAGGATATGGAGGA
ACTCAAAGGCTTACAAGATTGGTTGGAATGGCAAAAGCAAAAGAATTAAT
CTTTACAGGTCAAGTTATAAAAGCTGATGAAGCTGAAAAAATAGGGCTAG
TAAATAGAGTCGTTGAGCCAGACATTTTAATAGAAGAAGTTGAGAAATTA
GCTAAGATAATAGCTAAAAATGCTCAGCTTGCAGTTAGATACTCTAAAGA
AGCAATACAACTTGGTGCTCAAACTGATATAAATACTGGAATAGATATAG
AATCTAATTTATTTGGTCTTTGTTTTTCAACTAAAGACCAAAAAGAAGGA
ATGTCAGCTTTCGTTGAAAAGAGAGAAGCTAACTTTATAAAAGGGTAA pbt
ATGAGAAGTTTTGAAGAAGTAATTAAGTTTGCAAAAGAAAGAGGACCTAA (SEQ ID NO:
AACTATATCAGTAGCATGTTGCCAAGATAAAGAAGTTTTAATGGCAGTTG 45)
AAATGGCTAGAAAAGAAAAAATAGCAAATGCCATTTTAGTAGGAGATATA
GAAAAGACTAAAGAAATTGCAAAAAGCATAGACATGGATATCGAAAATTA
TGAACTGATAGATATAAAAGATTTAGCAGAAGCATCTCTAAAATCTGTTG
AATTAGTTTCACAAGGAAAAGCCGACATGGTAATGAAAGGCTTAGTAGAC
ACATCAATAATACTAAAAGCAGTTTTAAATAAAGAAGTAGGTCTTAGAAC
TGGAAATGTATTAAGTCACGTAGCAGTATTTGATGTAGAGGGATATGATA
GATTATTTTTCGTAACTGACGCAGCTATGAACTTAGCTCCTGATACAAAT
ACTAAAAAGCAAATCATAGAAAATGCTTGCACAGTAGCACATTCATTAGA
TATAAGTGAACCAAAAGTTGCTGCAATATGCGCAAAAGAAAAAGTAAATC
CAAAAATGAAAGATACAGTTGAAGCTAAAGAACTAGAAGAAATGTATGAA
AGAGGAGAAATCAAAGGTTGTATGGTTGGTGGGCCTTTTGCAATTGATAA
TGCAGTATCTTTAGAAGCAGCTAAACATAAAGGTATAAATCATCCTGTAG
CAGGACGAGCTGATATATTATTAGCCCCAGATATTGAAGGTGGTAACATA
TTATATAAAGCTTTGGTATTCTTCTCAAAATCAAAAAATGCAGGAGTTAT
AGTTGGGGCTAAAGCACCAATAATATTAACTTCTAGAGCAGACAGTGAAG
AAACTAAACTAAACTCAATAGCTTTAGGTGTTTTAATGGCAGCAAAGGCA TAA buk
ATGAGCAAAATATTTAAAATCTTAACAATAAATCCTGGTTCGACATCAAC (SEQ ID NO:
TAAAATAGCTGTATTTGATAATGAGGATTTAGTATTTGAAAAAACTTTAA 46)
GACATTCTTCAGAAGAAATAGGAAAATATGAGAAGGTGTCTGACCAATTT
GAATTTCGTAAACAAGTAATAGAAGAAGCTCTAAAAGAAGGTGGAGTAAA
AACATCTGAATTAGATGCTGTAGTAGGTAGAGGAGGACTTCTTAAACCTA
TAAAAGGTGGTACTTATTCAGTAAGTGCTGCTATGATTGAAGATTTAAAA
GTGGGAGTTTTAGGAGAACACGCTTCAAACCTAGGTGGAATAATAGCAAA
ACAAATAGGTGAAGAAGTAAATGTTCCTTCATACATAGTAGACCCTGTTG
TTGTAGATGAATTAGAAGATGTTGCTAGAATTTCTGGTATGCCTGAAATA
AGTAGAGCAAGTGTAGTACATGCTTTAAATCAAAAGGCAATAGCAAGAAG
ATATGCTAGAGAAATAAACAAGAAATATGAAGATATAAATCTTATAGTTG
CACACATGGGTGGAGGAGTTTCTGTTGGAGCTCATAAAAATGGTAAAATA
GTAGATGTTGCAAACGCATTAGATGGAGAAGGACCTTTCTCTCCAGAAAG
AAGTGGTGGACTACCAGTAGGTGCATTAGTAAAAATGTGCTTTAGTGGAA
AATATACTCAAGATGAAATTAAAAAGAAAATAAAAGGTAATGGCGGACTA
GTTGCATACTTAAACACTAATGATGCTAGAGAAGTTGAAGAAAGAATTGA
AGCTGGTGATGAAAAAGCTAAATTAGTATATGAAGCTATGGCATATCAAA
TCTCTAAAGAAATAGGAGCTAGTGCTGCAGTTCTTAAGGGAGATGTAAAA
GCAATATTATTAACTGGTGGAATCGCATATTCAAAAATGTTTACAGAAAT
GATTGCAGATAGAGTTAAATTTATAGCAGATGTAAAAGTTTATCCAGGTG
AAGATGAAATGATTGCATTAGCTCAAGGTGGACTTAGAGTTTTAACTGGT
GAAGAAGAGGCTCAAGTTTATGATAACTAA ter
ATGATCGTAAAACCTATGGTACGCAACAATATCTGCCTGAACGCCCATCC (SEQ ID NO:
TCAGGGCTGCAAGAAGGGAGTGGAAGATCAGATTGAATATACCAAGAAAC 47)
GCATTACCGCAGAAGTCAAAGCTGGCGCAAAAGCTCCAAAAAACGTTCTG
GTGCTTGGCTGCTCAAATGGTTACGGCCTGGCGAGCCGCATTACTGCTGC
GTTCGGATACGGGGCTGCGACCATCGGCGTGTCCTTTGAAAAAGCGGGTT
CAGAAACCAAATATGGTACACCGGGATGGTACAATAATTTGGCATTTGAT
GAAGCGGCAAAACGCGAGGGTCTTTATAGCGTGACGATCGACGGCGATGC
GTTTTCAGACGAGATCAAGGCCCAGGTAATTGAGGAAGCCAAAAAAAAAG
GTATCAAATTTGATCTGATCGTATACAGCTTGGCCAGCCCAGTACGTACT
GATCCTGATACAGGTATCATGCACAAAAGCGTTTTGAAACCCTTTGGAAA
AACGTTCACAGGCAAAACAGTAGATCCGTTTACTGGCGAGCTGAAGGAAA
TCTCCGCGGAACCAGCAAATGACGAGGAAGCAGCCGCCACTGTTAAAGTT
ATGGGGGGTGAAGATTGGGAACGTTGGATTAAGCAGCTGTCGAAGGAAGG
CCTCTTAGAAGAAGGCTGTATTACCTTGGCCTATAGTTATATTGGCCCTG
AAGCTACCCAAGCTTTGTACCGTAAAGGCACAATCGGCAAGGCCAAAGAA
CACCTGGAGGCCACAGCACACCGTCTCAACAAAGAGAACCCGTCAATCCG
TGCCTTCGTGAGCGTGAATAAAGGCCTGGTAACCCGCGCAAGCGCCGTAA
TCCCGGTAATCCCTCTGTATCTCGCCAGCTTGTTCAAAGTAATGAAAGAG
AAGGGCAATCATGAAGGTTGTATTGAACAGATCACGCGTCTGTACGCCGA
GCGCCTGTACCGTAAAGATGGTACAATTCCAGTTGATGAGGAAAATCGCA
TTCGCATTGATGATTGGGAGTTAGAAGAAGACGTCCAGAAAGCGGTATCC
GCGTTGATGGAGAAAGTCACGGGTGAAAACGCAGAATCTCTCACTGACTT
AGCGGGGTACCGCCATGATTTCTTAGCTAGTAACGGCTTTGATGTAGAAG
GTATTAATTATGAAGCGGAAGTTGAACGCTTCGACCGTATCTGA tesB
ATGAGTCAGGCGCTAAAAAATTTACTGACATTGTTAAATCTGGAAAAAAT SEQ ID NO:
TGAGGAAGGACTCTTTCGCGGCCAGAGTGAAGATTTAGGTTTACGCCAGG 48
TGTTTGGCGGCCAGGTCGTGGGTCAGGCCTTGTATGCTGCAAAAGAGACC
GTCCCTGAAGAGCGGCTGGTACATTCGTTTCACAGCTACTTTCTTCGCCC
TGGCGATAGTAAGAAGCCGATTATTTATGATGTCGAAACGCTGCGTGACG
GTAACAGCTTCAGCGCCCGCCGGGTTGCTGCTATTCAAAACGGCAAACCG
ATTTTTTATATGACTGCCTCTTTCCAGGCACCAGAAGCGGGTTTCGAACA
TCAAAAAACAATGCCGTCCGCGCCAGCGCCTGATGGCCTCCCTTCGGAAA
CGCAAATCGCCCAATCGCTGGCGCACCTGCTGCCGCCAGTGCTGAAAGAT
AAATTCATCTGCGATCGTCCGCTGGAAGTCCGTCCGGTGGAGTTTCATAA
CCCACTGAAAGGTCACGTCGCAGAACCACATCGTCAGGTGTGGATCCGCG
CAAATGGTAGCGTGCCGGATGACCTGCGCGTTCATCAGTATCTGCTCGGT
TACGCTTCTGATCTTAACTTCCTGCCGGTAGCTCTACAGCCGCACGGCAT
CGGTTTTCTCGAACCGGGGATTCAGATTGCCACCATTGACCATTCCATGT
GGTTCCATCGCCCGTTTAATTTGAATGAATGGCTGCTGTATAGCGTGGAG
AGCACCTCGGCGTCCAGCGCACGTGGCTTTGTGCGCGGTGAGTTTTATAC
CCAAGACGGCGTACTGGTTGCCTCGACCGTTCAGGAAGGGGTGATGCGTA ATCACAATTAA
[0283] The gene products of the bcd2, etfA3, and etfB3 genes in
Clostridium difficile form a complex that converts crotonyl-CoA to
butyryl-CoA, which may function as an oxygen-dependent co-oxidant.
In some embodiments, because the genetically engineered bacteria of
the invention are designed to produce butyrate in a microaerobic or
oxygen-limited environment, e.g., the mammalian gut,
oxygen-dependence could have a negative effect on butyrate
production in the gut. It has been shown that a single gene from
Treponema denticola (ter, encoding trans-2-enoynl-CoA reductase)
can functionally replace this three-gene complex in an
oxygen-independent manner. In some embodiments, the genetically
engineered bacteria comprise a ter gene, e.g., from Treponema
denticola, which can functionally replace all three of the bcd2,
etfB3, and etfA3 genes, e.g., from Peptoclostridium difficile. In
this embodiment, the genetically engineered bacteria comprise
thiA1, hbd, crt2, pbt, and buk, e.g., from Peptoclostridium
difficile, and ter, e.g., from Treponema denticola, and produce
butyrate in low-oxygen conditions, in the presence of HE-specific
molecules or metabolites, in the presence of molecules or
metabolites associated with liver damage, inflammation or an
inflammatory response, or in the presence of some other metabolite
that may or may not be present in the gut, such as arabinose. In
some embodiments, the genetically engineered bacteria comprise
genes for aerobic butyrate biosynthesis and/or genes for anaerobic
or microaerobic butyrate biosynthesis. In some embodiments, the
genetically engineered bacteria of the invention comprise thiA1,
hbd, crt2, pbt, and buk, e.g., from Peptoclostridium difficile;
ter, e.g., from Treponema denticola; one or more of bcd2, etfB3,
and etfA3, e.g., from Peptoclostridium difficile; and produce
butyrate in low-oxygen conditions or in the presence of HE-specific
molecules or metabolites. In some embodiments, one or more of the
butyrate biosynthesis genes is functionally replaced, modified,
and/or mutated in order to enhance stability and/or increase
butyrate production in low-oxygen conditions or in the presence of
HE-specific molecules or metabolites, or molecules or metabolites
associated with liver damage, or other condition(s) such as
inflammation or an inflammatory response, or in the presence of
some other metabolite that may or may not be present in the gut,
such as arabinose. In some embodiments, the local production of
butyrate induces the differentiation of regulatory T cells in the
gut and/or promotes the barrier function of colonic epithelial
cells.
[0284] The gene products of pbt and buk convert butyrylCoA to
Butyrate. In some embodiments, the pbt and buk genes can be
replaced by a tesB gene. tesB can be used to cleave off the CoA
from butyryl-coA. In one embodiment, the genetically engineered
bacteria comprise bcd2, etfB3, etfA3, thiA1, hbd, and crt2, e.g.,
from Peptoclostridium difficile, and tesB from E. Coli and produce
butyrate in low-oxygen conditions, in the presence of HE-specific
molecules or metabolites, in the presence of molecules or
metabolites associated with liver damage, inflammation or an
inflammatory response, or in the presence of some other metabolite
that may or may not be present in the gut, such as arabinose. In
one embodiment, the genetically engineered bacteria comprise ter
gene (encoding trans-2-enoynl-CoA reductase) e.g., from Treponema
denticola, thiA1, hbd, crt2, pbt, and buk, e.g., from
Peptoclostridium difficile, and tesB from E. Coli, and produce
butyrate in low-oxygen conditions, in the presence of HE-specific
molecules or metabolites, in the presence of molecules or
metabolites associated with liver damage, inflammation or an
inflammatory response, or in the presence of some other metabolite
that may or may not be present in the gut, such as arabinose. In
some embodiments, one or more of the butyrate biosynthesis genes is
functionally replaced, modified, and/or mutated in order to enhance
stability and/or increase butyrate production in low-oxygen
conditions or in the presence of HE-specific molecules or
metabolites, or molecules or metabolites associated with liver
damage, or other condition(s) such as inflammation or an
inflammatory response, or in the presence of some other metabolite
that may or may not be present in the gut, such as arabinose. In
some embodiments, the local production of butyrate induces the
differentiation of regulatory T cells in the gut and/or promotes
the barrier function of colonic epithelial cells.
[0285] In some embodiments, the genetically engineered bacteria of
the invention comprise a propionate gene cassette and are capable
of producing propionate in low-oxygen conditions or in the presence
of HE-specific molecules or metabolites. The genetically engineered
bacteria may express any suitable set of propionate biosynthesis
genes (see, e.g., Table 15). Unmodified bacteria that are capable
of producing propionate via an endogenous propionate biosynthesis
pathway include, but are not limited to, Clostridium propionicum,
Megasphaera elsdenii, and Prevotella ruminicola, and these
endogenous propionate biosynthesis pathways may be a source of
genes for the genetically engineered bacteria of the invention. In
some embodiments, the genetically engineered bacteria of the
invention comprise propionate biosynthesis genes from a different
species, strain, or substrain of bacteria. In some embodiments, the
genetically engineered bacteria comprise the genes pct, lcd, and
acr from Clostridium propionicum. In some embodiments, the
genetically engineered bacteria comprise acrylate pathway genes for
propionate biosynthesis, e.g., pct, lcdA, lcdB, lcdC, etfA, acre,
and acrC. In alternate embodiments, the genetically engineered
bacteria comprise pyruvate pathway genes for propionate
biosynthesis, e.g., thrA.sup.fbr, thrB, thrC, ilvA.sup.fbr, aceE,
aceF, and lpd, and optionally further comprise tesB. The genes may
be codon-optimized, and translational and transcriptional elements
may be added. Table 15 depicts the nucleic acid sequences of
exemplary genes in the propionate biosynthesis gene cassette. In
some embodiments, genetically engineered bacteria comprise a
nucleic acid sequence that is at least about 80%, at least about
85%, at least about 90%, at least about 95%, or at least about 99%
homologous to the DNA sequence of SEQ ID NO: 48, 49, 50, 51, 52,
53, 54, 55, 56, 57, 58, 59, 60, 61 or 62 a functional fragment
thereof. In some embodiments, genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61 or 62, or a functional
fragment thereof.
TABLE-US-00015 TABLE 15 Description Sequence pct
ATGCGCAAAGTGCCGATTATCACGGCTGACGAGGCCGCAAAACTGATCAA SEQ ID NO:
GGACGGCGACACCGTGACAACTAGCGGCTTTGTGGGTAACGCGATCCCTG 49
AGGCCCTTGACCGTGCAGTCGAAAAGCGTTTCCTGGAAACGGGCGAACCG
AAGAACATTACTTATGTATATTGCGGCAGTCAGGGCAATCGCGACGGTCG
TGGCGCAGAACATTTCGCGCATGAAGGCCTGCTGAAACGTTATATCGCTG
GCCATTGGGCGACCGTCCCGGCGTTAGGGAAAATGGCCATGGAGAATAAA
ATGGAGGCCTACAATGTCTCTCAGGGCGCCTTGTGTCATCTCTTTCGCGA
TATTGCGAGCCATAAACCGGGTGTGTTCACGAAAGTAGGAATCGGCACCT
TCATTGATCCACGTAACGGTGGTGGGAAGGTCAACGATATTACCAAGGAA
GATATCGTAGAACTGGTGGAAATTAAAGGGCAGGAATACCTGTTTTATCC
GGCGTTCCCGATCCATGTCGCGCTGATTCGTGGCACCTATGCGGACGAGA
GTGGTAACATCACCTTTGAAAAAGAGGTAGCGCCTTTGGAAGGGACTTCT
GTCTGTCAAGCGGTGAAGAACTCGGGTGGCATTGTCGTGGTTCAGGTTGA
GCGTGTCGTCAAAGCAGGCACGCTGGATCCGCGCCATGTGAAAGTTCCGG
GTATCTATGTAGATTACGTAGTCGTCGCGGATCCGGAGGACCATCAACAG
TCCCTTGACTGCGAATATGATCCTGCCCTTAGTGGAGAGCACCGTCGTCC
GGAGGTGGTGGGTGAACCACTGCCTTTATCCGCGAAGAAAGTCATCGGCC
GCCGTGGCGCGATTGAGCTCGAGAAAGACGTTGCAGTGAACCTTGGGGTA
GGTGCACCTGAGTATGTGGCCTCCGTGGCCGATGAAGAAGGCATTGTGGA
TTTTATGACTCTCACAGCGGAGTCCGGCGCTATCGGTGGCGTTCCAGCCG
GCGGTGTTCGCTTTGGGGCGAGCTACAATGCTGACGCCTTGATCGACCAG
GGCTACCAATTTGATTATTACGACGGTGGGGGTCTGGATCTTTGTTACCT
GGGTTTAGCTGAATGCGACGAAAAGGGTAATATCAATGTTAGCCGCTTCG
GTCCTCGTATCGCTGGGTGCGGCGGATTCATTAACATTACCCAAAACACG
CCGAAAGTCTTCTTTTGTGGGACCTTTACAGCCGGGGGGCTGAAAGTGAA
AATTGAAGATGGTAAGGTGATTATCGTTCAGGAAGGGAAACAGAAGAAAT
TCCTTAAGGCAGTGGAGCAAATCACCTTTAATGGAGACGTGGCCTTAGCG
AACAAGCAACAAGTTACCTACATCACGGAGCGTTGCGTCTTCCTCCTCAA
AGAAGACGGTTTACACCTTTCGGAAATCGCGCCAGGCATCGATCTGCAGA
CCCAGATTTTGGATGTTATGGACTTTGCCCCGATCATTGATCGTGACGCA
AACGGGCAGATTAAACTGATGGACGCGGCGTTATTCGCAGAAGGGCTGAT
GGGCTTGAAAGAAATGAAGTCTTAA lcdA
ATGAGCTTAACCCAAGGCATGAAAGCTAAACAACTGTTAGCATACTTTCA SEQ ID NO:
GGGTAAAGCCGATCAGGATGCACGTGAAGCGAAAGCCCGCGGTGAGCTGG 50
TCTGCTGGTCGGCGTCAGTCGCGCCGCCGGAATTTTGCGTAACAATGGGC
ATTGCCATGATCTACCCGGAGACTCATGCAGCGGGCATCGGTGCCCGCAA
AGGTGCGATGGACATGCTGGAAGTTGCGGACCGCAAAGGCTACAACGTGG
ATTGTTGTTCCTACGGCCGTGTAAATATGGGTTACATGGAATGTTTAAAA
GAAGCCGCCATCACGGGCGTCAAGCCGGAAGTTTTGGTTAATTCCCCTGC
TGCTGACGTTCCGCTTCCCGATTTGGTGATTACGTGTAATAATATCTGTA
ACACGCTGCTGAAATGGTACGAAAACTTAGCAGCAGAACTCGATATTCCT
TGCATCGTGATCGACGTACCGTTTAATCATACCATGCCGATTCCGGAATA
TGCCAAGGCCTACATCGCGGACCAGTTCCGCAATGCAATTTCTCAGCTGG
AAGTTATTTGTGGCCGTCCGTTCGATTGGAAGAAATTTAAGGAGGTCAAA
GATCAGACCCAGCGTAGCGTATACCACTGGAACCGCATTGCCGAGATGGC
GAAATACAAGCCTAGCCCGCTGAACGGCTTCGATCTGTTCAATTACATGG
CGTTAATCGTGGCGTGCCGCAGCCTGGATTATGCAGAAATTACCTTTAAA
GCGTTCGCGGACGAATTAGAAGAGAATTTGAAGGCGGGTATCTACGCCTT
TAAAGGTGCGGAAAAAACGCGCTTTCAATGGGAAGGTATCGCGGTGTGGC
CACATTTAGGTCACACGTTTAAATCTATGAAGAATCTGAATTCGATTATG
ACCGGTACGGCATACCCCGCCCTTTGGGACCTGCACTATGACGCTAACGA
CGAATCTATGCACTCTATGGCTGAAGCGTACACCCGTATTTATATTAATA
CTTGTCTGCAGAACAAAGTAGAGGTCCTGCTTGGGATCATGGAAAAAGGC
CAGGTGGATGGTACCGTATATCATCTGAATCGCAGCTGCAAACTGATGAG
TTTCCTGAACGTGGAAACGGCTGAAATTATTAAAGAGAAGAACGGTCTTC
CTTACGTCTCCATTGATGGCGATCAGACCGATCCTCGCGTTTTTTCTCCG
GCCCAGTTTGATACCCGTGTTCAGGCCCTGGTTGAGATGATGGAGGCCAA
TATGGCGGCAGCGGAATAA lcdB
ATGTCACGCGTGGAGGCAATCCTGTCGCAGCTGAAAGATGTCGCCGCGAA SEQ ID NO:
TCCGAAAAAAGCCATGGATGACTATAAAGCTGAAACAGGTAAGGGCGCGG 51
TTGGTATCATGCCGATCTACAGCCCCGAAGAAATGGTACACGCCGCTGGC
TATTTGCCGATGGGAATCTGGGGCGCCCAGGGCAAAACGATTAGTAAAGC
GCGCACCTATCTGCCTGCTTTTGCCTGCAGCGTAATGCAGCAGGTTATGG
AATTACAGTGCGAGGGCGCGTATGATGACCTGTCCGCAGTTATTTTTAGC
GTACCGTGCGACACTCTCAAATGTCTTAGCCAGAAATGGAAAGGTACGTC
CCCAGTGATTGTATTTACGCATCCGCAGAACCGCGGATTAGAAGCGGCGA
ACCAATTCTTGGTTACCGAGTATGAACTGGTAAAAGCACAACTGGAATCA
GTTCTGGGTGTGAAAATTTCAAACGCCGCCCTGGAAAATTCGATTGCAAT
TTATAACGAGAATCGTGCCGTGATGCGTGAGTTCGTGAAAGTGGCAGCGG
ACTATCCTCAAGTCATTGACGCAGTGAGCCGCCACGCGGTTTTTAAAGCG
CGCCAGTTTATGCTTAAGGAAAAACATACCGCACTTGTGAAAGAACTGAT
CGCTGAGATTAAAGCAACGCCAGTCCAGCCGTGGGACGGAAAAAAGGTTG
TAGTGACGGGCATTCTGTTGGAACCGAATGAGTTATTAGATATCTTTAAT
GAGTTTAAGATCGCGATTGTTGATGATGATTTAGCGCAGGAAAGCCGTCA
GATCCGTGTTGACGTTCTGGACGGAGAAGGCGGACCGCTCTACCGTATGG
CTAAAGCGTGGCAGCAAATGTATGGCTGCTCGCTGGCAACCGACACCAAG
AAGGGTCGCGGCCGTATGTTAATTAACAAAACGATTCAGACCGGTGCGGA
CGCTATCGTAGTTGCAATGATGAAGTTTTGCGACCCAGAAGAATGGGATT
ATCCGGTAATGTACCGTGAATTTGAAGAAAAAGGGGTCAAATCACTTATG
ATTGAGGTGGATCAGGAAGTATCGTCTTTCGAACAGATTAAAACCCGTCT
GCAGTCATTCGTCGAAATGCTTTAA lcdC
ATGTATACCTTGGGGATTGATGTCGGTTCTGCCTCTAGTAAAGCGGTGAT SEQ ID NO:
TCTGAAAGATGGAAAAGATATTGTCGCTGCCGAGGTTGTCCAAGTCGGTA 52
CCGGCTCCTCGGGTCCCCAACGCGCACTGGACAAAGCCTTTGAAGTCTCT
GGCTTAAAAAAGGAAGACATCAGCTACACAGTAGCTACGGGCTATGGGCG
CTTCAATTTTAGCGACGCGGATAAACAGATTTCGGAAATTAGCTGTCATG
CCAAAGGCATTTATTTCTTAGTACCAACTGCGCGCACTATTATTGACATT
GGCGGCCAAGATGCGAAAGCCATCCGCCTGGACGACAAGGGGGGTATTAA
GCAATTCTTCATGAATGATAAATGCGCGGCGGGCACGGGGCGTTTCCTGG
AAGTCATGGCTCGCGTACTTGAAACCACCCTGGATGAAATGGCTGAACTG
GATGAACAGGCGACTGACACCGCTCCCATTTCAAGCACCTGCACGGTTTT
CGCCGAAAGCGAAGTAATTAGCCAATTGAGCAATGGTGTCTCACGCAACA
ACATCATTAAAGGTGTCCATCTGAGCGTTGCGTCACGTGCGTGTGGTCTG
GCGTATCGCGGCGGTTTGGAGAAAGATGTTGTTATGACAGGTGGCGTGGC
AAAAAATGCAGGGGTGGTGCGCGCGGTGGCGGGCGTTCTGAAGACCGATG
TTATCGTTGCTCCGAATCCTCAGACGACCGGTGCACTGGGGGCAGCGCTG
TATGCTTATGAGGCCGCCCAGAAGAAGTA etfA
ATGGCCTTCAATAGCGCAGATATTAATTCTTTCCGCGATATTTGGGTGTT SEQ ID NO:
TTGTGAACAGCGTGAGGGCAAACTGATTAACACCGATTTCGAATTAATTA 53
GCGAAGGTCGTAAACTGGCTGACGAACGCGGAAGCAAACTGGTTGGAATT
TTGCTGGGGCACGAAGTTGAAGAAATCGCAAAAGAATTAGGCGGCTATGG
TGCGGACAAGGTAATTGTGTGCGATCATCCGGAACTTAAATTTTACACTA
CGGATGCTTATGCCAAAGTTTTATGTGACGTCGTGATGGAAGAGAAACCG
GAGGTAATTTTGATCGGTGCCACCAACATTGGCCGTGATCTCGGACCGCG
TTGTGCTGCACGCTTGCACACGGGGCTGACGGCTGATTGCACGCACCTGG
ATATTGATATGAATAAATATGTGGACTTTCTTAGCACCAGTAGCACCTTG
GATATCTCGTCGATGACTTTCCCTATGGAAGATACAAACCTTAAAATGAC
GCGCCCTGCATTTGGCGGACATCTGATGGCAACGATCATTTGTCCACGCT
TCCGTCCCTGTATGAGCACAGTGCGCCCCGGAGTGATGAAGAAAGCGGAG
TTCTCGCAGGAGATGGCGCAAGCATGTCAAGTAGTGACCCGTCACGTAAA
TTTGTCGGATGAAGACCTTAAAACTAAAGTAATTAATATCGTGAAGGAAA
CGAAAAAGATTGTGGATCTGATCGGCGCAGAAATTATTGTGTCAGTTGGT
CGTGGTATCTCGAAAGATGTCCAAGGTGGAATTGCACTGGCTGAAAAACT
TGCGGACGCATTTGGTAACGGTGTCGTGGGCGGCTCGCGCGCAGTGATTG
ATTCCGGCTGGTTACCTGCGGATCATCAGGTTGGACAAACCGGTAAGACC
GTGCACCCGAAAGTCTACGTGGCGCTGGGTATTAGTGGGGCTATCCAGCA
TAAGGCTGGGATGCAAGACTCTGAACTGATCATTGCCGTCAACAAAGACG
AAACGGCGCCTATCTTCGACTGCGCCGATTATGGCATCACCGGTGATTTA
TTTAAAATCGTACCGATGATGATCGACGCGATCAAAGAGGGTAAAAACGC ATGA acrB
ATGCGCATCTATGTGTGTGTGAAACAAGTCCCAGATACGAGCGGCAAGGT SEQ ID NO:
GGCCGTTAACCCTGATGGGACCCTTAACCGTGCCTCAATGGCAGCGATTA 54
TTAACCCGGACGATATGTCCGCGATCGAACAGGCATTAAAACTGAAAGAT
GAAACCGGATGCCAGGTTACGGCGCTTACGATGGGTCCTCCTCCTGCCGA
GGGCATGTTGCGCGAAATTATTGCAATGGGGGCCGACGATGGTGTGCTGA
TTTCGGCCCGTGAATTTGGGGGGTCCGATACCTTCGCAACCAGTCAAATT
ATTAGCGCGGCAATCCATAAATTAGGCTTAAGCAATGAAGACATGATCTT
TTGCGGTCGTCAGGCCATTGACGGTGATACGGCCCAAGTCGGCCCTCAAA
TTGCCGAAAAACTGAGCATCCCACAGGTAACCTATGGCGCAGGAATCAAA
AAATCTGGTGATTTAGTGCTGGTGAAGCGTATGTTGGAGGATGGTTATAT
GATGATCGAAGTCGAAACTCCATGTCTGATTACCTGCATTCAGGATAAAG
CGGTAAAACCACGTTACATGACTCTCAACGGTATTATGGAATGCTACTCC
AAGCCGCTCCTCGTTCTCGATTACGAAGCACTGAAAGATGAACCGCTGAT
CGAACTTGATACCATTGGGCTTAAAGGCTCCCCGACGAATATCTTTAAAT
CGTTTACGCCGCCTCAGAAAGGCGTTGGTGTCATGCTCCAAGGCACCGAT
AAGGAAAAAGTCGAGGATCTGGTGGATAAGCTGATGCAGAAACATGTCAT CTAA acrC
ATGTTCTTACTGAAGATTAAAAAAGAACGTATGAAACGCATGGACTTTAG SEQ ID NO:
TTTAACGCGTGAACAGGAGATGTTAAAAAAACTGGCGCGTCAGTTTGCTG 55
AGATCGAGCTGGAACCGGTGGCCGAAGAGATTGATCGTGAGCACGTTTTT
CCTGCAGAAAACTTTAAGAAGATGGCGGAAATTGGCTTAACCGGCATTGG
TATCCCGAAAGAATTTGGTGGCTCCGGTGGAGGCACCCTGGAGAAGGTCA
TTGCCGTGTCAGAATTCGGCAAAAAGTGTATGGCCTCAGCTTCCATTTTA
AGCATTCATCTTATCGCGCCGCAGGCAATCTACAAATATGGGACCAAAGA
ACAGAAAGAGACGTACCTGCCGCGTCTTACCAAAGGTGGTGAACTGGGCG
CCTTTGCGCTGACAGAACCAAACGCCGGAAGCGATGCCGGCGCGGTAAAA
ACGACCGCGATTCTGGACAGCCAGACAAACGAGTACGTGCTGAATGGCAC
CAAATGCTTTATCAGCGGGGGCGGGCGCGCGGGTGTTCTTGTAATTTTTG
CGCTTACTGAACCGAAAAAAGGTCTGAAAGGGATGAGCGCGATTATCGTG
GAGAAAGGGACCCCGGGCTTCAGCATCGGCAAGGTGGAGAGCAAGATGGG
GATCGCAGGTTCGGAAACCGCGGAACTTATCTTCGAAGATTGTCGCGTTC
CGGCTGCCAACCTTTTAGGTAAAGAAGGCAAAGGCTTTAAAATTGCTATG
GAAGCCCTGGATGGCGCCCGTATTGGCGTGGGCGCTCAAGCAATCGGAAT
TGCCGAGGGGGCGATCGACCTGAGTGTGAAGTACGTTCACGAGCGCATTC
AATTTGGTAAACCGATCGCGAATCTGCAGGGAATTCAATGGTATATCGCG
GATATGGCGACCAAAACCGCCGCGGCACGCGCACTTGTTGAGTTTGCAGC
GTATCTTGAAGACGCGGGTAAACCGTTCACAAAGGAATCTGCTATGTGCA
AGCTGAACGCCTCCGAAAACGCGCGTTTTGTGACAAATTTAGCTCTGCAG
ATTCACGGGGGTTACGGTTATATGAAAGATTATCCGTTAGAGCGTATGTA
TCGCGATGCTAAGATTACGGAAATTTACGAGGGGACATCAGAAATCCATA
AGGTGGTGATTGCGCGTGAAGTAATGAAACGCTAA thrA.sup.fbr
ATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTT SEQ ID NO:
TCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGG 56
CCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATG
ATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGC
CGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGG
GGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAA
ATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAG
CATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTA
TGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCG
GTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATAT
TGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACA
TGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTG
GTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTG
TTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATA
CCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCC
TACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCC
CCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAA
ATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGAT
GAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACATGGCAAT
GTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGC
GCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACG
CAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTG
TGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAG
AAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCG
GTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTT
TGCCGCACTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGAGAT
CTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCGACCACT
GGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGA
AGTGTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAAC
TGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTC
TGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAA
TCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATC
TCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTC
ATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTT
CCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCT
CGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGG
CGTAAATTCCTCTATGACACCAACGTTGGGGCTGGATTACCGGTTATTGA
GAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCG
GCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGC
ATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGA
ACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTAT
TGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAA
ATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGC
TTTTATGGCGAATCTGTCACAACTCGACGATCTCTTTGCCGCGCGCGTGG
CGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGAT
GAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCC
GCTGTTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACT
ATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGCAATGAC
GTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAA GTTAGGAGTCTGA
thrB ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTT SEQ ID NO:
TGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAG 57
ATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGA
CGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGA
TGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCC
TGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTA
TCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGT
ATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGA
CGGCAGAAGCCAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGC
ATTGCGCACGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCG
TCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT
ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCG
GAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGG
GTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTG
GATACGGCGGGCGCACGAGTACTGGAAAACTAA thrC
ATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGCGCA SEQ ID NO:
AGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACG 58
ACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGAT
TTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAAT
CCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGG
CTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCAC
GGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAAT
GCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCT
CCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAAT
GTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGA
AAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACG
GCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAA
GAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAG
CCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGC
CGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTC
GGCGATTTGACGGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAA
ACGTTTTATTGCTGCGACCAACGTGAACGATACCGTGCCACGTTTCCTGC
ACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCG
ATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCG
CCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATG
AAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCG
GAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCC
AGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAG
AGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTG
GCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTT
TGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAA ilvA.sup.fbr
ATGAGTGAAACATACGTGTCTGAGAAAAGTCCAGGAGTGATGGCTAGCGG SEQ ID NO:
AGCGGAGCTGATTCGTGCCGCCGACATTCAAACGGCGCAGGCACGAATTT 59
CCTCCGTCATTGCACCAACTCCATTGCAGTATTGCCCTCGTCTTTCTGAG
GAAACCGGAGCGGAAATCTACCTTAAGCGTGAGGATCTGCAGGATGTTCG
TTCCTACAAGATCCGCGGTGCGCTGAACTCTGGAGCGCAGCTCACCCAAG
AGCAGCGCGATGCAGGTATCGTTGCCGCATCTGCAGGTAACCATGCCCAG
GGCGTGGCCTATGTGTGCAAGTCCTTGGGCGTTCAGGGACGCATCTATGT
TCCTGTGCAGACTCCAAAGCAAAAGCGTGACCGCATCATGGTTCACGGCG
GAGAGTTTGTCTCCTTGGTGGTCACTGGCAATAACTTCGACGAAGCATCG
GCTGCAGCGCATGAAGATGCAGAGCGCACCGGCGCAACGCTGATCGAGCC
TTTCGATGCTCGCAACACCGTCATCGGTCAGGGCACCGTGGCTGCTGAGA
TCTTGTCGCAGCTGACTTCCATGGGCAAGAGTGCAGATCACGTGATGGTT
CCAGTCGGCGGTGGCGGACTTCTTGCAGGTGTGGTCAGCTACATGGCTGA
TATGGCACCTCGCACTGCGATCGTTGGTATCGAACCAGCGGGAGCAGCAT
CCATGCAGGCTGCATTGCACAATGGTGGACCAATCACTTTGGAGACTGTT
GATCCCTTTGTGGACGGCGCAGCAGTCAAACGTGTCGGAGATCTCAACTA
CACCATCGTGGAGAAGAACCAGGGTCGCGTGCACATGATGAGCGCGACCG
AGGGCGCTGTGTGTACTGAGATGCTCGATCTTTACCAAAACGAAGGCATC
ATCGCGGAGCCTGCTGGCGCGCTGTCTATCGCTGGGTTGAAGGAAATGTC
CTTTGCACCTGGTTCTGCAGTGGTGTGCATCATCTCTGGTGGCAACAACG
ATGTGCTGCGTTATGCGGAAATCGCTGAGCGCTCCTTGGTGCACCGCGGT
TTGAAGCACTACTTCTTGGTGAACTTCCCGCAAAAGCCTGGTCAGTTGCG
TCACTTCCTGGAAGATATCCTGGGACCGGATGATGACATCACGCTGTTTG
AGTACCTCAAGCGCAACAACCGTGAGACCGGTACTGCGTTGGTGGGTATT
CACTTGAGTGAAGCATCAGGATTGGATTCTTTGCTGGAACGTATGGAGGA
ATCGGCAATTGATTCCCGTCGCCTCGAGCCGGGCACCCCTGAGTACGAAT ACTTGACCTAA aceE
ATGTCAGAACGTTTCCCAAATGACGTGGATCCGATCGAAACTCGCGACTG SEQ ID NO:
GCTCCAGGCGATCGAATCGGTCATCCGTGAAGAAGGTGTTGAGCGTGCTC 60
AGTATCTGATCGACCAACTGCTTGCTGAAGCCCGCAAAGGCGGTGTAAAC
GTAGCCGCAGGCACAGGTATCAGCAACTACATCAACACCATCCCCGTTGA
AGAACAACCGGAGTATCCGGGTAATCTGGAACTGGAACGCCGTATTCGTT
CAGCTATCCGCTGGAACGCCATCATGACGGTGCTGCGTGCGTCGAAAAAA
GACCTCGAACTGGGCGGCCATATGGCGTCCTTCCAGTCTTCCGCAACCAT
TTATGATGTGTGCTTTAACCACTTCTTCCGTGCACGCAACGAGCAGGATG
GCGGCGACCTGGTTTACTTCCAGGGCCACATCTCCCCGGGCGTGTACGCT
CGTGCTTTCCTGGAAGGTCGTCTGACTCAGGAGCAGCTGGATAACTTCCG
TCAGGAAGTTCACGGCAATGGCCTCTCTTCCTATCCGCACCCGAAACTGA
TGCCGGAATTCTGGCAGTTCCCGACCGTATCTATGGGTCTGGGTCCGATT
GGTGCTATTTACCAGGCTAAATTCCTGAAATATCTGGAACACCGTGGCCT
GAAAGATACCTCTAAACAAACCGTTTACGCGTTCCTCGGTGACGGTGAAA
TGGACGAACCGGAATCCAAAGGTGCGATCACCATCGCTACCCGTGAAAAA
CTGGATAACCTGGTCTTCGTTATCAACTGTAACCTGCAGCGTCTTGACGG
CCCGGTCACCGGTAACGGCAAGATCATCAACGAACTGGAAGGCATCTTCG
AAGGTGCTGGCTGGAACGTGATCAAAGTGATGTGGGGTAGCCGTTGGGAT
GAACTGCTGCGTAAGGATACCAGCGGTAAACTGATCCAGCTGATGAACGA
AACCGTTGACGGCGACTACCAGACCTTCAAATCGAAAGATGGTGCGTACG
TTCGTGAACACTTCTTCGGTAAATATCCTGAAACCGCAGCACTGGTTGCA
GACTGGACTGACGAGCAGATCTGGGCACTGAACCGTGGTGGTCACGATCC
GAAGAAAATCTACGCTGCATTCAAGAAAGCGCAGGAAACCAAAGGCAAAG
CGACAGTAATCCTTGCTCATACCATTAAAGGTTACGGCATGGGCGACGCG
GCTGAAGGTAAAAACATCGCGCACCAGGTTAAGAAAATGAACATGGACGG
TGTGCGTCATATCCGCGACCGTTTCAATGTGCCGGTGTCTGATGCAGATA
TCGAAAAACTGCCGTACATCACCTTCCCGGAAGGTTCTGAAGAGCATACC
TATCTGCACGCTCAGCGTCAGAAACTGCACGGTTATCTGCCAAGCCGTCA
GCCGAACTTCACCGAGAAGCTTGAGCTGCCGAGCCTGCAAGACTTCGGCG
CGCTGTTGGAAGAGCAGAGCAAAGAGATCTCTACCACTATCGCTTTCGTT
CGTGCTCTGAACGTGATGCTGAAGAACAAGTCGATCAAAGATCGTCTGGT
ACCGATCATCGCCGACGAAGCGCGTACTTTCGGTATGGAAGGTCTGTTCC
GTCAGATTGGTATTTACAGCCCGAACGGTCAGCAGTACACCCCGCAGGAC
CGCGAGCAGGTTGCTTACTATAAAGAAGACGAGAAAGGTCAGATTCTGCA
GGAAGGGATCAACGAGCTGGGCGCAGGTTGTTCCTGGCTGGCAGCGGCGA
CCTCTTACAGCACCAACAATCTGCCGATGATCCCGTTCTACATCTATTAC
TCGATGTTCGGCTTCCAGCGTATTGGCGATCTGTGCTGGGCGGCTGGCGA
CCAGCAAGCGCGTGGCTTCCTGATCGGCGGTACTTCCGGTCGTACCACCC
TGAACGGCGAAGGTCTGCAGCACGAAGATGGTCACAGCCACATTCAGTCG
CTGACTATCCCGAACTGTATCTCTTACGACCCGGCTTACGCTTACGAAGT
TGCTGTCATCATGCATGACGGTCTGGAGCGTATGTACGGTGAAAAACAAG
AGAACGTTTACTACTACATCACTACGCTGAACGAAAACTACCACATGCCG
GCAATGCCGGAAGGTGCTGAGGAAGGTATCCGTAAAGGTATCTACAAACT
CGAAACTATTGAAGGTAGCAAAGGTAAAGTTCAGCTGCTCGGCTCCGGTT
CTATCCTGCGTCACGTCCGTGAAGCAGCTGAGATCCTGGCGAAAGATTAC
GGCGTAGGTTCTGACGTTTATAGCGTGACCTCCTTCACCGAGCTGGCGCG
TGATGGTCAGGATTGTGAACGCTGGAACATGCTGCACCCGCTGGAAACTC
CGCGCGTTCCGTATATCGCTCAGGTGATGAACGACGCTCCGGCAGTGGCA
TCTACCGACTATATGAAACTGTTCGCTGAGCAGGTCCGTACTTACGTACC
GGCTGACGACTACCGCGTACTGGGTACTGATGGCTTCGGTCGTTCCGACA
GCCGTGAGAACCTGCGTCACCACTTCGAAGTTGATGCTTCTTATGTCGTG
GTTGCGGCGCTGGGCGAACTGGCTAAACGTGGCGAAATCGATAAGAAAGT
GGTTGCTGACGCAATCGCCAAATTCAACATCGATGCAGATAAAGTTAACC CGCGTCTGGCGTAA
aceF ATGGCTATCGAAATCAAAGTACCGGACATCGGGGCTGATGAAGTTGAAAT SEQ ID NO:
CACCGAGATCCTGGTCAAAGTGGGCGACAAAGTTGAAGCCGAACAGTCGC 61
TGATCACCGTAGAAGGCGACAAAGCCTCTATGGAAGTTCCGTCTCCGCAG
GCGGGTATCGTTAAAGAGATCAAAGTCTCTGTTGGCGATAAAACCCAGAC
CGGCGCACTGATTATGATTTTCGATTCCGCCGACGGTGCAGCAGACGCTG
CACCTGCTCAGGCAGAAGAGAAGAAAGAAGCAGCTCCGGCAGCAGCACCA
GCGGCTGCGGCGGCAAAAGACGTTAACGTTCCGGATATCGGCAGCGACGA
AGTTGAAGTGACCGAAATCCTGGTGAAAGTTGGCGATAAAGTTGAAGCTG
AACAGTCGCTGATCACCGTAGAAGGCGACAAGGCTTCTATGGAAGTTCCG
GCTCCGTTTGCTGGCACCGTGAAAGAGATCAAAGTGAACGTGGGTGACAA
AGTGTCTACCGGCTCGCTGATTATGGTCTTCGAAGTCGCGGGTGAAGCAG
GCGCGGCAGCTCCGGCCGCTAAACAGGAAGCAGCTCCGGCAGCGGCCCCT
GCACCAGCGGCTGGCGTGAAAGAAGTTAACGTTCCGGATATCGGCGGTGA
CGAAGTTGAAGTGACTGAAGTGATGGTGAAAGTGGGCGACAAAGTTGCCG
CTGAACAGTCACTGATCACCGTAGAAGGCGACAAAGCTTCTATGGAAGTT
CCGGCGCCGTTTGCAGGCGTCGTGAAGGAACTGAAAGTCAACGTTGGCGA
TAAAGTGAAAACTGGCTCGCTGATTATGATCTTCGAAGTTGAAGGCGCAG
CGCCTGCGGCAGCTCCTGCGAAACAGGAAGCGGCAGCGCCGGCACCGGCA
GCAAAAGCTGAAGCCCCGGCAGCAGCACCAGCTGCGAAAGCGGAAGGCAA
ATCTGAATTTGCTGAAAACGACGCTTATGTTCACGCGACTCCGCTGATCC
GCCGTCTGGCACGCGAGTTTGGTGTTAACCTTGCGAAAGTGAAGGGCACT
GGCCGTAAAGGTCGTATCCTGCGCGAAGACGTTCAGGCTTACGTGAAAGA
AGCTATCAAACGTGCAGAAGCAGCTCCGGCAGCGACTGGCGGTGGTATCC
CTGGCATGCTGCCGTGGCCGAAGGTGGACTTCAGCAAGTTTGGTGAAATC
GAAGAAGTGGAACTGGGCCGCATCCAGAAAATCTCTGGTGCGAACCTGAG
CCGTAACTGGGTAATGATCCCGCATGTTACTCACTTCGACAAAACCGATA
TCACCGAGTTGGAAGCGTTCCGTAAACAGCAGAACGAAGAAGCGGCGAAA
CGTAAGCTGGATGTGAAGATCACCCCGGTTGTCTTCATCATGAAAGCCGT
TGCTGCAGCTCTTGAGCAGATGCCTCGCTTCAATAGTTCGCTGTCGGAAG
ACGGTCAGCGTCTGACCCTGAAGAAATACATCAACATCGGTGTGGCGGTG
GATACCCCGAACGGTCTGGTTGTTCCGGTATTCAAAGACGTCAACAAGAA
AGGCATCATCGAGCTGTCTCGCGAGCTGATGACTATTTCTAAGAAAGCGC
GTGACGGTAAGCTGACTGCGGGCGAAATGCAGGGCGGTTGCTTCACCATC
TCCAGCATCGGCGGCCTGGGTACTACCCACTTCGCGCCGATTGTGAACGC
GCCGGAAGTGGCTATCCTCGGCGTTTCCAAGTCCGCGATGGAGCCGGTGT
GGAATGGTAAAGAGTTCGTGCCGCGTCTGATGCTGCCGATTTCTCTCTCC
TTCGACCACCGCGTGATCGACGGTGCTGATGGTGCCCGTTTCATTACCAT
CATTAACAACACGCTGTCTGACATTCGCCGTCTGGTGATGTAA lpd
ATGAGTACTGAAATCAAAACTCAGGTCGTGGTACTTGGGGCAGGCCCCGC SEQ ID NO:
AGGTTACTCCGCTGCCTTCCGTTGCGCTGATTTAGGTCTGGAAACCGTAA 62
TCGTAGAACGTTACAACACCCTTGGCGGTGTTTGCCTGAACGTCGGCTGT
ATCCCTTCTAAAGCACTGCTGCACGTAGCAAAAGTTATCGAAGAAGCCAA
AGCGCTGGCTGAACACGGTATCGTCTTCGGCGAACCGAAAACCGATATCG
ACAAGATTCGTACCTGGAAAGAGAAAGTGATCAATCAGCTGACCGGTGGT
CTGGCTGGTATGGCGAAAGGCCGCAAAGTCAAAGTGGTCAACGGTCTGGG
TAAATTCACCGGGGCTAACACCCTGGAAGTTGAAGGTGAGAACGGCAAAA
CCGTGATCAACTTCGACAACGCGATCATTGCAGCGGGTTCTCGCCCGATC
CAACTGCCGTTTATTCCGCATGAAGATCCGCGTATCTGGGACTCCACTGA
CGCGCTGGAACTGAAAGAAGTACCAGAACGCCTGCTGGTAATGGGTGGCG
GTATCATCGGTCTGGAAATGGGCACCGTTTACCACGCGCTGGGTTCACAG
ATTGACGTGGTTGAAATGTTCGACCAGGTTATCCCGGCAGCTGACAAAGA
CATCGTTAAAGTCTTCACCAAGCGTATCAGCAAGAAATTCAACCTGATGC
TGGAAACCAAAGTTACCGCCGTTGAAGCGAAAGAAGACGGCATTTATGTG
ACGATGGAAGGCAAAAAAGCACCCGCTGAACCGCAGCGTTACGACGCCGT
GCTGGTAGCGATTGGTCGTGTGCCGAACGGTAAAAACCTCGACGCAGGCA
AAGCAGGCGTGGAAGTTGACGACCGTGGTTTCATCCGCGTTGACAAACAG
CTGCGTACCAACGTACCGCACATCTTTGCTATCGGCGATATCGTCGGTCA
ACCGATGCTGGCACACAAAGGTGTTCACGAAGGTCACGTTGCCGCTGAAG
TTATCGCCGGTAAGAAACACTACTTCGATCCGAAAGTTATCCCGTCCATC
GCCTATACCAAACCAGAAGTTGCATGGGTGGGTCTGACTGAGAAAGAAGC
GAAAGAGAAAGGCATCAGCTATGAAACCGCCACCTTCCCGTGGGCTGCTT
CTGGTCGTGCTATCGCTTCCGACTGCGCAGACGGTATGACCAAGCTGATT
TTCGACAAAGAATCTCACCGTGTGATCGGTGGTGCGATTGTCGGTACTAA
CGGCGGCGAGCTGCTGGGTGAAATCGGCCTGGCAATCGAAATGGGTTGTG
ATGCTGAAGACATCGCACTGACCATCCACGCGCACCCGACTCTGCACGAG
TCTGTGGGCCTGGCGGCAGAAGTGTTCGAAGGTAGCATTACCGACCTGCC
GAACCCGAAAGCGAAGAAGAAGTAA tesB
ATGAGTCAGGCGCTAAAAAATTTACTGACATTGTTAAATCTGGAAAAAAT SEQ ID NO:
TGAGGAAGGACTCTTTCGCGGCCAGAGTGAAGATTTAGGTTTACGCCAGG 48
TGTTTGGCGGCCAGGTCGTGGGTCAGGCCTTGTATGCTGCAAAAGAGACC
GTCCCTGAAGAGCGGCTGGTACATTCGTTTCACAGCTACTTTCTTCGCCC
TGGCGATAGTAAGAAGCCGATTATTTATGATGTCGAAACGCTGCGTGACG
GTAACAGCTTCAGCGCCCGCCGGGTTGCTGCTATTCAAAACGGCAAACCG
ATTTTTTATATGACTGCCTCTTTCCAGGCACCAGAAGCGGGTTTCGAACA
TCAAAAAACAATGCCGTCCGCGCCAGCGCCTGATGGCCTCCCTTCGGAAA
CGCAAATCGCCCAATCGCTGGCGCACCTGCTGCCGCCAGTGCTGAAAGAT
AAATTCATCTGCGATCGTCCGCTGGAAGTCCGTCCGGTGGAGTTTCATAA
CCCACTGAAAGGTCACGTCGCAGAACCACATCGTCAGGTGTGGATCCGCG
CAAATGGTAGCGTGCCGGATGACCTGCGCGTTCATCAGTATCTGCTCGGT
TACGCTTCTGATCTTAACTTCCTGCCGGTAGCTCTACAGCCGCACGGCAT
CGGTTTTCTCGAACCGGGGATTCAGATTGCCACCATTGACCATTCCATGT
GGTTCCATCGCCCGTTTAATTTGAATGAATGGCTGCTGTATAGCGTGGAG
AGCACCTCGGCGTCCAGCGCACGTGGCTTTGTGCGCGGTGAGTTTTATAC
CCAAGACGGCGTACTGGTTGCCTCGACCGTTCAGGAAGGGGTGATGCGTA ATCACAATTAA
[0286] In some embodiments, one or more of the propionate
biosynthesis genes is a synthetic propionate biosynthesis gene. In
some embodiments, one or more of the propionate biosynthesis genes
is an E. coli propionate biosynthesis gene. In some embodiments,
one or more of the propionate biosynthesis genes is a C. glutamicum
propionate biosynthesis gene. In some embodiments, one or more of
the propionate biosynthesis genes is a C. propionicum propionate
biosynthesis gene. The propionate gene cassette may comprise genes
for the aerobic biosynthesis of propionate and/or genes for the
anaerobic or microaerobic biosynthesis of propionate. One or more
of the propionate biosynthesis genes may be functionally replaced
or modified, e.g., codon optimized. In some embodiments, the
genetically engineered bacteria comprise a combination of
propionate biosynthesis genes from different species, strains,
and/or substrains of bacteria, and are capable of producing
propionate in low-oxygen conditions, in the presence of HE-specific
molecules or metabolites, in the presence of molecules or
metabolites associated with liver damage, inflammation or an
inflammatory response, or in the presence of some other metabolite
that may or may not be present in the gut, such as arabinose. In
some embodiments, one or more of the propionate biosynthesis genes
is functionally replaced, modified, and/or mutated in order to
enhance stability and/or increase propionate production in
low-oxygen conditions, in the presence of HE-specific molecules or
metabolites, in the presence of molecules or metabolites associated
with liver damage, inflammation or an inflammatory response, or in
the presence of some other metabolite that may or may not be
present in the gut, such as arabinose. In some embodiments, the
genetically engineered bacteria are capable of expressing the
propionate biosynthesis cassette and producing propionate in
low-oxygen conditions, in the presence of HE-specific molecules or
metabolites, in the presence of molecules or metabolites associated
with liver damage, inflammation or an inflammatory response, or in
the presence of some other metabolite that may or may not be
present in the gut, such as arabinose.
[0287] In some embodiments, the genetically engineered bacteria of
the invention comprise an acetate gene cassette and produce
acetate. The genetically engineered bacteria may include any
suitable set of acetate biosynthesis genes. Unmodified bacteria
comprising endogenous acetate biosynthesis genes are known in the
art and are capable of consuming various substrates to produce
acetate under aerobic and/or anaerobic conditions (see, e.g.,
Ragsdale et al., 2008). These endogenous acetate biosynthesis genes
may be a source of genes for the genetically engineered bacteria of
the invention. In some embodiments, the genetically engineered
bacteria of the invention comprise acetate biosynthesis genes from
a different species, strain, or substrain of bacteria. In some
embodiments, the native acetate biosynthesis genes in the
genetically engineered bacteria are enhanced. In some embodiments,
the genetically engineered bacteria comprise aerobic acetate
biosynthesis genes, e.g., from Escherichia coli. In some
embodiments, the genetically engineered bacteria comprise anaerobic
acetate biosynthesis genes, e.g., from Acetitomaculum,
Acetoanaerobium, Acetohalobium, Acetonema, Balutia,
Butyribacterium, Clostridium, Moorella, Oxobacter, Sporomusa,
and/or Thermoacetogenium. The genetically engineered bacteria may
comprise genes for aerobic acetate biosynthesis or genes for
anaerobic or microaerobic acetate biosynthesis. In some
embodiments, the genetically engineered bacteria comprise both
aerobic and anaerobic or microaerobic acetate biosynthesis genes.
In some embodiments, the genetically engineered bacteria comprise a
combination of acetate biosynthesis genes from different species,
strains, and/or substrains of bacteria, and are capable of
producing acetate. In some embodiments, one or more of the acetate
biosynthesis genes is functionally replaced, modified, and/or
mutated in order to enhance stability and/or acetate production. In
some embodiments, the genetically engineered bacteria are capable
of expressing the acetate biosynthesis cassette and producing
acetate in low-oxygen conditions or in the presence of HE-specific
molecules or metabolites. In some embodiments, the genetically
engineered bacteria are capable of producing an alternate
short-chain fatty acid.
[0288] One of skill in the art would appreciate that additional
genes and gene cassettes capable of producing gut barrier function
enhancer molecules are known in the art and may be expressed by the
genetically engineered bacteria of the invention. In some
embodiments, the gene or gene cassette for producing a therapeutic
molecule also comprises additional transcription and translation
elements, e.g., a ribosome binding site, to enhance expression of
the therapeutic molecule.
[0289] In some embodiments, the genetically engineered bacteria
produce two or more gut barrier function enhancer molecules. In
certain embodiments, the two or more molecules behave
synergistically to enhance gut barrier function. In certain
embodiments, the genetically engineered bacteria express butyrate
and propionate.
[0290] In some embodiments, the genetically engineered bacteria
comprising an ammonia conversion circuit further comprise one or
more circuits for producing a gut barrier enhancer molecule, e.g.,
butyrate (FIG. 43).
[0291] In some embodiments, the genetically engineered bacteria
comprise an ammonia conversion circuit, a GABA metabolic circuit,
and one or more circuits for producing a gut barrier enhancer
molecule, e.g., butyrate. In some embodiments, the genetically
engineered bacteria comprise an ammonia conversion circuit, a GABA
transport circuit, and one or more circuits for producing a gut
barrier enhancer molecule, e.g., butyrate. In some embodiments, the
genetically engineered bacteria comprise an ammonia conversion
circuit, a GABA transport circuit, a GABA metabolic circuit, and
one or more circuits for producing a gut barrier enhancer molecule,
e.g., butyrate. In some embodiments, the genetically engineered
bacteria comprise an ammonia conversion circuit, a manganese
transport circuit, a GABA metabolic circuit, and one or more
circuits for producing a gut barrier enhancer molecule, e.g.,
butyrate. In some embodiments, the genetically engineered bacteria
comprise an ammonia conversion circuit, a manganese transport
circuit, a GABA transport circuit, and one or more circuits for
producing a gut barrier enhancer molecule, e.g., butyrate. In some
embodiments, the genetically engineered bacteria comprise an
ammonia conversion circuit, a manganese transport circuit, a GABA
transport circuit, a GABA metabolic circuit, and one or more
circuits for producing a gut barrier enhancer molecule, e.g.,
butyrate. In some embodiments, the circuits are under the control
of the same promoter. In alternate embodiments, the circuits are
under the control of different promoters.
[0292] In some embodiments, the genetically engineered bacteria are
capable of expressing any one or more of the described circuits in
low-oxygen conditions, in the presence of HE-specific molecules or
metabolites, in the presence of molecules or metabolites associated
with liver damage, inflammation or an inflammatory response, or in
the presence of some other metabolite that may or may not be
present in the gut, such as arabinose. In some embodiments, any one
or more of the described circuits are present on one or more
plasmids (e.g., high copy or low copy) or are integrated into one
or more sites in the bacterial chromosome. Also, in some
embodiments, the genetically engineered bacteria are further
capable of expressing any one or more of the described circuits and
further comprise one or more of the following: (1) one or more
auxotrophies, such as any auxotrophies known in the art and
provided herein, e.g., thyA auxotrophy, (2) one or more kill switch
circuits, such as any of the kill-switches described herein or
otherwise known in the art, (3) one or more antibiotic resistance
circuits, (4) one or more transporters for importing biological
molecules or substrates, such any of the transporters described
herein or otherwise known in the art, (5) one or more secretion
circuits, such as any of the secretion circuits described herein
and otherwise known in the art, and (6) combinations of one or more
of such additional circuits.
[0293] In any of the embodiments described herein, the genetically
engineered bacteria may further comprise a resistance to rifaximin.
Resistance to rifaximin is caused primarily by mutations in the
rpoB gene. In some embodiments, the genetically engineered bacteria
comprise a known rifaximin resistance mutation, e.g., in the rpoB
gene. In other embodiments, a screen can be employed, exposing the
genetically engineered bacteria to increasing amounts of rifaximin,
to identify a useful mutation which confers rifaximin
resistance.
[0294] Inducible Promoters
[0295] In some embodiments, the bacterial cell comprises a stably
maintained plasmid or chromosome carrying the gene(s) encoding the
payload (s), such that the payload(s) can be expressed in the host
cell, and the host cell is capable of survival and/or growth in
vitro, e.g., in medium, and/or in vivo, e.g., in the gut. In some
embodiments, bacterial cell comprises two or more distinct payloads
or operons, e.g., two or more payload genes. In some embodiments,
bacterial cell comprises three or more distinct transporters or
operons, e.g., three or more payload genes. In some embodiments,
bacterial cell comprises 4, 5, 6, 7, 8, 9, 10, or more distinct
payloads or operons, e.g., 4, 5, 6, 7, 8, 9, 10, or more payload
genes.
[0296] In some embodiments, the genetically engineered bacteria
comprise multiple copies of the same payload gene(s). In some
embodiments, the gene encoding the payload is present on a plasmid
and operably linked to a directly or indirectly inducible promoter.
In some embodiments, the gene encoding the payload is present on a
plasmid and operably linked to a promoter that is induced under
low-oxygen or anaerobic conditions. In some embodiments, the gene
encoding the payload is present on a chromosome and operably linked
to a directly or indirectly inducible promoter. In some
embodiments, the gene encoding the payload is present in the
chromosome and operably linked to a promoter that is induced under
low-oxygen or anaerobic conditions. In some embodiments, the gene
encoding the payload is present on a plasmid and operably linked to
a promoter that is induced by exposure to tetracycline or
arabinose.
[0297] In some embodiments, the promoter that is operably linked to
the gene encoding the payload is directly induced by exogenous
environmental conditions. In some embodiments, the promoter that is
operably linked to the gene encoding the payload is indirectly
induced by exogenous environmental conditions. In some embodiments,
the promoter is directly or indirectly induced by exogenous
environmental conditions specific to the gut of a mammal. In some
embodiments, the promoter is directly or indirectly induced by
exogenous environmental conditions specific to the small intestine
of a mammal. In some embodiments, the promoter is directly or
indirectly induced by low-oxygen or anaerobic conditions such as
the environment of the mammalian gut. In some embodiments, the
promoter is directly or indirectly induced by molecules or
metabolites that are specific to the gut of a mammal. In some
embodiments, the promoter is directly or indirectly induced by a
molecule that is co-administered with the bacterial cell.
[0298] In certain embodiments, the bacterial cell comprises a gene
encoding a payload expressed under the control of a fumarate and
nitrate reductase regulator (FNR) responsive promoter. In E. coli,
FNR is a major transcriptional activator that controls the switch
from aerobic to anaerobic metabolism (Unden et al., 1997). In the
anaerobic state, FNR dimerizes into an active DNA binding protein
that activates hundreds of genes responsible for adapting to
anaerobic growth. In the aerobic state, FNR is prevented from
dimerizing by oxygen and is inactive. FNR responsive promoters
include, but are not limited to, the FNR responsive promoters
listed in the chart, below. Underlined sequences are predicted
ribosome binding sites, and bolded sequences are restriction sites
used for cloning.
[0299] FNR promoter sequences are known in the art, and any
suitable FNR promoter sequence(s) may be used in the genetically
engineered bacteria of the invention. Any suitable FNR promoter(s)
may be combined with any suitable payload (e.g., the exemplary
argA.sup.fbr sequence shown in Table 7). Non-limiting FNR promoter
sequences are provided in Table 6. Table 6 depicts the nucleic acid
sequences of exemplary regulatory region sequences comprising a
FNR-responsive promoter sequence. Underlined sequences are
predicted ribosome binding sites, and bolded sequences are
restriction sites used for cloning. In some embodiments, the
genetically engineered bacteria of the invention comprise one or
more of: SEQ ID NO: 18, SEQ ID NO: 19, nirB1 promoter (SEQ ID NO:
20), nirB2 promoter (SEQ ID NO: 21), nirB3 promoter (SEQ ID NO:
22), ydfZ promoter (SEQ ID NO: 23), nirB promoter fused to a strong
ribosome binding site (SEQ ID NO: 24), ydfZ promoter fused to a
strong ribosome binding site (SEQ ID NO: 25), fnrS, an
anaerobically induced small RNA gene (fnrS1 promoter SEQ ID NO: 26
or fnrS2 promoter SEQ ID NO: 27), nirB promoter fused to a crp
binding site (SEQ ID NO: 28), and fnrS fused to a crp binding site
(SEQ ID NO: 29).
[0300] In some embodiments, genetically engineered bacteria
comprise a nucleic acid sequence that is at least about 80%, at
least about 85%, at least about 90%, at least about 95%, or at
least about 99% homologous to the DNA sequence of SEQ ID NO: 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29, or a functional
fragment thereof.
[0301] In one embodiment, the FNR responsive promoter comprises SEQ
ID NO:1. In another embodiment, the FNR responsive promoter
comprises SEQ ID NO:2. In another embodiment, the FNR responsive
promoter comprises SEQ ID NO:3. In another embodiment, the FNR
responsive promoter comprises SEQ ID NO:4. In yet another
embodiment, the FNR responsive promoter comprises SEQ ID NO:5.
[0302] In some embodiments, multiple distinct FNR nucleic acid
sequences are inserted in the genetically engineered bacteria. In
alternate embodiments, the genetically engineered bacteria comprise
a gene encoding a payload expressed under the control of an
alternate oxygen level-dependent promoter, e.g., DNR (Trunk et al.,
2010) or ANR (Ray et al., 1997). In these embodiments, expression
of the payload gene is particularly activated in a low-oxygen or
anaerobic environment, such as in the gut. In some embodiments,
gene expression is further optimized by methods known in the art,
e.g., by optimizing ribosomal binding sites and/or increasing mRNA
stability. In one embodiment, the mammalian gut is a human
mammalian gut.
[0303] In some embodiments, the bacterial cell comprises an
oxygen-level dependent transcriptional regulator, e.g., FNR, ANR,
or DNR, and corresponding promoter from a different bacterial
species. The heterologous oxygen-level dependent transcriptional
regulator and promoter increase the transcription of genes operably
linked to said promoter, e.g., the gene encoding the payload, in a
low-oxygen or anaerobic environment, as compared to the native
gene(s) and promoter in the bacteria under the same conditions. In
certain embodiments, the non-native oxygen-level dependent
transcriptional regulator is an FNR protein from N. gonorrhoeae
(see, e.g., Isabella et al., 2011). In some embodiments, the
corresponding wild-type transcriptional regulator is left intact
and retains wild-type activity. In alternate embodiments, the
corresponding wild-type transcriptional regulator is deleted or
mutated to reduce or eliminate wild-type activity.
[0304] In some embodiments, the genetically engineered bacteria
comprise a wild-type oxygen-level dependent transcriptional
regulator, e.g., FNR, ANR, or DNR, and corresponding promoter that
is mutated relative to the wild-type promoter from bacteria of the
same subtype. The mutated promoter enhances binding to the
wild-type transcriptional regulator and increases the transcription
of genes operably linked to said promoter, e.g., the gene encoding
the payload, in a low-oxygen or anaerobic environment, as compared
to the wild-type promoter under the same conditions. In some
embodiments, the genetically engineered bacteria comprise a
wild-type oxygen-level dependent promoter, e.g., FNR, ANR, or DNR
promoter, and corresponding transcriptional regulator that is
mutated relative to the wild-type transcriptional regulator from
bacteria of the same subtype. The mutated transcriptional regulator
enhances binding to the wild-type promoter and increases the
transcription of genes operably linked to said promoter, e.g., the
gene encoding the payload, in a low-oxygen or anaerobic
environment, as compared to the wild-type transcriptional regulator
under the same conditions. In certain embodiments, the mutant
oxygen-level dependent transcriptional regulator is an FNR protein
comprising amino acid substitutions that enhance dimerization and
FNR activity (see, e.g., Moore et al., (2006).
[0305] In some embodiments, the bacterial cells comprise multiple
copies of the endogenous gene encoding the oxygen level-sensing
transcriptional regulator, e.g., the FNR gene. In some embodiments,
the gene encoding the oxygen level-sensing transcriptional
regulator is present on a plasmid. In some embodiments, the gene
encoding the oxygen level-sensing transcriptional regulator and the
gene encoding the payload are present on different plasmids. In
some embodiments, the gene encoding the oxygen level-sensing
transcriptional regulator and the gene encoding the payload are
present on the same plasmid. In some embodiments, the gene encoding
the oxygen level-sensing transcriptional regulator is present on a
chromosome. In some embodiments, the gene encoding the oxygen
level-sensing transcriptional regulator and the gene encoding the
payload are present on different chromosomes. In some embodiments,
the gene encoding the oxygen level-sensing transcriptional
regulator and the gene encoding the payload are present on the same
chromosome. In some instances, it may be advantageous to express
the oxygen level-sensing transcriptional regulator under the
control of an inducible promoter in order to enhance expression
stability. In some embodiments, expression of the transcriptional
regulator is controlled by a different promoter than the promoter
that controls expression of the gene encoding the payload. In some
embodiments, expression of the transcriptional regulator is
controlled by the same promoter that controls expression of the
payload. In some embodiments, the transcriptional regulator and the
payload are divergently transcribed from a promoter region.
[0306] RNS-Dependent Regulation
[0307] In some embodiments, the genetically engineered bacteria or
genetically engineered virus comprise a gene encoding a payload
that is expressed under the control of an inducible promoter. In
some embodiments, the genetically engineered bacterium or
genetically engineered virus that expresses a payload under the
control of a promoter that is activated by inflammatory conditions.
In one embodiment, the gene for producing the payload is expressed
under the control of an inflammatory-dependent promoter that is
activated in inflammatory environments, e.g., a reactive nitrogen
species or RNS promoter.
[0308] As used herein, "reactive nitrogen species" and "RNS" are
used interchangeably to refer to highly active molecules, ions,
and/or radicals derived from molecular nitrogen. RNS can cause
deleterious cellular effects such as nitrosative stress. RNS
includes, but is not limited to, nitric oxide (NO.), peroxynitrite
or peroxynitrite anion (ONOO--), nitrogen dioxide (.NO2),
dinitrogen trioxide (N2O3), peroxynitrous acid (ONOOH), and
nitroperoxycarbonate (ONOOCO2-) (unpaired electrons denoted by .).
Bacteria have evolved transcription factors that are capable of
sensing RNS levels. Different RNS signaling pathways are triggered
by different RNS levels and occur with different kinetics.
[0309] As used herein, "RNS-inducible regulatory region" refers to
a nucleic acid sequence to which one or more RNS-sensing
transcription factors is capable of binding, wherein the binding
and/or activation of the corresponding transcription factor
activates downstream gene expression; in the presence of RNS, the
transcription factor binds to and/or activates the regulatory
region. In some embodiments, the RNS-inducible regulatory region
comprises a promoter sequence. In some embodiments, the
transcription factor senses RNS and subsequently binds to the
RNS-inducible regulatory region, thereby activating downstream gene
expression. In alternate embodiments, the transcription factor is
bound to the RNS-inducible regulatory region in the absence of RNS;
in the presence of RNS, the transcription factor undergoes a
conformational change, thereby activating downstream gene
expression. The RNS-inducible regulatory region may be operatively
linked to a gene or genes, e.g., a payload gene sequence(s), e.g.,
any of the payloads described herein. For example, in the presence
of RNS, a transcription factor senses RNS and activates a
corresponding RNS-inducible regulatory region, thereby driving
expression of an operatively linked gene sequence. Thus, RNS
induces expression of the gene or gene sequences.
[0310] As used herein, "RNS-derepressible regulatory region" refers
to a nucleic acid sequence to which one or more RNS-sensing
transcription factors is capable of binding, wherein the binding of
the corresponding transcription factor represses downstream gene
expression; in the presence of RNS, the transcription factor does
not bind to and does not repress the regulatory region. In some
embodiments, the RNS-derepressible regulatory region comprises a
promoter sequence. The RNS-derepressible regulatory region may be
operatively linked to a gene or genes, e.g., a payload gene
sequence(s). For example, in the presence of RNS, a transcription
factor senses RNS and no longer binds to and/or represses the
regulatory region, thereby derepressing an operatively linked gene
sequence or gene cassette. Thus, RNS derepresses expression of the
gene or genes.
[0311] As used herein, "RNS-repressible regulatory region" refers
to a nucleic acid sequence to which one or more RNS-sensing
transcription factors is capable of binding, wherein the binding of
the corresponding transcription factor represses downstream gene
expression; in the presence of RNS, the transcription factor binds
to and represses the regulatory region. In some embodiments, the
RNS-repressible regulatory region comprises a promoter sequence. In
some embodiments, the transcription factor that senses RNS is
capable of binding to a regulatory region that overlaps with part
of the promoter sequence. In alternate embodiments, the
transcription factor that senses RNS is capable of binding to a
regulatory region that is upstream or downstream of the promoter
sequence. The RNS-repressible regulatory region may be operatively
linked to a gene sequence or gene cassette. For example, in the
presence of RNS, a transcription factor senses RNS and binds to a
corresponding RNS-repressible regulatory region, thereby blocking
expression of an operatively linked gene sequence or gene
sequences. Thus, RNS represses expression of the gene or gene
sequences.
[0312] As used herein, a "RNS-responsive regulatory region" refers
to a RNS-inducible regulatory region, a RNS-repressible regulatory
region, and/or a RNS-derepressible regulatory region. In some
embodiments, the RNS-responsive regulatory region comprises a
promoter sequence. Each regulatory region is capable of binding at
least one corresponding RNS-sensing transcription factor. Examples
of transcription factors that sense RNS and their corresponding
RNS-responsive genes, promoters, and/or regulatory regions include,
but are not limited to, those shown in Table A.
TABLE-US-00016 TABLE A Examples of RNS-sensing transcription
factors and RNS-responsive genes Primarily RNS-sensing capable of
Examples of responsive genes, transcription factor: sensing:
promoters, and/or regulatory regions: NsrR NO norB, aniA, nsrR,
hmpA, ytfE, ygbA, hcp, hcr, nrfA, aox NorR NO norVW, norR DNR NO
norCB, nir, nor, nos
[0313] In some embodiments, the genetically engineered bacteria of
the invention comprise a tunable regulatory region that is directly
or indirectly controlled by a transcription factor that is capable
of sensing at least one reactive nitrogen species. The tunable
regulatory region is operatively linked to a gene or genes capable
of directly or indirectly driving the expression of a payload, thus
controlling expression of the payload relative to RNS levels. For
example, the tunable regulatory region is a RNS-inducible
regulatory region, and the payload is a payload, such as any of the
payloads provided herein; when RNS is present, e.g., in an inflamed
tissue, a RNS-sensing transcription factor binds to and/or
activates the regulatory region and drives expression of the
payload gene or genes. Subsequently, when inflammation is
ameliorated, RNS levels are reduced, and production of the payload
is decreased or eliminated.
[0314] In some embodiments, the tunable regulatory region is a
RNS-inducible regulatory region; in the presence of RNS, a
transcription factor senses RNS and activates the RNS-inducible
regulatory region, thereby driving expression of an operatively
linked gene or genes. In some embodiments, the transcription factor
senses RNS and subsequently binds to the RNS-inducible regulatory
region, thereby activating downstream gene expression. In alternate
embodiments, the transcription factor is bound to the RNS-inducible
regulatory region in the absence of RNS; when the transcription
factor senses RNS, it undergoes a conformational change, thereby
inducing downstream gene expression.
[0315] In some embodiments, the tunable regulatory region is a
RNS-inducible regulatory region, and the transcription factor that
senses RNS is NorR. NorR "is an NO-responsive transcriptional
activator that regulates expression of the norVW genes encoding
flavorubredoxin and an associated flavoprotein, which reduce NO to
nitrous oxide" (Spiro 2006). The genetically engineered bacteria of
the invention may comprise any suitable RNS-responsive regulatory
region from a gene that is activated by NorR. Genes that are
capable of being activated by NorR are known in the art (see, e.g.,
Spiro 2006; Vine et al., 2011; Karlinsey et al., 2012). In certain
embodiments, the genetically engineered bacteria of the invention
comprise a RNS-inducible regulatory region from norVW that is
operatively linked to a gene or genes, e.g., one or more payload
gene sequence(s). In the presence of RNS, a NorR transcription
factor senses RNS and activates to the norVW regulatory region,
thereby driving expression of the operatively linked gene(s) and
producing the payload.
[0316] In some embodiments, the tunable regulatory region is a
RNS-inducible regulatory region, and the transcription factor that
senses RNS is DNR. DNR (dissimilatory nitrate respiration
regulator) "promotes the expression of the nir, the nor and the nos
genes" in the presence of nitric oxide (Castiglione et al., 2009).
The genetically engineered bacteria of the invention may comprise
any suitable RNS-responsive regulatory region from a gene that is
activated by DNR. Genes that are capable of being activated by DNR
are known in the art (see, e.g., Castiglione et al., 2009; Giardina
et al., 2008). In certain embodiments, the genetically engineered
bacteria of the invention comprise a RNS-inducible regulatory
region from norCB that is operatively linked to a gene or gene
cassette, e.g., a butyrogenic gene cassette. In the presence of
RNS, a DNR transcription factor senses RNS and activates to the
norCB regulatory region, thereby driving expression of the
operatively linked gene or genes and producing one or more
payloads. In some embodiments, the DNR is Pseudomonas aeruginosa
DNR.
[0317] In some embodiments, the tunable regulatory region is a
RNS-derepressible regulatory region, and binding of a corresponding
transcription factor represses downstream gene expression; in the
presence of RNS, the transcription factor no longer binds to the
regulatory region, thereby derepressing the operatively linked gene
or gene cassette.
[0318] In some embodiments, the tunable regulatory region is a
RNS-derepressible regulatory region, and the transcription factor
that senses RNS is NsrR. NsrR is "an Rrf2-type transcriptional
repressor [that] can sense NO and control the expression of genes
responsible for NO metabolism" (Isabella et al., 2009). The
genetically engineered bacteria of the invention may comprise any
suitable RNS-responsive regulatory region from a gene that is
repressed by NsrR. In some embodiments, the NsrR is Neisseria
gonorrhoeae NsrR. Genes that are capable of being repressed by NsrR
are known in the art (see, e.g., Isabella et al., 2009; Dunn et
al., 2010). In certain embodiments, the genetically engineered
bacteria of the invention comprise a RNS-derepressible regulatory
region from norB that is operatively linked to a gene or genes,
e.g., a payload gene or genes. In the presence of RNS, an NsrR
transcription factor senses RNS and no longer binds to the norB
regulatory region, thereby derepressing the operatively linked a
payload gene or genes and producing the encoding a payload(s).
[0319] In some embodiments, it is advantageous for the genetically
engineered bacteria to express a RNS-sensing transcription factor
that does not regulate the expression of a significant number of
native genes in the bacteria. In some embodiments, the genetically
engineered bacterium of the invention expresses a RNS-sensing
transcription factor from a different species, strain, or substrain
of bacteria, wherein the transcription factor does not bind to
regulatory sequences in the genetically engineered bacterium of the
invention. In some embodiments, the genetically engineered
bacterium of the invention is Escherichia coli, and the RNS-sensing
transcription factor is NsrR, e.g., from is Neisseria gonorrhoeae,
wherein the Escherichia coli does not comprise binding sites for
said NsrR. In some embodiments, the heterologous transcription
factor minimizes or eliminates off-target effects on endogenous
regulatory regions and genes in the genetically engineered
bacteria.
[0320] In some embodiments, the tunable regulatory region is a
RNS-repressible regulatory region, and binding of a corresponding
transcription factor represses downstream gene expression; in the
presence of RNS, the transcription factor senses RNS and binds to
the RNS-repressible regulatory region, thereby repressing
expression of the operatively linked gene or gene cassette. In some
embodiments, the RNS-sensing transcription factor is capable of
binding to a regulatory region that overlaps with part of the
promoter sequence. In alternate embodiments, the RNS-sensing
transcription factor is capable of binding to a regulatory region
that is upstream or downstream of the promoter sequence.
[0321] In these embodiments, the genetically engineered bacteria
may comprise a two repressor activation regulatory circuit, which
is used to express a payload. The two repressor activation
regulatory circuit comprises a first RNS-sensing repressor and a
second repressor, which is operatively linked to a gene or gene
cassette, e.g., encoding a payload. In one aspect of these
embodiments, the RNS-sensing repressor inhibits transcription of
the second repressor, which inhibits the transcription of the gene
or gene cassette. Examples of second repressors useful in these
embodiments include, but are not limited to, TetR, C1, and LexA. In
the absence of binding by the first repressor (which occurs in the
absence of RNS), the second repressor is transcribed, which
represses expression of the gene or genes. In the presence of
binding by the first repressor (which occurs in the presence of
RNS), expression of the second repressor is repressed, and the gene
or genes, e.g., a payload gene or genes is expressed.
[0322] A RNS-responsive transcription factor may induce, derepress,
or repress gene expression depending upon the regulatory region
sequence used in the genetically engineered bacteria. One or more
types of RNS-sensing transcription factors and corresponding
regulatory region sequences may be present in genetically
engineered bacteria. In some embodiments, the genetically
engineered bacteria comprise one type of RNS-sensing transcription
factor, e.g., NsrR, and one corresponding regulatory region
sequence, e.g., from norB. In some embodiments, the genetically
engineered bacteria comprise one type of RNS-sensing transcription
factor, e.g., NsrR, and two or more different corresponding
regulatory region sequences, e.g., from norB and aniA. In some
embodiments, the genetically engineered bacteria comprise two or
more types of RNS-sensing transcription factors, e.g., NsrR and
NorR, and two or more corresponding regulatory region sequences,
e.g., from norB and norR, respectively. One RNS-responsive
regulatory region may be capable of binding more than one
transcription factor. In some embodiments, the genetically
engineered bacteria comprise two or more types of RNS-sensing
transcription factors and one corresponding regulatory region
sequence. Nucleic acid sequences of several RNS-regulated
regulatory regions are known in the art (see, e.g., Spiro 2006;
Isabella et al., 2009; Dunn et al., 2010; Vine et al., 2011;
Karlinsey et al., 2012).
[0323] In some embodiments, the genetically engineered bacteria of
the invention comprise a gene encoding a RNS-sensing transcription
factor, e.g., the nsrR gene, that is controlled by its native
promoter, an inducible promoter, a promoter that is stronger than
the native promoter, e.g., the GlnRS promoter or the P(Bla)
promoter, or a constitutive promoter. In some instances, it may be
advantageous to express the RNS-sensing transcription factor under
the control of an inducible promoter in order to enhance expression
stability. In some embodiments, expression of the RNS-sensing
transcription factor is controlled by a different promoter than the
promoter that controls expression of the therapeutic molecule. In
some embodiments, expression of the RNS-sensing transcription
factor is controlled by the same promoter that controls expression
of the therapeutic molecule. In some embodiments, the RNS-sensing
transcription factor and therapeutic molecule are divergently
transcribed from a promoter region.
[0324] In some embodiments, the genetically engineered bacteria of
the invention comprise a gene for a RNS-sensing transcription
factor from a different species, strain, or substrain of bacteria.
In some embodiments, the genetically engineered bacteria comprise a
RNS-responsive regulatory region from a different species, strain,
or substrain of bacteria. In some embodiments, the genetically
engineered bacteria comprise a RNS-sensing transcription factor and
corresponding RNS-responsive regulatory region from a different
species, strain, or substrain of bacteria. The heterologous
RNS-sensing transcription factor and regulatory region may increase
the transcription of genes operatively linked to said regulatory
region in the presence of RNS, as compared to the native
transcription factor and regulatory region from bacteria of the
same subtype under the same conditions.
[0325] In some embodiments, the genetically engineered bacteria
comprise a RNS-sensing transcription factor, NsrR, and
corresponding regulatory region, nsrR, from Neisseria gonorrhoeae.
In some embodiments, the native RNS-sensing transcription factor,
e.g., NsrR, is left intact and retains wild-type activity. In
alternate embodiments, the native RNS-sensing transcription factor,
e.g., NsrR, is deleted or mutated to reduce or eliminate wild-type
activity.
[0326] In some embodiments, the genetically engineered bacteria of
the invention comprise multiple copies of the endogenous gene
encoding the RNS-sensing transcription factor, e.g., the nsrR gene.
In some embodiments, the gene encoding the RNS-sensing
transcription factor is present on a plasmid. In some embodiments,
the gene encoding the RNS-sensing transcription factor and the gene
or gene cassette for producing the therapeutic molecule are present
on different plasmids. In some embodiments, the gene encoding the
RNS-sensing transcription factor and the gene or gene cassette for
producing the therapeutic molecule are present on the same plasmid.
In some embodiments, the gene encoding the RNS-sensing
transcription factor is present on a chromosome. In some
embodiments, the gene encoding the RNS-sensing transcription factor
and the gene or gene cassette for producing the therapeutic
molecule are present on different chromosomes. In some embodiments,
the gene encoding the RNS-sensing transcription factor and the gene
or gene cassette for producing the therapeutic molecule are present
on the same chromosome.
[0327] In some embodiments, the genetically engineered bacteria
comprise a wild-type gene encoding a RNS-sensing transcription
factor, e.g., the NsrR gene, and a corresponding regulatory region,
e.g., a norB regulatory region, that is mutated relative to the
wild-type regulatory region from bacteria of the same subtype. The
mutated regulatory region increases the expression of the payload
in the presence of RNS, as compared to the wild-type regulatory
region under the same conditions. In some embodiments, the
genetically engineered bacteria comprise a wild-type RNS-responsive
regulatory region, e.g., the norB regulatory region, and a
corresponding transcription factor, e.g., NsrR, that is mutated
relative to the wild-type transcription factor from bacteria of the
same subtype. The mutant transcription factor increases the
expression of the payload in the presence of RNS, as compared to
the wild-type transcription factor under the same conditions. In
some embodiments, both the RNS-sensing transcription factor and
corresponding regulatory region are mutated relative to the
wild-type sequences from bacteria of the same subtype in order to
increase expression of the payload in the presence of RNS.
[0328] In some embodiments, the gene or gene cassette for producing
the anti-inflammation and/or gut barrier function enhancer molecule
is present on a plasmid and operably linked to a promoter that is
induced by RNS. In some embodiments, expression is further
optimized by methods known in the art, e.g., by optimizing
ribosomal binding sites, manipulating transcriptional regulators,
and/or increasing mRNA stability.
[0329] In some embodiments, any of the gene(s) of the present
disclosure may be integrated into the bacterial chromosome at one
or more integration sites. For example, one or more copies of one
or more encoding a payload gene(s) may be integrated into the
bacterial chromosome. Having multiple copies of the gene or gen(s)
integrated into the chromosome allows for greater production of the
payload(s) and also permits fine-tuning of the level of expression.
Alternatively, different circuits described herein, such as any of
the secretion or exporter circuits, in addition to the therapeutic
gene(s) or gene cassette(s) could be integrated into the bacterial
chromosome at one or more different integration sites to perform
multiple different functions.
[0330] ROS-Dependent Regulation
[0331] In some embodiments, the genetically engineered bacteria or
genetically engineered virus comprise a gene for producing a
payload that is expressed under the control of an inducible
promoter. In some embodiments, the genetically engineered bacterium
or genetically engineered virus that expresses a payload under the
control of a promoter that is activated by conditions of cellular
damage. In one embodiment, the gene for producing the payload is
expressed under the control of an cellular damaged-dependent
promoter that is activated in environments in which there is
cellular or tissue damage, e.g., a reactive oxygen species or ROS
promoter.
[0332] As used herein, "reactive oxygen species" and "ROS" are used
interchangeably to refer to highly active molecules, ions, and/or
radicals derived from molecular oxygen. ROS can be produced as
byproducts of aerobic respiration or metal-catalyzed oxidation and
may cause deleterious cellular effects such as oxidative damage.
ROS includes, but is not limited to, hydrogen peroxide (H2O2),
organic peroxide (ROOH), hydroxyl ion (OH--), hydroxyl radical
(.OH), superoxide or superoxide anion (.O2-), singlet oxygen (1O2),
ozone (O3), carbonate radical, peroxide or peroxyl radical (.O2-2),
hypochlorous acid (HOCl), hypochlorite ion (OCl--), sodium
hypochlorite (NaOCl), nitric oxide (NO.), and peroxynitrite or
peroxynitrite anion (ONOO--) (unpaired electrons denoted by .).
Bacteria have evolved transcription factors that are capable of
sensing ROS levels. Different ROS signaling pathways are triggered
by different ROS levels and occur with different kinetics (Marinho
et al., 2014).
[0333] As used herein, "ROS-inducible regulatory region" refers to
a nucleic acid sequence to which one or more ROS-sensing
transcription factors is capable of binding, wherein the binding
and/or activation of the corresponding transcription factor
activates downstream gene expression; in the presence of ROS, the
transcription factor binds to and/or activates the regulatory
region. In some embodiments, the ROS-inducible regulatory region
comprises a promoter sequence. In some embodiments, the
transcription factor senses ROS and subsequently binds to the
ROS-inducible regulatory region, thereby activating downstream gene
expression. In alternate embodiments, the transcription factor is
bound to the ROS-inducible regulatory region in the absence of ROS;
in the presence of ROS, the transcription factor undergoes a
conformational change, thereby activating downstream gene
expression. The ROS-inducible regulatory region may be operatively
linked to a gene sequence or gene sequence, e.g., a sequence or
sequences encoding one or more payload(s). For example, in the
presence of ROS, a transcription factor, e.g., OxyR, senses ROS and
activates a corresponding ROS-inducible regulatory region, thereby
driving expression of an operatively linked gene sequence or gene
sequences. Thus, ROS induces expression of the gene or genes.
[0334] As used herein, "ROS-derepressible regulatory region" refers
to a nucleic acid sequence to which one or more ROS-sensing
transcription factors is capable of binding, wherein the binding of
the corresponding transcription factor represses downstream gene
expression; in the presence of ROS, the transcription factor does
not bind to and does not repress the regulatory region. In some
embodiments, the ROS-derepressible regulatory region comprises a
promoter sequence. The ROS-derepressible regulatory region may be
operatively linked to a gene or genes, e.g., one or more genes
encoding one or more payload(s). For example, in the presence of
ROS, a transcription factor, e.g., OhrR, senses ROS and no longer
binds to and/or represses the regulatory region, thereby
derepressing an operatively linked gene sequence or gene cassette.
Thus, ROS derepresses expression of the gene or gene cassette.
[0335] As used herein, "ROS-repressible regulatory region" refers
to a nucleic acid sequence to which one or more ROS-sensing
transcription factors is capable of binding, wherein the binding of
the corresponding transcription factor represses downstream gene
expression; in the presence of ROS, the transcription factor binds
to and represses the regulatory region. In some embodiments, the
ROS-repressible regulatory region comprises a promoter sequence. In
some embodiments, the transcription factor that senses ROS is
capable of binding to a regulatory region that overlaps with part
of the promoter sequence. In alternate embodiments, the
transcription factor that senses ROS is capable of binding to a
regulatory region that is upstream or downstream of the promoter
sequence. The ROS-repressible regulatory region may be operatively
linked to a gene sequence or gene sequences. For example, in the
presence of ROS, a transcription factor, e.g., PerR, senses ROS and
binds to a corresponding ROS-repressible regulatory region, thereby
blocking expression of an operatively linked gene sequence or gene
sequences. Thus, ROS represses expression of the gene or genes.
[0336] As used herein, a "ROS-responsive regulatory region" refers
to a ROS-inducible regulatory region, a ROS-repressible regulatory
region, and/or a ROS-derepressible regulatory region. In some
embodiments, the ROS-responsive regulatory region comprises a
promoter sequence. Each regulatory region is capable of binding at
least one corresponding ROS-sensing transcription factor. Examples
of transcription factors that sense ROS and their corresponding
ROS-responsive genes, promoters, and/or regulatory regions include,
but are not limited to, those shown in Table B.
TABLE-US-00017 TABLE B Examples of ROS-sensing transcription
factors and ROS-responsive genes ROS-sensing Primarily
transcription capable of Examples of responsive genes, factor:
sensing: promoters, and/or regulatory regions: OxyR H.sub.2O.sub.2
ahpC; ahpF; dps; dsbG; fhuF; flu; fur; gor; grxA; hemH; katG; oxyS;
sufA; sufB; sufC; sufD; sufE; sufS; trxC; uxuA; yaaA; yaeH; yaiA;
ybjM; ydcH; ydeN; ygaQ; yljA; ytfK PerR H.sub.2O.sub.2 katA; ahpCF;
mrgA; zoaA; fur; hemAXCDBL; srfA OhrR Organic ohrA peroxides NaOCl
SoxR .cndot.O.sub.2.sup.- soxS NO.cndot. (also capable of sensing
H.sub.2O.sub.2) RosR H.sub.2O.sub.2 rbtT; tnp16a; rluC1; tnp5a;
mscL; tnp2d; phoD; tnp15b; pstA; tnp5b; xylC; gabD1; rluC2; cgtS9;
azlC; narKGHJI; rosR
[0337] In some embodiments, the genetically engineered bacteria
comprise a tunable regulatory region that is directly or indirectly
controlled by a transcription factor that is capable of sensing at
least one reactive oxygen species. The tunable regulatory region is
operatively linked to a gene or gene cassette capable of directly
or indirectly driving the expression of a payload, thus controlling
expression of the payload relative to ROS levels. For example, the
tunable regulatory region is a ROS-inducible regulatory region, and
the molecule is a payload; when ROS is present, e.g., in an
inflamed tissue, a ROS-sensing transcription factor binds to and/or
activates the regulatory region and drives expression of the gene
sequence for the payload, thereby producing the payload.
Subsequently, when inflammation is ameliorated, ROS levels are
reduced, and production of the payload is decreased or
eliminated.
[0338] In some embodiments, the tunable regulatory region is a
ROS-inducible regulatory region; in the presence of ROS, a
transcription factor senses ROS and activates the ROS-inducible
regulatory region, thereby driving expression of an operatively
linked gene or gene cassette. In some embodiments, the
transcription factor senses ROS and subsequently binds to the
ROS-inducible regulatory region, thereby activating downstream gene
expression. In alternate embodiments, the transcription factor is
bound to the ROS-inducible regulatory region in the absence of ROS;
when the transcription factor senses ROS, it undergoes a
conformational change, thereby inducing downstream gene
expression.
[0339] In some embodiments, the tunable regulatory region is a
ROS-inducible regulatory region, and the transcription factor that
senses ROS is OxyR. OxyR "functions primarily as a global regulator
of the peroxide stress response" and is capable of regulating
dozens of genes, e.g., "genes involved in H2O2 detoxification
(katE, ahpCF), heme biosynthesis (hem H), reductant supply (grxA,
gor, trxC), thiol-disulfide isomerization (dsbG), Fe--S center
repair (sufA-E, sufS), iron binding (yaaA), repression of iron
import systems (fur)" and "OxyS, a small regulatory RNA" (Dubbs et
al., 2012). The genetically engineered bacteria may comprise any
suitable ROS-responsive regulatory region from a gene that is
activated by OxyR. Genes that are capable of being activated by
OxyR are known in the art (see, e.g., Zheng et al., 2001; Dubbs et
al., 2012). In certain embodiments, the genetically engineered
bacteria of the invention comprise a ROS-inducible regulatory
region from oxyS that is operatively linked to a gene, e.g., a
payload gene. In the presence of ROS, e.g., H2O2, an OxyR
transcription factor senses ROS and activates to the oxyS
regulatory region, thereby driving expression of the operatively
linked payload gene and producing the payload. In some embodiments,
OxyR is encoded by an E. coli oxyR gene. In some embodiments, the
oxyS regulatory region is an E. coli oxyS regulatory region. In
some embodiments, the ROS-inducible regulatory region is selected
from the regulatory region of katG, dps, and ahpC.
[0340] In alternate embodiments, the tunable regulatory region is a
ROS-inducible regulatory region, and the corresponding
transcription factor that senses ROS is SoxR. When SoxR is
"activated by oxidation of its [2Fe-2S] cluster, it increases the
synthesis of SoxS, which then activates its target gene expression"
(Koo et al., 2003). "SoxR is known to respond primarily to
superoxide and nitric oxide" (Koo et al., 2003), and is also
capable of responding to H2O2. The genetically engineered bacteria
of the invention may comprise any suitable ROS-responsive
regulatory region from a gene that is activated by SoxR. Genes that
are capable of being activated by SoxR are known in the art (see,
e.g., Koo et al., 2003). In certain embodiments, the genetically
engineered bacteria of the invention comprise a ROS-inducible
regulatory region from soxS that is operatively linked to a gene,
e.g., a payload. In the presence of ROS, the SoxR transcription
factor senses ROS and activates the soxS regulatory region, thereby
driving expression of the operatively linked a payload gene and
producing the a payload.
[0341] In some embodiments, the tunable regulatory region is a
ROS-derepressible regulatory region, and binding of a corresponding
transcription factor represses downstream gene expression; in the
presence of ROS, the transcription factor no longer binds to the
regulatory region, thereby derepressing the operatively linked gene
or gene cassette.
[0342] In some embodiments, the tunable regulatory region is a
ROS-derepressible regulatory region, and the transcription factor
that senses ROS is OhrR. OhrR "binds to a pair of inverted repeat
DNA sequences overlapping the ohrA promoter site and thereby
represses the transcription event," but oxidized OhrR is "unable to
bind its DNA target" (Duarte et al., 2010). OhrR is a
"transcriptional repressor [that] . . . senses both organic
peroxides and NaOCl" (Dubbs et al., 2012) and is "weakly activated
by H2O2 but it shows much higher reactivity for organic
hydroperoxides" (Duarte et al., 2010). The genetically engineered
bacteria of the invention may comprise any suitable ROS-responsive
regulatory region from a gene that is repressed by OhrR. Genes that
are capable of being repressed by OhrR are known in the art (see,
e.g., Dubbs et al., 2012). In certain embodiments, the genetically
engineered bacteria of the invention comprise a ROS-derepressible
regulatory region from ohrA that is operatively linked to a gene or
gene cassette, e.g., a payload gene. In the presence of ROS, e.g.,
NaOCl, an OhrR transcription factor senses ROS and no longer binds
to the ohrA regulatory region, thereby derepressing the operatively
linked payload gene and producing the payload.
[0343] OhrR is a member of the MarR family of ROS-responsive
regulators. "Most members of the MarR family are transcriptional
repressors and often bind to the -10 or -35 region in the promoter
causing a steric inhibition of RNA polymerase binding" (Bussmann et
al., 2010). Other members of this family are known in the art and
include, but are not limited to, OspR, MgrA, RosR, and SarZ. In
some embodiments, the transcription factor that senses ROS is OspR,
MgRA, RosR, and/or SarZ, and the genetically engineered bacteria of
the invention comprises one or more corresponding regulatory region
sequences from a gene that is repressed by OspR, MgRA, RosR, and/or
SarZ. Genes that are capable of being repressed by OspR, MgRA,
RosR, and/or SarZ are known in the art (see, e.g., Dubbs et al.,
2012).
[0344] In some embodiments, the tunable regulatory region is a
ROS-derepressible regulatory region, and the corresponding
transcription factor that senses ROS is RosR. RosR is "a MarR-type
transcriptional regulator" that binds to an "18-bp inverted repeat
with the consensus sequence TTGTTGAYRYRTCAACWA" (SEQ ID NO: 122)
and is "reversibly inhibited by the oxidant H2O2" (Bussmann et al.,
2010). RosR is capable of repressing numerous genes and putative
genes, including but not limited to "a putative
polyisoprenoid-binding protein (cg1322, gene upstream of and
divergent from rosR), a sensory histidine kinase (cgtS9), a
putative transcriptional regulator of the Crp/FNR family (cg3291),
a protein of the glutathione S-transferase family (cg1426), two
putative FMN reductases (cg1150 and cg1850), and four putative
monooxygenases (cg0823, cg1848, cg2329, and cg3084)" (Bussmann et
al., 2010). The genetically engineered bacteria of the invention
may comprise any suitable ROS-responsive regulatory region from a
gene that is repressed by RosR. Genes that are capable of being
repressed by RosR are known in the art (see, e.g., Bussmann et al.,
2010). In certain embodiments, the genetically engineered bacteria
of the invention comprise a ROS-derepressible regulatory region
from cgtS9 that is operatively linked to a gene or gene cassette,
e.g., a payload. In the presence of ROS, e.g., H2O2, a RosR
transcription factor senses ROS and no longer binds to the cgtS9
regulatory region, thereby derepressing the operatively linked
payload gene and producing the payload.
[0345] In some embodiments, it is advantageous for the genetically
engineered bacteria to express a ROS-sensing transcription factor
that does not regulate the expression of a significant number of
native genes in the bacteria. In some embodiments, the genetically
engineered bacterium of the invention expresses a ROS-sensing
transcription factor from a different species, strain, or substrain
of bacteria, wherein the transcription factor does not bind to
regulatory sequences in the genetically engineered bacterium of the
invention. In some embodiments, the genetically engineered
bacterium of the invention is Escherichia coli, and the ROS-sensing
transcription factor is RosR, e.g., from Corynebacterium
glutamicum, wherein the Escherichia coli does not comprise binding
sites for said RosR. In some embodiments, the heterologous
transcription factor minimizes or eliminates off-target effects on
endogenous regulatory regions and genes in the genetically
engineered bacteria.
[0346] In some embodiments, the tunable regulatory region is a
ROS-repressible regulatory region, and binding of a corresponding
transcription factor represses downstream gene expression; in the
presence of ROS, the transcription factor senses ROS and binds to
the ROS-repressible regulatory region, thereby repressing
expression of the operatively linked gene or gene cassette. In some
embodiments, the ROS-sensing transcription factor is capable of
binding to a regulatory region that overlaps with part of the
promoter sequence. In alternate embodiments, the ROS-sensing
transcription factor is capable of binding to a regulatory region
that is upstream or downstream of the promoter sequence.
[0347] In some embodiments, the tunable regulatory region is a
ROS-repressible regulatory region, and the transcription factor
that senses ROS is PerR. In Bacillus subtilis, PerR "when bound to
DNA, represses the genes coding for proteins involved in the
oxidative stress response (katA, ahpC, and mrgA), metal homeostasis
(hemAXCDBL, fur, and zoaA) and its own synthesis (perR)" (Marinho
et al., 2014). PerR is a "global regulator that responds primarily
to H2O2" (Dubbs et al., 2012) and "interacts with DNA at the per
box, a specific palindromic consensus sequence (TTATAATNATTATAA)
(SEQ ID NO: 123) residing within and near the promoter sequences of
PerR-controlled genes" (Marinho et al., 2014). PerR is capable of
binding a regulatory region that "overlaps part of the promoter or
is immediately downstream from it" (Dubbs et al., 2012). The
genetically engineered bacteria of the invention may comprise any
suitable ROS-responsive regulatory region from a gene that is
repressed by PerR. Genes that are capable of being repressed by
PerR are known in the art (see, e.g., Dubbs et al., 2012).
[0348] In these embodiments, the genetically engineered bacteria
may comprise a two repressor activation regulatory circuit, which
is used to express a payload. The two repressor activation
regulatory circuit comprises a first ROS-sensing repressor, e.g.,
PerR, and a second repressor, e.g., TetR, which is operatively
linked to a gene or gene cassette, e.g., a payload. In one aspect
of these embodiments, the ROS-sensing repressor inhibits
transcription of the second repressor, which inhibits the
transcription of the gene or gene cassette. Examples of second
repressors useful in these embodiments include, but are not limited
to, TetR, C1, and LexA. In some embodiments, the ROS-sensing
repressor is PerR. In some embodiments, the second repressor is
TetR. In this embodiment, a PerR-repressible regulatory region
drives expression of TetR, and a TetR-repressible regulatory region
drives expression of the gene or gene cassette, e.g., a payload. In
the absence of PerR binding (which occurs in the absence of ROS),
tetR is transcribed, and TetR represses expression of the gene or
gene cassette, e.g., a payload. In the presence of PerR binding
(which occurs in the presence of ROS), tetR expression is
repressed, and the gene or gene cassette, e.g., a payload, is
expressed.
[0349] A ROS-responsive transcription factor may induce, derepress,
or repress gene expression depending upon the regulatory region
sequence used in the genetically engineered bacteria. For example,
although "OxyR is primarily thought of as a transcriptional
activator under oxidizing conditions . . . OxyR can function as
either a repressor or activator under both oxidizing and reducing
conditions" (Dubbs et al., 2012), and OxyR "has been shown to be a
repressor of its own expression as well as that of fhuF (encoding a
ferric ion reductase) and flu (encoding the antigen 43 outer
membrane protein)" (Zheng et al., 2001). The genetically engineered
bacteria of the invention may comprise any suitable ROS-responsive
regulatory region from a gene that is repressed by OxyR. In some
embodiments, OxyR is used in a two repressor activation regulatory
circuit, as described above. Genes that are capable of being
repressed by OxyR are known in the art (see, e.g., Zheng et al.,
2001). Or, for example, although RosR is capable of repressing a
number of genes, it is also capable of activating certain genes,
e.g., the narKGHJI operon. In some embodiments, the genetically
engineered bacteria comprise any suitable ROS-responsive regulatory
region from a gene that is activated by RosR. In addition,
"PerR-mediated positive regulation has also been observed . . . and
appears to involve PerR binding to distant upstream sites" (Dubbs
et al., 2012). In some embodiments, the genetically engineered
bacteria comprise any suitable ROS-responsive regulatory region
from a gene that is activated by PerR.
[0350] One or more types of ROS-sensing transcription factors and
corresponding regulatory region sequences may be present in
genetically engineered bacteria. For example, "OhrR is found in
both Gram-positive and Gram-negative bacteria and can 0 with either
OxyR or PerR or both" (Dubbs et al., 2012). In some embodiments,
the genetically engineered bacteria comprise one type of
ROS-sensing transcription factor, e.g., OxyR, and one corresponding
regulatory region sequence, e.g., from oxyS. In some embodiments,
the genetically engineered bacteria comprise one type of
ROS-sensing transcription factor, e.g., OxyR, and two or more
different corresponding regulatory region sequences, e.g., from
oxyS and katG. In some embodiments, the genetically engineered
bacteria comprise two or more types of ROS-sensing transcription
factors, e.g., OxyR and PerR, and two or more corresponding
regulatory region sequences, e.g., from oxyS and katA,
respectively. One ROS-responsive regulatory region may be capable
of binding more than one transcription factor. In some embodiments,
the genetically engineered bacteria comprise two or more types of
ROS-sensing transcription factors and one corresponding regulatory
region sequence.
[0351] Nucleic acid sequences of several exemplary OxyR-regulated
regulatory regions are shown in Table C. OxyR binding sites are
underlined and bolded. In some embodiments, genetically engineered
bacteria comprise a nucleic acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the DNA sequence of SEQ ID NO: 63,
64, 65, or 66, or a functional fragment thereof.
TABLE-US-00018 TABLE C Nucleotide sequences of exemplary
OxyR-regulated regulatory regions Regulatory sequence Sequence katG
TGTGGCTTTTATGAAAATCACACAGTGATCACAAATTTTAAACA (SEQ ID NO: 63)
GAGCACAAAATGCTGCCTCGAAATGAGGGCGGGAAAATAAGGT
TATCAGCCTTGTTTTCTCCCTCATTACTTGAAGGATATGAAGCTA
AAACCCTTTTTTATAAAGCATTTGTCCGAATTCGGACATAATCA
AAAAAGCTTAATTAAGATCAATTTGATCTACATCTCTTTAACCA
ACAATATGTAAGATCTCAACTATCGCATCCGTGGATTAATTC
AATTATAACTTCTCTCTAACGCTGTGTATCGTAACGGTAACACT
GTAGAGGGGAGCACATTGATGCGAATTCATTAAAGAGGAGAAA GGTACC dps
TTCCGAAAATTCCTGGCGAGCAGATAAATAAGAATTGTTCTTAT (SEQ ID NO: 64)
CAATATATCTAACTCATTGAATCTTTATTAGTTTTGTTTTTCACG
CTTGTTACCACTATTAGTGTGATAGGAACAGCCAGAATAGCG
GAACACATAGCCGGTGCTATACTTAATCTCGTTAATTACTGGGA
CATAACATCAAGAGGATATGAAATTCGAATTCATTAAAGAGGA GAAAGGTACC ahpC
GCTTAGATCAGGTGATTGCCCTTTGTTTATGAGGGTGTTGTAATC (SEQ ID NO: 65)
CATGTCGTTGTTGCATTTGTAAGGGCAACACCTCAGCCTGCAGG
CAGGCACTGAAGATACCAAAGGGTAGTTCAGATTACACGGTCA
CCTGGAAAGGGGGCCATTTTACTTTTTATCGCCGCTGGCGGTGC
AAAGTTCACAAAGTTGTCTTACGAAGGTTGTAAGGTAAAACTT
ATCGATTTGATAATGGAAACGCATTAGCCGAATCGGCAAAAAT
TGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATG
CGAATTCATTAAAGAGGAGAAAGGTACC oxyS
CTCGAGTTCATTATCCATCCTCCATCGCCACGATAGTTCATGGC (SEQ ID NO: 66)
GATAGGTAGAATAGCAATGAACGATTATCCCTATCAAGCATTC
TGACTGATAATTGCTCACACGAATTCATTAAAGAGGAGAAAGGT ACC
[0352] In some embodiments, the genetically engineered bacteria of
the invention comprise a gene encoding a ROS-sensing transcription
factor, e.g., the oxyR gene, that is controlled by its native
promoter, an inducible promoter, a promoter that is stronger than
the native promoter, e.g., the GlnRS promoter or the P(Bla)
promoter, or a constitutive promoter. In some instances, it may be
advantageous to express the ROS-sensing transcription factor under
the control of an inducible promoter in order to enhance expression
stability. In some embodiments, expression of the ROS-sensing
transcription factor is controlled by a different promoter than the
promoter that controls expression of the therapeutic molecule. In
some embodiments, expression of the ROS-sensing transcription
factor is controlled by the same promoter that controls expression
of the therapeutic molecule. In some embodiments, the ROS-sensing
transcription factor and therapeutic molecule are divergently
transcribed from a promoter region.
[0353] In some embodiments, the genetically engineered bacteria of
the invention comprise a gene for a ROS-sensing transcription
factor from a different species, strain, or substrain of bacteria.
In some embodiments, the genetically engineered bacteria comprise a
ROS-responsive regulatory region from a different species, strain,
or substrain of bacteria. In some embodiments, the genetically
engineered bacteria comprise a ROS-sensing transcription factor and
corresponding ROS-responsive regulatory region from a different
species, strain, or substrain of bacteria. The heterologous
ROS-sensing transcription factor and regulatory region may increase
the transcription of genes operatively linked to said regulatory
region in the presence of ROS, as compared to the native
transcription factor and regulatory region from bacteria of the
same subtype under the same conditions.
[0354] In some embodiments, the genetically engineered bacteria
comprise a ROS-sensing transcription factor, OxyR, and
corresponding regulatory region, oxyS, from Escherichia coli. In
some embodiments, the native ROS-sensing transcription factor,
e.g., OxyR, is left intact and retains wild-type activity. In
alternate embodiments, the native ROS-sensing transcription factor,
e.g., OxyR, is deleted or mutated to reduce or eliminate wild-type
activity.
[0355] In some embodiments, the genetically engineered bacteria of
the invention comprise multiple copies of the endogenous gene
encoding the ROS-sensing transcription factor, e.g., the oxyR gene.
In some embodiments, the gene encoding the ROS-sensing
transcription factor is present on a plasmid. In some embodiments,
the gene encoding the ROS-sensing transcription factor and the gene
or gene cassette for producing the therapeutic molecule are present
on different plasmids. In some embodiments, the gene encoding the
ROS-sensing transcription factor and the gene or gene cassette for
producing the therapeutic molecule are present on the same. In some
embodiments, the gene encoding the ROS-sensing transcription factor
is present on a chromosome. In some embodiments, the gene encoding
the ROS-sensing transcription factor and the gene or gene cassette
for producing the therapeutic molecule are present on different
chromosomes. In some embodiments, the gene encoding the ROS-sensing
transcription factor and the gene or gene cassette for producing
the therapeutic molecule are present on the same chromosome.
[0356] In some embodiments, the genetically engineered bacteria
comprise a wild-type gene encoding a ROS-sensing transcription
factor, e.g., the soxR gene, and a corresponding regulatory region,
e.g., a soxS regulatory region, that is mutated relative to the
wild-type regulatory region from bacteria of the same subtype. The
mutated regulatory region increases the expression of the payload
in the presence of ROS, as compared to the wild-type regulatory
region under the same conditions. In some embodiments, the
genetically engineered bacteria comprise a wild-type ROS-responsive
regulatory region, e.g., the oxyS regulatory region, and a
corresponding transcription factor, e.g., OxyR, that is mutated
relative to the wild-type transcription factor from bacteria of the
same subtype. The mutant transcription factor increases the
expression of the payload in the presence of ROS, as compared to
the wild-type transcription factor under the same conditions. In
some embodiments, both the ROS-sensing transcription factor and
corresponding regulatory region are mutated relative to the
wild-type sequences from bacteria of the same subtype in order to
increase expression of the payload in the presence of ROS.
[0357] In some embodiments, the gene or gene cassette for producing
the payload is present on a plasmid and operably linked to a
promoter that is induced by ROS. In some embodiments, the gene or
gene cassette for producing the payload is present in the
chromosome and operably linked to a promoter that is induced by
ROS. In some embodiments, the gene or gene cassette for producing
the payload is present on a chromosome and operably linked to a
promoter that is induced by exposure to tetracycline. In some
embodiments, the gene or gene cassette for producing the payload is
present on a plasmid and operably linked to a promoter that is
induced by exposure to tetracycline. In some embodiments,
expression is further optimized by methods known in the art, e.g.,
by optimizing ribosomal binding sites, manipulating transcriptional
regulators, and/or increasing mRNA stability.
[0358] In some embodiments, the genetically engineered bacteria may
comprise multiple copies of the gene(s) capable of producing a
payload(s). In some embodiments, the gene(s) capable of producing a
payload(s) is present on a plasmid and operatively linked to a
ROS-responsive regulatory region. In some embodiments, the gene(s)
capable of producing a payload is present in a chromosome and
operatively linked to a ROS-responsive regulatory region.
[0359] Thus, in some embodiments, the genetically engineered
bacteria or genetically engineered virus produce one or more
payloads under the control of an oxygen level-dependent promoter, a
reactive oxygen species (ROS)-dependent promoter, or a reactive
nitrogen species (RNS)-dependent promoter, and a corresponding
transcription factor.
[0360] In some embodiments, the genetically engineered bacteria
comprise a stably maintained plasmid or chromosome carrying a gene
for producing a payload, such that the payload can be expressed in
the host cell, and the host cell is capable of survival and/or
growth in vitro, e.g., in medium, and/or in vivo. In some
embodiments, a bacterium may comprise multiple copies of the gene
encoding the payload. In some embodiments, the gene encoding the
payload is expressed on a low-copy plasmid. In some embodiments,
the low-copy plasmid may be useful for increasing stability of
expression. In some embodiments, the low-copy plasmid may be useful
for decreasing leaky expression under non-inducing conditions. In
some embodiments, the gene encoding the payload is expressed on a
high-copy plasmid. In some embodiments, the high-copy plasmid may
be useful for increasing expression of the payload. In some
embodiments, the gene encoding the payload is expressed on a
chromosome.
[0361] In some embodiments, the bacteria are genetically engineered
to include multiple mechanisms of action (MOAs), e.g., circuits
producing multiple copies of the same product (e.g., to enhance
copy number) or circuits performing multiple different functions.
For example, the genetically engineered bacteria may include four
copies of the gene encoding a particular payload inserted at four
different insertion sites. Alternatively, the genetically
engineered bacteria may include three copies of the gene encoding a
particular payload inserted at three different insertion sites and
three copies of the gene encoding a different payload inserted at
three different insertion sites.
[0362] In some embodiments, under conditions where the payload is
expressed, the genetically engineered bacteria of the disclosure
produce at least about 1.5-fold, at least about 2-fold, at least
about 10-fold, at least about 15-fold, at least about 20-fold, at
least about 30-fold, at least about 50-fold, at least about
100-fold, at least about 200-fold, at least about 300-fold, at
least about 400-fold, at least about 500-fold, at least about
600-fold, at least about 700-fold, at least about 800-fold, at
least about 900-fold, at least about 1,000-fold, or at least about
1,500-fold more of the payload, and/or transcript of the gene(s) in
the operon as compared to unmodified bacteria of the same subtype
under the same conditions.
[0363] In some embodiments, quantitative PCR (qPCR) is used to
amplify, detect, and/or quantify mRNA expression levels of the
payload gene(s). Primers specific for payload the gene(s) may be
designed and used to detect mRNA in a sample according to methods
known in the art. In some embodiments, a fluorophore is added to a
sample reaction mixture that may contain payload mRNA, and a
thermal cycler is used to illuminate the sample reaction mixture
with a specific wavelength of light and detect the subsequent
emission by the fluorophore. The reaction mixture is heated and
cooled to predetermined temperatures for predetermined time
periods. In certain embodiments, the heating and cooling is
repeated for a predetermined number of cycles. In some embodiments,
the reaction mixture is heated and cooled to 90-100.degree. C.,
60-70.degree. C., and 30-50.degree. C. for a predetermined number
of cycles. In a certain embodiment, the reaction mixture is heated
and cooled to 93-97.degree. C., 55-65.degree. C., and 35-45.degree.
C. for a predetermined number of cycles. In some embodiments, the
accumulating amplicon is quantified after each cycle of the qPCR.
The number of cycles at which fluorescence exceeds the threshold is
the threshold cycle (CT). At least one CT result for each sample is
generated, and the CT result(s) may be used to determine mRNA
expression levels of the payload gene(s).
[0364] In some embodiments, quantitative PCR (qPCR) is used to
amplify, detect, and/or quantify mRNA expression levels of the
payload gene(s). Primers specific for payload the gene(s) may be
designed and used to detect mRNA in a sample according to methods
known in the art. In some embodiments, a fluorophore is added to a
sample reaction mixture that may contain payload mRNA, and a
thermal cycler is used to illuminate the sample reaction mixture
with a specific wavelength of light and detect the subsequent
emission by the fluorophore. The reaction mixture is heated and
cooled to predetermined temperatures for predetermined time
periods. In certain embodiments, the heating and cooling is
repeated for a predetermined number of cycles. In some embodiments,
the reaction mixture is heated and cooled to 90-100.degree. C.,
60-70.degree. C., and 30-50.degree. C. for a predetermined number
of cycles. In a certain embodiment, the reaction mixture is heated
and cooled to 93-97.degree. C., 55-65.degree. C., and 35-45.degree.
C. for a predetermined number of cycles. In some embodiments, the
accumulating amplicon is quantified after each cycle of the qPCR.
The number of cycles at which fluorescence exceeds the threshold is
the threshold cycle (CT). At least one CT result for each sample is
generated, and the CT result(s) may be used to determine mRNA
expression levels of the payload gene(s).
[0365] Multiple Mechanisms of Action
[0366] In some embodiments, the bacteria are genetically engineered
to include multiple mechanisms of action (MoAs), e.g., circuits
producing multiple copies of the same product or circuits
performing multiple different functions. Examples of insertion
sites include, but are not limited to, malE/K, insB/I, araC/BAD,
lacZ, dapA, cea, and other shown in FIG. 18. For example, the
genetically engineered bacteria may include four copies of
argA.sup.fbr inserted at four different insertion sites, e.g.,
malE/K, insB/I, araC/BAD, and lacZ. Alternatively, the genetically
engineered bacteria may include three copies of argA.sup.fbr
inserted at three different insertion sites, e.g., malE/K, insB/I,
and lacZ, and three mutant arginine regulons, e.g., two producing
citrulline and one producing arginine, inserted at three different
insertion sites dapA, cea, and araC/BAD. In some embodiments, the
genetically engineered bacteria may include one or more ammonia
conversion circuit(s) inserted at one or more different insertion
sites and one or more additional circuits inserted at one or more
other insertion sites. For example, the genetically engineered
bacteria may include one or more copies of argA.sup.fbr (and/or
other ammonia conversion circuit(s)) inserted at one or more
different insertion sites, and one or more gut barrier enhancing
circuits, e.g., one or more butyrate production circuit(s) (or
other gut barrier enhancing circuit(s)) at other insertion sites.
In other exemplary embodiments, the genetically engineered bacteria
may include one or more copies of argA.sup.fbr and/or other ammonia
conversion circuit(s)) inserted at one or more different insertion
sites, and one or more GABA reducing circuits, e.g., GABA transport
and/or GABA metabolic circuit(s), inserted at other insertion
site(s). In other exemplary embodiments, the genetically engineered
bacteria may include one or more copies of argA.sup.fbr (and/or
other ammonia conversion circuit(s)) inserted at one or more
different insertion sites, and one or more manganese transport
circuit(s) inserted at other insertion sites (FIG. 47A). In some
embodiments, one or more ammonia conversion circuit(s) (e.g.,
argA.sup.fbr and/or other ammonia conversion circuit(s)), one or
more gut barrier enhancing circuit (e.g., butyrate, propionate,
acetate biosynthetic circuit(s)), one or more GABA reducing
circuit(s) (e.g., GABA transport and/or GABA metabolic circuit),
and one or more manganese transport circuit(s) are inserted at four
or more different chromosomal insertion sites (e.g., FIG. 45). In
some embodiments, an ammonia conversion circuit, a gut barrier
enhancing circuit, a GABA transport and/or GABA metabolic circuit
are inserted at three different chromosomal insertion sites. In
some embodiments, an ammonia conversion circuit, a GABA
transport/metabolic circuit, and a manganese transport circuit are
inserted at three different chromosomal insertion sites (FIG. 46B).
In other embodiments, an ammonia conversion circuit, and a
manganese transport circuit are inserted at two different
chromosomal insertion sites (FIG. 47A). In still other embodiments,
an ammonia conversion circuit, and a GABA transport and/or GABA
metabolic circuit are inserted at two different chromosomal
insertion sites. In still other embodiments, an ammonia conversion
circuit, and a gut barrier enhancing circuit are inserted at two
different chromosomal insertion sites. In still other embodiments,
an ammonia conversion circuit, and a manganese reducing circuit are
inserted at two different chromosomal insertion sites.
[0367] Table 14 lists non-limiting examples of embodiments of the
disclosure.
TABLE-US-00019 TABLE 14 Non-limiting examples of embodiments of the
disclosure Anti- Code Name ARG box ArgR argA.sup.fb ThyA biotic
Other Control Strains SYN- Wild type Wild type none Wild Strep none
UCD103 ARG Box ArgR type ThyA SYN- Wild type Wild type none Wild
Kan none UCD107 ARG Box ArgR type ThyA .DELTA.ARG box SYN-
.DELTA.ARG box Wild type none Wild none none UCD101 ArgR type ThyA
SYN- .DELTA.ARG box Wild type tetracycline- Wild Amp none UCD102
ArgR inducible type argA.sup.fbr on a ThyA low copy plasmid SYN-
.DELTA.ARG box Wild type tetracycline- Wild Amp, Inducible UCD104
ArgR inducible type Cam ArgG argA.sup.fbr on a ThyA low copy
plasmid (Amp) SYN- .DELTA.ARG box Wild type tetracycline- Wild Amp
constitutively UCD105 ArgR inducible type expressed argA.sup.fbr on
a ThyA argG low copy (BBa_J23100 plasmid constitutive (Amp)
promoter) .DELTA.ArgR SYN- Wild type .DELTA.ArgR none .DELTA.ThyA
Cam none UCD106 ARG Box SYN- Wild type .DELTA.ArgR none Wild none
none UCD201/ ARG Box type SYN- ThyA UCD312 SYN- Wild type
.DELTA.ArgR tetracycline- Wild Amp none UCD202 ARG Box inducible
type argAfbr on a ThyA high-copy plasmid (Amp) SYN- Wild type
.DELTA.ArgR tetracycline- Wild Amp none UCD203 ARG Box inducible
type argAfbr on a ThyA low-copy plasmid (Amp) SYN- Wild type
.DELTA.ArgR tet-ArgAfbr Wild Amp none UCD204 ARG Box on a low- type
copy plasmid ThyA (Amp) SYN- Wild type .DELTA.ArgR PfnrS- Wild Amp
none UCD205 ARG Box ArgAfbr on a type low-copy ThyA plasmid (Amp)
SYN- Wild type .DELTA.ArgR PfnrS- .DELTA.ThyA Amp, none UCD206 ARG
Box ArgAfbr on a Cam low-copy plasmid (Amp) Integrated FNRS-argAfbr
SYN- Wild type .DELTA.ArgR PfnrS- Wild Cam none UCD301 ARG Box
ArgAfbr type integrated ThyA into the chromosome at the maIEK locus
SYN- Wild type .DELTA.ArgR PfnrS- .DELTA.ThyA Cam none UCD302 ARG
Box ArgAfbr integrated into the chromosome at the maIEK locus SYN-
Wild type .DELTA.ArgR PfnrS- .DELTA.ThyA Kan none UCD303 ARG Box
ArgAfbr integrated into the chromosome at the maIEK locus SYN- Wild
type .DELTA.ArgR PfnrS- .DELTA.ThyA None none UCD305 ARG Box
ArgAfbr integrated into the chromosome at the maIEK locus SYN- Wild
type .DELTA.ArgR PfnrS- Wild None none UCD304 ARG Box ArgAfbr type
integrated ThyA into the chromosome at the maIEK locus SYN- Wild
type .DELTA.ArgR PfnrS- Wild Kan none UCD306 ARG Box ArgAfbr type
integrated ThyA into the chromosome at the maIEK locus SYN- Wild
type Wild type PfnrS- .DELTA.ThyA Kan none UCD307 ARG Box ArgR
ArgAfbr integrated into the chromosome at the maIEK locus SYN- Wild
type Wild type PfnrS- .DELTA.ThyA none none UCD308 ARG Box ArgR
ArgAfbr integrated into the chromosome at the maIEK locus SYN- Wild
type Wild type PfnrS- Wild Kan none UCD309 ARG Box ArgR ArgAfbr
type integrated ThyA into the chromosome at the maIEK locus SYN-
Wild type Wild type PfnrS- Wild none none UCD310 ARG Box ArgR
ArgAfbr type integrated ThyA into the chromosome at the maIEK locus
SYN- Wild type .DELTA.ArgR none Wild Kan none UCD311 ARG Box type
ThyA SYN- Wild type .DELTA.ArgR none Wild none none UCD312/ ARG Box
type SYN- ThyA UCD201 SYN- Wild type .DELTA.ArgR none .DELTA.ThyA
Kan none UCD313 ARG Box SYN- Wild type .DELTA.ArgR none .DELTA.ThyA
none none UCD314 ARG Box Rifaximin resistance SYN- Wild type
.DELTA.ArgR PfnrS- .DELTA.ThyA Kan Rifaximin UCD403 ARG Box ArgAfbr
resistance integrated into the chromosome at the maIEK locus SYN-
Wild type .DELTA.ArgR PfnrS- .DELTA.ThyA None Rifaximin UCD405 ARG
Box ArgAfbr resistance integrated into the chromosome at the maIEK
locus SYN- Wild type .DELTA.ArgR PfnrS- Wild None Rifaximin UCD404
ARG Box ArgAfbr type resistance integrated ThyA into the chromosome
at the maIEK locus SYN- Wild type .DELTA.ArgR PfnrS- Wild Kan
Rifaximin UCD406 ARG Box ArgAfbr type resistance integrated ThyA
into the chromosome at the maIEK locus SYN- Wild type Wild type
PfnrS- .DELTA.ThyA Kan Rifaximin UCD407 ARG Box ArgR ArgAfbr
resistance integrated into the chromosome at the maIEK locus SYN-
Wild type Wild type PfnrS- .DELTA.ThyA none Rifaximin UCD408 ARG
Box ArgR ArgAfbr resistance integrated into the chromosome at the
maIEK locus SYN- Wild type Wild type PfnrS- Wild Kan Rifaximin
UCD409 ARG Box ArgR ArgAfbr type resistance integrated ThyA into
the chromosome at the maIEK locus SYN- Wild type Wild type PfnrS-
Wild none Rifaximin UCD410 ARG Box ArgR ArgAfbr type resistance
integrated ThyA into the chromosome at the maIEK locus SYN- Wild
type .DELTA.ArgR none Wild Kan Rifaximin UCD411 ARG Box type
resistance ThyA SYN- Wild type .DELTA.ArgR none Wild none Rifaximin
UCD412 ARG Box type resistance ThyA SYN- Wild type .DELTA.ArgR none
.DELTA.ThyA Kan Rifaximin UCD413 ARG Box resistance SYN- Wild type
.DELTA.ArgR none .DELTA.ThyA none Rifaximin UCD414 ARG Box
resistance Butyrate Circuits SYN- Wild type Wild none Wild Amp
Logic156 UCD500 ARG Box type type (pSC101 ArgR ThyA PydfZ-Bcd
butyrate plasmid; amp resistance) SYN- Wild type Wild type none
Wild Amp Logic156 UCD501 ARG Box ArgR type (pSC101 ThyA PydfZ-ter
butyrate plasmid; amp resistance) SYN- Wild type Wild type none
Wild None PydfZ-ter UCD502 ARG Box ArgR type butyrate ThyA cassette
integrated on the chromosome SYN- Wild type Wild type none Wild Amp
pLogic031 UCD503 ARG Box ArgR type (bdc2 butyrate ThyA cassette
under control of tet promoter on a plasmid) SYN- Wild type Wild
type none Wild None pLogic046 (ter UCD504 ARG Box ArgR type
butyrate ThyA cassette under control of tet promoter on a plasmid)
SYN- Wild type Wild type none Wild Amp pLOGIC046- UCD505 ARG Box
ArgR type delta.pbt- ThyA buk/tesB+
(tesB butyrate cassette under control of tet promoter on a plasmid)
SYN- Wild type Wild type none Wild Amp Logic156 UCD506 ARG Box ArgR
type (pSC101 nirB- ThyA Bcd butyrate plasmid; amp resistance) SYN-
Wild type Wild type none Wild Amp pLogic031- UCD507 ARG Box ArgR
type nsrR-norB- ThyA butyrate construct SYN- Wild type Wild type
none Wild Amp pLogic046- UCD508 ARG Box ArgR type nsrR-norB- ThyA
butyrate construct SYN- Wild type Wild type none Wild Amp
tesB-butyrate UCD509 ARG Box ArgR type cassette ThyA integrated
into chromosome under control of FNR promoter SYN- Wild type Wild
type none Wild None pLogic031 UCD510 ARG Box ArgR type (bdc2
butyrate ThyA cassette under control of tet promoter on a plasmid);
nuoB deletion SYN- Wild type Wild type none Wild None pLogic046
(ter UCD511 ARG Box ArgR type butyrate ThyA cassette under control
of tet promoter on a plasmid); nuoB deletion Butyrate and Ammonium
Circuits SYN- Wild type .DELTA.ArgR PfnrS- .DELTA.ThyA Amp Logic156
UCD601 ARG Box ArgAfbr (pSC101 integrated PydfZ-ter into the
butyrate chromosome plasmid; amp at the maIEK resistance) locus
SYN- Wild type .DELTA.ArgR PfnrS- .DELTA.ThyA Kan PydfZ-ter UCD603
ARG Box ArgAfbr butyrate integrated cassette into the integrated on
chromosome the at the maIEK chromosome locus SYN- Wild type
.DELTA.ArgR PfnrS- .DELTA.ThyA None PydfZ-ter UCD605 ARG Box
ArgAfbr butyrate integrated cassette into the integrated on
chromosome the at the maIEK chromosome locus SYN- Wild type
.DELTA.ArgR PfnrS- Wild None PydfZ-ter UCD604 ARG Box ArgAfbr type
butyrate integrated ThyA cassette into the integrated on chromosome
the at the maIEK chromosome locus SYN- Wild type .DELTA.ArgR PfnrS-
Wild Kan PydfZ-ter UCD606 ARG Box ArgAfbr type butyrate integrated
ThyA cassette into the integrated on chromosome the at the maIEK
chromosome locus SYN- Wild type Wild type PfnrS- .DELTA.ThyA Kan
PydfZ-ter UCD607 ARG Box ArgR ArgAfbr butyrate integrated cassette
into the integrated on chromosome the at the maIEK chromosome locus
SYN- Wild type Wild type PfnrS- .DELTA.ThyA none PydfZ-ter UCD608
ARG Box ArgR ArgAfbr butyrate integrated cassette into the
integrated on chromosome the at the maIEK chromosome locus SYN-
Wild type Wild type PfnrS- Wild Kan PydfZ-ter UCD609 ARG Box ArgR
ArgAfbr type butyrate integrated ThyA cassette into the integrated
on chromosome the at the maIEK chromosome locus SYN- Wild type Wild
type PfnrS- Wild none PydfZ-ter UCD610 ARG Box ArgR ArgAfbr type
butyrate integrated ThyA cassette into the integrated on chromosome
the at the maIEK chromosome locus SYN- Wild type .DELTA.ArgR none
Wild Kan PydfZ-ter UCD611 ARG Box type butyrate ThyA cassette
integrated on the chromosome SYN- Wild type .DELTA.ArgR none Wild
none PydfZ-ter UCD612 ARG Box type butyrate ThyA cassette
integrated on the chromosome SYN- Wild type .DELTA.ArgR none
.DELTA.ThyA Kan PydfZ-ter UCD613 ARG Box butyrate cassette
integrated on the chromosome SYN- Wild type .DELTA.ArgR none
.DELTA.ThyA none PydfZ-ter UCD614 ARG Box butyrate cassette
integrated on the chromosome SYN- Wild type .DELTA.ArgR PfnrS-
.DELTA.ThyA Kan PydfZ-ter UCD703 ARG Box ArgAfbr butyrate
integrated cassette into the integrated on chromosome the at the
maIEK chromosome; locus Rifaximin resistance SYN- Wild type
.DELTA.ArgR PfnrS- .DELTA.ThyA None PydfZ-ter UCD705 ARG Box
ArgAfbr butyrate integrated cassette into the integrated on
chromosome the at the maIEK chromosome; locus Rifaximin resistance
SYN- Wild type .DELTA.ArgR PfnrS- Wild None PydfZ-ter UCD704 ARG
Box ArgAfbr type butyrate integrated ThyA cassette into the
integrated on chromosome the at the maIEK chromosome; locus
Rifaximin resistance SYN- Wild type .DELTA.ArgR PfnrS- Wild Kan
PydfZ-ter UCD706 ARG Box ArgAfbr type butyrate integrated ThyA
cassette into the integrated on chromosome the at the maIEK
chromosome; locus Rifaximin resistance SYN- Wild type Wild type
PfnrS- .DELTA.ThyA Kan PydfZ-ter UCD707 ARG Box ArgR ArgAfbr
butyrate integrated cassette into the integrated on chromosome the
at the maIEK chromosome; locus Rifaximin resistance SYN- Wild type
Wild type PfnrS- .DELTA.ThyA none PydfZ-ter UCD708 ARG Box ArgR
ArgAfbr butyrate integrated cassette into the integrated on
chromosome the at the maIEK chromosome; locus Rifaximin resistance
SYN- Wild type Wild type PfnrS- Wild Kan PydfZ-ter UCD709 ARG Box
ArgR ArgAfbr type butyrate integrated ThyA cassette into the
integrated on chromosome the at the maIEK chromosome; locus
Rifaximin resistance SYN- Wild type Wild type PfnrS- Wild none
PydfZ-ter UCD710 ARG Box ArgR ArgAfbr type butyrate integrated ThyA
cassette into the integrated on chromosome the at the maIEK
chromosome; locus Rifaximin resistance SYN- Wild type .DELTA.ArgR
none Wild Kan PydfZ-ter UCD711 ARG Box type butyrate ThyA cassette
integrated on the chromosome; Rifaximin resistance SYN- Wild type
.DELTA.ArgR none Wild none PydfZ-ter UCD712 ARG Box type butyrate
ThyA cassette integrated on the chromosome; Rifaximin resistance
SYN- Wild type .DELTA.ArgR none .DELTA.ThyA Kan PydfZ-ter UCD713
ARG Box butyrate cassette integrated on the chromosome; Rifaximin
resistance SYN- Wild type .DELTA.ArgR none .DELTA.ThyA none
PydfZ-ter UCD714 ARG Box butyrate cassette integrated on the
chromosome; Rifaximin resistance SYN- Wild type .DELTA.ArgR PfnrS-
ArgAfbr .DELTA.ThyA Kan tesB-butyrate UCD715 ARG Box integrated
into cassette the integrated into chromosome chromosome at maIEK
under control of locus FNR promoter SYN- Wild type .DELTA.ArgR
PfnrS- ArgAfbr .DELTA.ThyA None tesB-butyrate UCD716 ARG Box
integrated into cassette the integrated into chromosome chromosome
at maIEK under control of locus FNR promoter SYN- Wild type
.DELTA.ArgR PfnrS- ArgAfbr Wild None tesB-butyrate UCD717 ARG Box
integrated into type cassette the ThyA integrated into chromosome
chromosome at maIEK under control of locus FNR promoter SYN- Wild
type .DELTA.ArgR PfnrS- ArgAfbr Wild Kan tesB-butyrate UCD718 ARG
Box integrated into type cassette the ThyA integrated into
chromosome chromosome at maIEK under control of locus FNR promoter
SYN- Wild type Wild PfnrS- ArgAfbr .DELTA.ThyA Kan tesB-butyrate
UCD719 ARG Box type integrated into cassette ArgR the integrated
into chromosome chromosome
at maIEK under control of locus FNR promoter SYN- Wild type Wild
PfnrS- ArgAfbr .DELTA.ThyA none tesB-butyrate UCD720 ARG Box type
integrated into cassette ArgR the integrated into chromosome
chromosome at maIEK under control of locus FNR promoter SYN- Wild
type Wild PfnrS- ArgAfbr Wild Kan tesB-butyrate UCD721 ARG Box type
integrated into type cassette ArgR the ThyA integrated into
chromosome chromosome at maIEK under control of locus FNR promoter
SYN- Wild type Wild PfnrS- ArgAfbr Wild none tesB-butyrate UCD722
ARG Box type integrated into type cassette ArgR the ThyA integrated
into chromosome chromosome at maIEK under control of locus FNR
promoter SYN- Wild type .DELTA.ArgR none Wild Kan tesB-butyrate
UCD723 ARG Box type cassette ThyA integrated into chromosome under
control of FNR promoter SYN- Wild type .DELTA.ArgR none Wild none
tesB-butyrate UCD724 ARG Box type cassette ThyA integrated into
chromosome under control of FNR promoter SYN- Wild type .DELTA.ArgR
none .DELTA.ThyA Kan tesB-butyrate UCD725 ARG Box cassette
integrated into chromosome under control of FNR promoter SYN- Wild
type .DELTA.ArgR none .DELTA.ThyA none tesB-butyrate UCD726 ARG Box
cassette integrated into chromosome under control of FNR promoter
SYN- Wild type .DELTA.ArgR PfnrS- ArgAfbr .DELTA.ThyA Kan
tesB-butyrate UCD727 ARG Box integrated into cassette the
integrated into chromosome chromosome at maIEK under control of
locus FNR promoter; Rifaximin resistance SYN- Wild type .DELTA.ArgR
PfnrS- ArgAfbr .DELTA.ThyA None tesB-butyrate UCD728 ARG Box
integrated into cassette the integrated into chromosome chromosome
at maIEK under control of locus FNR promoter; Rifaximin resistance
SYN- Wild type .DELTA.ArgR PfnrS- ArgAfbr Wild None tesB-butyrate
UCD729 ARG Box integrated into type cassette the ThyA integrated
into chromosome chromosome at maIEK under control of locus FNR
promoter; Rifaximin resistance SYN- Wild type .DELTA.ArgR PfnrS-
ArgAfbr Wild Kan tesB-butyrate UCD730 ARG Box integrated into type
cassette the ThyA integrated into chromosome chromosome at maIEK
under control of locus FNR promoter; Rifaximin resistance SYN- Wild
type Wild PfnrS- ArgAfbr .DELTA.ThyA Kan tesB-butyrate UCD731 ARG
Box type integrated into cassette ArgR the integrated into
chromosome chromosome at maIEK under control of locus FNR promoter;
Rifaximin resistance SYN- Wild type Wild PfnrS- ArgAfbr .DELTA.ThyA
none tesB-butyrate UCD732 ARG Box type integrated into cassette
ArgR the integrated into chromosome chromosome at maIEK under
control of locus FNR promoter; Rifaximin resistance SYN- Wild type
Wild PfnrS- ArgAfbr Wild Kan tesB-butyrate UCD733 ARG Box type
integrated into type cassette ArgR the ThyA integrated into
chromosome chromosome at maIEK under control of locus FNR promoter;
Rifaximin resistance SYN- Wild type Wild PfnrS- ArgAfbr Wild none
tesB-butyrate UCD734 ARG Box type integrated into type cassette
ArgR the ThyA integrated into chromosome chromosome at maIEK under
control of locus FNR promoter; Rifaximin resistance SYN- Wild type
.DELTA.ArgR none Wild Kan tesB-butyrate UCD735 ARG Box type
cassette ThyA integrated into chromosome under control of FNR
promoter; Rifaximin resistance SYN- Wild type .DELTA.ArgR none Wild
none tesB-butyrate UCD736 ARG Box type cassette ThyA integrated
into chromosome under control of FNR promoter; Rifaximin resistance
SYN- Wild type .DELTA.ArgR none .DELTA.ThyA Kan tesB-butyrate
UCD737 ARG Box cassette integrated into chromosome under control of
FNR promoter; Rifaximin resistance SYN- Wild type .DELTA.ArgR none
.DELTA.ThyA none tesB-butyrate UCD38 ARG Box cassette integrated
into chromosome under control of FNR promoter; Rifaximin
resistance
[0368] In some embodiments, butyrate production by the genetically
engineered bacteria can be further enhanced by additional
modifications. Butyrate production under anaerobic conditions
depends on endogenous NADH pools. In some embodiments, the flux
through the butyrate pathway may be enhanced by eliminating
competing routes for NADH utilization. A non-limiting example is
the mutation/deletion of frdA, which utilizes NADH to catalyze the
conversion of phosphoenolpyruvate to succinate. In some
embodiments, any of the genetically engineered bacteria described
herein further comprise a mutation, which eliminates competing
routes for NADH utilization, e.g., a mutation/deletion of frdA.
[0369] Secretion
[0370] In some embodiments, the genetically engineered bacteria
further comprise a native secretion mechanism (e.g., gram positive
bacteria) or non-native secretion mechanism (e.g., gram negative
bacteria) that is capable of secreting the protein(s) of interest
or therapeutic protein(s), from the bacterial cytoplasm. Many
bacteria have evolved sophisticated secretion systems to transport
substrates across the bacterial cell envelope. Substrates, such as
small molecules, proteins, and DNA, may be released into the
extracellular space or periplasm (such as the gut lumen or other
space), injected into a target cell, or associated with the
bacterial membrane.
[0371] In Gram-negative bacteria, secretion machineries may span
one or both of the inner and outer membranes. In some embodiments,
the genetically engineered bacteria further comprise a non-native
double membrane-spanning secretion system. Double membrane-spanning
secretion systems include, but are not limited to, the type I
secretion system (T1SS), the type II secretion system (T2SS), the
type III secretion system (T3SS), the type IV secretion system
(T4SS), the type VI secretion system (T6SS), and the
resistance-nodulation-division (RND) family of multi-drug efflux
pumps (Pugsley 1993; Gerlach et al., 2007; Collinson et al., 2015;
Costa et al., 2015; Reeves et al., 2015; WO2014138324A1,
incorporated herein by reference). Examples of such secretion
systems are shown in FIGS. 69-73. Mycobacteria, which have a
Gram-negative-like cell envelope, may also encode a type VII
secretion system (T7SS) (Stanley et al., 2003). With the exception
of the T2SS, double membrane-spanning secretions generally
transport substrates from the bacterial cytoplasm directly into the
extracellular space or into the target cell. In contrast, the T2SS
and secretion systems that span only the outer membrane may use a
two-step mechanism, wherein substrates are first translocated to
the periplasm by inner membrane-spanning transporters, and then
transferred to the outer membrane or secreted into the
extracellular space. Outer membrane-spanning secretion systems
include, but are not limited to, the type V secretion or
autotransporter system (T5SS), the curli secretion system, and the
chaperone-usher pathway for pili assembly (Saier, 2006; Costa et
al., 2015).
[0372] In some embodiments, the genetically engineered bacteria of
the invention further comprise a type III or a type III-like
secretion system (T3SS) from Shigella, Salmonella, E. coli, Bivrio,
Burkholderia, Yersinia, Chlamydia, or Pseudomonas. The T3SS is
capable of transporting a protein from the bacterial cytoplasm to
the host cytoplasm through a needle complex. The T3SS may be
modified to secrete the molecule from the bacterial cytoplasm, but
not inject the molecule into the host cytoplasm. Thus, the molecule
is secreted into the gut lumen or other extracellular space. In
some embodiments, the genetically engineered bacteria comprise said
modified T3SS and are capable of secreting the protein(s) of
interest or therapeutic protein(s) from the bacterial cytoplasm. In
some embodiments, the secreted molecule, such as a heterologous
protein or peptide, e.g., the protein of interest or therapeutic
protein, comprises a type III secretion sequence that allows the
protein(s) of interest or therapeutic protein(s) to be secreted
from the bacteria.
[0373] In some embodiments, a flagellar type III secretion pathway
is used to secrete the molecule of interest. In some embodiments,
an incomplete flagellum is used to secrete a therapeutic peptide of
interest, by recombinantly fusing the peptide to an N-terminal
flagellar secretion signal of a native flagellar component. In this
manner, the intracellularly expressed chimeric peptide can be
mobilized across the inner and outer membranes into the surrounding
host environment.
[0374] In some embodiments, a Type V Autotransporter Secretion
System is used to secrete the therapeutic peptide. Due to the
simplicity of the machinery and capacity to handle relatively large
protein fluxes, the Type V secretion system is attractive for the
extracellular production of recombinant proteins. As shown in FIG.
70, a therapeutic peptide (star) can be fused to an N-terminal
secretion signal, a linker, and the beta-domain of an
autotransporter. The N-terminal signal sequence directs the protein
to the SecA-YEG machinery which moves the protein across the inner
membrane into the periplasm, followed by subsequent cleavage of the
signal sequence. The Beta-domain is recruited to the Bam complex
(`Beta-barrel assembly machinery`) where the beta-domain is folded
and inserted into the outer membrane as a beta-barrel structure.
The therapeutic peptide, is threaded through the hollow pore of the
beta-barrel structure ahead of the linker sequence. Once exposed to
the extracellular environment, the therapeutic peptide, can be
freed from the linker system by an autocatalytic cleavage (left
side of Bam complex) or by targeting of a membrane-associated
peptidase (black scissors; right side of Barn complex) to a
complimentary protease cut site in the linker. Thus, in some
embodiments, the secreted molecule, such as a heterologous protein
or peptide, e.g., the protein of interest or therapeutic protein,
comprises an N-terminal secretion signal, a linker, and beta-domain
of an autotransporter so as to allow the molecule to be secreted
from the bacteria.
[0375] In some embodiments, a Hemolysin-based Secretion System is
used to secrete the molecule of interest. Type I Secretion systems
offer the advantage of translocating their passenger peptide
directly from the cytoplasm to the extracellular space, obviating
the two-step process of other secretion types. FIG. 71 shows the
alpha-hemolysin (HlyA) of uropathogenic Escherichia coli. This
pathway uses HlyB, an ATP-binding cassette transporter; HlyD, a
membrane fusion protein; and TolC, an outer membrane protein. The
assembly of these three proteins forms a channel through both the
inner and outer membranes. Natively, this channel is used to
secrete HlyA, however, to secrete the therapeutic peptide of the
present disclosure, the secretion signal-containing C-terminal
portion of HlyA is fused to the C-terminal portion of a therapeutic
peptide (star) to mediate secretion of this peptide.
[0376] In alternate embodiments, the genetically engineered
bacteria further comprise a non-native single membrane-spanning
secretion system. Single membrane-spanning exporters may act as a
component of a secretion system, or may export substrates
independently. Such exporters include, but are not limited to,
ATP-binding cassette translocases, flagellum/virulence-related
translocases, conjugation-related translocases, the general
secretory system (e.g., the SecYEG complex in E. coli), the
accessory secretory system in mycobacteria and several types of
Gram-positive bacteria (e.g., Bacillus anthracis, Lactobacillus
johnsonii, Corynebacterium glutamicum, Streptococcus gordonii,
Staphylococcus aureus), and the twin-arginine translocation (TAT)
system (Saier, 2006; Rigel and Braunstein, 2008; Albiniak et al.,
2013). It is known that the general secretory and TAT systems can
both export substrates with cleavable N-terminal signal peptides
into the periplasm, and have been explored in the context of
biopharmaceutical production. The TAT system may offer particular
advantages, however, in that it is able to transport folded
substrates, thus eliminating the potential for premature or
incorrect folding. In certain embodiments, the genetically
engineered bacteria comprise a TAT or a TAT-like system and are
capable of secreting the protein(s) of interest or therapeutic
protein(s), from the bacterial cytoplasm. One of ordinary skill in
the art would appreciate that the secretion systems disclosed
herein may be modified to act in different species, strains, and
subtypes of bacteria, and/or adapted to deliver different
payloads.
[0377] In order to translocate a protein, e.g., therapeutic
polypeptide, to the extracellular space, the polypeptide must first
be translated intracellularly, mobilized across the inner membrane
and finally mobilized across the outer membrane. Many effector
proteins (e.g., therapeutic polypeptides)--particularly those of
eukaryotic origin--contain disulphide bonds to stabilize the
tertiary and quaternary structures. While these bonds are capable
of correctly forming in the oxidizing periplasmic compartment with
the help of periplasmic chaperones, in order to translocate the
polypeptide across the outer membrane the disulphide bonds must be
reduced and the protein unfolded again.
[0378] One way to secrete properly folded proteins in gram-negative
bacteria-particularly those requiring disulphide bonds--is to
target the periplasm in a bacterium with a destabilized outer
membrane. In this manner the protein is mobilized into the
oxidizing environment and allowed to fold properly. In contrast to
orchestrated extracellular secretion systems, the protein is then
able to escape the periplasmic space in a correctly folded form by
membrane leakage. These "leaky" gram-negative mutants are therefore
capable of secreting bioactive, properly disulphide-bonded
polypeptides. In some embodiments, the genetically engineered
bacteria have a "leaky" or destabilized outer membrane.
Destabilizing the bacterial outer membrane to induce leakiness can
be accomplished by deleting or mutagenizing genes responsible for
tethering the outer membrane to the rigid peptidoglycan skeleton,
including for example, lpp, ompC, ompA, ompF, tolA, tolB, paI,
degS, degP, and nlpI. Lpp is the most abundant polypeptide in the
bacterial cell existing at .about.500,000 copies per cell and
functions as the primary `staple` of the bacterial cell wall to the
peptidoglycan. Silhavy, T. J., Kahne, D. & Walker, S. The
bacterial cell envelope. Cold Spring Harb Perspect Biol 2, a000414
(2010). TolA-PAL and OmpA complexes function similarly to Lpp and
are other deletion targets to generate a leaky phenotype.
Additionally, leaky phenotypes have been observed when periplasmic
proteases are deactivated. The periplasm is very densely packed
with protein and therefore encode several periplasmic proteins to
facilitate protein turnover. Removal of periplasmic proteases such
as degS, degP or nlpI can induce leaky phenotypes by promoting an
excessive build-up of periplasmic protein. Mutation of the
proteases can also preserve the effector polypeptide by preventing
targeted degradation by these proteases. Moreover, a combination of
these mutations may synergistically enhance the leaky phenotype of
the cell without major sacrifices in cell viability. Thus, in some
embodiments, the engineered bacteria have one or more deleted or
mutated membrane genes. In some embodiments, the engineered
bacteria have a deleted or mutated lpp gene. In some embodiments,
the engineered bacteria have one or more deleted or mutated
gene(s), selected from ompA, ompA, and ompF genes. In some
embodiments, the engineered bacteria have one or more deleted or
mutated gene(s), selected from tolA, tolB, and paI genes. in some
embodiments, the engineered bacteria have one or more deleted or
mutated periplasmic protease genes. In some embodiments, the
engineered bacteria have one or more deleted or mutated periplasmic
protease genes selected from degS, degP, and nlpI. In some
embodiments, the engineered bacteria have one or more deleted or
mutated gene(s), selected from lpp, ompA, ompA, ompF, tolA, tolB,
paI, degS, degP, and nlpI genes.
[0379] To minimize disturbances to cell viability, the leaky
phenotype can be made inducible by placing one or more membrane or
periplasmic protease genes, e.g., selected from lpp, ompA, ompA,
ompF, tolA, tolB, paI, degS, degP, and nlpI, under the control of
an inducible promoter. For example, expression of lpp or other cell
wall stability protein or periplasmic protease can be repressed in
conditions where the therapeutic polypeptide needs to be delivered
(secreted). For instance, under inducing conditions a
transcriptional repressor protein or a designed antisense RNA can
be expressed which reduces transcription or translation of a target
membrane or periplasmic protease gene. Conversely, overexpression
of certain peptides can result in a destabilized phenotype, e.g.,
overexpression of colicins or the third topological domain of TolA,
wherein peptide overexpression can be induced in conditions in
which the therapeutic polypeptide needs to be delivered (secreted).
These sorts of strategies would decouple the fragile, leaky
phenotypes from biomass production. Thus, in some embodiments, the
engineered bacteria have one or more membrane and/or periplasmic
protease genes under the control of an inducible promoter.
[0380] Table 15 and Table 16 list secretion systems for Gram
positive bacteria and Gram negative bacteria. These can be used to
secrete polypeptides, proteins of interest or therapeutic
protein(s) from the engineered bacteria, which are reviewed in
Milton H. Saier, Jr. Microbe/Volume 1, Number 9, 2006 "Protein
Secretion Systems in Gram-Negative Bacteria Gram-negative bacteria
possess many protein secretion-membrane insertion systems that
apparently evolved independently", the contents of which is herein
incorporated by reference in its entirety.
TABLE-US-00020 TABLE 15 Secretion systems for gram positive
bacteria Bacterial Strain Relevant Secretion System C. novyi-NT
(Gram+) Sec pathway Twin-arginine (TAT) pathway C. butryicum
(Gram+) Sec pathway Twin-arginine (TAT) pathway Listeria
monocytogenes (Gram+) Sec pathway Twin-arginine (TAT) pathway
TABLE-US-00021 TABLE 16 Secretion Systems for Gram negative
bacteria Protein secretary pathways (SP) in gram-negative bacteria
and their descendants Type # Proteins/ Energy (Abbreviation) Name
TC#.sup.2 Bacteria Archaea Eukarya System Source IMPS -
Gram-negative bacterial inner membrane channel-forming translocases
ABC (SIP) ATP binding 3.A.1 + + + 3-4 ATP cassette translocase SEC
(IISP) General 3.A.5 + + + ~12 GTP secretory OR translocase ATP +
PMF Fla/Path Flagellum/ 3.A.6 + - - >10 ATP (IIISP) virulence-
related translocase Conj Conjugation- 3.A.7 + - - >10 ATP (IVSP)
related translocase Tat (IISP) Twin-arginine 2.A.64 + + + 2-4 PMF
targeting (chloroplasts) translocase Oxa1 Cytochrome 2.A.9 + + + 1
None (YidC) oxidase (mitochondria or biogenesis chloroplasts) PMF
family MscL Large 1.A.22 + + + 1 None conductance mechanosensitive
channel family Holins Holin 1.E.1 + - - 1 None functional .cndot.21
superfamily Eukaryotic Organelles MPT Mitochondrial 3.A.B - - +
>20 ATP protein (mitochondrial) translocase CEPT Chloroplast
3.A.9 (+) - + .gtoreq.3 GTP envelope (chloroplasts) protein
translocase Bcl-2 Eukaryotic Bcl- 1.A.21 - - + 1? None 2 family
(programmed cell death) Gram-negative bacterial outer membrane
channel-forming translocases MTB (IISP) Main terminal 3.A.15 .sup.
+.sup.b - - ~14 ATP; branch of the PMF general secretory
translocase FUP AT-1 Fimbrial usher 1.B.11 .sup. +.sup.b - - 1 None
protein 1.B.12 .sup. +.sup.b - 1 None Autotransporter-1 AT-2 OMF
Autotransporter-2 1.B.40 .sup. +.sup.b - - 1 None (ISP) 1.B.17
.sup. +.sup.b .sup. +(?) 1 None TPS 1.B.20 + - + 1 None Secretin
1.B.22 .sup. +.sup.b - 1 None (IISP and IISP) OmpIP Outer 1.B.33 +
- + .gtoreq.4 None? membrane (mitochondria; insertion porin
chloroplasts)
[0381] In some embodiments, the genetically engineered bacterial
comprise a native or non-native secretion system described herein
for the secretion of therapeutic enzyme. In some embodiments, the
secretion system is selected from the modified type III flagellar,
type I (e.g., hemolysin secretion system), type II, type IV, type
V, type VI, and type VII secretion systems,
resistance-nodulation-division (RND) multi-drug efflux pumps, a
single membrane secretion system, Sec and, TAT secretion
systems.
[0382] In some embodiments, the therapeutic proteins secreted by
the genetically engineered bacteria are modified to increase
resistance to proteases, e.g. intestinal proteases.
[0383] In some embodiments, the one or more proteins of interest or
therapeutic proteins for secretion are under the control of an
inducible promoter, as described herein. In one example, the one or
more proteins of interest or therapeutic proteins are under the
control of the FNR promoter and are produced and secreted under
anaerobic conditions. In some embodiments, the one or more proteins
of interest or therapeutic proteins for secretion are under the
control of a constitutive promoter.
[0384] In some embodiments in which the one or more proteins of
interest or therapeutic proteins are secreted or exported from the
microorganism, the engineered microorganism comprises gene
sequence(s) that includes a secretion tag. In some embodiments, the
one or more proteins of interest or therapeutic proteins include a
"secretion tag" of either RNA or peptide origin to direct the one
or more proteins of interest or therapeutic proteins to specific
secretion systems. For example, a secretion tag for the Type I
Hemolysin secretion system is encoded in the C-terminal 53 amino
acids of the alpha hemolysin protein (HlyA). HlyA secretion
signal.
[0385] HlyB inserts into inner membrane to form a pore, HlyD aligns
HlyB with TolC (outer membrane pore) thereby forming a channel
through inner and outer membrane. The C-terminal secretion tag can
be removed by either an autocatalytic or protease-catalyzed e.g.,
OmpT cleavage thereby releasing the one or more proteins of
interest or therapeutic proteins into the extracellular milieu.
[0386] The Type V Auto-secretion System utilizes an N-terminal
Sec-dependent peptide tag (inner membrane) and C-terminal tag
(outer-membrane). This uses Sec-system to get from cytoplasm to
periplasm. C-terminal tag then inserts into the outer membrane
forming a pore through which the "passenger protein" threads
through. Once across the outer membrane, the passenger (anti-cancer
molecule) is released from the membrane-embedded C-terminal tag by
either an autocatalytic, intein-like mechanism or via a
membrane-bound protease (I.e., OmpT). The N-terminal tag is removed
by the Sec system. Thus, in some embodiments, the secretion system
is able to remove this tag before secreting the one or more
proteins of interest or therapeutic proteins, from the engineered
bacteria. In the Type V auto-secretion-mediated secretion the
N-terminal peptide secretion tag is removed upon translocation of
the "passenger" peptide from the cytoplasm into the periplasmic
compartment by the native Sec system. Further, once the
auto-secretor is translocated across the outer membrane the
C-terminal secretion tag can be removed by either an autocatalytic
or protease-catalyzed e.g., OmpT cleavage thereby releasing the
anti-cancer molecule(s) into the extracellular milieu.
[0387] In the Flagellar modified Type III Secretion, the tag is
encoded in 5'untranslated region of the mRNA and thus there is no
peptide tag to cleave/remove. This modified system does not contain
the "syringe" portion and instead uses the basal body of the
flagella structure as the pore to translocate across both membranes
and out through the forming flagella. If the fliC/fliD genes
(encoding the flagella "tail"/whip) are disrupted the flagella
cannot fully form and this promotes overall secretion. In some
embodiments, the tail portion can be removed entirely. In the Type
III traditional secretion system, the basal body closely resembles
the flagella, however, instead of a "tail"/whip, the traditional
T3SS has a syringe to inject the passenger proteins into host
cells. The secretion tag is encoded by an N-terminal peptide
(lengths vary and there are several different tags, see
PCT/US14/020972). The N-terminal tag is not removed from the
polypeptides in this secretion system.
[0388] In some embodiments the one or more proteins of interest or
therapeutic proteins contain expressed as fusion protein with the
53 amino acids of the C termini of alpha-hemolysin (hlyA) of E.
coli CFT073 (C terminal secretion tag).
[0389] Essential Genes and Auxotrophs
[0390] As used herein, the term "essential gene" refers to a gene
which is necessary to for cell growth and/or survival. Bacterial
essential genes are well known to one of ordinary skill in the art,
and can be identified by directed deletion of genes and/or random
mutagenesis and screening (see, for example, Zhang and Lin, 2009,
DEG 5.0, a database of essential genes in both prokaryotes and
eukaryotes, Nucl. Acids Res., 37:D455-D458 and Gerdes et al.,
Essential genes on metabolic maps, Curr. Opin. Biotechnol.,
17(5):448-456, the entire contents of each of which are expressly
incorporated herein by reference).
[0391] An "essential gene" may be dependent on the circumstances
and environment in which an organism lives. For example, a mutation
of, modification of, or excision of an essential gene may result in
the recombinant bacteria of the disclosure becoming an auxotroph.
An auxotrophic modification is intended to cause bacteria to die in
the absence of an exogenously added nutrient essential for survival
or growth because they lack the gene(s) necessary to produce that
essential nutrient.
[0392] Exemplary bacterial genes which may be disrupted or deleted
to produce an auxotrophic strain are shown below. These include,
but are not limited to, genes required for oligonucleotide
synthesis, amino acid synthesis, and cell wall synthesis.
[0393] An auxotrophic modification is intended to cause bacteria to
die in the absence of an exogenously added nutrient essential for
survival or growth because they lack the gene(s) necessary to
produce that essential nutrient. In some embodiments, any of the
genetically engineered bacteria described herein also comprise a
deletion or mutation in a gene required for cell survival and/or
growth. In one embodiment, the essential gene is a DNA synthesis
gene, for example, thyA. In another embodiment, the essential gene
is a cell wall synthesis gene, for example, dapA. In yet another
embodiment, the essential gene is an amino acid gene, for example,
serA or MetA. Any gene required for cell survival and/or growth may
be targeted, including but not limited to, cysE, glnA, ilvD, leuB,
lysA, serA, metA, glyA, hisB, ilvA, pheA, proA, thrC, trpC, tyrA,
thyA, uraA, dapA, dapB, dapD, dapE, dapF, flhD, metB, metC, proAB,
and thi1, as long as the corresponding wild-type gene product is
not produced in the bacteria. Table 17 lists depicts exemplary
bacterial genes which may be disrupted or deleted to produce an
auxotrophic strain. These include, but are not limited to, genes
required for oligonucleotide synthesis, amino acid synthesis, and
cell wall synthesis.
TABLE-US-00022 TABLE 17 Non-limiting Examples of Bacterial Genes
Useful for Generation of an Auxotroph Amino Acid Oligonucleotide
Cell Wall cysE thyA dapA glnA uraA dapB ilvD dapD leuB dapE lysA
dapF serA metA glyA hisB ilvA pheA proA thrC trpC tyrA
[0394] Table 18 shows the survival of various amino acid auxotrophs
in the mouse gut, as detected 24 hrs and 48 hrs post-gavage. These
auxotrophs were generated using BW25113, a non-Nissle strain of E.
coli.
TABLE-US-00023 TABLE 18 Survival of amino acid auxotrophs in the
mouse gut Gene AA Auxotroph Pre-Gavage 24 hours 48 hours argA
Arginine Present Present Absent cysE Cysteine Present Present
Absent glnA Glutamine Present Present Absent glyA Glycine Present
Present Absent hisB Histidine Present Present Present ilvA
Isoleucine Present Present Absent leuB Leucine Present Present
Absent lysA Lysine Present Present Absent metA Methionine Present
Present Present pheA Phenylalanine Present Present Present proA
Proline Present Present Absent serA Serine Present Present Present
thrC Threonine Present Present Present trpC Tryptophan Present
Present Present tyrA Tyrosine Present Present Present ilvD
Valine/Isoleucine/ Present Present Absent Leucine thyA Thiamine
Present Absent Absent uraA Uracil Present Absent Absent flhD FlhD
Present Present Present
[0395] For example, thymine is a nucleic acid that is required for
bacterial cell growth; in its absence, bacteria undergo cell death.
The thyA gene encodes thimidylate synthetase, an enzyme that
catalyzes the first step in thymine synthesis by converting dUMP to
dTMP (Sat et al., 2003). In some embodiments, the bacterial cell of
the disclosure is a thyA auxotroph in which the thyA gene is
deleted and/or replaced with an unrelated gene. A thyA auxotroph
can grow only when sufficient amounts of thymine are present, e.g.,
by adding thymine to growth media in vitro, or in the presence of
high thymine levels found naturally in the human gut in vivo. In
some embodiments, the bacterial cell of the disclosure is
auxotrophic in a gene that is complemented when the bacterium is
present in the mammalian gut. Without sufficient amounts of
thymine, the thyA auxotroph dies. In some embodiments, the
auxotrophic modification is used to ensure that the bacterial cell
does not survive in the absence of the auxotrophic gene product
(e.g., outside of the gut).
[0396] Diaminopimelic acid (DAP) is an amino acid synthetized
within the lysine biosynthetic pathway and is required for
bacterial cell wall growth (Meadow et al., 1959; Clarkson et al.,
1971). In some embodiments, any of the genetically engineered
bacteria described herein is a dapD auxotroph in which dapD is
deleted and/or replaced with an unrelated gene. A dapD auxotroph
can grow only when sufficient amounts of DAP are present, e.g., by
adding DAP to growth media in vitro. Without sufficient amounts of
DAP, the dapD auxotroph dies. In some embodiments, the auxotrophic
modification is used to ensure that the bacterial cell does not
survive in the absence of the auxotrophic gene product (e.g.,
outside of the gut).
[0397] In other embodiments, the genetically engineered bacterium
of the present disclosure is a uraA auxotroph in which uraA is
deleted and/or replaced with an unrelated gene. The uraA gene codes
for UraA, a membrane-bound transporter that facilitates the uptake
and subsequent metabolism of the pyrimidine uracil (Andersen et
al., 1995). A uraA auxotroph can grow only when sufficient amounts
of uracil are present, e.g., by adding uracil to growth media in
vitro. Without sufficient amounts of uracil, the uraA auxotroph
dies. In some embodiments, auxotrophic modifications are used to
ensure that the bacteria do not survive in the absence of the
auxotrophic gene product (e.g., outside of the gut).
[0398] In complex communities, it is possible for bacteria to share
DNA. In very rare circumstances, an auxotrophic bacterial strain
may receive DNA from a non-auxotrophic strain, which repairs the
genomic deletion and permanently rescues the auxotroph. Therefore,
engineering a bacterial strain with more than one auxotroph may
greatly decrease the probability that DNA transfer will occur
enough times to rescue the auxotrophy. In some embodiments, the
genetically engineered bacteria of the invention comprise a
deletion or mutation in two or more genes required for cell
survival and/or growth.
[0399] Other examples of essential genes include, but are not
limited to yhbV, yagG, hemB, secD, secF, ribD, ribE, thiL, dxs,
ispA, dnaX, adk, hemH, lpxH, cysS, fold, rplT, infC, thrS, nadE,
gapA, yeaZ, aspS, argS, pgsA, yefM, metG, folE, yejM, gyrA, nrdA,
nrdB, folC, accD, fabB, gltX, ligA, zipA, dapE, dapA, der, hisS,
ispG, suhB, tadA, acpS, era, rnc, ftsB, eno, pyrG, chpR, lgt, fbaA,
pgk, yqgD, metK, yqgF, plsC, ygiT, pare, ribB, cca, ygjD, tdcF,
yraL, yihA, ftsN, murI, murB, birA, secE, nusG, rplJ, rplL, rpoB,
rpoC, ubiA, plsB, lexA, dnaB, ssb, alsK, groS, psd, orn, yjeE,
rpsR, chpS, ppa, valS, yjgP, yjgQ, dnaC, ribF, lspA, ispH, dapB,
folA, imp, yabQ, ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG,
murC, ftsQ, ftsA, ftsZ, lpxC, secM, secA, can, folk, hemL, yadR,
dapD, map, rpsB, infB, nusA, ftsH, obgE, rpmA, rplU, ispB, murA,
yrbB, yrbK, yhbN, rpsI, rplM, degS, mreD, mreC, mreB, accB, accC,
yrdC, def, fmt, rplQ, rpoA, rpsD, rpsK, rpsM, entD, mrdB, mrdA,
nadD, hlepB, rpoE, pssA, yfiO, rplS, trmD, rpsP, ffh, grpE, yfjB,
csrA, ispF, ispD, rplW, rplD, rplC, rpsJ, fusA, rpsG, rpsL, trpS,
yrfF, asd, rpoH, ftsX, ftsE, ftsY, frr, dxr, ispU, rfaK, kdtA,
coaD, rpmB, dfp, dut, gmk, spot, gyrB, dnaN, dnaA, rpmH, mpA, yidC,
tnaB, glmS, glmU, wzyE, hemD, hemC, yigP, ubiB, ubiD, hemG, secY,
rplO, rpmD, rpsE, rplR, rplF, rpsH, rpsN, rplE, rplX, rplN, rpsQ,
rpmC, rplP, rpsC, rplV, rpsS, rplB, cdsA, yaeL, yaeT, lpxD, fabZ,
lpxA, lpxB, dnaE, accA, tilS, proS, yafF, tsf, pyrH, olA, rlpB,
leuS, lnt, glnS, fldA, cydA, infA, cydC, ftsK, lolA, serS, rpsA,
msbA, lpxK, kdsB, mukF, mukE, mukB, asnS, fabA, mviN, rne, yceQ,
fabD, fabG, acpP, tmk, holB, lolC, lolD, lolE, purB, ymfK, minE,
mind, pth, rsA, ispE, lolB, hemA, prfA, prmC, kdsA, topA, ribA,
fabI, racR, dicA, ydfB, tyrS, ribC, ydiL, pheT, pheS, yhhQ, bcsB,
glyQ, yibJ, and gpsA. Other essential genes are known to those of
ordinary skill in the art.
[0400] In some embodiments, the genetically engineered bacterium of
the present disclosure is a synthetic ligand-dependent essential
gene (SLiDE) bacterial cell. SLiDE bacterial cells are synthetic
auxotrophs with a mutation in one or more essential genes that only
grow in the presence of a particular ligand (see Lopez and Anderson
"Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a
BL21 (DE3 Biosafety Strain," ACS Synthetic Biology (2015) DOI:
10.1021/acssynbio.5b00085, the entire contents of which are
expressly incorporated herein by reference).
[0401] In some embodiments, the SLiDE bacterial cell comprises a
mutation in an essential gene. In some embodiments, the essential
gene is selected from the group consisting of pheS, dnaN, tyrS,
metG, and adk. In some embodiments, the essential gene is dnaN
comprising one or more of the following mutations: H191N, R240C,
I317S, F319V, L340T, V347I, and S345C. In some embodiments, the
essential gene is dnaN comprising the mutations H191N, R240C,
I317S, F319V, L340T, V347I, and S345C. In some embodiments, the
essential gene is pheS comprising one or more of the following
mutations: F125G, P183T, P184A, R186A, and I188L. In some
embodiments, the essential gene is pheS comprising the mutations
F125G, P183T, P184A, R186A, and I188L. In some embodiments, the
essential gene is tyrS comprising one or more of the following
mutations: L36V, C38A, and F40G. In some embodiments, the essential
gene is tyrS comprising the mutations L36V, C38A, and F40G. In some
embodiments, the essential gene is metG comprising one or more of
the following mutations: E45Q, N47R, I49G, and A51C. In some
embodiments, the essential gene is metG comprising the mutations
E45Q, N47R, I49G, and A51C. In some embodiments, the essential gene
is adk comprising one or more of the following mutations: I4L, L5I,
and L6G. In some embodiments, the essential gene is adk comprising
the mutations I4L, L5I, and L6G.
[0402] In some embodiments, the genetically engineered bacterium is
complemented by a ligand. In some embodiments, the ligand is
selected from the group consisting of benzothiazole, indole,
2-aminobenzothiazole, indole-3-butyric acid, indole-3-acetic acid,
and L-histidine methyl ester. For example, bacterial cells
comprising mutations in metG (E45Q, N47R, I49G, and A51C) are
complemented by benzothiazole, indole, 2-aminobenzothiazole,
indole-3-butyric acid, indole-3-acetic acid or L-histidine methyl
ester. Bacterial cells comprising mutations in dnaN (H191N, R240C,
I317S, F319V, L340T, V347I, and S345C) are complemented by
benzothiazole, indole or 2-aminobenzothiazole. Bacterial cells
comprising mutations in pheS (F125G, P183T, P184A, R186A, and
I188L) are complemented by benzothiazole or 2-aminobenzothiazole.
Bacterial cells comprising mutations in tyrS (L36V, C38A, and F40G)
are complemented by benzothiazole or 2-aminobenzothiazole.
Bacterial cells comprising mutations in adk (I4L, L5I, and L6G) are
complemented by benzothiazole or indole.
[0403] In some embodiments, the genetically engineered bacterium
comprises more than one mutant essential gene that renders it
auxotrophic to a ligand. In some embodiments, the bacterial cell
comprises mutations in two essential genes. For example, in some
embodiments, the bacterial cell comprises mutations in tyrS (L36V,
C38A, and F40G) and metG (E45Q, N47R, I49G, and A51C). In other
embodiments, the bacterial cell comprises mutations in three
essential genes. For example, in some embodiments, the bacterial
cell comprises mutations in tyrS (L36V, C38A, and F40G), metG
(E45Q, N47R, I49G, and A51C), and pheS (F125G, P183T, P184A, R186A,
and I188L).
[0404] In some embodiments, the genetically engineered bacterium is
a conditional auxotroph whose essential gene(s) is replaced using
the arabinose system, e.g., as shown in FIG. 66.
[0405] In some embodiments, the genetically engineered bacterium of
the disclosure is an auxotroph and also comprises kill-switch
circuitry, such as any of the kill-switch components and systems
described herein. For example, the recombinant bacteria may
comprise a deletion or mutation in an essential gene required for
cell survival and/or growth, for example, in a DNA synthesis gene,
for example, thyA, cell wall synthesis gene, for example, dapA
and/or an amino acid gene, for example, serA or MetA and may also
comprise a toxin gene that is regulated by one or more
transcriptional activators that are expressed in response to an
environmental condition(s) and/or signal(s) (such as the described
arabinose system) or regulated by one or more recombinases that are
expressed upon sensing an exogenous environmental condition(s)
and/or signal(s) (such as the recombinase systems described herein
and in FIGS. 62-65. Other embodiments are described in Wright et
al., "GeneGuard: A Modular Plasmid System Designed for Biosafety,"
ACS Synthetic Biology (2015) 4: 307-316, the entire contents of
which are expressly incorporated herein by reference). In some
embodiments, the genetically engineered bacterium of the disclosure
is an auxotroph and also comprises kill-switch circuitry, such as
any of the kill-switch components and systems described herein, as
well as another biosecurity system, such a conditional origin of
replication (Wright et al., 2015).
[0406] In other embodiments, auxotrophic modifications may also be
used to screen for mutant bacteria that consume excess ammonia. In
a more specific aspect, auxotrophic modifications may be used to
screen for mutant bacteria that consume excess ammonia by
overproducing arginine. As described herein, many genes involved in
arginine metabolism are subject to repression by arginine via its
interaction with ArgR. The astC gene promoter is unique in that the
arginine-ArgR complex acts as a transcriptional activator, as
opposed to a transcriptional repressor. AstC encodes
succinylornithine aminotransferase, the third enzyme of the
ammonia-producing arginine succinyltransferase (AST) pathway and
the first of the astCADBE operon in E. coli (Schneider et al.,
1998). In certain embodiments, the genetically engineered bacteria
are auxotrophic for a gene, and express the auxotrophic gene
product under the control of an astC promoter. In these
embodiments, the auxotrophy is subject to a positive feedback
mechanism and used to select for mutant bacteria which consume
excess ammonia by overproducing arginine. A non-limiting example of
a positive feedback auxotroph is shown in FIGS. 60A and 60B.
[0407] Genetic Regulatory Circuits
[0408] In some embodiments, the genetically engineered bacteria
comprise multilayered genetic regulatory circuits for expressing
the constructs described herein (see, e.g., U.S. Provisional
Application No. 62/184,811, incorporated herein by reference in its
entirety).
[0409] In certain embodiments, the invention provides methods for
selecting genetically engineered bacteria that overproduce
arginine. In some embodiments, the invention provides methods for
selecting genetically engineered bacteria that consume excess
ammonia via an alternative metabolic pathway, e.g., a histidine
biosynthesis pathway, a methionine biosynthesis pathway, a lysine
biosynthesis pathway, an asparagine biosynthesis pathway, a
glutamine biosynthesis pathway, and a tryptophan biosynthesis
pathway. In some embodiments, the invention provides genetically
engineered bacteria comprising a mutant arginine regulon and an
ArgR-regulated two-repressor activation genetic regulatory circuit.
The two-repressor activation genetic regulatory circuit is useful
to screen for mutant bacteria that reduce ammonia or rescue an
auxotroph. In some constructs, high levels of arginine and the
resultant activation of ArgR by arginine can cause expression of a
detectable label or an essential gene that is required for cell
survival.
[0410] The two-repressor activation regulatory circuit comprises a
first ArgR and a second repressor, e.g., the Tet repressor. In one
aspect of these embodiments, ArgR inhibits transcription of a
second repressor, which inhibits the transcription of a particular
gene of interest, e.g., a detectable product, which may be used to
screen for mutants that consume excess ammonia, and/or an essential
gene that is required for cell survival. Any detectable product may
be used, including but not limited to, luciferase,
.beta.-galactosidase, and fluorescent proteins such as GFP. In some
embodiments, the second repressor is a Tet repressor protein
(TetR). In this embodiment, an ArgR-repressible promoter comprising
wild-type ARG boxes drives the expression of TetR, and a
TetR-repressible promoter drives the expression of at least one
gene of interest, e.g., GFP. In the absence of ArgR binding (which
occurs at low arginine concentrations), tetR is transcribed, and
TetR represses GFP expression. In the presence of ArgR binding
(which occurs at high arginine concentrations), tetR expression is
repressed, and GFP is generated. Examples of other second
repressors useful in these embodiments include, but are not limited
to, ArsR, AscG, LacI, CscR, DeoR, DgoR, FruR, GalR, GatR, Cl, LexA,
RafR, QacR, and PtxS (US20030166191). In some embodiments, the
mutant arginine regulon comprising a switch is subjected to
mutagenesis, and mutants that reduce ammonia by overproducing
arginine are selected based upon the level of detectable product,
e.g., by flow cytometry, fluorescence-activated cell sorting (FACS)
when the detectable product fluoresces.
[0411] In some embodiments, the gene of interest is one required
for survival and/or growth of the bacteria. Any such gene may be
used, including but not limited to, cysE, glnA, ilvD, leuB, lysA,
serA, metA, glyA, hisB, ilvA, pheA, proA, thrC, trpC, tyrA, thyA,
uraA, dapA, dapB, dapD, dapE, dapF, flhD, metB, metC, proAB, and
thi1, as long as the corresponding wild-type gene has been removed
or mutated so as not to produce the gene product except under
control of ArgR. In some embodiments, an ArgR-repressible promoter
comprising wild-type ARG boxes drives the expression of a TetR
protein, and a TetR-repressible promoter drives the expression of
at least one gene required for survival and/or growth of the
bacteria, e.g., thyA, uraA (Sat et al., 2003). In some embodiments,
the genetically engineered bacterium is auxotrophic in a gene that
is not complemented when the bacterium is present in the mammalian
gut, wherein said gene is complemented by a second inducible gene
present in the bacterium; transcription of the second gene is
ArgR-repressible and induced in the presence of sufficiently high
concentrations of arginine (thus complementing the auxotrophic
gene). In some embodiments, the mutant arginine regulon comprising
a two-repressor activation circuit is subjected to mutagenesis, and
mutants that reduce excess ammonia are selected by growth in the
absence of the gene product required for survival and/or growth. In
some embodiments, the mutant arginine regulon comprising a
two-repressor activation circuit is used to ensure that the
bacteria do not survive in the absence of high levels of arginine
(e.g., outside of the gut).
[0412] Host-Plasmid Mutual Dependency
[0413] In some embodiments, the genetically engineered bacteria of
the invention also comprise a plasmid that has been modified to
create a host-plasmid mutual dependency. In certain embodiments,
the mutually dependent host-plasmid platform is GeneGuard (Wright
et al., 2015). In some embodiments, the GeneGuard plasmid comprises
(i) a conditional origin of replication, in which the requisite
replication initiator protein is provided in trans; (ii) an
auxotrophic modification that is rescued by the host via genomic
translocation and is also compatible for use in rich media; and/or
(iii) a nucleic acid sequence which encodes a broad-spectrum toxin.
The toxin gene may be used to select against plasmid spread by
making the plasmid DNA itself disadvantageous for strains not
expressing the anti-toxin (e.g., a wild-type bacterium). In some
embodiments, the GeneGuard plasmid is stable for at least 100
generations without antibiotic selection. In some embodiments, the
GeneGuard plasmid does not disrupt growth of the host. The
GeneGuard plasmid is used to greatly reduce unintentional plasmid
propagation in the genetically engineered bacteria of the
invention.
[0414] The mutually dependent host-plasmid platform may be used
alone or in combination with other biosafety mechanisms, such as
those described herein (e.g., kill switches, auxotrophies). In some
embodiments, the genetically engineered bacteria comprise a
GeneGuard plasmid. In other embodiments, the genetically engineered
bacteria comprise a GeneGuard plasmid and/or one or more kill
switches. In other embodiments, the genetically engineered bacteria
comprise a GeneGuard plasmid and/or one or more auxotrophies. In
still other embodiments, the genetically engineered bacteria
comprise a GeneGuard plasmid, one or more kill switches, and/or one
or more auxotrophies.
[0415] Synthetic gene circuits express on plasmids may function
well in the short term but lose ability and/or function in the long
term (Danino et al., 2015). In some embodiments, the genetically
engineered bacteria comprise stable circuits for expressing genes
of interest over prolonged periods. In some embodiments, the
genetically engineered bacteria are capable of producing a gut
enhancer molecule and further comprise a toxin-anti-toxin system
that simultaneously produces a toxin (hok) and a short-lived
anti-toxin (sok), wherein loss of the plasmid causes the cell to be
killed by the long-lived toxin (Danino et al., 2015; FIG. 68). In
some embodiments, the genetically engineered bacteria further
comprise alp7 from B. subtilis plasmid pL20 and produces filaments
that are capable of pushing plasmids to the poles of the cells in
order to ensure equal segregation during cell division (Danino et
al., 2015).
[0416] Kill Switch
[0417] In some embodiments, the genetically engineered bacteria of
the invention also comprise a kill switch (see, e.g., U.S.
Provisional Application Nos. 62/183,935, 62/263,329, and
62/277,654, each of which is incorporated herein by reference in
their entireties). The kill switch is intended to actively kill
engineered microbes in response to external stimuli. As opposed to
an auxotrophic mutation where bacteria die because they lack an
essential nutrient for survival, the kill switch is triggered by a
particular factor in the environment that induces the production of
toxic molecules within the microbe that cause cell death.
[0418] Bacteria engineered with kill switches have been engineered
for in vitro research purposes, e.g., to limit the spread of a
biofuel-producing microorganism outside of a laboratory
environment. Bacteria engineered for in vivo administration to
treat a disease or disorder may also be programmed to die at a
specific time after the expression and delivery of a heterologous
gene or genes, for example, a therapeutic gene(s) or after the
subject has experienced the therapeutic effect. For example, in
some embodiments, the kill switch is activated to kill the bacteria
after a period of time following oxygen level-dependent expression
of arg.sup.Afbr. In some embodiments, the kill switch is activated
in a delayed fashion following oxygen level-dependent expression of
arg.sup.Afbr, for example, after the production of arginine or
citrulline. Alternatively, the bacteria may be engineered to die
after the bacteria has spread outside of a disease site.
Specifically, it may be useful to prevent long-term colonization of
subjects by the microorganism, spread of the microorganism outside
the area of interest (for example, outside the gut) within the
subject, or spread of the microorganism outside of the subject into
the environment (for example, spread to the environment through the
stool of the subject). Examples of such toxins that can be used in
kill-switches include, but are not limited to, bacteriocins,
lysins, and other molecules that cause cell death by lysing cell
membranes, degrading cellular DNA, or other mechanisms. Such toxins
can be used individually or in combination. The switches that
control their production can be based on, for example,
transcriptional activation (toggle switches; see, e.g., Gardner et
al., 2000), translation (riboregulators), or DNA recombination
(recombinase-based switches), and can sense environmental stimuli
such as anaerobiosis or reactive oxygen species. These switches can
be activated by a single environmental factor or may require
several activators in AND, OR, NAND and NOR logic configurations to
induce cell death. For example, an AND riboregulator switch is
activated by tetracycline, isopropyl
.beta.-D-1-thiogalactopyranoside (IPTG), and arabinose to induce
the expression of lysins, which permeabilize the cell membrane and
kill the cell. IPTG induces the expression of the endolysin and
holin mRNAs, which are then derepressed by the addition of
arabinose and tetracycline. All three inducers must be present to
cause cell death. Examples of kill switches are known in the art
(Callura et al., 2010). In some embodiments, the kill switch is
activated to kill the bacteria after a period of time following
oxygen level-dependent expression of arg.sup.Afbr. In some
embodiments, the kill switch is activated in a delayed fashion
following oxygen level-dependent expression of argA.sup.fbr.
[0419] Kill-switches can be designed such that a toxin is produced
in response to an environmental condition or external signal (e.g.,
the bacteria is killed in response to an external cue) or,
alternatively designed such that a toxin is produced once an
environmental condition no longer exists or an external signal is
ceased.
[0420] Thus, in some embodiments, the genetically engineered
bacteria of the disclosure are further programmed to die after
sensing an exogenous environmental signal, for example, in a
low-oxygen environment. In some embodiments, the genetically
engineered bacteria of the present disclosure, e.g., bacteria
expressing argA.sup.fbr and repressor ArgR, comprise one or more
genes encoding one or more recombinase(s), whose expression is
induced in response to an environmental condition or signal and
causes one or more recombination events that ultimately leads to
the expression of a toxin which kills the cell. In some
embodiments, the at least one recombination event is the flipping
of an inverted heterologous gene encoding a bacterial toxin which
is then constitutively expressed after it is flipped by the first
recombinase. In one embodiment, constitutive expression of the
bacterial toxin kills the genetically engineered bacterium. In
these types of kill-switch systems once the engineered bacterial
cell senses the exogenous environmental condition and expresses the
heterologous gene of interest, the recombinant bacterial cell is no
longer viable.
[0421] In another embodiment in which the genetically engineered
bacteria of the present disclosure, e.g., bacteria expressing
argA.sup.fbr and repressor ArgR, express one or more recombinase(s)
in response to an environmental condition or signal causing at
least one recombination event, the genetically engineered bacterium
further expresses a heterologous gene encoding an anti-toxin in
response to an exogenous environmental condition or signal. In one
embodiment, the at least one recombination event is flipping of an
inverted heterologous gene encoding a bacterial toxin by a first
recombinase. In one embodiment, the inverted heterologous gene
encoding the bacterial toxin is located between a first forward
recombinase recognition sequence and a first reverse recombinase
recognition sequence. In one embodiment, the heterologous gene
encoding the bacterial toxin is constitutively expressed after it
is flipped by the first recombinase. In one embodiment, the
anti-toxin inhibits the activity of the toxin, thereby delaying
death of the genetically engineered bacterium. In one embodiment,
the genetically engineered bacterium is killed by the bacterial
toxin when the heterologous gene encoding the anti-toxin is no
longer expressed when the exogenous environmental condition is no
longer present.
[0422] In another embodiment, the at least one recombination event
is flipping of an inverted heterologous gene encoding a second
recombinase by a first recombinase, followed by the flipping of an
inverted heterologous gene encoding a bacterial toxin by the second
recombinase. In one embodiment, the inverted heterologous gene
encoding the second recombinase is located between a first forward
recombinase recognition sequence and a first reverse recombinase
recognition sequence. In one embodiment, the inverted heterologous
gene encoding the bacterial toxin is located between a second
forward recombinase recognition sequence and a second reverse
recombinase recognition sequence. In one embodiment, the
heterologous gene encoding the second recombinase is constitutively
expressed after it is flipped by the first recombinase. In one
embodiment, the heterologous gene encoding the bacterial toxin is
constitutively expressed after it is flipped by the second
recombinase. In one embodiment, the genetically engineered
bacterium is killed by the bacterial toxin. In one embodiment, the
genetically engineered bacterium further expresses a heterologous
gene encoding an anti-toxin in response to the exogenous
environmental condition. In one embodiment, the anti-toxin inhibits
the activity of the toxin when the exogenous environmental
condition is present, thereby delaying death of the genetically
engineered bacterium. In one embodiment, the genetically engineered
bacterium is killed by the bacterial toxin when the heterologous
gene encoding the anti-toxin is no longer expressed when the
exogenous environmental condition is no longer present.
[0423] In one embodiment, the at least one recombination event is
flipping of an inverted heterologous gene encoding a second
recombinase by a first recombinase, followed by flipping of an
inverted heterologous gene encoding a third recombinase by the
second recombinase, followed by flipping of an inverted
heterologous gene encoding a bacterial toxin by the third
recombinase.
[0424] In one embodiment, the at least one recombination event is
flipping of an inverted heterologous gene encoding a first excision
enzyme by a first recombinase. In one embodiment, the inverted
heterologous gene encoding the first excision enzyme is located
between a first forward recombinase recognition sequence and a
first reverse recombinase recognition sequence. In one embodiment,
the heterologous gene encoding the first excision enzyme is
constitutively expressed after it is flipped by the first
recombinase. In one embodiment, the first excision enzyme excises a
first essential gene. In one embodiment, the programmed recombinant
bacterial cell is not viable after the first essential gene is
excised.
[0425] In one embodiment, the first recombinase further flips an
inverted heterologous gene encoding a second excision enzyme. In
one embodiment, the wherein the inverted heterologous gene encoding
the second excision enzyme is located between a second forward
recombinase recognition sequence and a second reverse recombinase
recognition sequence. In one embodiment, the heterologous gene
encoding the second excision enzyme is constitutively expressed
after it is flipped by the first recombinase. In one embodiment,
the genetically engineered bacterium dies or is no longer viable
when the first essential gene and the second essential gene are
both excised. In one embodiment, the genetically engineered
bacterium dies or is no longer viable when either the first
essential gene is excised or the second essential gene is excised
by the first recombinase.
[0426] In one embodiment, the genetically engineered bacterium dies
after the at least one recombination event occurs. In another
embodiment, the genetically engineered bacterium is no longer
viable after the at least one recombination event occurs.
[0427] In any of these embodiment, the recombinase can be a
recombinase selected from the group consisting of: BxbI, PhiC31,
TP901, BxbI, PhiC31, TP901, HK022, HP1, R4, Int1, Int2, Int3, Int4,
Int5, Int6, Int7, Int8, Int9, Int10, Int11, Int12, Int13, Int14,
Int15, Int16, Int17, Int18, Int19, Int20, Int21, Int22, Int23,
Int24, Int25, Int26, Int27, Int28, Int29, Int30, Int31, Int32,
Int33, and Int34, or a biologically active fragment thereof.
[0428] In the above-described kill-switch circuits, a toxin is
produced in the presence of an environmental factor or signal. In
another aspect of kill-switch circuitry, a toxin may be repressed
in the presence of an environmental factor (not produced) and then
produced once the environmental condition or external signal is no
longer present. An exemplary kill-switch in which the toxin is
repressed in the presence of an external factor or signal (and
activated once the external signal is removed) is shown in FIGS.
66-68. The disclosure provides recombinant bacterial cells which
express one or more heterologous gene(s) upon sensing arabinose or
other sugar in the exogenous environment. In this aspect, the
recombinant bacterial cells contain the araC gene, which encodes
the AraC transcription factor, as well as one or more genes under
the control of the araBAD promoter. In the absence of arabinose,
the AraC transcription factor adopts a conformation that represses
transcription of genes under the control of the araBAD promoter. In
the presence of arabinose, the AraC transcription factor undergoes
a conformational change that allows it to bind to and activate the
araBAD promoter, which induces expression of the desired gene, for
example tetR, which represses expression of a toxin gene. In this
embodiment, the toxin gene is repressed in the presence of
arabinose or other sugar. In an environment where arabinose is not
present, the tetR gene is not activated and the toxin is expressed,
thereby killing the bacteria. The arabinose system can also be used
to express an essential gene, in which the essential gene is only
expressed in the presence of arabinose or other sugar and is not
expressed when arabinose or other sugar is absent from the
environment.
[0429] Thus, in some embodiments in which one or more heterologous
gene(s) are expressed upon sensing arabinose in the exogenous
environment, the one or more heterologous genes are directly or
indirectly under the control of the araBAD promoter. In some
embodiments, the expressed heterologous gene is selected from one
or more of the following: a heterologous therapeutic gene, a
heterologous gene encoding an anti-toxin, a heterologous gene
encoding a repressor protein or polypeptide, for example, a TetR
repressor, a heterologous gene encoding an essential protein not
found in the bacterial cell, and/or a heterologous encoding a
regulatory protein or polypeptide.
[0430] In some embodiments, the argA.sup.fbr gene is directly or
indirectly under the control of the araBAD promoter. FIG. 13
depicts a schematic diagram of an exemplary BAD promoter-driven
argA.sup.fbr construct. In this embodiment, the argA.sup.fbr gene
is inserted between the araC and araD genes. ArgA.sup.fbr is
flanked by a ribosome binding site, a FRT site, and one or more
transcription terminator sequences. The nucleic acid sequence of an
exemplary BAD promoter-driven argA.sup.fbr construct is shown in
Table 19. All bolded sequences are Nissle genomic DNA. A portion of
the araC gene is bolded and underlined, the argA.sup.fbr gene is ,
and the bolded sequence in between is the promoter that is
activated by the presence of arabinose. The ribosome binding site
is in italics, the terminator sequences are , and the FRT site is
boxed. A portion of the araD gene is in dashes. In some
embodiments, genetically engineered bacteria comprise a nucleic
acid sequence that is at least about 80%, at least about 85%, at
least about 90%, at least about 95%, or at least about 99%
homologous to the BAD promoter sequence of SEQ ID NO: 67 or a
functional fragment thereof. In some embodiments, genetically
engineered bacteria comprise the BAD promoter sequence of SEQ ID
NO: 67 or a functional fragment thereof.
TABLE-US-00024 TABLE 19 Nucleotide sequence of exemplary BAD
promoter-driven argA.sup.fbr (SEQ ID NO: 67)
cgacggtggcgataggcatccgggtggtgctcaaaagcagcttcgcctgactgatgcgct
ggtcctcgcgccagcttaatacgctaatccctaactgctggcggaacaaatgcgacagac
gcgacggcgacaggcagacatgctgtgcgacgctggcgatatcaaaattactgtctgcca
ggtgatcgctgatgtactgacaagcctcgcgtacccgattatccatcggtggatggagcg
actcgttaatcgcttccatgcgccgcagtaacaattgctcaagcagatttatcgccagca
attccgaatagcgcccttccccttgtccggcattaatgatttgcccaaacaggtcgctga
aatgcggctggtgcgcttcatccgggcgaaagaaaccggtattggcaaatatcgacggcc
agttaagccattcatgccagtaggcgcgcggacgaaagtaaacccactggtgataccatt
cgtgagcctccggatgacgaccgtagtgatgaatctctccaggcgggaacagcaaaatat
cacccggtcggcagacaaattctcgtccctgatttttcaccaccccctgaccgcgaatgg
tgagattgagaatataacctttcattcccagcggtcggtcgataaaaaaatcgagataac
cgttggcctcaatcggcgttaaacccgccaccagatgggcgttaaacgagtatcccggca
gcaggggatcattttgcgcttcagccatacttttcatactcccgccattcagagaagaaa
ccaattgtccatattgcatcagacattgccgtcactgcgtcttttactggctcttctcgc
taacccaaccggtaaccccgcttattaaaagcattctgtaacaaagcgggaccaaagcca
tgacaaaaacgcgtaacaaaagtgtctataatcacggcagaaaagtccacattgattatt
tgcacggcgtcacactttgctatgccatagcatttttatccataagattagcggatccag
##STR00126## ##STR00127##
[0431] Arabinose inducible promoters are known in the art,
including P.sub.ara, P.sub.araB, P.sub.araC, and P.sub.araBAD. In
one embodiment, the arabinose inducible promoter is from E. coli.
In some embodiments, the P.sub.araC promoter and the P.sub.araBAD
promoter operate as a bidirectional promoter, with the P.sub.araBAD
promoter controlling expression of a heterologous gene(s) in one
direction, and the P.sub.araC (in close proximity to, and on the
opposite strand from the P.sub.araBAD promoter), controlling
expression of a heterologous gene(s) in the other direction. In the
presence of arabinose, transcription of both heterologous genes
from both promoters is induced. However, in the absence of
arabinose, transcription of both heterologous genes from both
promoters is not induced.
[0432] In one exemplary embodiment of the disclosure, the
engineered bacteria of the present disclosure contains a
kill-switch having at least the following sequences: a P.sub.araBAD
promoter operably linked to a heterologous gene encoding a
tetracycline repressor protein (TetR), a P.sub.araC promoter
operably linked to a heterologous gene encoding AraC transcription
factor, and a heterologous gene encoding a bacterial toxin operably
linked to a promoter which is repressed by the tetracycline
repressor protein (P.sub.TetR). In the presence of arabinose, the
AraC transcription factor activates the P.sub.araBAD promoter,
which activates transcription of the TetR protein which, in turn,
represses transcription of the toxin. In the absence of arabinose,
however, AraC suppresses transcription from the P.sub.araBAD
promoter and no TetR protein is expressed. In this case, expression
of the heterologous toxin gene is activated, and the toxin is
expressed. The toxin builds up in the recombinant bacterial cell,
and the recombinant bacterial cell is killed. In one embodiment,
the araC gene encoding the AraC transcription factor is under the
control of a constitutive promoter and is therefore constitutively
expressed.
[0433] In one embodiment of the disclosure, the recombinant
bacterial cell further comprises an anti-toxin under the control of
a constitutive promoter. In this situation, in the presence of
arabinose, the toxin is not expressed due to repression by TetR
protein, and the anti-toxin protein builds-up in the cell. However,
in the absence of arabinose, TetR protein is not expressed, and
expression of the toxin is induced. The toxin begins to build-up
within the recombinant bacterial cell. The recombinant bacterial
cell is no longer viable once the toxin protein is present at
either equal or greater amounts than that of the anti-toxin protein
in the cell, and the recombinant bacterial cell will be killed by
the toxin.
[0434] In another embodiment of the disclosure, the recombinant
bacterial cell further comprises an anti-toxin under the control of
the P.sub.araBAD promoter. In this situation, in the presence of
arabinose, TetR and the anti-toxin are expressed, the anti-toxin
builds up in the cell, and the toxin is not expressed due to
repression by TetR protein. However, in the absence of arabinose,
both the TetR protein and the anti-toxin are not expressed, and
expression of the toxin is induced. The toxin begins to build-up
within the recombinant bacterial cell. The recombinant bacterial
cell is no longer viable once the toxin protein is expressed, and
the recombinant bacterial cell will be killed by the toxin.
[0435] In another exemplary embodiment of the disclosure, the
engineered bacteria of the present disclosure contain a kill-switch
having at least the following sequences: a P.sub.araBAD promoter
operably linked to a heterologous gene encoding an essential
polypeptide not found in the recombinant bacterial cell (and
required for survival), and a P araC promoter operably linked to a
heterologous gene encoding the AraC transcription factor. In the
presence of arabinose, the AraC transcription factor activates the
P.sub.araBAD promoter, which activates transcription of the
heterologous gene encoding the essential polypeptide, allowing the
recombinant bacterial cell to survive. In the absence of arabinose,
however, AraC suppresses transcription from the P.sub.araBAD
promoter and the essential protein required for survival is not
expressed. In this case, the recombinant bacterial cell dies in the
absence of arabinose. In some embodiments, the sequence of
P.sub.araBAD promoter operably linked to a heterologous gene
encoding an essential polypeptide not found in the recombinant
bacterial cell can be present in the bacterial cell in conjunction
with the TetR/toxin kill-switch system described directly above. In
some embodiments, the sequence of P.sub.araBAD promoter operably
linked to a heterologous gene encoding an essential polypeptide not
found in the recombinant bacterial cell can be present in the
bacterial cell in conjunction with the TetR/toxin/anti-toxin
kill-switch system described directly above.
[0436] In yet other embodiments, the bacteria may comprise a
plasmid stability system with a plasmid that produces both a
short-lived anti-toxin and a long-lived toxin. In this system, the
bacterial cell produces equal amounts of toxin and anti-toxin to
neutralize the toxin. However, if/when the cell loses the plasmid,
the short-lived anti-toxin begins to decay. When the anti-toxin
decays completely the cell dies as a result of the longer-lived
toxin killing it.
[0437] In some embodiments, the engineered bacteria of the present
disclosure, for example, bacteria expressing argA.sup.fbr and
repressor ArgR further comprise the gene(s) encoding the components
of any of the above-described kill-switch circuits.
[0438] In any of the above-described embodiments, the bacterial
toxin is selected from the group consisting of a lysin, Hok, Fst,
TisB, LdrD, Kid, SymE, MazF, FlmA, Ibs, XCV2162, dinJ, CcdB, MazF,
ParE, YafO, Zeta, hicB, relB, yhaV, yoeB, chpBK, hipA, microcin B,
microcin B17, microcin C, microcin C7-C51, microcin J25, microcin
ColV, microcin 24, microcin L, microcin D93, microcin L, microcin
E492, microcin H47, microcin 147, microcin M, colicin A, colicin
E1, colicin K, colicin N, colicin U, colicin B, colicin Ia, colicin
Ib, colicin 5, colicin10, colicin S4, colicin Y, colicin E2,
colicin E7, colicin E8, colicin E9, colicin E3, colicin E4, colicin
E6; colicin E5, colicin D, colicin M, and cloacin DF13, or a
biologically active fragment thereof.
[0439] In any of the above-described embodiments, the anti-toxin is
selected from the group consisting of an anti-lysin, Sok, RNAII,
IstR, RdlD, Kis, SymR, MazE, FlmB, Sib, ptaRNA1, yafQ, CcdA, MazE,
ParD, yafN, Epsilon, HicA, relE, prlF, yefM, chpBI, hipB, MccE,
MccE.sup.CTD, MccF, Cai, ImmE1, Cki, Cni, Cui, Cbi, Iia, Imm, Cfi,
Im10, Csi, Cyi, Im2, Im7, Im8, Im9, Im3, Im4, ImmE6, cloacin
immunity protein (Cim), ImmE5, ImmD, and Cmi, or a biologically
active fragment thereof.
[0440] In one embodiment, the bacterial toxin is bactericidal to
the genetically engineered bacterium. In one embodiment, the
bacterial toxin is bacteriostatic to the genetically engineered
bacterium.
[0441] In some embodiments, the engineered bacteria provided herein
have an arginine regulon comprising one or more nucleic acid
mutations that reduce or eliminate arginine-mediated repression of
each of the operons that encode the enzymes responsible for
converting glutamate to arginine and/or an intermediate byproduct,
e.g., citrulline, in the arginine biosynthesis pathway, such that
the mutant arginine regulon produces more arginine and/or
intermediate byproduct than an unmodified regulon from the same
bacterial subtype under the same conditions. In some embodiments,
the genetically engineered bacteria comprise an arginine feedback
resistant N-acetylglutamate synthase mutant, e.g., argA.sup.fbr. In
some embodiments, the genetically engineered bacteria comprise a
mutant arginine regulon comprising one or more nucleic acid
mutations in at least one ARG box for each of the operons that
encode the arginine biosynthesis enzymes N-acetylglutamate kinase,
N-acetylglutamylphosphate reductase, acetylornithine am
inotransferase, N-acetylornithinase, ornithine transcarbamylase,
argininosuccinate synthase, argininosuccinate lyase, and
carbamoylphosphate synthase, thereby derepressing the regulon and
enhancing arginine and/or intermediate byproduct biosynthesis. In
some embodiments, the genetically engineered bacteria further
comprise an arginine feedback resistant N-acetylglutamate synthase
mutant. In some embodiments, the arginine feedback resistant
N-acetylglutamate synthase mutant is controlled by an oxygen
level-dependent promoter. In some embodiments, the arginine
feedback resistant N-acetylglutamate synthase mutant is controlled
by a promoter that is induced under low-oxygen or anaerobic
conditions. In some embodiments, the promoter is selected from the
fumarate and nitrate reductase regulator (FNR) promoter, arginine
deiminiase and nitrate reduction (ANR) promoter, and dissimilatory
nitrate respiration regulator (DNR) promoter. In some embodiments,
the arginine feedback resistant N-acetylglutamate synthase mutant
is argA.sup.fbr.
[0442] In some embodiments, the genetically engineered bacteria
comprise a mutant arginine regulon comprising one or more nucleic
acid mutations in at least one ARG box for each of the operons that
encode the arginine biosynthesis enzymes and an arginine feedback
resistant N-acetylglutamate synthase mutant. In some embodiments,
the genetically engineered bacteria comprise a mutant arginine
regulon, wherein the bacterium comprises a gene encoding a
functional N-acetylglutamate synthetase that is mutated to reduce
arginine feedback inhibition as compared to a wild-type
N-acetylglutamate synthetase from the same bacterial subtype under
the same conditions, wherein expression of the gene encoding the
mutated N-acetylglutamate synthetase is controlled by a promoter
that is induced under low-oxygen or anaerobic conditions, wherein
the mutant arginine regulon comprises one or more operons
comprising genes that encode arginine biosynthesis enzymes
N-acetylglutamate kinase, N-acetylglutamate phosphate reductase,
acetylornithine aminotransferase, N-acetylornithinase,
carbamoylphosphate synthase, ornithine transcarbamylase,
argininosuccinate synthase, and argininosuccinate lyase, and
wherein each operon comprises one or more mutated ARG box(es)
characterized by one or more nucleic acid mutations that reduces
arginine-mediated repression of the operon via ArgR repressor
binding, and retains RNA polymerase binding with sufficient
affinity to promote transcription of the genes in the operon.
[0443] In some embodiments, the genetically engineered bacteria is
an auxotroph comprising a mutant arginine regulon comprising one or
more nucleic acid mutations in at least one ARG box for each of the
operons that encode the arginine biosynthesis enzymes and an
arginine feedback resistant N-acetylglutamate synthase mutant. In
one embodiment, the genetically engineered bacteria comprising a
mutant arginine regulon comprising one or more nucleic acid
mutations in at least one ARG box for each of the operons that
encode the arginine biosynthesis enzymes and an arginine feedback
resistant N-acetylglutamate synthase mutant is an auxotroph
selected from a cysE, glnA, ilvD, leuB, lysA, serA, metA, glyA,
hisB, ilvA, pheA, proA, thrC, trpC, tyrA, thyA, uraA, dapA, dapB,
dapD, dapE, dapF, flhD, metB, metC, proAB, and thi1 auxotroph. In
some embodiments, the engineered bacteria have more than one
auxotrophy, for example, they may be a .DELTA.thyA and .DELTA.dapA
auxotroph.
[0444] In some embodiments, the genetically engineered bacteria
comprising a mutant arginine regulon comprising one or more nucleic
acid mutations in at least one ARG box for each of the operons that
encode the arginine biosynthesis enzymes and an arginine feedback
resistant N-acetylglutamate synthase mutant further comprises a
kill-switch circuit, such as any of the kill-switch circuits
provided herein. For example, in some embodiments, the genetically
engineered bacteria further comprise one or more genes encoding one
or more recombinase(s) under the control of an inducible promoter
and an inverted toxin sequence. In some embodiments, the
genetically engineered bacteria further comprise one or more genes
encoding an anti-toxin. In some embodiments, the engineered
bacteria further comprise one or more genes encoding one or more
recombinase(s) under the control of an inducible promoter and one
or more inverted excision genes, wherein the excision gene(s)
encode an enzyme that deletes an essential gene. In some
embodiments, the genetically engineered bacteria further comprise
one or more genes encoding an anti-toxin. In some embodiments, the
engineered bacteria further comprise one or more genes encoding a
toxin under the control of a promoter having a TetR repressor
binding site and a gene encoding the TetR under the control of an
inducible promoter that is induced by arabinose, such as
P.sub.araBAD. In some embodiments, the genetically engineered
bacteria further comprise one or more genes encoding an
anti-toxin.
[0445] In some embodiments, the genetically engineered bacteria is
an auxotroph comprising a mutant arginine regulon comprising one or
more nucleic acid mutations in at least one ARG box for each of the
operons that encode the arginine biosynthesis enzymes and an
arginine feedback resistant N-acetylglutamate synthase mutant and
further comprises a kill-switch circuit, such as any of the
kill-switch circuits described herein.
[0446] In some embodiments of the above described genetically
engineered bacteria, the gene encoding the arginine feedback
resistant N-acetylglutamate synthetase is present on a plasmid in
the bacterium and operatively linked on the plasmid to the promoter
that is induced under low-oxygen or anaerobic conditions. In other
embodiments, the gene encoding the arginine feedback resistant
N-acetylglutamate synthetase is present in the bacterial chromosome
and is operatively linked in the chromosome to the promoter that is
induced under low-oxygen or anaerobic conditions.
[0447] In some embodiments, the genetically engineered bacteria
comprise a mutant arginine repressor comprising one or more nucleic
acid mutations such that arginine repressor function is decreased
or inactive, or the genetically engineered bacteria do not have an
arginine repressor (e.g., the arginine repressor gene has been
deleted), resulting in derepression of the regulon and enhancement
of arginine and/or intermediate byproduct biosynthesis. In some
embodiments, the genetically engineered bacteria further comprise
an arginine feedback resistant N-acetylglutamate synthase mutant.
In some embodiments, the arginine feedback resistant
N-acetylglutamate synthase mutant is controlled by an oxygen
level-dependent promoter. In some embodiments, the arginine
feedback resistant N-acetylglutamate synthase mutant is controlled
by a promoter that is induced under low-oxygen or anaerobic
conditions. In some embodiments, the promoter is selected from the
fumarate and nitrate reductase regulator (FNR) promoter, arginine
deiminiase and nitrate reduction (ANR) promoter, and dissimilatory
nitrate respiration regulator (DNR) promoter. In some embodiments,
the arginine feedback resistant N-acetylglutamate synthase mutant
is argA.sup.fbr.
[0448] In some embodiments, the genetically engineered bacteria
comprise a mutant or deleted arginine repressor and an arginine
feedback resistant N-acetylglutamate synthase mutant. In some
embodiments, the genetically engineered bacterium comprise an
arginine regulon, wherein the bacterium comprises a gene encoding a
functional N-acetylglutamate synthetase with reduced arginine
feedback inhibition as compared to a wild-type N-acetylglutamate
synthetase from the same bacterial subtype under the same
conditions, wherein expression of the gene encoding arginine
feedback resistant N-acetylglutamate synthetase is controlled by a
promoter that is induced by exogenous environmental conditions and
wherein the bacterium has been genetically engineered to lack a
functional ArgR repressor.
[0449] In some embodiments, the genetically engineered bacteria
comprising a mutant or deleted arginine repressor and an arginine
feedback resistant N-acetylglutamate synthase mutant is an
auxotroph. In one embodiment, the genetically engineered bacteria
comprising a mutant or deleted arginine repressor and an arginine
feedback resistant N-acetylglutamate synthase mutant is an
auxotroph selected from a cysE, glnA, ilvD, leuB, lysA, serA, metA,
glyA, hisB, ilvA, pheA, proA, thrC, trpC, tyrA, thyA, uraA, dapA,
dapB, dapD, dapE, dapF, flhD, metB, metC, proAB, and thi1
auxotroph. In some embodiments, the engineered bacteria have more
than one auxotrophy, for example, they may be a .DELTA.thyA and
.DELTA.dapA auxotroph.
[0450] In some embodiments, the genetically engineered bacteria
comprising a mutant or deleted arginine repressor and an arginine
feedback resistant N-acetylglutamate synthase mutant further
comprise a kill-switch circuit, such as any of the kill-switch
circuits provided herein. For example, in some embodiments, the
genetically engineered bacteria further comprise one or more genes
encoding one or more recombinase(s) under the control of an
inducible promoter, and an inverted toxin sequence. In some
embodiments, the genetically engineered bacteria further comprise
one or more genes encoding an anti-toxin. In some embodiments, the
engineered bacteria further comprise one or more genes encoding one
or more recombinase(s) under the control of an inducible promoter
and one or more inverted excision genes, wherein the excision
gene(s) encode an enzyme that deletes an essential gene. In some
embodiments, the genetically engineered bacteria further comprise
one or more genes encoding an anti-toxin. In some embodiments, the
engineered bacteria further comprise one or more genes encoding a
toxin under the control of a promoter having a TetR repressor
binding site and a gene encoding the TetR under the control of an
inducible promoter that is induced by arabinose, such as
P.sub.araBAD. In some embodiments, the genetically engineered
bacteria further comprise one or more genes encoding an
anti-toxin.
[0451] In some embodiments, the genetically engineered bacterium is
an auxotroph comprising a mutant or deleted arginine repressor and
an arginine feedback resistant N-acetylglutamate synthase mutant
and further comprises a kill-switch circuit, such as any of the
kill-switch circuits described herein.
[0452] In some embodiments of the above described genetically
engineered bacteria, the gene encoding the arginine feedback
resistant N-acetylglutamate synthetase is present on a plasmid in
the bacterium and operatively linked on the plasmid to the promoter
that is induced under low-oxygen or anaerobic conditions. In other
embodiments, the gene encoding the arginine feedback resistant
N-acetylglutamate synthetase is present in the bacterial chromosome
and is operatively linked in the chromosome to the promoter that is
induced under low-oxygen or anaerobic conditions.
[0453] Ammonia Transport
[0454] Ammonia transporters may further be expressed or modified in
the genetically engineered bacteria of the invention in order to
enhance ammonia transport into the cell. AmtB is a membrane
transport protein that transports ammonia into bacterial cells. In
some embodiments, the genetically engineered bacteria of the
invention also comprise multiple copies of the native amtB gene. In
some embodiments, the genetically engineered bacteria of the
invention also comprise an amtB gene from a different bacterial
species. In some embodiments, the genetically engineered bacteria
of the invention comprise multiple copies of an amtB gene from a
different bacterial species. In some embodiments, the native amtB
gene in the genetically engineered bacteria of the invention is not
modified. In some embodiments, the genetically engineered bacteria
of the invention comprise an amtB gene that is controlled by its
native promoter, an inducible promoter, or a promoter that is
stronger than the native promoter, e.g., a GlnRS promoter, a P(Bla)
promoter, or a constitutive promoter.
[0455] In some embodiments, the native amtB gene in the genetically
engineered bacteria is not modified, and one or more additional
copies of the native amtB gene are inserted into the genome under
the control of the same inducible promoter that controls expression
of argA.sup.fbr, e.g., a FNR promoter, or a different inducible
promoter than the one that controls expression of argA.sup.fbr or a
constitutive promoter. In alternate embodiments, the native amtB
gene is not modified, and a copy of a non-native amtB gene from a
different bacterial species is inserted into the genome under the
control of the same inducible promoter that controls expression of
argA.sup.fbr, e.g., a FNR promoter, or a different inducible
promoter than the one that controls expression of argA.sup.fbr or a
constitutive promoter.
[0456] In some embodiments, the native amtB gene in the genetically
engineered bacteria is not modified, and one or more additional
copies of the native amtB gene are present in the bacteria on a
plasmid and under the control of the same inducible promoter that
controls expression of argA.sup.fbr, e.g., a FNR promoter, or a
different inducible promoter than the one that controls expression
of argA.sup.fbr or a constitutive promoter. In alternate
embodiments, the native amtB gene is not modified, and a copy of a
non-native amtB gene from a different bacterial species is present
in the bacteria on a plasmid and under the control of the same
inducible promoter that controls expression of argA.sup.fbr, e.g.,
a FNR promoter, or a different inducible promoter than the one that
controls expression of argA.sup.fbr or a constitutive promoter.
[0457] In some embodiments, the native amtB gene is mutagenized,
the mutants exhibiting increased ammonia transport are selected,
and the mutagenized amtB gene is isolated and inserted into the
genetically engineered bacteria. In some embodiments, the native
amtB gene is mutagenized, mutants exhibiting increased ammonia
transport are selected, and those mutants are used to produce the
bacteria of the invention. The ammonia transporter modifications
described herein may be present on a plasmid or chromosome.
[0458] In some embodiments, the genetically engineered bacterium is
E. coli Nissle, and the native amtB gene in E. coli Nissle is not
modified; one or more additional copies the native E. coli Nissle
amtB genes are inserted into the E. coli Nissle genome under the
control of the same inducible promoter that controls expression of
argA.sup.fbr, e.g., a FNR promoter, or a different inducible
promoter than the one that controls expression of argA.sup.fbr or a
constitutive promoter. In an alternate embodiment, the native amtB
gene in E. coli Nissle is not modified, and a copy of a non-native
amtB gene from a different bacterium, e.g., Lactobacillus
plantarum, is inserted into the E. coli Nissle genome under the
control of the same inducible promoter that controls expression of
argA.sup.fbr, e.g., a FNR promoter, or a different inducible
promoter than the one that controls expression of argA.sup.fbr or a
constitutive promoter.
[0459] In some embodiments, the genetically engineered bacterium is
E. coli Nissle, and the native amtB gene in E. coli Nissle is not
modified; one or more additional copies the native E. coli Nissle
amtB genes are present in the bacterium on a plasmid and under the
control of the same inducible promoter that controls expression of
argA.sup.fbr, e.g., a FNR promoter, or a different inducible
promoter than the one that controls expression of argA.sup.fbr, or
a constitutive promoter. In an alternate embodiment, the native
amtB gene in E. coli Nissle is not modified, and a copy of a
non-native amtB gene from a different bacterium, e.g.,
Lactobacillus plantarum, are present in the bacterium on a plasmid
and under the control of the same inducible promoter that controls
expression of argA.sup.fbr, e.g., a FNR promoter, or a different
inducible promoter than the one that controls expression of
argA.sup.fbr, or a constitutive promoter.
[0460] Pharmaceutical Compositions and Formulations
[0461] Pharmaceutical compositions comprising the genetically
engineered bacteria described herein may be used to treat, manage,
ameliorate, and/or prevent a disorder associated with
hyperammonemia or symptom(s) associated with hyperammonemia.
Pharmaceutical compositions comprising one or more genetically
engineered bacteria, alone or in combination with prophylactic
agents, therapeutic agents, and/or pharmaceutically acceptable
carriers are provided.
[0462] In certain embodiments, the pharmaceutical composition
comprises one species, strain, or subtype of bacteria that are
engineered to comprise the genetic modifications described herein.
In alternate embodiments, the pharmaceutical composition comprises
two or more species, strains, and/or subtypes of bacteria that are
each engineered to comprise the genetic modifications described
herein.
[0463] The pharmaceutical compositions described herein may be
formulated in a conventional manner using one or more
physiologically acceptable carriers comprising excipients and
auxiliaries, which facilitate processing of the active ingredients
into compositions for pharmaceutical use. Methods of formulating
pharmaceutical compositions are known in the art (see, e.g.,
"Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton,
Pa.). In some embodiments, the pharmaceutical compositions are
subjected to tabletting, lyophilizing, direct compression,
conventional mixing, dissolving, granulating, levigating,
emulsifying, encapsulating, entrapping, or spray drying to form
tablets, granulates, nanoparticles, nanocapsules, microcapsules,
microtablets, pellets, or powders, which may be enterically coated
or uncoated. Appropriate formulation depends on the route of
administration.
[0464] The genetically engineered bacteria described herein may be
formulated into pharmaceutical compositions in any suitable dosage
form (e.g., liquids, capsules, sachet, hard capsules, soft
capsules, tablets, enteric coated tablets, suspension powders,
granules, or matrix sustained release formations for oral
administration) and for any suitable type of administration (e.g.,
oral, topical, injectable, immediate-release, pulsatile-release,
delayed-release, or sustained release). Suitable dosage amounts for
the genetically engineered bacteria may range from about 10.sup.5
to 10.sup.12 bacteria, e.g., approximately 10.sup.5 bacteria,
approximately 10.sup.6 bacteria, approximately 10.sup.7 bacteria,
approximately 10.sup.8 bacteria, approximately 10.sup.9 bacteria,
approximately 10.sup.10 bacteria, approximately 10.sup.11 bacteria,
or approximately 10.sup.11 bacteria. The composition may be
administered once or more daily, weekly, or monthly. The
composition may be administered before, during, or following a
meal. In one embodiment, the pharmaceutical composition is
administered before the subject eats a meal. In one embodiment, the
pharmaceutical composition is administered currently with a meal.
In one embodiment, the pharmaceutical composition is administered
after the subject eats a meal.
[0465] The composition may be administered once or more daily,
weekly, or monthly. The genetically engineered bacteria may be
formulated into pharmaceutical compositions comprising one or more
pharmaceutically acceptable carriers, thickeners, diluents,
buffers, buffering agents, surface active agents, neutral or
cationic lipids, lipid complexes, liposomes, penetration enhancers,
carrier compounds, and other pharmaceutically acceptable carriers
or agents. For example, the pharmaceutical composition may include,
but is not limited to, the addition of calcium bicarbonate, sodium
bicarbonate, calcium phosphate, various sugars and types of starch,
cellulose derivatives, gelatin, vegetable oils, polyethylene
glycols, and surfactants, including, for example, polysorbate 20.
In some embodiments, the genetically engineered bacteria of the
invention may be formulated in a solution of sodium bicarbonate,
e.g., 1 molar solution of sodium bicarbonate (to buffer an acidic
cellular environment, such as the stomach, for example). The
genetically engineered bacteria may be administered and formulated
as neutral or salt forms. Pharmaceutically acceptable salts include
those formed with anions such as those derived from hydrochloric,
phosphoric, acetic, oxalic, tartaric acids, etc., and those formed
with cations such as those derived from sodium, potassium,
ammonium, calcium, ferric hydroxides, isopropylamine,
triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
[0466] The genetically engineered bacteria disclosed herein may be
administered topically and formulated in the form of an ointment,
cream, transdermal patch, lotion, gel, shampoo, spray, aerosol,
solution, emulsion, or other form well-known to one of skill in the
art. See, e.g., "Remington's Pharmaceutical Sciences," Mack
Publishing Co., Easton, Pa. In an embodiment, for non-sprayable
topical dosage forms, viscous to semi-solid or solid forms
comprising a carrier or one or more excipients compatible with
topical application and having a dynamic viscosity greater than
water are employed. Suitable formulations include, but are not
limited to, solutions, suspensions, emulsions, creams, ointments,
powders, liniments, salves, etc., which may be sterilized or mixed
with auxiliary agents (e.g., preservatives, stabilizers, wetting
agents, buffers, or salts) for influencing various properties,
e.g., osmotic pressure. Other suitable topical dosage forms include
sprayable aerosol preparations wherein the active ingredient in
combination with a solid or liquid inert carrier, is packaged in a
mixture with a pressurized volatile (e.g., a gaseous propellant,
such as freon) or in a squeeze bottle. Moisturizers or humectants
can also be added to pharmaceutical compositions and dosage forms.
Examples of such additional ingredients are well known in the art.
In one embodiment, the pharmaceutical composition comprising the
recombinant bacteria of the invention may be formulated as a
hygiene product. For example, the hygiene product may be an
antibacterial formulation, or a fermentation product such as a
fermentation broth. Hygiene products may be, for example, shampoos,
conditioners, creams, pastes, lotions, and lip balms.
[0467] The genetically engineered bacteria disclosed herein may be
administered orally and formulated as tablets, pills, dragees,
capsules, liquids, gels, syrups, slurries, suspensions, etc.
Pharmacological compositions for oral use can be made using a solid
excipient, optionally grinding the resulting mixture, and
processing the mixture of granules, after adding suitable
auxiliaries if desired, to obtain tablets or dragee cores. Suitable
excipients include, but are not limited to, fillers such as sugars,
including lactose, sucrose, mannitol, or sorbitol; cellulose
compositions such as maize starch, wheat starch, rice starch,
potato starch, gelatin, gum tragacanth, methyl cellulose,
hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and/or
physiologically acceptable polymers such as polyvinylpyrrolidone
(PVP) or polyethylene glycol (PEG). Disintegrating agents may also
be added, such as cross-linked polyvinylpyrrolidone, agar, alginic
acid or a salt thereof such as sodium alginate.
[0468] Tablets or capsules can be prepared by conventional means
with pharmaceutically acceptable excipients such as binding agents
(e.g., pregelatinised maize starch, polyvinylpyrrolidone,
hydroxypropyl methylcellulose, carboxymethylcellulose, polyethylene
glycol, sucrose, glucose, sorbitol, starch, gum, kaolin, and
tragacanth); fillers (e.g., lactose, microcrystalline cellulose, or
calcium hydrogen phosphate); lubricants (e.g., calcium, aluminum,
zinc, stearic acid, polyethylene glycol, sodium lauryl sulfate,
starch, sodium benzoate, L-leucine, magnesium stearate, talc, or
silica); disintegrants (e.g., starch, potato starch, sodium starch
glycolate, sugars, cellulose derivatives, silica powders); or
wetting agents (e.g., sodium lauryl sulphate). The tablets may be
coated by methods well known in the art. A coating shell may be
present, and common membranes include, but are not limited to,
polylactide, polyglycolic acid, polyanhydride, other biodegradable
polymers, alginate-polylysine-alginate (APA),
alginate-polymethylene-co-guanidine-alginate (A-PMCG-A),
hydroymethylacrylate-methyl methacrylate (HEMA-MMA), multilayered
HEMA-MMA-MAA, polyacrylonitrilevinylchloride (PAN-PVC),
acrylonitrile/sodium methallylsulfonate (AN-69), polyethylene
glycol/poly pentamethylcyclopentasiloxane/polydimethylsiloxane
(PEG/PD5/PDMS), poly N,N-dimethyl acrylamide (PDMAAm), siliceous
encapsulates, cellulose sulphate/sodium
alginate/polymethylene-co-guanidine (CS/A/PMCG), cellulose acetate
phthalate, calcium alginate, k-carrageenan-locust bean gum gel
beads, gellan-xanthan beads, poly(lactide-co-glycolides),
carrageenan, starch polyanhydrides, starch polymethacrylates,
polyamino acids, and enteric coating polymers.
[0469] In some embodiments, the genetically engineered bacteria are
enterically coated for release into the gut or a particular region
of the gut, for example, the large intestine. The typical pH
profile from the stomach to the colon is about 1-4 (stomach), 5.5-6
(duodenum), 7.3-8.0 (ileum), and 5.5-6.5 (colon). In some diseases,
the pH profile may be modified. In some embodiments, the coating is
degraded in specific pH environments in order to specify the site
of release. In some embodiments, at least two coatings are used. In
some embodiments, the outside coating and the inside coating are
degraded at different pH levels.
[0470] Liquid preparations for oral administration may take the
form of solutions, syrups, suspensions, or a dry product for
constitution with water or other suitable vehicle before use. Such
liquid preparations may be prepared by conventional means with
pharmaceutically acceptable agents such as suspending agents (e.g.,
sorbitol syrup, cellulose derivatives, or hydrogenated edible
fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous
vehicles (e.g., almond oil, oily esters, ethyl alcohol, or
fractionated vegetable oils); and preservatives (e.g., methyl or
propyl-p-hydroxybenzoates or sorbic acid). The preparations may
also contain buffer salts, flavoring, coloring, and sweetening
agents as appropriate. Preparations for oral administration may be
suitably formulated for slow release, controlled release, or
sustained release of the genetically engineered bacteria described
herein.
[0471] In one embodiment, the genetically engineered bacteria of
the disclosure may be formulated in a composition suitable for
administration to pediatric subjects. As is well known in the art,
children differ from adults in many aspects, including different
rates of gastric emptying, pH, gastrointestinal permeability, etc.
(Ivanovska et al., 2014). Moreover, pediatric formulation
acceptability and preferences, such as route of administration and
taste attributes, are critical for achieving acceptable pediatric
compliance. Thus, in one embodiment, the composition suitable for
administration to pediatric subjects may include easy-to-swallow or
dissolvable dosage forms, or more palatable compositions, such as
compositions with added flavors, sweeteners, or taste blockers. In
one embodiment, a composition suitable for administration to
pediatric subjects may also be suitable for administration to
adults.
[0472] In one embodiment, the composition suitable for
administration to pediatric subjects may include a solution, syrup,
suspension, elixir, powder for reconstitution as suspension or
solution, dispersible/effervescent tablet, chewable tablet, gummy
candy, lollipop, freezer pop, troche, chewing gum, oral thin strip,
orally disintegrating tablet, sachet, soft gelatin capsule,
sprinkle oral powder, or granules. In one embodiment, the
composition is a gummy candy, which is made from a gelatin base,
giving the candy elasticity, desired chewy consistency, and longer
shelf-life. In some embodiments, the gummy candy may also comprise
sweeteners or flavors.
[0473] In one embodiment, the composition suitable for
administration to pediatric subjects may include a flavor. As used
herein, "flavor" is a substance (liquid or solid) that provides a
distinct taste and aroma to the formulation. Flavors also help to
improve the palatability of the formulation. Flavors include, but
are not limited to, strawberry, vanilla, lemon, grape, bubble gum,
and cherry.
[0474] In certain embodiments, the genetically engineered bacteria
may be orally administered, for example, with an inert diluent or
an assimilable edible carrier. The compound may also be enclosed in
a hard or soft shell gelatin capsule, compressed into tablets, or
incorporated directly into the subject's diet. For oral therapeutic
administration, the compounds may be incorporated with excipients
and used in the form of ingestible tablets, buccal tablets,
troches, capsules, elixirs, suspensions, syrups, wafers, and the
like. To administer a compound by other than parenteral
administration, it may be necessary to coat the compound with, or
co-administer the compound with, a material to prevent its
inactivation.
[0475] In another embodiment, the pharmaceutical composition
comprising the recombinant bacteria of the invention may be a
comestible product, for example, a food product. In one embodiment,
the food product is milk, concentrated milk, fermented milk
(yogurt, sour milk, frozen yogurt, lactic acid bacteria-fermented
beverages), milk powder, ice cream, cream cheeses, dry cheeses,
soybean milk, fermented soybean milk, vegetable-fruit juices, fruit
juices, sports drinks, confectionery, candies, infant foods (such
as infant cakes), nutritional food products, animal feeds, or
dietary supplements. In one embodiment, the food product is a
fermented food, such as a fermented dairy product. In one
embodiment, the fermented dairy product is yogurt. In another
embodiment, the fermented dairy product is cheese, milk, cream, ice
cream, milk shake, or kefir. In another embodiment, the recombinant
bacteria of the invention are combined in a preparation containing
other live bacterial cells intended to serve as probiotics. In
another embodiment, the food product is a beverage. In one
embodiment, the beverage is a fruit juice-based beverage or a
beverage containing plant or herbal extracts. In another
embodiment, the food product is a jelly or a pudding. Other food
products suitable for administration of the recombinant bacteria of
the invention are well known in the art. For example, see U.S.
2015/0359894 and US 2015/0238545, the entire contents of each of
which are expressly incorporated herein by reference. In yet
another embodiment, the pharmaceutical composition of the invention
is injected into, sprayed onto, or sprinkled onto a food product,
such as bread, yogurt, or cheese.
[0476] In some embodiments, the composition is formulated for
intraintestinal administration, intrajejunal administration,
intraduodenal administration, intraileal administration, gastric
shunt administration, or intracolic administration, via
nanoparticles, nanocapsules, microcapsules, or microtablets, which
are enterically coated or uncoated. The pharmaceutical compositions
may also be formulated in rectal compositions such as suppositories
or retention enemas, using, e.g., conventional suppository bases
such as cocoa butter or other glycerides. The compositions may be
suspensions, solutions, or emulsions in oily or aqueous vehicles,
and may contain suspending, stabilizing and/or dispersing
agents.
[0477] The genetically engineered bacteria described herein may be
administered intranasally, formulated in an aerosol form, spray,
mist, or in the form of drops, and conveniently delivered in the
form of an aerosol spray presentation from pressurized packs or a
nebuliser, with the use of a suitable propellant (e.g.,
dichlorodifluoromethane, trichlorofluoromethane,
dichlorotetrafluoroethane, carbon dioxide or other suitable gas).
Pressurized aerosol dosage units may be determined by providing a
valve to deliver a metered amount. Capsules and cartridges (e.g.,
of gelatin) for use in an inhaler or insufflator may be formulated
containing a powder mix of the compound and a suitable powder base
such as lactose or starch.
[0478] The genetically engineered bacteria may be administered and
formulated as depot preparations. Such long acting formulations may
be administered by implantation or by injection, including
intravenous injection, subcutaneous injection, local injection,
direct injection, or infusion. For example, the compositions may be
formulated with suitable polymeric or hydrophobic materials (e.g.,
as an emulsion in an acceptable oil) or ion exchange resins, or as
sparingly soluble derivatives (e.g., as a sparingly soluble
salt).
[0479] In some embodiments, disclosed herein are pharmaceutically
acceptable compositions in single dosage forms. Single dosage forms
may be in a liquid or a solid form. Single dosage forms may be
administered directly to a patient without modification or may be
diluted or reconstituted prior to administration. In certain
embodiments, a single dosage form may be administered in bolus
form, e.g., single injection, single oral dose, including an oral
dose that comprises multiple tablets, capsule, pills, etc. In
alternate embodiments, a single dosage form may be administered
over a period of time, e.g., by infusion.
[0480] Single dosage forms of the pharmaceutical composition may be
prepared by portioning the pharmaceutical composition into smaller
aliquots, single dose containers, single dose liquid forms, or
single dose solid forms, such as tablets, granulates,
nanoparticles, nanocapsules, microcapsules, microtablets, pellets,
or powders, which may be enterically coated or uncoated. A single
dose in a solid form may be reconstituted by adding liquid,
typically sterile water or saline solution, prior to administration
to a patient.
[0481] In other embodiments, the composition can be delivered in a
controlled release or sustained release system. In one embodiment,
a pump may be used to achieve controlled or sustained release. In
another embodiment, polymeric materials can be used to achieve
controlled or sustained release of the therapies of the present
disclosure (see, e.g., U.S. Pat. No. 5,989,463). Examples of
polymers used in sustained release formulations include, but are
not limited to, poly(2-hydroxy ethyl methacrylate), poly(methyl
methacrylate), poly(acrylic acid), poly(ethylene-co-vinyl acetate),
poly(methacrylic acid), polyglycolides (PLG), polyanhydrides,
poly(N-vinyl pyrrolidone), poly(vinyl alcohol), polyacrylamide,
poly(ethylene glycol), polylactides (PLA),
poly(lactide-co-glycolides) (PLGA), and polyorthoesters. The
polymer used in a sustained release formulation may be inert, free
of leachable impurities, stable on storage, sterile, and
biodegradable. In some embodiments, a controlled or sustained
release system can be placed in proximity of the prophylactic or
therapeutic target, thus requiring only a fraction of the systemic
dose. Any suitable technique known to one of skill in the art may
be used.
[0482] Dosage regimens may be adjusted to provide a therapeutic
response. Dosing can depend on several factors, including severity
and responsiveness of the disease, route of administration, time
course of treatment (days to months to years), and time to
amelioration of the disease. For example, a single bolus may be
administered at one time, several divided doses may be administered
over a predetermined period of time, or the dose may be reduced or
increased as indicated by the therapeutic situation. The
specification for the dosage is dictated by the unique
characteristics of the active compound and the particular
therapeutic effect to be achieved. Dosage values may vary with the
type and severity of the condition to be alleviated. For any
particular subject, specific dosage regimens may be adjusted over
time according to the individual need and the professional judgment
of the treating clinician. Toxicity and therapeutic efficacy of
compounds provided herein can be determined by standard
pharmaceutical procedures in cell culture or animal models. For
example, LD.sub.50, ED.sub.50, EC.sub.50, and IC.sub.50 may be
determined, and the dose ratio between toxic and therapeutic
effects (LD.sub.50/ED.sub.50) may be calculated as the therapeutic
index. Compositions that exhibit toxic side effects may be used,
with careful modifications to minimize potential damage to reduce
side effects. Dosing may be estimated initially from cell culture
assays and animal models. The data obtained from in vitro and in
vivo assays and animal studies can be used in formulating a range
of dosage for use in humans.
[0483] The ingredients are supplied either separately or mixed
together in unit dosage form, for example, as a dry lyophilized
powder or water-free concentrate in a hermetically sealed container
such as an ampoule or sachet indicating the quantity of active
agent. If the mode of administration is by injection, an ampoule of
sterile water for injection or saline can be provided so that the
ingredients may be mixed prior to administration.
[0484] The pharmaceutical compositions may be packaged in a
hermetically sealed container such as an ampoule or sachet
indicating the quantity of the agent. In one embodiment, one or
more of the pharmaceutical compositions is supplied as a dry
sterilized lyophilized powder or water-free concentrate in a
hermetically sealed container and can be reconstituted (e.g., with
water or saline) to the appropriate concentration for
administration to a subject. In an embodiment, one or more of the
prophylactic or therapeutic agents or pharmaceutical compositions
is supplied as a dry sterile lyophilized powder in a hermetically
sealed container stored between 2.degree. C. and 8.degree. C. and
administered within 1 hour, within 3 hours, within 5 hours, within
6 hours, within 12 hours, within 24 hours, within 48 hours, within
72 hours, or within one week after being reconstituted.
Cryoprotectants can be included for a lyophilized dosage form,
principally 0-10% sucrose (optimally 0.5-1.0%). Other suitable
cryoprotectants include trehalose and lactose. Other suitable
bulking agents include glycine and arginine, either of which can be
included at a concentration of 0-0.05%, and polysorbate-80
(optimally included at a concentration of 0.005-0.01%). Additional
surfactants include but are not limited to polysorbate 20 and BRIJ
surfactants. The pharmaceutical composition may be prepared as an
injectable solution and can further comprise an agent useful as an
adjuvant, such as those used to increase absorption or dispersion,
e.g., hyaluronidase.
[0485] Methods of Treatment
[0486] Another aspect of the invention provides methods of treating
a disease or disorder associated with hyperammonemia. In some
embodiments, the invention provides methods for reducing,
ameliorating, or eliminating one or more symptom(s) associated with
these diseases or disorders. In some embodiments, the disorder is a
urea cycle disorder such as argininosuccinic aciduria, arginase
deficiency, carbamoylphosphate synthetase deficiency,
citrullinemia, N-acetylglutamate synthetase deficiency, and
ornithine transcarbamylase deficiency. In alternate embodiments,
the disorder is a liver disorder such as hepatic encephalopathy,
acute liver failure, or chronic liver failure; organic acid
disorders; isovaleric aciduria; 3-methylcrotonylglycinuria;
methylmalonic acidemia; propionic aciduria; fatty acid oxidation
defects; carnitine cycle defects; carnitine deficiency;
.beta.-oxidation deficiency; lysinuric protein intolerance;
pyrroline-5-carboxylate synthetase deficiency; pyruvate carboxylase
deficiency; ornithine aminotransferase deficiency; carbonic
anhydrase deficiency; hyperinsulinism-hyperammonemia syndrome;
mitochondrial disorders; valproate therapy; asparaginase therapy;
total parenteral nutrition; cystoscopy with glycine-containing
solutions; post-lung/bone marrow transplantation; portosystemic
shunting; urinary tract infections; ureter dilation; multiple
myeloma; chemotherapy; infection; neurogenic bladder; or intestinal
bacterial overgrowth. In some embodiments, the symptom(s)
associated thereof include, but are not limited to, seizures,
ataxia, stroke-like lesions, coma, psychosis, vision loss, acute
encephalopathy, cerebral edema, as well as vomiting, respiratory
alkalosis, and hypothermia.
[0487] The method may comprise preparing a pharmaceutical
composition with at least one genetically engineered species,
strain, or subtype of bacteria described herein, and administering
the pharmaceutical composition to a subject in a therapeutically
effective amount. In some embodiments, the genetically engineered
bacteria of the invention are administered orally, e.g., in a
liquid suspension. In some embodiments, the genetically engineered
bacteria of the invention are lyophilized in a gel cap and
administered orally. In some embodiments, the genetically
engineered bacteria of the invention are administered via a feeding
tube or gastric shunt. In some embodiments, the genetically
engineered bacteria of the invention are administered rectally,
e.g., by enema. In some embodiments, the genetically engineered
bacteria of the invention are administered topically,
intraintestinally, intrajejunally, intraduodenally, intraileally,
and/or intracolically.
[0488] In certain embodiments, administering the pharmaceutical
composition to the subject reduces ammonia concentrations in a
subject. In some embodiments, the methods of the present disclosure
may reduce the ammonia concentration in a subject by at least about
10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or
more as compared to levels in an untreated or control subject. In
some embodiments, reduction is measured by comparing the ammonia
concentration in a subject before and after administration of the
pharmaceutical composition. In some embodiments, the method of
treating or ameliorating hyperammonemia allows one or more symptoms
of the condition or disorder to improve by at least about 10%, 20%,
30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more.
[0489] Before, during, and after the administration of the
pharmaceutical composition, ammonia concentrations in the subject
may be measured in a biological sample, such as blood, serum,
plasma, urine, fecal matter, peritoneal fluid, intestinal mucosal
scrapings, a sample collected from a tissue, and/or a sample
collected from the contents of one or more of the following: the
stomach, duodenum, jejunum, ileum, cecum, colon, rectum, and anal
canal. In some embodiments, the methods may include administration
of the compositions of the invention to reduce ammonia
concentrations in a subject to undetectable levels, or to less than
about 1%, 2%, 5%, 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, or
80% of the subject's ammonia concentrations prior to treatment.
[0490] In certain embodiments, the genetically engineered bacteria
comprising the mutant arginine regulon is E. coli Nissle. The
genetically engineered bacteria may be destroyed, e.g., by defense
factors in the gut or blood serum (Sonnenborn et al., 2009), or by
activation of a kill switch, several hours or days after
administration. Thus, the pharmaceutical composition comprising the
mutant arginine regulon may be re-administered at a therapeutically
effective dose and frequency. Length of Nissle residence in vivo in
mice is shown in FIGS. 34 and 35. In alternate embodiments, the
genetically engineered bacteria are not destroyed within hours or
days after administration and may propagate and colonize the
gut.
[0491] The pharmaceutical composition may be administered alone or
in combination with one or more additional therapeutic agents,
including but not limited to, sodium phenylbutyrate, sodium
benzoate, and glycerol phenylbutyrate. An important consideration
in the selection of the one or more additional therapeutic agents
is that the agent(s) should be compatible with the genetically
engineered bacteria of the invention, e.g., the agent(s) must not
kill the bacteria.
[0492] In one embodiment, the genetically engineered bacteria are
administered for prevention, treatment or management of HE. In some
embodiments, the genetically engineered bacteria are administered
in combination with another therapeutic approach to prevent HE
reoccurrence. In one embodiment, the genetically engineered
bacteria are administered in combination with branched-chain amino
acid supplementation. In one embodiment, the genetically engineered
bacteria are administered in combination with acetyl-l-carnitine
and/or sodium benzoate and/or zinc and/or acarbose and/or ornithine
aspartate. In one embodiment, the genetically engineered bacteria
are administered in combination with non-absorbable disaccharides,
which are commonly applied to both treat and prevent HE in
patients. In one embodiment, the genetically engineered bacteria
are administered in combination with lactulose and/or lactitol.
[0493] In one embodiment, the genetically engineered bacteria are
administered in combination with one or more antibiotics, for
example for the treatment of HE. Examples of such antibiotics
include, but are not limited to, non-absorbable antibiotics, such
as aminoglicosides, e.g., neomycin and/or paramomycin. In one
embodiment, the antibiotic is rifamycin. In one embodiment, the
antibiotic is a rifamycin derivative, e.g., a synthetic derivative,
including but not limited to, rifaximin.
[0494] Rifaximin has been shown to significantly reduce the risk of
an episode of hepatic encephalopathy, as compared with placebo,
over a 6-month period (Bass et a., Rifaximin Treatment in Hepatic
Encephalopathy; N Engl J Med 2010; 362:1071-1081). Rifaximin is a
semi-synthetic derivative of rifampin and acts by binding to the
beta-subunit of bacterial DNA-dependent RNA polymerase, and thereby
blocking transcription. As a result, bacterial protein synthesis
and growth is inhibited.
[0495] Rifaximin has been shown to be active against E. coli both
in vitro and in clinical studies. It therefore is understood that,
for a combination treatment with rifaximin to be effective, the
genetically engineered bacteria must further comprise a rifaximin
resistance.
[0496] Resistance to rifaximin is caused primarily by mutations in
the rpoB gene. This changes the binding site on DNA dependent RNA
polymerase and decreases rifaximin binding affinity, thereby
reducing efficacy. In one embodiment, the rifaximin resistance is a
mutation in the rpoB gene. Non-limiting examples of such mutations
are described in e.g., Rodriguez-Verdugo, Evolution of Escherichia
coli rifampicin resistance in an antibiotic-free environment during
thermal stress. BMC Evol Biol. 2013 Feb. 22; 13:50. Of note,
mutations in the same three codons of the rpoB consensus sequence
occur repeatedly in unrelated rifaximin-resistant clinical isolates
of several different bacterial species (as reviewed in Goldstein,
Resistance to rifampicin: a review; The Journal of Antibiotics
(2014), 1-6, the contents of which is herein incorporated by
reference in its entirety. In some embodiments, the genetically
engineered bacteria comprise a known rifaximin resistance mutation,
e.g., in the rpoB gene. In other embodiments, a screen can be
employed, exposing the genetically engineered bacteria to
increasing amounts of rifaximin, to identify a useful mutation
which confers rifaximin resistance.
[0497] In some embodiments, the pharmaceutical composition is
administered with food. In alternate embodiments, the
pharmaceutical composition is administered before or after eating
food. The pharmaceutical composition may be administered in
combination with one or more dietary modifications, e.g.,
low-protein diet and amino acid supplementation. The dosage of the
pharmaceutical composition and the frequency of administration may
be selected based on the severity of the symptoms and the
progression of the disorder. The appropriate therapeutically
effective dose and/or frequency of administration can be selected
by a treating clinician.
[0498] Table 20 shows non-limiting examples of target degradation
rates, based on levels of phenylalanine on average in) in
hyperammonemic patients (UCD<HE).
TABLE-US-00025 TABLE 20 Target Ammonia Degradation/Arginine
Production Rates Parameter Value Maximum burden of NH.sub.4.sup.+
(in blood) in 825 .mu.mols total excess NH.sub.4.sup.+
hyperammonemic patients (UCD < HE) Total blood ammonia levels:
~1000 .mu.mols; 5 L blood (adult) Arginine production target: 275
.mu.mol/day (1 Arg = 3 NH.sub.4.sup.+) NH.sub.4.sup.+ burden Target
arginine production rate: NH.sub.4.sup.+ 275 .mu.mol/day/10.sup.11
bacteria burden Lab assay target: NH.sub.4.sup.+ burden 0.11
.mu.mol/hr/10.sup.9 bacteria Current arginine production rate 1.25
.mu.mol/hr/10.sup.9 bacteria Maximum flux of NH.sub.4.sup.+ (in
blood from 800 .mu.mols/hr colon); in healthy individuals > UCD
Arginine production target: NH.sub.4.sup.+ flux 267 .mu.mols/hr
Target arginine production rate: 267 .mu.mols/hr/10.sup.11 bacteria
NH.sub.4.sup.+ flux Lab assay target: NH.sub.4.sup.+ flux 2.67
mol/hr/10.sup.9 bacteria
[0499] Treatment In Vivo
[0500] The genetically engineered bacteria of the invention may be
evaluated in vivo, e.g., in an animal model. Any suitable animal
model of a disease or condition associated with hyperammonemia may
be used (see, e.g., Deignan et al., 2008; Nicaise et al., 2008),
for example, a mouse model of acute liver failure and
hyperammonemia. This acute liver failure and hyperammonemia may be
induced by treatment with thiol acetamide (TAA) (Basile et al.,
1990; Nicaise et al., 2008). Alternatively, liver damage may be
modeled using physical bile duct ligation (Rivera-Mancia et al.,
2012). Hyperammonemia may also be induced by oral supplementation
with ammonium acetate and/or magnesium chloride (Azorin et al.,
1989; Rivera-Mancia et al., 2012).
[0501] Additionally, CCl4 is often used to induce hepaticfibrosis
and cirrhosis in animals (Nhung et al., Establishment of a
standardized mouse model of hepatic fibrosis for biomedical
research; Biomedical Research and Therapy 2014, 1(2):43-49).
[0502] The genetically engineered bacteria of the invention may be
administered to the animal, e.g., by oral gavage, and treatment
efficacy determined, e.g., by measuring ammonia in blood samples
and/or arginine, citrulline, or other byproducts in fecal
samples.
[0503] Full citations for the references cited throughout the
specification include: [0504] 1. Alifano et al. Histidine
biosynthetic pathway and genes: structure, regulation, and
evolution. Microbiol Rev. 1996 March; 60(1):44-69. PMID: 8852895.
[0505] 2. Altenhoefer et al. The probiotic Escherichia coli strain
Nissle 1917 interferes with invasion of human intestinal epithelial
cells by different enteroinvasive bacterial pathogens. FEMS Immunol
Med Microbiol. 2004 Apr. 9; 40(3):223-229. PMID: 15039098. [0506]
3. Andersen et al. Uracil uptake in Escherichia coli K-12:
isolation of uraA mutants and cloning of the gene. J Bacteriol.
1995 April; 177(8):2008-2013. PMID: 7721693. [0507] 4. Arthur et
al. Intestinal inflammation targets cancer-inducing activity of the
microbiota. Science. 2012 Oct. 5; 338(6103):120-123. PMID:
22903521. [0508] 5. Aoyagi et al. Gastrointestinal urease in man.
Activity of mucosal urease. Gut. 1966 December; 7(6):631-635. PMID:
5957514. [0509] 6. Arai et al. Expression of the nir and nor genes
for denitrification of Pseudomonas aeruginosa requires a novel
CRP/FNR-related transcriptional regulator, DNR, in addition to ANR.
FEBS Lett. 1995 Aug. 28; 371(1):73-76. PMID: 7664887. [0510] 7.
Aschner et al. Manganese uptake and distribution in the central
nervous system (CNS). Neurotoxicology. 1999 April-June;
20(2-3):173-180. PMID: 10385881. [0511] 8. Azorin et al. A simple
animal model of hyperammonemia. Hepatology. 1989 September;
10(3):311-314. PMID: 2759549. [0512] 9. Bansky et al. Reversal of
hepatic coma by benzodiazepene antagonists (Rol5-1788). Lancet.
1985; 1:1324-1325. [0513] 10. Basile et al. Brain concentrations of
benzodiazepines are elevated in an animal model of hepatic
encephalopathy. Proc Natl Acad Sci USA. 1990 July;
87(14):5263-5267. PMID: 1973539. [0514] 11. Bearden S W, Perry R D.
The Yfe system of Yersinia pestis transports iron and manganese and
is required for full virulence of plague. Mol Microbiol. 1999
April; 32(2):403-414. PMID: 10231495. [0515] 12. Berk D P, Chalmers
T. Deafness complicating antibiotic therapy of hepatic
encephalopathy. Ann Intern Med. 1970 September; 73(3):393-396.
PMID: 5455989. [0516] 13. Blanc et al. Lactitol or lactulose in the
treatment of chronic hepatic encephalopathy: results of a
meta-analysis. Hepatology. 1992 February; 15(2):222-228. PMID:
1531204. [0517] 14. Caldara et al. The arginine regulon of
Escherichia coli: whole-system transcriptome analysis discovers new
genes and provides an integrated view of arginine regulation.
Microbiology. 2006 November; 152(Pt 11):3343-3354. PMID: 17074904.
[0518] 15. Caldara et al. Arginine biosynthesis in Escherichia
coli: experimental perturbation and mathematical modeling. J Biol
Chem. 2008 Mar. 7; 283(10):6347-6358. PMID: 18165237. [0519] 16.
Caldovic et al. N-acetylglutamate synthase: structure, function and
defects. Mol Genet Metab. 2010; 100 Suppl 1:S13-S19. Review. PMID:
20303810. [0520] 17. Callura et al. Tracking, tuning, and
terminating microbial physiology using synthetic riboregulators.
Proc Natl Acad Sci USA. 2010 Sep. 7; 107(36):15898-15903. PMID:
20713708. [0521] 18. Cash et al. Current concepts in the assessment
and treatment of hepatic encephalopathy. QJM. 2010 January;
103(1):9-16. PMID: 19903725. [0522] 19. Castiglione et al. The
transcription factor DNR from Pseudomonas aeruginosa specifically
requires nitric oxide and haem for the activation of a target
promoter in Escherichia coli. Microbiology. 2009 September; 155(Pt
9):2838-2844. PMID: 19477902. [0523] 20. Cellier et al. Resistance
to intracellular infections: comparative genomic analysis of Nramp.
Trends Genet. 1996 June; 12(6):201-204. PMID: 8928221. [0524] 21.
Charlier et al. Arginine regulon of Escherichia coli K-12. A study
of repressor-operator interactions and of in vitro binding
affinities versus in vivo repression. J Mol Biol. 1992 Jul. 20;
226(2):367-386. PMID: 1640456. [0525] 22. Chiang et al.
Dysregulation of C/EBPalpha by mutant Huntingtin causes the urea
cycle deficiency in Huntington's disease. Hum Mol Genet. 2007 Mar.
1; 16(5):483-498. PMID: 17213233. [0526] 23. Collinson et al.
Channel crossing: how are proteins shipped across the bacterial
plasma membrane? Philos Trans R Soc Lond B Biol Sci. 2015;
370:20150025. PMID: 26370937. [0527] 24. Cordoba J, Minguez B.
Hepatic Encephalopathy. Semin Liver Dis. 2008; 28(1):70-80. PMID:
18293278. [0528] 25. Costa et al. Secretion systems in
Gram-negative bacteria: structural and mechanistic insights. Nat
Rev Microbiol. 2015; 13(6):343-359. PMID: 25978706. [0529] 26.
Crabeel et al. Characterization of the Saccharomyces cerevisiae
ARG7 gene encoding ornithine acetyltransferase, an enzyme also
endowed with acetylglutamate synthase activity. Eur J Biochem. 1997
Dec. 1; 250(2):232-241. PMID: 9428669. [0530] 27. Cuevas-Ramos et
al. Escherichia coli induces DNA damage in vivo and triggers
genomic instability in mammalian cells. Proc Natl Acad Sci USA.
2010 Jun. 22; 107(25):11537-42. PMID: 20534522. [0531] 28. Cunin et
al. Molecular basis for modulated regulation of gene expression in
the arginine regulon of Escherichia coli K-12. Nucleic Acids Res.
1983 Aug. 11; 11(15):5007-5019. PMID: 6348703. [0532] 29. Cunin et
al. Biosynthesis and metabolism of arginine in bacteria. Microbiol
Rev. 1986 September; 50(3):314-52. Review. Erratum in: Microbiol
Rev. 1987 March; 51(1):178. PMID: 3534538. [0533] 30. Danino et al.
Programmable probiotics for detection of cancer in urine. Sci
Transl Med. 2015 May 27; 7(289):289ra84. PMID: 26019220. [0534] 31.
Deignan et al. Contrasting features of urea cycle disorders in
human patients. Mol Genet Metab. 2008 January; 93(1):7-14. PMID:
17933574. [0535] 32. Deutscher. The mechanisms of carbon catabolite
repression in bacteria. Curr Opin Microbiol. 2008 April;
11(2):87-93. PMID: 18359269. [0536] 33. Diaz et al. Ammonia control
and neurocognitive outcome among urea cycle disorder patients
treated with glycerol phenylbutyrate. Hepatology. 2013 June;
57(6):2171-9. PMID: 22961727. [0537] 34. Dinleyici et al.
Saccharomyces boulardii CNCM I-745 in different clinical
conditions. Expert Opin Biol Ther. 2014 November; 14(11): 1593-609.
PMID: 24995675. [0538] 35. Doolittle. A new allele of the sparse
fur gene in the mouse. J Hered. 1974 May-June; 65(3):194-5. PMID:
4603259. [0539] 36. Eckhardt et al. Isolation and characterization
of mutants with a feedback resistant N-acetylglutamate synthase in
Escherichia coli K 12. Mol Gen Genet. 1975 Jun. 19; 138(3):225-32.
PMID: 1102931. [0540] 37. Eiglmeier et al. Molecular genetic
analysis of FNR-dependent promoters. Mol Microbiol. 1989 July;
3(7):869-78. PMID: 2677602. [0541] 38. Fraga et al. (2008).
Real-Time PCR. Current Protocols Essential Laboratory Techniques
(10.3.1-10.3.33). John Wiley & Sons, Inc. [0542] 39. Galimand
et al. Positive FNR-like control of anaerobic arginine degradation
and nitrate respiration in Pseudomonas aeruginosa. J Bacteriol.
1991 March; 173(5):1598-606. PMID: 1900277. [0543] 40. Gamper et
al. Anaerobic regulation of transcription initiation in the arcDABC
operon of Pseudomonas aeruginosa. J Bacteriol. 1991 August;
173(15):4742-50. PMID: 1906871. [0544] 41. Gardner et al.
Construction of a genetic toggle switch in Escherichia coli.
Nature. 2000; 403:339-42. PMID: 10659857. [0545] 42. Gorke B et al.
Carbon catabolite repression in bacteria: many ways to make the
most out of nutrients. Nat Rev Microbiol. 2008 August; 6(8):613-24.
PMID: 18628769. [0546] 43. Haberle et al. Suggested guidelines for
the diagnosis and management of urea cycle disorders. Orphanet J
Rare Dis. 2012 May 29; 7:32. Review. PMID: 22642880. [0547] 44.
Haberle J. Clinical and biochemical aspects of primary and
secondary hyperammonemic disorders. Arch Biochem Biophys. 2013 Aug.
15; 536(2):101-8. Review. PMID: 23628343. [0548] 45. Hasegawa et
al. Activation of a consensus FNR-dependent promoter by DNR of
Pseudomonas aeruginosa in response to nitrite. FEMS Microbiol Lett.
1998 Sep. 15; 166(2):213-7. PMID: 9770276. [0549] 46. Hodges et al.
The spfash mouse: a missense mutation in the ornithine
transcarbamylase gene also causes aberrant mRNA splicing. Proc Natl
Acad Sci USA. 1989 June; 86(11):4142-6. PMID: 2471197. [0550] 47.
Hoeren et al. Sequence and expression of the gene encoding the
respiratory nitrous-oxide reductase from Paracoccus denitrificans.
Eur J Biochem. 1993 Nov. 15; 218(1):49-57. PMID: 8243476. [0551]
48. Hoffmann et al. Defects in amino acid catabolism and the urea
cycle. Handb Clin Neurol. 2013; 113:1755-73. Review. PMID:
23622399. [0552] 49. Hosseini et al. Proprionate as a
health-promoting microbial metabolite in the human gut. Nutr Rev.
2011 May; 69(5):245-58. PMID: 21521227. [0553] 50. Isabella et al.
Deep sequencing-based analysis of the anaerobic stimulon in
Neisseria gonorrhoeae. BMC Genomics. 2011 Jan. 20; 12:51. PMID:
21251255. [0554] 51. Konieczna et al. Bacterial urease and its role
in long-lasting human diseases. Curr Protein Pept Sci. 2012
December; 13(8):789-806. Review. PMID: 23305365. [0555] 52. Lazier
et al. Hyperammonemic encephalopathy in an adenocarcinoma patient
managed with carglumic acid. Curr Oncol. 2014 October;
21(5):e736-9. PMID: 25302046. [0556] 53. Leonard (2006). Disorders
of the urea cycle and related enzymes. Inborn Metabolic Diseases,
4.sup.th ed (pp. 263-272). Springer Medizin Verlag Heidelberg.
[0557] 54. Lim et al. Nucleotide sequence of the argR gene of
Escherichia coli K-12 and isolation of its product, the arginine
repressor. Proc Natl Acad Sci USA. 1987 October; 84(19):6697-701.
PMID: 3116542. [0558] 55. Makarova et al. Conservation of the
binding site for the arginine repressor in all bacterial lineages.
Genome Biol. 2001; 2(4). PMID: 11305941. [0559] 56. Maas et al.
Studies on the mechanism of repression of arginine biosynthesis in
Escherichia coli. Dominance of repressibility in diploids. J Mol
Biol. 1964 March; 8:365-70. PMID: 14168690. [0560] 57. Maas. The
arginine repressor of Escherichia coli. Microbiol Rev. 1994
December; 58(4):631-40. PMID: 7854250. [0561] 58. Meng et al.
Nucleotide sequence of the Escherichia coli cad operon: a system
for neutralization of low extracellular pH. J Bacteriol. 1992
April; 174(8):2659-69. PMID: 1556085. [0562] 59. Moore et al.
Regulation of FNR dimerization by subunit charge repulsion. J Biol
Chem. 2006 Nov. 3; 281(44):33268-75. PMID: 16959764. [0563] 60.
Mountain et al. Cloning of a Bacillus subtilis restriction fragment
complementing auxotrophic mutants of eight Escherichia coli genes
of arginine biosynthesis. Mol Gen Genet. 1984; 197(1):82-9. PMID:
6096675. [0564] 61. Nagamani et al. Optimizing therapy for
argininosuccinic aciduria. Mol Genet Metab. 2012 September;
107(1-2):10-4. Review. PMID: 22841516. [0565] 62. Nicaise et al.
Control of acute, chronic, and constitutive hyperammonemia by
wild-type and genetically engineered Lactobacillus plantarum in
rodents. Hepatology. 2008 October; 48(4):1184-92. PMID: 18697211.
[0566] 63. Nicoloff et al. Two arginine repressors regulate
arginine biosynthesis in Lactobacillus plantarum. J Bacteriol. 2004
September; 186(18):6059-69. PMID: 15342575. [0567] 64. Nougayrede
et al. Escherichia coli induces DNA double-strand breaks in
eukaryotic cells. Science. 2006 Aug. 11; 313(5788):848-51. PMID:
16902142. [0568] 65. Olier et al. Genotoxicity of Escherichia coli
Nissle 1917 strain cannot be dissociated from its probiotic
activity. Gut Microbes. 2012 November-December; 3(6):501-9. PMID:
22895085. [0569] 66. Pham et al. Multiple myeloma-induced
hyperammonemic encephalopathy: an entity associated with high
in-patient mortality. Leuk Res. 2013 October; 37(10):1229-32.
Review. PMID: 23932549. [0570] 67. Rajagopal et al. Use of
inducible feedback-resistant N-acetylglutamate synthetase (argA)
genes for enhanced arginine biosynthesis by genetically engineered
Escherichia coli K-12 strains. Appl Environ Microbiol. 1998 May;
64(5):1805-11. PMID: 9572954. [0571] 68. Ray et al. The effects of
mutation of the anr gene on the aerobic respiratory chain of
Pseudomonas aeruginosa. FEMS Microbiol Lett. 1997 Nov. 15;
156(2):227-32. PMID: 9513270. [0572] 69. Reister et al. Complete
genome sequence of the Gram-negative probiotic Escherichia coli
strain Nissle 1917. J Biotechnol. 2014 Oct. 10; 187:106-7. PMID:
25093936. [0573] 70. Rembacken et al. Non-pathogenic Escherichia
coli versus mesalazine for the treatment of ulcerative colitis: a
randomised trial. Lancet. 1999 Aug. 21; 354(9179):635-9. PMID:
10466665. [0574] 71. Remington's Pharmaceutical Sciences, 22.sup.nd
ed. Mack Publishing Co. [0575] 72. Salmon et al. Global gene
expression profiling in Escherichia coli K12. The effects of oxygen
availability and FNR. J Biol Chem. 2003 Aug. 8; 278(32):29837-55.
PMID: 12754220. [0576] 73. Sat et al. The Escherichia coli mazEF
suicide module mediates thymineless death. J Bacteriol. 2003 March;
185(6):1803-7. PMID: 12618443. [0577] 74. Sawers. Identification
and molecular characterization of a transcriptional regulator from
Pseudomonas aeruginosa PAO1 exhibiting structural and functional
similarity to the FNR protein of Escherichia coli. Mol Microbiol.
1991 June; 5(6):1469-81. PMID: 1787797. [0578] 75. Schneider et al.
Arginine catabolism and the arginine succinyltransferase pathway in
Escherichia coli. J Bacteriol. 1998 August; 180(16): 4278-86. PMID:
9696779. [0579] 76. Schultz. Clinical use of E. coli Nissle 1917 in
inflammatory bowel disease. Inflamm Bowel Dis. 2008 July;
14(7):1012-8. Review. PMID: 18240278. [0580] 77. Sonnenborn et al.
The non-pathogenic Escherichia coli strain Nissle 1917-features of
a versatile probiotic. Microbial Ecology in Health and Disease.
2009; 21:122-58. [0581] 78. Suiter et al. Fitness consequences of a
regulatory polymorphism in a seasonal environment. Proc Natl Acad
Sci USA. 2003 Oct. 28; 100(22):12782-6. PMID: 14555766. [0582] 79.
Summerskill. On the origin and transfer of ammonia in the human
gastrointestinal tract. Medicine (Baltimore). 1966 November;
45(6):491-6. PMID: 5925900. [0583] 80. Szwajkajzer et al.
Quantitative analysis of DNA binding by the Escherichia coli
arginine repressor. J Mol Biol. 2001 Oct. 5; 312(5):949-62. PMID:
11580241. [0584] 81. Tian et al. Binding of the arginine repressor
of Escherichia coli K12 to its operator sites. J Mol Biol. 1992
Jul. 20; 226(2):387-97. PMID: 1640457. [0585] 82. Tian et al.
Explanation for different types of regulation of arginine
biosynthesis in Escherichia coli B and Escherichia coli K12 caused
by a difference between their arginine repressors. J Mol Biol. 1994
Jan. 7; 235(1):221-30. PMID: 8289243. [0586] 83. Torres-Vega et al.
Delivery of glutamine synthetase gene by baculovirus vectors: a
proof of concept for the treatment of acute hyperammonemia. Gene
Ther. 2014 Oct. 23; 22(1):58-64. PMID: 25338921. [0587] 84. Trunk
et al. Anaerobic adaptation in Pseudomonas aeruginosa: definition
of the Anr and Dnr regulons. Environ Microbiol. 2010 June;
12(6):1719-33. PMID: 20553552.
[0588] 85. Tuchman et al. Enhanced production of arginine and urea
by genetically engineered Escherichia coli K-12 strains. Appl
Environ Microbiol. 1997 January; 63(1):33-8. PMID: 8979336. [0589]
86. Ukena et al. Probiotic Escherichia coli Nissle 1917 inhibits
leaky gut by enhancing mucosal integrity. PLoS One. 2007 Dec. 12;
2(12):e1308. PMID: 18074031. [0590] 87. Unden et al. Alternative
respiratory pathways of Escherichia coli: energetics and
transcriptional regulation in response to electron acceptors.
Biochim Biophys Acta. 1997 Jul. 4; 1320(3):217-34. Review. PMID:
9230919. [0591] 88. Vander Wauven et al. Pseudomonas aeruginosa
mutants affected in anaerobic growth on arginine: evidence for a
four-gene cluster encoding the arginine deiminase pathway. J
Bacteriol. 1984 December; 160(3):928-34. PMID: 6438064. [0592] 89.
Walker. Severe hyperammonaemia in adults not explained by liver
disease. Ann Clin Biochem. 2012 May; 49(Pt 3):214-28. Review. PMID:
22349554. [0593] 90. Winteler et al. The homologous regulators ANR
of Pseudomonas aeruginosa and FNR of Escherichia coli have
overlapping but distinct specificities for anaerobically inducible
promoters. Microbiology. 1996 March; 142 (Pt 3):685-93. PMID:
8868444. [0594] 91. Wu et al. Direct regulation of the natural
competence regulator gene tfoX by cyclic AMP (cAMP) and cAMP
receptor protein in Vibrios. Sci Rep. 2015 Oct. 7; 5:14921. PMID:
26442598. [0595] 92. Zimmermann et al. Anaerobic growth and cyanide
synthesis of Pseudomonas aeruginosa depend on anr, a regulatory
gene homologous with fnr of Escherichia coli. Mol Microbiol. 1991
June; 5(6):1483-90. PMID: 1787798. [0596] 93. Wright O, Delmans M,
Stan G B, Ellis T. GeneGuard: A modular plasmid system designed for
biosafety. ACS Synth Biol. 2015 Mar. 20; 4(3):307-16. PMID:
24847673. [0597] 94. Liu Y, White R H, Whitman W B. Methanococci
use the diaminopimelate aminotransferase (DapL) pathway for lysine
biosynthesis. J Bacteriol. 2010 July; 192(13):3304-10. PMID:
20418392. [0598] 95. Dogovski et al. (2012) Enzymology of Bacterial
Lysine Biosynthesis, Biochemistry, Prof. Deniz Ekinci (Ed.), ISBN:
978-953-51-0076-8, InTech, Available from: [0599] 96.
http://www.intechopen.com/books/biochemistry/enzymology-of-bacterial-lysi-
ne-biosynthesis. [0600] 97. Feng et al. Role of phosphorylated
metabolic intermediates in the regulation of glutamine synthetase
synthesis in Escherichia coli. J Bacteriol. 1992 October;
174(19):6061-70. PMID: 1356964. [0601] 98. Lodeiro et al.
Robustness in Escherichia coli glutamate and glutamine synthesis
studied by a kinetic model. J Biol Phys. 2008 April;
34(1-2):91-106. PMID: 19669495. [0602] 99. Reboul et al. Structural
and dynamic requirements for optimal activity of the essential
bacterial enzyme dihydrodipicolinate synthase. PLoS Comput Biol.
2012; 8(6):e1002537. PMID: 22685390. [0603] 100. Saint-Girons et
al. Structure and autoregulation of the metJ regulatory gene in
Escherichia coli. J Biol Chem. 1984 Nov. 25; 259(22):14282-5. PMID:
6094549. [0604] 101. Shoeman et al. Regulation of methionine
synthesis in Escherichia coli: Effect of metJ gene product and
S-adenosylmethionine on the expression of the metF gene. Proc Natl
Acad Sci USA. 1985 June; 82(11):3601-5. PMID: 16593564. [0605] 102.
van Heeswijk et al. Nitrogen assimilation in Escherichia coli:
putting molecular data into a systems perspective. Microbiol Mol
Biol Rev. 2013 December; 77(4):628-95. PMID: 24296575.
EXAMPLES
[0606] The following examples provide illustrative embodiments of
the disclosure. One of ordinary skill in the art will recognize the
numerous modifications and variations that may be performed without
altering the spirit or scope of the disclosure. Such modifications
and variations are encompassed within the scope of the disclosure.
The Examples do not in any way limit the disclosure.
Arginine Repressor Binding Sites (ARG Boxes)
Example 1
ARG Box Mutations
[0607] The wild-type genomic sequences comprising ArgR binding
sites for each arginine biosynthesis operon in E. coli Nissle is
shown in Table 3. Modifications to those sequences are designed
according to the following parameters. For each wild-type sequence,
the ARG boxes are shown in italics. The ARG boxes of the arginine
regulon overlap with the promoter region of each operon. The
underlined sequences represent RNA polymerase binding sites and
those sequences were not altered. Bases that are protected from DNA
methylation during ArgR binding are , and bases that are protected
from hydroxyl radical attack during ArgR binding are bolded. The
and bolded bases were the primary targets for mutations to disrupt
ArgR binding.
Example 2
Lambda Red Recombination
[0608] Lambda red recombination is used to make chromosomal
modifications, e.g., ARG box mutations. Lambda red is a procedure
using recombination enzymes from a bacteriophage lambda to insert a
piece of custom DNA into the chromosome of E. coli. A pKD46 plasmid
is transformed into the E. coli Nissle host strain. E. coli Nissle
cells are grown overnight in LB media. The overnight culture is
diluted 1:100 in 5 mL of LB media and grown until it reaches an
OD.sub.600 of 0.4-0.6. All tubes, solutions, and cuvettes are
pre-chilled to 4.degree. C. The E. coli cells are centrifuged at
2,000 rpm for 5 min. at 4.degree. C., the supernatant is removed,
and the cells are resuspended in 1 mL of 4.degree. C. water. The E.
coli are centrifuged at 2,000 rpm for 5 min. at 4.degree. C., the
supernatant is removed, and the cells are resuspended in 0.5 mL of
4.degree. C. water. The E. coli are centrifuged at 2,000 rpm for 5
min. at 4.degree. C., the supernatant is removed, and the cells are
resuspended in 0.1 mL of 4.degree. C. water. The electroporator is
set to 2.5 kV. 1 ng of pKD46 plasmid DNA is added to the E. coli
cells, mixed by pipetting, and pipetted into a sterile, chilled
cuvette. The dry cuvette is placed into the sample chamber, and the
electric pulse is applied. 1 mL of room-temperature SOC media is
immediately added, and the mixture is transferred to a culture tube
and incubated at 30.degree. C. for 1 hr. The cells are spread out
on a selective media plate and incubated overnight at 30.degree.
C.
[0609] DNA sequences comprising the desired ARG box sequences shown
in Table 3 were ordered from a gene synthesis company. For the argA
operon, the mutant regulatory region comprises the following
nucleic acid sequence (SEQ ID NO: 2):
TABLE-US-00026 gcaaaaaaacaCTTtaaaaaCTTaataatttcCTTtaatcaCTTaaagag
gtgtaccgtg.
[0610] The lambda enzymes are used to insert this construct into
the genome of E. coli Nissle through homologous recombination. The
construct is inserted into a specific site in the genome of E. coli
Nissle based on its DNA sequence. To insert the construct into a
specific site, the homologous DNA sequence flanking the construct
is identified. The homologous sequence of DNA includes
approximately 50 bases on either side of the mutated sequence. The
homologous sequences are ordered as part of the synthesized gene.
Alternatively, the homologous sequences may be added by PCR. The
construct is used to replace the natural sequence upstream of argA
in the E. coli Nissle genome. The construct includes an antibiotic
resistance marker that may be removed by recombination. The
resulting mutant argA construct comprises approximately 50 bases of
homology upstream of argA, a kanamycin resistance marker that can
be removed by recombination,
gcaaaaaaacaCTTtaaaaaCTTaataatttcCTTtaatcaCTTaaagaggtgtaccgtg (SEQ
ID NO: 2), and approximately 50 bases of homology to argA.
[0611] In some embodiments, the ARG boxes were mutated in the argG
regulatory region as described above, and a BBa_J23100 constitutive
promoter was inserted into the regulatory region using lambda red
recombination (SYN-UCD105). These bacteria were capable of
producing arginine. In alternate embodiments, the argG regulatory
region (SEQ ID NO: 16) remained ArgR-repressible (SYN-UCD104), and
the bacteria were capable of producing citrulline.
Example 3
Transforming E. coli Nissle
[0612] The mutated ARG box construct is transformed into E. coli
Nissle comprising pKD46. All tubes, solutions, and cuvettes are
pre-chilled to 4.degree. C. An overnight culture is diluted 1:100
in 5 mL of LB media containing ampicillin and grown until it
reaches an OD.sub.600 of 0.1. 0.05 mL of 100.times. L-arabinose
stock solution is added to induce pKD46 lambda red expression. The
culture is grown until it reaches an OD.sub.600 of 0.4-0.6. The E.
coli cells are centrifuged at 2,000 rpm for 5 min. at 4.degree. C.,
the supernatant is removed, and the cells are resuspended in 1 mL
of 4.degree. C. water. The E. coli are centrifuged at 2,000 rpm for
5 min. at 4.degree. C., the supernatant is removed, and the cells
are resuspended in 0.5 mL of 4.degree. C. water. The E. coli are
centrifuged at 2,000 rpm for 5 min. at 4.degree. C., the
supernatant is removed, and the cells are resuspended in 0.1 mL of
4.degree. C. water. The electroporator is set to 2.5 kV. 0.5 .mu.g
of the mutated ARG box construct is added to the cells, mixed by
pipetting, and pipetted into a sterile, chilled cuvette. The dry
cuvette is placed into the sample chamber, and the electric pulse
is applied. 1 mL of room-temperature SOC media is immediately
added, and the mixture is transferred to a culture tube and
incubated at 37.degree. C. for 1 hr. The cells are spread out on an
LB plate containing kanamycin and incubated overnight.
Example 4
Verifying Mutants
[0613] The presence of the mutation is verified by colony PCR.
Colonies are picked with a pipette tip and resuspended in 20 .mu.l
of cold ddH.sub.2O by pipetting up and down. 3 .mu.L of the
suspension is pipetted onto an index plate with appropriate
antibiotic for use later. The index plate is grown at 37.degree. C.
overnight. A PCR master mix is made using 5 .mu.L of 10.times.PCR
buffer, 0.6 .mu.l of 10 mM dNTPs, 0.4 .mu.L of 50 mM
Mg.sub.2SO.sub.4, 6.0 .mu.L of 10.times. enhancer, and 3.0 .mu.L of
ddH.sub.2O (15 .mu.L of master mix per PCR reaction). A 10 .mu.M
primer mix is made by mixing 2 .mu.L of primers unique to the argA
mutant construct (100 .mu.M stock) into 16 .mu.L of ddH.sub.2O. For
each 20 .mu.L reaction, 15 .mu.L of the PCR master mix, 2.0 .mu.L
of the colony suspension (template), 2.0 .mu.L of the primer mix,
and 1.0 .mu.L of Pfx Platinum DNA Pol are mixed in a PCR tube. The
PCR thermocycler is programmed as follows, with steps 2-4 repeating
34 times: 1) 94.degree. C. at 5:00 min., 2) 94.degree. C. at 0:15
min., 3) 55.degree. C. at 0:30 min., 4) 68.degree. C. at 2:00 min.,
5) 68.degree. C. at 7:00 min., and then cooled to 4.degree. C. The
PCR products are analyzed by gel electrophoresis using 10 .mu.L of
each amplicon and 2.5 .mu.L 5.times. dye. The PCR product only
forms if the mutation has inserted into the genome.
Example 5
Removing Selection Marker
[0614] The antibiotic resistance gene is removed with pCP20. Each
strain with the mutated ARG boxes is grown in LB media containing
antibiotics at 37.degree. C. until it reaches an OD.sub.600 of
0.4-0.6. All tubes, solutions, and cuvettes are pre-chilled to
4.degree. C. The cells are centrifuged at 2,000 rpm for 5 min. at
4.degree. C., the supernatant is removed, and the cells are
resuspended in 1 mL of 4.degree. C. water. The E. coli are
centrifuged at 2,000 rpm for 5 min. at 4.degree. C., the
supernatant is removed, and the cells are resuspended in 0.5 mL of
4.degree. C. water. The E. coli are centrifuged at 2,000 rpm for 5
min. at 4.degree. C., the supernatant is removed, and the cells are
resuspended in 0.1 mL of 4.degree. C. water. The electroporator is
set to 2.5 kV. 1 ng of pCP20 plasmid DNA is added to the cells,
mixed by pipetting, and pipetted into a sterile, chilled cuvette.
The dry cuvette was placed into the sample chamber, and the
electric pulse was applied. 1 mL of room-temperature SOC media is
immediately added, and the mixture is transferred to a culture tube
and incubated at 30.degree. C. for 1-3 hrs. The cells are spread
out on an LB plate containing kanamycin and incubated overnight.
Colonies that do not grow to a sufficient OD.sub.600 overnight are
further incubated for an additional 24 hrs. 200 .mu.L of cells are
spread on ampicillin plates, 200 .mu.L of cells are spread on
kanamycin plates, and both are grown at 37.degree. C. overnight.
The ampicillin plate contains cells with pCP20. The kanamycin plate
provides an indication of how many cells survived the
electroporation. Transformants from the ampicillin plate are
purified non-selectively at 43.degree. C. and allowed to grow
overnight.
Example 6
Verifying Transformants
[0615] The purified transformants are tested for sensitivity to
ampicillin and kanamycin. A colony from the plate grown at
43.degree. C. is picked and resuspended in 10 .mu.L of LB media. 3
.mu.L of the cell suspension is pipetted onto each of three plates:
1) an LB plate with kanamycin incubated at 37.degree. C., which
tests for the presence or absence of the kanR gene in the genome of
the host strain; 2) an LB plate with ampicillin incubated at
30.degree. C., which tests for the presence or absence of the ampR
gene from the pCP20 plasmid; and 3) an LB plate without antibiotic
incubated at 37.degree. C. If no growth is observed on the
kanamycin or ampicillin plates for a particular colony, then both
the kanR gene and the pCP20 plasmid were lost, and the colony is
saved for further analysis. The saved colonies are restreaked onto
an LB plate to obtain single colonies and grown overnight at
37.degree. C. The presence of the mutated genomic ARG box is
confirmed by sequencing the argA region of the genome.
[0616] The methods for lambda red recombination, transforming E.
coli Nissle, verifying the mutation, removing the selection marker,
and verifying/sequencing the transformants are repeated for each of
the ARG box mutations and operons shown in Table 3. The resulting
bacteria comprise mutations in each ARG box for one or more operons
encoding the arginine biosynthesis enzymes, such that ArgR binding
to the ARG boxes is reduced and total ArgR binding to the
regulatory region of said operons is reduced.
Example 7
Arginine Feedback Resistant N-Acetylglutamate Synthetase
(argA.sup.fbr)
[0617] In addition to the ARG box mutations described above, the E.
coli Nissle bacteria further comprise an arginine feedback
resistant N-acetylglutamate synthetase (argA.sup.fbr, SEQ ID NO:
30) gene expressed under the control of each of the following
promoters: tetracycline-inducible promoter, FNR promoter selected
from SEQ ID NOs: 18-29. As discussed herein, other promoters may be
used.
[0618] The argA.sup.fbr gene is expressed on a high-copy plasmid, a
low-copy plasmid, or a chromosome. SYN-UCD101 comprises wild-type
ArgR, wild-type ArgA, tetracycline-inducible argA.sup.fbr on a
plasmid, and mutations in each ARG box for each arginine
biosynthesis operon. The plasmid does not comprise functional ArgR
binding sites, i.e., ARG boxes. SYN-UCD101 was used to generate
SYN-UCD102, which comprises wild-type ArgR, wild-type ArgA,
tetracycline-inducible argA.sup.fbr on a plasmid, and mutations in
each ARG box for each arginine biosynthesis operon. The plasmid
further comprises functional ArgR binding sites, i.e., ARG boxes.
In some instances, the presence and/or build-up of functional ArgR
may result in off-target binding at sites other than the ARG boxes.
Introducing functional ARG boxes in this plasmid may be useful for
reducing or eliminating off-target ArgR binding, i.e., by acting as
an ArgR sink. SYN-UCD104 comprises wild-type ArgR, wild-type ArgA,
tetracycline-inducible argA.sup.fbr on a low-copy plasmid,
tetracycline-inducible argG, and mutations in each ARG box for each
arginine biosynthesis operon except for argG. SYN-UCD105 comprises
wild-type ArgR, wild-type ArgA, tetracycline-inducible argA.sup.fbr
on a low-copy plasmid, constitutively expressed argG (SEQ ID NO: 17
comprising the BBa_J23100 constitutive promoter), and mutations in
each ARG box for each arginine biosynthesis operon. SYN-UCD103 is a
control Nissle construct.
[0619] The argA.sup.fbr gene is inserted into the bacterial genome
at one or more of the following insertion sites in E. coli Nissle:
malE/K, araC/BAD, lacZ, thyA, malP/T. Any suitable insertion site
may be used, see, e.g., FIG. 18. The insertion site may be anywhere
in the genome, e.g., in a gene required for survival and/or growth,
such as thyA (to create an auxotroph); in an active area of the
genome, such as near the site of genome replication; and/or in
between divergent promoters in order to reduce the risk of
unintended transcription, such as between AraB and AraC of the
arabinose operon. At the site of insertion, DNA primers that are
homologous to the site of insertion and to the argA.sup.fbr
construct are designed. A linear DNA fragment containing the
construct with homology to the target site is generated by PCR, and
lambda red recombination is performed as described above.
[0620] The resulting E. coli Nissle bacteria are genetically
engineered to include nucleic acid mutations that reduce
arginine-mediated repression--via ArgR binding and arginine binding
to N-acetylglutamate synthetase--of one or more of the operons that
encode the arginine biosynthesis enzymes, thereby enhancing
arginine and/or citrulline biosynthesis.
[0621] Arginine Repressor (ArgR) sequences The wild-type argR
nucleotide sequence in E. coli Nissle and the nucleotide sequence
following argR deletion are shown below in Table 21 and Table
22.
TABLE-US-00027 TABLE 21 Wild-type argR nucleotide sequence SEQ ID
NO: 69 Sequence argR nucleotide
atgcgaagctcggctaagcaagaagaactagttaaagcatttaaagcatt sequence
acttaaagaagagaaatttagctcccagggcgaaatcgtcgccgcgttg
caggagcaaggctttgacaatattaatcagtctaaagtctcgcggatgttg
accaagtttggtgctgtacgtacacgcaatgccaaaatggaaatggtttac
tgcctgccagctgaactgggtgtaccaaccacctccagtccattgaagaa
tctggtactggatatcgactacaacgatgcagttgtcgtgattcataccagc
cctggtgcggcgcagttaattgctcgcctgctggactcactgggcaaagc
agaaggtattctgggcaccatcgctggcgatgacaccatctttactacccc
tgctaacggtttcaccgtcaaagagctgtacgaagcgattttagagctgttc
gaccaggagctttaa
TABLE-US-00028 TABLE 22 Nucleotide sequence following argR deletion
SEQ ID NO: 124 Sequence argR-deleted
atgcgaagctcggctaagcaagaagagagctg nucleotide ttcgaccaggagctttaa
sequence
Example 9
Deleting ArgR
[0622] A pKD46 plasmid is transformed into the E. coli Nissle host
strain. E. coli Nissle cells are grown overnight in LB media. The
overnight culture is diluted 1:100 in 5 mL of LB media and grown
until it reaches an OD.sub.600 of 0.4-0.6. All tubes, solutions,
and cuvettes are pre-chilled to 4.degree. C. The E. coli cells are
centrifuged at 2,000 rpm for 5 min. at 4.degree. C., the
supernatant is removed, and the cells are resuspended in 1 mL of
4.degree. C. water. The E. coli are centrifuged at 2,000 rpm for 5
min. at 4.degree. C., the supernatant is removed, and the cells are
resuspended in 0.5 mL of 4.degree. C. water. The E. coli are
centrifuged at 2,000 rpm for 5 min. at 4.degree. C., the
supernatant is removed, and the cells are resuspended in 0.1 mL of
4.degree. C. water. The electroporator is set to 2.5 kV. 1 ng of
pKD46 plasmid DNA is added to the E. coli cells, mixed by
pipetting, and pipetted into a sterile, chilled cuvette. The dry
cuvette is placed into the sample chamber, and the electric pulse
is applied. 1 mL of room-temperature SOC media is immediately
added, and the mixture is transferred to a culture tube and
incubated at 30.degree. C. for 1 hr. The cells are spread out on a
selective media plate and incubated overnight at 30.degree. C.
[0623] Approximately 50 bases of homology upstream and downstream
of the ArgR gene are added by PCR to the kanamycin resistance gene
in the pKD4 plasmid to generate the following KanR construct:
(.about.50 bases upstream of ArgR) (terminator) (kanR gene flanked
by FRT sites from pKD4) (DNA downstream of argR).
[0624] In some embodiments, both argR and argG genes are deleted
using lambda red recombination as described above, and the bacteria
are capable of producing citrulline.
Example 10
Bacterial Strains Having Arginine Feedback Resistant
N-Acetylglutamate Synthetase (argA.sup.fbr) and ArgR Deletion
[0625] In addition to the ArgR deletion described above, the E.
coli Nissle bacteria further comprise an arginine feedback
resistant N-acetylglutamate synthetase (argA.sup.fbr, SEQ ID NO:
30) gene expressed under the control of each of the following
promoters: tetracycline-inducible promoter, FNR promoter selected
from SEQ ID NOs: 18-29. As discussed herein, other promoters may be
used.
[0626] The argA.sup.fbr gene is expressed on a high-copy plasmid, a
low-copy plasmid, or a chromosome. ArgR is deleted (.DELTA.ArgR) in
each of SYN-UCD201, SYN-UCD202, and SYN-UCD203. SYN-UCD201 further
comprises wild-type argA, but lacks inducible argA.sup.fbr.
SYN-UCD202 comprises .DELTA.ArgR and argA.sup.fbr expressed under
the control of a tetracycline-inducible promoter on a high-copy
plasmid. SYN-UCD203 comprises .DELTA.ArgR and argA.sup.fbr
expressed under the control of a tetracycline-inducible promoter on
a low-copy plasmid. SYN-UCD204 comprises .DELTA.ArgR and
argA.sup.fbr expressed under the control of a
tetracycline-inducible promoter on a low-copy plasmid. SYN-UCD205
comprises .DELTA.ArgR and argA.sup.fbr expressed under the control
of a FNR-inducible promoter (fnrS2) on a low-copy plasmid.
[0627] The argA.sup.fbr gene is inserted into the bacterial genome
at one or more of the following insertion sites in E. coli Nissle:
malE/K, araC/BAD, lacZ, thyA, malP/T. Any suitable insertion site
may be used, see, e.g., FIG. 18. The insertion site may be anywhere
in the genome, e.g., in a gene required for survival and/or growth,
such as thyA (to create an auxotroph); in an active area of the
genome, such as near the site of genome replication; and/or in
between divergent promoters in order to reduce the risk of
unintended transcription, such as between AraB and AraC of the
arabinose operon. At the site of insertion, DNA primers that are
homologous to the site of insertion and to the argA.sup.fbr
construct are designed. A linear DNA fragment containing the
construct with homology to the target site is generated by PCR, and
lambda red recombination is performed as described above. The
resulting E. coli Nissle bacteria have deleted ArgR and inserted
feedback resistant N-acetylglutamate synthetase, thereby increasing
arginine or citrulline biosynthesis.
Example 11
Generation of .DELTA.ThyA
[0628] An auxotrophic mutation causes bacteria to die in the
absence of an exogenously added nutrient essential for survival or
growth because they lack the gene(s) necessary to produce that
essential nutrient. In order to generate genetically engineered
bacteria with an auxotrophic modification, the thyA, a gene
essential for oligonucleotide synthesis was deleted. Deletion of
the thyA gene in E. coli Nissle yields a strain that cannot form a
colony on LB plates unless they are supplemented with
thymidine.
[0629] A thyA::cam PCR fragment was amplified using 3 rounds of PCR
as follows. Sequences of the primers used at a 100 um concentration
are found in Table 23.
TABLE-US-00029 TABLE 23 Primer Sequences SEQ ID Name Sequence
Description NO SR36 tagaactgatgcaaaaaggct Round 1: binds SEQ ID
tcgacgaaggcacacagaTG on pKD3 NO: 68 TGTAGGCTGGAGCTG CTTC SR38
gtttcgtaattagatagccacc Round 1: binds SEQ ID ggcgctttaatgcccggaCAT
on pKD3 NO: 125 ATGAATATCCTCCTTAG SR33 caacacgtttcctgaggaacc Round
2: binds SEQ ID atgaaacagtatttagaactg to round 1 PCR NO: 70
atgcaaaaag product SR34 cgcacactggcgtcggctctgg Round 2: binds SEQ
ID caggatgtttcgtaattagat to round 1 PCR NO: 71 agc product SR43
atatcgtcgcagcccacagcaa Round 3: binds SEQ ID cacgtttcctgagg to
round 2 PCR NO: 72 product SR44 aagaatttaacggagggcaaa Round 3:
binds SEQ ID aaaaaccgacgcacact to round 2 PCR NO: 73 ggcgtcggc
product
[0630] For the first PCR round, 4.times.50 ul PCR reactions
containing 1 ng pKD3 as template, 25 ul 2.times. phusion, 0.2 ul
primer SR36 and SR38, and either 0, 0.2, 0.4 or 0.6 ul DMSO were
brought up to 50 ul volume with nuclease free water and amplified
under the following cycle conditions:
[0631] step1: 98c for 30 s
[0632] step2: 98c for 10 s
[0633] step3: 55c for 15 s
[0634] step4: 72c for 20 s
[0635] repeat step 2-4 for 30 cycles
[0636] step5: 72c for 5 min
[0637] Subsequently, 5 ul of each PCR reaction was run on an
agarose gel to confirm PCR product of the appropriate size. The PCR
product was purified from the remaining PCR reaction using a
Zymoclean gel DNA recovery kit according to the manufacturer's
instructions and eluted in 30 ul nuclease free water.
[0638] For the second round of PCR, 1 ul purified PCR product from
round 1 was used as template, in 4.times.50 ul PCR reactions as
described above except with 0.2 ul of primers SR33 and SR34. Cycle
conditions were the same as noted above for the first PCR reaction.
The PCR product run on an agarose gel to verify amplification,
purified, and eluted in 30 ul as described above.
[0639] For the third round of PCR, 1 ul of purified PCR product
from round 2 was used as template in 4.times.50 ul PCR reactions as
described except with primer SR43 and SR44. Cycle conditions were
the same as described for rounds 1 and 2. Amplification was
verified, the PCR product purified, and eluted as described above.
The concentration and purity was measured using a
spectrophotometer. The resulting linear DNA fragment, which
contains 92 bp homologous to upstream of thyA, the chloramphenicol
cassette flanked by frt sites, and 98 bp homologous to downstream
of the thyA gene, was transformed into a E. coli Nissle 1917 strain
containing pKD46 grown for recombineering. Following
electroporation, 1 ml SOC medium containing 3 mM thymidine was
added, and cells were allowed to recover at 37 C for 2 h with
shaking. Cells were then pelleted at 10,000.times.g for 1 minute,
the supernatant was discarded, and the cell pellet was resuspended
in 100 ul LB containing 3 mM thymidine and spread on LB agar plates
containing 3 mM thy and 20 ug/ml chloramphenicol. Cells were
incubated at 37 C overnight. Colonies that appeared on LB plates
were restreaked. + cam 20 ug/ml+ or - thy 3 mM. (thyA auxotrophs
will only grow in media supplemented with thy 3 mM).
[0640] Next, the antibiotic resistance was removed with pCP20
transformation. pCP20 has the yeast Flp recombinase gene, FLP,
chloramphenicol and ampicillin resistant genes, and temperature
sensitive replication. Bacteria were grown in LB media containing
the selecting antibiotic at 37.degree. C. until OD600=0.4-0.6. 1 mL
of cells were washed as follows: cells were pelleted at
16,000.times.g for 1 minute. The supernatant was discarded and the
pellet was resuspended in 1 mL ice-cold 10% glycerol. This wash
step was repeated 3.times. times. The final pellet was resuspended
in 70 ul ice-cold 10% glycerol. Next, cells were electroporated
with 1 ng pCP20 plasmid DNA, and 1 mL SOC supplemented with 3 mM
thymidine was immediately added to the cuvette. Cells were
resuspended and transferred to a culture tube and grown at
30.degree. C. for 1 hours. Cells were then pelleted at
10,000.times.g for 1 minute, the supernatant was discarded, and the
cell pellet was resuspended in 100 ul LB containing 3 mM thymidine
and spread on LB agar plates containing 3 mM thy and 100 ug/ml
carbenicillin and grown at 30.degree. C. for 16-24 hours. Next,
transformants were colony purified non-selectively (no antibiotics)
at 42.degree. C.
[0641] To test the colony-purified transformants, a colony was
picked from the 42.degree. C. plate with a pipette tip and
resuspended in 10 .mu.L LB. 3 .mu.L of the cell suspension was
pipetted onto a set of 3 plates: Cam, (37.degree. C.; tests for the
presence/absence of CamR gene in the genome of the host strain),
Amp, (30.degree. C., tests for the presence/absence of AmpR from
the pCP20 plasmid) and LB only (desired cells that have lost the
chloramphenicol cassette and the pCP20 plasmid), 37.degree. C.
Colonies were considered cured if there is no growth in neither the
Cam or Amp plate, picked, and restreaked on an LB plate to get
single colonies, and grown overnight at 37.degree. C.
Example 12
Quantifying Ammonia
[0642] The genetically engineered bacteria described above were
grown overnight in 5 mL LB. The next day, cells were pelleted and
washed in M9+glucose, pelleted, and resuspended in 3 mL M9+glucose.
Cell cultures were incubated with shaking (250 rpm) for 4 hrs and
incubated aerobically or anaerobically in a Coy anaerobic chamber
(supplying 90% N.sub.2, 5% CO.sub.2, 5% H.sub.2) at 37.degree. C.
At baseline (t=0), 2 hours, and 4 hours, the OD.sub.600 of each
cell culture was measured in order to determine the relative
abundance of each cell.
[0643] At t=0, 2 hrs, and 4 hrs, a 1 mL aliquot of each cell
culture was analyzed on the Nova Biomedical Bioprofile Analyzer 300
in order to determine the concentration of ammonia in the media.
Both SYN-UCD101 and SYN-UCD102 were capable of consuming ammonia in
vitro (FIG. 26). FIGS. 25, 26, and 27 depict bar graphs of ammonia
concentrations using SYN-UCD202, SYN-UCD204, SYN-UCD103, and blank
controls.
Example 13
Quantifying Arginine and Citrulline
[0644] In some embodiments, the genetically engineered bacteria
described above are grown overnight in LB at 37.degree. C. with
shaking. The bacteria are diluted 1:100 in 5 mL LB and grown at
37.degree. C. with shaking for 1.5 hr. The bacteria cultures are
induced as follows: (1) bacteria comprising FNR-inducible
argA.sup.fbr are induced in LB at 37.degree. C. for up to 4 hrs in
anaerobic conditions in a Coy anaerobic chamber (supplying 90%
N.sub.2, 5% CO.sub.2, 5% H.sub.2, and 20 mM nitrate) at 37.degree.
C.; (2) bacteria comprising tetracycline-inducible argA.sup.fbr are
induced with anhydrotetracycline (100 ng/mL); (3) bacteria
comprising arabinose-inducible argA.sup.fbr are induced with 1%
arabinose in media lacking glucose. After induction, bacterial
cells are removed from the incubator and spun down at maximum speed
for 5 min. The cells are resuspended in 1 mL M9 glucose, and the
OD.sub.600 is measured. Cells are diluted until the OD.sub.600 is
between 0.6-0.8. Resuspended cells in M9 glucose media are grown
aerobically with shaking at 37 C. 100 .mu.L of the cell
resuspension is removed and the OD.sub.600 is measured at time=0. A
100 .mu.L aliquot is frozen at -20.degree. C. in a round-bottom
96-well plate for mass spectrometry analysis (LC-MS/MS). At each
subsequent time point, 100 .mu.L of the cell suspension is removed
and the OD.sub.600 is measured; a 100 .mu.L aliquot is frozen at
-20 C in a round-bottom 96-well plate for mass spectrometry
analysis. Samples are analyzed for arginine and/or citrulline
concentrations. At each time point, normalized concentrations as
determined by mass spectrometry vs. OD.sub.600 are used to
determine the rate of arginine and/or citrulline production per
cell per unit time.
[0645] In some embodiments, the genetically engineered bacteria
described above are streaked from glycerol stocks for single
colonies on agar. A colony is picked and grown in 3 mL LB for 4 hrs
or overnight, then centrifuged for 5 min at 2,500 rcf. The cultures
are washed in M9 media with 0.5% glucose. The cultures are
resuspended in 3 mL of M9 media with 0.5% glucose, and the
OD.sub.600 is measured. The cultures are diluted in M9 media with
0.5% glucose, with or without ATC (100 ng/mL), with or without 20
mM glutamine, so that all of the OD.sub.600 are between 0.4 and
0.5. A 0.5 mL aliquot of each sample is removed, centrifuged for 5
min. at 14,000 rpm, and the supernatant is removed and saved. The
supernatant is frozen at -80.degree. C., and the cell pellets are
frozen at -80.degree. C. (t=0). The remaining cells are grown with
shaking (250 rpm) for 4-6 hrs and incubated aerobically or
anaerobically in a Coy anaerobic chamber (supplying 90% N.sub.2, 5%
CO.sub.2, 5% H.sub.2) at 37.degree. C. One 0.5 mL aliquot is
removed from each sample every two hours and the OD.sub.600 is
measured. The aliquots are centrifuged for 5 min at 14,000 rpm, and
the supernatant is removed. The supernatant is frozen at
-80.degree. C., and the cell pellets are frozen at -80.degree. C.
(t=2, 4, and 6 hrs). The samples are placed on ice, and arginine
and citrulline levels are determined using mass spectrometry.
[0646] For bacterial culture supernatants, samples of 500, 100, 20,
4, and 0.8 .mu.g/mL arginine and citrulline standards in water are
prepared. In a round-bottom 96-well plate, 20 .mu.L of sample
(bacterial supernatant or standards) is added to 80 .mu.L of water
with L-Arginine-.sup.13C.sub.6, .sup.15N.sub.4 (Sigma) and
L-Citrulline-2,3,3,4,4,5,5-d7 (CDN isotope) internal standards at a
final 2 .mu.g/mL concentration. The plate is heat-sealed with a
PierceASeal foil and mixed well. In a V-bottom 96-well
polypropylene plate, 5 .mu.L of diluted samples is added to 95
.mu.L of derivatization mix (85 .mu.L 10 mM NaHCO.sub.3 pH 9.7 and
10 .mu.L 10 mg/mL dansyl-chloride (diluted in acetonitrile). The
plate is heat-sealed with a ThermASeal foil and mixed well. The
samples are incubated at 60.degree. C. for 45 min for
derivatization and centrifuged at 4000 rpm for 5 min. In a
round-bottom 96-well plate, 20 .mu.L of the derivatized samples are
added to 180 .mu.L of water with 0.1% formic acid. The plate is
heat-sealed with a ClearASeal sheet and mixed well.
[0647] Arginine and citrulline are measured by liquid
chromatography coupled to tandem mass spectrometry (LC-MS/MS) using
a Thermo TSQ Quantum Max triple quadrupole mass spectrometer. Table
24 below provides a summary of a LC-MS/MS method.
TABLE-US-00030 TABLE 24 a LC-MS/MS Method Summary HPLC Column Luna
C18(2) column, 5 .mu.m (50 .times. 2.1 mm) Mobile Phase A 100%
H.sub.2O, 0.1% Formic Acid) Mobile Phase B 100% ACN, 0.1% Formic
Acid Total Time (min) Flow Rate (.mu.L/min) A % B % HPLC Method
0.00 400 90.0 10.0 0.50 400 90.0 10.0 2.00 400 10.0 90.0 3.25 400
10.0 90.0 3.26 400 90.0 10.0 4.30 400 90.0 10.0 Injection Volume 10
.mu.L Tandem Mass Spectrometry Ion Source HESI-II Polarity Positive
SRM transitions L-Arginine: 408.1/170.1 L-Arginine-.sup.13C.sub.6,
.sup.15N.sub.4: 418.1/170.0 L-Citrulline: 409.1/170.2
L-Citrulline-2,3,3,4,4,5,5-d7: 416.1/170.1
[0648] Intracellular arginine and secreted (supernatant) arginine
production in the genetically engineered bacteria in the presence
or absence an ATC or anaerobic inducer is measured and compared to
control bacteria of the same strain under the same conditions.
[0649] Total arginine production over 6 hrs in the genetically
engineered bacteria in the genetically engineered bacteria in the
presence or absence an ATC or anaerobic inducer is measured and
compared to control bacteria of the same strain under the same
conditions.
Example 14
Efficacy of Genetically Engineered Bacteria in a Mouse Model of
Hyperammonemia and Acute Liver Failure
[0650] Wild-type C57BL6/J mice are treated with thiol acetamide
(TAA), which causes acute liver failure and hyperammonemia (Nicaise
et al., 2008). The TAA mouse model is an industry-accepted in vivo
model for HE. Mice are treated with unmodified control Nissle
bacteria or Nissle bacteria engineered to produce high levels of
arginine or citrulline as described above.
[0651] On day 1, 50 mL of the bacterial cultures are grown
overnight and pelleted. The pellets are resuspended in 5 mL of PBS
at a final concentration of approximately 10.sup.11 CFU/mL. Blood
ammonia levels in mice are measured by mandibular bleed, and
ammonia levels are determined by the PocketChem Ammonia Analyzer
(Arkray). Mice are gavaged with 100 .mu.L of bacteria
(approximately 10.sup.10 CFU). Drinking water for the mice is
changed to contain 0.1 mg/mL anhydrotetracycline (ATC) and 5%
sucrose for palatability.
[0652] On day 2, the bacterial gavage solution is prepared as
described above, and mice are gavaged with 100 .mu.L of bacteria.
The mice continue to receive drinking water containing 0.1 mg/mL
ATC and 5% sucrose.
[0653] On day 3, the bacterial gavage solution is prepared as
described above, and mice are gavaged with 100 .mu.L of bacteria.
The mice continue to receive drinking water containing 0.1 mg/mL
ATC and 5% sucrose. Mice receive an intraperitoneal (IP) injection
of 100 .mu.L of TAA (250 mg/kg body weight in 0.5% NaCl).
[0654] On day 4, the bacterial gavage solution is prepared as
described above, and mice are gavaged with 100 .mu.L of bacteria.
The mice continue to receive drinking water containing 0.1 mg/mL
ATC and 5% sucrose. Mice receive another IP injection of 100 .mu.L
of TAA (250 mg/kg body weight in 0.5% NaCl). Blood ammonia levels
in the mice are measured by mandibular bleed, and ammonia levels
are determined by the PocketChem Ammonia Analyzer (Arkray).
[0655] On day 5, blood ammonia levels in mice are measured by
mandibular bleed, and ammonia levels are determined by the
PocketChem Ammonia Analyzer (Arkray). Fecal pellets are collected
from mice to determine arginine content by liquid
chromatography-mass spectrometry (LC-MS). Ammonia levels in mice
treated with genetically engineered Nissle and unmodified control
Nissle are compared.
Example 15
Efficacy of Genetically Engineered Bacteria in a Mouse Model of
Hyperammonemia and UCD
[0656] Ornithine transcarbamylase is urea cycle enzyme, and mice
comprising an spf-ash mutation exhibit partial ornithine
transcarbamylase deficiency, which serves as a model for human UCD.
Mice are treated with unmodified control Nissle bacteria or Nissle
bacteria engineered to produce high levels of arginine or
citrulline as described above.
[0657] 60 spf-ash mice were treated with the genetically engineered
bacteria of the invention (SYN-UCD103, SYN-UCD204) or H2O control
at 100 ul PO QD: H2O control, normal chow (n=15); H2O control, high
protein chow (n=15); SYN-UCD103, high protein chow (n=15);
SYN-UCD204, high protein chow (n=15). On Day 1, mice were weighed
and sorted into groups to minimize variance in mouse weight per
cage. Mice were gavaged and water with 20 mg/L ATC was added to the
cages. On day 2, mice were gavaged in the morning and afternoon. On
day 3, mice were gavaged in the morning and weighed, and blood was
drawn 4 h post-dosing to obtain baseline ammonia levels. Mice were
gavaged in the afternoon and chow changed to 70% protein chow. On
day 4, mice were gavaged in the morning and afternoon. On day 5,
mice were gavaged in the morning and weighed, and blood was drawn 4
h post-dosing to obtain ammonia levels. On days 6 and 7, mice were
gavaged in the morning. On day 8, mice were gavaged in the morning
and weighed, and blood was drawn 4 h post-dosing to obtain ammonia
levels. On day 9, mice were gavaged in the morning and afternoon.
On day 10, mice were gavaged in the morning and weighed, and blood
was drawn 4 h post-dosing to obtain ammonia levels. On day 12, mice
were gavaged in the morning and afternoon. On day 13, mice were
gavaged in the morning and weighed, and blood was drawn 4 h
post-dosing to obtain ammonia levels. Blood ammonia levels, body
weight, and survival rates are analyzed (FIG. 29).
Example 16
Efficacy of Genetically Engineered Bacteria in a Mouse Model of
Hyperammonemia and UCD (Spf-Ash) Maintained on a High Protein
Diet
[0658] The hyperammonia/UCD (spf-ash) model described in Example 14
was used to assess the in vivo efficacy of genetically engineered
bacteria encoding ArgAfbr driven by a fnr promoter on a low copy
plasmid on ammonia levels upon administration of a high protein
diet.
[0659] Two strains encoding ArgAfbr driven by a fnr promoter on a
low copy plasmid, SYN-UCD206 (comprising .DELTA.ArgR and
.DELTA.ThyA and argAfbr expressed under the control of a
FNR-inducible promoter (fnrS2) on a low-copy plasmid) and
SYN-UCD205 (comprising .DELTA.ArgR and argAfbr expressed under the
control of a FNR-inducible promoter (fnrS2) on a low-copy plasmid)
were compared to determine whether thymidine auxotrophy can
influence the efficacy of ammonia removal from the blood.
[0660] Spf-ash mice were treated by oral administration with the
genetically engineered bacteria (SYN-UCD205, SYN-UCD206) or H2O
control. Normal or high protein chow was provided as follows:
SYN-UCD205, high protein chow (n=10); SYN-UCD206, high protein chow
(n=10); H2O control, normal chow (n=10); H2O control, high protein
chow (n=10). For SYN-UCD205 and SYN-UCD206, a dose of 100 ul of
>1.times.10.sup.10 cells/ml was administered twice a day for 12
days, with the exception of days 1, 5, 6, and 7, where bacteria
were administered once. On Day 1, mice were weighed and randomized.
T=0 NH4 levels were determined from mandibular bleeds using the
PocketChem Ammonia Analyzer (Arkray), and mice were subsequently
and gavaged. On day 2, mice were gavaged in the morning and
afternoon. On day 3, mice were gavaged in the morning and afternoon
and the chow was changed from normal chow to 70% protein chow. On
day 4, mice were gavaged in the morning and afternoon. On day 5,
mice were gavaged in the morning and weighed, and blood was drawn 4
h post-dosing to obtain ammonia levels. On days 8 through 12, mice
were gavaged in the morning and afternoon.
[0661] As seen in FIG. 30, ammonia levels of spf-ash mice in a high
protein diet were reduced 48 hours after switch to high protein
chow in the SYN-UCD205 and SYN-UCD206 groups as compared to the H2O
high protein diet control group, indicating that the FNR inducible
promoter can drive ArgAfbr expression, resulting in decreased
ammonia levels in the blood of the mice treated with the engineered
bacteria. The observed reduction in ammonia levels was similar in
both SYN-UCD205 and SYN-UCD206, indicating that ThyA auxotrophy
does not have a significant effect on efficacy of SYN-UCD206.
Example 17
Engineering Bacterial Strains Using Chromosomal Insertions
[0662] Bacterial strains, in which ArgAfbr is integrated directly
into the E. coli Nissle genome under the control of an
FNR-responsive promoter at the MALEK site were constructed.
[0663] To create a vector capable of integrating the PfnrS-ArgAfbr
into the chromosome at the Nissle MalE and MalK loci, Gibson
assembly was used to add 1000 bp sequences of DNA homologous to the
Nissle MALE/K locus to both sides of a flippase recombination
target (FRT) site-flanked chloramphenicol resistance (cmR) cassette
on a knock-in knock-out (KIKO) plasmid. Gibson assembly was then
used to clone the PfnrS-ArgAfbr DNA sequence between these homology
arms, adjacent to the FRT-cmR-FRT site. Successful insertion of the
fragment was validated by sequencing. PCR is used to amplify the
entire MalEK::FRT-cmR-FRT::PfnrS-ArgAfbr::MalK region. This
knock-in PCR fragment was used to transform an electrocompetent
Nissle strain that contains a temperature-sensitive plasmid
encoding the lambda red recombinase genes. After transformation,
cells were grown for 2 hrs at 37.degree. C. Growth at 37.degree. C.
cures the temperature-sensitive plasmid. Transformants with
successful chromosomal integration of the fragment were selected on
chloramphenicol at 20 .mu.g/m L.
[0664] In some embodiments, recombinase-based switches may be used
to activate PfnrS-ArgAfbr expression. To construct a strain
allowing recombinase-based switches to regulate ArgAfbr expression,
the PfnrS-driven Int5 gene and the rrnBUP-driven, recombinase
site-flanked ArgAfbrare synthesized by Genewiz (Cambridge, Mass.).
Gibson assembly is used to add 1000 bp sequences of DNA homologous
to the Nissle malE and malK loci on either side of the PfnrS-Int5,
rrnBUP-ArgAfbr sequence and to clone this sequence between the
homology arms. Successful insertion of the fragment into a KIKO
plasmid is validated by sequencing. PCR is used to amplify the
entire PfnrS-Int5, rrnBUP-ArgAfbr region. This knock-in PCR
fragment is used to transform an electrocompetent Nissle strain
expressing the lambda red recombinase genes. After transformation,
cells are grown for 2 hrs at 37.degree. C. Transformants with
successful integration of the PfnrS-ArgAfbr at the malEK intergenic
region are selected on kanamycin at 50 .mu.g/mL. This strategy may
also be used to construct a recombinase-based strain requiring T7
polymerase activity for ArgAfbr expression.
Example 18
Comparison of In Vitro Efficacy of Chromosomal Insertion and
Plasmid-Bearing Engineered Bacterial Strains
[0665] To compare the in vitro efficacy between engineered
bacterial strains harboring a chromosomal insertion of ArgAfbr
driven by an fnr inducible promoter at the malEK locus and strains
with a low copy plasmid comprising ArgAfbr driven by an fnr
inducible promoter, arginine levels in the media were measured at
various time points post anaerobic induction. Additionally, to
assess whether auxotrophy for thymidine may have an effect on
arginine production efficiency, arginine production of engineered
bacterial strains with or without a ThyA deletion, comprising the
fnr-ArgAfbr on a low copy plasmid or integrated on the chromosome,
were compared.
[0666] Overnight cultures were diluted 1:100 in LB and grown with
shaking (250 rpm) at 37.degree. C. After 1.5 hrs of growth, the
bacteria cultures were induced as follows: (1) bacteria comprising
FNR-inducible argAfbr were induced in LB at 37.degree. C. for 4 hrs
in anaerobic conditions in a Coy anaerobic chamber (supplying 90%
N2, 5% CO2, 5% H2, and 20 mM nitrate) at 37.degree. C.; (2)
bacteria comprising tetracycline-inducible argAfbr were induced
with anhydrotetracycline (100 ng/m L). After induction, bacteria
were removed from the incubator and spun down at maximum speed for
5 min. The cells were resuspended in 1 mL M9 glucose, and the OD600
was measured. Cells were diluted until the OD600 was between
0.6-0.8. Resuspended cells in M9 glucose media were grown
aerobically with shaking at 37 C. 100 .mu.L of the cell
resuspension was removed and the OD600 is measured at time=0. A 100
.mu.L aliquot was frozen at -20.degree. C. in a round-bottom
96-well plate for mass spectrometry analysis (LC-MS/MS). At each
subsequent time point (e.g., 30, 60, and 120 min), 100 .mu.L of the
cell suspension was removed and the OD600 was measured; a 100 .mu.L
aliquot was frozen at -20 C in a round-bottom 96-well plate for
mass spectrometry analysis. Samples were analyzed for arginine
concentrations. At each time point, normalized concentrations as
determined by mass spectrometry vs. OD600 were used to determine
the rate of arginine production per cell per unit time. A summary
of the LC-MS/MS method is provided above.
[0667] Arginine production at 30, 60, and 120 min post induction
was compared between (1) Syn-UCD301 (SYN825; comprising .DELTA.ArgR
and argAfbr expressed under the control of a FNR-inducible promoter
integrated into the chromosome at the malEK locus), (2) SYN-UCD205
(comprising .DELTA.ArgR and argAfbr expressed under the control of
a FNR-inducible promoter on a low-copy plasmid), and (3) SYN-UCD206
(comprising .DELTA.ArgR and .DELTA.ThyA and argAfbr expressed under
the control of a FNR-inducible promoter on a low-copy plasmid.
SYN-UCD103 was used as is a control Nissle construct and results
are shown in FIG. 31A.
[0668] FIG. 31A shows the levels of arginine production of
SYN-UCD205, SYN-UCD206, and SYN-UCD301 measured at 0, 30, 60, and
120 minutes. Arginine production was comparable between all three
strains, with the greatest arginine production seen with SYN-UCD301
at 120 minutes, indicating that chromosomal integration of FNR ArgA
fbr results in similar levels of arginine production as seen with
the low copy plasmid strains expressing the same construct, and may
even slightly increase the rate of arginine production. SYN-UCD206
exhibited attenuated arginine production as compared to SYN-UCD205
and SYN-UCD-301 (lower arginine levels at 60 minutes), but reached
comparable arginine production levels at 120 minutes, indicating
that .DELTA.ThyA may have a slight attenuating effect on arginine
production. No arginine production was detected for the SYN-UCD103
control.
[0669] Next, samples were prepared as described above and arginine
production at 120 min post induction was compared between (1)
SYN-UCD204 (comprising .DELTA.ArgR and argAfbr expressed under the
control of a tetracycline-inducible promoter on a low-copy
plasmid), and (2) SYN-UCD301 (comprising .DELTA.ArgR, CmR and
argAfbr expressed under the control of a FNR-inducible promoter
integrated into the chromosome at the malEK locus), (3) SYN-UCD302
(comprising .DELTA.ArgR, .DELTA.ThyA, CmR (chloramphenicol
resistance) and argAfbr expressed under the control of a
FNR-inducible promoter integrated into the chromosome at the malEK
locus), and (4) SYN-UCD303 (comprising .DELTA.ArgR, .DELTA.ThyA,
KanR (kanamycin resistance) and argAfbr expressed under the control
of a FNR-inducible promoter integrated into the chromosome at the
malEK locus).
[0670] SYN-UCD106, comprising .DELTA.ArgR and .DELTA.ThyA was used
as is a control Nissle construct. Results are shown in FIG. 31B. As
seen in FIG. 31B, arginine production was elevated to between 0.7
and 0.9 umol/1.times.109 cells, indicating that arginine production
is at similar levels in strains bearing ArgAfbr on a plasmid and
strains with integrated copies of ArgAfbr.
Example 19
Efficacy of Genetically Engineered Bacteria in a Mouse Model of
Hyperammonemia and UCD (Spf-Ash) Maintained on a High Protein
Diet
[0671] The hyperammonia/UCD (spf-ash) model described in Example 14
was used to assess the in vivo efficacy of genetically engineered
bacteria encoding ArgAfbr driven by a fnr promoter integrated into
the bacterial chromosome on ammonia levels upon administration of a
high protein diet. Mice were treated with unmodified control Nissle
bacteria or Nissle bacteria engineered to produce high levels of
arginine or citrulline as described above.
[0672] Two strains, one with a ThyA deletion (SYN-UCD303) and one
without a ThyA deletion (SYN-UCD301) were tested for efficacy and
compared to determine whether .DELTA.ThyA may influence the
efficacy of ammonia removal from the blood with these stains
harboring chromosomal fnr-ArgAfbr.
[0673] Spf-ash mice were treated by oral administration with the
genetically engineered bacteria (SYN-UCD301, SYN-UCD303) or H2O
control. Normal and high protein chow was provided as follows:
SYN-UCD301, high protein chow (n=10); SYN-UCD303, high protein chow
(n=10); H2O control, normal chow (n=10); H2O control, high protein
chow (n=10). For SYN-UCD301, SYN-UCD303, and SYN-UCD106, a dose of
100 ul of >1.times.10.sup.10 cells/ml was administered twice a
day for 12 days, with the exception of days 1, 5, 6, and 7, where
bacteria were administered once. Essentially the same protocol was
followed as described in Example 16, with blood being drawn on day
5 to obtain ammonia levels (FIG. 32A). On day 10, survival rates
were analyzed and a time course of survival is shown in FIG.
32B.
[0674] As depicted in FIG. 32A, ammonia levels of spf-ash mice in a
high protein diet were reduced in the SYN-UCD301 and SYN-UCD303
groups as compared to the H2O high protein diet control group,
indicating that the FNR inducible promoter can drive ArgAfbr
expression when the construct is integrated into the chromosome,
resulting in decreased ammonia levels in the blood of the mice
treated with the engineered bacteria. The observed reduction in
ammonia levels was similar in both SYN-UCD301 and SYN-UCD303,
indicating that ThyA auxotrophy does not have a significant effect
on efficacy of SYN-UCD303. As seen in FIG. 32B, SYN-UCD301 and
SYN-UCD303 showed prolonged survival as compared to controls.
Experiments were conducted twice sequentially with similar
results.
Example 20
Comparison of Efficacy at Various Doses
[0675] To determine the lowest dose which can be used, while
achieving optimal arginine production in the hyperammonia/UCD
(spf-ash) model described in Example 14, three doses of SYN-UCD303
were administered.
[0676] Spf-ash mice were treated by gavage with the genetically
engineered bacteria (SYN-UCD303) or H2O control. For SYN-UCD303,
doses of 1.times.10.sup.7, 1.times.10.sup.8, 1.times.10.sup.9, and
1.times.10.sup.10 CFUs were administered in a volume of 100 ul
twice a day for 12 days, with the exception of days 1, 5, 6, and 7,
where bacteria were administered once. Normal chow or high protein
chow was provided as follows: SYN-UCD303 (1.times.10.sup.7 CFU),
high protein chow (n=10); SYN-UCD303 (1.times.10.sup.8 CFU), high
protein chow (n=10); SYN-UCD303 (1.times.10.sup.9 CFU), high
protein chow (n=10); H2O control, normal chow (n=10); H2O control,
high protein chow (n=10). Essentially the same protocol was
followed as described in Example 16, with blood being drawn on day
5 to obtain ammonia levels. Blood ammonia levels were analyzed for
each dose on day 5. Results are depicted in FIG. 33. Both doses of
1.times.10.sup.8 and 1.times.10.sup.9 were sufficient to result in
a significant reduction of blood ammonia levels in this model.
Example 21
Nissle Residence
[0677] Unmodified E. coli Nissle and the genetically engineered
bacteria of the invention may be destroyed, e.g., by defense
factors in the gut or blood serum. The residence time of bacteria
in vivo may be calculated. A non-limiting example using a
streptomycin-resistant strain of E. coli Nissle is described below.
In alternate embodiments, residence time is calculated for the
genetically engineered bacteria of the invention.
[0678] C57BL/6 mice were acclimated in the animal facility for 1
week. After one week of acclimation (i.e., day 0),
streptomycin-resistant Nissle (SYN-UCD103) was administered to the
mice via oral gavage on days 1-3. Mice were not pre-treated with
antibiotic. The amount of bacteria administered, i.e., the
inoculant, is shown in Table 25. In order to determine the CFU of
the inoculant, the inoculant was serially diluted, and plated onto
LB plates containing streptomycin (300 .mu.g/mL). The plates were
incubated at 37.degree. C. overnight, and colonies were
counted.
TABLE-US-00031 TABLE 25 CFU administered via oral gavage CFU
administered via oral gavage Strain Day 1 Day 2 Day 3 SYN-UCD103
1.30E+08 8.50E+08 1.90E+09
[0679] On days 2-10, fecal pellets were collected from up to 6 mice
(ID NOs. 1-6; Table 14). The pellets were weighed in tubes
containing PBS and homogenized. In order to determine the CFU of
Nissle in the fecal pellet, the homogenized fecal pellet was
serially diluted, and plated onto LB plates containing streptomycin
(300 .mu.g/mL). The plates were incubated at 37.degree. C.
overnight, and colonies were counted.
[0680] Fecal pellets from day 1 were also collected and plated on
LB plates containing streptomycin (300 .mu.g/mL) to determine if
there were any strains native to the mouse gastrointestinal tract
that were streptomycin resistant. The time course and amount of
administered Nissle still residing within the mouse
gastrointestinal tract is shown in Table 26.
[0681] FIG. 34 depicts a graph of Nissle residence in vivo.
Streptomycin-resistant Nissle was administered to mice via oral
gavage without antibiotic pre-treatment. Fecal pellets from six
total mice were monitored post-administration to determine the
amount of administered Nissle still residing within the mouse
gastrointestinal tract. The bars represent the number of bacteria
administered to the mice. The line represents the number of Nissle
recovered from the fecal samples each day for 10 consecutive
days.
TABLE-US-00032 TABLE 26 Nissle residence in vivo ID Day 2 Day 3 Day
4 Day 5 1 2.40E+05 6.50E+03 6.00E+04 2.00E+03 2 1.00E+05 1.00E+04
3.30E+04 3.00E+03 3 6.00E+04 1.70E+04 6.30E+04 2.00E+02 4 3.00E+04
1.50E+04 1.10E+05 3.00E+02 5 1.00E+04 3.00E+05 1.50E+04 6 1.00E+06
4.00E+05 2.30E+04 Avg 1.08E+05 1.76E+05 1.61E+05 7.25E+03 ID Day 6
Day 7 Day 8 Day 9 Day 10 1 9.10E+03 1.70E+03 4.30E+03 6.40E+03
2.77E+03 2 6.00E+03 7.00E+02 6.00E+02 0.00E+00 0.00E+00 3 1.00E+02
2.00E+02 0.00E+00 0.00E+00 0.00E+00 4 1.50E+03 1.00E+02 0.00E+00
0.00E+00 5 3.10E+04 3.60E+03 0.00E+00 0.00E+00 6 1.50E+03 1.40E+03
4.20E+03 1.00E+02 0.00E+00 Avg 8.20E+03 1.28E+03 2.28E+03 1.08E+03
4.62E+02
Example 22
Intestinal Residence and Survival of Bacterial Strains In Vivo
[0682] Localization and intestinal residence time of SYN-UCD303
(integrated fnrS inducible promoter driving ArgAfbr, kanamycin
resistance, .DELTA.ThyA, FIG. 35C) was compared to SYN-UCD106
(.DELTA.ArgR, .DELTA.ThyA, and chloramphenicol resistance, FIG.
35B) and SYN-UCD103 (streptomycin resistant Nissle, FIG. 35A). Mice
were gavaged, sacrificed at various time points, and effluents were
collected from various areas of the small intestine cecum and
colon.
[0683] Bacterial cultures were grown overnight and pelleted. The
pellets were resuspended in PBS at a final concentration of
approximately 10.sup.10 CFU/mL. Mice (C57BL6/J, 10-12 weeks old)
were gavaged with 100 .mu.L of bacteria (approximately 109 CFU).
Drinking water for the mice was changed to contain 0.1 mg/mL
anhydrotetracycline (ATC) and 5% sucrose for palatability. At each
timepoint (1, 4, 8, 12, 24, and 30 hours post-gavage), animals
(n=4) were euthanized, and intestine, cecum, and colon were
removed. The small intestine was cut into three sections, and the
large intestine and colon each into two sections. Each section was
flushed with 0.5 ml cold PBS and collected in separate 1.5 ml
tubes. The cecum was harvested, contents were squeezed out, and
flushed with 0.5 ml cold PBS and collected in a 1.5 ml tube.
Intestinal effluents were placed on ice for serial dilution
plating.
[0684] In order to determine the CFU of bacteria in each effluent,
the effluent was serially diluted, and plated onto LB plates
containing kanamycin. The plates were incubated at 37.degree. C.
overnight, and colonies were counted. The amount of bacteria and
residence time of SYN-UCD103, SYN-UCD106, and SYN-UCD303 seen in
each compartment is shown in FIG. 35. As seen in FIG. 35, all three
strains behave in a similar manner. Comparing FIG. 35A with FIG.
35B, .DELTA.ThyA auxotrophy and .DELTA.ArgR does not seem to have
any substantial effect on residency and transit time.
Example 23
Effect of Auxotrophy on Intestinal Residence Time
[0685] To determine if auxotrophy may have an effect on
localization and time of residence, the mouse model described above
is used to compare the residency of SYN-UCD303 (.DELTA.ThyA) with
SYN-UCD304 (wild type ThyA). SYN-UCD103 (streptomycin resistant
control Nissle) is administered in parallel to determine whether
the Arg R deletion and argAfbr have an effect on residence.
[0686] Bacteria are prepared and mice are gavaged, euthanized and
intestinal effluents collected at various time points as described
in Example 22. To determine the CFU of bacteria in each effluent,
the effluent is serially diluted and plated as described in Example
20. For SYN-UCD103 streptomycin containing plates and for
SYN-UCD301 chloramphenicol containing plates are used.
Example 24
TAA Model of Hyperammonemia
[0687] TAA treatment of mice has previously been employed in the
literature to model increased blood ammonia levels associated with
UCDs, acute and chronic liver disease and HE (Wallace M C, et al.,
Lab Anim. 2015 April; 49(1 Suppl):21-9. Standard operating
procedures in experimental liver research: thioacetamide model in
mice and rat)s. In some embodiments, a TAA-induced mouse model of
hyperammonemia is employed to investigate the ability of the
genetically engineered bacteria to reduce blood ammonia levels. The
TAA serves as an alternative to the spf-ash model. Because spf-ash
is a genetic model, the numbers of mice are limiting so developing
an inducible model in wild-type mice would greatly facilitate in
vivo testing of potential strains of interest.
[0688] To investigate the effects of engineered bacteria on
prolonged elevations of blood ammonia, the bacteria are
administered to C57BL6 mice that are also administered a dose of
300 mpk thioacetamide (TAA).
[0689] C57BL6 (10 weeks old) are administered one daily dose of
SYN-UCD103 or SYN-UCD303 (100 ul of >1.times.10.sup.10 cells/ml)
or vehicle control. Alternatively, mice are administered 2 daily
doses of bacteria (100 ul of >1.times.10.sup.10 cells/ml) (n=5
for each treatment group), once in the AM and once in the PM. After
three days of pre-dosing with the bacteria, the mice are treated
intraperitoneally with thioacetamide (TAA) at 300 mpk or with H2O
as control. Alternatively, the mice are treated twice daily, once
in the AM and once in the PM with 250 mpk. The duration of the
study is five days. Ammonium levels are measured and overall health
survival, body weight change is monitored.
[0690] In brief, animals are acclimated for 7 days. On day 1 of the
time course, animals are weighed, bled to measure baseline ammonia
and collect fecal pellets (per cage), and are randomized based on
initial blood ammonia levels. Animals are dosed by oral gavage
either once or twice (AM and PM) with H2O, SYN-UCD103 or SYN-UCD303
(100 ul/dose/animal). Water is changed to H2O (+)20 mg/ml ATC. On
day 2, animals are dosed by oral gavage either once or twice (AM
and PM) with H2O, SYN-UCD103 or SYN-UCD303 (100 ul/dose/animal). On
day 3, animals are weighed and dosed by oral gavage either once or
twice (AM and PM) with H2O, SYN-UCD103 or SYN-UCD303 (100
ul/dose/animal). Additionally, animals are dosed intraperitoneally
with 300 mpk TAA (or saline control). Alternatively, animals are
dosed with 250 mpk TAA (or saline control) once in the AM and once
in the PM. On day 4, animals are weighed, bled, and blood ammonia
is measured. Fecal pellets are collected per cage. Animals are
dosed per oral gavage either once or twice (AM and PM) with H2O,
SYN-UCD103 or SYN-UCD303 (100 ul/dose/animal). Animals may also be
dosed with 250 mpk TAA (or saline control). On day 5, animals are
weighed, bled, and blood ammonia levels are measured. Fecal pellets
are collected (per cage). Animals are dosed by oral gavage either
once or twice (AM and PM) with H2O, SYN-UCD103 or SYN-UCD303 (100
ul/dose/animal). Ammonium levels, bacterial load in the fecal
pellets, and overall health survival, and body weight changes are
monitored.
Example 25
Model of Hyperammonemia Using Arginase Inhibitors
[0691] As an alternative to the genetic spf-ash model, arginase
inhibitors +/- high protein chow are used as an inducible model of
hyperammonemia. Arginase inhibitors fall into at least 2 classes
(described in Steppan et al., Front Immunol. 2013; 4: 278.
Development of Novel Arginase Inhibitors for Therapy of Endothelial
Dysfunction). The first group of arginase inhibitors consisted of
the boronic acid analogs of 1-arginine (2)S-amino-6-hexanoic acid
(ABH) and S-2-BEC both of which inhibit the catalytic activity of
arginase. Another category of arginase inhibitors, that is mainly
represented by N-hydroxy-l-arginine (NOHA) and
N-hydroxy-nor-l-arginine (nor-NOHA), is characterized by
N-hydroxy-guanidinium side chains and inhibit arginase by
displacing the metal-bridging hydroxide ion of arginase with their
N-hydroxy group. The model development study employs an arginase
inhibitor from each group, BEC and nor-NOHA +/- high protein chow
(70% protein).
[0692] To determine if engineered bacteria can change ammonium
levels in the blood, inducible models using an arginase inhibitor
from each group, BEC and nor-NOHA, +/- high protein chow (70%
protein) (70% protein) in wild type mice are employed. C57BL6
(Female, 8 weeks) are treated by oral gavage with the genetically
engineered bacteria (100 ul of >1.times.10.sup.10 cells/ml) or a
vehicle control and intraperitoneally either with BEC or norNOHA,
and are kept either on a normal chow (n=5 per treatment group) or a
high protein chow diet (n=5 per treatment group). Administration
groups are as follows for SYN-UCD303 and a vehicle control-treated
animals: normal chow (n=5); high protein chow (70% protein chow;
n=5); high protein chow (+)BEC (n=5); high protein chow (+)norNOHA
(n=5).
[0693] On day 1 of the time course, animals are weighed, bled to
measure baseline ammonia, and are randomized based on initial blood
ammonia levels. Fecal pellets are collected (per cage). Animals are
dosed by oral gavage with H2O, SYN-UCD303 or SYN-UCD103 (100
ul/dose/animal). Water is changed to H2O (+)20 mg/ml ATC. On day 2,
animals are dosed by oral gavage either once or twice (AM and PM)
with H2O, SYN-UCD303 or SYN-UCD103 (100 ul/dose/animal). On day 3,
animals are weighed and dosed by oral gavage either once or twice
(AM and PM) with H2O, SYN-UCD303 or SYN-UCD103 (100
ul/dose/animal). Additionally, animals are dosed intraperitoneally
with BEC (25 mpk) or norNOHA (100 mpk) or saline control. For the
high protein diet groups, the chow is changed from normal chow to
70% protein chow. On day 4, animals are weighed, bled, and blood
ammonia is measured. Fecal pellets are collected per cage. Animals
are dosed per oral gavage either once or twice (AM and PM) with
H2O, SYN-UCD303 or SYN-UCD103 (100 ul/dose/animal). Animals are
dosed intraperitoneally with BEC (25 mpk) or norNOHA (100 mpk). On
day 4, animals are dosed per oral gavage either once or twice (AM
and PM) with H2O, SYN-UCD303 or SYN-UCD103 (100 ul/dose/animal).
Animals are weighed, bled 1 h post dose, and blood ammonia is
measured. Fecal pellets are collected per cage. Animals are also
dosed intraperitoneally with BEC (25 mpk) or norNOHA (100 mpk). On
day 5, Animals are dosed by oral gavage either once or twice (AM
and PM) with H2O, SYN-UCD303 or SYN-UCD103 (100 ul/dose/animal).
Animals are weighed, bled 1 h post dose, and ammonia levels are
measured.
[0694] A similar study was conducted using strains SYN-UCD202,
SYN-UCD204, and SYN-UCD103, and results are shown in FIG. 28.
Example 26
Effect of Proliferation Potential and Metabolic Activity on
Arginine Production
[0695] The requirement of cell division and/or active metabolism
for arginine production from the genetically engineered bacteria
was investigated in strain SYNUCD-303.
[0696] SYNUCD-301 were incubated with 70% isopropanol or phosphate
buffered saline (PBS) as a control for 1 hour with shaking. 70%
isopropanol disrupted the cellular membrane, which prevented cell
division, but should allow cell metabolism. PBS incubation had no
effect on the cells (not shown). After treatment, the cells were
mixed at specific ratios in M9 media supplemented with 0.5% glucose
and 3 mM thymidine. Cells were incubated with shaking at 37 C for 2
hours. Cells can use the ammonium chloride contained in the M9
media to form arginine. Arginine concentration was measured in the
media at time zero and again after the 2 hour incubation, and the
amount of arginine produced per hour per billion cells was
calculated. As seen in FIGS. 36A and 36B, a greater ratio of
isopropanol treated cells to untreated in a culture results in
fewer CFUs as determined by plating, and lower levels of arginine
production. Arginine production relative to amount of bacteria
present remained constant across the various cultures (FIG. 36C).
These results indicate that only viable bacteria are contributing
to arginine production.
Example 27
Repeat-Dose Pharmacokinetic and Pharmacodynamic Study of
SYN-UCD-303 Following Daily Nasogastric Gavage Dose Administration
for 28-Days in Cynomolgus Monkeys (Non-GLP)
[0697] To evaluate any potential toxicities arising from
administration of the genetically engineered bacteria or E coli
Nissle alone, the pharmacokinetics and pharmacodynamics of
SYN-UCD303 and an E. coli Nissle with kanamycin resistance
(SYN-UCD107) were studied following daily nasogastric gavage (NG)
dose administration for 28-days to female cynomolgus monkeys.
Cynomolgus monkeys were selected because this species is closely
related, both phylogenetically and physiologically, to humans and
is a species commonly used for nonclinical toxicity evaluations.
The genetically engineered bacteria were administered by nasal
gastric gavage, consistent with the proposed route of
administration in humans. Animals overall well-being (clinical
observations), weight clinical pathology (serum chemistry,
hematology, and coagulation) were tracked. Fecal samples were
examined for bacterial load. Plasma is analyzed for ammonia
levels.
[0698] A. Materials, Animals and Dosing Regimen:
[0699] The study was conducted in compliance with nonclinical
Laboratory Studies Good Laboratory Practice Regulations issued by
the U.S. Food and Drug Administration (Title 21 of the Code of
Federal Regulations, Part 58; effective Jun. 20, 1979) and the OECD
Principles on Good Laboratory Practice (C[97]186/Final; effective
1997). The animals were individually housed based on the
recommendations set forth in the Guide for the Care and Use of
Laboratory Animals (National Research Council 2011).
[0700] Animals used in the study were Female Purpose-bred,
non-naive cynomolgus monkey (Macaca fascicularis) with 3 to 6 kg
(at initial physical exam) 3 to 8 years (at initial physical exam)
of age (SNBL USA stock, Origin: Cambodia).
[0701] For control of bias, animals were randomized to groups in a
weight-stratified manner to achieve similar group body weight
distributions. The number of animals selected for randomization and
their weights and ages are included in Table 27.
TABLE-US-00033 TABLE 27 Animals for randomization Sex Number of
Animals Age Weight Female 17 3 to 6 years 3.1 to 4.7 kg Animals
were identified by unique tattoo numbers.
[0702] Seventeen animals were acclimated for 7 days prior to dose
initiation and fifteen animals were assigned to treatment groups.
Spare animals were removed from the study after Day 1.
[0703] For the duration of the study, animals were offered PMI
LabDiet.RTM. Fiber-Plus.RTM. Monkey Diet 5049 biscuits twice daily.
Animal were fasted for at least 2 hours prior to dose
administration and fed within 1 hour post dose. Animals also were
fasted as required by specific procedures (e.g., prior to blood
draws for serum chemistry, fecal collection). The diet was
routinely analyzed for contaminants and found to be within
manufacturer's specifications. No contaminants were expected to be
present at levels that would interfere with the outcome of the
study.
[0704] Fresh drinking water was provided ad libitum to all animals.
The water was routinely analyzed for contaminants. No contaminants
were present at levels that would interfere with the outcome of the
study. Animals were given fruits, vegetables, other dietary
supplements, and cage enrichment devices throughout the course of
the study.
[0705] Previously quarantined animals were acclimated to the study
room for 7 days prior to initiation of dosing (day 1). The last
dosing occurred on day 28. A stratified randomization scheme
incorporating body weights was used to assign animals to study
groups. Animals were assigned to groups and treated as indicated in
Table 28.
TABLE-US-00034 TABLE 28 Group Assignments Dose Test/ Flush* Number
of Control Dose Level Conc. Volume Bicarb. Volume Females Group
Articles (cfu/Animal) (cfu/mL) (mL/Animal) Conc. (M) (mL/Animal)
(Animal NO.) 1 Control 0 0 10 0.36 5 3 (1, 3, 5) Article* 2
SYN-UCD107 1 .times. 10.sup.9 1 .times. 10.sup.9 1 0.12 14 3 (1, 3,
5) 3 SYN-UCD107 1 .times. 10.sup.12 1 .times. 10.sup.11 10 0.36 5 3
(1, 3, 5) 4 SYN-UCD303 1 .times. 10.sup.9 1 .times. 10.sup.9 1 0.12
14 3 (19, 21, 23) 5 SYN-UCD303 1 .times. 10.sup.12 1 .times.
10.sup.11 10 0.36 5 3 (25, 27, 29) *Concentration of Sodium
Bicarbonate: .36M or 0.12M (0.36M for the control article)
[0706] SYN-UCD107 and SYN-UCD303 stocks were prepared at
1.times.109 cfu/mL and 1.times.10.sup.11 cfu/mL in 15% glycerol in
1.times.PBS with 2.2% glucose and 3 mM thymidine and were kept at
86 to -60.degree. C. (see Table 28). PBS made in 20% glycerol with
sodium bicarbonate was used as a control vehicle. Carbonate
concentration was 0.36M and 0.12M for sodium bicarbonate (see Table
28). On the day of each dosing, bacteria and vehicle control were
removed from the freezer and put on ice and thawed and placed on
ice until dosing.
[0707] Animals were dosed at 0, 1.times.10.sup.9, or
1.times.10.sup.12 cfu/animal. All animals were dosed via nasal
gastric gavage (NG) followed by control/vehicle flush once daily
for 28-days. The concentration of bicarbonate and volume for each
group is specified in Table 28. Vials were inverted at least 3
times prior to drawing the dose in the syringe. The dose site and
dose time (end of flush time) was recorded. On Day 6, Animals 19,
21, and 23 in Group 4 (SYN-UCD303, 1.times.109/animal) received 5
mL bicarbonate flush instead of 14 mL followed by test article dose
administration.
[0708] B. Analysis
[0709] Overall Condition and Weight
[0710] Overall condition: Clinical observations were performed
twice daily, beginning on Day -6 through 44. The first observation
was in the AM. The second observation was no sooner than 4 hours
after the AM observation. During the dosing phase, the second
observation was performed 4 hour (.+-.10 minutes) post dose
administration. Additional clinical observations were performed, as
necessary.
[0711] No test article-related clinical observations were
identified in this study.
[0712] Incidental and/or procedural findings, commonly noted in
similarly housed animals, occurred sporadically among individuals,
were noted in control animals, were also present during the
acclimation phase, and did not increase in severity and incidence
among dose groups. These included findings related to skin
(scab/crust, wounds, abrasions, abnormal skin discoloration,
bruising), hair loss, kinked tail, sunken eyes, inappetence,
emesis, and urogenital discharge.
[0713] Weight: Body weights were measured on Days -6, 1, 8, 11, 15,
22, 29, 36, and 43 prior to the first feeding and dose
administration, as applicable.
[0714] No test article-related effects on body weights were
identified in this study. Decreases of 5 to 10% body weight,
relative to baseline (Day 1), was apparent across all groups,
including control, by Day 36 and determined to be study
procedure-related. Compared to Day 36, an upward trend was noted in
the available body weight data on Day 43, albeit values did not
completely return to baseline.
Clinical Pathology
[0715] Blood Collection: Animals were fasted overnight prior to
daily dose administration and at least 4 hours prior to each series
of collections that included specimens for serum chemistry and
plasma bioanalysis. In these instances, associated clinical
pathology evaluations were from fasted animals. Blood was collected
by venipuncture from a peripheral vein of restrained, conscious
animals via a single draw (if possible) and divided into
appropriate tubes for analysis, as follows: Hematology:
approximately 1.3 mL, K2EDTA tube; Coagulation: approximately 1.8
mL, 3.2% sodium citrate tube; Serum chemistry: approximately 1.0
mL, serum separator tube (SST); Plasma sample: approximately 1.0
mL, Lithium Heparin; The blood for clinical pathology assessment
was processed to serum or plasma, or used intact, according to SNBL
USA SOPs.
[0716] Whenever possible, blood was collected via a single draw and
then divided appropriately. Specimen collection frequency is
summarized in Table 29.
TABLE-US-00035 TABLE 29 Specimen collection frequency Plasma Fecal
Serum Sample sample (on Time Point Hematology Coagulation Chemistry
(on ice) ice) Acclimation 1x 1x 1x 1x 1x Week 1 Dosing Week 1 Day 2
Day 2 Day 2 Days 2 and 7 Days 2, 4 (Predose) (Predose) (Predose)
(Predose) and 7 (Postdose) Dosing Week 2 Day 14 Day 14 Day 14 Day
14 Day 14 (Predose) (Predose) (Predose) (Predose) (Postdose) Dosing
Week 3 -- -- -- -- Once daily Days 18 through 21 (Predose) Dosing
Week 4 -- -- -- Day28 Once daily (Predose) Days 22 through 28
(Predose) Dosing Day 30 Day 30 Day 30 Day 30 Once daily Weeks 5
Days 29,, 30, and 35 Dosing -- -- -- -- Day 40 Weeks 6 Dosing -- --
-- -- Days 46 and Weeks 6 50 -- = Not applicable x =Number of times
procedure performed within the week
[0717] Table 30 Summarizes the Clinical Pathology Assay
Information.
TABLE-US-00036 TABLE 30 Clinical pathology assay information
Residual Analyzed Sample Sample Assay Collection Days Parameters
Measured Disposition Hematology Days -6, 2, 14, Hematocrit,
Hemoglobin, Mean Stored at and 30 corpuscular hemoglobin, Mean 2 to
8.degree. C..sup.a corpuscular hemoglobin concentration, Mean
corpuscular volume, Mean platelet volume, Platelets, Red blood
cells, Red cell distribution width, Reticulocyte absolute count,
Reticulocyte percent, White blood cells, and Differential leukocyte
absolute count: Basophils, Eosinophils, Lymphocytes, Monocytes, and
Neutrophils Coagulation Days -6, 2, 14, Activated partial
thromboplastin time, Stored and 30 Fibrinogen, and Prothrombin time
at -60 to -86.degree. C..sup.a Serum Days -6, 2, 14, Alanine
Aminotransferase, Albumin, Stored Chemistry and 30 Albumin/Globulin
Ratio, Alkaline at -60 to -86.degree. C..sup.a Phosphatase,
Aspartate Aminotransferase, Blood Urea Nitrogen, Calcium, Chloride,
Creatine Kinase, Creatinine, Gamma Glutamyltransferase, Globulin,
Glucose, Inorganic Phosphorus, Potassium, Sodium, Total Bilirubin,
Total Cholesterol, Total Protein, and Triglyceride .sup.aResidual
samples were discarded prior to study finalization
[0718] No test article-related effects in hematology, coagulation,
and serum chemistry parameters were identified in this study.
[0719] Plasma Samples: Animals were fasted for 4 hours prior to
removal of the sample. Approximately 1 mL of blood were collected
from the femoral vein and transferred into 2 mL lithium heparin
tubes on Days -1 and 30, and prior to dose administration on Days
2, 7, 14, and 28. After collection of the target volume of blood in
the tube, approximately 0.05 (on Days -1 and 2) or 0.1 mL (on Days
7, 14, 28, and 30) of mineral oil was added to cover the surface of
blood in the tubes. Tubes were not inverted and were placed on wet
ice.
[0720] The samples were centrifuged within 15 minutes of collection
at 2 to 8.degree. C. to obtain plasma and the plasma was maintained
on dry ice prior to storage at -60 to -86.degree. C.
[0721] Analysis of specimens is conducted using a blood ammonia
analyzer instrument.
[0722] Fecal Sample Collection: Two fecal samples per animal were
collected at the target time points listed in Table 29. Sample
collection dates and times were recorded. 50 mL falcon tube with
approximately 5 mL PBS were used as the container (If feces is
liquid, no PBS is added). To get the fecal sample weight, pre- and
post-sampling weight of container was taken. Samples were collected
from the bottom of the cage from each animal. To get fresh and
un-contaminated samples, remaining food was removed and the cage
pan was cleaned and squeegeed to remove debris and/or water before
the collection. On Days -5, 2, 4, 7, and 14, food removals and pan
cleanings were performed after the first feeding and/or dose
administration. On Days 18, 20, 24, 28, 30, 35, 40, 46, and 50, the
food removals and pan cleanings were performed the night before
each collection. Visually fresh fecal samples were also collected
in the morning before any procedures, except clinical observations,
occurred.
[0723] Fecal Swab Collection: When fecal samples were not collected
by the end of the scheduled day, fecal swab samples were collected
with a cotton tip applicator from the rectum of animals restrained
in a procedure cage.
[0724] Samples were put on wet ice immediately after the
collection. Samples were stored at -20 to -15.degree. C. until
analysis. Analysis of specimens was conducted using a PCR
analytical method as described in Example 31.
[0725] Two fecal samples per animal were collected on Day -5 and
after dose administration on Days 2, 4, 7, and 14, and three fecal
samples per animal were collected on Days 29, 30, 35, 40, 46, and
50, and prior to dose administration on Days 18 through 28. Fifty
milliliter falcon tubes with approximately 5 mL PBS were used for
the collections on Days -5 through 14, and 50 mL falcon tubes with
approximately 5 mL PBS for Tube 1, 20 mL of 50% glycerol and 10 mM
thymidine for Tube 2, and 20 mL of 50% glycerol/PBS for Tube 3,
were used for the collections on Days 18 through 50. Specimens were
put on wet ice immediately after the collection and the contents of
each tube collected on Days 18 through 50 were broken-up and mixed
using a sterile tongue depressor.
[0726] Since no fecal samples were collected from the animals
listed in Table 29 by the end of the collection day, two fecal swab
samples were collected per animal. After sample collection, the
cotton part of the swab was transferred to a 5 mL cryovial with 1
mL of PBS and immediately put on wet ice.
[0727] Results are shown in FIG. 37, and show that the amount of
bacteria quantified from fecal samples follows a similar pattern
for Kanamycin resistant control Nissle (SYN-UCD107) and SYN-UCD303.
Bacteria in the fecal samples reach a level of less than 1000
bacteria/per ml of feces by day 35. Results indicate that under
these dosing conditions, similar amounts of bacteria were recovered
with the auxotroph SYN-UCD303 as control kanamycin resistant Nissle
in the feces. Similar results have been observed in mice. In
conclusion, SYN-UCD303 appeared to be present in the NHP feces at
nearly the same concentration as Nissle (SYN-UCD107).
[0728] In overall conclusion, the test article, SYN-UCD303, was
well tolerated by female cynomolgus monkeys after 28 days of daily
NG dose administration at doses up to 1.times.10.sup.12 CFU/animal.
No test article-related mortality occurred and no test
article-related effects were identified upon clinical observation,
body weight, and clinical pathology assessment.
Example 28
Repeat-Dose Pharmacokinetic and Pharmacodynamic Study of
SYN-UCD-303 Following Daily Nasogastric Gavage Dose Administration
for 28-Days in Cynomolgus Monkeys (Non-GLP)
[0729] Pharmacokinetics and pharmacodynamics of SYN-UCD303,
SYN-UCD304, SYN-UCD305, and SYN-UCD306 and are studied following
daily nasogastric gavage (NG) dose administration for 28-days to
female cynomolgus monkeys essentially as described in Example 27.
Cynomolgus monkeys are selected because this species is closely
related, both phylogenetically and physiologically, to humans and
is a species commonly used for nonclinical toxicity evaluations.
The genetically engineered bacteria are administered by nasal
gastric gavage, consistent with the proposed route of
administration in humans. Animals overall well-being (clinical
observations), weight clinical pathology (serum chemistry,
hematology, and coagulation) are tracked. Plasma is analyzed for
ammonia levels, and fecal samples are examined for bacterial
load.
Example 29
4-Week Toxicity Study in Cynomolgus Monkeys with a 4-Week Recovery
(GLP)
[0730] To evaluate any potential toxicities arising from
administration of the genetically engineered bacteria, the
pharmacokinetics and pharmacodynamics of SYN-UCD303 is studied
following daily nasogastric gavage (NG) dose administration for
28-days to female cynomolgus monkeys under GLP conditions.
[0731] In other embodiments, the study is conducted SYN-UCD304,
SYN-UCD305, and/or SYN-UCD306.
[0732] The study is conducted in compliance with nonclinical
Laboratory Studies Good Laboratory Practice Regulations issued by
the U.S. Food and Drug Administration (Title 21 of the Code of
Federal Regulations, Part 58; effective Jun. 20, 1979) and the OECD
Principles on Good Laboratory Practice (C[97]186/Final; effective
1997). The animals are individually housed based on the
recommendations set forth in the Guide for the Care and Use of
Laboratory Animals (National Research Council 2011).
[0733] Animals are administered SYN-UCD303 or control vehicle
essentially as described in the Example 27, except that all
materials are manufactured under GMP standards. Dosing is tabulated
in Table 31. Additionally, animals are acclimated for 14 days and
the dosing period is daily for 28 days followed by a recovery
period of 28 days. Additionally, animals are euthanized at the end
of the study to conduct histological analysis.
TABLE-US-00037 TABLE 31 Dosing Period and Regimen ACCLIMATION 14
days TEST ARTICLE PREP Daily DOSING PERIOD Daily for 28 days
RECOVERY PERIOD 28 days REGULATIONS FDA GLP TEST DOSE DOSE NUMBER
OF ANIMALS GROUP ARTICLE LEVEL ROUTE MALES ( ) FEMALES ( ) 1
Vehicle 0 NG 3.sup.a + 2.sup.b 3.sup.a + 2.sup.b 2 SYN- 1 .times.
10{circumflex over ( )}9 NG 3.sup.a 3.sup.a UCD303 3 SYN- 1 .times.
10{circumflex over ( )}10 NG 3.sup.a 3.sup.a UCD303 4 SYN- 1
.times. 10{circumflex over ( )}11 NG 3.sup.a + 2.sup.b 3.sup.a +
2.sup.b UCD303 .sup.aTerminal Necropsy, Day 29 .sup.bRecovery
Necropsy, Day 56
[0734] Study Analysis is conducted as described in Table 32.
Hematology, Coagulation, Serum Chemistry and Plasma Samples
parameters are essentially as described in Example 27, and are
analyzed using the methods described in Example 27. Collection and
analysis of fecal samples is essentially conducted as described in
Example 27.
TABLE-US-00038 TABLE 32 Study Analysis PROCEDURE TIME POINTS DOSE
CONCENTRATION Day 1 and Day 28 ANALYSIS CLINICAL Twice Daily
(cageside observations) OBSERVATIONS FOOD CONSUMPTION Daily
(qualitative) BODY WEIGHTS Weekly OPHTHALMOLOGY Once during
acclimation, Week 4, and Week 8 ECGs/HR/BP Once during acclimation,
Week 4, and Week 8 HEMATOLOGY Twice during acclimation, Day 2 (pre-
dose), Day 15 (pre-dose), Day 29, Day 42, and Day 56 COAGULATION
Twice during acclimation, Day 2 (pre- dose), Day 15 (pre-dose), Day
29, Day 42, and Day 56 SERUM CHEMISTRY Twice during acclimation,
Day 2 (pre- dose), Day 15 (pre-dose), Day 29, Day 42, and Day 56
BODY (RECTAL) Twice during acclimation (with at least 7 TEMPERATURE
days between measurements); once weekly during dosing (~6 hrs
post-dose), and Weeks 5 and 8 STOOL SAMPLE Once during acclimation,
prior to dosing COLLECTION on Days 2, 7, and 14, Day 29, Day 33,
(BACTERIAL CULTURE) and Week 8 Rectal/Fecal swabs are collected via
cotton tip applicator; the cotton part of the swab is transferred
to a tube with an appropriate broth/media and immediately put on
wet ice. Fecal samples are stored at 2 to 8.degree. C. until time
of analysis. CYTOKINE BLOOD Once during acclimation, Days 1, 3, 7,
14 COLLECTIONS and 28 (6 hrs post-dose), and Day 56 ARCHIVE BLOOD
SAMPLE Once during acclimation, Days 1, 3, 7, 14 COLLECTION (SAMPLE
and 28 (6 hrs post-dose), and Day 56; TO BE HELD FOR Blood samples
are processed to serum; POSSIBLE ANALYSIS) samples are stored
frozen. NECROPSY & TISSUE All animals (e.g., colon, intestine,
cecum, COLLECTION liver, spleen) ORGAN WEIGHTS All animals TISSUE
COLLECTION All animals FOR PK/PD ASSESSMENT HISTOPATHOLOGY All
animals STATISTICAL ANALYSIS Comparative (Anova/Bartletts)
Example 30
4-Week Repeat Dose Toxicity Study in Mice with a 2-Week Recovery
(GLP)
[0735] To evaluate any potential toxicities arising from
administration of the genetically engineered bacteria, the
pharmacokinetics and pharmacodynamics of SYN-UCD303 is studied
following daily gavage dose administration for 4 weeks followed by
a two week recovery under GLP conditions.
[0736] All materials are manufactured under GLP conditions. CD-1
Mice, 6-8 weeks of age at initiation of study are acclimated for 7
days. Groups of males and female mice are studied separately.
SYN-UCD303 or vehicle control are administered as described in
Table 33.
[0737] In certain embodiments, the study is conducted SYN-UCD304,
SYN-UCD305, and/or SYN-UCD306.
TABLE-US-00039 TABLE 33 Study Design NUMBER DOSE OF ANIMALS TEST
LEVEL DOSE MALES GROUP ARTICLE (MG/KG) ROUTE ( ) FEMALES ( ) 1
Vehicle 0 NG 10.sup.a + 6.sup.b 10.sup.a + 6.sup.b 2 SYN-UCD303 1
.times. 10{circumflex over ( )}9 NG 10.sup.a + 6.sup.b 10.sup.a +
6.sup.b 3 SYN-UCD303 1 .times. 10{circumflex over ( )}10 NG
10.sup.a + 6.sup.b 10.sup.a + 6.sup.b 4 SYN-UCD303 1 .times.
10{circumflex over ( )}11 NG 10.sup.a + 6.sup.b 10.sup.a + 6.sup.b
.sup.aToxicity (Tox) Animals, Terminal Necropsy Day 29;
.sup.bToxicity (Tox) Animals, Recovery Necropsy Day 42
[0738] The study analysis is described in Table 34. Hematology,
Coagulation, Serum Chemistry and Plasma Samples parameters are
essentially as described in Example 27, and are analyzed using the
methods described in Example 27. Collection and analysis of fecal
samples is essentially conducted as described in Example 27.
Histology is conducted as in Example 29.
TABLE-US-00040 TABLE 34 Study Analysis PROCEDURE TIME POINTS DOSE
CONCENTRATION Day 1 and Day 28 ANALYSIS CLINICAL Daily (Cageside
Observations) OBSERVATIONS FOOD CONSUMPTION Weekly (Quantitative)
BODY WEIGHTS Twice during acclimation, weekly during study and
recovery OPHTHALMOLOGY Once during acclimation, Week 4, and Week 8
HEMATOLOGY At each necropsy; Day 29: 5 animals/sex/group; Day 42: 3
animals/sex/group; Standard panel as in Example 27 COAGULATION At
each necropsy; Day 29: 5 animals/sex/group; Day 42: 3
animals/sex/group; Standard panel as in Example 27 SERUM CHEMISTRY
At each necropsy; Day 29: 5 animals/sex/group; Day 56: 3
animals/sex/group; Standard panel as in Example 27 FECAL SAMPLE
Once during acclimation, Days 2, 7, 14, 29, COLLECTION 33, and 42.
Samples will be collected for (BACTERIAL CULTURE) up to a 2 hour
period. For sample collection, animals, as a group of 6, are placed
in or above a sterile surface. Fecal pellets (for each sex and
group) are transferred to a tube with an appropriate broth/media
and immediately put on wet ice. NECROPSY AND TISSUE At each
necropsy Standard panel as in COLLECTION Example 29 ORGAN WEIGHTS
At each necropsy Standard panel as in Example 29. HISTOPATHOLOGY
Tox animals: Control & High dose groups only Example 29.
STATISTICAL Comparative (Anova/Bartletts) ANALYSIS
Example 31
Determination of Presence of Nissle in Fecal Samples of Non-Human
Primates
[0739] To analyze fecal samples from non-human primates (NHPs) for
the presence of Nissle, the number of bacteria from NHP samples was
quantified based on the quantity of DNA in the sample using qPCR.
In some embodiments, this protocol is used for the analysis of
fecal samples from other mammals, including, but not limited to,
mice and humans.
[0740] Sample Homogenization: Fecal samples (stored at -20.degree.
C.) were thawed at room temperature for 90 minutes. For solid fecal
samples, the approximate solid volume was estimated, and phosphate
buffered saline (PBS) was added to double the volume. For liquid
fecal samples, no additional PBS was added. Samples were then
vortexed for 30 seconds per tube. Fecal samples were homogenized
using a disposable Pestle (Fisher 12-141-363) in PBS in Eppendorf
tubes and kept on ice for subsequent procedures.
[0741] DNA purification: The homogenized samples (250 .mu.L) were
removed using sterilized filter tips (Racked Gilson Expert
Sterilized Filter Tips) cut at the first gradation line and
transferred to Eppendorf tubes. DNA was purified from the
homogenized samples (250 .mu.l) using the MoBio PowerLyzer
PowerSoil DNA Isolation Kit (12855-100) following manufacturer's
protocol. The amount of purified DNA recovered from each sample was
quantified by measuring the OD260 of the sample on a Eppendorf
BioSpectrometer Basic.
[0742] PCR reaction: Two reactions (Reaction 1 and Reaction 2) were
assembled and run in triplicate. The first reaction served to
quantify the amount of Nissle, and the second to quantify the total
amount of bacteria present in the fecal samples. For the first qPCR
reaction, purified DNA (5 ng), 0.4 .mu.L of Primer 1 (10 .mu.M),
0.4 .mu.L of Primer 2 (10 .mu.M), and 10 .mu.L of SYBR Green PCR
Master Mix (Thermo Fisher Scientific: 4368577) were brought up to
20 .mu.L with water. For the second qPCR reaction, purified DNA (5
ng), 0.4 .mu.L of Primer 3 (10 .mu.M), 0.4 .mu.L of Primer 4 (10
.mu.M), and 10 .mu.L of SYBR Green PCR Master Mix (Thermo Fisher
Scientific: 4368577) were brought up to 20 .mu.L with water.
[0743] The sequences of primers used in the reactions at a
concentration of 10 .mu.M are found in Table 35.
TABLE-US-00041 TABLE 35 Primer Sequences Primer Size of SEQ ID Name
Primer Sequence Product Identifies NO 1 GCAACTGGCCCGTAATT 191 bp
Nissle 74 2 ATCCACGCATCGCACG 75 TAGGTTT 3 ggcaggcctaacacatgc 240 bp
Total 76 aag Bacteria 4 gtcgcctaggtgagcctt 77 tacc
[0744] For quantification of the amount of bacterial DNA amplified,
a standard curve was run for each reaction. To generate the
standard curve, Fragment #1 (synthesized at a set concentration)
(Table 36) was diluted in 10-fold serial dilutions, resulting in
the following amounts: no DNA, 1 copy of Fragment #1, 10 copies of
Fragment #1, 100 copies of Fragment #1, and so on, until the eighth
well has 106 copies of fragment #1. Standard DNAs were then added
to the qPCR reaction mix for Reaction #1.
TABLE-US-00042 TABLE 36 Standard DNA Sequence (Fragment #1) SEQ ID
Description Sequence NO Fragment 1 gcaactggcccgtaattatccatagctgtag
78 tgatcactcggtccgaattaaacgcaatgat ggcgagctgagaacgattagcatcaaacg
ctttaacgaagattttgaacgagtggagcat gatgagtatcgcaaaatatgtgccgaaata
gagcaggaaacaaacctgaaaaacctac gtgcgatgcgt
[0745] PCR reaction conditions for standard curve, and Reactions 1
and 2 are shown in Table 37.
TABLE-US-00043 TABLE 37 PCR Reaction Conditions Transition
Temperature Time Speed (.degree. C.) (seconds) (.degree. C./second)
Repeats 95 15 N/A 40 60 60 N/A Melt Curve 95 15 N/A 1 60 60 0.3 95
15
[0746] As a quality control measure, the melt-curves of the test
qPCR reactions were compared to the positive control for each
primer set, to ensure that the melt-curve of the positive controls
matched the melt-curve of the test samples. The presence and
quantity of Nissle and total bacteria was determined by analyzing
CT values (Cycle threshold values) against the standard curve.
Example 32
Construction of Vectors for Overproducing Butyrate
[0747] In addition to the ammonia conversion circuit, GABA
transport circuit, GABA metabolic circuit, and/or manganese
transport circuit described above, the E. coli Nissle bacteria
further comprise one or more circuits for producing a gut barrier
enhancer molecule.
[0748] To facilitate inducible production of butyrate in E. coli
Nissle, the eight genes of the butyrate production pathway from
Peptoclostridium difficile 630 (bcd2, etfB3, etfA3, thiA1, hbd,
crt2, bpt, and buk; NCBI), as well as transcriptional and
translational elements, were synthesized (Gen9, Cambridge, Mass.)
and cloned into vector pBR322. The butyrate gene cassette is placed
under the control of a FNR regulatory region selected from SEQ ID
NOs: 18-29 (Table 6). In certain constructs, the FNR-responsive
promoter is further fused to a strong ribosome binding site
sequence. For efficient translation of butyrate genes, each
synthetic gene in the operon was separated by a 15 base pair
ribosome binding site derived from the T7 promoter/translational
start site.
[0749] In certain constructs, the butyrate gene cassette is placed
under the control of an RNS-responsive regulatory region, e.g.,
norB, and the bacteria further comprises a gene encoding a
corresponding RNS-responsive transcription factor, e.g., nsrR (see,
e.g., Tables 38 and 39). In certain constructs, the butyrate gene
cassette is placed under the control of an ROS-responsive
regulatory region, e.g., oxyS, and the bacteria further comprises a
gene encoding a corresponding ROS-responsive transcription factor,
e.g., oxyR (see, e.g., Tables 14-17). In certain constructs, the
butyrate gene cassette is placed under the control of a
tetracycline-inducible or constitutive promoter.
TABLE-US-00044 TABLE 38 pLogic031-nsrR-norB-butyrate construct (SEQ
ID NO: 79) Nucleotide sequences of pLogic031-nsrR- Description
norB-butyrate construct (SEQ ID NO: 79) Nucleic acid
ttattatcgcaccgcaatcgggattttcgattcataaagcaggt sequence of an
cgtaggtcggcttgttgagcaggtcttgcagcgtgaaaccgtcc exemplary RNS-
agatacgtgaaaaacgacttcattgcaccgccgagtatgcccgt regulated construct
cagccggcaggacggcgtaatcaggcattcgttgttcgggccca comprising a gene
tacactcgaccagctgcatcggttcgaggtggcggacgaccgcg encoding nsrR, a
ccgatattgatgcgttcgggcggcgcggccagcctcagcccgcc regulatory region of
gcctttcccgcgtacgctgtgcaagaacccgcctttgaccagcg norB, and a
cggtaaccactttcatcaaatggcttttggaaatgccgtaggtc butyrogenic gene
gaggcgatggtggcgatattgaccagcgcgtcgtcgttgacggc cassette (pLogic031-
ggtgtagatgaggacgcgcagcccgtagtcggtatgttgggtca nsrR-norB-butyrate
gatacatacaacctccttagtacatgcaaaattatttctagagc construct; SEQ ID
aacatacgagccggaagcataaagtgtaaagcctggggtgccta NO: 79). The
atgagttgagttgaggaattataacaggaagaaatattcctcat sequence encoding
acgcttgtaattcctctatggttgttgacaattaatcatcggct NsrR is underlined
##STR00128## and bolded, and the
gaaataattttgtttaactttaagaaggagatatacatatggat NsrR binding site,
ttaaattctaaaaaatatcagatgcttaaagagctatatgtaag i.e., a regulatory
cttcgctgaaaatgaagttaaacctttagcaacagaacttgatg region of norB is
aagaagaaagatttccttatgaaacagtggaaaaaatggcaaaa ##STR00129##
gcaggaatgatgggtataccatatccaaaagaatatggtggaga
aggtggagacactgtaggatatataatggcagttgaagaattgt
ctagagtttgtggtactacaggagttatattatcagctcataca
tctcttggctcatggcctatatatcaatatggtaatgaagaaca
aaaacaaaaattcttaagaccactagcaagtggagaaaaattag
gagcatttggtcttactgagcctaatgctggtacagatgcgtct
ggccaacaaacaactgctgttttagacggggatgaatacatact
taatggctcaaaaatatttataacaaacgcaatagctggtgaca
tatatgtagtaatggcaatgactgataaatctaaggggaacaaa
ggaatatcagcatttatagttgaaaaaggaactcctgggtttag
ctttggagttaaagaaaagaaaatgggtataagaggttcagcta
cgagtgaattaatatttgaggattgcagaatacctaaagaaaat
ttacttggaaaagaaggtcaaggatttaagatagcaatgtctac
tcttgatggtggtagaattggtatagctgcacaagctttaggtt
tagcacaaggtgctcttgatgaaactgttaaatatgtaaaagaa
agagtacaatttggtagaccattatcaaaattccaaaatacaca
attccaattagctgatatggaagttaaggtacaagcggctagac
accttgtatatcaagcagctataaataaagacttaggaaaacct
tatggagtagaagcagcaatggcaaaattatttgcagctgaaac
agctatggaagttactacaaaagctgtacaacttcatggaggat
atggatacactcgtgactatccagtagaaagaatgatgagagat
gctaagataactgaaatatatgaaggaactagtgaagttcaaag
aatggttatttcaggaaaactattaaaatagtaagaaggagata
tacatatggaggaaggatttatgaatatagtcgtttgtataaaa
caagttccagatacaacagaagttaaactagatcctaatacagg
tactttaattagagatggagtaccaagtataataaaccctgatg
ataaagcaggtttagaagaagctataaaattaaaagaagaaatg
ggtgctcatgtaactgttataacaatgggacctcctcaagcaga
tatggctttaaaagaagctttagcaatgggtgcagatagaggta
tattattaacagatagagcatttgcgggtgctgatacttgggca
acttcatcagcattagcaggagcattaaaaaatatagattttga
tattataatagctggaagacaggcgatagatggagatactgcac
aagttggacctcaaatagctgaacatttaaatcttccatcaata
acatatgctgaagaaataaaaactgaaggtgaatatgtattagt
aaaaagacaatttgaagattgttgccatgacttaaaagttaaaa
tgccatgccttataacaactcttaaagatatgaacacaccaaga
tacatgaaagttggaagaatatatgatgctttcgaaaatgatgt
agtagaaacatggactgtaaaagatatagaagttgacccttcta
atttaggtcttaaaggttctccaactagtgtatttaaatcattt
acaaaatcagttaaaccagctggtacaatatacaatgaagatgc
gaaaacatcagctggaattatcatagataaattaaaagagaagt
atatcatataataagaaggagatatacatatgggtaacgtttta
gtagtaatagaacaaagagaaaatgtaattcaaactgtttcttt
agaattactaggaaaggctacagaaatagcaaaagattatgata
caaaagtttctgcattacttttaggtagtaaggtagaaggttta
atagatacattagcacactatggtgcagatgaggtaatagtagt
agatgatgaagctttagcagtgtatacaactgaaccatatacaa
aagcagcttatgaagcaataaaagcagctgaccctatagttgta
ttatttggtgcaacttcaataggtagagatttagcgcctagagt
ttctgctagaatacatacaggtcttactgctgactgtacaggtc
ttgcagtagctgaagatacaaaattattattaatgacaagacct
gcctttggtggaaatataatggcaacaatagtttgtaaagattt
cagacctcaaatgtctacagttagaccaggggttatgaagaaaa
atgaacctgatgaaactaaagaagctgtaattaaccgtttcaag
gtagaatttaatgatgctgataaattagttcaagttgtacaagt
aataaaagaagctaaaaaacaagttaaaatagaagatgctaaga
tattagtttctgctggacgtggaatgggtggaaaagaaaactta
gacatactttatgaattagctgaaattataggtggagaagtttc
tggttctcgtgccactatagatgcaggttggttagataaagcaa
gacaagttggtcaaactggtaaaactgtaagaccagacctttat
atagcatgtggtatatctggagcaatacaacatatagctggtat
ggaagatgctgagtttatagttgctataaataaaaatccagaag
ctccaatatttaaatatgctgatgttggtatagttggagatgtt
cataaagtgcttccagaacttatcagtcagttaagtgttgcaaa
agaaaaaggtgaagttttagctaactaataagaaggagatatac
atatgagagaagtagtaattgccagtgcagctagaacagcagta
ggaagttttggaggagcatttaaatcagtttcagcggtagagtt
aggggtaacagcagctaaagaagctataaaaagagctaacataa
ctccagatatgatagatgaatctcttttagggggagtacttaca
gcaggtcttggacaaaatatagcaagacaaatagcattaggagc
aggaataccagtagaaaaaccagctatgactataaatatagttt
gtggttctggattaagatctgtttcaatggcatctcaacttata
gcattaggtgatgctgatataatgttagttggtggagctgaaaa
catgagtatgtctccttatttagtaccaagtgcgagatatggtg
caagaatgggtgatgctgcttttgttgattcaatgataaaagat
ggattatcagacatatttaataactatcacatgggtattactgc
tgaaaacatagcagagcaatggaatataactagagaagaacaag
atgaattagctcttgcaagtcaaaataaagctgaaaaagctcaa
gctgaaggaaaatttgatgaagaaatagttcctgttgttataaa
aggaagaaaaggtgacactgtagtagataaagatgaatatatta
agcctggcactacaatggagaaacttgctaagttaagacctgca
tttaaaaaagatggaacagttactgctggtaatgcatcaggaat
aaatgatggtgctgctatgttagtagtaatggctaaagaaaaag
ctgaagaactaggaatagagcctcttgcaactatagtttcttat
ggaacagctggtgttgaccctaaaataatgggatatggaccagt
tccagcaactaaaaaagctttagaagctgctaatatgactattg
aagatatagatttagttgaagctaatgaggcatttgctgcccaa
tctgtagctgtaataagagacttaaatatagatatgaataaagt
taatgttaatggtggagcaatagctataggacatccaataggat
gctcaggagcaagaatacttactacacttttatatgaaatgaag
agaagagatgctaaaactggtcttgctacactttgtataggcgg
tggaatgggaactactttaatagttaagagatagtaagaaggag
atatacatatgaaattagctgtaataggtagtggaactatggga
agtggtattgtacaaacttttgcaagttgtggacatgatgtatg
tttaaagagtagaactcaaggtgctatagataaatgtttagctt
tattagataaaaatttaactaagttagttactaagggaaaaatg
gatgaagctacaaaagcagaaatattaagtcatgttagttcaac
tactaattatgaagatttaaaagatatggatttaataatagaag
catctgtagaagacatgaatataaagaaagatgttttcaagtta
ctagatgaattatgtaaagaagatactatcttggcaacaaatac
ttcatcattatctataacagaaatagcttcttctactaagcgcc
cagataaagttataggaatgcatttctttaatccagttcctatg
atgaaattagttgaagttataagtggtcagttaacatcaaaagt
tacttttgatacagtatttgaattatctaagagtatcaataaag
taccagtagatgtatctgaatctcctggatttgtagtaaataga
atacttatacctatgataaatgaagctgttggtatatatgcaga
tggtgttgcaagtaaagaagaaatagatgaagctatgaaattag
gagcaaaccatccaatgggaccactagcattaggtgatttaatc
ggattagatgttgttttagctataatgaacgttttatatactga
atttggagatactaaatatagacctcatccacttttagctaaaa
tggttagagctaatcaattaggaagaaaaactaagataggattc
tatgattataataaataataagaaggagatatacatatgagtac
aagtgatgttaaagtttatgagaatgtagctgttgaagtagatg
gaaatatatgtacagtgaaaatgaatagacctaaagcccttaat
gcaataaattcaaagactttagaagaactttatgaagtatttgt
agatattaataatgatgaaactattgatgttgtaatattgacag
gggaaggaaaggcatttgtagctggagcagatattgcatacatg
aaagatttagatgctgtagctgctaaagattttagtatcttagg
agcaaaagcttttggagaaatagaaaatagtaaaaaagtagtga
tagctgctgtaaacggatttgctttaggtggaggatgtgaactt
gcaatggcatgtgatataagaattgcatctgctaaagctaaatt
tggtcagccagaagtaactcttggaataactccaggatatggag
gaactcaaaggcttacaagattggttggaatggcaaaagcaaaa
gaattaatctttacaggtcaagttataaaagctgatgaagctga
aaaaatagggctagtaaatagagtcgttgagccagacattttaa
tagaagaagttgagaaattagctaagataatagctaaaaatgct
cagcttgcagttagatactctaaagaagcaatacaacttggtgc
tcaaactgatataaatactggaatagatatagaatctaatttat
ttggtctttgtttttcaactaaagaccaaaaagaaggaatgtca
gctttcgttgaaaagagagaagctaactttataaaagggtaata
agaaggagatatacatatgagaagttttgaagaagtaattaagt
ttgcaaaagaaagaggacctaaaactatatcagtagcatgttgc
caagataaagaagttttaatggcagttgaaatggctagaaaaga
aaaaatagcaaatgccattttagtaggagatatagaaaagacta
aagaaattgcaaaaagcatagacatggatatcgaaaattatgaa
ctgatagatataaaagatttagcagaagcatctctaaaatctgt
tgaattagtttcacaaggaaaagccgacatggtaatgaaaggct
tagtagacacatcaataatactaaaagcagttttaaataaagaa
gtaggtcttagaactggaaatgtattaagtcacgtagcagtatt
tgatgtagagggatatgatagattatttttcgtaactgacgcag
ctatgaacttagctcctgatacaaatactaaaaagcaaatcata
gaaaatgcttgcacagtagcacattcattagatataagtgaacc
aaaagttgctgcaatatgcgcaaaagaaaaagtaaatccaaaaa
tgaaagatacagttgaagctaaagaactagaagaaatgtatgaa
agaggagaaatcaaaggttgtatggttggtgggccttttgcaat
tgataatgcagtatctttagaagcagctaaacataaaggtataa
atcatcctgtagcaggacgagctgatatattattagccccagat
attgaaggtggtaacatattatataaagctttggtattcttctc
aaaatcaaaaaatgcaggagttatagttggggctaaagcaccaa
taatattaacttctagagcagacagtgaagaaactaaactaaac
tcaatagctttaggtgttttaatggcagcaaaggcataataaga
aggagatatacatatgagcaaaatatttaaaatcttaacaataa
atcctggttcgacatcaactaaaatagctgtatttgataatgag
gatttagtatttgaaaaaactttaagacattcttcagaagaaat
aggaaaatatgagaaggtgtctgaccaatttgaatttcgtaaac
aagtaatagaagaagctctaaaagaaggtggagtaaaaacatct
gaattagatgctgtagtaggtagaggaggacttcttaaacctat
aaaaggtggtacttattcagtaagtgctgctatgattgaagatt
taaaagtgggagttttaggagaacacgcttcaaacctaggtgga
ataatagcaaaacaaataggtgaagaagtaaatgttccttcata
catagtagaccctgttgttgtagatgaattagaagatgttgcta
gaatttctggtatgcctgaaataagtagagcaagtgtagtacat
gctttaaatcaaaaggcaatagcaagaagatatgctagagaaat
aaacaagaaatatgaagatataaatcttatagttgcacacatgg
gtggaggagtttctgttggagctcataaaaatggtaaaatagta
gatgttgcaaacgcattagatggagaaggacctttctctccaga
aagaagtggtggactaccagtaggtgcattagtaaaaatgtgct
ttagtggaaaatatactcaagatgaaattaaaaagaaaataaaa
ggtaatggcggactagttgcatacttaaacactaatgatgctag
agaagttgaagaaagaattgaagctggtgatgaaaaagctaaat
tagtatatgaagctatggcatatcaaatctctaaagaaatagga
gctagtgctgcagttcttaagggagatgtaaaagcaatattatt
aactggtggaatcgcatattcaaaaatgtttacagaaatgattg
cagatagagttaaatttatagcagatgtaaaagtttatccaggt
gaagatgaaatgattgcattagctcaaggtggacttagagtttt
aactggtgaagaagaggctcaagtttatgataactaataa
TABLE-US-00045 TABLE 39 Nucleotide sequences of
pLogic046-nsrR-norB-butyrate construct Nucleotide sequences of
pLogic046-nsrR-norB- Description butyrate construct (SEQ ID NO: 80)
Nucleic acid ttattatcgcaccgcaatcgggattttcgattcataaagcaggtcgta
sequence of an ggtcggcttgttgagcaggtcttgcagcgtgaaaccgtccagatacgt
exemplary RNS- gaaaaacgacttcattgcaccgccgagtatgcccgtcagccggcagga
regulated cggcgtaatcaggcattcgttgttcgggcccatacactcgaccagctg
construct catcggttcgaggtggcggacgaccgcgccgatattgatgcgttcggg
comprising a cggcgcggccagcctcagcccgccgcctttcccgcgtacgctgtgcaa gene
encoding gaacccgcctttgaccagcgcggtaaccactttcatcaaatggctttt nsrR, a
ggaaatgccgtaggtcgaggcgatggtggcgatattgaccagcgcgtc regulatory
gtcgttgacggcggtgtagatgaggacgcgcagcccgtagtcggtatg region of norB,
ttgggtcagatacatacaacctccttagtacatgcaaaattatttcta and a
gagcaacatacgagccggaagcataaagtgtaaagcctggggtgccta butyrogenic
atgagttgagttgaggaattataacaggaagaaatattcctcatacgc gene cassette
ttgtaattcctctatggttgttgacaattaatcatcggctcgtataat pLogic046-nsrR-
##STR00130## norB-butyrate
ttaactttaagaaggagatatacatatgatcgtaaaacctatggtacg construct; SEQ
caacaatatctgcctgaacgcccatcctcagggctgcaagaagggagt ID NO: 80).
ggaagatcagattgaatataccaagaaacgcattaccgcagaagtcaa
agctggcgcaaaagctccaaaaaacgttctggtgcttggctgctcaaa
tggttacggcctggcgagccgcattactgctgcgttcggatacggggc
tgcgaccatcggcgtgtcctttgaaaaagcgggttcagaaaccaaata
tggtacaccgggatggtacaataatttggcatttgatgaagcggcaaa
acgcgagggtctttatagcgtgacgatcgacggcgatgcgttttcaga
cgagatcaaggcccaggtaattgaggaagccaaaaaaaaaggtatcaa
atttgatctgatcgtatacagcttggccagcccagtacgtactgatcc
tgatacaggtatcatgcacaaaagcgttttgaaaccctttggaaaaac
gttcacaggcaaaacagtagatccgtttactggcgagctgaaggaaat
ctccgcggaaccagcaaatgacgaggaagcagccgccactgttaaagt
tatggggggtgaagattgggaacgttggattaagcagctgtcgaagga
aggcctcttagaagaaggctgtattaccttggcctatagttatattgg
ccctgaagctacccaagctttgtaccgtaaaggcacaatcggcaaggc
caaagaacacctggaggccacagcacaccgtctcaacaaagagaaccc
gtcaatccgtgccttcgtgagcgtgaataaaggcctggtaacccgcgc
aagcgccgtaatcccggtaatccctctgtatctcgccagcttgttcaa
agtaatgaaagagaagggcaatcatgaaggttgtattgaacagatcac
gcgtctgtacgccgagcgcctgtaccgtaaagatggtacaattccagt
tgatgaggaaaatcgcattcgcattgatgattgggagttagaagaaga
cgtccagaaagcggtatccgcgttgatggagaaagtcacgggtgaaaa
cgcagaatctctcactgacttagcggggtaccgccatgatttcttagc
tagtaacggctttgatgtagaaggtattaattatgaagcggaagttga
acgcttcgaccgtatctgataagaaggagatatacatatgagagaagt
agtaattgccagtgcagctagaacagcagtaggaagttttggaggagc
atttaaatcagtttcagcggtagagttaggggtaacagcagctaaaga
agctataaaaagagctaacataactccagatatgatagatgaatctct
tttagggggagtacttacagcaggtcttggacaaaatatagcaagaca
aatagcattaggagcaggaataccagtagaaaaaccagctatgactat
aaatatagtttgtggttctggattaagatctgtttcaatggcatctca
acttatagcattaggtgatgctgatataatgttagttggtggagctga
aaacatgagtatgtctccttatttagtaccaagtgcgagatatggtgc
aagaatgggtgatgctgcttttgttgattcaatgataaaagatggatt
atcagacatatttaataactatcacatgggtattactgctgaaaacat
agcagagcaatggaatataactagagaagaacaagatgaattagctct
tgcaagtcaaaataaagctgaaaaagctcaagctgaaggaaaatttga
tgaagaaatagttcctgttgttataaaaggaagaaaaggtgacactgt
agtagataaagatgaatatattaagcctggcactacaatggagaaact
tgctaagttaagacctgcatttaaaaaagatggaacagttactgctgg
taatgcatcaggaataaatgatggtgctgctatgttagtagtaatggc
taaagaaaaagctgaagaactaggaatagagcctcttgcaactatagt
ttcttatggaacagctggtgttgaccctaaaataatgggatatggacc
agttccagcaactaaaaaagctttagaagctgctaatatgactattga
agatatagatttagttgaagctaatgaggcatttgctgcccaatctgt
agctgtaataagagacttaaatatagatatgaataaagttaatgttaa
tggtggagcaatagctataggacatccaataggatgctcaggagcaag
aatacttactacacttttatatgaaatgaagagaagagatgctaaaac
tggtcttgctacactttgtataggcggtggaatgggaactactttaat
agttaagagatagtaagaaggagatatacatatgaaattagctgtaat
aggtagtggaactatgggaagtggtattgtacaaacttttgcaagttg
tggacatgatgtatgtttaaagagtagaactcaaggtgctatagataa
atgtttagctttattagataaaaatttaactaagttagttactaaggg
aaaaatggatgaagctacaaaagcagaaatattaagtcatgttagttc
aactactaattatgaagatttaaaagatatggatttaataatagaagc
atctgtagaagacatgaatataaagaaagatgttttcaagttactaga
tgaattatgtaaagaagatactatcttggcaacaaatacttcatcatt
atctataacagaaatagcttcttctactaagcgcccagataaagttat
aggaatgcatttctttaatccagttcctatgatgaaattagttgaagt
tataagtggtcagttaacatcaaaagttacttttgatacagtatttga
attatctaagagtatcaataaagtaccagtagatgtatctgaatctcc
tggatttgtagtaaatagaatacttatacctatgataaatgaagctgt
tggtatatatgcagatggtgttgcaagtaaagaagaaatagatgaagc
tatgaaattaggagcaaaccatccaatgggaccactagcattaggtga
tttaatcggattagatgttgttttagctataatgaacgttttatatac
tgaatttggagatactaaatatagacctcatccacttttagctaaaat
ggttagagctaatcaattaggaagaaaaactaagataggattctatga
ttataataaataataagaaggagatatacatatgagtacaagtgatgt
taaagtttatgagaatgtagctgttgaagtagatggaaatatatgtac
agtgaaaatgaatagacctaaagcccttaatgcaataaattcaaagac
tttagaagaactttatgaagtatttgtagatattaataatgatgaaac
tattgatgttgtaatattgacaggggaaggaaaggcatttgtagctgg
agcagatattgcatacatgaaagatttagatgctgtagctgctaaaga
ttttagtatcttaggagcaaaagcttttggagaaatagaaaatagtaa
aaaagtagtgatagctgctgtaaacggatttgctttaggtggaggatg
tgaacttgcaatggcatgtgatataagaattgcatctgctaaagctaa
atttggtcagccagaagtaactcttggaataactccaggatatggagg
aactcaaaggcttacaagattggttggaatggcaaaagcaaaagaatt
aatctttacaggtcaagttataaaagctgatgaagctgaaaaaatagg
gctagtaaatagagtcgttgagccagacattttaatagaagaagttga
gaaattagctaagataatagctaaaaatgctcagcttgcagttagata
ctctaaagaagcaatacaacttggtgctcaaactgatataaatactgg
aatagatatagaatctaatttatttggtctttgtttttcaactaaaga
ccaaaaagaaggaatgtcagctttcgttgaaaagagagaagctaactt
tataaaagggtaataagaaggagatatacatatgagaagttttgaaga
agtaattaagtttgcaaaagaaagaggacctaaaactatatcagtagc
atgttgccaagataaagaagttttaatggcagttgaaatggctagaaa
agaaaaaatagcaaatgccattttagtaggagatatagaaaagactaa
agaaattgcaaaaagcatagacatggatatcgaaaattatgaactgat
agatataaaagatttagcagaagcatctctaaaatctgttgaattagt
ttcacaaggaaaagccgacatggtaatgaaaggcttagtagacacatc
aataatactaaaagcagttttaaataaagaagtaggtcttagaactgg
aaatgtattaagtcacgtagcagtatttgatgtagagggatatgatag
attatttttcgtaactgacgcagctatgaacttagctcctgatacaaa
tactaaaaagcaaatcatagaaaatgcttgcacagtagcacattcatt
agatataagtgaaccaaaagttgctgcaatatgcgcaaaagaaaaagt
aaatccaaaaatgaaagatacagttgaagctaaagaactagaagaaat
gtatgaaagaggagaaatcaaaggttgtatggttggtgggccttttgc
aattgataatgcagtatctttagaagcagctaaacataaaggtataaa
tcatcctgtagcaggacgagctgatatattattagccccagatattga
aggtggtaacatattatataaagctttggtattcttctcaaaatcaaa
aaatgcaggagttatagttggggctaaagcaccaataatattaacttc
tagagcagacagtgaagaaactaaactaaactcaatagctttaggtgt
tttaatggcagcaaaggcataataagaaggagatatacatatgagcaa
aatatttaaaatcttaacaataaatcctggttcgacatcaactaaaat
agctgtatttgataatgaggatttagtatttgaaaaaactttaagaca
ttcttcagaagaaataggaaaatatgagaaggtgtctgaccaatttga
atttcgtaaacaagtaatagaagaagctctaaaagaaggtggagtaaa
aacatctgaattagatgctgtagtaggtagaggaggacttcttaaacc
tataaaaggtggtacttattcagtaagtgctgctatgattgaagattt
aaaagtgggagttttaggagaacacgcttcaaacctaggtggaataat
agcaaaacaaataggtgaagaagtaaatgttccttcatacatagtaga
ccctgttgttgtagatgaattagaagatgttgctagaatttctggtat
gcctgaaataagtagagcaagtgtagtacatgctttaaatcaaaaggc
aatagcaagaagatatgctagagaaataaacaagaaatatgaagatat
aaatcttatagttgcacacatgggtggaggagtttctgttggagctca
taaaaatggtaaaatagtagatgttgcaaacgcattagatggagaagg
acctttctctccagaaagaagtggtggactaccagtaggtgcattagt
aaaaatgtgctttagtggaaaatatactcaagatgaaattaaaaagaa
aataaaaggtaatggcggactagttgcatacttaaacactaatgatgc
tagagaagttgaagaaagaattgaagctggtgatgaaaaagctaaatt
agtatatgaagctatggcatatcaaatctctaaagaaataggagctag
tgctgcagttcttaagggagatgtaaaagcaatattattaactggtgg
aatcgcatattcaaaaatgtttacagaaatgattgcagatagagttaa
atttatagcagatgtaaaagtttatccaggtgaagatgaaatgattgc
attagctcaaggtggacttagagttttaactggtgaagaagaggctca
agtttatgataactaataa
[0750] The gene products of the bcd2-etfA3-etfB3 genes form a
complex that converts crotonyl-CoA to butyryl-CoA and may exhibit
dependence on oxygen as a co-oxidant. Because the recombinant
bacteria of the invention are designed to produce butyrate in an
oxygen-limited environment (e.g. the mammalian gut), that
dependence on oxygen could have a negative effect of butyrate
production in the gut. It has been shown that a single gene from
Treponema denticola, trans-2-enoynl-CoA reductase (ter), can
functionally replace this three gene complex in an
oxygen-independent manner. Therefore, a second butyrate gene
cassette in which the ter gene replaces the bcd2-etfA3-etfB3 genes
of the first butyrate cassette is synthesized (Genewiz, Cambridge,
Mass.). The ter gene is codon-optimized for E. coli codon usage
using Integrated DNA Technologies online codon optimization tool
(https://www.idtdna.com/CodonOpt). The second butyrate gene
cassette, as well as transcriptional and translational elements, is
synthesized (Gen9, Cambridge, Mass.) and cloned into vector pBR322.
The second butyrate gene cassette is placed under control of a FNR
regulatory region as described above. In certain constructs, the
butyrate gene cassette is placed under the control of an
RNS-responsive regulatory region, e.g., norB, and the bacteria
further comprises a gene encoding a corresponding RNS-responsive
transcription factor, e.g., nsrR (see, e.g., Table 38 and Table
39). In certain constructs, the butyrate gene cassette is placed
under the control of an ROS-responsive regulatory region, e.g.,
oxyS, and the bacteria further comprises a gene encoding a
corresponding ROS-responsive transcription factor, e.g., oxyR (see,
e.g., Table C and Table 40).
TABLE-US-00046 TABLE 40 ROS regulated constructs, OxyR construct,
Tet-regulated constructs Description Sequence Nucleotide
ctcgagttcattatccatcctccatcgccacgatagttcatggcgataggtagaatagc
sequences of
aatgaacgattatccctatcaagcattctgactgataattgctcacacgaattcattaa
pLogic031-
agaggagaaaggtaccatggatttaaattctaaaaaatatcagatgcttaaagagctat oxyS-
atgtaagcttcgctgaaaatgaagttaaacctttagcaacagaacttgatgaagaagaa
butyrate
agatttccttatgaaacagtggaaaaaatggcaaaagcaggaatgatgggtataccata
construct
tccaaaagaatatggtggagaaggtggagacactgtaggatatataatggcagttgaag (SEQ ID
NO: aattgtctagagtttgtggtactacaggagttatattatcagctcatacatctcttggc 81)
tcatggcctatatatcaatatggtaatgaagaacaaaaacaaaaattcttaagaccact
agcaagtggagaaaaattaggagcatttggtcttactgagcctaatgctggtacagatg
cgtctggccaacaaacaactgctgttttagacggggatgaatacatacttaatggctca
aaaatatttataacaaacgcaatagctggtgacatatatgtagtaatggcaatgactga
taaatctaaggggaacaaaggaatatcagcatttatagttgaaaaaggaactcctgggt
ttagctttggagttaaagaaaagaaaatgggtataagaggttcagctacgagtgaatta
atatttgaggattgcagaatacctaaagaaaatttacttggaaaagaaggtcaaggatt
taagatagcaatgtctactcttgatggtggtagaattggtatagctgcacaagctttag
gtttagcacaaggtgctcttgatgaaactgttaaatatgtaaaagaaagagtacaattt
ggtagaccattatcaaaattccaaaatacacaattccaattagctgatatggaagttaa
ggtacaagcggctagacaccttgtatatcaagcagctataaataaagacttaggaaaac
cttatggagtagaagcagcaatggcaaaattatttgcagctgaaacagctatggaagtt
actacaaaagctgtacaacttcatggaggatatggatacactcgtgactatccagtaga
aagaatgatgagagatgctaagataactgaaatatatgaaggaactagtgaagttcaaa
gaatggttatttcaggaaaactattaaaatagtaagaaggagatatacatatggaggaa
ggatttatgaatatagtcgtttgtataaaacaagttccagatacaacagaagttaaact
agatcctaatacaggtactttaattagagatggagtaccaagtataataaaccctgatg
ataaagcaggtttagaagaagctataaaattaaaagaagaaatgggtgctcatgtaact
gttataacaatgggacctcctcaagcagatatggctttaaaagaagctttagcaatggg
tgcagatagaggtatattattaacagatagagcatttgcgggtgctgatacttgggcaa
cttcatcagcattagcaggagcattaaaaaatatagattttgatattataatagctgga
agacaggcgatagatggagatactgcacaagttggacctcaaatagctgaacatttaaa
tcttccatcaataacatatgctgaagaaataaaaactgaaggtgaatatgtattagtaa
aaagacaatttgaagattgttgccatgacttaaaagttaaaatgccatgccttataaca
actcttaaagatatgaacacaccaagatacatgaaagttggaagaatatatgatgcttt
cgaaaatgatgtagtagaaacatggactgtaaaagatatagaagttgacccttctaatt
taggtcttaaaggttctccaactagtgtatttaaatcatttacaaaatcagttaaacca
gctggtacaatatacaatgaagatgcgaaaacatcagctggaattatcatagataaatt
aaaagagaagtatatcatataataagaaggagatatacatatgggtaacgttttagtag
taatagaacaaagagaaaatgtaattcaaactgtttctttagaattactaggaaaggct
acagaaatagcaaaagattatgatacaaaagtttctgcattacttttaggtagtaaggt
agaaggtttaatagatacattagcacactatggtgcagatgaggtaatagtagtagatg
atgaagctttagcagtgtatacaactgaaccatatacaaaagcagcttatgaagcaata
aaagcagctgaccctatagttgtattatttggtgcaacttcaataggtagagatttagc
gcctagagtttctgctagaatacatacaggtcttactgctgactgtacaggtcttgcag
tagctgaagatacaaaattattattaatgacaagacctgcctttggtggaaatataatg
gcaacaatagtttgtaaagatttcagacctcaaatgtctacagttagaccaggggttat
gaagaaaaatgaacctgatgaaactaaagaagctgtaattaaccgtttcaaggtagaat
ttaatgatgctgataaattagttcaagttgtacaagtaataaaagaagctaaaaaacaa
gttaaaatagaagatgctaagatattagtttctgctggacgtggaatgggtggaaaaga
aaacttagacatactttatgaattagctgaaattataggtggagaagtttctggttctc
gtgccactatagatgcaggttggttagataaagcaagacaagttggtcaaactggtaaa
actgtaagaccagacctttatatagcatgtggtatatctggagcaatacaacatatagc
tggtatggaagatgctgagtttatagttgctataaataaaaatccagaagctccaatat
ttaaatatgctgatgttggtatagttggagatgttcataaagtgcttccagaacttatc
agtcagttaagtgttgcaaaagaaaaaggtgaagttttagctaactaataagaaggaga
tatacatatgagagaagtagtaattgccagtgcagctagaacagcagtaggaagttttg
gaggagcatttaaatcagtttcagcggtagagttaggggtaacagcagctaaagaagct
ataaaaagagctaacataactccagatatgatagatgaatctcttttagggggagtact
tacagcaggtcttggacaaaatatagcaagacaaatagcattaggagcaggaataccag
tagaaaaaccagctatgactataaatatagtttgtggttctggattaagatctgtttca
atggcatctcaacttatagcattaggtgatgctgatataatgttagttggtggagctga
aaacatgagtatgtctccttatttagtaccaagtgcgagatatggtgcaagaatgggtg
atgctgcttttgttgattcaatgataaaagatggattatcagacatatttaataactat
cacatgggtattactgctgaaaacatagcagagcaatggaatataactagagaagaaca
agatgaattagctcttgcaagtcaaaataaagctgaaaaagctcaagctgaaggaaaat
ttgatgaagaaatagttcctgttgttataaaaggaagaaaaggtgacactgtagtagat
aaagatgaatatattaagcctggcactacaatggagaaacttgctaagttaagacctgc
atttaaaaaagatggaacagttactgctggtaatgcatcaggaataaatgatggtgctg
ctatgttagtagtaatggctaaagaaaaagctgaagaactaggaatagagcctcttgca
actatagtttcttatggaacagctggtgttgaccctaaaataatgggatatggaccagt
tccagcaactaaaaaagctttagaagctgctaatatgactattgaagatatagatttag
ttgaagctaatgaggcatttgctgcccaatctgtagctgtaataagagacttaaatata
gatatgaataaagttaatgttaatggtggagcaatagctataggacatccaataggatg
ctcaggagcaagaatacttactacacttttatatgaaatgaagagaagagatgctaaaa
ctggtcttgctacactttgtataggcggtggaatgggaactactttaatagttaagaga
tagtaagaaggagatatacatatgaaattagctgtaataggtagtggaactatgggaag
tggtattgtacaaacttttgcaagttgtggacatgatgtatgtttaaagagtagaactc
aaggtgctatagataaatgtttagctttattagataaaaatttaactaagttagttact
aagggaaaaatggatgaagctacaaaagcagaaatattaagtcatgttagttcaactac
taattatgaagatttaaaagatatggatttaataatagaagcatctgtagaagacatga
atataaagaaagatgttttcaagttactagatgaattatgtaaagaagatactatcttg
gcaacaaatacttcatcattatctataacagaaatagcttcttctactaagcgcccaga
taaagttataggaatgcatttctttaatccagttcctatgatgaaattagttgaagtta
taagtggtcagttaacatcaaaagttacttttgatacagtatttgaattatctaagagt
atcaataaagtaccagtagatgtatctgaatctcctggatttgtagtaaatagaatact
tatacctatgataaatgaagctgttggtatatatgcagatggtgttgcaagtaaagaag
aaatagatgaagctatgaaattaggagcaaaccatccaatgggaccactagcattaggt
gatttaatcggattagatgttgttttagctataatgaacgttttatatactgaatttgg
agatactaaatatagacctcatccacttttagctaaaatggttagagctaatcaattag
gaagaaaaactaagataggattctatgattataataaataataagaaggagatatacat
atgagtacaagtgatgttaaagtttatgagaatgtagctgttgaagtagatggaaatat
atgtacagtgaaaatgaatagacctaaagcccttaatgcaataaattcaaagactttag
aagaactttatgaagtatttgtagatattaataatgatgaaactattgatgttgtaata
ttgacaggggaaggaaaggcatttgtagctggagcagatattgcatacatgaaagattt
agatgctgtagctgctaaagattttagtatcttaggagcaaaagcttttggagaaatag
aaaatagtaaaaaagtagtgatagctgctgtaaacggatttgctttaggtggaggatgt
gaacttgcaatggcatgtgatataagaattgcatctgctaaagctaaatttggtcagcc
agaagtaactcttggaataactccaggatatggaggaactcaaaggcttacaagattgg
ttggaatggcaaaagcaaaagaattaatctttacaggtcaagttataaaagctgatgaa
gctgaaaaaatagggctagtaaatagagtcgttgagccagacattttaatagaagaagt
tgagaaattagctaagataatagctaaaaatgctcagcttgcagttagatactctaaag
aagcaatacaacttggtgctcaaactgatataaatactggaatagatatagaatctaat
ttatttggtctttgtttttcaactaaagaccaaaaagaaggaatgtcagctttcgttga
aaagagagaagctaactttataaaagggtaataagaaggagatatacatatgagaagtt
ttgaagaagtaattaagtttgcaaaagaaagaggacctaaaactatatcagtagcatgt
tgccaagataaagaagttttaatggcagttgaaatggctagaaaagaaaaaatagcaaa
tgccattttagtaggagatatagaaaagactaaagaaattgcaaaaagcatagacatgg
atatcgaaaattatgaactgatagatataaaagatttagcagaagcatctctaaaatct
gttgaattagtttcacaaggaaaagccgacatggtaatgaaaggcttagtagacacatc
aataatactaaaagcagttttaaataaagaagtaggtcttagaactggaaatgtattaa
gtcacgtagcagtatttgatgtagagggatatgatagattatttttcgtaactgacgca
gctatgaacttagctcctgatacaaatactaaaaagcaaatcatagaaaatgcttgcac
agtagcacattcattagatataagtgaaccaaaagttgctgcaatatgcgcaaaagaaa
aagtaaatccaaaaatgaaagatacagttgaagctaaagaactagaagaaatgtatgaa
agaggagaaatcaaaggttgtatggttggtgggccttttgcaattgataatgcagtatc
tttagaagcagctaaacataaaggtataaatcatcctgtagcaggacgagctgatatat
tattagccccagatattgaaggtggtaacatattatataaagctttggtattcttctca
aaatcaaaaaatgcaggagttatagttggggctaaagcaccaataatattaacttctag
agcagacagtgaagaaactaaactaaactcaatagctttaggtgttttaatggcagcaa
aggcataataagaaggagatatacatatgagcaaaatatttaaaatcttaacaataaat
cctggttcgacatcaactaaaatagctgtatttgataatgaggatttagtatttgaaaa
aactttaagacattcttcagaagaaataggaaaatatgagaaggtgtctgaccaatttg
aatttcgtaaacaagtaatagaagaagctctaaaagaaggtggagtaaaaacatctgaa
ttagatgctgtagtaggtagaggaggacttcttaaacctataaaaggtggtacttattc
agtaagtgctgctatgattgaagatttaaaagtgggagttttaggagaacacgcttcaa
acctaggtggaataatagcaaaacaaataggtgaagaagtaaatgttccttcatacata
gtagaccctgttgttgtagatgaattagaagatgttgctagaatttctggtatgcctga
aataagtagagcaagtgtagtacatgctttaaatcaaaaggcaatagcaagaagatatg
ctagagaaataaacaagaaatatgaagatataaatcttatagttgcacacatgggtgga
ggagtttctgttggagctcataaaaatggtaaaatagtagatgttgcaaacgcattaga
tggagaaggacctttctctccagaaagaagtggtggactaccagtaggtgcattagtaa
aaatgtgctttagtggaaaatatactcaagatgaaattaaaaagaaaataaaaggtaat
ggcggactagttgcatacttaaacactaatgatgctagagaagttgaagaaagaattga
agctggtgatgaaaaagctaaattagtatatgaagctatggcatatcaaatctctaaag
aaataggagctagtgctgcagttcttaagggagatgtaaaagcaatattattaactggt
ggaatcgcatattcaaaaatgtttacagaaatgattgcagatagagttaaatttatagc
agatgtaaaagtttatccaggtgaagatgaaatgattgcattagctcaaggtggactta
gagttttaactggtgaagaagaggctcaagtttatgataactaataa Nucleotide
ctcgagttcattatccatcctccatcgccacgatagttcatggcgataggtagaatagc
sequences of
aatgaacgattatccctatcaagcattctgactgataattgctcacacgaattcattaa
pLogic046-
agaggagaaaggtaccatgatcgtaaaacctatggtacgcaacaatatctgcctgaacg oxyS-
cccatcctcagggctgcaagaagggagtggaagatcagattgaatataccaagaaacgc
butyrate
attaccgcagaagtcaaagctggcgcaaaagctccaaaaaacgttctggtgcttggctg
construct
ctcaaatggttacggcctggcgagccgcattactgctgcgttcggatacggggctgcga (SEQ ID
NO: ccatcggcgtgtcctttgaaaaagcgggttcagaaaccaaatatggtacaccgggatgg 82)
tacaataatttggcatttgatgaagcggcaaaacgcgagggtctttatagcgtgacgat
cgacggcgatgcgttttcagacgagatcaaggcccaggtaattgaggaagccaaaaaaa
aaggtatcaaatttgatctgatcgtatacagcttggccagcccagtacgtactgatcct
gatacaggtatcatgcacaaaagcgttttgaaaccctttggaaaaacgttcacaggcaa
aacagtagatccgtttactggcgagctgaaggaaatctccgcggaaccagcaaatgacg
aggaagcagccgccactgttaaagttatggggggtgaagattgggaacgttggattaag
cagctgtcgaaggaaggcctcttagaagaaggctgtattaccttggcctatagttatat
tggccctgaagctacccaagctttgtaccgtaaaggcacaatcggcaaggccaaagaac
acctggaggccacagcacaccgtctcaacaaagagaacccgtcaatccgtgccttcgtg
agcgtgaataaaggcctggtaacccgcgcaagcgccgtaatcccggtaatccctctgta
tctcgccagcttgttcaaagtaatgaaagagaagggcaatcatgaaggttgtattgaac
agatcacgcgtctgtacgccgagcgcctgtaccgtaaagatggtacaattccagttgat
gaggaaaatcgcattcgcattgatgattgggagttagaagaagacgtccagaaagcggt
atccgcgttgatggagaaagtcacgggtgaaaacgcagaatctctcactgacttagcgg
ggtaccgccatgatttcttagctagtaacggctttgatgtagaaggtattaattatgaa
gcggaagttgaacgcttcgaccgtatctgataagaaggagatatacatatgagagaagt
agtaattgccagtgcagctagaacagcagtaggaagttttggaggagcatttaaatcag
tttcagcggtagagttaggggtaacagcagctaaagaagctataaaaagagctaacata
actccagatatgatagatgaatctcttttagggggagtacttacagcaggtcttggaca
aaatatagcaagacaaatagcattaggagcaggaataccagtagaaaaaccagctatga
ctataaatatagtttgtggttctggattaagatctgtttcaatggcatctcaacttata
gcattaggtgatgctgatataatgttagttggtggagctgaaaacatgagtatgtctcc
ttatttagtaccaagtgcgagatatggtgcaagaatgggtgatgctgcttttgttgatt
caatgataaaagatggattatcagacatatttaataactatcacatgggtattactgct
gaaaacatagcagagcaatggaatataactagagaagaacaagatgaattagctcttgc
aagtcaaaataaagctgaaaaagctcaagctgaaggaaaatttgatgaagaaatagttc
ctgttgttataaaaggaagaaaaggtgacactgtagtagataaagatgaatatattaag
cctggcactacaatggagaaacttgctaagttaagacctgcatttaaaaaagatggaac
agttactgctggtaatgcatcaggaataaatgatggtgctgctatgttagtagtaatgg
ctaaagaaaaagctgaagaactaggaatagagcctcttgcaactatagtttcttatgga
acagctggtgttgaccctaaaataatgggatatggaccagttccagcaactaaaaaagc
tttagaagctgctaatatgactattgaagatatagatttagttgaagctaatgaggcat
ttgctgcccaatctgtagctgtaataagagacttaaatatagatatgaataaagttaat
gttaatggtggagcaatagctataggacatccaataggatgctcaggagcaagaatact
tactacacttttatatgaaatgaagagaagagatgctaaaactggtcttgctacacttt
gtataggcggtggaatgggaactactttaatagttaagagatagtaagaaggagatata
catatgaaattagctgtaataggtagtggaactatgggaagtggtattgtacaaacttt
tgcaagttgtggacatgatgtatgtttaaagagtagaactcaaggtgctatagataaat
gtttagctttattagataaaaatttaactaagttagttactaagggaaaaatggatgaa
gctacaaaagcagaaatattaagtcatgttagttcaactactaattatgaagatttaaa
agatatggatttaataatagaagcatctgtagaagacatgaatataaagaaagatgttt
tcaagttactagatgaattatgtaaagaagatactatcttggcaacaaatacttcatca
ttatctataacagaaatagcttcttctactaagcgcccagataaagttataggaatgca
tttctttaatccagttcctatgatgaaattagttgaagttataagtggtcagttaacat
caaaagttacttttgatacagtatttgaattatctaagagtatcaataaagtaccagta
gatgtatctgaatctcctggatttgtagtaaatagaatacttatacctatgataaatga
agctgttggtatatatgcagatggtgttgcaagtaaagaagaaatagatgaagctatga
aattaggagcaaaccatccaatgggaccactagcattaggtgatttaatcggattagat
gttgttttagctataatgaacgttttatatactgaatttggagatactaaatatagacc
tcatccacttttagctaaaatggttagagctaatcaattaggaagaaaaactaagatag
gattctatgattataataaataataagaaggagatatacatatgagtacaagtgatgtt
aaagtttatgagaatgtagctgttgaagtagatggaaatatatgtacagtgaaaatgaa
tagacctaaagcccttaatgcaataaattcaaagactttagaagaactttatgaagtat
ttgtagatattaataatgatgaaactattgatgttgtaatattgacaggggaaggaaag
gcatttgtagctggagcagatattgcatacatgaaagatttagatgctgtagctgctaa
agattttagtatcttaggagcaaaagcttttggagaaatagaaaatagtaaaaaagtag
tgatagctgctgtaaacggatttgctttaggtggaggatgtgaacttgcaatggcatgt
gatataagaattgcatctgctaaagctaaatttggtcagccagaagtaactcttggaat
aactccaggatatggaggaactcaaaggcttacaagattggttggaatggcaaaagcaa
aagaattaatctttacaggtcaagttataaaagctgatgaagctgaaaaaatagggcta
gtaaatagagtcgttgagccagacattttaatagaagaagttgagaaattagctaagat
aatagctaaaaatgctcagcttgcagttagatactctaaagaagcaatacaacttggtg
ctcaaactgatataaatactggaatagatatagaatctaatttatttggtctttgtttt
tcaactaaagaccaaaaagaaggaatgtcagctttcgttgaaaagagagaagctaactt
tataaaagggtaataagaaggagatatacatatgagaagttttgaagaagtaattaagt
ttgcaaaagaaagaggacctaaaactatatcagtagcatgttgccaagataaagaagtt
ttaatggcagttgaaatggctagaaaagaaaaaatagcaaatgccattttagtaggaga
tatagaaaagactaaagaaattgcaaaaagcatagacatggatatcgaaaattatgaac
tgatagatataaaagatttagcagaagcatctctaaaatctgttgaattagtttcacaa
ggaaaagccgacatggtaatgaaaggcttagtagacacatcaataatactaaaagcagt
tttaaataaagaagtaggtcttagaactggaaatgtattaagtcacgtagcagtatttg
atgtagagggatatgatagattatttttcgtaactgacgcagctatgaacttagctcct
gatacaaatactaaaaagcaaatcatagaaaatgcttgcacagtagcacattcattaga
tataagtgaaccaaaagttgctgcaatatgcgcaaaagaaaaagtaaatccaaaaatga
aagatacagttgaagctaaagaactagaagaaatgtatgaaagaggagaaatcaaaggt
tgtatggttggtgggccttttgcaattgataatgcagtatctttagaagcagctaaaca
taaaggtataaatcatcctgtagcaggacgagctgatatattattagccccagatattg
aaggtggtaacatattatataaagctttggtattcttctcaaaatcaaaaaatgcagga
gttatagttggggctaaagcaccaataatattaacttctagagcagacagtgaagaaac
taaactaaactcaatagctttaggtgttttaatggcagcaaaggcataataagaaggag
atatacatatgagcaaaatatttaaaatcttaacaataaatcctggttcgacatcaact
aaaatagctgtatttgataatgaggatttagtatttgaaaaaactttaagacattcttc
agaagaaataggaaaatatgagaaggtgtctgaccaatttgaatttcgtaaacaagtaa
tagaagaagctctaaaagaaggtggagtaaaaacatctgaattagatgctgtagtaggt
agaggaggacttcttaaacctataaaaggtggtacttattcagtaagtgctgctatgat
tgaagatttaaaagtgggagttttaggagaacacgcttcaaacctaggtggaataatag
caaaacaaataggtgaagaagtaaatgttccttcatacatagtagaccctgttgttgta
gatgaattagaagatgttgctagaatttctggtatgcctgaaataagtagagcaagtgt
agtacatgctttaaatcaaaaggcaatagcaagaagatatgctagagaaataaacaaga
aatatgaagatataaatcttatagttgcacacatgggtggaggagtttctgttggagct
TCTGTACCGTCCCAATCATGGCTCGCTGGAAAAAGTTGGTCTTATGGCAGAAGACCCCT
GTACACAACACCCGT neered bacteria comprise the nucleic acid
ttaaacactaatgatgctagagaagttgaagaaagaattgaagctggtgatgaaaaagc
taaattagtatatgaagctatggcatatcaaatctctaaagaaataggagctagtgctg
cagttcttaagggagatgtaaaagcaatattattaactggtggaatcgcatattcaaaa
atgtttacagaaatgattgcagatagagttaaatttatagcagatgtaaaagtttatcc
aggtgaagatgaaatgattgcattagctcaaggtggacttagagttttaactggtgaag
aagaggctcaagtttatgataactaataa Nucleotide
ctcgagatgctagcaattgtgagcggataacaattgacattgtgagcggataacaagat
sequences of
actgagcacatcagcaggacgcactgaccttaattaaaagaattcattaaagaggagaa
pZA22-oxyR
aggtaccatgaatattcgtgatcttgagtacctggtggcattggctgaacaccgccatt
constrcut
ttcggcgtgcggcagattcctgccacgttagccagccgacgcttagcgggcaaattcgt (SEQ ID
NO: aagctggaagatgagctgggcgtgatgttgctggagcggaccagccgtaaagtgttgtt 83)
cacccaggcgggaatgctgctggtggatcaggcgcgtaccgtgctgcgtgaggtgaaag
tccttaaagagatggcaagccagcagggcgagacgatgtccggaccgctgcacattggt
ttgattcccacagttggaccgtacctgctaccgcatattatccctatgctgcaccagac
ctttccaaagctggaaatgtatctgcatgaagcacagacccaccagttactggcgcaac
tggacagcggcaaactcgattgcgtgatcctcgcgctggtgaaagagagcgaagcattc
attgaagtgccgttgtttgatgagccaatgttgctggctatctatgaagatcacccgtg
ggcgaaccgcgaatgcgtaccgatggccgatctggcaggggaaaaactgctgatgctgg
aagatggtcactgtttgcgcgatcaggcaatgggtttctgttttgaagccggggcggat
gaagatacacacttccgcgcgaccagcctggaaactctgcgcaacatggtggcggcagg
tagcgggatcactttactgccagcgctggctgtgccgccggagcgcaaacgcgatgggg
ttgtttatctgccgtgcattaagccggaaccacgccgcactattggcctggtttatcgt
cctggctcaccgctgcgcagccgctatgagcagctggcagaggccatccgcgcaagaat
ggatggccatttcgataaagttttaaaacaggcggtttaaggatcccatggtacgcgtg
ctagaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatct
gttgtttgtcggtgaacgctctcctgagtaggacaaatccgccgccctagacctagggg
atatattccgcttcctcgctcactgactcgctacgctcggtcgttcgactgcggcgagc
ggaaatggcttacgaacggggcggagatttcctggaagatgccaggaagatacttaaca
gggaagtgagagggccgcggcaaagccgtttttccataggctccgcccccctgacaagc
atcacgaaatctgacgctcaaatcagtggtggcgaaacccgacaggactataaagatac
caggcgtttccccctggcggctccctcgtgcgctctcctgttcctgcctttcggtttac
cggtgtcattccgctgttatggccgcgtttgtctcattccacgcctgacactcagttcc
gggtaggcagttcgctccaagctggactgtatgcacgaaccccccgttcagtccgaccg
ctgcgccttatccggtaactatcgtcttgagtccaacccggaaagacatgcaaaagcac
cactggcagcagccactggtaattgatttagaggagttagtcttgaagtcatgcgccgg
ttaaggctaaactgaaaggacaagttttggtgactgcgctcctccaagccagttacctc
ggttcaaagagttggtagctcagagaaccttcgaaaaaccgccctgcaaggcggttttt
tcgttttcagagcaagagattacgcgcagaccaaaacgatctcaagaagatcatcttat
taatcagataaaatatttctagatttcagtgcaatttatctcttcaaatgtagcacctg
aagtcagccccatacgatataagttgttactagtgcttggattctcaccaataaaaaac
gcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactgg
atctatcaacaggagtccaagcgagctctcgaaccccagagtcccgctcagaagaactc
gtcaagaaggcgatagaaggcgatgcgctgcgaatcgggagcggcgataccgtaaagca
cgaggaagcggtcagcccattcgccgccaagctcttcagcaatatcacgggtagccaac
gctatgtcctgatagcggtccgccacacccagccggccacagtcgatgaatccagaaaa
gcggccattttccaccatgatattcggcaagcaggcatcgccatgggtcacgacgagat
cctcgccgtcgggcatgcgcgccttgagcctggcgaacagttcggctggcgcgagcccc
tgatgctcttcgtccagatcatcctgatcgacaagaccggcttccatccgagtacgtgc
tcgctcgatgcgatgtttcgcttggtggtcgaatgggcaggtagccggatcaagcgtat
gcagccgccgcattgcatcagccatgatggatactttctcggcaggagcaaggtgagat
gacaggagatcctgccccggcacttcgcccaatagcagccagtcccttcccgcttcagt
gacaacgtcgagcacagctgcgcaaggaacgcccgtcgtggccagccacgatagccgcg
ctgcctcgtcctgcagttcattcagggcaccggacaggtcggtcttgacaaaaagaacc
gggcgcccctgcgctgacagccggaacacggcggcatcagagcagccgattgtctgttg
tgcccagtcatagccgaatagcctctccacccaagcggccggagaacctgcgtgcaatc
catcttgttcaatcatgcgaaacgatcctcatcctgtctcttgatcagatcttgatccc
ctgcgccatcagatccttggcggcaagaaagccatccagtttactttgcagggcttccc
aaccttaccagagggcgccccagctggcaattccgacgtctaagaaaccattattatca
tgacattaacctataaaaataggcgtatcacgaggccctttcgtcttcac Nucleotide
gtaaaacgacggccagtgaattcgttaagacccactttcacatttaagttgtttttcta
sequences of
atccgcatatgatcaattcaaggccgaataagaaggctggctctgcaccttggtgatca
pLogic031-
aataattcgatagcttgtcgtaataatggcggcatactatcagtagtaggtgtttccct
tet-butyrate
ttcttctttagcgacttgatgctcttgatcttccaatacgcaacctaaagtaaaatgcc
construct
ccacagcgctgagtgcatataatgcattctctagtgaaaaaccttgttggcataaaaag (SEQ ID
NO: gctaattgattttcgagagtttcatactgtttttctgtaggccgtgtacctaaatgtac 84)
The ttttgctccatcgcgatgacttagtaaagcacatctaaaacttttagcgttattacgta
sequence
aaaaatcttgccagctttccccttctaaagggcaaaagtgagtatggtgcctatctaac
encoding
atctcaatggctaaggcgtcgagcaaagcccgcttattttttacatgccaatacaatgt TetR is
aggctgctctacacctagcttctgggcgagtttacgggttgttaaaccttcgattccga
underlined,
cctcattaagcagctctaatgcgctgttaatcactttacttttatctaatctagacatc and the
##STR00131## overlapping ##STR00132## tetR/tetA
tacatatggatttaaattctaaaaaatatcagatgcttaaagagctatatgtaagcttc
promoters
gctgaaaatgaagttaaacctttagcaacagaacttgatgaagaagaaagatttcctta are
tgaaacagtggaaaaaatggcaaaagcaggaatgatgggtataccatatccaaaagaat
##STR00133##
atggtggagaaggtggagacactgtaggatatataatggcagttgaagaattgtctaga
gtttgtggtactacaggagttatattatcagctcatacatctcttggctcatggcctat
atatcaatatggtaatgaagaacaaaaacaaaaattcttaagaccactagcaagtggag
aaaaattaggagcatttggtcttactgagcctaatgctggtacagatgcgtctggccaa
caaacaactgctgttttagacggggatgaatacatacttaatggctcaaaaatatttat
aacaaacgcaatagctggtgacatatatgtagtaatggcaatgactgataaatctaagg
ggaacaaaggaatatcagcatttatagttgaaaaaggaactcctgggtttagctttgga
gttaaagaaaagaaaatgggtataagaggttcagctacgagtgaattaatatttgagga
ttgcagaatacctaaagaaaatttacttggaaaagaaggtcaaggatttaagatagcaa
tgtctactcttgatggtggtagaattggtatagctgcacaagctttaggtttagcacaa
ggtgctcttgatgaaactgttaaatatgtaaaagaaagagtacaatttggtagaccatt
atcaaaattccaaaatacacaattccaattagctgatatggaagttaaggtacaagcgg
ctagacaccttgtatatcaagcagctataaataaagacttaggaaaaccttatggagta
gaagcagcaatggcaaaattatttgcagctgaaacagctatggaagttactacaaaagc
tgtacaacttcatggaggatatggatacactcgtgactatccagtagaaagaatgatga
gagatgctaagataactgaaatatatgaaggaactagtgaagttcaaagaatggttatt
tcaggaaaactattaaaatagtaagaaggagatatacatatggaggaaggatttatgaa
tatagtcgtttgtataaaacaagttccagatacaacagaagttaaactagatcctaata
caggtactttaattagagatggagtaccaagtataataaaccctgatgataaagcaggt
ttagaagaagctataaaattaaaagaagaaatgggtgctcatgtaactgttataacaat
gggacctcctcaagcagatatggctttaaaagaagctttagcaatgggtgcagatagag
gtatattattaacagatagagcatttgcgggtgctgatacttgggcaacttcatcagca
ttagcaggagcattaaaaaatatagattttgatattataatagctggaagacaggcgat
agatggagatactgcacaagttggacctcaaatagctgaacatttaaatcttccatcaa
taacatatgctgaagaaataaaaactgaaggtgaatatgtattagtaaaaagacaattt
gaagattgttgccatgacttaaaagttaaaatgccatgccttataacaactcttaaaga
tatgaacacaccaagatacatgaaagttggaagaatatatgatgctttcgaaaatgatg
tagtagaaacatggactgtaaaagatatagaagttgacccttctaatttaggtcttaaa
ggttctccaactagtgtatttaaatcatttacaaaatcagttaaaccagctggtacaat
atacaatgaagatgcgaaaacatcagctggaattatcatagataaattaaaagagaagt
atatcatataataagaaggagatatacatatgggtaacgttttagtagtaatagaacaa
agagaaaatgtaattcaaactgtttctttagaattactaggaaaggctacagaaatagc
aaaagattatgatacaaaagtttctgcattacttttaggtagtaaggtagaaggtttaa
tagatacattagcacactatggtgcagatgaggtaatagtagtagatgatgaagcttta
gcagtgtatacaactgaaccatatacaaaagcagcttatgaagcaataaaagcagctga
ccctatagttgtattatttggtgcaacttcaataggtagagatttagcgcctagagttt
ctgctagaatacatacaggtcttactgctgactgtacaggtcttgcagtagctgaagat
acaaaattattattaatgacaagacctgcctttggtggaaatataatggcaacaatagt
ttgtaaagatttcagacctcaaatgtctacagttagaccaggggttatgaagaaaaatg
aacctgatgaaactaaagaagctgtaattaaccgtttcaaggtagaatttaatgatgct
gataaattagttcaagttgtacaagtaataaaagaagctaaaaaacaagttaaaataga
agatgctaagatattagtttctgctggacgtggaatgggtggaaaagaaaacttagaca
tactttatgaattagctgaaattataggtggagaagtttctggttctcgtgccactata
gatgcaggttggttagataaagcaagacaagttggtcaaactggtaaaactgtaagacc
agacctttatatagcatgtggtatatctggagcaatacaacatatagctggtatggaag
atgctgagtttatagttgctataaataaaaatccagaagctccaatatttaaatatgct
gatgttggtatagttggagatgttcataaagtgcttccagaacttatcagtcagttaag
tgttgcaaaagaaaaaggtgaagttttagctaactaataagaaggagatatacatatga
gagaagtagtaattgccagtgcagctagaacagcagtaggaagttttggaggagcattt
aaatcagtttcagcggtagagttaggggtaacagcagctaaagaagctataaaaagagc
taacataactccagatatgatagatgaatctcttttagggggagtacttacagcaggtc
ttggacaaaatatagcaagacaaatagcattaggagcaggaataccagtagaaaaacca
gctatgactataaatatagtttgtggttctggattaagatctgtttcaatggcatctca
acttatagcattaggtgatgctgatataatgttagttggtggagctgaaaacatgagta
tgtctccttatttagtaccaagtgcgagatatggtgcaagaatgggtgatgctgctttt
gttgattcaatgataaaagatggattatcagacatatttaataactatcacatgggtat
tactgctgaaaacatagcagagcaatggaatataactagagaagaacaagatgaattag
ctcttgcaagtcaaaataaagctgaaaaagctcaagctgaaggaaaatttgatgaagaa
atagttcctgttgttataaaaggaagaaaaggtgacactgtagtagataaagatgaata
tattaagcctggcactacaatggagaaacttgctaagttaagacctgcatttaaaaaag
atggaacagttactgctggtaatgcatcaggaataaatgatggtgctgctatgttagta
gtaatggctaaagaaaaagctgaagaactaggaatagagcctcttgcaactatagtttc
ttatggaacagctggtgttgaccctaaaataatgggatatggaccagttccagcaacta
aaaaagctttagaagctgctaatatgactattgaagatatagatttagttgaagctaat
gaggcatttgctgcccaatctgtagctgtaataagagacttaaatatagatatgaataa
agttaatgttaatggtggagcaatagctataggacatccaataggatgctcaggagcaa
gaatacttactacacttttatatgaaatgaagagaagagatgctaaaactggtcttgct
acactttgtataggcggtggaatgggaactactttaatagttaagagatagtaagaagg
agatatacatatgaaattagctgtaataggtagtggaactatgggaagtggtattgtac
aaacttttgcaagttgtggacatgatgtatgtttaaagagtagaactcaaggtgctata
gataaatgtttagctttattagataaaaatttaactaagttagttactaagggaaaaat
ggatgaagctacaaaagcagaaatattaagtcatgttagttcaactactaattatgaag
atttaaaagatatggatttaataatagaagcatctgtagaagacatgaatataaagaaa
gatgttttcaagttactagatgaattatgtaaagaagatactatcttggcaacaaatac
ttcatcattatctataacagaaatagcttcttctactaagcgcccagataaagttatag
gaatgcatttctttaatccagttcctatgatgaaattagttgaagttataagtggtcag
ttaacatcaaaagttacttttgatacagtatttgaattatctaagagtatcaataaagt
accagtagatgtatctgaatctcctggatttgtagtaaatagaatacttatacctatga
taaatgaagctgttggtatatatgcagatggtgttgcaagtaaagaagaaatagatgaa
gctatgaaattaggagcaaaccatccaatgggaccactagcattaggtgatttaatcgg
attagatgttgttttagctataatgaacgttttatatactgaatttggagatactaaat
atagacctcatccacttttagctaaaatggttagagctaatcaattaggaagaaaaact
aagataggattctatgattataataaataataagaaggagatatacatatgagtacaag
tgatgttaaagtttatgagaatgtagctgttgaagtagatggaaatatatgtacagtga
aaatgaatagacctaaagcccttaatgcaataaattcaaagactttagaagaactttat
gaagtatttgtagatattaataatgatgaaactattgatgttgtaatattgacagggga
aggaaaggcatttgtagctggagcagatattgcatacatgaaagatttagatgctgtag
ctgctaaagattttagtatcttaggagcaaaagcttttggagaaatagaaaatagtaaa
aaagtagtgatagctgctgtaaacggatttgctttaggtggaggatgtgaacttgcaat
ggcatgtgatataagaattgcatctgctaaagctaaatttggtcagccagaagtaactc
ttggaataactccaggatatggaggaactcaaaggcttacaagattggttggaatggca
aaagcaaaagaattaatctttacaggtcaagttataaaagctgatgaagctgaaaaaat
agggctagtaaatagagtcgttgagccagacattttaatagaagaagttgagaaattag
ctaagataatagctaaaaatgctcagcttgcagttagatactctaaagaagcaatacaa
cttggtgctcaaactgatataaatactggaatagatatagaatctaatttatttggtct
ttgtttttcaactaaagaccaaaaagaaggaatgtcagctttcgttgaaaagagagaag
ctaactttataaaagggtaataagaaggagatatacatatgagaagttttgaagaagta
attaagtttgcaaaagaaagaggacctaaaactatatcagtagcatgttgccaagataa
agaagttttaatggcagttgaaatggctagaaaagaaaaaatagcaaatgccattttag
taggagatatagaaaagactaaagaaattgcaaaaagcatagacatggatatcgaaaat
tatgaactgatagatataaaagatttagcagaagcatctctaaaatctgttgaattagt
ttcacaaggaaaagccgacatggtaatgaaaggcttagtagacacatcaataatactaa
aagcagttttaaataaagaagtaggtcttagaactggaaatgtattaagtcacgtagca
gtatttgatgtagagggatatgatagattatttttcgtaactgacgcagctatgaactt
agctcctgatacaaatactaaaaagcaaatcatagaaaatgcttgcacagtagcacatt
cattagatataagtgaaccaaaagttgctgcaatatgcgcaaaagaaaaagtaaatcca
aaaatgaaagatacagttgaagctaaagaactagaagaaatgtatgaaagaggagaaat
caaaggttgtatggttggtgggccttttgcaattgataatgcagtatctttagaagcag
ctaaacataaaggtataaatcatcctgtagcaggacgagctgatatattattagcccca
gatattgaaggtggtaacatattatataaagctttggtattcttctcaaaatcaaaaaa
tgcaggagttatagttggggctaaagcaccaataatattaacttctagagcagacagtg
aagaaactaaactaaactcaatagctttaggtgttttaatggcagcaaaggcataataa
gaaggagatatacatatgagcaaaatatttaaaatcttaacaataaatcctggttcgac
atcaactaaaatagctgtatttgataatgaggatttagtatttgaaaaaactttaagac
attcttcagaagaaataggaaaatatgagaaggtgtctgaccaatttgaatttcgtaaa
caagtaatagaagaagctctaaaagaaggtggagtaaaaacatctgaattagatgctgt
agtaggtagaggaggacttcttaaacctataaaaggtggtacttattcagtaagtgctg
ctatgattgaagatttaaaagtgggagttttaggagaacacgcttcaaacctaggtgga
ataatagcaaaacaaataggtgaagaagtaaatgttccttcatacatagtagaccctgt
tgttgtagatgaattagaagatgttgctagaatttctggtatgcctgaaataagtagag
caagtgtagtacatgctttaaatcaaaaggcaatagcaagaagatatgctagagaaata
aacaagaaatatgaagatataaatcttatagttgcacacatgggtggaggagtttctgt
tggagctcataaaaatggtaaaatagtagatgttgcaaacgcattagatggagaaggac
ctttctctccagaaagaagtggtggactaccagtaggtgcattagtaaaaatgtgcttt
agtggaaaatatactcaagatgaaattaaaaagaaaataaaaggtaatggcggactagt
tgcatacttaaacactaatgatgctagagaagttgaagaaagaattgaagctggtgatg
aaaaagctaaattagtatatgaagctatggcatatcaaatctctaaagaaataggagct
agtgctgcagttcttaagggagatgtaaaagcaatattattaactggtggaatcgcata
ttcaaaaatgtttacagaaatgattgcagatagagttaaatttatagcagatgtaaaag
tttatccaggtgaagatgaaatgattgcattagctcaaggtggacttagagttttaact
ggtgaagaagaggctcaagtttatgataactaataa Nucleotide
gtaaaacgacggccagtgaattcgttaagacccactttcacatttaagttgtttttcta
sequences of
atccgcatatgatcaattcaaggccgaataagaaggctggctctgcaccttggtgatca
pLogic046-
aataattcgatagcttgtcgtaataatggcggcatactatcagtagtaggtgtttccct
tet-butyrate
ttcttctttagcgacttgatgctcttgatcttccaatacgcaacctaaagtaaaatgcc
construct
ccacagcgctgagtgcatataatgcattctctagtgaaaaaccttgttggcataaaaag (SEQ ID
NO: gctaattgattttcgagagtttcatactgtttttctgtaggccgtgtacctaaatgtac 85)
The ttttgctccatcgcgatgacttagtaaagcacatctaaaacttttagcgttattacgta
sequence
aaaaatcttgccagctttccccttctaaagggcaaaagtgagtatggtgcctatctaac
encoding
atctcaatggctaaggcgtcgagcaaagcccgcttattttttacatgccaatacaatgt TetR is
aggctgctctacacctagcttctgggcgagtttacgggttgttaaaccttcgattccga
underlined,
cctcattaagcagctctaatgcgctgttaatcactttacttttatctaatctagacatc and the
##STR00134## overlapping ##STR00135## tetR/tetA
tacatatgatcgtaaaacctatggtacgcaacaatatctgcctgaacgcccatcctcag
promoters
ggctgcaagaagggagtggaagatcagattgaatataccaagaaacgcattaccgcaga are
agtcaaagctggcgcaaaagctccaaaaaacgttctggtgcttggctgctcaaatggtt
##STR00136##
acggcctggcgagccgcattactgctgcgttcggatacggggctgcgaccatcggcgtg
tcctttgaaaaagcgggttcagaaaccaaatatggtacaccgggatggtacaataattt
ggcatttgatgaagcggcaaaacgcgagggtctttatagcgtgacgatcgacggcgatg
cgttttcagacgagatcaaggcccaggtaattgaggaagccaaaaaaaaaggtatcaaa
tttgatctgatcgtatacagcttggccagcccagtacgtactgatcctgatacaggtat
catgcacaaaagcgttttgaaaccctttggaaaaacgttcacaggcaaaacagtagatc
cgtttactggcgagctgaaggaaatctccgcggaaccagcaaatgacgaggaagcagcc
gccactgttaaagttatggggggtgaagattgggaacgttggattaagcagctgtcgaa
ggaaggcctcttagaagaaggctgtattaccttggcctatagttatattggccctgaag
ctacccaagctttgtaccgtaaaggcacaatcggcaaggccaaagaacacctggaggcc
acagcacaccgtctcaacaaagagaacccgtcaatccgtgccttcgtgagcgtgaataa
aggcctggtaacccgcgcaagcgccgtaatcccggtaatccctctgtatctcgccagct
tgttcaaagtaatgaaagagaagggcaatcatgaaggttgtattgaacagatcacgcgt
ctgtacgccgagcgcctgtaccgtaaagatggtacaattccagttgatgaggaaaatcg
cattcgcattgatgattgggagttagaagaagacgtccagaaagcggtatccgcgttga
tggagaaagtcacgggtgaaaacgcagaatctctcactgacttagcggggtaccgccat
gatttcttagctagtaacggctttgatgtagaaggtattaattatgaagcggaagttga
acgcttcgaccgtatctgataagaaggagatatacatatgagagaagtagtaattgcca
gtgcagctagaacagcagtaggaagttttggaggagcatttaaatcagtttcagcggta
gagttaggggtaacagcagctaaagaagctataaaaagagctaacataactccagatat
gatagatgaatctcttttagggggagtacttacagcaggtcttggacaaaatatagcaa
gacaaatagcattaggagcaggaataccagtagaaaaaccagctatgactataaatata
gtttgtggttctggattaagatctgtttcaatggcatctcaacttatagcattaggtga
tgctgatataatgttagttggtggagctgaaaacatgagtatgtctccttatttagtac
caagtgcgagatatggtgcaagaatgggtgatgctgcttttgttgattcaatgataaaa
gatggattatcagacatatttaataactatcacatgggtattactgctgaaaacatagc
agagcaatggaatataactagagaagaacaagatgaattagctcttgcaagtcaaaata
aagctgaaaaagctcaagctgaaggaaaatttgatgaagaaatagttcctgttgttata
aaaggaagaaaaggtgacactgtagtagataaagatgaatatattaagcctggcactac
aatggagaaacttgctaagttaagacctgcatttaaaaaagatggaacagttactgctg
gtaatgcatcaggaataaatgatggtgctgctatgttagtagtaatggctaaagaaaaa
gctgaagaactaggaatagagcctcttgcaactatagtttcttatggaacagctggtgt
tgaccctaaaataatgggatatggaccagttccagcaactaaaaaagctttagaagctg
ctaatatgactattgaagatatagatttagttgaagctaatgaggcatttgctgcccaa
tctgtagctgtaataagagacttaaatatagatatgaataaagttaatgttaatggtgg
agcaatagctataggacatccaataggatgctcaggagcaagaatacttactacacttt
tatatgaaatgaagagaagagatgctaaaactggtcttgctacactttgtataggcggt
ggaatgggaactactttaatagttaagagatagtaagaaggagatatacatatgaaatt
agctgtaataggtagtggaactatgggaagtggtattgtacaaacttttgcaagttgtg
gacatgatgtatgtttaaagagtagaactcaaggtgctatagataaatgtttagcttta
ttagataaaaatttaactaagttagttactaagggaaaaatggatgaagctacaaaagc
agaaatattaagtcatgttagttcaactactaattatgaagatttaaaagatatggatt
taataatagaagcatctgtagaagacatgaatataaagaaagatgttttcaagttacta
gatgaattatgtaaagaagatactatcttggcaacaaatacttcatcattatctataac
agaaatagcttcttctactaagcgcccagataaagttataggaatgcatttctttaatc
cagttcctatgatgaaattagttgaagttataagtggtcagttaacatcaaaagttact
tttgatacagtatttgaattatctaagagtatcaataaagtaccagtagatgtatctga
atctcctggatttgtagtaaatagaatacttatacctatgataaatgaagctgttggta
tatatgcagatggtgttgcaagtaaagaagaaatagatgaagctatgaaattaggagca
aaccatccaatgggaccactagcattaggtgatttaatcggattagatgttgttttagc
tataatgaacgttttatatactgaatttggagatactaaatatagacctcatccacttt
tagctaaaatggttagagctaatcaattaggaagaaaaactaagataggattctatgat
tataataaataataagaaggagatatacatatgagtacaagtgatgttaaagtttatga
gaatgtagctgttgaagtagatggaaatatatgtacagtgaaaatgaatagacctaaag
cccttaatgcaataaattcaaagactttagaagaactttatgaagtatttgtagatatt
aataatgatgaaactattgatgttgtaatattgacaggggaaggaaaggcatttgtagc
tggagcagatattgcatacatgaaagatttagatgctgtagctgctaaagattttagta
tcttaggagcaaaagcttttggagaaatagaaaatagtaaaaaagtagtgatagctgct
gtaaacggatttgctttaggtggaggatgtgaacttgcaatggcatgtgatataagaat
tgcatctgctaaagctaaatttggtcagccagaagtaactcttggaataactccaggat
atggaggaactcaaaggcttacaagattggttggaatggcaaaagcaaaagaattaatc
tttacaggtcaagttataaaagctgatgaagctgaaaaaatagggctagtaaatagagt
cgttgagccagacattttaatagaagaagttgagaaattagctaagataatagctaaaa
atgctcagcttgcagttagatactctaaagaagcaatacaacttggtgctcaaactgat
ataaatactggaatagatatagaatctaatttatttggtctttgtttttcaactaaaga
ccaaaaagaaggaatgtcagctttcgttgaaaagagagaagctaactttataaaagggt
aataagaaggagatatacatatgagaagttttgaagaagtaattaagtttgcaaaagaa
agaggacctaaaactatatcagtagcatgttgccaagataaagaagttttaatggcagt
tgaaatggctagaaaagaaaaaatagcaaatgccattttagtaggagatatagaaaaga
ctaaagaaattgcaaaaagcatagacatggatatcgaaaattatgaactgatagatata
aaagatttagcagaagcatctctaaaatctgttgaattagtttcacaaggaaaagccga
catggtaatgaaaggcttagtagacacatcaataatactaaaagcagttttaaataaag
aagtaggtcttagaactggaaatgtattaagtcacgtagcagtatttgatgtagaggga
tatgatagattatttttcgtaactgacgcagctatgaacttagctcctgatacaaatac
taaaaagcaaatcatagaaaatgcttgcacagtagcacattcattagatataagtgaac
caaaagttgctgcaatatgcgcaaaagaaaaagtaaatccaaaaatgaaagatacagtt
gaagctaaagaactagaagaaatgtatgaaagaggagaaatcaaaggttgtatggttgg
tgggccttttgcaattgataatgcagtatctttagaagcagctaaacataaaggtataa
atcatcctgtagcaggacgagctgatatattattagccccagatattgaaggtggtaac
atattatataaagctttggtattcttctcaaaatcaaaaaatgcaggagttatagttgg
ggctaaagcaccaataatattaacttctagagcagacagtgaagaaactaaactaaact
caatagctttaggtgttttaatggcagcaaaggcataataagaaggagatatacatatg
agcaaaatatttaaaatcttaacaataaatcctggttcgacatcaactaaaatagctgt
atttgataatgaggatttagtatttgaaaaaactttaagacattcttcagaagaaatag
gaaaatatgagaaggtgtctgaccaatttgaatttcgtaaacaagtaatagaagaagct
ctaaaagaaggtggagtaaaaacatctgaattagatgctgtagtaggtagaggaggact
tcttaaacctataaaaggtggtacttattcagtaagtgctgctatgattgaagatttaa
aagtgggagttttaggagaacacgcttcaaacctaggtggaataatagcaaaacaaata
ggtgaagaagtaaatgttccttcatacatagtagaccctgttgttgtagatgaattaga
agatgttgctagaatttctggtatgcctgaaataagtagagcaagtgtagtacatgctt
taaatcaaaaggcaatagcaagaagatatgctagagaaataaacaagaaatatgaagat
ataaatcttatagttgcacacatgggtggaggagtttctgttggagctcataaaaatgg
taaaatagtagatgttgcaaacgcattagatggagaaggacctttctctccagaaagaa
gtggtggactaccagtaggtgcattagtaaaaatgtgctttagtggaaaatatactcaa
gatgaaattaaaaagaaaataaaaggtaatggcggactagttgcatacttaaacactaa
tgatgctagagaagttgaagaaagaattgaagctggtgatgaaaaagctaaattagtat
atgaagctatggcatatcaaatctctaaagaaataggagctagtgctgcagttcttaag
ggagatgtaaaagcaatattattaactggtggaatcgcatattcaaaaatgtttacaga
aatgattgcagatagagttaaatttatagcagatgtaaaagtttatccaggtgaagatg
aaatgattgcattagctcaaggtggacttagagttttaactggtgaagaagaggctcaa
gtttatgataactaataa
[0751] In certain constructs, the butyrate gene cassette is placed
under the control of a tetracycline-inducible or constitutive
promoter.
In a third butyrate gene cassette, the pbt and buk genes are
replaced with tesB. TesB is a thioesterase found in E. Coli that
cleaves off the butyrate from butyryl-coA, thus obviating the need
for pbt-buk.
[0752] In one embodiment, tesB is placed under the control of a FNR
regulatory region selected from any of the sequences in Table 6. In
an alternate embodiment, tesB is placed under the control of an
RNS-responsive regulatory region, e.g., norB, and the bacteria
further comprises a gene encoding a corresponding RNS-responsive
transcription factor, e.g., nsrR. In yet another embodiment, tesB
is placed under the control of an ROS-responsive regulatory region,
e.g., oxyS, and the bacteria further comprises a gene encoding a
corresponding ROS-responsive transcription factor, e.g., oxyR. In
certain constructs, the different described butyrate gene cassettes
are each placed under the control of a tetracycline-inducible or
constitutive promoter. For example, genetically engineered Nissle
are generated comprising a butyrate gene cassette in which the pbt
and buk genes are replaced with tesB expressed under the control of
a nitric oxide-responsive regulatory element. SEQ ID NO: 86
comprises a reverse complement of the nsrR repressor gene from
Neisseria gonorrhoeae (underlined), intergenic region containing
divergent promoters controlling nsrR and the butyrogenic gene
cassette and their respective RBS (bold), and the butyrate genes
(ter-thiA-hbd-crt-tesB) separated by RBS.
TABLE-US-00047 TABLE 41 SEQ ID NO: 86 SEQ ID NO: 86
ttattatcgcaccgcaatcgggattttcgattcataaagcaggtcgtagg
tcggcttgttgagcaggtcttgcagcgtgaaaccgtccagatacgtgaaa
aacgacttcattgcaccgccgagtatgcccgtcagccggcaggacggcgt
aatcaggcattcgttgttcgggcccatacactcgaccagctgcatcggtt
cgaggtggcggacgaccgcgccgatattgatgcgttcgggcggcgcggcc
agcctcagcccgccgcctttcccgcgtacgctgtgcaagaacccgccttt
gaccagcgcggtaaccactttcatcaaatggcttttggaaatgccgtagg
tcgaggcgatggtggcgatattgaccagcgcgtcgtcgttgacggcggtg
tagatgaggacgcgcagcccgtagtcggtatgttgggtcagatacataca
acctccttagtacatgcaaaattatttctagagcaacatacgagccggaa
gcataaagtgtaaagcctggggtgcctaatgagttgagttgaggaattat
aacaggaagaaatattcctcatacgcttgtaattcctctatggttgttga
caattaatcatcggctcgtataatgtataacattcatattttgtgaattt
taaactctagaaataattttgtttaactttaagaaggagatatacatatg
atcgtaaaacctatggtacgcaacaatatctgcctgaacgcccatcctca
gggctgcaagaagggagtggaagatcagattgaatataccaagaaacgca
ttaccgcagaagtcaaagctggcgcaaaagctccaaaaaacgttctggtg
cttggctgctcaaatggttacggcctggcgagccgcattactgctgcgtt
cggatacggggctgcgaccatcggcgtgtcctttgaaaaagcgggttcag
aaaccaaatatggtacaccgggatggtacaataatttggcatttgatgaa
gcggcaaaacgcgagggtctttatagcgtgacgatcgacggcgatgcgtt
ttcagacgagatcaaggcccaggtaattgaggaagccaaaaaaaaaggta
tcaaatttgatctgatcgtatacagcttggccagcccagtacgtactgat
cctgatacaggtatcatgcacaaaagcgttttgaaaccctttggaaaaac
gttcacaggcaaaacagtagatccgtttactggcgagctgaaggaaatct
ccgcggaaccagcaaatgacgaggaagcagccgccactgttaaagttatg
gggggtgaagattgggaacgttggattaagcagctgtcgaaggaaggcct
cttagaagaaggctgtattaccttggcctatagttatattggccctgaag
ctacccaagctttgtaccgtaaaggcacaatcggcaaggccaaagaacac
ctggaggccacagcacaccgtctcaacaaagagaacccgtcaatccgtgc
cttcgtgagcgtgaataaaggcctggtaacccgcgcaagcgccgtaatcc
cggtaatccctctgtatctcgccagcttgttcaaagtaatgaaagagaag
ggcaatcatgaaggttgtattgaacagatcacgcgtctgtacgccgagcg
cctgtaccgtaaagatggtacaattccagttgatgaggaaaatcgcattc
gcattgatgattgggagttagaagaagacgtccagaaagcggtatccgcg
ttgatggagaaagtcacgggtgaaaacgcagaatctctcactgacttagc
ggggtaccgccatgatttcttagctagtaacggctttgatgtagaaggta
ttaattatgaagcggaagttgaacgcttcgaccgtatctgataagaagga
gatatacatatgagagaagtagtaattgccagtgcagctagaacagcagt
aggaagttttggaggagcatttaaatcagtttcagcggtagagttagggg
taacagcagctaaagaagctataaaaagagctaacataactccagatatg
atagatgaatctcttttagggggagtacttacagcaggtcttggacaaaa
tatagcaagacaaatagcattaggagcaggaataccagtagaaaaaccag
ctatgactataaatatagtttgtggttctggattaagatctgtttcaatg
gcatctcaacttatagcattaggtgatgctgatataatgttagttggtgg
agctgaaaacatgagtatgtctccttatttagtaccaagtgcgagatatg
gtgcaagaatgggtgatgctgcttttgttgattcaatgataaaagatgga
ttatcagacatatttaataactatcacatgggtattactgctgaaaacat
agcagagcaatggaatataactagagaagaacaagatgaattagctcttg
caagtcaaaataaagctgaaaaagctcaagctgaaggaaaatttgatgaa
gaaatagttcctgttgttataaaaggaagaaaaggtgacactgtagtaga
taaagatgaatatattaagcctggcactacaatggagaaacttgctaagt
taagacctgcatttaaaaaagatggaacagttactgctggtaatgcatca
ggaataaatgatggtgctgctatgttagtagtaatggctaaagaaaaagc
tgaagaactaggaatagagcctcttgcaactatagtttcttatggaacag
ctggtgttgaccctaaaataatgggatatggaccagttccagcaactaaa
aaagctttagaagctgctaatatgactattgaagatatagatttagttga
agctaatgaggcatttgctgcccaatctgtagctgtaataagagacttaa
atatagatatgaataaagttaatgttaatggtggagcaatagctatagga
catccaataggatgctcaggagcaagaatacttactacacttttatatga
aatgaagagaagagatgctaaaactggtcttgctacactttgtataggcg
gtggaatgggaactactttaatagttaagagatagtaagaaggagatata
catatgaaattagctgtaataggtagtggaactatgggaagtggtattgt
acaaacttttgcaagttgtggacatgatgtatgtttaaagagtagaactc
aaggtgctatagataaatgtttagctttattagataaaaatttaactaag
ttagttactaagggaaaaatggatgaagctacaaaagcagaaatattaag
tcatgttagttcaactactaattatgaagatttaaaagatatggatttaa
taatagaagcatctgtagaagacatgaatataaagaaagatgttttcaag
ttactagatgaattatgtaaagaagatactatcttggcaacaaatacttc
atcattatctataacagaaatagcttcttctactaagcgcccagataaag
ttataggaatgcatttctttaatccagttcctatgatgaaattagttgaa
gttataagtggtcagttaacatcaaaagttacttttgatacagtatttga
attatctaagagtatcaataaagtaccagtagatgtatctgaatctcctg
gatttgtagtaaatagaatacttatacctatgataaatgaagctgttggt
atatatgcagatggtgttgcaagtaaagaagaaatagatgaagctatgaa
attaggagcaaaccatccaatgggaccactagcattaggtgatttaatcg
gattagatgttgttttagctataatgaacgttttatatactgaatttgga
gatactaaatatagacctcatccacttttagctaaaatggttagagctaa
tcaattaggaagaaaaactaagataggattctatgattataataaataat
aagaaggagatatacatatgagtacaagtgatgttaaagtttatgagaat
gtagctgttgaagtagatggaaatatatgtacagtgaaaatgaatagacc
taaagcccttaatgcaataaattcaaagactttagaagaactttatgaag
tatttgtagatattaataatgatgaaactattgatgttgtaatattgaca
ggggaaggaaaggcatttgtagctggagcagatattgcatacatgaaaga
tttagatgctgtagctgctaaagattttagtatcttaggagcaaaagctt
ttggagaaatagaaaatagtaaaaaagtagtgatagctgctgtaaacgga
tttgctttaggtggaggatgtgaacttgcaatggcatgtgatataagaat
tgcatctgctaaagctaaatttggtcagccagaagtaactcttggaataa
ctccaggatatggaggaactcaaaggcttacaagattggttggaatggca
aaagcaaaagaattaatctttacaggtcaagttataaaagctgatgaagc
tgaaaaaatagggctagtaaatagagtcgttgagccagacattttaatag
aagaagttgagaaattagctaagataatagctaaaaatgctcagcttgca
gttagatactctaaagaagcaatacaacttggtgctcaaactgatataaa
tactggaatagatatagaatctaatttatttggtctttgtttttcaacta
aagaccaaaaagaaggaatgtcagctttcgttgaaaagagagaagctaac
tttataaaagggtaataagaaggagatatacatatgAGTCAGGCGCTAAA
AAATTTACTGACATTGTTAAATCTGGAAAAAATTGAGGAAGGACTCTTTC
GCGGCCAGAGTGAAGATTTAGGTTTACGCCAGGTGTTTGGCGGCCAGGTC
GTGGGTCAGGCCTTGTATGCTGCAAAAGAGACCGTCCCTGAAGAGCGGCT
GGTACATTCGTTTCACAGCTACTTTCTTCGCCCTGGCGATAGTAAGAAGC
CGATTATTTATGATGTCGAAACGCTGCGTGACGGTAACAGCTTCAGCGCC
CGCCGGGTTGCTGCTATTCAAAACGGCAAACCGATTTTTTATATGACTGC
CTCTTTCCAGGCACCAGAAGCGGGTTTCGAACATCAAAAAACAATGCCGT
CCGCGCCAGCGCCTGATGGCCTCCCTTCGGAAACGCAAATCGCCCAATCG
CTGGCGCACCTGCTGCCGCCAGTGCTGAAAGATAAATTCATCTGCGATCG
TCCGCTGGAAGTCCGTCCGGTGGAGTTTCATAACCCACTGAAAGGTCACG
TCGCAGAACCACATCGTCAGGTGTGGATCCGCGCAAATGGTAGCGTGCCG
GATGACCTGCGCGTTCATCAGTATCTGCTCGGTTACGCTTCTGATCTTAA
CTTCCTGCCGGTAGCTCTACAGCCGCACGGCATCGGTTTTCTCGAACCGG
GGATTCAGATTGCCACCATTGACCATTCCATGTGGTTCCATCGCCCGTTT
AATTTGAATGAATGGCTGCTGTATAGCGTGGAGAGCACCTCGGCGTCCAG
CGCACGTGGCTTTGTGCGCGGTGAGTTTTATACCCAAGACGGCGTACTGG
TTGCCTCGACCGTTCAGGAAGGGGTGATGCGTAATCACAATtaa
Example 33
Construction of Vectors for Overproducing Butyrate Using a
Tet-Inducible Promoter
[0753] To facilitate inducible production of butyrate in
Escherichia coli Nissle, the eight genes of the butyrate production
pathway from Peptoclostridium difficile (bcd, etfB, etfA, thiA,
hbd, crt, bpt, and buk; NCBI), as well as transcriptional and
translational elements, were synthesized (Gen, Cambridge, Mass.)
and cloned into vector pBR to create pLogic. As synthesized, the
genes were placed under control of a tetracycline-inducible
promoter, with the tet repressor (tetR) expressed constitutively,
divergent from the tet-inducible synthetic butyrate operon. For
efficient translation of butyrate genes, each synthetic gene in the
operon was separated by a base pair ribosome binding site derived
from the T promoter.
[0754] The gene products of bcd-etfA-etfB form a complex that
convert crotonyl-CoA to butyryl-CoA, and may show some dependence
on oxygen as a co-oxidant. Because an effective probiotic should be
able to function in an oxygen-limited environment (e.g. the
mammalian gut), and because it has been shown that a single gene
from Treponema denticola can functionally replace this three gene
complex in an oxygen-independent manner (trans-enoynl-CoA
reductase; ter), we created a second plasmid capable of butyrate
production in E. coli. Inverse PCR was used to amplify the entire
sequence of pLogic outside of the bcd-etfA-etfB region. The ter
gene was codon optimized for E. coli codon usage using Integrated
DNA technologies online codon optimization tool
(https://www.idtdna.com/CodonOpt), synthesized (Genewiz, Cambridge,
Mass.), and cloned into this inverse PCR fragment using Gibson
assembly to create pLogic.
Example 34
Transforming E. coli
[0755] Each plasmid is transformed into E. coli Nissle or E. coli
DH5a. All tubes, solutions, and cuvettes are pre-chilled to
4.degree. C. An overnight culture of E. coli Nissle or E. coli DH5a
is diluted 1:100 in 5 mL of lysogeny broth (LB) and grown until it
reached an OD600 of 0.4-0.6. The cell culture medium contains a
selection marker, e.g., ampicillin, that is suitable for the
plasmid. The E. coli cells are then centrifuged at 2,000 rpm for 5
min. at 4.degree. C., the supernatant is removed, and the cells are
resuspended in 1 mL of 4.degree. C. water. The E. coli are again
centrifuged at 2,000 rpm for 5 min. at 4.degree. C., the
supernatant is removed, and the cells are resuspended in 0.5 mL of
4.degree. C. water. The E. coli are again centrifuged at 2,000 rpm
for 5 min. at 4.degree. C., the supernatant is removed, and the
cells are finally resuspended in 0.1 mL of 4.degree. C. water. The
electroporator is set to 2.5 kV. 0.5 .mu.g of one of the above
plasmids is added to the cells, mixed by pipetting, and pipetted
into a sterile, chilled cuvette. The dry cuvette is placed into the
sample chamber, and the electric pulse is applied. One mL of
room-temperature SOC media is immediately added, and the mixture is
transferred to a culture tube and incubated at 37.degree. C. for 1
hr. The cells are spread out on an LB plate containing ampicillin
and incubated overnight.
[0756] In alternate embodiments, the butyrate cassette can be
inserted into the Nissle genome through homologous recombination
(Genewiz, Cambridge, Mass.). Organization of the constructs and
nucleotide sequences are provided herein. To create a vector
capable of integrating the synthesized butyrate cassette construct
into the chromosome, Gibson assembly was first used to add 1000 bp
sequences of DNA homologous to the Nissle lacZ locus into the R6K
origin plasmid pKD3. This targets DNA cloned between these homology
arms to be integrated into the lacZ locus in the Nissle genome.
Gibson assembly was used to clone the fragment between these arms.
PCR was used to amplify the region from this plasmid containing the
entire sequence of the homology arms, as well as the butyrate
cassette between them. This PCR fragment was used to transform
electrocompetent Nissle-pKD46, a strain that contains a
temperature-sensitive plasmid encoding the lambda red recombinase
genes. After transformation, cells were grown out for 2 hours
before plating on chloramphenicol at 20 ug/mL at 37 degrees C.
Growth at 37 degrees C. also cures the pKD46 plasmid. Transformants
containing cassette were chloramphenicol resistant and lac-minus
(lac-).
Example 35
Production of Butyrate in Recombinant E. coli
[0757] Production of butyrate is assessed in E. coli Nissle strains
containing the butyrate cassettes described above in order to
determine the effect of oxygen on butyrate production. All
incubations are performed at 37.degree. C. Cultures of E. coli
strains DH5a and Nissle transformed with the butyrate cassettes are
grown overnight in LB and then diluted 1:200 into 4 mL of M9
minimal medium containing 0.5% glucose. The cells are grown with
shaking (250 rpm) for 4-6 h and incubated aerobically or
anaerobically in a Coy anaerobic chamber (supplying 90% N2, 5% CO2,
5% H2). One mL culture aliquots are prepared in 1.5 mL capped tubes
and incubated in a stationary incubator to limit culture aeration.
One tube is removed at each time point (0, 1, 2, 4, and 20 hrs) and
analyzed for butyrate concentration by LC-MS to confirm that
butyrate production in these recombinant strains can be achieved in
a low-oxygen environment.
Example 36
Production of Butyrate in Recombinant E. coli
[0758] Production of butyrate is assessed in E. coli Nissle strains
containing the butyrate cassettes described above in order to
determine the effect of oxygen on butyrate production. All
incubations are performed at 37.degree. C. Cultures of E. coli
strains DH5a and Nissle transformed with the butyrate cassettes are
grown overnight in LB and then diluted 1:200 into 4 mL of M9
minimal medium containing 0.5% glucose. The cells are grown with
shaking (250 rpm) for 4-6 h and incubated aerobically or
anaerobically in a Coy anaerobic chamber (supplying 90% N2, 5% CO2,
5% H2). One mL culture aliquots are prepared in 1.5 mL capped tubes
and incubated in a stationary incubator to limit culture aeration.
One tube is removed at each time point (0, 1, 2, 4, and 20 hrs) and
analyzed for butyrate concentration by LC-MS to confirm that
butyrate production in these recombinant strains can be achieved in
a low-oxygen environment.
Example 37
Production of Butyrate in Recombinant E. coli Using Tet-Inducible
Promoter
[0759] FIG. 48 shows butyrate cassettes described above under the
control of a tet-inducible promoter. Production of butyrate is
assessed using the methods described below in Example 40. The
tet-inducible cassettes tested include (1) tet-butyrate cassette
comprising all eight genes (pLOGIC031); (2) tet-butyrate cassette
in which the ter is substituted (pLOGIC046) and (3) tet-butyarte
cassette in which tesB is substituted in place of pbt and buk
genes. FIG. 51A shows butyrate production in strains pLOGIC031 and
pLOGIC046 in the presence and absence of oxygen, in which there is
no significant difference in butyrate production. Enhanced butyrate
production was shown in Nissle in low copy plasmid expressing
pLOGIC046 which contain a deletion of the final two genes (ptb-buk)
and their replacement with the endogenous E. Coli tesB gene (a
thioesterase that cleaves off the butyrate portion from butyryl
CoA).
[0760] Overnight cultures of cells were diluted 1:100 in Lb and
grown for 1.5 hours until early log phase was reached at which
point anhydrous tet was added at a final concentration of 100 ng/ml
to induce plasmid expression. After 2 hours induction, cells were
washed and resuspended in M9 minimal media containing 0.5% glucose
at OD600=0.5. Samples were removed at indicated times and cells
spun down. The supernatant was tested for butyrate production using
LC-MS. FIG. 51B shows butyrate production in strains comprising a
tet-butyrate cassette having ter substitution (pLOGIC046) or the
tesB substitution (ptb-buk deletion), demonstrating that the tesB
substituted strain has greater butyrate production.
[0761] FIG. 52 shows the BW25113 strain of E. Coli, which is a
common cloning strain and the background of the KEIO collection of
E. Coli mutants. NuoB mutants having NuoB deletion were obtained.
NuoB is a protein complex involved in the oxidation of NADH during
respiratory growth (form of growth requiring electron transport).
Preventing the coupling of NADH oxidation to electron transport
allows an increase in the amount of NADH being used to support
butyrate production. FIG. 52 shows that compared with wild-type
Nissle, deletion of NuoB results in grater production of
butyrate.
TABLE-US-00048 TABLE 42 pLOGIC046-tesB-butyrate
pLOGIC046-tesB-butyrate: SEQ ID NO: 87
gtaaaacgacggccagtgaattcgttaagacccactttcacatttaagtt
gtttttctaatccgcatatgatcaattcaaggccgaataagaaggctggc
tctgcaccttggtgatcaaataattcgatagcttgtcgtaataatggcgg
catactatcagtagtaggtgtttccctttcttctttagcgacttgatgct
cttgatcttccaatacgcaacctaaagtaaaatgccccacagcgctgagt
gcatataatgcattctctagtgaaaaaccttgttggcataaaaaggctaa
ttgattttcgagagtttcatactgtttttctgtaggccgtgtacctaaat
gtacttttgctccatcgcgatgacttagtaaagcacatctaaaactttta
gcgttattacgtaaaaaatcttgccagctttccccttctaaagggcaaaa
gtgagtatggtgcctatctaacatctcaatggctaaggcgtcgagcaaag
cccgcttattttttacatgccaatacaatgtaggctgctctacacctagc
ttctgggcgagtttacgggttgttaaaccttcgattccgacctcattaag
cagctctaatgcgctgttaatcactttacttttatctaatctagacatca
ttaattcctaatttttgttgacactctatcattgatagagttattttacc
actccctatcagtgatagagaaaagtgaactctagaaataattttgttta
actttaagaaggagatatacatatgatcgtaaaacctatggtacgcaaca
atatctgcctgaacgcccatcctcagggctgcaagaagggagtggaagat
cagattgaatataccaagaaacgcattaccgcagaagtcaaagctggcgc
aaaagctccaaaaaacgttctggtgcttggctgctcaaatggttacggcc
tggcgagccgcattactgctgcgttcggatacggggctgcgaccatcggc
gtgtcctttgaaaaagcgggttcagaaaccaaatatggtacaccgggatg
gtacaataatttggcatttgatgaagcggcaaaacgcgagggtctttata
gcgtgacgatcgacggcgatgcgttttcagacgagatcaaggcccaggta
attgaggaagccaaaaaaaaaggtatcaaatttgatctgatcgtatacag
cttggccagcccagtacgtactgatcctgatacaggtatcatgcacaaaa
gcgttttgaaaccctttggaaaaacgttcacaggcaaaacagtagatccg
tttactggcgagctgaaggaaatctccgcggaaccagcaaatgacgagga
agcagccgccactgttaaagttatggggggtgaagattgggaacgttgga
ttaagcagctgtcgaaggaaggcctcttagaagaaggctgtattaccttg
gcctatagttatattggccctgaagctacccaagctttgtaccgtaaagg
cacaatcggcaaggccaaagaacacctggaggccacagcacaccgtctca
acaaagagaacccgtcaatccgtgccttcgtgagcgtgaataaaggcctg
gtaacccgcgcaagcgccgtaatcccggtaatccctctgtatctcgccag
cttgttcaaagtaatgaaagagaagggcaatcatgaaggttgtattgaac
agatcacgcgtctgtacgccgagcgcctgtaccgtaaagatggtacaatt
ccagttgatgaggaaaatcgcattcgcattgatgattgggagttagaaga
agacgtccagaaagcggtatccgcgttgatggagaaagtcacgggtgaaa
acgcagaatctctcactgacttagcggggtaccgccatgatttcttagct
agtaacggctttgatgtagaaggtattaattatgaagcggaagttgaacg
cttcgaccgtatctgataagaaggagatatacatatgagagaagtagtaa
ttgccagtgcagctagaacagcagtaggaagttttggaggagcatttaaa
tcagtttcagcggtagagttaggggtaacagcagctaaagaagctataaa
aagagctaacataactccagatatgatagatgaatctcttttagggggag
tacttacagcaggtcttggacaaaatatagcaagacaaatagcattagga
gcaggaataccagtagaaaaaccagctatgactataaatatagtttgtgg
ttctggattaagatctgtttcaatggcatctcaacttatagcattaggtg
atgctgatataatgttagttggtggagctgaaaacatgagtatgtctcct
tatttagtaccaagtgcgagatatggtgcaagaatgggtgatgctgcttt
tgttgattcaatgataaaagatggattatcagacatatttaataactatc
acatgggtattactgctgaaaacatagcagagcaatggaatataactaga
gaagaacaagatgaattagctcttgcaagtcaaaataaagctgaaaaagc
tcaagctgaaggaaaatttgatgaagaaatagttcctgttgttataaaag
gaagaaaaggtgacactgtagtagataaagatgaatatattaagcctggc
actacaatggagaaacttgctaagttaagacctgcatttaaaaaagatgg
aacagttactgctggtaatgcatcaggaataaatgatggtgctgctatgt
tagtagtaatggctaaagaaaaagctgaagaactaggaatagagcctctt
gcaactatagtttcttatggaacagctggtgttgaccctaaaataatggg
atatggaccagttccagcaactaaaaaagctttagaagctgctaatatga
ctattgaagatatagatttagttgaagctaatgaggcatttgctgcccaa
tctgtagctgtaataagagacttaaatatagatatgaataaagttaatgt
taatggtggagcaatagctataggacatccaataggatgctcaggagcaa
gaatacttactacacttttatatgaaatgaagagaagagatgctaaaact
ggtcttgctacactttgtataggcggtggaatgggaactactttaatagt
taagagatagtaagaaggagatatacatatgaaattagctgtaataggta
gtggaactatgggaagtggtattgtacaaacttttgcaagttgtggacat
gatgtatgtttaaagagtagaactcaaggtgctatagataaatgtttagc
tttattagataaaaatttaactaagttagttactaagggaaaaatggatg
aagctacaaaagcagaaatattaagtcatgttagttcaactactaattat
gaagatttaaaagatatggatttaataatagaagcatctgtagaagacat
gaatataaagaaagatgttttcaagttactagatgaattatgtaaagaag
atactatcttggcaacaaatacttcatcattatctataacagaaatagct
tcttctactaagcgcccagataaagttataggaatgcatttctttaatcc
agttcctatgatgaaattagttgaagttataagtggtcagttaacatcaa
aagttacttttgatacagtatttgaattatctaagagtatcaataaagta
ccagtagatgtatctgaatctcctggatttgtagtaaatagaatacttat
acctatgataaatgaagctgttggtatatatgcagatggtgttgcaagta
aagaagaaatagatgaagctatgaaattaggagcaaaccatccaatggga
ccactagcattaggtgatttaatcggattagatgttgttttagctataat
gaacgttttatatactgaatttggagatactaaatatagacctcatccac
ttttagctaaaatggttagagctaatcaattaggaagaaaaactaagata
ggattctatgattataataaataataagaaggagatatacatatgagtac
aagtgatgttaaagtttatgagaatgtagctgttgaagtagatggaaata
tatgtacagtgaaaatgaatagacctaaagcccttaatgcaataaattca
aagactttagaagaactttatgaagtatttgtagatattaataatgatga
aactattgatgttgtaatattgacaggggaaggaaaggcatttgtagctg
gagcagatattgcatacatgaaagatttagatgctgtagctgctaaagat
tttagtatcttaggagcaaaagcttttggagaaatagaaaatagtaaaaa
agtagtgatagctgctgtaaacggatttgctttaggtggaggatgtgaac
ttgcaatggcatgtgatataagaattgcatctgctaaagctaaatttggt
cagccagaagtaactcttggaataactccaggatatggaggaactcaaag
gcttacaagattggttggaatggcaaaagcaaaagaattaatctttacag
gtcaagttataaaagctgatgaagctgaaaaaatagggctagtaaataga
gtcgttgagccagacattttaatagaagaagttgagaaattagctaagat
aatagctaaaaatgctcagcttgcagttagatactctaaagaagcaatac
aacttggtgctcaaactgatataaatactggaatagatatagaatctaat
ttatttggtctttgtttttcaactaaagaccaaaaagaaggaatgtcagc
tttcgttgaaaagagagaagctaactttataaaagggtaataagaaggag
atatacatatgAGTCAGGCGCTAAAAAATTTACTGACATTGTTAAATCTG
GAAAAAATTGAGGAAGGACTCTTTCGCGGCCAGAGTGAAGATTTAGGTTT
ACGCCAGGTGTTTGGCGGCCAGGTCGTGGGTCAGGCCTTGTATGCTGCAA
AAGAGACCGTCCCTGAAGAGCGGCTGGTACATTCGTTTCACAGCTACTTT
CTTCGCCCTGGCGATAGTAAGAAGCCGATTATTTATGATGTCGAAACGCT
GCGTGACGGTAACAGCTTCAGCGCCCGCCGGGTTGCTGCTATTCAAAACG
GCAAACCGATTTTTTATATGACTGCCTCTTTCCAGGCACCAGAAGCGGGT
TTCGAACATCAAAAAACAATGCCGTCCGCGCCAGCGCCTGATGGCCTCCC
TTCGGAAACGCAAATCGCCCAATCGCTGGCGCACCTGCTGCCGCCAGTGC
TGAAAGATAAATTCATCTGCGATCGTCCGCTGGAAGTCCGTCCGGTGGAG
TTTCATAACCCACTGAAAGGTCACGTCGCAGAACCACATCGTCAGGTGTG
GATCCGCGCAAATGGTAGCGTGCCGGATGACCTGCGCGTTCATCAGTATC
TGCTCGGTTACGCTTCTGATCTTAACTTCCTGCCGGTAGCTCTACAGCCG
CACGGCATCGGTTTTCTCGAACCGGGGATTCAGATTGCCACCATTGACCA
TTCCATGTGGTTCCATCGCCCGTTTAATTTGAATGAATGGCTGCTGTATA
GCGTGGAGAGCACCTCGGCGTCCAGCGCACGTGGCTTTGTGCGCGGTGAG
TTTTATACCCAAGACGGCGTACTGGTTGCCTCGACCGTTCAGGAAGGGGT
GATGCGTAATCACAATtaa
Example 38
Production of Butyrate in Recombinant E. coli
[0762] Production of butyrate is assessed in E. coli Nissle strains
containing the butyrate cassettes described above in order to
determine the effect of oxygen on butyrate production. All
incubations are performed at 37.degree. C. Cultures of E. coli
strains DH5a and Nissle transformed with the butyrate cassettes are
grown overnight in LB and then diluted 1:200 into 4 mL of M9
minimal medium containing 0.5% glucose. The cells are grown with
shaking (250 rpm) for 4-6 h and incubated aerobically or
anaerobically in a Coy anaerobic chamber (supplying 90% N2, 5% CO2,
5% H2). One mL culture aliquots are prepared in 1.5 mL capped tubes
and incubated in a stationary incubator to limit culture aeration.
One tube is removed at each time point (0, 1, 2, 4, and 20 hours)
and analyzed for butyrate concentration by LC-MS to confirm that
butyrate production in these recombinant strains can be achieved in
a low-oxygen environment.
[0763] In an alternate embodiment, overnight bacterial cultures
were diluted 1:100 into fresh LB and grown for 1.5 hrs to allow
entry into early log phase. At this point, long half-life nitric
oxide donor (DETA-NO; diethylenetriamine-nitric oxide adduct) was
added to cultures at a final concentration of 0.3 mM to induce
expression from plasmid. After 2 hours of induction, cells were
spun down, supernatant was discarded, and the cells were
resuspended in M9 minimal media containing 0.5% glucose. Culture
supernatant was then analyzed at indicated time points to assess
levels of butyrate production. Genetically engineered Nissle
comprising pLogic031-nsrR-norB-butyrate operon construct;
SYN-UCD507) or (pLogic046-nsrR-norB-butyrate operon construct;
SYN-UCD508) produce significantly more butyrate as compared to
wild-type Nissle.
[0764] Genetically engineered Nissle were generated comprising a
butyrate gene cassette in which the pbt and buk genes are replaced
with tesB (SEQ ID NO: 48) expressed under the control of a
tetracycline promoter (pLOGIC046-tesB-butyrate; SEQ ID NO: 88). SEQ
ID NO: 88 comprises a reverse complement of the tetR repressor
(underlined), an intergenic region containing divergent promoters
controlling tetR and the butyrate operon and their respective RBS
(bold), and the butyrate genes (ter-thiA1-hbd-crt2-tesB) separated
by RBS.
TABLE-US-00049 TABLE 43 pLOGIC046-tesB-butyrate sequence SEQ ID NO:
88 gtaaaacgacggccagtgaattcgttaagacccactttcacatttaagtt
gtttttctaatccgcatatgatcaattcaaggccgaataagaaggctggc
tctgcaccttggtgatcaaataattcgatagcttgtcgtaataatggcgg
catactatcagtagtaggtgtttccctttcttctttagcgacttgatgct
cttgatcttccaatacgcaacctaaagtaaaatgccccacagcgctgagt
gcatataatgcattctctagtgaaaaaccttgttggcataaaaaggctaa
ttgattttcgagagtttcatactgtttttctgtaggccgtgtacctaaat
gtacttttgctccatcgcgatgacttagtaaagcacatctaaaactttta
gcgttattacgtaaaaaatcttgccagctttccccttctaaagggcaaaa
gtgagtatggtgcctatctaacatctcaatggctaaggcgtcgagcaaag
cccgcttattttttacatgccaatacaatgtaggctgctctacacctagc
ttctgggcgagtttacgggttgttaaaccttcgattccgacctcattaag
cagctctaatgcgctgttaatcactttacttttatctaatctagacatca
ttaattcctaatttttgttgacactctatcattgatagagttattttacc
actccctatcagtgatagagaaaagtgaactctagaaataattttgttta
actttaagaaggagatatacatatgatcgtaaaacctatggtacgcaaca
atatctgcctgaacgcccatcctcagggctgcaagaagggagtggaagat
cagattgaatataccaagaaacgcattaccgcagaagtcaaagctggcgc
aaaagctccaaaaaacgttctggtgcttggctgctcaaatggttacggcc
tggcgagccgcattactgctgcgttcggatacggggctgcgaccatcggc
gtgtcctttgaaaaagcgggttcagaaaccaaatatggtacaccgggatg
gtacaataatttggcatttgatgaagcggcaaaacgcgagggtctttata
gcgtgacgatcgacggcgatgcgttttcagacgagatcaaggcccaggta
attgaggaagccaaaaaaaaaggtatcaaatttgatctgatcgtatacag
cttggccagcccagtacgtactgatcctgatacaggtatcatgcacaaaa
gcgttttgaaaccctttggaaaaacgttcacaggcaaaacagtagatccg
tttactggcgagctgaaggaaatctccgcggaaccagcaaatgacgagga
agcagccgccactgttaaagttatggggggtgaagattgggaacgttgga
ttaagcagctgtcgaaggaaggcctcttagaagaaggctgtattaccttg
gcctatagttatattggccctgaagctacccaagctttgtaccgtaaagg
cacaatcggcaaggccaaagaacacctggaggccacagcacaccgtctca
acaaagagaacccgtcaatccgtgccttcgtgagcgtgaataaaggcctg
gtaacccgcgcaagcgccgtaatcccggtaatccctctgtatctcgccag
cttgttcaaagtaatgaaagagaagggcaatcatgaaggttgtattgaac
agatcacgcgtctgtacgccgagcgcctgtaccgtaaagatggtacaatt
ccagttgatgaggaaaatcgcattcgcattgatgattgggagttagaaga
agacgtccagaaagcggtatccgcgttgatggagaaagtcacgggtgaaa
acgcagaatctctcactgacttagcggggtaccgccatgatttcttagct
agtaacggctttgatgtagaaggtattaattatgaagcggaagttgaacg
cttcgaccgtatctgataagaaggagatatacatatgagagaagtagtaa
ttgccagtgcagctagaacagcagtaggaagttttggaggagcatttaaa
tcagtttcagcggtagagttaggggtaacagcagctaaagaagctataaa
aagagctaacataactccagatatgatagatgaatctcttttagggggag
tacttacagcaggtcttggacaaaatatagcaagacaaatagcattagga
gcaggaataccagtagaaaaaccagctatgactataaatatagtttgtgg
ttctggattaagatctgtttcaatggcatctcaacttatagcattaggtg
atgctgatataatgttagttggtggagctgaaaacatgagtatgtctcct
tatttagtaccaagtgcgagatatggtgcaagaatgggtgatgctgcttt
tgttgattcaatgataaaagatggattatcagacatatttaataactatc
acatgggtattactgctgaaaacatagcagagcaatggaatataactaga
gaagaacaagatgaattagctcttgcaagtcaaaataaagctgaaaaagc
tcaagctgaaggaaaatttgatgaagaaatagttcctgttgttataaaag
gaagaaaaggtgacactgtagtagataaagatgaatatattaagcctggc
actacaatggagaaacttgctaagttaagacctgcatttaaaaaagatgg
aacagttactgctggtaatgcatcaggaataaatgatggtgctgctatgt
tagtagtaatggctaaagaaaaagctgaagaactaggaatagagcctctt
gcaactatagtttcttatggaacagctggtgttgaccctaaaataatggg
atatggaccagttccagcaactaaaaaagctttagaagctgctaatatga
ctattgaagatatagatttagttgaagctaatgaggcatttgctgcccaa
tctgtagctgtaataagagacttaaatatagatatgaataaagttaatgt
taatggtggagcaatagctataggacatccaataggatgctcaggagcaa
gaatacttactacacttttatatgaaatgaagagaagagatgctaaaact
ggtcttgctacactttgtataggcggtggaatgggaactactttaatagt
taagagatagtaagaaggagatatacatatgaaattagctgtaataggta
gtggaactatgggaagtggtattgtacaaacttttgcaagttgtggacat
gatgtatgtttaaagagtagaactcaaggtgctatagataaatgtttagc
tttattagataaaaatttaactaagttagttactaagggaaaaatggatg
aagctacaaaagcagaaatattaagtcatgttagttcaactactaattat
gaagatttaaaagatatggatttaataatagaagcatctgtagaagacat
gaatataaagaaagatgttttcaagttactagatgaattatgtaaagaag
atactatcttggcaacaaatacttcatcattatctataacagaaatagct
tcttctactaagcgcccagataaagttataggaatgcatttctttaatcc
agttcctatgatgaaattagttgaagttataagtggtcagttaacatcaa
aagttacttttgatacagtatttgaattatctaagagtatcaataaagta
ccagtagatgtatctgaatctcctggatttgtagtaaatagaatacttat
acctatgataaatgaagctgttggtatatatgcagatggtgttgcaagta
aagaagaaatagatgaagctatgaaattaggagcaaaccatccaatggga
ccactagcattaggtgatttaatcggattagatgttgttttagctataat
gaacgttttatatactgaatttggagatactaaatatagacctcatccac
ttttagctaaaatggttagagctaatcaattaggaagaaaaactaagata
ggattctatgattataataaataataagaaggagatatacatatgagtac
aagtgatgttaaagtttatgagaatgtagctgttgaagtagatggaaata
tatgtacagtgaaaatgaatagacctaaagcccttaatgcaataaattca
aagactttagaagaactttatgaagtatttgtagatattaataatgatga
aactattgatgttgtaatattgacaggggaaggaaaggcatttgtagctg
gagcagatattgcatacatgaaagatttagatgctgtagctgctaaagat
tttagtatcttaggagcaaaagcttttggagaaatagaaaatagtaaaaa
agtagtgatagctgctgtaaacggatttgctttaggtggaggatgtgaac
ttgcaatggcatgtgatataagaattgcatctgctaaagctaaatttggt
cagccagaagtaactcttggaataactccaggatatggaggaactcaaag
gcttacaagattggttggaatggcaaaagcaaaagaattaatctttacag
gtcaagttataaaagctgatgaagctgaaaaaatagggctagtaaataga
gtcgttgagccagacattttaatagaagaagttgagaaattagctaagat
aatagctaaaaatgctcagcttgcagttagatactctaaagaagcaatac
aacttggtgctcaaactgatataaatactggaatagatatagaatctaat
ttatttggtctttgtttttcaactaaagaccaaaaagaaggaatgtcagc
tttcgttgaaaagagagaagctaactttataaaagggtaataagaaggag
atatacatatgAGTCAGGCGCTAAAAAATTTACTGACATTGTTAAATCTG
GAAAAAATTGAGGAAGGACTCTTTCGCGGCCAGAGTGAAGATTTAGGTTT
ACGCCAGGTGTTTGGCGGCCAGGTCGTGGGTCAGGCCTTGTATGCTGCAA
AAGAGACCGTCCCTGAAGAGCGGCTGGTACATTCGTTTCACAGCTACTTT
CTTCGCCCTGGCGATAGTAAGAAGCCGATTATTTATGATGTCGAAACGCT
GCGTGACGGTAACAGCTTCAGCGCCCGCCGGGTTGCTGCTATTCAAAACG
GCAAACCGATTTTTTATATGACTGCCTCTTTCCAGGCACCAGAAGCGGGT
TTCGAACATCAAAAAACAATGCCGTCCGCGCCAGCGCCTGATGGCCTCCC
TTCGGAAACGCAAATCGCCCAATCGCTGGCGCACCTGCTGCCGCCAGTGC
TGAAAGATAAATTCATCTGCGATCGTCCGCTGGAAGTCCGTCCGGTGGAG
TTTCATAACCCACTGAAAGGTCACGTCGCAGAACCACATCGTCAGGTGTG
GATCCGCGCAAATGGTAGCGTGCCGGATGACCTGCGCGTTCATCAGTATC
TGCTCGGTTACGCTTCTGATCTTAACTTCCTGCCGGTAGCTCTACAGCCG
CACGGCATCGGTTTTCTCGAACCGGGGATTCAGATTGCCACCATTGACCA
TTCCATGTGGTTCCATCGCCCGTTTAATTTGAATGAATGGCTGCTGTATA
GCGTGGAGAGCACCTCGGCGTCCAGCGCACGTGGCTTTGTGCGCGGTGAG
TTTTATACCCAAGACGGCGTACTGGTTGCCTCGACCGTTCAGGAAGGGGT
GATGCGTAATCACAATtaa
[0765] Overnight bacterial cultures were diluted 1:100 into fresh
LB and grown for 1.5 hrs to allow entry into early log phase. At
this point, anhydrous tetracycline (ATC) was added to cultures at a
final concentration of 100 ng/mL to induce expression of butyrate
genes from plasmid. After 2 hours of induction, cells were spun
down, supernatant was discarded, and the cells were resuspended in
M9 minimal media containing 0.5% glucose. Culture supernatant was
then analyzed at indicated time points to assess levels of butyrate
production. Replacement of pbt and buk with tesB leads to greater
levels of butyrate production.
[0766] FIG. 53C shows butyrate production in strains comprising an
FNR-butyrate cassette syn 363 (having the ter substitution) in the
presence/absence of glucose and oxygen. FIG. 53C shows that
bacteria need both glucose and anaerobic conditions for butyrate
production from the FNR promoter. Cells were grown aerobically or
anaerobically in media containg no glucose (LB) or in media
containing glucose at 0.5% (RMC). Culture samples were taken at
indicaed time pints and supernatant fractions were assessed for
butyrate concentration using LC-MS. These data show that SYN 363
requires glucose for butyrate production and that in the presence
of glucose butyrate production can be enhanced under anaerobic
conditions when under the control of the anaerobic FNR-regulated
ydfZ promoter.
Example 39
In Vitro Activity of Bacterial Strain Comprising
Ammonia-Metabolizing and Butyrate Producing Circuits
[0767] Do determine whether ammonia uptake and conversion to
arginine and production of butyrate could be accomplished in one
strain, a plasmid (Logic156) comprising a butyrate production
cassette construct, was used for initial proof-of-concept
experiments. The following strains were generated using the
plasmid: SYN-UCD501 (comprising Logic156 (pSC101 PydfZ-ter butyrate
plasmid; amp resistance); and SYN-UCD601, which is SYN-UCD-305,
additionally comprising Logic156 (i.e., SYN-UCD601 comprises
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and Logic156 (pSC101 PydfZ-ter butyrate
plasmid; amp resistance)). Arginine and butyrate production was the
compared between the butyrate only producer SYN-UCD501, the
arginine only producer SYN-UCD305, and the combined
butyrate/arginine producer SYN-UCD-601. Sequences for the butyrate
cassette used are shown in Table 38.
[0768] Briefly, 3 ml LB (containing selective antibiotics (Amp for
SYN-UCD501 and SYN-UCD601) and 3 mM thymidine for SYN-UCD-305 and
SYN-UCD601) with bacteria from frozen glycerol stocks. Bacteria
were grown overnight at 37 C with shaking. Overnight cultures were
diluted 1:100 dilution into 10 ml LB (containing antibiotics and
thymidine where necessary as above) in a 125 ml baffled flask.
Cultures were grown aerobically at 37 C with shaking for about 1.5
h, and then transferred to the anaerobic chamber at 37 C for 4 h.
Bacteria (2.times.108 CFU) were added to 1 ml M9 media containing
50 mM MOPS with 0.5% glucose in microcentrifuge tubes. Cells were
plated to determine cell counts. The assay tubes were placed in the
anaerobic chamber at 37 C. At indicated times (1, 2, 24 h), 120 ul
cells were removed and pelleted at 14,000 rpm for 1 min, and 100 ul
of the supernatant was transferred to a 96-well assay plate and
sealed with aluminum foil, and stored at -80 C until analysis by
LC-MS for arginine and butyrate concentrations (as described in
Example 13 and Example 40).
[0769] Results are depicted in FIG. 53A and FIG. 53B, and show that
SYN-UCD601 is able to produce similar levels of arginine as
SYN-UCD305 and similar levels of butyrate as SYN-UCD501 in
vitro.
TABLE-US-00050 TABLE 44 Butyrate cassette sequences SEQ Description
Sequence ID NO ydfZ + RBS CATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTC SEQ
(RBS is bolded) CCCCGACTTATGGCTCATGCATGCATCAAAAAAGATG ID NO:
TGAGCTTGATCAAAAACAAAAAATATTTCACTCGACA 89
GGAGTATTTATATTGCGCCCGGATCCCTCTAGAAATA
ATTTTGTTTAACTTTAAGAAGGAGATATACAT Ter
atgatcgtaaaacctatggtacgcaacaatatctgcctgaacgcccatcctca SEQ
(polynucleotide gggctgcaagaagggagtggaagatcagattgaatataccaagaaacgca
ID NO: sequence)
ttaccgcagaagtcaaagctggcgcaaaagctccaaaaaacgttctggtgctt 90
ggctgctcaaatggttacggcctggcgagccgcattactgctgcgttcggatac
ggggctgcgaccatcggcgtgtcctttgaaaaagcgggttcagaaaccaaat
atggtacaccgggatggtacaataatttggcatttgatgaagcggcaaaacgc
gagggtctttatagcgtgacgatcgacggcgatgcgttttcagacgagatcaa
ggcccaggtaattgaggaagccaaaaaaaaaggtatcaaatttgatctgatc
gtatacagcttggccagcccagtacgtactgatcctgatacaggtatcatgcac
aaaagcgttttgaaaccctttggaaaaacgttcacaggcaaaacagtagatc
cgtttactggcgagctgaaggaaatctccgcggaaccagcaaatgacgagg
aagcagccgccactgttaaagttatggggggtgaagattgggaacgttggatt
aagcagctgtcgaaggaaggcctcttagaagaaggctgtattaccttggccta
tagttatattggccctgaagctacccaagctttgtaccgtaaaggcacaatcgg
caaggccaaagaacacctggaggccacagcacaccgtctcaacaaagag
aacccgtcaatccgtgccttcgtgagcgtgaataaaggcctggtaacccgcg
caagcgccgtaatcccggtaatccctctgtatctcgccagcttgttcaaagtaat
gaaagagaagggcaatcatgaaggttgtattgaacagatcacgcgtctgtac
gccgagcgcctgtaccgtaaagatggtacaattccagttgatgaggaaaatc
gcattcgcattgatgattgggagttagaagaagacgtccagaaagcggtatcc
gcgttgatggagaaagtcacgggtgaaaacgcagaatctctcactgacttag
cggggtaccgccatgatttcttagctagtaacggctttgatgtagaaggtattaat
tatgaagcggaagttgaacgcttcgaccgtatctga Ter (polypeptide
MIVKPMVRNNICLNAHPQGCKKGVEDQIEYTKKRITAEV SEQ sequence)
KAGAKAPKNVLVLGCSNGYGLASRITAAFGYGAATIGV ID NO:
SFEKAGSETKYGTPGWYNNLAFDEAAKREGLYSVTIDG 91
DAFSDEIKAQVIEEAKKKGIKFDLIVYSLASPVRTDPDTGI
MHKSVLKPFGKTFTGKTVDPFTGELKEISAEPANDEEA
AATVKVMGGEDWERWIKQLSKEGLLEEGCITLAYSYIG
PEATQALYRKGTIGKAKEHLEATAHRLNKENPSIRAFVS
VNKGLVTRASAVIPVIPLYLASLFKVMKEKGNHEGCIEQI
TRLYAERLYRKDGTIPVDEENRIRIDDWELEEDVQKAVS
ALMEKVTGENAESLTDLAGYRHDFLASNGFDVEGINYE AEVERFDRI ThiA
atgagagaagtagtaattgccagtgcagctagaacagcagtaggaagttttg SEQ
(polynucleotide
gaggagcatttaaatcagtttcagcggtagagttaggggtaacagcagctaa ID NO:
sequence) agaagctataaaaagagctaacataactccagatatgatagatgaatctctttt 92
agggggagtacttacagcaggtcttggacaaaatatagcaagacaaatagc
attaggagcaggaataccagtagaaaaaccagctatgactataaatatagttt
gtggttctggattaagatctgtttcaatggcatctcaacttatagcattaggtgatg
ctgatataatgttagttggtggagctgaaaacatgagtatgtctccttatttagtac
caagtgcgagatatggtgcaagaatgggtgatgctgcttttgttgattcaatgat
aaaagatggattatcagacatatttaataactatcacatgggtattactgctgaa
aacatagcagagcaatggaatataactagagaagaacaagatgaattagct
cttgcaagtcaaaataaagctgaaaaagctcaagctgaaggaaaatttgatg
aagaaatagttcctgttgttataaaaggaagaaaaggtgacactgtagtagat
aaagatgaatatattaagcctggcactacaatggagaaacttgctaagttaag
acctgcatttaaaaaagatggaacagttactgctggtaatgcatcaggaataa
atgatggtgctgctatgttagtagtaatggctaaagaaaaagctgaagaacta
ggaatagagcctcttgcaactatagtttcttatggaacagctggtgttgacccta
aaataatgggatatggaccagttccagcaactaaaaaagctttagaagctgct
aatatgactattgaagatatagatttagttgaagctaatgaggcatttgctgccc
aatctgtagctgtaataagagacttaaatatagatatgaataaagttaatgttaat
ggtggagcaatagctataggacatccaataggatgctcaggagcaagaata
cttactacacttttatatgaaatgaagagaagagatgctaaaactggtcttgcta
cactttgtataggcggtggaatgggaactactttaatagttaagagatag ThiA
MREVVIASAARTAVGSFGGAFKSVSAVELGVTAAKEAIK SEQ (polypeptide
RANITPDMIDESLLGGVLTAGLGQNIARQIALGAGIPVEK ID NO: sequence)
PAMTINIVCGSGLRSVSMASQLIALGDADIMLVGGAENM 93
SMSPYLVPSARYGARMGDAAFVDSMIKDGLSDIFNNYH
MGITAENIAEQWNITREEQDELALASQNKAEKAQAEGK
FDEEIVPVVIKGRKGDTVVDKDEYIKPGTTMEKLAKLRP
AFKKDGTVTAGNASGINDGAAMLWMAKEKAEELGIEP
LATIVSYGTAGVDPKIMGYGPVPATKKALEAANMTIEDID
LVEANEAFAAQSVAVIRDLNIDMNKVNVNGGAIAIGHPIG
CSGARILTTLLYEMKRRDAKTGLATLCIGGGMGTTLIVKR Hbd
atgaaattagctgtaataggtagtggaactatgggaagtggtattgtacaaactt SEQ
(polynucleotide
ttgcaagttgtggacatgatgtatgtttaaagagtagaactcaaggtgctataga ID NO:
sequence) taaatgtttagctttattagataaaaatttaactaagttagttactaagggaaaaat
94 ggatgaagctacaaaagcagaaatattaagtcatgttagttcaactactaatta
tgaagatttaaaagatatggatttaataatagaagcatctgtagaagacatgaa
tataaagaaagatgttttcaagttactagatgaattatgtaaagaagatactatct
tggcaacaaatacttcatcattatctataacagaaatagcttcttctactaagcgc
ccagataaagttataggaatgcatttctttaatccagttcctatgatgaaattagtt
gaagttataagtggtcagttaacatcaaaagttacttttgatacagtatttgaatta
tctaagagtatcaataaagtaccagtagatgtatctgaatctcctggatttgtagt
aaatagaatacttatacctatgataaatgaagctgttggtatatatgcagatggt
gttgcaagtaaagaagaaatagatgaagctatgaaattaggagcaaaccat
ccaatgggaccactagcattaggtgatttaatcggattagatgttgttttagctata
atgaacgttttatatactgaatttggagatactaaatatagacctcatccactttta
gctaaaatggttagagctaatcaattaggaagaaaaactaagataggattcta
tgattataataaataa Hbd MKLAVIGSGTMGSGIVQTFASCGHDVCLKSRTQGAIDK SEQ
(polypeptide CLALLDKNLTKLVTKGKMDEATKAEILSHVSSTTNYEDL ID NO:
sequence) KDMDLIIEASVEDMNIKKDVFKLLDELCKEDTILATNTSS 95
LSITEIASSTKRPDKVIGMHFFNPVPMMKLVEVISGQLTS
KVTFDTVFELSKSINKVPVDVSESPGFVVNRILIPMINEA
VGIYADGVASKEEIDEAMKLGANHPMGPLALGDLIGLDV
VLAIMNVLYTEFGDTKYRPHPLLAKMVRANQLGRKTKIG FYDYNK Crt2
atgagtacaagtgatgttaaagtttatgagaatgtagctgttgaagtagatgga SEQ
(polynucleotide
aatatatgtacagtgaaaatgaatagacctaaagcccttaatgcaataaattca ID NO:
sequence) aagactttagaagaactttatgaagtatttgtagatattaataatgatgaaactatt
96 gatgttgtaatattgacaggggaaggaaaggcatttgtagctggagcagatatt
gcatacatgaaagatttagatgctgtagctgctaaagattttagtatcttaggag
caaaagcttttggagaaatagaaaatagtaaaaaagtagtgatagctgctgta
aacggatttgctttaggtggaggatgtgaacttgcaatggcatgtgatataaga
attgcatctgctaaagctaaatttggtcagccagaagtaactcttggaataactc
caggatatggaggaactcaaaggcttacaagattggttggaatggcaaaag
caaaagaattaatctttacaggtcaagttataaaagctgatgaagctgaaaaa
atagggctagtaaatagagtcgttgagccagacattttaatagaagaagttga
gaaattagctaagataatagctaaaaatgctcagcttgcagttagatactctaa
agaagcaatacaacttggtgctcaaactgatataaatactggaatagatatag
aatctaatttatttggtctttgtttttcaactaaagaccaaaaagaaggaatgtca
gctttcgttgaaaagagagaagctaactttataaaagggtaa Crt2
MSTSDVKVYENVAVEVDGNICTVKMNRPKALNAINSKT SEQ (polypeptide
LEELYEVFVDINNDETIDWILTGEGKAFVAGADIAYMKD ID NO: sequence)
LDAVAAKDFSILGAKAFGEIENSKKVVIAAVNGFALGGG 97
CELAMACDIRIASAKAKFGQPEVTLGITPGYGGTQRLTR
LVGMAKAKELIFTGQVIKADEAEKIGLVNRWEPDILIEEV
EKLAKIIAKNAQLAVRYSKEAIQLGAQTDINTGIDIESNLF
GLCFSTKDQKEGMSAFVEKREANFIKG Pbt
atgagaagttttgaagaagtaattaagtttgcaaaagaaagaggacctaaaa SEQ
(polynucleotide
ctatatcagtagcatgttgccaagataaagaagttttaatggcagttgaaatgg ID NO:
sequence) ctagaaaagaaaaaatagcaaatgccattttagtaggagatatagaaaaga 98
ctaaagaaattgcaaaaagcatagacatggatatcgaaaattatgaactgat
agatataaaagatttagcagaagcatctctaaaatctgttgaattagtttcacaa
ggaaaagccgacatggtaatgaaaggcttagtagacacatcaataatactaa
aagcagttttaaataaagaagtaggtcttagaactggaaatgtattaagtcacg
tagcagtatttgatgtagagggatatgatagattatttttcgtaactgacgcagct
atgaacttagctcctgatacaaatactaaaaagcaaatcatagaaaatgcttg
cacagtagcacattcattagatataagtgaaccaaaagttgctgcaatatgcg
caaaagaaaaagtaaatccaaaaatgaaagatacagttgaagctaaagaa
ctagaagaaatgtatgaaagaggagaaatcaaaggttgtatggttggtgggc
cttttgcaattgataatgcagtatctttagaagcagctaaacataaaggtataaa
tcatcctgtagcaggacgagctgatatattattagccccagatattgaaggtggt
aacatattatataaagctttggtattcttctcaaaatcaaaaaatgcaggagttat
agttggggctaaagcaccaataatattaacttctagagcagacagtgaagaa
actaaactaaactcaatagctttaggtgttttaatggcagcaaaggcataa Pbt
(polypeptide MRSFEEVIKFAKERGPKTISVACCQDKEVLMAVEMARK SEQ sequence)
EKIANAILVGDIEKTKEIAKSIDMDIENYELIDIKDLAEASL ID NO:
KSVELVSQGKADMVMKGLVDTSIILKAVLNKEVGLRTG 99
NVLSHVAVFDVEGYDRLFFVTDAAMNLAPDTNTKKQIIE
NACTVAHSLDISEPKVAAICAKEKVNPKMKDTVEAKELE
EMYERGEIKGCMVGGPFAIDNAVSLEAAKHKGINHPVA
GRADILLAPDIEGGNILYKALVFFSKSKNAGVIVGAKAPII LTSRADSEETKLNSIALGVLMAAKA
Buk atgagcaaaatatttaaaatcttaacaataaatcctggttcgacatcaactaaa SEQ
(polynucleotide
atagctgtatttgataatgaggatttagtatttgaaaaaactttaagacattcttca ID NO:
sequence) gaagaaataggaaaatatgagaaggtgtctgaccaatttgaatttcgtaaaca 100
agtaatagaagaagctctaaaagaaggtggagtaaaaacatctgaattagat
gctgtagtaggtagaggaggacttcttaaacctataaaaggtggtacttattca
gtaagtgctgctatgattgaagatttaaaagtgggagttttaggagaacacgctt
caaacctaggtggaataatagcaaaacaaataggtgaagaagtaaatgttc
cttcatacatagtagaccctgttgttgtagatgaattagaagatgttgctagaattt
ctggtatgcctgaaataagtagagcaagtgtagtacatgctttaaatcaaaag
gcaatagcaagaagatatgctagagaaataaacaagaaatatgaagatata
aatcttatagttgcacacatgggtggaggagtttctgttggagctcataaaaatg
gtaaaatagtagatgttgcaaacgcattagatggagaaggacctttctctccag
aaagaagtggtggactaccagtaggtgcattagtaaaaatgtgctttagtgga
aaatatactcaagatgaaattaaaaagaaaataaaaggtaatggcggacta
gttgcatacttaaacactaatgatgctagagaagttgaagaaagaattgaagc
tggtgatgaaaaagctaaattagtatatgaagctatggcatatcaaatctctaa
agaaataggagctagtgctgcagttcttaagggagatgtaaaagcaatattatt
aactggtggaatcgcatattcaaaaatgtttacagaaatgattgcagatagagt
taaatttatagcagatgtaaaagtttatccaggtgaagatgaaatgattgcatta
gctcaaggtggacttagagttttaactggtgaagaagaggctcaagtttatgat aactaa Buk
MSKIFKILTINPGSTSTKIAVFDNEDLVFEKTLRHSSEEIG SEQ (polypeptide
KYEKVSDQFEFRKQVIEEALKEGGVKTSELDAVVGRGG ID NO: sequence)
LLKPIKGGTYSVSAAMIEDLKVGVLGEHASNLGGIIAKQI 101
GEEVNVPSYIVDPVVVDELEDVARISGMPEISRASVVHA
LNQKAIARRYAREINKKYEDINLIVAHMGGGVSVGAHKN
GKIVDVANALDGEGPFSPERSGGLPVGALVKMCFSGK
YTQDEIKKKIKGNGGLVAYLNTNDAREVEERIEAGDEKA
KLVYEAMAYQISKEIGASAAVLKGDVKAILLTGGIAYSKM
FTEMIADRVKFIADVKVYPGEDEMIALAQGGLRVLTGEE EAQVYDN First RBS (in
TTTGTTTAACTTTAAGAAGGAGA SEQ ydfZ = RBS) ID NO: 102 Internal RBS
taagaaggagatatacat SEQ between genes ID NO: 103 Butryate
CATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTC SEQ cassette under
CCCCGACTTATGGCTCATGCATGCATCAAAAAAGATG ID NO: the control of
TGAGCTTGATCAAAAACAAAAAATATTTCACTCGACA 104 the ydfZ
GGAGTATTTATATTGCGCCCGGATCCCTCTAGAAATA promoter
ATTTTGTTTAACTTTAAGAAGGAGATATACATatgatcgt (uppercase:
aaaacctatggtacgcaacaatatctgcctgaacgcccatcctcagggctgc ydfZ promoter,
aagaagggagtggaagatcagattgaatataccaagaaacgcattaccgca with RBS in
gaagtcaaagctggcgcaaaagctccaaaaaacgttctggtgcttggctgctc bold; lower
aaatggttacggcctggcgagccgcattactgctgcgttcggatacggggctg case: coding
cgaccatcggcgtgtcctttgaaaaagcgggttcagaaaccaaatatggtac regions in the
accgggatggtacaataatttggcatttgatgaagcggcaaaacgcgagggt following
order: ctttatagcgtgacgatcgacggcgatgcgttttcagacgagatcaaggccca ter,
thiA, hbd, ggtaattgaggaagccaaaaaaaaaggtatcaaatttgatctgatcgtataca
crt2, pbt, buk,
gcttggccagcccagtacgtactgatcctgatacaggtatcatgcacaaaagc separated by
gttttgaaaccctttggaaaaacgttcacaggcaaaacagtagatccgtttact internal RBS
ggcgagctgaaggaaatctccgcggaaccagcaaatgacgaggaagcag (uppercase and
ccgccactgttaaagttatggggggtgaagattgggaacgttggattaagcag underlined)
ctgtcgaaggaaggcctcttagaagaaggctgtattaccttggcctatagttata
ttggccctgaagctacccaagctttgtaccgtaaaggcacaatcggcaaggc
caaagaacacctggaggccacagcacaccgtctcaacaaagagaacccg
tcaatccgtgccttcgtgagcgtgaataaaggcctggtaacccgcgcaagcg
ccgtaatcccggtaatccctctgtatctcgccagcttgttcaaagtaatgaaaga
gaagggcaatcatgaaggttgtattgaacagatcacgcgtctgtacgccgag
cgcctgtaccgtaaagatggtacaattccagttgatgaggaaaatcgcattcg
cattgatgattgggagttagaagaagacgtccagaaagcggtatccgcgttga
tggagaaagtcacgggtgaaaacgcagaatctctcactgacttagcggggta
ccgccatgatttcttagctagtaacggctttgatgtagaaggtattaattatgaag
cggaagttgaacgcttcgaccgtatctgaTAAGAAGGAGATATACA
Tatgagagaagtagtaattgccagtgcagctagaacagcagtaggaagtttt
ggaggagcatttaaatcagtttcagcggtagagttaggggtaacagcagcta
aagaagctataaaaagagctaacataactccagatatgatagatgaatctcttt
tagggggagtacttacagcaggtcttggacaaaatatagcaagacaaatagc
attaggagcaggaataccagtagaaaaaccagctatgactataaatatagttt
gtggttctggattaagatctgtttcaatggcatctcaacttatagcattaggtgatg
ctgatataatgttagttggtggagctgaaaacatgagtatgtctccttatttagtac
caagtgcgagatatggtgcaagaatgggtgatgctgcttttgttgattcaatgat
aaaagatggattatcagacatatttaataactatcacatgggtattactgctgaa
aacatagcagagcaatggaatataactagagaagaacaagatgaattagct
cttgcaagtcaaaataaagctgaaaaagctcaagctgaaggaaaatttgatg
aagaaatagttcctgttgttataaaaggaagaaaaggtgacactgtagtagat
aaagatgaatatattaagcctggcactacaatggagaaacttgctaagttaag
acctgcatttaaaaaagatggaacagttactgctggtaatgcatcaggaataa
atgatggtgctgctatgttagtagtaatggctaaagaaaaagctgaagaacta
ggaatagagcctcttgcaactatagtttcttatggaacagctggtgttgacccta
aaataatgggatatggaccagttccagcaactaaaaaagctttagaagctgct
aatatgactattgaagatatagatttagttgaagctaatgaggcatttgctgccc
aatctgtagctgtaataagagacttaaatatagatatgaataaagttaatgttaat
ggtggagcaatagctataggacatccaataggatgctcaggagcaagaata
cttactacacttttatatgaaatgaagagaagagatgctaaaactggtcttgcta
cactttgtataggcggtggaatgggaactactttaatagttaagagatagTAA
GAAGGAGATATACATatgaaattagctgtaataggtagtggaactat
gggaagtggtattgtacaaacttttgcaagttgtggacatgatgtatgtttaaaga
gtagaactcaaggtgctatagataaatgtttagctttattagataaaaatttaact
aagttagttactaagggaaaaatggatgaagctacaaaagcagaaatattaa
gtcatgttagttcaactactaattatgaagatttaaaagatatggatttaataatag
aagcatctgtagaagacatgaatataaagaaagatgttttcaagttactagatg
aattatgtaaagaagatactatcttggcaacaaatacttcatcattatctataaca
gaaatagcttcttctactaagcgcccagataaagttataggaatgcatttctttaa
tccagttcctatgatgaaattagttgaagttataagtggtcagttaacatcaaaa
gttacttttgatacagtatttgaattatctaagagtatcaataaagtaccagtagat
gtatctgaatctcctggatttgtagtaaatagaatacttatacctatgataaatga
agctgttggtatatatgcagatggtgttgcaagtaaagaagaaatagatgaag
ctatgaaattaggagcaaaccatccaatgggaccactagcattaggtgattta
atcggattagatgttgttttagctataatgaacgttttatatactgaatttggagata
ctaaatatagacctcatccacttttagctaaaatggttagagctaatcaattagg
aagaaaaactaagataggattctatgattataataaataaTAAGAAGGA
GATATACATatgagtacaagtgatgttaaagtttatgagaatgtagctgttg
aagtagatggaaatatatgtacagtgaaaatgaatagacctaaagcccttaat
gcaataaattcaaagactttagaagaactttatgaagtatttgtagatattaataa
tgatgaaactattgatgttgtaatattgacaggggaaggaaaggcatttgtagct
ggagcagatattgcatacatgaaagatttagatgctgtagctgctaaagatttta
gtatcttaggagcaaaagcttttggagaaatagaaaatagtaaaaaagtagtg
atagctgctgtaaacggatttgctttaggtggaggatgtgaacttgcaatggcat
gtgatataagaattgcatctgctaaagctaaatttggtcagccagaagtaactct
tggaataactccaggatatggaggaactcaaaggcttacaagattggttgga
atggcaaaagcaaaagaattaatctttacaggtcaagttataaaagctgatga
agctgaaaaaatagggctagtaaatagagtcgttgagccagacattttaatag
aagaagttgagaaattagctaagataatagctaaaaatgctcagcttgcagtt
agatactctaaagaagcaatacaacttggtgctcaaactgatataaatactgg
aatagatatagaatctaatttatttggtctttgtttttcaactaaagaccaaaaaga
aggaatgtcagctttcgttgaaaagagagaagctaactttataaaagggtaaT
AAGAAGGAGATATACATatgagaagttttgaagaagtaattaagttt
gcaaaagaaagaggacctaaaactatatcagtagcatgttgccaagataaa
gaagttttaatggcagttgaaatggctagaaaagaaaaaatagcaaatgcca
ttttagtaggagatatagaaaagactaaagaaattgcaaaaagcatagacat
ggatatcgaaaattatgaactgatagatataaaagatttagcagaagcatctct
aaaatctgttgaattagtttcacaaggaaaagccgacatggtaatgaaaggct
tagtagacacatcaataatactaaaagcagttttaaataaagaagtaggtctta
gaactggaaatgtattaagtcacgtagcagtatttgatgtagagggatatgata
gattatttttcgtaactgacgcagctatgaacttagctcctgatacaaatactaaa
aagcaaatcatagaaaatgcttgcacagtagcacattcattagatataagtga
accaaaagttgctgcaatatgcgcaaaagaaaaagtaaatccaaaaatgaa
agatacagttgaagctaaagaactagaagaaatgtatgaaagaggagaaat
caaaggttgtatggttggtgggccttttgcaattgataatgcagtatctttagaag
cagctaaacataaaggtataaatcatcctgtagcaggacgagctgatatattat
tagccccagatattgaaggtggtaacatattatataaagctttggtattcttctcaa
aatcaaaaaatgcaggagttatagttggggctaaagcaccaataatattaact
tctagagcagacagtgaagaaactaaactaaactcaatagctttaggtgtttta
atggcagcaaaggcataaTAAGAAGGAGATATACATatgagcaa
aatatttaaaatcttaacaataaatcctggttcgacatcaactaaaatagctgtat
ttgataatgaggatttagtatttgaaaaaactttaagacattcttcagaagaaata
ggaaaatatgagaaggtgtctgaccaatttgaatttcgtaaacaagtaataga
agaagctctaaaagaaggtggagtaaaaacatctgaattagatgctgtagta
ggtagaggaggacttcttaaacctataaaaggtggtacttattcagtaagtgct
gctatgattgaagatttaaaagtgggagttttaggagaacacgcttcaaaccta
ggtggaataatagcaaaacaaataggtgaagaagtaaatgttccttcatacat
agtagaccctgttgttgtagatgaattagaagatgttgctagaatttctggtatgc
ctgaaataagtagagcaagtgtagtacatgctttaaatcaaaaggcaatagc
aagaagatatgctagagaaataaacaagaaatatgaagatataaatcttata
gttgcacacatgggtggaggagtttctgttggagctcataaaaatggtaaaata
gtagatgttgcaaacgcattagatggagaaggacctttctctccagaaagaag
tggtggactaccagtaggtgcattagtaaaaatgtgctttagtggaaaatatact
caagatgaaattaaaaagaaaataaaaggtaatggcggactagttgcatact
taaacactaatgatgctagagaagttgaagaaagaattgaagctggtgatga
aaaagctaaattagtatatgaagctatggcatatcaaatctctaaagaaatag
gagctagtgctgcagttcttaagggagatgtaaaagcaatattattaactggtg
gaatcgcatattcaaaaatgtttacagaaatgattgcagatagagttaaatttat
agcagatgtaaaagtttatccaggtgaagatgaaatgattgcattagctcaag
gtggacttagagttttaactggtgaagaagaggctcaagtttatgataactaataa
[0770] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 90 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 90 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 90 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 90 or a functional
fragment thereof.
[0771] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 92 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 92 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 92 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 92 or a functional
fragment thereof.
[0772] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 94 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 94 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 94 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 94 or a functional
fragment thereof.
[0773] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 96 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 96 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 96 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 96 or a functional
fragment thereof.
[0774] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 98 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 98 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 98 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 98 or a functional
fragment thereof.
[0775] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 100 or a
functional fragment thereof. In some embodiments, the genetically
engineered bacteria comprise a nucleic acid sequence that, but for
the redundancy of the genetic code, encodes the same polypeptide as
SEQ ID NO: 100 or a functional fragment thereof. In some
embodiments, genetically engineered bacteria comprise a nucleic
acid sequence that is at least about 80%, at least about 85%, at
least about 90%, at least about 95%, or at least about 99%
homologous to the DNA sequence of SEQ ID NO: 100 or a functional
fragment thereof, or a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 100 or a functional fragment thereof.
[0776] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 104 or a
functional fragment thereof. In some embodiments, the genetically
engineered bacteria comprise a nucleic acid sequence that, but for
the redundancy of the genetic code, encodes the same polypeptide as
SEQ ID NO: 104 or a functional fragment thereof. In some
embodiments, genetically engineered bacteria comprise a nucleic
acid sequence that is at least about 80%, at least about 85%, at
least about 90%, at least about 95%, or at least about 99%
homologous to the DNA sequence of SEQ ID NO: 104 or a functional
fragment thereof, or a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 104 or a functional fragment thereof.
[0777] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 48 or a functional
fragment thereof. In some embodiments, the genetically engineered
bacteria comprise a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 48 or a functional fragment thereof. In some embodiments,
genetically engineered bacteria comprise a nucleic acid sequence
that is at least about 80%, at least about 85%, at least about 90%,
at least about 95%, or at least about 99% homologous to the DNA
sequence of SEQ ID NO: 48 or a functional fragment thereof, or a
nucleic acid sequence that, but for the redundancy of the genetic
code, encodes the same polypeptide as SEQ ID NO: 48 or a functional
fragment thereof.
[0778] In alternate embodiments, pbt and buk are replaced with TesB
(SEQ ID NO: 48)
[0779] In some embodiments, the butyrate cassette is driven by an
inducible promoter. For example, other FNR promotors can be used in
lieu of ydfZ, e.g., in SEQ ID NO:.
[0780] Non-limiting FNR promoter sequences are provided herein. In
some embodiments, the genetically engineered bacteria of the
invention comprise a butyrate cassette under the control of one or
more of promoter sequences found in Table 6, e.g., nirB promoter,
ydfZ promoter, nirB promoter fused to a strong ribosome binding
site, ydfZ promoter fused to a strong ribosome binding site, fnrS,
an anaerobically induced small RNA gene (fnrS promoter), nirB
promoter fused to a crp binding site, and fnrS fused to a crp
binding site.
[0781] In some embodiments, the butyrate cassetted is under the
control of a promoter which is inducible by metabolites present in
the gut. In some embodiments the butyrate cassette is induced by
HE-specific molecules or metabolites indicative of liver damage,
e.g., bilirubin. In some embodiments, the butyrate cassette is
placed under the control of promoter, which is inducible by
inflammation or an inflammatory response (e.g., RNS or ROS
promoter).
[0782] In some embodiments, the genetically engineered bacteria
comprise a butyrate cassette driven by a promoter induced by a
molecule or metabolite, e.g., bilirubin, aspartate
aminotransferase, alanine aminotransferase, blood coagulation
factors II, VII, IX, and X, alkaline phosphatase, gamma glutamyl
transferase, hepatitis antigens and antibodies, alpha fetoprotein,
anti-mitochondrial, smooth muscle, and anti-nuclear antibodies,
iron, transferrin, ferritin, copper, ceruloplasmin, ammonia, and
manganese in their blood and intestines. Promoters that respond to
one of these molecules or their metabolites may be used in the
genetically engineered bacteria provided herein.
[0783] In some embodiments, the butyrate cassette is inducible by
arabinose and is driven by the AraBAD promoter.
Example 40
Quantification of Butyrate by LC-MS/MS
[0784] To obtain the butyrate measurements in Example 37 a LC-MS/MS
protocol for butyrate quantification was used.
Sample Preparation
[0785] First, fresh sodium butyrate stock solution (10 mg/m), and
1000, 500, 250, 100, 20, 4 and 0.8 .mu.g/mL of sodium butyrate
standards were prepared in water. Then, 10 .mu.L of sample
(bacterial supernatants and standards) were pipetted into a
V-bottom polypropylene 96-well plate, and 90 .mu.L of 67% ACN (60
uL ACN+30 uL water per reaction) with 4 ug/mL of butyrate-d7 (CDN
isotope) internal standard in final solution were added to each
sample. The plate was heat-sealed, mixed well, and centrifuged at
4000 rpm for 5 minutes. In a round-bottom 96-well polypropylene
plate, 20 .mu.L of diluted samples were added to 180 .mu.L of a
buffer containing 10 mM MES pH4.5, 20 mM EDC
(N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide), and 20 mM TFEA
(2,2,2-trifluroethylamine). The plate was again heat-sealed and
mixed well, and samples were incubated at room temperature for 1
hour.
LC-MS/MS Method
[0786] Butyrate was measured by liquid chromatography coupled to
tandem mass spectrometry (LC-MS/MS) using a Thermo TSQ Quantum Max
triple quadrupole mass spectrometer. HPLC Details are listed in
Table 45 and Table 46. Tandem Mass Spectrometry details are found
in Table 47.
TABLE-US-00051 TABLE 45 HPLC Details Column Thermo Aquasil C18
column, 5 .mu.m (50 .times. 2.1 mm) Mobile 100% H2O, 0.1% Formic
Acid Phase A Mobile 100% ACN, 0.1% Formic Acid Phase B Injection 10
uL volume
TABLE-US-00052 TABLE 46 HPLC Method Total Flow Time Rate (min)
(.mu.L/min) A % B % 0 0.5 100 0 1 0.5 100 0 2 0.5 10 90 4 0.5 10 90
4.01 0.5 100 0 4.25 0.5 100 0
TABLE-US-00053 TABLE 47 Tandem Mass Spectrometry Details Ion Source
HESI-II Polarity Positive SRM Butyrate 170.0/71.1, transitions
Butyrate d7 177.1/78.3
Example 41
Efficacy of Genetically Engineered Bacteria Producing Arginine
and/or Butyrate in a Bile Duct Ligation Model
[0787] Ligation of the common bile duct in rodents has used as an
experimental procedure in research for many years to induce liver
cholestasis and fibrosis (see e.g., Tag et a., Bile Duct Ligation
in Mice: Induction of Inflammatory Liver Injury and Fibrosis by
Obstructive Cholestasis, Journal of Visualized Experiments,
February 2015; 96; e52438, and references therein).
[0788] To determine the efficacy of a strain comprising an arginine
and butyrate producing circuit in reducing symptoms of liver
inflammation and fibrosis, a bile duct ligation model is used. A
Nissle control (SYN-UCD107, kanamycin resistant Nissle), an
arginine producing strain (SYN-UCD305), a butyrate producing strain
(SYN-UCD502), and a strain producing both butyrate and arginine
(SYN-UCD605) are compared in the study. ALT/AST levels, fibrosis
(portal, perisinusoidal and total) and hepatic inflammation are the
primary endpoints of the study; overall animal health is the
secondary endpoint of the study.
[0789] Animals (C57BL6, 8 weeks) are treated by oral gavage with
either H2O control (n=12), or SYN-UCD107 (n=12; kanamycin resistant
Nissle), or arginine producing SYN-UCD305 (n=12; comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and no antibiotic resistance), or
butyrate producing SYN-UCD502 (n=12; comprising a PydfZ-ter
butyrate cassette integrated on the chromosome) or SYN-UCD605
(n=12; comprising .DELTA.ArgR, PfnrS-ArgAfbr integrated into the
chromosome at the malEK locus, .DELTA.ThyA, and PydfZ-ter butyrate
cassette integrated on the chromosome, and no antibiotic
resistance). Bacteria are administered at a dose of >10e10
cells/ml.
[0790] In some embodiments, SYN-UCD501 (comprising wild type ArgR,
no FNR-ArgAfbr, wild type ThyA, and Logic156 (pSC101 PydfZ-ter
butyrate plasmid; amp resistance) and SYN-UCD602 (comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and Logic156 (pSC101 PydfZ-ter butyrate
plasmid; amp resistance)) are used instead of SYN-UCD502 and
SYN-UCD605.
[0791] On Day 0, bile duct ligation surgery is performed as
described in Example 40. On day 1, mice are weighed and randomized.
Mice are gavaged with 100 ul H2O, SYN-UCD107, SYN-UCD305,
SYN-UCD502 or SYN-UCD605 in the AM and PM. On day two, mice are
gavaged with 100 ul H2O, SYN798 and SYN993-in the AM and PM. On day
three, mice are gavaged with 100 ul H2O, SYN-UCD107, SYN-UCD305,
SYN-UCD502 or SYN-UCD605 in the AM and PM. At 4 h post AM dose,
blood is collected for ALT/AST analysis. On days 4-6, mice are
gavaged with 100 ul H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502 or
SYN-UCD605 in the AM and PM. On day 7, mice are gavaged with 100 ul
H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502 or SYN-UCD605 in the AM and
PM. At 4 h post AM dose, blood is collected for ALT/AST analysis.
On days 8-9, mice are gavaged with 100 ul H2O, SYN-UCD107,
SYN-UCD305, SYN-UCD502 or SYN-UCD605 in the AM and PM. On day 10,
mice are gavaged with 100 ul H2O, SYN-UCD107, SYN-UCD305,
SYN-UCD502 or SYN-UCD605 in the AM and PM. At 4 h post AM dose,
blood is collected for ALT/AST analysis. On days 11-13, mice are
gavaged with 100 ul H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502 or
SYN-UCD605 in the AM and PM. On day 14, animals are gavaged with
100 ul H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502 or SYN-UCD605 in the
AM. Then, 4 h post dose animals are euthanized, and blood is
collected by cardiac bleed for ALT/AST analysis. The liver tissue
is harvested for fibrosis analysis by histological assessment.
Example 42
Bile Duct Ligation Procedure
Bile Duct Ligation
Pre-Surgical Preparation:
[0792] During the complete experimentation, the animal is kept on a
warming plate at a temperature of 37.degree. C., permanently
connected to an anesthesia system, and the operational area is
covered overall with fluid-impermeable, self-adhesive drapes.
[0793] The mouse is anaesthetized with inhalation of 4 vol %
isoflurane in 100% oxygen at a flow rate of 4 L/min for the
induction of the anesthesia. The depth of anesthetization is
sufficient when the following vital criteria are reached: regular
spontaneous breathing, no reflex after setting of pain stimuli
between toes, and no response to pain. The abdominal fur of the
mouse is shaved with an electric fur shaver and the eyes are
protected from drying out by usage of eye and nose ointment. The
mouse is placed on a 37.degree. C. heated hot plate, the mouse
snout is inserted in the Fluovac mask of a Fluovac anesthesia
system, and the legs of the animal are fixed with stripes of silk
tape. Anesthesia of the mouse is maintained by inhalation of 1.5-3
vol % isoflurane in 100% oxygen at a flow rate of 1 L/min and
induct perioperative analgesia via intraperitoneal injection of
buprenorphine solution (0.1 mg/kg BW dissolved in 0.9% NaCl
solution).
[0794] The shaved abdominal skin is sterilized with a gauze swab
that is moistened with a standard antiseptic, ready to use
alcoholic solution for preoperative treatment of the skin.
Surgical Procedures:
[0795] The abdomen is opened with a midline laparotomy of a length
of approximately 2 cm by cutting the cutis plus fascia at the same
time with an 11.5 cm surgical scissor. The connective tissue on top
of the peritoneum is dissected by using the scissor as a spreader.
The peritoneum is cut along the linea alba to open the peritoneal
cavity. The cavity is enlarged by inserting a holding suture in the
sternum, raising the filament of the suture, and fixing it on top
of the Fluovac mask. The operation area is spread by inserting a
Colibri retractor in the peritoneal cavity. The liver is lifted
with a moisturized (0.9% NaCl solution) cotton swab so that the
ventral side of it sticks to the diaphragm and the hilum is clearly
visible. The bile duct is expoed by caudal movement of the gut. The
bile duct is separated carefully from the flanking portal vein and
hepatic artery using a micro-serrations forceps. The 5-0 suture is
placed around the bile duct and secured with two surgical knots.
When tying the knots the tractive force is increased continuously
to ensure effective obstruction without severing the bile duct. A
second cranial ligation is added in the same manner without
dissecting the bile duct in between. The ends of the sutures are
cut, the sternum lowered, and the retractor removed. The peritoneal
cavity is rinsed with 0.9% NaCl solution and the abdominal organs
replaced to the physiological positions. Both abdominal layers
(peritoneum and cutis plus facia) are closed with separate running
sutures with 6-0 Mersilk. The ends of the sutures are cut and the
operation area is sterilized with a gauze swab moistened with
antiseptic solution.
Postoperative Treatment and Follow-Up:
[0796] The mouse is allowed to recover in a cage warmed up by an
infrared lamp until the mouse is fully awake and active.
Afterwards, the mouse is moved to a normal cage and provided ad
libitum access to water and food. After the surgery, the animals
are monitored at regular intervals and follow-up postoperative
treatments are carried out with suitable analgesia (e.g.,
buprenorphine solution) following the local recommendation of the
internal animal care and use committees. Animals are kept with free
access to food and water ad libitum until the end of the
experiment.
Example 43
TAA Model of Hepatic Encephalopathy
[0797] TAA treatment of mice has previously been employed in the
literature to model increased blood ammonia levels associated with
UCDs, acute and chronic liver disease and HE (Wallace M C, et al.,
Lab Anim. 2015 April; 49(1 Suppl):21-9. Standard operating
procedures in experimental liver research: thioacetamide model in
mice and rat)s. In some embodiments, a TAA-induced mouse model of
hyperammonemia is employed to investigate the duration of activity
of the genetically engineered bacteria and to generate additional
data to support this approach to the treatment of hepatic
encephalopathy.
[0798] To determine the efficacy of a strain comprising an arginine
and butyrate producing circuit in alleviating symptoms of liver
inflammation and fibrosis, Nissle control (SYN-UCD107, kanamycin
resistant Nissle), an arginine producing strain (SYN-UCD305), a
butyrate producing strain (SYN-UCD502), and a strain producing both
butyrate and arginine (SYN-UCD605) are compared in a TAA model
study. ALT/AST levels, fibrosis (portal, perisinusoidal and total)
and hepatic inflammation are the primary endpoints of the study.
Overall animal health is the secondary endpoint of the study.
[0799] To investigate the effects of engineered bacteria on
prolonged elevations of blood ammonia, the bacteria are
administered to C57BL6 mice that are also administered a dose of
300 mpk thioacetamide (TAA).
[0800] C57BL6 (10 weeks old) are administered one daily dose of
SYN-UCD107, or SYN-UCD305 (n=12), SYN-UCD502 (n=12), or SYN-UCD605
(n=12) (100 ul of >1.times.10.sup.10 cells/ml) or vehicle
control. Alternatively, mice are administered 2 daily doses of
bacteria (100 ul of >1.times.10.sup.10 cells/ml) (n=5 for each
treatment group), once in the AM and once in the PM. After three
days of pre-dosing with the bacteria, the mice are treated
intraperitoneally with thioacetamide (TAA) at 300 mpk or with H2O
as control. Alternatively, the mice are treated twice daily, once
in the AM and once in the PM with 250 mpk. The duration of the
study is five days. Ammonium levels are measured and overall health
survival, body weight change is monitored.
[0801] In brief, animals are acclimated for 7 days. On day 1 of the
time course, animals are weighed, bled to measure baseline ALT/AST
and collect fecal pellets (per cage), and are randomized based on
ALT/AST levels. Animals are dosed by oral gavage either once or
twice (AM and PM) with H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502, or
SYN-UCD605 (100 ul/dose/animal). Water is changed to H2O (+)20
mg/ml ATC. On day 2, animals are dosed by oral gavage either once
or twice (AM and PM) with H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502,
or SYN-UCD605 (100 ul/dose/animal). On day 3, animals are weighed
and dosed by oral gavage either once or twice (AM and PM) with H2O,
SYN-UCD107, SYN-UCD305, SYN-UCD502, or SYN-UCD605 (100
ul/dose/animal). Additionally, animals are dosed intraperitoneally
with 300 mpk TAA (or saline control). Alternatively, animals are
dosed with 250 mpk TAA (or saline control) once in the AM and once
in the PM. On day 4, animals are weighed and blood is collected for
ALT/AST analysis. Fecal pellets are collected per cage. Animals are
dosed per oral gavage either once or twice (AM and PM) with H2O,
SYN-UCD107, SYN-UCD305, SYN-UCD502, or SYN-UCD605 (100
ul/dose/animal). Animals may also be dosed with 250 mpk TAA (or
saline control). On day 5, animals are weighed and blood is
collected for ALT/AST analysis. Fecal pellets are collected (per
cage). Animals are dosed by oral gavage either once or twice (AM
and PM) with H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502, or SYN-UCD605
(100 ul/dose/animal). ALT/AST levels, bacterial load in the fecal
pellets, and overall health survival, and body weight changes are
monitored. The liver tissue is harvested for fibrosis analysis by
histological assessment.
Example 44
Carbontetrachloride (CCl4) Model of Hepatic Encephalopathy
[0802] CCl4 is often used to induce hepaticfibrosis and cirrhosis
in animals because the underlying iochemical mechanisms and
histological characteristics are similar to those observed in human
liver cirrhosis (Nhung et al., Establishment of a standardized
mouse model of hepatic fibrosis for biomedical research; Biomedical
Research and Therapy 2014, 1(2):43-49).
[0803] CYP2E1 is an enzyme which is expressed in perivenular
hepatocytes, and which converts CCl4 into a CCl3+ radical. The
accumulation of the CCl3+ radical causes centrilobular necrosis and
changes the permeability of the hepatocyte plasma and mitochondrial
membranes. As a result, an increase in inflammation and
fibrogenesis, and extracellular matrix deposition is observed.
Chronic CCl4 exposure causes the formation of nodules and fibrosis,
products of the wound healing process. CCl4 treatment has been
shown to cause fibrosis after 2-4 weeks, significant bridging
fibrosis after 5-7 weeks, cirrhosis after 9-11 weeks, and
micronodular cirrhosis after 10-20 weeks (Nhung et al.,
Establishment of a standardized mouse model of hepatic fibrosis for
biomedical research; Biomedical Research and Therapy 2014,
1(2):43-49, and references therein).
[0804] To determine the efficacy of a strain comprising an arginine
and butyrate producing circuit in alleviating symptoms of liver
inflammation and fibrosis, a CCl4 mouse model of liver cirrhosis is
used. A Nissle control (SYN-UCD107, kanamycin resistant Nissle), an
arginine producing strain (SYN-UCD305), a butyrate producing strain
(SYN-UCD502), and a strain producing both butyrate and arginine
(SYN-UCD605) are compared in the study. ALT/AST levels, fibrosis
(portal, perisinusoidal and total) and hepatic inflammation are the
primary endpoints of the study. Overall animal health is the
secondary endpoint of the study. Study duration is 8 weeks.
[0805] Animals (C57BL6, 8 weeks) are treated by oral gavage with
either H2O control (n=12), or SYN-UCD107 (n=12; kanamycin resistant
Nissle), or arginine producing SYN-UCD305 (n=12; comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and no antibiotic resistance), or
butyrate producing SYN-UCD502 (n=12; comprising wild type ArgR, no
FNR-ArgAfbr, wild type ThyA, and a PydfZ-ter butyrate cassette
integrated on the chromosome) or SYN-UCD605 (n=12; comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, PydfZ-ter butyrate cassette integrated on
the chromosome, and no antibiotic resistance. Bacteria are
administered at a dose of >10e10 cells/ml in 100 ul.
[0806] In some embodiments, SYN-UCD501 (comprising Wild type ArgR,
no FNR-ArgAfbr, wild type ThyA, and Logic156 (pSC101 PydfZ-ter
butyrate plasmid; amp resistance) and SYN-UCD602 (comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and Logic156 (pSC101 PydfZ-ter butyrate
plasmid; amp resistance)) are used instead of SYN-UCD502 and
SYN-UCD605.
[0807] On Day 1, mice are weighed and randomized. Animals are
gavaged with 100 ul H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502, or
SYN-UCD605 in the AM. Additionally animals are gavaged with olive
oil (sham control) or 1 ml/kg CCL4 in olive oil (all other
treatment groups). Animals are gavaged with 100 ul H2O, SYN-UCD107,
SYN-UCD305, SYN-UCD502, or SYN-UCD605 in the PM.
[0808] Through Week 1-8, animals are gavaged BID with 100 ul H2O,
SYN-UCD107, SYN-UCD305, SYN-UCD502, or SYN-UCD605. Additionally,
animals are gavaged 3.times./week with olive oil (sham control) or
1 ml/kg CCL4 in olive oil (all other treatment groups). Animals are
weighed 3.times./week, and blood for ALT/AST analysis is collected
1.times./week.
[0809] At the end of Week 8 animals are gavaged with 100 ul with
100 ul H2O, SYN-UCD107, SYN-UCD305, SYN-UCD502, or SYN-UCD605 in
the AM. At 4 h post dose, animals are weighed, euthanized and blood
is collected by cardiac bleed for ALT/AST analysis. The liver is
harvested for fibrosis analysis by histological assessment.
Example 45
Efficacy of Butyrate-Expressing Bacteria in a DSS Mouse Model
[0810] Bacteria harboring the butyrate cassettes described above
are grown overnight in LB. Bacteria are then diluted 1:100 into LB
containing a suitable selection marker, e.g., ampicillin, and grown
to an optical density of 0.4-0.5 and then pelleted by
centrifugation. Bacteria are resuspended in phosphate buffered
saline and 100 microliters is administered by oral gavage to mice.
Damage to the gut is induced in mice by supplementing drinking
water with 3% dextran sodium sulfate for 7 days prior to bacterial
gavage. Mice are treated daily for 1 week and bacteria in stool
samples are detected by plating stool homogenate on agar plates
supplemented with a suitable selection marker, e.g., ampicillin.
After 5 days of bacterial treatment, gut damage is scored in live
mice using endoscopy. Endoscopic damage score is determined by
assessing colon translucency, fibrin attachment, mucosal and
vascular pathology, and/or stool characteristics. Mice are
sacrificed and colonic tissues are isolated. Distal colonic
sections are fixed and scored for inflammation and ulceration.
Colonic tissue is homogenized and measurements are made for
myeloperoxidase activity using an enzymatic assay kit and for
cytokine levels (IL-1.beta., TNF-.alpha., IL-6, IFN-.gamma. and
IL-10).
Example 46
Generating a DSS-Induced Mouse Model of HE
[0811] The genetically engineered bacteria described can be tested
in the dextran sodium sulfate (DSS)-induced mouse model. The
administration of DSS to animals results in chemical injury to the
intestinal epithelium, allowing proinflammatory intestinal contents
(e.g., luminal antigens, enteric bacteria, bacterial products) to
disseminate and trigger inflammation (Low et al., 2013). To prepare
mice for DSS treatment, mice are labeled using ear punch, or any
other suitable labeling method. Labeling individual mice allows the
investigator to track disease progression in each mouse, since mice
show differential susceptibilities and responsiveness to DSS
induction. Mice are then weighed, and if required, the average
group weight is equilibrated to eliminate any significant weight
differences between groups. Stool is also collected prior to DSS
administration, as a control for subsequent assays. Exemplary
assays for fecal markers of inflammation (e.g., cytokine levels or
myeloperoxidase activity) are described below.
[0812] For DSS administration, a 3% solution of DSS (MP
Biomedicals, Santa Ana, Calif.; Cat. No. 160110) in autoclaved
water is prepared. Cage water bottles are then filled with 100 mL
of DSS water, and control mice are given the same amount of water
without DSS supplementation. This amount is generally sufficient
for 5 mice for 2-3 days. Although DSS is stable at room
temperature, both types of water are changed every 2 days, or when
turbidity in the bottles is observed.
[0813] Acute, chronic, and resolving models of intestinal
inflammation are achieved by modifying the dosage of DSS (usually
1-5%) and the duration of DSS administration (Chassaing et al.,
2014). For example, acute and resolving gut damage may be achieved
after a single continuous exposure to DSS over one week or less,
whereas chronic gut damage is typically induced by cyclical
administration of DSS punctuated with recovery periods (e.g., four
cycles of DSS treatment for 7 days, followed by 7-10 days of
water).
[0814] FIG. 53D shows that butyrate produced in vivo in DSS mouse
models under the control of an FNR promoter can be gut protective.
LCN2 and calprotectin are both a measure of gut barrier disruption
(measure by ELISA in this assay). FIG. 53D shows that Syn 363 (ter
substitution) reduces inflammation and/or protects gut barrier as
compared to Syn 94 (wildtype Nissle).
Example 47
Monitoring Disease Progression In Vivo
[0815] Following initial administration of DSS, stool is collected
from each animal daily, by placing a single mouse in an empty cage
(without bedding material) for 15-30 min. However, as DSS
administration progresses and inflammation becomes more robust, the
time period required for collection increases. Stool samples are
collected using sterile forceps, and placed in a microfuge tube. A
single pellet is used to monitor occult blood according to the
following scoring system: 0, normal stool consistency with negative
hemoccult; 1, soft stools with positive hemoccult; 2, very soft
stools with traces of blood; and 3, watery stools with visible
rectal bleeding. This scale is used for comparative analysis of
intestinal bleeding. All remaining stool is reserved for the
measurement of inflammatory markers, and frozen at -20.degree.
C.
[0816] The body weight of each animal is also measured daily. Body
weights may increase slightly during the first three days following
initial DSS administration, and then begin to decrease gradually
upon initiation of bleeding. For mouse models of acute colitis, DSS
is typically administered for 7 days. However, this length of time
may be modified at the discretion of the investigator.
Example 48
In Vivo Efficacy of Genetically Engineered Bacteria Following DSS
Induction
[0817] The genetically engineered bacteria described herein can be
tested in DSS-induced animal models of HE. Bacteria are grown
overnight in LB supplemented with the appropriate antibiotic.
Bacteria are then diluted 1:100 in fresh LB containing selective
antibiotic, grown to an optical density of 0.4-0.5, and pelleted by
centrifugation. Bacteria are then resuspended in phosphate buffered
saline (PBS). Gut damage is induced in mice by supplementing
drinking water with 3% DSS for 7 days prior to bacterial gavage. On
day 7 of DSS treatment, 100 .mu.L of bacteria (or vehicle) is
administered to mice by oral gavage. Bacterial treatment is
repeated once daily for 1 week, and bacteria in stool samples are
detected by plating stool homogenate on selective agar plates.
[0818] After 5 days of bacterial treatment, gut damage is scored in
live mice using the Coloview system (Karl Storz Veterinary
Endoscopy, Goleta, Calif.). In mice under 1.5-2.0% isoflurane
anesthesia, colons are inflated with air and approximately 3 cm of
the proximal colon can be visualized (Chassaing et al., 2014).
Endoscopic damage is scored by assessing colon translucency (score
0-3), fibrin attachment to the bowel wall (score 0-3), mucosal
granularity (score 0-3), vascular pathology (score 0-3), stool
characteristics (normal to diarrhea; score 0-3), and the presence
of blood in the lumen (score 0-3), to generate a maximum score of
18. Mice are sacrificed and colonic tissues are isolated using
protocols described in Examples 8 and 9. Distal colonic sections
are fixed and scored for inflammation and ulceration. Remaining
colonic tissue is homogenized and cytokine levels (e.g.,
IL-1.beta., TNF-.alpha., IL-6, IFN-.gamma., and IL-10), as well as
myeloperoxidase activity, are measured using methods described
below.
Example 49
Euthanasia Procedures for Rodent Models of HE
[0819] Four and 24 hours prior to sacrifice,
5-bromo-2'-deooxyuridine (BrdU) (Invitrogen, Waltham, Mass.; Cat.
No. B23151) may be intraperitoneally administered to mice, as
recommended by the supplier. BrdU is used to monitor intestinal
epithelial cell proliferation and/or migration via
immunohistochemistry with standard anti-BrdU antibodies (Abcam,
Cambridge, Mass.).
[0820] On the day of sacrifice, mice are deprived of food for 4
hours, and then gavaged with FITC-dextran tracer (4 kDa, 0.6 mg/g
body weight). Fecal pellets are collected, and mice are euthanized
3 hours following FITC-dextran administration. Animals are then
cardiac bled to collect hemolysis-free serum. Intestinal
permeability correlates with fluorescence intensity of
appropriately diluted serum (excitation, 488 nm; emission, 520 nm),
and is measured using spectrophotometry. Serial dilutions of a
known amount of FITC-dextran in mouse serum are used to prepare a
standard curve.
[0821] Alternatively, intestinal inflammation is quantified
according to levels of serum keratinocyte-derived chemokine (KC),
lipocalin 2, calprotectin, and/or CRP-1. These proteins are
reliable biomarkers of inflammatory disease activity, and are
measured using DuoSet ELISA kits (R&D Systems, Minneapolis,
Minn.) according to manufacturer's instructions. For these assays,
control serum samples are diluted 1:2 or 1:4 for KC, and 1:200 for
lipocalin 2. Samples from DSS-treated mice require a significantly
higher dilution.
Example 42
Non-Obese Diabetes (NOD) Model of Hepatic Encephalopathy
[0822] NOD mice can be used as an in vivo model for testing the
efficacy of bacteria comprising a gut-barrier enhancing circuit,
e.g., a butyrate biosynthetic cassette, as these mice exhibit a
pronounced "leaky gut" phenotype, which is evidenced by a decrease
in the level of tight junction proteins (e.g., occludin, zonula
occludin, mucin, E-cadherin).
[0823] To determine the efficacy of a strain comprising an arginine
and butyrate producing circuit in alleviating symptoms associated
with "leaky gut", a NOD mouse model is used. NOD mice result from
the autoimmune destruction of pancreatic islet .beta. cells. A
Nissle control (SYN-UCD107, kanamycin resistant Nissle), an
arginine producing strain (SYN-UCD305), a butyrate producing strain
(SYN-UCD502), and a strain producing both butyrate and arginine
(SYN-UCD605) are compared in the study. Epithelial gut integrity
(occludin and other tight junction markers) and gut inflammation
(inflammatory biomarkers, e.g., IL-1A, IL-6, TNFa, IL-21) are the
primary endpoints of the study. Overall animal health is the
secondary endpoint of the study. Study duration is 8 weeks.
[0824] Animals (C57BL6, 8 weeks) are treated by oral gavage with
either H2O control (n=12), or 100 mM butyrate (n=12), or arginine
producing SYN-UCD305 (n=12; comprising .DELTA.ArgR, PfnrS-ArgAfbr
integrated into the chromosome at the malEK locus, .DELTA.ThyA, and
no antibiotic resistance), or butyrate producing SYN-UCD502 (n=12;
comprising wild type ArgR, no FNR-ArgAfbr, wild type ThyA, and a
PydfZ-ter butyrate cassette integrated on the chromosome) or
SYN-UCD605 (n=12; comprising .DELTA.ArgR, PfnrS-ArgAfbr integrated
into the chromosome at the malEK locus, .DELTA.ThyA, PydfZ-ter
butyrate cassette integrated on the chromosome, and no antibiotic
resistance. Bacteria are administered at a dose of >10e10
cells/ml in 100 ul.
[0825] In some embodiments, SYN-UCD501 (comprising Wild type ArgR,
no FNR-ArgAfbr, wild type ThyA, and Logic156 (pSC101 PydfZ-ter
butyrate plasmid; amp resistance) and SYN-UCD602 (comprising
.DELTA.ArgR, PfnrS-ArgAfbr integrated into the chromosome at the
malEK locus, .DELTA.ThyA, and Logic156 (pSC101 PydfZ-ter butyrate
plasmid; amp resistance)) are used instead of SYN-UCD502 and
SYN-UCD605.
[0826] On Day 1, mice are weighed and randomized. Animals are
gavaged with 100 ul H2O, 100 mM butyrate, SYN-UCD305, SYN-UCD502,
or SYN-UCD605 in the AM. Animals are gavaged with 100 ul H2O, 100
mM butyrate, SYN-UCD305, SYN-UCD502, or SYN-UCD605 in the PM.
Animals are gavaged BID with 100 ul H2O, 100 mM butyrate,
SYN-UCD305, SYN-UCD502, or SYN-UCD605. Animals are weighed
daily.
[0827] On day 5, mice are fasted for 4 h and then gavaged with 0.6
mg/g FITC-dextran (40 kD). 3 h post FITC-dex administration mice
are weighed, and blood is collected by cardiac bleed and colons and
fecal pellets are harvested.
[0828] Haptoglobin/zonulin and Lcn2 are measured. RNA levels of
TJP1, OCLN, CLDN25, and EPCAM are measured in colon samples
(increased levels of these markers indicate therapeutic effect).
RNA levels of inflammatory biomarkers are measured in the blood
samples (decreased levels of these biomarkers indicate therapeutic
effect).
Example 51
GABA Transport and Metabolic Circuits
[0829] In addition to the ammonia conversion circuit described
above, the E. coli Nissle bacteria further comprise one or more
GABA transport and/or one or more GABA metabolic circuits.
Genetically engineered strains comprising at least one GABA
transport circuit comprise a gene encoding an exemplary GABA
transport protein, such as GabP (SEQ ID NO: 105, Table 48; SEQ ID
NO: 106, Table 49), and are constructed using methods described
above. Genetically engineered strains comprising at least one GABA
metabolic circuit comprise genes encoding enzymes required for GABA
catabolism, including, but not limited to GSST and SSDH, and are
constructed using methods described above.
[0830] The genes encoding GabP, GSST, and SSDH are expressed under
the control of a tetracycline-inducible promoter, a FNR promoter
selected from SEQ ID NOs: 18-29, or a promoter induced by
HE-related molecules or metabolites. The genes encoding GabP, GSST,
and SSDH may be expressed under the control of the same or
different promoters. As discussed herein, other promoters may be
used. The genes encoding GabP, GSST, and SSDH are expressed on a
high-copy plasmid, a low-copy plasmid, or a chromosome. The genes
encoding GabP, GSST, and SSDH are inserted into the bacterial
genome at one or more of the following insertion sites in E. coli
Nissle: malE/K, araC/BAD, lacZ, thyA, malP/T. Any suitable
insertion site may be used, see, e.g., FIG. 18.
TABLE-US-00054 TABLE 48 Amino acid sequence of GabP transporter
(SEQ ID NO: 105) MGQSSQPHELGGGLKSRHVTMLSIAGVIGASLFVGSSVAIAEAGPAVLLA
YLFAGLLVVMIMRMLAEMAVATPDTGSFSTYADKAIGRWAGYTIGWLYWW
FWVLVIPLEANIAAMILHSWVPGIPIWLFSLVITLALTGSNLLSVKNYGE
FEFWLALCKVIAILAFIFLGAVAISGFYPYAEVSGISRLWDSGGFMPNGF
GAVLSAMLITMFSFMGAEIVTIAAAESDTPEKHIVRATNSVIWRISIFYL
CSIFVVVALIPWNMPGLKAVGSYRSVLELLNIPHAKLIMDCVILLSVTSC
LNSALYTASRMLYSLSRRGDAPAVMGKINRSKTPYVAVLLSTGAAFLTVV
VNYYAPAKVFKFLIDSSGAIALLVYLVIAVSQLRMRKILRAEGSEIRLRM
WLYPWLTWLVIGFITFVLVVMLFRPAQQLEVISTGLLAIGIICTVPIMAR
WKKLVLWQKTPVHNTR
TABLE-US-00055 TABLE 49 Codon optimized polynucleotide sequence of
GabP transporter (SEQ ID NO: 106)
ATGGGACAGTCTTCACAACCACACGAACTTGGGGGTGGATTGAAATCGCG
CCATGTGACCATGTTAAGTATCGCAGGCGTGATTGGCGCCTCCTTATTTG
TGGGGTCCTCCGTGGCGATTGCAGAGGCGGGTCCGGCTGTACTTTTGGCA
TATCTTTTTGCGGGTTTACTGGTTGTGATGATCATGCGCATGCTTGCCGA
AATGGCTGTGGCCACGCCGGACACGGGGTCATTTTCCACTTATGCGGACA
AGGCGATTGGCCGCTGGGCCGGGTACACAATCGGGTGGCTGTATTGGTGG
TTCTGGGTGTTAGTTATCCCCTTGGAGGCCAACATCGCCGCAATGATTCT
GCACTCCTGGGTTCCGGGTATCCCGATCTGGCTGTTCAGCTTGGTGATCA
CCCTGGCACTGACGGGCAGCAACTTATTGAGTGTGAAAAACTATGGAGAG
TTTGAATTTTGGCTGGCCCTGTGTAAAGTCATTGCTATCTTGGCATTCAT
TTTTTTAGGAGCGGTAGCAATCAGTGGCTTCTACCCTTATGCAGAAGTTT
CGGGGATTTCCCGTCTTTGGGATAGTGGCGGATTCATGCCAAACGGGTTT
GGAGCTGTACTGTCAGCCATGTTGATTACCATGTTTAGCTTTATGGGTGC
CGAGATCGTGACAATCGCCGCAGCCGAGAGTGATACCCCGGAAAAGCACA
TTGTTCGTGCGACGAATTCGGTAATTTGGCGTATTTCGATTTTTTACTTA
TGCTCCATTTTCGTTGTGGTCGCCCTTATCCCCTGGAACATGCCAGGCTT
AAAAGCAGTAGGCAGCTACCGCTCAGTCCTGGAATTACTGAACATTCCTC
ACGCGAAGTTAATTATGGATTGCGTAATCCTGTTATCGGTAACGAGCTGC
CTTAACAGTGCTCTGTACACGGCTTCACGTATGCTGTACTCTTTAAGTCG
CCGTGGCGATGCACCTGCCGTTATGGGCAAGATTAACCGCAGTAAGACGC
CGTATGTAGCTGTTTTGCTGTCGACTGGAGCTGCGTTTCTTACAGTCGTA
GTAAACTATTACGCACCAGCTAAAGTTTTCAAATTCCTTATTGATTCGTC
TGGGGCAATCGCACTTCTGGTGTACCTGGTCATCGCGGTGTCACAACTTC
GCATGCGCAAGATCTTGCGTGCGGAGGGCAGTGAGATTCGTTTGCGTATG
TGGCTGTATCCGTGGCTGACGTGGCTTGTTATTGGTTTCATTACTTTTGT
GTTGGTAGTGATGCTGTTTCGTCCAGCGCAACAGCTGGAGGTGATTTCTA
CCGGACTGTTGGCAATCGGCATCATCTGTACCGTCCCAATCATGGCTCGC
TGGAAAAAGTTGGTCTTATGGCAGAAGACCCCTGTACACAACACCCGT
[0831] In some embodiments, the genetically engineered bacteria
comprise the nucleic acid sequence of SEQ ID NO: 106 or a
functional fragment thereof. In some embodiments, the genetically
engineered bacteria comprise a nucleic acid sequence that, but for
the redundancy of the genetic code, encodes the same polypeptide as
SEQ ID NO: 106 or a functional fragment thereof. In some
embodiments, genetically engineered bacteria comprise a nucleic
acid sequence that is at least about 80%, at least about 85%, at
least about 90%, at least about 95%, or at least about 99%
homologous to the DNA sequence of SEQ ID NO: 106 or a functional
fragment thereof, or a nucleic acid sequence that, but for the
redundancy of the genetic code, encodes the same polypeptide as SEQ
ID NO: 106 or a functional fragment thereof.
Example 52
Manganese Transport Circuit
[0832] In addition to the circuits described above, the E. coli
Nissle bacteria further comprise one or more manganese transport
circuits. Genetically engineered strains comprising at least one
manganese transport circuit comprise a gene encoding an exemplary
manganese transport protein, such as MntH (SEQ ID NO: 107, Table
50, SEQ ID NO: 108, Table 51), and are constructed using methods
described above.
[0833] The gene encoding MntH is expressed under the control of a
tetracycline-inducible promoter, a FNR promoter selected from SEQ
ID NOs: 18-29, or a promoter induced by HE-related molecules or
metabolites. As discussed herein, other promoters may be used. The
gene encoding MntH is expressed on a high-copy plasmid, a low-copy
plasmid, or a chromosome. The gene encoding MntH is inserted into
the bacterial genome at one or more of the following insertion
sites in E. coli Nissle: malE/K, araC/BAD, lacZ, thyA, malP/T. Any
suitable insertion site may be used, see, e.g., FIG. 18.
TABLE-US-00056 TABLE 50 Amino acid sequence of MntH transporter
(SEQ ID NO: 107) MTNYRVESSSGRAARKMRLALMGPAFIAAIGYIDPGNFATNIQAGASFGY
QLLWVVVWANLMAMLIQILSAKLGIATGKNLAEQIRDHYPRPVVWFYWVQ
AEIIAMATDLAEFIGAAIGFKLILGVSLLQGAVLTGIATFLILMLQRRGQ
KPLEKVIGGLLLFVAAAYIVELIFSQPNLAQLGKGMVIPSLPTSEAVFLA
AGVLGATIMPHVIYLHSSLTQHLHGGSRQQRYSATKWDVAIAMTIAGFVN
LAMMATAAAAFHFSGHTGVADLDEAYLTLQPLLSHAAATVFGLSLVAAGL
SSTVVGTLAGQVVMQGFIRFHIPLWVRRTVTMLPSFIVILMGLDPTRILV
MSQVLLSFGIALALVPLLIFTSDSKLMGDLVNSKRVKQTGWVIVVLVVAL NIWLLVGTALGL
TABLE-US-00057 TABLE 51 Polynucleotide sequence of MntH transporter
(SEQ ID NO: 108) ATGACCAATTATCGTGTTGAAAGTAGTAGTGGCCGCGCGGCTCGTAAAAT
GCGTCTGGCCTTAATGGGCCCGGCGTTTATTGCTGCGATTGGATACATTG
ATCCGGGCAATTTCGCTACAAACATCCAAGCAGGTGCATCCTTCGGTTAC
CAGCTTCTGTGGGTAGTGGTATGGGCTAACCTGATGGCCATGCTTATTCA
AATTCTTTCAGCTAAGCTTGGTATTGCCACAGGAAAGAATTTAGCCGAGC
AGATTCGTGACCACTATCCCCGCCCCGTGGTCTGGTTCTATTGGGTCCAG
GCAGAGATTATCGCGATGGCGACTGATTTAGCCGAATTTATTGGGGCAGC
TATTGGATTTAAGCTGATCCTTGGCGTATCTCTGTTGCAAGGCGCGGTAT
TGACCGGAATTGCAACCTTTTTGATTCTTATGTTGCAACGTCGTGGGCAG
AAGCCTCTGGAAAAAGTCATCGGCGGGTTATTGCTTTTTGTTGCCGCGGC
CTACATTGTGGAACTGATCTTTTCTCAACCTAACCTGGCGCAGCTTGGTA
AAGGCATGGTAATCCCGTCACTTCCTACATCTGAGGCAGTATTCTTAGCA
GCCGGCGTCTTGGGCGCAACTATCATGCCCCATGTCATCTACTTACACAG
TTCTCTGACTCAGCACTTACACGGTGGGTCGCGCCAACAGCGTTACTCCG
CAACAAAGTGGGACGTTGCAATTGCCATGACCATTGCCGGTTTTGTTAAC
CTGGCGATGATGGCCACGGCTGCTGCCGCCTTTCATTTCAGTGGCCACAC
TGGTGTAGCCGATCTGGATGAGGCATACCTGACCTTGCAGCCTCTGTTGT
CTCATGCAGCCGCCACCGTTTTTGGTTTAAGCTTAGTAGCCGCCGGCTTG
AGTAGCACGGTGGTAGGCACATTGGCTGGACAGGTCGTGATGCAAGGTTT
CATTCGTTTCCATATTCCGTTATGGGTACGTCGCACGGTAACGATGCTGC
CGTCATTTATCGTCATCCTGATGGGATTAGACCCGACGCGCATCCTGGTA
ATGTCGCAAGTTTTACTGAGCTTTGGAATCGCGTTGGCCCTGGTGCCATT
ACTTATCTTCACTAGCGATAGTAAGTTGATGGGTGATCTTGTCAATAGCA
AACGTGTGAAGCAAACAGGCTGGGTCATTGTGGTACTGGTTGTGGCCTTA
AACATTTGGTTGTTAGTGGGCACGGCCCTTGGCTTG
Example 53
Circuit Comprising TesB
[0834] The nucleic acid sequence of TesB is translated as
follows.
TABLE-US-00058 TABLE 52 TesB sequences tesB
ATGAGTCAGGCGCTAAAAAATTTACTGACATTGTTAAATCTGGAAAAAAT SEQ ID NO:
TGAGGAAGGACTCTTTCGCGGCCAGAGTGAAGATTTAGGTTTACGCCAGG 48
TGTTTGGCGGCCAGGTCGTGGGTCAGGCCTTGTATGCTGCAAAAGAGACC
GTCCCTGAAGAGCGGCTGGTACATTCGTTTCACAGCTACTTTCTTCGCCC
TGGCGATAGTAAGAAGCCGATTATTTATGATGTCGAAACGCTGCGTGACG
GTAACAGCTTCAGCGCCCGCCGGGTTGCTGCTATTCAAAACGGCAAACCG
ATTTTTTATATGACTGCCTCTTTCCAGGCACCAGAAGCGGGTTTCGAACA
TCAAAAAACAATGCCGTCCGCGCCAGCGCCTGATGGCCTCCCTTCGGAAA
CGCAAATCGCCCAATCGCTGGCGCACCTGCTGCCGCCAGTGCTGAAAGAT
AAATTCATCTGCGATCGTCCGCTGGAAGTCCGTCCGGTGGAGTTTCATAA
CCCACTGAAAGGTCACGTCGCAGAACCACATCGTCAGGTGTGGATCCGCG
CAAATGGTAGCGTGCCGGATGACCTGCGCGTTCATCAGTATCTGCTCGGT
TACGCTTCTGATCTTAACTTCCTGCCGGTAGCTCTACAGCCGCACGGCAT
CGGTTTTCTCGAACCGGGGATTCAGATTGCCACCATTGACCATTCCATGT
GGTTCCATCGCCCGTTTAATTTGAATGAATGGCTGCTGTATAGCGTGGAG
AGCACCTCGGCGTCCAGCGCACGTGGCTTTGTGCGCGGTGAGTTTTATAC
CCAAGACGGCGTACTGGTTGCCTCGACCGTTCAGGAAGGGGTGATGCGTA ATCACAATTAA
tesB: SEQ MSQALKNLLTLLNLEKIEEGLFRGQSEDLGLRQVFGGQVVGQALYAAKET ID NO:
109 VPEERLVHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKP
IFYMTASFQAPEAGFEHQKTMPSAPAPDGLPSETQIAQSLAHLLPPVLKD
KFICDRPLEVRPVEFHNPLKGHVAEPHRQVWIRANGSVPDDLRVHQYLLG
YASDLNFLPVALQPHGIGFLEPGIQIATIDHSMWFHRPFNLNEWLLYSVE
STSASSARGFVRGEFYTQDGVLVASTVQEGVMRNHN
[0835] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 109 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 109 or a functional fragment thereof, or a nucleic acid
sequence that, but for the redundancy of the genetic code, encodes
the same polypeptide as SEQ ID NO: 109 or a functional fragment
thereof.
[0836] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 91 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 91 or a functional fragment thereof, or a nucleic acid sequence
that, but for the redundancy of the genetic code, encodes the same
polypeptide as SEQ ID NO: 91 or a functional fragment thereof.
[0837] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 93 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 93 or a functional fragment thereof, or a nucleic acid sequence
that, but for the redundancy of the genetic code, encodes the same
polypeptide as SEQ ID NO: 93 or a functional fragment thereof.
[0838] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 95 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 95 or a functional fragment thereof, or a nucleic acid sequence
that, but for the redundancy of the genetic code, encodes the same
polypeptide as SEQ ID NO: 95 or a functional fragment thereof.
[0839] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 97 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 97 or a functional fragment thereof, or a nucleic acid sequence
that, but for the redundancy of the genetic code, encodes the same
polypeptide as SEQ ID NO: 97 or a functional fragment thereof.
[0840] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 99 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 99 or a functional fragment thereof, or a nucleic acid sequence
that, but for the redundancy of the genetic code, encodes the same
polypeptide as SEQ ID NO: 99 or a functional fragment thereof.
TABLE-US-00059 TABLE 53 FNRS-fbrArgA and no antibiotic resistance
Description Sequence SEQ ID Terminator
CAAATAAAATGAAAGGCTCAGTCGAAAGACTGGGCC SEQ ID NO: 110 sequence
TTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTC CTGAGTAGGACAAAT Terminator
AGAAGGCCATCCTGACGGATGGCCTTTT SEQ ID NO: 111 FRT site SEQ ID NO: 112
FNRS GTACCAGTTGTTCTTATTGGTGGTGTTGCTTTATGG SEQ ID NO: 113 promoter
TTGCATCGTAGTAAATGGTTGTAACAAAAGCAATTT
TTCCGGCTGTCTGTATACAAAAACGCCGTAAAGTTT
GAGCGAAGTCAATAAACTCTCTACCCATTCAGGGCA ATATCTCTCTTGGATCC ArgAfbr
ATGGTAAAGGAACGTAAAACCGAGTTGGTCGAGGGA SEQ ID NO: 114
TTCCGCCATTCGGTTCCCTGTATCAATACCCACCGG
GGAAAAACGTTTGTCATCATGCTCGGCGGTGAAGCC
ATTGAGCATGAGAATTTCTCCAGTATCGTTAATGAT
ATCGGGTTGTTGCACAGCCTCGGCATCCGTCTGGTG
GTGGTCTATGGCGCACGTCCGCAGATCGACGCAAAT
CTGGCTGCGCATCACCACGAACCGCTGTATCACAAG
AATATACGTGTGACCGACGCCAAAACACTGGAACTG
GTGAAGCAGGCTGCGGGAACATTGCAACTGGATATT
ACTGCTCGCCTGTCGATGAGTCTCAATAACACGCCG
CTGCAGGGCGCGCATATCAACGTCGTCAGTGGCAAT
TTTATTATTGCCCAGCCGCTGGGCGTCGATGACGGC
GTGGATTACTGCCATAGCGGGCGTATCCGGCGGATT
GATGAAGACGCGATCCATCGTCAACTGGACAGCGGT
GCAATAGTGCTAATGGGGCCGGTCGCTGTTTCAGTC
ACTGGCGAGAGCTTTAACCTGACCTCGGAAGAGATT
GCCACTCAACTGGCCATCAAACTGAAAGCTGAAAAG
ATGATTGGTTTTTGCTCTTCCCAGGGCGTCACTAAT
GACGACGGTGATATTGTCTCCGAACTTTTCCCTAAC
GAAGCGCAAGCGCGGGTAGAAGCCCAGGAAGAGAAA
GGCGATTACAACTCCGGTACGGTGCGCTTTTTGCGT
GGCGCAGTGAAAGCCTGCCGCAGCGGCGTGCGTCGC
TGTCATTTAATCAGTTATCAGGAAGATGGCGCGCTG
TTGCAAGAGTTGTTCTCACGCGACGGTATCGGTACG
CAGATTGTGATGGAAAGCGCCGAGCAGATTCGTCGC
GCAACAATCAACGATATTGGCGGTATTCTGGAGTTG
ATTCGCCCACTGGAGCAGCAAGGTATTCTGGTACGC
CGTTCTCGCGAGCAGCTGGAGATGGAAATCGACAAA
TTCACCATTATTCAGCGCGATAACACGACTATTGCC
TGCGCCGCGCTCTATCCGTTCCCGGAAGAGAAGATT
GGGGAAATGGCCTGTGTGGCAGTTCACCCGGATTAC
CGCAGTTCATCAAGGGGTGAAGTTCTGCTGGAACGC
ATTGCCGCTCAGGCTAAGCAGAGCGGCTTAAGCAAA
TTGTTTGTGCTGACCACGCGCAGTATTCACTGGTTC
CAGGAACGTGGATTTACCCCAGTGGATATTGATTTA
CTGCCCGAGAGCAAAAAGCAGTTGTACAACTACCAG
CGTAAATCCAAAGTGTTGATGGCGGATTTAGGGTAA SEQ ID NO: 115 KanR gene
atgattgaacaagatggattgcacgcaggttctccg SEQ ID NO: 116
gccgcttgggtggagaggctattcggctatgactgg
gcacaacagacaatcggctgctctgatgccgccgtg
ttccggctgtcagcgcaggggcgcccggttcttttt
gtcaagaccgacctgtccggtgccctgaatgaactg
caggacgaggcagcgcggctatcgtggctggccacg
acgggcgttccttgcgcagctgtgctcgacgttgtc
actgaagcgggaagggactggctgctattgggcgaa
gtgccggggcaggatctcctgtcatctcaccttgct
cctgccgagaaagtatccatcatggctgatgcaatg
cggcggctgcatacgcttgatccggctacctgccca
ttcgaccaccaagcgaaacatcgcatcgagcgagca
cgtactcggatggaagccggtcttgtcgatcaggat
gatctggacgaagagcatcaggggctcgcgccagcc
gaactgttcgccaggctcaaggcgcgcatgcccgac
ggcgaggatctcgtcgtgacccatggcgatgcctgc
ttgccgaatatcatggtggaaaatggccgcttttct
ggattcatcgactgtggccggctgggtgtggcggac
cgctatcaggacatagcgttggctacccgtgatatt
gctgaagagcttggcggcgaatgggctgaccgcttc
ctcgtgctttacggtatcgccgctcccgattcgcag
cgcatcgccttctatcgccttcttgacgagttcttc
tgagcgggactctggggttcgaaatgaccgaccaag
cgacgcccaacctgccatcacgagatttcgattcca
ccgccgccttctatgaaaggttgggcttcggaatcg
ttttccgggacgccggctggatgatcctccagcgcg
gggatctcatgctggagttcttcgcccaccccagct tcaaaagcgctct KanR
ggttgggaagccctgcaaagtaaactggatggcttt SEQ ID NO: 117 promoter
cttgccgccaaggatctgatggcgcaggggatcaag
atctgatcaagagacaggatgaggatcgtttcgc CamR gene
TCATCGCAGTACTGTTGTATTCATTAAGCATCTGCC SEQ ID NO: 118
GACATGGAAGCCATCACAAACGGCATGATGAACCTG
AATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGT
ATAATATTTGCCCATGGTGAAAACGGGGGCGAAGAA
GTTGTCCATATTGGCCACGTTTAAATCAAAACTGGT
GAAACTCACCCAGGGATTGGCTGAGACGAAAAACAT
ATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTT
TTCACCGTAACACGCCACATCTTGCGAATATATGTG
TAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCA
GAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAAC
GGTGTAACAAGGGTGAACACTATCCCATATCACCAG
CTCACCGTCTTTCATTGCCATACGTAATTCCGGATG
AGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGC
CGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTT
TAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTT
ATAGGTACATTGAGCAACTGACTGAAATGCCTCAAA
ATGTTCTTTACGATGCCATTGGGATATATCAACGGT GGTATATCCAGTGATTTTTTTCTCCAT
CamR TTTAGCTTCCTTAGCTCCTGAAAATCTCGACAACTC SEQ ID NO: 119 promoter
AAAAAATACGCCCGGTAGTGATCTTATTTCATTATG
GTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTC
TCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCCGGT
ATCAACAGGGACACCAGGATTTATTTATTCTGCGAA
GTGATCTTCCGTCACAGGTAGGCGCGCC
[0841] In some embodiments, the genetically engineered bacteria
comprise the amino acid sequence of SEQ ID NO: 101 or a functional
fragment thereof. In some embodiments, genetically engineered
bacteria comprise an amino acid sequence that is at least about
80%, at least about 85%, at least about 90%, at least about 95%, or
at least about 99% homologous to the amino acid sequence of SEQ ID
NO: 101 or a functional fragment thereof, or a nucleic acid
sequence that, but for the redundancy of the genetic code, encodes
the same polypeptide as SEQ ID NO: 101 or a functional fragment
thereof.
Sequence CWU 1
1
125160DNAEscherichia coli 1gcaaaaaaac agaataaaaa tacaataatt
tcgaataatc atgcaaagag gtgtaccgtg 60260DNAEscherichia coli
2gcaaaaaaac actttaaaaa cttaataatt tcctttaatc acttaaagag gtgtaccgtg
60376DNAEscherichia coli 3agacttgcaa atgaataatc atccatatag
attgaatttt aattcattaa ggcgttagcc 60acaggaggga tctatg
76476DNAEscherichia coli 4agacttgcaa acttatactt atccatatag
attttgtttt aatttgttaa ggcgttagcc 60acaggaggga tctatg
765160DNAEscherichia coli 5tcattgttga cacacctctg gtcatgatag
tatcaatatt catgcagtat ttatgaataa 60aaatacacta acgttgagcg taataaaacc
caccagccgt aaggtgaatg ttttacgttt 120aacctggcaa ccagacataa
gaaggtgaat agccccgatg 1606160DNAEscherichia coli 6tcattgttga
cacacctctg gtcatgatag tatcaaactt catgggatat ttatctttaa 60aaatacttga
acgttgagcg taataaaacc caccagccgt aaggtgaatg ttttacgttt
120aacctggcaa ccagacataa gaaggtgaat agccccgatg
1607160DNAEscherichia coli 7catcggggct attcaccttc ttatgtctgg
ttgccaggtt aaacgtaaaa cattcacctt 60acggctggtg ggttttatta cgctcaacgt
tagtgtattt ttattcataa atactgcatg 120aatattgata ctatcatgac
cagaggtgtg tcaacaatga 1608160DNAEscherichia coli 8catcggggct
attcaccttc ttatgtctgg ttgccaggtt aaacgtaaaa cattcacctt 60acggctggtg
ggttttatta cgctcaacgt tcaagtattt ttaaagataa atatcccatg
120aagtttgata ctatcatgac cagaggtgtg tcaacaatga 160981DNAEscherichia
coli 9agcagatttg cattgattta cgtcatcatt gtgaattaat atgcaaataa
agtgagtgaa 60tattctctgg agggtgtttt g 811081DNAEscherichia coli
10agcagatttg cattgattta cgtcatcatt gtcttttaat atcttaataa ctggagtgac
60gtttctctgg agggtgtttt g 811188DNAEscherichia coli 11tttctgattg
ccattcagtg attttttatg catattttgt gattataatt tcatatttat 60ttatgcgtaa
cagggtgatc atgagatg 881288DNAEscherichia coli 12tttctgattg
ccattcagtc tttttttact tatattttgt ctttataatc ttatatttat 60ttatgcgtaa
cagggtgatc atgagatg 8813219DNAEscherichia coli 13ctaatcacgt
gaatgaatat ccagttcact ttcatttgtt gaatactttt accttctcct 60gctttccctt
aagcgcatta ttttacaaaa aacacactaa actcttcctg tctccgataa
120aagatgatta aatgaaaact catttatttt gcataaaaat tcagtgaaag
cagaaatcca 180ggctcatcat cagttaatta agcagggtgt tattttatg
21914219DNAEscherichia coli 14ctaatcacct taatgaatct tcagttcact
ttcatttgtt gaatactttt accttctcct 60gctttccctt aagcgcatta ttttacaaaa
aacacactaa actcttcctg tctccgataa 120aagatgatct tatgaaaacc
tttttatttc ttataaaaat cttgtgaaag cagaaatcca 180ggctcatcat
cagttaatta agcagggtgt tattttatg 21915233DNAEscherichia coli
15cctgaaacgt ggcaaattct actcgttttg ggtaaaaaat gcaaatactg ctgggatttg
60gtgtaccgag acgggacgta aaatctgcag gcattatagt gatccacgcc acattttgtc
120aacgtttatt gctaatcatt gacggctagc tcagtcctag gtacagtgct
agcacccgtt 180tttttgggct agaaataatt ttgtttaact ttaagaagga
gatatacata ccc 233161053DNAEscherichia coli 16gtgatccacg ccacattttg
tcaacgttta ttgctaatca cgtgaatgaa tatccagttc 60actttcattt gttgaatact
tttaccttct cctgctttcc cttaagcgca ttattttaca 120aaaaacacac
taaactcttc ctgtctccga taaaagatga ttaaatgaaa actcatttat
180tttgcataaa aattcagtga aagcagaaat ccaggctcat catcagttaa
ttaagcaggg 240tgttatttta tgacgacgat tctcaagcat ctcccggtag
gtcaacgtat tggtatcgct 300ttttccggcg gtctggacac cagtgccgca
ctgctgtgga tgcgacaaaa gggagcggtt 360ccttatgcat atactgcaaa
cctgggccag ccagacgaag aggattatga tgcgatccct 420cgtcgtgcca
tggaatacgg cgcggagaac gcacgtctga tcgactgccg caaacaactg
480gtggccgaag gtattgccgc tattcagtgt ggcgcatttc ataacaccac
tggtggactg 540acctatttca acacgacgcc gctgggccgc gccgtgaccg
gcaccatgct ggttgctgct 600atgaaagaag atggcgtgaa tatctggggt
gacggcagca cctataaagg aaacgatatc 660gaacgtttct accgttacgg
tctgctgacc aatgctgaac tgcagattta caaaccgtgg 720cttgatactg
actttattga tgaactgggt ggccgtcatg agatgtctga atttatgatt
780gcctgcggtt tcgactacaa aatgtctgtc gaaaaagctt actccacgga
ctccaacatg 840cttggtgcaa cgcatgaagc gaaggatctg gaatacctca
actccagcgt caaaatcgtc 900aacccaatta tgggcgtgaa gttttgggat
gagagcgtga aaatcccggc agaagaagtc 960acagtacgct ttgagcaagg
tcatccggtg gcgctgaacg gtaaaacctt tagcgacgac 1020gtagaaatga
tgctggaagc taaccgcatc ggc 105317734DNAEscherichia coli 17ttgacggcta
gctcagtcct aggtacagtg ctagcacccg tttttttggg ctagaaataa 60ttttgtttaa
ctttaagaag gagatataca tacccatgac gacgattctc aagcatctcc
120cggtaggtca acgtattggt atcgcttttt ccggcggtct ggacaccagt
gccgcactgc 180tgtggatgcg acaaaaggga gcggttcctt atgcatatac
tgcaaacctg ggccagccag 240acgaagagga ttatgatgcg atccctcgtc
gtgccatgga atacggcgcg gagaacgcac 300gtctgatcga ctgccgcaaa
caactggtgg ccgaaggtat tgccgctatt cagtgtggcg 360catttcataa
caccactggt ggactgacct atttcaacac gacgccgctg ggccgcgccg
420tgaccggcac catgctggtt gctgctatga aagaagatgg cgtgaatatc
tggggtgacg 480gcagcaccta taaaggaaac gatatcgaac gtttctaccg
ttacggtctg ctgaccaatg 540ctgaactgca gatttacaaa ccgtggcttg
atactgactt tattgatgaa ctgggtggcc 600gtcatgagat gtctgaattt
atgattgcct gcggtttcga ctacaaaatg tctgtcgaaa 660aagcttactc
cacggactcc aacatgcttg gtgcaacgca tgaagcgaag gatctggaat
720acctcaactc cagc 73418117DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 18atccccatca
ctcttgatgg agatcaattc cccaagctgc tagagcgtta ccttgccctt 60aaacattagc
aatgtcgatt tatcagaggg ccgacaggct cccacaggag aaaaccg
11719108DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 19ctcttgatcg ttatcaattc ccacgctgtt
tcagagcgtt accttgccct taaacattag 60caatgtcgat ttatcagagg gccgacaggc
tcccacagga gaaaaccg 10820290DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 20gtcagcataa
caccctgacc tctcattaat tgttcatgcc gggcggcact atcgtcgtcc 60ggccttttcc
tctcttactc tgctacgtac atctatttct ataaatccgt tcaatttgtc
120tgttttttgc acaaacatga aatatcagac aattccgtga cttaagaaaa
tttatacaaa 180tcagcaatat accccttaag gagtatataa aggtgaattt
gatttacatc aataagcggg 240gttgctgaat cgttaaggta ggcggtaata
gaaaagaaat cgaggcaaaa 29021433DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 21cggcccgatc
gttgaacata gcggtccgca ggcggcactg cttacagcaa acggtctgta 60cgctgtcgtc
tttgtgatgt gcttcctgtt aggtttcgtc agccgtcacc gtcagcataa
120caccctgacc tctcattaat tgctcatgcc ggacggcact atcgtcgtcc
ggccttttcc 180tctcttcccc cgctacgtgc atctatttct ataaacccgc
tcattttgtc tattttttgc 240acaaacatga aatatcagac aattccgtga
cttaagaaaa tttatacaaa tcagcaatat 300acccattaag gagtatataa
aggtgaattt gatttacatc aataagcggg gttgctgaat 360cgttaaggta
ggcggtaata gaaaagaaat cgaggcaaaa atgtttgttt aactttaaga
420aggagatata cat 43322290DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 22gtcagcataa
caccctgacc tctcattaat tgctcatgcc ggacggcact atcgtcgtcc 60ggccttttcc
tctcttcccc cgctacgtgc atctatttct ataaacccgc tcattttgtc
120tattttttgc acaaacatga aatatcagac aattccgtga cttaagaaaa
tttatacaaa 180tcagcaatat acccattaag gagtatataa aggtgaattt
gatttacatc aataagcggg 240gttgctgaat cgttaaggta ggcggtaata
gaaaagaaat cgaggcaaaa 29023173DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 23atttcctctc
atcccatccg gggtgagagt cttttccccc gacttatggc tcatgcatgc 60atcaaaaaag
atgtgagctt gatcaaaaac aaaaaatatt tcactcgaca ggagtattta
120tattgcgccc gttacgtggg cttcgactgt aaatcagaaa ggagaaaaca cct
17324305DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 24gtcagcataa caccctgacc tctcattaat
tgttcatgcc gggcggcact atcgtcgtcc 60ggccttttcc tctcttactc tgctacgtac
atctatttct ataaatccgt tcaatttgtc 120tgttttttgc acaaacatga
aatatcagac aattccgtga cttaagaaaa tttatacaaa 180tcagcaatat
accccttaag gagtatataa aggtgaattt gatttacatc aataagcggg
240gttgctgaat cgttaaggat ccctctagaa ataattttgt ttaactttaa
gaaggagata 300tacat 30525180DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 25catttcctct
catcccatcc ggggtgagag tcttttcccc cgacttatgg ctcatgcatg 60catcaaaaaa
gatgtgagct tgatcaaaaa caaaaaatat ttcactcgac aggagtattt
120atattgcgcc cggatccctc tagaaataat tttgtttaac tttaagaagg
agatatacat 18026199DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 26agttgttctt attggtggtg
ttgctttatg gttgcatcgt agtaaatggt tgtaacaaaa 60gcaatttttc cggctgtctg
tatacaaaaa cgccgtaaag tttgagcgaa gtcaataaac 120tctctaccca
ttcagggcaa tatctctctt ggatccctct agaaataatt ttgtttaact
180ttaagaagga gatatacat 19927207DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 27agttgttctt
attggtggtg ttgctttatg gttgcatcgt agtaaatggt tgtaacaaaa 60gcaatttttc
cggctgtctg tatacaaaaa cgccgcaaag tttgagcgaa gtcaataaac
120tctctaccca ttcagggcaa tatctctctt ggatccaaag tgaactctag
aaataatttt 180gtttaacttt aagaaggaga tatacat 20728390DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
28tcgtctttgt gatgtgcttc ctgttaggtt tcgtcagccg tcaccgtcag cataacaccc
60tgacctctca ttaattgctc atgccggacg gcactatcgt cgtccggcct tttcctctct
120tcccccgcta cgtgcatcta tttctataaa cccgctcatt ttgtctattt
tttgcacaaa 180catgaaatat cagacaattc cgtgacttaa gaaaatttat
acaaatcagc aatataccca 240ttaaggagta tataaaggtg aatttgattt
acatcaataa gcggggttgc tgaatcgtta 300aggtagaaat gtgatctagt
tcacatttgc ggtaatagaa aagaaatcga ggcaaaaatg 360tttgtttaac
tttaagaagg agatatacat 39029200DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 29agttgttctt
attggtggtg ttgctttatg gttgcatcgt agtaaatggt tgtaacaaaa 60gcaatttttc
cggctgtctg tatacaaaaa cgccgcaaag tttgagcgaa gtcaataaac
120tctctaccca ttcagggcaa tatctctcaa atgtgatcta gttcacattt
tttgtttaac 180tttaagaagg agatatacat 200301332DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
30atggtaaagg aacgtaaaac cgagttggtc gagggattcc gccattcggt tccctgtatc
60aatacccacc ggggaaaaac gtttgtcatc atgctcggcg gtgaagccat tgagcatgag
120aatttctcca gtatcgttaa tgatatcggg ttgttgcaca gcctcggcat
ccgtctggtg 180gtggtctatg gcgcacgtcc gcagatcgac gcaaatctgg
ctgcgcatca ccacgaaccg 240ctgtatcaca agaatatacg tgtgaccgac
gccaaaacac tggaactggt gaagcaggct 300gcgggaacat tgcaactgga
tattactgct cgcctgtcga tgagtctcaa taacacgccg 360ctgcagggcg
cgcatatcaa cgtcgtcagt ggcaatttta ttattgccca gccgctgggc
420gtcgatgacg gcgtggatta ctgccatagc gggcgtatcc ggcggattga
tgaagacgcg 480atccatcgtc aactggacag cggtgcaata gtgctaatgg
ggccggtcgc tgtttcagtc 540actggcgaga gctttaacct gacctcggaa
gagattgcca ctcaactggc catcaaactg 600aaagctgaaa agatgattgg
tttttgctct tcccagggcg tcactaatga cgacggtgat 660attgtctccg
aacttttccc taacgaagcg caagcgcggg tagaagccca ggaagagaaa
720ggcgattaca actccggtac ggtgcgcttt ttgcgtggcg cagtgaaagc
ctgccgcagc 780ggcgtgcgtc gctgtcattt aatcagttat caggaagatg
gcgcgctgtt gcaagagttg 840ttctcacgcg acggtatcgg tacgcagatt
gtgatggaaa gcgccgagca gattcgtcgc 900gcaacaatca acgatattgg
cggtattctg gagttgattc gcccactgga gcagcaaggt 960attctggtac
gccgttctcg cgagcagctg gagatggaaa tcgacaaatt caccattatt
1020cagcgcgata acacgactat tgcctgcgcc gcgctctatc cgttcccgga
agagaagatt 1080ggggaaatgg cctgtgtggc agttcacccg gattaccgca
gttcatcaag gggtgaagtt 1140ctgctggaac gcattgccgc tcaggctaag
cagagcggct taagcaaatt gtttgtgctg 1200accacgcgca gtattcactg
gttccaggaa cgtggattta ccccagtgga tattgattta 1260ctgcccgaga
gcaaaaagca gttgtacaac taccagcgta aatccaaagt gttgatggcg
1320gatttagggt aa 133231443PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 31Met Val Lys Glu Arg Lys
Thr Glu Leu Val Glu Gly Phe Arg His Ser 1 5 10 15 Val Pro Cys Ile
Asn Thr His Arg Gly Lys Thr Phe Val Ile Met Leu 20 25 30 Gly Gly
Glu Ala Ile Glu His Glu Asn Phe Ser Ser Ile Val Asn Asp 35 40 45
Ile Gly Leu Leu His Ser Leu Gly Ile Arg Leu Val Val Val Tyr Gly 50
55 60 Ala Arg Pro Gln Ile Asp Ala Asn Leu Ala Ala His His His Glu
Pro 65 70 75 80 Leu Tyr His Lys Asn Ile Arg Val Thr Asp Ala Lys Thr
Leu Glu Leu 85 90 95 Val Lys Gln Ala Ala Gly Thr Leu Gln Leu Asp
Ile Thr Ala Arg Leu 100 105 110 Ser Met Ser Leu Asn Asn Thr Pro Leu
Gln Gly Ala His Ile Asn Val 115 120 125 Val Ser Gly Asn Phe Ile Ile
Ala Gln Pro Leu Gly Val Asp Asp Gly 130 135 140 Val Asp Tyr Cys His
Ser Gly Arg Ile Arg Arg Ile Asp Glu Asp Ala 145 150 155 160 Ile His
Arg Gln Leu Asp Ser Gly Ala Ile Val Leu Met Gly Pro Val 165 170 175
Ala Val Ser Val Thr Gly Glu Ser Phe Asn Leu Thr Ser Glu Glu Ile 180
185 190 Ala Thr Gln Leu Ala Ile Lys Leu Lys Ala Glu Lys Met Ile Gly
Phe 195 200 205 Cys Ser Ser Gln Gly Val Thr Asn Asp Asp Gly Asp Ile
Val Ser Glu 210 215 220 Leu Phe Pro Asn Glu Ala Gln Ala Arg Val Glu
Ala Gln Glu Glu Lys 225 230 235 240 Gly Asp Tyr Asn Ser Gly Thr Val
Arg Phe Leu Arg Gly Ala Val Lys 245 250 255 Ala Cys Arg Ser Gly Val
Arg Arg Cys His Leu Ile Ser Tyr Gln Glu 260 265 270 Asp Gly Ala Leu
Leu Gln Glu Leu Phe Ser Arg Asp Gly Ile Gly Thr 275 280 285 Gln Ile
Val Met Glu Ser Ala Glu Gln Ile Arg Arg Ala Thr Ile Asn 290 295 300
Asp Ile Gly Gly Ile Leu Glu Leu Ile Arg Pro Leu Glu Gln Gln Gly 305
310 315 320 Ile Leu Val Arg Arg Ser Arg Glu Gln Leu Glu Met Glu Ile
Asp Lys 325 330 335 Phe Thr Ile Ile Gln Arg Asp Asn Thr Thr Ile Ala
Cys Ala Ala Leu 340 345 350 Tyr Pro Phe Pro Glu Glu Lys Ile Gly Glu
Met Ala Cys Val Ala Val 355 360 365 His Pro Asp Tyr Arg Ser Ser Ser
Arg Gly Glu Val Leu Leu Glu Arg 370 375 380 Ile Ala Ala Gln Ala Lys
Gln Ser Gly Leu Ser Lys Leu Phe Val Leu 385 390 395 400 Thr Thr Arg
Ser Ile His Trp Phe Gln Glu Arg Gly Phe Thr Pro Val 405 410 415 Asp
Ile Asp Leu Leu Pro Glu Ser Lys Lys Gln Leu Tyr Asn Tyr Gln 420 425
430 Arg Lys Ser Lys Val Leu Met Ala Asp Leu Gly 435 440
321539DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 32agttgttctt attggtggtg ttgctttatg
gttgcatcgt agtaaatggt tgtaacaaaa 60gcaatttttc cggctgtctg tatacaaaaa
cgccgcaaag tttgagcgaa gtcaataaac 120tctctaccca ttcagggcaa
tatctctctt ggatccaaag tgaactctag aaataatttt 180gtttaacttt
aagaaggaga tatacatatg gtaaaggaac gtaaaaccga gttggtcgag
240ggattccgcc attcggttcc ctgtatcaat acccaccggg gaaaaacgtt
tgtcatcatg 300ctcggcggtg aagccattga gcatgagaat ttctccagta
tcgttaatga tatcgggttg 360ttgcacagcc tcggcatccg tctggtggtg
gtctatggcg cacgtccgca gatcgacgca 420aatctggctg cgcatcacca
cgaaccgctg tatcacaaga atatacgtgt gaccgacgcc 480aaaacactgg
aactggtgaa gcaggctgcg ggaacattgc aactggatat tactgctcgc
540ctgtcgatga gtctcaataa cacgccgctg cagggcgcgc atatcaacgt
cgtcagtggc 600aattttatta ttgcccagcc gctgggcgtc gatgacggcg
tggattactg ccatagcggg 660cgtatccggc ggattgatga agacgcgatc
catcgtcaac tggacagcgg tgcaatagtg 720ctaatggggc cggtcgctgt
ttcagtcact ggcgagagct ttaacctgac ctcggaagag 780attgccactc
aactggccat caaactgaaa gctgaaaaga tgattggttt ttgctcttcc
840cagggcgtca ctaatgacga cggtgatatt gtctccgaac ttttccctaa
cgaagcgcaa 900gcgcgggtag aagcccagga agagaaaggc gattacaact
ccggtacggt gcgctttttg 960cgtggcgcag tgaaagcctg ccgcagcggc
gtgcgtcgct gtcatttaat cagttatcag 1020gaagatggcg cgctgttgca
agagttgttc tcacgcgacg gtatcggtac gcagattgtg 1080atggaaagcg
ccgagcagat tcgtcgcgca acaatcaacg atattggcgg tattctggag
1140ttgattcgcc cactggagca gcaaggtatt ctggtacgcc gttctcgcga
gcagctggag 1200atggaaatcg acaaattcac cattattcag cgcgataaca
cgactattgc ctgcgccgcg 1260ctctatccgt tcccggaaga gaagattggg
gaaatggcct gtgtggcagt tcacccggat 1320taccgcagtt catcaagggg
tgaagttctg ctggaacgca ttgccgctca ggctaagcag 1380agcggcttaa
gcaaattgtt tgtgctgacc acgcgcagta ttcactggtt ccaggaacgt
1440ggatttaccc cagtggatat tgatttactg cccgagagca aaaagcagtt
gtacaactac 1500cagcgtaaat ccaaagtgtt gatggcggat ttagggtaa
1539335417DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 33gtaaaacgac ggccagtgaa ttcgagctcg
gtaccatccc catcactctt gatggagatc 60aattccccaa gctgctagag
cgttaccttg
cccttaaaca ttagcaatgt cgatttatca 120gagggccgac aggctcccac
aggagaaaac cgatggtaaa ggaacgtaaa accgagttgg 180tcgagggatt
ccgccattcg gttccctgta tcaataccca ccggggaaaa acgtttgtca
240tcatgctcgg cggtgaagcc attgagcatg agaatttctc cagtatcgtt
aatgatatcg 300ggttgttgca cagcctcggc atccgtctgg tggtggtcta
tggcgcacgt ccgcagatcg 360acgcaaatct ggctgcgcat caccacgaac
cgctgtatca caagaatata cgtgtgaccg 420acgccaaaac actggaactg
gtgaagcagg ctgcgggaac attgcaactg gatattactg 480ctcgcctgtc
gatgagtctc aataacacgc cgctgcaggg cgcgcatatc aacgtcgtca
540gtggcaattt tattattgcc cagccgctgg gcgtcgatga cggcgtggat
tactgccata 600gcgggcgtat ccggcggatt gatgaagacg cgatccatcg
tcaactggac agcggtgcaa 660tagtgctaat ggggccggtc gctgtttcag
tcactggcga gagctttaac ctgacctcgg 720aagagattgc cactcaactg
gccatcaaac tgaaagctga aaagatgatt ggtttttgct 780cttcccaggg
cgtcactaat gacgacggtg atattgtctc cgaacttttc cctaacgaag
840cgcaagcgcg ggtagaagcc caggaagaga aaggcgatta caactccggt
acggtgcgct 900ttttgcgtgg cgcagtgaaa gcctgccgca gcggcgtgcg
tcgctgtcat ttaatcagtt 960atcaggaaga tggcgcgctg ttgcaagagt
tgttctcacg cgacggtatc ggtacgcaga 1020ttgtgatgga aagcgccgag
cagattcgtc gcgcaacaat caacgatatt ggcggtattc 1080tggagttgat
tcgcccactg gagcagcaag gtattctggt acgccgttct cgcgagcagc
1140tggagatgga aatcgacaaa ttcaccatta ttcagcgcga taacacgact
attgcctgcg 1200ccgcgctcta tccgttcccg gaagagaaga ttggggaaat
ggcctgtgtg gcagttcacc 1260cggattaccg cagttcatca aggggtgaag
ttctgctgga acgcattgcc gctcaggcta 1320agcagagcgg cttaagcaaa
ttgtttgtgc tgaccacgcg cagtattcac tggttccagg 1380aacgtggatt
taccccagtg gatattgatt tactgcccga gagcaaaaag cagttgtaca
1440actaccagcg taaatccaaa gtgttgatgg cggatttagg gtaaacagaa
taaaaataca 1500ataatttcga ataatcatgc aaagcttggc gtaatcatgg
tcatagctgt ttcctgtgtg 1560aaattgttat ccgctcacaa ttccacacaa
catacgagcc ggaagcatgt acgggttttg 1620ctgcccgcaa acgggctgtt
ctggtgttgc tagtttgtta tcagaatcgc agatccggct 1680tcaggtttgc
cggctgaaag cgctatttct tccagaattg ccatgatttt ttccccacgg
1740gaggcgtcac tggctcccgt gttgtcggca gctttgattc gataagcagc
atcgcctgtt 1800tcaggctgtc tatgtgtgac tgttgagctg taacaagttg
tctcaggtgt tcaatttcat 1860gttctagttg ctttgtttta ctggtttcac
ctgttctatt aggtgttaca tgctgttcat 1920ctgttacatt gtcgatctgt
tcatggtgaa cagctttaaa tgcaccaaaa actcgtaaaa 1980gctctgatgt
atctatcttt tttacaccgt tttcatctgt gcatatggac agttttccct
2040ttgatatcta acggtgaaca gttgttctac ttttgtttgt tagtcttgat
gcttcactga 2100tagatacaag agccataaga acctcagatc cttccgtatt
tagccagtat gttctctagt 2160gtggttcgtt gtttttgcgt gagccatgag
aacgaaccat tgagatcatg cttactttgc 2220atgtcactca aaaattttgc
ctcaaaactg gtgagctgaa tttttgcagt taaagcatcg 2280tgtagtgttt
ttcttagtcc gttacgtagg taggaatctg atgtaatggt tgttggtatt
2340ttgtcaccat tcatttttat ctggttgttc tcaagttcgg ttacgagatc
catttgtcta 2400tctagttcaa cttggaaaat caacgtatca gtcgggcggc
ctcgcttatc aaccaccaat 2460ttcatattgc tgtaagtgtt taaatcttta
cttattggtt tcaaaaccca ttggttaagc 2520cttttaaact catggtagtt
attttcaagc attaacatga acttaaattc atcaaggcta 2580atctctatat
ttgccttgtg agttttcttt tgtgttagtt cttttaataa ccactcataa
2640atcctcatag agtatttgtt ttcaaaagac ttaacatgtt ccagattata
ttttatgaat 2700ttttttaact ggaaaagata aggcaatatc tcttcactaa
aaactaattc taatttttcg 2760cttgagaact tggcatagtt tgtccactgg
aaaatctcaa agcctttaac caaaggattc 2820ctgatttcca cagttctcgt
catcagctct ctggttgctt tagctaatac accataagca 2880ttttccctac
tgatgttcat catctgagcg tattggttat aagtgaacga taccgtccgt
2940tctttccttg tagggttttc aatcgtgggg ttgagtagtg ccacacagca
taaaattagc 3000ttggtttcat gctccgttaa gtcatagcga ctaatcgcta
gttcatttgc tttgaaaaca 3060actaattcag acatacatct caattggtct
aggtgatttt aatcactata ccaattgaga 3120tgggctagtc aatgataatt
actagtcctt ttcctttgag ttgtgggtat ctgtaaattc 3180tgctagacct
ttgctggaaa acttgtaaat tctgctagac cctctgtaaa ttccgctaga
3240cctttgtgtg ttttttttgt ttatattcaa gtggttataa tttatagaat
aaagaaagaa 3300taaaaaaaga taaaaagaat agatcccagc cctgtgtata
actcactact ttagtcagtt 3360ccgcagtatt acaaaaggat gtcgcaaacg
ctgtttgctc ctctacaaaa cagaccttaa 3420aaccctaaag gcttaagtag
caccctcgca agctcgggca aatcgctgaa tattcctttt 3480gtctccgacc
atcaggcacc tgagtcgctg tctttttcgt gacattcagt tcgctgcgct
3540cacggctctg gcagtgaatg ggggtaaatg gcactacagg cgccttttat
ggattcatgc 3600aaggaaacta cccataatac aagaaaagcc cgtcacgggc
ttctcagggc gttttatggc 3660gggtctgcta tgtggtgcta tctgactttt
tgctgttcag cagttcctgc cctctgattt 3720tccagtctga ccacttcgga
ttatcccgtg acaggtcatt cagactggct aatgcaccca 3780gtaaggcagc
ggtatcatca acaggcttac ccgtcttact gtcttttcta cggggtctga
3840cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat
caaaaaggat 3900cttcacctag atccttttaa attaaaaatg aagttttaaa
tcaatctaaa gtatatatga 3960gtaaacttgg tctgacagtt accaatgctt
aatcagtgag gcacctatct cagcgatctg 4020tctatttcgt tcatccatag
ttgcctgact ccccgtcgtg tagataacta cgatacggga 4080gggcttacca
tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc
4140agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg
gtcctgcaac 4200tttatccgcc tccatccagt ctattaattg ttgccgggaa
gctagagtaa gtagttcgcc 4260agttaatagt ttgcgcaacg ttgttgccat
tgctacaggc atcgtggtgt cacgctcgtc 4320gtttggtatg gcttcattca
gctccggttc ccaacgatca aggcgagtta catgatcccc 4380catgttgtgc
aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt
4440ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta
ctgtcatgcc 4500atccgtaaga tgcttttctg tgactggtga gtactcaacc
aagtcattct gagaatagtg 4560tatgcggcga ccgagttgct cttgcccggc
gtcaatacgg gataataccg cgccacatag 4620cagaacttta aaagtgctca
tcattggaaa acgttcttcg gggcgaaaac tctcaaggat 4680cttaccgctg
ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc
4740atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa
atgccgcaaa 4800aaagggaata agggcgacac ggaaatgttg aatactcata
ctcttccttt ttcaatatta 4860ttgaagcatt tatcagggtt attgtctcat
gagcggatac atatttgaat gtatttagaa 4920aaataaacaa ataggggttc
cgcgcacatt tccccgaaaa gtgccacctg acgtctaaga 4980aaccattatt
atcatgacat taacctataa aaataggcgt atcacgaggc cctttcgtct
5040cgcgcgtttc ggtgatgacg gtgaaaacct ctgacacatg cagctcccgg
agacggtcac 5100agcttgtctg taagcggatg ccgggagcag acaagcccgt
cagggcgcgt cagcgggtgt 5160tggcgggtgt cggggctggc ttaactatgc
ggcatcagag cagattgtac tgagagtgca 5220ccatatgcgg tgtgaaatac
cgcacagatg cgtaaggaga aaataccgca tcaggcgcca 5280ttcgccattc
aggctgcgca actgttggga agggcgatcg gtgcgggcct cttcgctatt
5340acgccagctg gcgaaagggg gatgtgctgc aaggcgatta agttgggtaa
cgccagggtt 5400ttcccagtca cgacgtt 5417343995DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
34attaagttgg gtaacgccag ggttttccca gtcacgacgt tattgcgttg cgctcactgc
60ccgctttcca gtcgggaaac ctgtcgtgcc agctgcatta atgaatcggc caacgcgcgg
120ggagaggcgg tttgcgtatt gggcgctctt ccgcttcctc gctcactgac
tcgctgcgct 180cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa
ggcggtagta cgggttttgc 240tgcccgcaaa cgggctgttc tggtgttgct
agtttgttat cagaatcgca gatccggctt 300caggtttgcc ggctgaaagc
gctatttctt ccagaattgc catgattttt tccccacggg 360aggcgtcact
ggctcccgtg ttgtcggcag ctttgattcg ataagcagca tcgcctgttt
420caggctgtct atgtgtgact gttgagctgt aacaagttgt ctcaggtgtt
caatttcatg 480ttctagttgc tttgttttac tggtttcacc tgttctatta
ggtgttacat gctgttcatc 540tgttacattg tcgatctgtt catggtgaac
agctttaaat gcaccaaaaa ctcgtaaaag 600ctctgatgta tctatctttt
ttacaccgtt ttcatctgtg catatggaca gttttccctt 660tgatatctaa
cggtgaacag ttgttctact tttgtttgtt agtcttgatg cttcactgat
720agatacaaga gccataagaa cctcagatcc ttccgtattt agccagtatg
ttctctagtg 780tggttcgttg tttttgcgtg agccatgaga acgaaccatt
gagatcatgc ttactttgca 840tgtcactcaa aaattttgcc tcaaaactgg
tgagctgaat ttttgcagtt aaagcatcgt 900gtagtgtttt tcttagtccg
ttacgtaggt aggaatctga tgtaatggtt gttggtattt 960tgtcaccatt
catttttatc tggttgttct caagttcggt tacgagatcc atttgtctat
1020ctagttcaac ttggaaaatc aacgtatcag tcgggcggcc tcgcttatca
accaccaatt 1080tcatattgct gtaagtgttt aaatctttac ttattggttt
caaaacccat tggttaagcc 1140ttttaaactc atggtagtta ttttcaagca
ttaacatgaa cttaaattca tcaaggctaa 1200tctctatatt tgccttgtga
gttttctttt gtgttagttc ttttaataac cactcataaa 1260tcctcataga
gtatttgttt tcaaaagact taacatgttc cagattatat tttatgaatt
1320tttttaactg gaaaagataa ggcaatatct cttcactaaa aactaattct
aatttttcgc 1380ttgagaactt ggcatagttt gtccactgga aaatctcaaa
gcctttaacc aaaggattcc 1440tgatttccac agttctcgtc atcagctctc
tggttgcttt agctaataca ccataagcat 1500tttccctact gatgttcatc
atctgagcgt attggttata agtgaacgat accgtccgtt 1560ctttccttgt
agggttttca atcgtggggt tgagtagtgc cacacagcat aaaattagct
1620tggtttcatg ctccgttaag tcatagcgac taatcgctag ttcatttgct
ttgaaaacaa 1680ctaattcaga catacatctc aattggtcta ggtgatttta
atcactatac caattgagat 1740gggctagtca atgataatta ctagtccttt
tcctttgagt tgtgggtatc tgtaaattct 1800gctagacctt tgctggaaaa
cttgtaaatt ctgctagacc ctctgtaaat tccgctagac 1860ctttgtgtgt
tttttttgtt tatattcaag tggttataat ttatagaata aagaaagaat
1920aaaaaaagat aaaaagaata gatcccagcc ctgtgtataa ctcactactt
tagtcagttc 1980cgcagtatta caaaaggatg tcgcaaacgc tgtttgctcc
tctacaaaac agaccttaaa 2040accctaaagg cttaagtagc accctcgcaa
gctcgggcaa atcgctgaat attccttttg 2100tctccgacca tcaggcacct
gagtcgctgt ctttttcgtg acattcagtt cgctgcgctc 2160acggctctgg
cagtgaatgg gggtaaatgg cactacaggc gccttttatg gattcatgca
2220aggaaactac ccataataca agaaaagccc gtcacgggct tctcagggcg
ttttatggcg 2280ggtctgctat gtggtgctat ctgacttttt gctgttcagc
agttcctgcc ctctgatttt 2340ccagtctgac cacttcggat tatcccgtga
caggtcattc agactggcta atgcacccag 2400taaggcagcg gtatcatcaa
caggcttacc cgtcttactg tcttttctac ggggtctgac 2460gctcagtgga
acgaaaactc acgttaaggg attttggtca tgagattatc aaaaaggatc
2520ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag
tatatatgag 2580taaacttggt ctgacagtta ccaatgctta atcagtgagg
cacctatctc agcgatctgt 2640ctatttcgtt catccatagt tgcctgactc
cccgtcgtgt agataactac gatacgggag 2700ggcttaccat ctggccccag
tgctgcaatg ataccgcgag acccacgctc accggctcca 2760gatttatcag
caataaacca gccagccgga agggccgagc gcagaagtgg tcctgcaact
2820ttatccgcct ccatccagtc tattaattgt tgccgggaag ctagagtaag
tagttcgcca 2880gttaatagtt tgcgcaacgt tgttgccatt gctacaggca
tcgtggtgtc acgctcgtcg 2940tttggtatgg cttcattcag ctccggttcc
caacgatcaa ggcgagttac atgatccccc 3000atgttgtgca aaaaagcggt
tagctccttc ggtcctccga tcgttgtcag aagtaagttg 3060gccgcagtgt
tatcactcat ggttatggca gcactgcata attctcttac tgtcatgcca
3120tccgtaagat gcttttctgt gactggtgag tactcaacca agtcattctg
agaatagtgt 3180atgcggcgac cgagttgctc ttgcccggcg tcaatacggg
ataataccgc gccacatagc 3240agaactttaa aagtgctcat cattggaaaa
cgttcttcgg ggcgaaaact ctcaaggatc 3300ttaccgctgt tgagatccag
ttcgatgtaa cccactcgtg cacccaactg atcttcagca 3360tcttttactt
tcaccagcgt ttctgggtga gcaaaaacag gaaggcaaaa tgccgcaaaa
3420aagggaataa gggcgacacg gaaatgttga atactcatac tcttcctttt
tcaatattat 3480tgaagcattt atcagggtta ttgtctcatg agcggataca
tatttgaatg tatttagaaa 3540aataaacaaa taggggttcc gcgcacattt
ccccgaaaag tgccacctga cgtctaagaa 3600accattatta tcatgacatt
aacctataaa aataggcgta tcacgaggcc ctttcgtctc 3660gcgcgtttcg
gtgatgacgg tgaaaacctc tgacacatgc agctcccgga gacggtcaca
3720gcttgtctgt aagcggatgc cgggagcaga caagcccgtc agggcgcgtc
agcgggtgtt 3780ggcgggtgtc ggggctggct taactatgcg gcatcagagc
agattgtact gagagtgcac 3840catatgcggt gtgaaatacc gcacagatgc
gtaaggagaa aataccgcat caggcgccat 3900tcgccattca ggctgcgcaa
ctgttgggaa gggcgatcgg tgcgggcctc ttcgctatta 3960cgccagctgg
cgaaaggggg atgtgctgca aggcg 3995355660DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
35ggtaccagtt gttcttattg gtggtgttgc tttatggttg catcgtagta aatggttgta
60acaaaagcaa tttttccggc tgtctgtata caaaaacgcc gcaaagtttg agcgaagtca
120ataaactctc tacccattca gggcaatatc tctcttggat ccaaagtgaa
ctctagaaat 180aattttgttt aactttaaga aggagatata catatggtaa
aggaacgtaa aaccgagttg 240gtcgagggat tccgccattc ggttccctgt
atcaataccc accggggaaa aacgtttgtc 300atcatgctcg gcggtgaagc
cattgagcat gagaatttct ccagtatcgt taatgatatc 360gggttgttgc
acagcctcgg catccgtctg gtggtggtct atggcgcacg tccgcagatc
420gacgcaaatc tggctgcgca tcaccacgaa ccgctgtatc acaagaatat
acgtgtgacc 480gacgccaaaa cactggaact ggtgaagcag gctgcgggaa
cattgcaact ggatattact 540gctcgcctgt cgatgagtct caataacacg
ccgctgcagg gcgcgcatat caacgtcgtc 600agtggcaatt ttattattgc
ccagccgctg ggcgtcgatg acggcgtgga ttactgccat 660agcgggcgta
tccggcggat tgatgaagac gcgatccatc gtcaactgga cagcggtgca
720atagtgctaa tggggccggt cgctgtttca gtcactggcg agagctttaa
cctgacctcg 780gaagagattg ccactcaact ggccatcaaa ctgaaagctg
aaaagatgat tggtttttgc 840tcttcccagg gcgtcactaa tgacgacggt
gatattgtct ccgaactttt ccctaacgaa 900gcgcaagcgc gggtagaagc
ccaggaagag aaaggcgatt acaactccgg tacggtgcgc 960tttttgcgtg
gcgcagtgaa agcctgccgc agcggcgtgc gtcgctgtca tttaatcagt
1020tatcaggaag atggcgcgct gttgcaagag ttgttctcac gcgacggtat
cggtacgcag 1080attgtgatgg aaagcgccga gcagattcgt cgcgcaacaa
tcaacgatat tggcggtatt 1140ctggagttga ttcgcccact ggagcagcaa
ggtattctgg tacgccgttc tcgcgagcag 1200ctggagatgg aaatcgacaa
attcaccatt attcagcgcg ataacacgac tattgcctgc 1260gccgcgctct
atccgttccc ggaagagaag attggggaaa tggcctgtgt ggcagttcac
1320ccggattacc gcagttcatc aaggggtgaa gttctgctgg aacgcattgc
cgctcaggct 1380aagcagagcg gcttaagcaa attgtttgtg ctgaccacgc
gcagtattca ctggttccag 1440gaacgtggat ttaccccagt ggatattgat
ttactgcccg agagcaaaaa gcagttgtac 1500aactaccagc gtaaatccaa
agtgttgatg gcggatttag ggtaaggaag tttgtctaga 1560tctcaggcgt
ggatggcttg gcgtaatcat ggtcatagct gtttcctgtg tgaaattgtt
1620atccgctcac aattccacac aacatacgag ccggaagcat aaagtgtaaa
gcctggggtg 1680cctaatgagt gagctaactc acattaattg cgttgcgctc
actgcccgct ttccagtcgg 1740gaaacctgtc gtgccagctg cattaatgaa
tcggccaacg cgcggggaga ggcggtttgc 1800gtattgggcg ctcttccgct
tcctcgctca ctgactcgct gcgctcggtc gttcggctgc 1860ggcgagcggt
atcagctcac tcaaaggcgg tagtacgggt tttgctgccc gcaaacgggc
1920tgttctggtg ttgctagttt gttatcagaa tcgcagatcc ggcttcaggt
ttgccggctg 1980aaagcgctat ttcttccaga attgccatga ttttttcccc
acgggaggcg tcactggctc 2040ccgtgttgtc ggcagctttg attcgataag
cagcatcgcc tgtttcaggc tgtctatgtg 2100tgactgttga gctgtaacaa
gttgtctcag gtgttcaatt tcatgttcta gttgctttgt 2160tttactggtt
tcacctgttc tattaggtgt tacatgctgt tcatctgtta cattgtcgat
2220ctgttcatgg tgaacagctt taaatgcacc aaaaactcgt aaaagctctg
atgtatctat 2280cttttttaca ccgttttcat ctgtgcatat ggacagtttt
ccctttgata tctaacggtg 2340aacagttgtt ctacttttgt ttgttagtct
tgatgcttca ctgatagata caagagccat 2400aagaacctca gatccttccg
tatttagcca gtatgttctc tagtgtggtt cgttgttttt 2460gcgtgagcca
tgagaacgaa ccattgagat catgcttact ttgcatgtca ctcaaaaatt
2520ttgcctcaaa actggtgagc tgaatttttg cagttaaagc atcgtgtagt
gtttttctta 2580gtccgttacg taggtaggaa tctgatgtaa tggttgttgg
tattttgtca ccattcattt 2640ttatctggtt gttctcaagt tcggttacga
gatccatttg tctatctagt tcaacttgga 2700aaatcaacgt atcagtcggg
cggcctcgct tatcaaccac caatttcata ttgctgtaag 2760tgtttaaatc
tttacttatt ggtttcaaaa cccattggtt aagcctttta aactcatggt
2820agttattttc aagcattaac atgaacttaa attcatcaag gctaatctct
atatttgcct 2880tgtgagtttt cttttgtgtt agttctttta ataaccactc
ataaatcctc atagagtatt 2940tgttttcaaa agacttaaca tgttccagat
tatattttat gaattttttt aactggaaaa 3000gataaggcaa tatctcttca
ctaaaaacta attctaattt ttcgcttgag aacttggcat 3060agtttgtcca
ctggaaaatc tcaaagcctt taaccaaagg attcctgatt tccacagttc
3120tcgtcatcag ctctctggtt gctttagcta atacaccata agcattttcc
ctactgatgt 3180tcatcatctg agcgtattgg ttataagtga acgataccgt
ccgttctttc cttgtagggt 3240tttcaatcgt ggggttgagt agtgccacac
agcataaaat tagcttggtt tcatgctccg 3300ttaagtcata gcgactaatc
gctagttcat ttgctttgaa aacaactaat tcagacatac 3360atctcaattg
gtctaggtga ttttaatcac tataccaatt gagatgggct agtcaatgat
3420aattactagt ccttttcctt tgagttgtgg gtatctgtaa attctgctag
acctttgctg 3480gaaaacttgt aaattctgct agaccctctg taaattccgc
tagacctttg tgtgtttttt 3540ttgtttatat tcaagtggtt ataatttata
gaataaagaa agaataaaaa aagataaaaa 3600gaatagatcc cagccctgtg
tataactcac tactttagtc agttccgcag tattacaaaa 3660ggatgtcgca
aacgctgttt gctcctctac aaaacagacc ttaaaaccct aaaggcttaa
3720gtagcaccct cgcaagctcg ggcaaatcgc tgaatattcc ttttgtctcc
gaccatcagg 3780cacctgagtc gctgtctttt tcgtgacatt cagttcgctg
cgctcacggc tctggcagtg 3840aatgggggta aatggcacta caggcgcctt
ttatggattc atgcaaggaa actacccata 3900atacaagaaa agcccgtcac
gggcttctca gggcgtttta tggcgggtct gctatgtggt 3960gctatctgac
tttttgctgt tcagcagttc ctgccctctg attttccagt ctgaccactt
4020cggattatcc cgtgacaggt cattcagact ggctaatgca cccagtaagg
cagcggtatc 4080atcaacaggc ttacccgtct tactgtcttt tctacggggt
ctgacgctca gtggaacgaa 4140aactcacgtt aagggatttt ggtcatgaga
ttatcaaaaa ggatcttcac ctagatcctt 4200ttaaattaaa aatgaagttt
taaatcaatc taaagtatat atgagtaaac ttggtctgac 4260agttaccaat
gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc
4320atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
accatctggc 4380cccagtgctg caatgatacc gcgagaccca cgctcaccgg
ctccagattt atcagcaata 4440aaccagccag ccggaagggc cgagcgcaga
agtggtcctg caactttatc cgcctccatc 4500cagtctatta attgttgccg
ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc 4560aacgttgttg
ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca
4620ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
gtgcaaaaaa 4680gcggttagct ccttcggtcc tccgatcgtt gtcagaagta
agttggccgc agtgttatca 4740ctcatggtta tggcagcact gcataattct
cttactgtca tgccatccgt aagatgcttt 4800tctgtgactg gtgagtactc
aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt 4860tgctcttgcc
cggcgtcaat acgggataat accgcgccac atagcagaac tttaaaagtg
4920ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
gctgttgaga 4980tccagttcga tgtaacccac tcgtgcaccc aactgatctt
cagcatcttt tactttcacc 5040agcgtttctg ggtgagcaaa aacaggaagg
caaaatgccg caaaaaaggg aataagggcg 5100acacggaaat gttgaatact
catactcttc ctttttcaat attattgaag catttatcag 5160ggttattgtc
tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg
5220gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat
tattatcatg 5280acattaacct ataaaaatag gcgtatcacg aggccctttc
gtctcgcgcg tttcggtgat 5340gacggtgaaa acctctgaca catgcagctc
ccggagacgg tcacagcttg tctgtaagcg 5400gatgccggga gcagacaagc
ccgtcagggc gcgtcagcgg gtgttggcgg gtgtcggggc 5460tggcttaact
atgcggcatc agagcagatt
gtactgagag tgcaccatat gcggtgtgaa 5520ataccgcaca gatgcgtaag
gagaaaatac cgcatcaggc gccattcgcc attcaggctg 5580cgcaactgtt
gggaagggcg atcggtgcgg gcctcttcgc tattacgcca gctggcgaaa
5640gggggatgtg ctgcaaggcg 5660363115DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
36ctacgcccca tcgttgcttt gtgtgatctc tgttacagaa ttggcggtaa tgtggagatg
60cgcacataaa atcgccatga tttttgcaag caacatcacg aaattcctta catgacctcg
120gtttagttca caggacgtcc catggctcga gcatgcgaga gtagggaact
gccaggcatc 180aaataaaatg aaaggctcag tcgaaagact gggcctttcg
ttttatctgt tgtttgtcgg 240tgaacgctct cctgagtagg acaaatccgc
cgggagcgga tttgaacgtt gcgaagcaac 300ggcccggagg gtggcgggca
ggacgcccgc cataaactgc caggcatcaa attaagcaga 360aggccatcct
gacggatggc ctttttgcgt ggccagtgcc aagcttgcat gcagattgca
420gcattacacg tcttgagcga ttgtgtaggc tggagctgct tcgaagttcc
tatactttct 480agagaatagg aacttcggaa taggaacttc atttaaatgg
cgcgccttac gccccgccct 540gccactcatc gcagtactgt tgtattcatt
aagcatctgc cgacatggaa gccatcacaa 600acggcatgat gaacctgaat
cgccagcggc atcagcacct tgtcgccttg cgtataatat 660ttgcccatgg
tgaaaacggg ggcgaagaag ttgtccatat tggccacgtt taaatcaaaa
720ctggtgaaac tcacccaggg attggctgag acgaaaaaca tattctcaat
aaacccttta 780gggaaatagg ccaggttttc accgtaacac gccacatctt
gcgaatatat gtgtagaaac 840tgccggaaat cgtcgtggta ttcactccag
agcgatgaaa acgtttcagt ttgctcatgg 900aaaacggtgt aacaagggtg
aacactatcc catatcacca gctcaccgtc tttcattgcc 960atacgtaatt
ccggatgagc attcatcagg cgggcaagaa tgtgaataaa ggccggataa
1020aacttgtgct tatttttctt tacggtcttt aaaaaggccg taatatccag
ctgaacggtc 1080tggttatagg tacattgagc aactgactga aatgcctcaa
aatgttcttt acgatgccat 1140tgggatatat caacggtggt atatccagtg
atttttttct ccattttagc ttccttagct 1200cctgaaaatc tcgacaactc
aaaaaatacg cccggtagtg atcttatttc attatggtga 1260aagttggaac
ctcttacgtg ccgatcaacg tctcattttc gccaaaagtt ggcccagggc
1320ttcccggtat caacagggac accaggattt atttattctg cgaagtgatc
ttccgtcaca 1380ggtaggcgcg ccgaagttcc tatactttct agagaatagg
aacttcggaa taggaactaa 1440ggaggatatt catatggacc atggctaatt
cccaggtacc agttgttctt attggtggtg 1500ttgctttatg gttgcatcgt
agtaaatggt tgtaacaaaa gcaatttttc cggctgtctg 1560tatacaaaaa
cgccgtaaag tttgagcgaa gtcaataaac tctctaccca ttcagggcaa
1620tatctctctt ggatccaaag tgaactctag aaataatttt gtttaacttt
aagaaggaga 1680tatacatatg gtaaaggaac gtaaaaccga gttggtcgag
ggattccgcc attcggttcc 1740ctgtatcaat acccaccggg gaaaaacgtt
tgtcatcatg ctcggcggtg aagccattga 1800gcatgagaat ttctccagta
tcgttaatga tatcgggttg ttgcacagcc tcggcatccg 1860tctggtggtg
gtctatggcg cacgtccgca gatcgacgca aatctggctg cgcatcacca
1920cgaaccgctg tatcacaaga atatacgtgt gaccgacgcc aaaacactgg
aactggtgaa 1980gcaggctgcg ggaacattgc aactggatat tactgctcgc
ctgtcgatga gtctcaataa 2040cacgccgctg cagggcgcgc atatcaacgt
cgtcagtggc aattttatta ttgcccagcc 2100gctgggcgtc gatgacggcg
tggattactg ccatagcggg cgtatccggc ggattgatga 2160agacgcgatc
catcgtcaac tggacagcgg tgcaatagtg ctaatggggc cggtcgctgt
2220ttcagtcact ggcgagagct ttaacctgac ctcggaagag attgccactc
aactggccat 2280caaactgaaa gctgaaaaga tgattggttt ttgctcttcc
cagggcgtca ctaatgacga 2340cggtgatatt gtctccgaac ttttccctaa
cgaagcgcaa gcgcgggtag aagcccagga 2400agagaaaggc gattacaact
ccggtacggt gcgctttttg cgtggcgcag tgaaagcctg 2460ccgcagcggc
gtgcgtcgct gtcatttaat cagttatcag gaagatggcg cgctgttgca
2520agagttgttc tcacgcgacg gtatcggtac gcagattgtg atggaaagcg
ccgagcagat 2580tcgtcgcgca acaatcaacg atattggcgg tattctggag
ttgattcgcc cactggagca 2640gcaaggtatt ctggtacgcc gttctcgcga
gcagctggag atggaaatcg acaaattcac 2700cattattcag cgcgataaca
cgactattgc ctgcgccgcg ctctatccgt tcccggaaga 2760gaagattggg
gaaatggcct gtgtggcagt tcacccggat taccgcagtt catcaagggg
2820tgaagttctg ctggaacgca ttgccgctca ggctaagcag agcggcttaa
gcaaattgtt 2880tgtgctgacc acgcgcagta ttcactggtt ccaggaacgt
ggatttaccc cagtggatat 2940tgatttactg cccgagagca aaaagcagtt
gtacaactac cagcgtaaat ccaaagtgtt 3000gatggcggat ttagggtaag
tcgacgcatg catcgataag ccgcgttctc atcctcccgc 3060ctcctccccc
ataaaaaagc cagggggtgg aggatttaag ccatctcctg atgac
3115373583DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 37ctacgcccca tcgttgcttt gtgtgatctc
tgttacagaa ttggcggtaa tgtggagatg 60cgcacataaa atcgccatga tttttgcaag
caacatcacg aaattcctta catgacctcg 120gtttagttca caggacgtcc
catggctcga gcatgcgaga gtagggaact gccaggcatc 180aaataaaatg
aaaggctcag tcgaaagact gggcctttcg ttttatctgt tgtttgtcgg
240tgaacgctct cctgagtagg acaaatccgc cgggagcgga tttgaacgtt
gcgaagcaac 300ggcccggagg gtggcgggca ggacgcccgc cataaactgc
caggcatcaa attaagcaga 360aggccatcct gacggatggc ctttttgcgt
ggccagtgcc aagcttgcat gcagattgca 420gcattacacg tcttgagcga
ttgtgtaggc tggagctgct tcgaagttcc tatactttct 480agagaatagg
aacttcggaa taggaacttc aagatcccct cacgctgccg caagcactca
540gggcgcaagg gctgctaaag gaagcggaac acgtagaaag ccagtccgca
gaaacggtgc 600tgaccccgga tgaatgtcag ctactgggct atctggacaa
gggaaaacgc aagcgcaaag 660agaaagcagg tagcttgcag tgggcttaca
tggcgatagc tagactgggc ggttttatgg 720acagcaagcg aaccggaatt
gccagctggg gcgccctctg gtaaggttgg gaagccctgc 780aaagtaaact
ggatggcttt cttgccgcca aggatctgat ggcgcagggg atcaagatct
840gatcaagaga caggatgagg atcgtttcgc atgattgaac aagatggatt
gcacgcaggt 900tctccggccg cttgggtgga gaggctattc ggctatgact
gggcacaaca gacaatcggc 960tgctctgatg ccgccgtgtt ccggctgtca
gcgcaggggc gcccggttct ttttgtcaag 1020accgacctgt ccggtgccct
gaatgaactg caggacgagg cagcgcggct atcgtggctg 1080gccacgacgg
gcgttccttg cgcagctgtg ctcgacgttg tcactgaagc gggaagggac
1140tggctgctat tgggcgaagt gccggggcag gatctcctgt catctcacct
tgctcctgcc 1200gagaaagtat ccatcatggc tgatgcaatg cggcggctgc
atacgcttga tccggctacc 1260tgcccattcg accaccaagc gaaacatcgc
atcgagcgag cacgtactcg gatggaagcc 1320ggtcttgtcg atcaggatga
tctggacgaa gagcatcagg ggctcgcgcc agccgaactg 1380ttcgccaggc
tcaaggcgcg catgcccgac ggcgaggatc tcgtcgtgac ccatggcgat
1440gcctgcttgc cgaatatcat ggtggaaaat ggccgctttt ctggattcat
cgactgtggc 1500cggctgggtg tggcggaccg ctatcaggac atagcgttgg
ctacccgtga tattgctgaa 1560gagcttggcg gcgaatgggc tgaccgcttc
ctcgtgcttt acggtatcgc cgctcccgat 1620tcgcagcgca tcgccttcta
tcgccttctt gacgagttct tctgagcggg actctggggt 1680tcgaaatgac
cgaccaagcg acgcccaacc tgccatcacg agatttcgat tccaccgccg
1740ccttctatga aaggttgggc ttcggaatcg ttttccggga cgccggctgg
atgatcctcc 1800agcgcgggga tctcatgctg gagttcttcg cccaccccag
cttcaaaagc gctctgaagt 1860tcctatactt tctagagaat aggaacttcg
gaataggaac taaggaggat attcatatgg 1920accatggcta attcccagat
atggtaccag ttgttcttat tggtggtgtt gctttatggt 1980tgcatcgtag
taaatggttg taacaaaagc aatttttccg gctgtctgta tacaaaaacg
2040ccgtaaagtt tgagcgaagt caataaactc tctacccatt cagggcaata
tctctcttgg 2100atccaaagtg aactctagaa ataattttgt ttaactttaa
gaaggagata tacatatggt 2160aaaggaacgt aaaaccgagt tggtcgaggg
attccgccat tcggttccct gtatcaatac 2220ccaccgggga aaaacgtttg
tcatcatgct cggcggtgaa gccattgagc atgagaattt 2280ctccagtatc
gttaatgata tcgggttgtt gcacagcctc ggcatccgtc tggtggtggt
2340ctatggcgca cgtccgcaga tcgacgcaaa tctggctgcg catcaccacg
aaccgctgta 2400tcacaagaat atacgtgtga ccgacgccaa aacactggaa
ctggtgaagc aggctgcggg 2460aacattgcaa ctggatatta ctgctcgcct
gtcgatgagt ctcaataaca cgccgctgca 2520gggcgcgcat atcaacgtcg
tcagtggcaa ttttattatt gcccagccgc tgggcgtcga 2580tgacggcgtg
gattactgcc atagcgggcg tatccggcgg attgatgaag acgcgatcca
2640tcgtcaactg gacagcggtg caatagtgct aatggggccg gtcgctgttt
cagtcactgg 2700cgagagcttt aacctgacct cggaagagat tgccactcaa
ctggccatca aactgaaagc 2760tgaaaagatg attggttttt gctcttccca
gggcgtcact aatgacgacg gtgatattgt 2820ctccgaactt ttccctaacg
aagcgcaagc gcgggtagaa gcccaggaag agaaaggcga 2880ttacaactcc
ggtacggtgc gctttttgcg tggcgcagtg aaagcctgcc gcagcggcgt
2940gcgtcgctgt catttaatca gttatcagga agatggcgcg ctgttgcaag
agttgttctc 3000acgcgacggt atcggtacgc agattgtgat ggaaagcgcc
gagcagattc gtcgcgcaac 3060aatcaacgat attggcggta ttctggagtt
gattcgccca ctggagcagc aaggtattct 3120ggtacgccgt tctcgcgagc
agctggagat ggaaatcgac aaattcacca ttattcagcg 3180cgataacacg
actattgcct gcgccgcgct ctatccgttc ccggaagaga agattgggga
3240aatggcctgt gtggcagttc acccggatta ccgcagttca tcaaggggtg
aagttctgct 3300ggaacgcatt gccgctcagg ctaagcagag cggcttaagc
aaattgtttg tgctgaccac 3360gcgcagtatt cactggttcc aggaacgtgg
atttacccca gtggatattg atttactgcc 3420cgagagcaaa aagcagttgt
acaactacca gcgtaaatcc aaagtgttga tggcggattt 3480agggtaagtc
gacgcatgca tcgataagcc gcgttctcat cctcccgcct cctcccccat
3540aaaaaagcca gggggtggag gatttaagcc atctcctgat gac
3583382185DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 38ctacgcccca tcgttgcttt gtgtgatctc
tgttacagaa ttggcggtaa tgtggagatg 60cgcacataaa atcgccatga tttttgcaag
caacatcacg aaattcctta catgacctcg 120gtttagttca caggacgtcc
catggctcga gcatgcgaga gtagggaact gccaggcatc 180aaataaaatg
aaaggctcag tcgaaagact gggcctttcg ttttatctgt tgtttgtcgg
240tgaacgctct cctgagtagg acaaatccgc cgggagcgga tttgaacgtt
gcgaagcaac 300ggcccggagg gtggcgggca ggacgcccgc cataaactgc
caggcatcaa attaagcaga 360aggccatcct gacggatggc ctttttgcgt
ggccagtgcc aagcttgcat gcagattgca 420gcattacacg tcttgagcga
ttgtgtaggc tggagctgct tcgaagttcc tatactttct 480agagaatagg
aacttcggaa taggaactaa ggaggatatt catatggacc atggctaatt
540cccaggtacc agttgttctt attggtggtg ttgctttatg gttgcatcgt
agtaaatggt 600tgtaacaaaa gcaatttttc cggctgtctg tatacaaaaa
cgccgtaaag tttgagcgaa 660gtcaataaac tctctaccca ttcagggcaa
tatctctctt ggatccaaag tgaactctag 720aaataatttt gtttaacttt
aagaaggaga tatacatatg gtaaaggaac gtaaaaccga 780gttggtcgag
ggattccgcc attcggttcc ctgtatcaat acccaccggg gaaaaacgtt
840tgtcatcatg ctcggcggtg aagccattga gcatgagaat ttctccagta
tcgttaatga 900tatcgggttg ttgcacagcc tcggcatccg tctggtggtg
gtctatggcg cacgtccgca 960gatcgacgca aatctggctg cgcatcacca
cgaaccgctg tatcacaaga atatacgtgt 1020gaccgacgcc aaaacactgg
aactggtgaa gcaggctgcg ggaacattgc aactggatat 1080tactgctcgc
ctgtcgatga gtctcaataa cacgccgctg cagggcgcgc atatcaacgt
1140cgtcagtggc aattttatta ttgcccagcc gctgggcgtc gatgacggcg
tggattactg 1200ccatagcggg cgtatccggc ggattgatga agacgcgatc
catcgtcaac tggacagcgg 1260tgcaatagtg ctaatggggc cggtcgctgt
ttcagtcact ggcgagagct ttaacctgac 1320ctcggaagag attgccactc
aactggccat caaactgaaa gctgaaaaga tgattggttt 1380ttgctcttcc
cagggcgtca ctaatgacga cggtgatatt gtctccgaac ttttccctaa
1440cgaagcgcaa gcgcgggtag aagcccagga agagaaaggc gattacaact
ccggtacggt 1500gcgctttttg cgtggcgcag tgaaagcctg ccgcagcggc
gtgcgtcgct gtcatttaat 1560cagttatcag gaagatggcg cgctgttgca
agagttgttc tcacgcgacg gtatcggtac 1620gcagattgtg atggaaagcg
ccgagcagat tcgtcgcgca acaatcaacg atattggcgg 1680tattctggag
ttgattcgcc cactggagca gcaaggtatt ctggtacgcc gttctcgcga
1740gcagctggag atggaaatcg acaaattcac cattattcag cgcgataaca
cgactattgc 1800ctgcgccgcg ctctatccgt tcccggaaga gaagattggg
gaaatggcct gtgtggcagt 1860tcacccggat taccgcagtt catcaagggg
tgaagttctg ctggaacgca ttgccgctca 1920ggctaagcag agcggcttaa
gcaaattgtt tgtgctgacc acgcgcagta ttcactggtt 1980ccaggaacgt
ggatttaccc cagtggatat tgatttactg cccgagagca aaaagcagtt
2040gtacaactac cagcgtaaat ccaaagtgtt gatggcggat ttagggtaag
tcgacgcatg 2100catcgataag ccgcgttctc atcctcccgc ctcctccccc
ataaaaaagc cagggggtgg 2160aggatttaag ccatctcctg atgac
2185391137DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 39atggatttaa attctaaaaa atatcagatg
cttaaagagc tatatgtaag cttcgctgaa 60aatgaagtta aacctttagc aacagaactt
gatgaagaag aaagatttcc ttatgaaaca 120gtggaaaaaa tggcaaaagc
aggaatgatg ggtataccat atccaaaaga atatggtgga 180gaaggtggag
acactgtagg atatataatg gcagttgaag aattgtctag agtttgtggt
240actacaggag ttatattatc agctcataca tctcttggct catggcctat
atatcaatat 300ggtaatgaag aacaaaaaca aaaattctta agaccactag
caagtggaga aaaattagga 360gcatttggtc ttactgagcc taatgctggt
acagatgcgt ctggccaaca aacaactgct 420gttttagacg gggatgaata
catacttaat ggctcaaaaa tatttataac aaacgcaata 480gctggtgaca
tatatgtagt aatggcaatg actgataaat ctaaggggaa caaaggaata
540tcagcattta tagttgaaaa aggaactcct gggtttagct ttggagttaa
agaaaagaaa 600atgggtataa gaggttcagc tacgagtgaa ttaatatttg
aggattgcag aatacctaaa 660gaaaatttac ttggaaaaga aggtcaagga
tttaagatag caatgtctac tcttgatggt 720ggtagaattg gtatagctgc
acaagcttta ggtttagcac aaggtgctct tgatgaaact 780gttaaatatg
taaaagaaag agtacaattt ggtagaccat tatcaaaatt ccaaaataca
840caattccaat tagctgatat ggaagttaag gtacaagcgg ctagacacct
tgtatatcaa 900gcagctataa ataaagactt aggaaaacct tatggagtag
aagcagcaat ggcaaaatta 960tttgcagctg aaacagctat ggaagttact
acaaaagctg tacaacttca tggaggatat 1020ggatacactc gtgactatcc
agtagaaaga atgatgagag atgctaagat aactgaaata 1080tatgaaggaa
ctagtgaagt tcaaagaatg gttatttcag gaaaactatt aaaatag
113740783DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 40atgaatatag tcgtttgtat aaaacaagtt
ccagatacaa cagaagttaa actagatcct 60aatacaggta ctttaattag agatggagta
ccaagtataa taaaccctga tgataaagca 120ggtttagaag aagctataaa
attaaaagaa gaaatgggtg ctcatgtaac tgttataaca 180atgggacctc
ctcaagcaga tatggcttta aaagaagctt tagcaatggg tgcagataga
240ggtatattat taacagatag agcatttgcg ggtgctgata cttgggcaac
ttcatcagca 300ttagcaggag cattaaaaaa tatagatttt gatattataa
tagctggaag acaggcgata 360gatggagata ctgcacaagt tggacctcaa
atagctgaac atttaaatct tccatcaata 420acatatgctg aagaaataaa
aactgaaggt gaatatgtat tagtaaaaag acaatttgaa 480gattgttgcc
atgacttaaa agttaaaatg ccatgcctta taacaactct taaagatatg
540aacacaccaa gatacatgaa agttggaaga atatatgatg ctttcgaaaa
tgatgtagta 600gaaacatgga ctgtaaaaga tatagaagtt gacccttcta
atttaggtct taaaggttct 660ccaactagtg tatttaaatc atttacaaaa
tcagttaaac cagctggtac aatatacaat 720gaagatgcga aaacatcagc
tggaattatc atagataaat taaaagagaa gtatatcata 780taa
783411011DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 41atgggtaacg ttttagtagt aatagaacaa
agagaaaatg taattcaaac tgtttcttta 60gaattactag gaaaggctac agaaatagca
aaagattatg atacaaaagt ttctgcatta 120cttttaggta gtaaggtaga
aggtttaata gatacattag cacactatgg tgcagatgag 180gtaatagtag
tagatgatga agctttagca gtgtatacaa ctgaaccata tacaaaagca
240gcttatgaag caataaaagc agctgaccct atagttgtat tatttggtgc
aacttcaata 300ggtagagatt tagcgcctag agtttctgct agaatacata
caggtcttac tgctgactgt 360acaggtcttg cagtagctga agatacaaaa
ttattattaa tgacaagacc tgcctttggt 420ggaaatataa tggcaacaat
agtttgtaaa gatttcagac ctcaaatgtc tacagttaga 480ccaggggtta
tgaagaaaaa tgaacctgat gaaactaaag aagctgtaat taaccgtttc
540aaggtagaat ttaatgatgc tgataaatta gttcaagttg tacaagtaat
aaaagaagct 600aaaaaacaag ttaaaataga agatgctaag atattagttt
ctgctggacg tggaatgggt 660ggaaaagaaa acttagacat actttatgaa
ttagctgaaa ttataggtgg agaagtttct 720ggttctcgtg ccactataga
tgcaggttgg ttagataaag caagacaagt tggtcaaact 780ggtaaaactg
taagaccaga cctttatata gcatgtggta tatctggagc aatacaacat
840atagctggta tggaagatgc tgagtttata gttgctataa ataaaaatcc
agaagctcca 900atatttaaat atgctgatgt tggtatagtt ggagatgttc
ataaagtgct tccagaactt 960atcagtcagt taagtgttgc aaaagaaaaa
ggtgaagttt tagctaacta a 1011421176DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 42atgagagaag
tagtaattgc cagtgcagct agaacagcag taggaagttt tggaggagca 60tttaaatcag
tttcagcggt agagttaggg gtaacagcag ctaaagaagc tataaaaaga
120gctaacataa ctccagatat gatagatgaa tctcttttag ggggagtact
tacagcaggt 180cttggacaaa atatagcaag acaaatagca ttaggagcag
gaataccagt agaaaaacca 240gctatgacta taaatatagt ttgtggttct
ggattaagat ctgtttcaat ggcatctcaa 300cttatagcat taggtgatgc
tgatataatg ttagttggtg gagctgaaaa catgagtatg 360tctccttatt
tagtaccaag tgcgagatat ggtgcaagaa tgggtgatgc tgcttttgtt
420gattcaatga taaaagatgg attatcagac atatttaata actatcacat
gggtattact 480gctgaaaaca tagcagagca atggaatata actagagaag
aacaagatga attagctctt 540gcaagtcaaa ataaagctga aaaagctcaa
gctgaaggaa aatttgatga agaaatagtt 600cctgttgtta taaaaggaag
aaaaggtgac actgtagtag ataaagatga atatattaag 660cctggcacta
caatggagaa acttgctaag ttaagacctg catttaaaaa agatggaaca
720gttactgctg gtaatgcatc aggaataaat gatggtgctg ctatgttagt
agtaatggct 780aaagaaaaag ctgaagaact aggaatagag cctcttgcaa
ctatagtttc ttatggaaca 840gctggtgttg accctaaaat aatgggatat
ggaccagttc cagcaactaa aaaagcttta 900gaagctgcta atatgactat
tgaagatata gatttagttg aagctaatga ggcatttgct 960gcccaatctg
tagctgtaat aagagactta aatatagata tgaataaagt taatgttaat
1020ggtggagcaa tagctatagg acatccaata ggatgctcag gagcaagaat
acttactaca 1080cttttatatg aaatgaagag aagagatgct aaaactggtc
ttgctacact ttgtataggc 1140ggtggaatgg gaactacttt aatagttaag agatag
117643846DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 43atgaaattag ctgtaatagg tagtggaact
atgggaagtg gtattgtaca aacttttgca 60agttgtggac atgatgtatg tttaaagagt
agaactcaag gtgctataga taaatgttta 120gctttattag ataaaaattt
aactaagtta gttactaagg gaaaaatgga tgaagctaca 180aaagcagaaa
tattaagtca tgttagttca actactaatt atgaagattt aaaagatatg
240gatttaataa tagaagcatc tgtagaagac atgaatataa agaaagatgt
tttcaagtta 300ctagatgaat tatgtaaaga agatactatc ttggcaacaa
atacttcatc attatctata 360acagaaatag cttcttctac taagcgccca
gataaagtta taggaatgca tttctttaat 420ccagttccta tgatgaaatt
agttgaagtt ataagtggtc agttaacatc aaaagttact 480tttgatacag
tatttgaatt atctaagagt atcaataaag taccagtaga tgtatctgaa
540tctcctggat ttgtagtaaa tagaatactt atacctatga taaatgaagc
tgttggtata 600tatgcagatg gtgttgcaag taaagaagaa atagatgaag
ctatgaaatt aggagcaaac 660catccaatgg gaccactagc attaggtgat
ttaatcggat tagatgttgt tttagctata 720atgaacgttt tatatactga
atttggagat actaaatata gacctcatcc acttttagct 780aaaatggtta
gagctaatca attaggaaga aaaactaaga taggattcta tgattataat 840aaataa
84644798DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide
44atgagtacaa gtgatgttaa agtttatgag aatgtagctg ttgaagtaga tggaaatata
60tgtacagtga aaatgaatag acctaaagcc cttaatgcaa taaattcaaa gactttagaa
120gaactttatg aagtatttgt agatattaat aatgatgaaa ctattgatgt
tgtaatattg 180acaggggaag gaaaggcatt tgtagctgga gcagatattg
catacatgaa agatttagat 240gctgtagctg ctaaagattt tagtatctta
ggagcaaaag cttttggaga aatagaaaat 300agtaaaaaag tagtgatagc
tgctgtaaac ggatttgctt taggtggagg atgtgaactt 360gcaatggcat
gtgatataag aattgcatct gctaaagcta aatttggtca gccagaagta
420actcttggaa taactccagg atatggagga actcaaaggc ttacaagatt
ggttggaatg 480gcaaaagcaa aagaattaat ctttacaggt caagttataa
aagctgatga agctgaaaaa 540atagggctag taaatagagt cgttgagcca
gacattttaa tagaagaagt tgagaaatta 600gctaagataa tagctaaaaa
tgctcagctt gcagttagat actctaaaga agcaatacaa 660cttggtgctc
aaactgatat aaatactgga atagatatag aatctaattt atttggtctt
720tgtttttcaa ctaaagacca aaaagaagga atgtcagctt tcgttgaaaa
gagagaagct 780aactttataa aagggtaa 79845903DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
45atgagaagtt ttgaagaagt aattaagttt gcaaaagaaa gaggacctaa aactatatca
60gtagcatgtt gccaagataa agaagtttta atggcagttg aaatggctag aaaagaaaaa
120atagcaaatg ccattttagt aggagatata gaaaagacta aagaaattgc
aaaaagcata 180gacatggata tcgaaaatta tgaactgata gatataaaag
atttagcaga agcatctcta 240aaatctgttg aattagtttc acaaggaaaa
gccgacatgg taatgaaagg cttagtagac 300acatcaataa tactaaaagc
agttttaaat aaagaagtag gtcttagaac tggaaatgta 360ttaagtcacg
tagcagtatt tgatgtagag ggatatgata gattattttt cgtaactgac
420gcagctatga acttagctcc tgatacaaat actaaaaagc aaatcataga
aaatgcttgc 480acagtagcac attcattaga tataagtgaa ccaaaagttg
ctgcaatatg cgcaaaagaa 540aaagtaaatc caaaaatgaa agatacagtt
gaagctaaag aactagaaga aatgtatgaa 600agaggagaaa tcaaaggttg
tatggttggt gggccttttg caattgataa tgcagtatct 660ttagaagcag
ctaaacataa aggtataaat catcctgtag caggacgagc tgatatatta
720ttagccccag atattgaagg tggtaacata ttatataaag ctttggtatt
cttctcaaaa 780tcaaaaaatg caggagttat agttggggct aaagcaccaa
taatattaac ttctagagca 840gacagtgaag aaactaaact aaactcaata
gctttaggtg ttttaatggc agcaaaggca 900taa 903461080DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
46atgagcaaaa tatttaaaat cttaacaata aatcctggtt cgacatcaac taaaatagct
60gtatttgata atgaggattt agtatttgaa aaaactttaa gacattcttc agaagaaata
120ggaaaatatg agaaggtgtc tgaccaattt gaatttcgta aacaagtaat
agaagaagct 180ctaaaagaag gtggagtaaa aacatctgaa ttagatgctg
tagtaggtag aggaggactt 240cttaaaccta taaaaggtgg tacttattca
gtaagtgctg ctatgattga agatttaaaa 300gtgggagttt taggagaaca
cgcttcaaac ctaggtggaa taatagcaaa acaaataggt 360gaagaagtaa
atgttccttc atacatagta gaccctgttg ttgtagatga attagaagat
420gttgctagaa tttctggtat gcctgaaata agtagagcaa gtgtagtaca
tgctttaaat 480caaaaggcaa tagcaagaag atatgctaga gaaataaaca
agaaatatga agatataaat 540cttatagttg cacacatggg tggaggagtt
tctgttggag ctcataaaaa tggtaaaata 600gtagatgttg caaacgcatt
agatggagaa ggacctttct ctccagaaag aagtggtgga 660ctaccagtag
gtgcattagt aaaaatgtgc tttagtggaa aatatactca agatgaaatt
720aaaaagaaaa taaaaggtaa tggcggacta gttgcatact taaacactaa
tgatgctaga 780gaagttgaag aaagaattga agctggtgat gaaaaagcta
aattagtata tgaagctatg 840gcatatcaaa tctctaaaga aataggagct
agtgctgcag ttcttaaggg agatgtaaaa 900gcaatattat taactggtgg
aatcgcatat tcaaaaatgt ttacagaaat gattgcagat 960agagttaaat
ttatagcaga tgtaaaagtt tatccaggtg aagatgaaat gattgcatta
1020gctcaaggtg gacttagagt tttaactggt gaagaagagg ctcaagttta
tgataactaa 1080471194DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 47atgatcgtaa
aacctatggt acgcaacaat atctgcctga acgcccatcc tcagggctgc 60aagaagggag
tggaagatca gattgaatat accaagaaac gcattaccgc agaagtcaaa
120gctggcgcaa aagctccaaa aaacgttctg gtgcttggct gctcaaatgg
ttacggcctg 180gcgagccgca ttactgctgc gttcggatac ggggctgcga
ccatcggcgt gtcctttgaa 240aaagcgggtt cagaaaccaa atatggtaca
ccgggatggt acaataattt ggcatttgat 300gaagcggcaa aacgcgaggg
tctttatagc gtgacgatcg acggcgatgc gttttcagac 360gagatcaagg
cccaggtaat tgaggaagcc aaaaaaaaag gtatcaaatt tgatctgatc
420gtatacagct tggccagccc agtacgtact gatcctgata caggtatcat
gcacaaaagc 480gttttgaaac cctttggaaa aacgttcaca ggcaaaacag
tagatccgtt tactggcgag 540ctgaaggaaa tctccgcgga accagcaaat
gacgaggaag cagccgccac tgttaaagtt 600atggggggtg aagattggga
acgttggatt aagcagctgt cgaaggaagg cctcttagaa 660gaaggctgta
ttaccttggc ctatagttat attggccctg aagctaccca agctttgtac
720cgtaaaggca caatcggcaa ggccaaagaa cacctggagg ccacagcaca
ccgtctcaac 780aaagagaacc cgtcaatccg tgccttcgtg agcgtgaata
aaggcctggt aacccgcgca 840agcgccgtaa tcccggtaat ccctctgtat
ctcgccagct tgttcaaagt aatgaaagag 900aagggcaatc atgaaggttg
tattgaacag atcacgcgtc tgtacgccga gcgcctgtac 960cgtaaagatg
gtacaattcc agttgatgag gaaaatcgca ttcgcattga tgattgggag
1020ttagaagaag acgtccagaa agcggtatcc gcgttgatgg agaaagtcac
gggtgaaaac 1080gcagaatctc tcactgactt agcggggtac cgccatgatt
tcttagctag taacggcttt 1140gatgtagaag gtattaatta tgaagcggaa
gttgaacgct tcgaccgtat ctga 119448861DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
48atgagtcagg cgctaaaaaa tttactgaca ttgttaaatc tggaaaaaat tgaggaagga
60ctctttcgcg gccagagtga agatttaggt ttacgccagg tgtttggcgg ccaggtcgtg
120ggtcaggcct tgtatgctgc aaaagagacc gtccctgaag agcggctggt
acattcgttt 180cacagctact ttcttcgccc tggcgatagt aagaagccga
ttatttatga tgtcgaaacg 240ctgcgtgacg gtaacagctt cagcgcccgc
cgggttgctg ctattcaaaa cggcaaaccg 300attttttata tgactgcctc
tttccaggca ccagaagcgg gtttcgaaca tcaaaaaaca 360atgccgtccg
cgccagcgcc tgatggcctc ccttcggaaa cgcaaatcgc ccaatcgctg
420gcgcacctgc tgccgccagt gctgaaagat aaattcatct gcgatcgtcc
gctggaagtc 480cgtccggtgg agtttcataa cccactgaaa ggtcacgtcg
cagaaccaca tcgtcaggtg 540tggatccgcg caaatggtag cgtgccggat
gacctgcgcg ttcatcagta tctgctcggt 600tacgcttctg atcttaactt
cctgccggta gctctacagc cgcacggcat cggttttctc 660gaaccgggga
ttcagattgc caccattgac cattccatgt ggttccatcg cccgtttaat
720ttgaatgaat ggctgctgta tagcgtggag agcacctcgg cgtccagcgc
acgtggcttt 780gtgcgcggtg agttttatac ccaagacggc gtactggttg
cctcgaccgt tcaggaaggg 840gtgatgcgta atcacaatta a
861491575DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 49atgcgcaaag tgccgattat cacggctgac
gaggccgcaa aactgatcaa ggacggcgac 60accgtgacaa ctagcggctt tgtgggtaac
gcgatccctg aggcccttga ccgtgcagtc 120gaaaagcgtt tcctggaaac
gggcgaaccg aagaacatta cttatgtata ttgcggcagt 180cagggcaatc
gcgacggtcg tggcgcagaa catttcgcgc atgaaggcct gctgaaacgt
240tatatcgctg gccattgggc gaccgtcccg gcgttaggga aaatggccat
ggagaataaa 300atggaggcct acaatgtctc tcagggcgcc ttgtgtcatc
tctttcgcga tattgcgagc 360cataaaccgg gtgtgttcac gaaagtagga
atcggcacct tcattgatcc acgtaacggt 420ggtgggaagg tcaacgatat
taccaaggaa gatatcgtag aactggtgga aattaaaggg 480caggaatacc
tgttttatcc ggcgttcccg atccatgtcg cgctgattcg tggcacctat
540gcggacgaga gtggtaacat cacctttgaa aaagaggtag cgcctttgga
agggacttct 600gtctgtcaag cggtgaagaa ctcgggtggc attgtcgtgg
ttcaggttga gcgtgtcgtc 660aaagcaggca cgctggatcc gcgccatgtg
aaagttccgg gtatctatgt agattacgta 720gtcgtcgcgg atccggagga
ccatcaacag tcccttgact gcgaatatga tcctgccctt 780agtggagagc
accgtcgtcc ggaggtggtg ggtgaaccac tgcctttatc cgcgaagaaa
840gtcatcggcc gccgtggcgc gattgagctc gagaaagacg ttgcagtgaa
ccttggggta 900ggtgcacctg agtatgtggc ctccgtggcc gatgaagaag
gcattgtgga ttttatgact 960ctcacagcgg agtccggcgc tatcggtggc
gttccagccg gcggtgttcg ctttggggcg 1020agctacaatg ctgacgcctt
gatcgaccag ggctaccaat ttgattatta cgacggtggg 1080ggtctggatc
tttgttacct gggtttagct gaatgcgacg aaaagggtaa tatcaatgtt
1140agccgcttcg gtcctcgtat cgctgggtgc ggcggattca ttaacattac
ccaaaacacg 1200ccgaaagtct tcttttgtgg gacctttaca gccggggggc
tgaaagtgaa aattgaagat 1260ggtaaggtga ttatcgttca ggaagggaaa
cagaagaaat tccttaaggc agtggagcaa 1320atcaccttta atggagacgt
ggccttagcg aacaagcaac aagttaccta catcacggag 1380cgttgcgtct
tcctcctcaa agaagacggt ttacaccttt cggaaatcgc gccaggcatc
1440gatctgcaga cccagatttt ggatgttatg gactttgccc cgatcattga
tcgtgacgca 1500aacgggcaga ttaaactgat ggacgcggcg ttattcgcag
aagggctgat gggcttgaaa 1560gaaatgaagt cttaa 1575501269DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
50atgagcttaa cccaaggcat gaaagctaaa caactgttag catactttca gggtaaagcc
60gatcaggatg cacgtgaagc gaaagcccgc ggtgagctgg tctgctggtc ggcgtcagtc
120gcgccgccgg aattttgcgt aacaatgggc attgccatga tctacccgga
gactcatgca 180gcgggcatcg gtgcccgcaa aggtgcgatg gacatgctgg
aagttgcgga ccgcaaaggc 240tacaacgtgg attgttgttc ctacggccgt
gtaaatatgg gttacatgga atgtttaaaa 300gaagccgcca tcacgggcgt
caagccggaa gttttggtta attcccctgc tgctgacgtt 360ccgcttcccg
atttggtgat tacgtgtaat aatatctgta acacgctgct gaaatggtac
420gaaaacttag cagcagaact cgatattcct tgcatcgtga tcgacgtacc
gtttaatcat 480accatgccga ttccggaata tgccaaggcc tacatcgcgg
accagttccg caatgcaatt 540tctcagctgg aagttatttg tggccgtccg
ttcgattgga agaaatttaa ggaggtcaaa 600gatcagaccc agcgtagcgt
ataccactgg aaccgcattg ccgagatggc gaaatacaag 660cctagcccgc
tgaacggctt cgatctgttc aattacatgg cgttaatcgt ggcgtgccgc
720agcctggatt atgcagaaat tacctttaaa gcgttcgcgg acgaattaga
agagaatttg 780aaggcgggta tctacgcctt taaaggtgcg gaaaaaacgc
gctttcaatg ggaaggtatc 840gcggtgtggc cacatttagg tcacacgttt
aaatctatga agaatctgaa ttcgattatg 900accggtacgg cataccccgc
cctttgggac ctgcactatg acgctaacga cgaatctatg 960cactctatgg
ctgaagcgta cacccgtatt tatattaata cttgtctgca gaacaaagta
1020gaggtcctgc ttgggatcat ggaaaaaggc caggtggatg gtaccgtata
tcatctgaat 1080cgcagctgca aactgatgag tttcctgaac gtggaaacgg
ctgaaattat taaagagaag 1140aacggtcttc cttacgtctc cattgatggc
gatcagaccg atcctcgcgt tttttctccg 1200gcccagtttg atacccgtgt
tcaggccctg gttgagatga tggaggccaa tatggcggca 1260gcggaataa
1269511125DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 51atgtcacgcg tggaggcaat cctgtcgcag
ctgaaagatg tcgccgcgaa tccgaaaaaa 60gccatggatg actataaagc tgaaacaggt
aagggcgcgg ttggtatcat gccgatctac 120agccccgaag aaatggtaca
cgccgctggc tatttgccga tgggaatctg gggcgcccag 180ggcaaaacga
ttagtaaagc gcgcacctat ctgcctgctt ttgcctgcag cgtaatgcag
240caggttatgg aattacagtg cgagggcgcg tatgatgacc tgtccgcagt
tatttttagc 300gtaccgtgcg acactctcaa atgtcttagc cagaaatgga
aaggtacgtc cccagtgatt 360gtatttacgc atccgcagaa ccgcggatta
gaagcggcga accaattctt ggttaccgag 420tatgaactgg taaaagcaca
actggaatca gttctgggtg tgaaaatttc aaacgccgcc 480ctggaaaatt
cgattgcaat ttataacgag aatcgtgccg tgatgcgtga gttcgtgaaa
540gtggcagcgg actatcctca agtcattgac gcagtgagcc gccacgcggt
ttttaaagcg 600cgccagttta tgcttaagga aaaacatacc gcacttgtga
aagaactgat cgctgagatt 660aaagcaacgc cagtccagcc gtgggacgga
aaaaaggttg tagtgacggg cattctgttg 720gaaccgaatg agttattaga
tatctttaat gagtttaaga tcgcgattgt tgatgatgat 780ttagcgcagg
aaagccgtca gatccgtgtt gacgttctgg acggagaagg cggaccgctc
840taccgtatgg ctaaagcgtg gcagcaaatg tatggctgct cgctggcaac
cgacaccaag 900aagggtcgcg gccgtatgtt aattaacaaa acgattcaga
ccggtgcgga cgctatcgta 960gttgcaatga tgaagttttg cgacccagaa
gaatgggatt atccggtaat gtaccgtgaa 1020tttgaagaaa aaggggtcaa
atcacttatg attgaggtgg atcaggaagt atcgtctttc 1080gaacagatta
aaacccgtct gcagtcattc gtcgaaatgc tttaa 112552779DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
52atgtatacct tggggattga tgtcggttct gcctctagta aagcggtgat tctgaaagat
60ggaaaagata ttgtcgctgc cgaggttgtc caagtcggta ccggctcctc gggtccccaa
120cgcgcactgg acaaagcctt tgaagtctct ggcttaaaaa aggaagacat
cagctacaca 180gtagctacgg gctatgggcg cttcaatttt agcgacgcgg
ataaacagat ttcggaaatt 240agctgtcatg ccaaaggcat ttatttctta
gtaccaactg cgcgcactat tattgacatt 300ggcggccaag atgcgaaagc
catccgcctg gacgacaagg ggggtattaa gcaattcttc 360atgaatgata
aatgcgcggc gggcacgggg cgtttcctgg aagtcatggc tcgcgtactt
420gaaaccaccc tggatgaaat ggctgaactg gatgaacagg cgactgacac
cgctcccatt 480tcaagcacct gcacggtttt cgccgaaagc gaagtaatta
gccaattgag caatggtgtc 540tcacgcaaca acatcattaa aggtgtccat
ctgagcgttg cgtcacgtgc gtgtggtctg 600gcgtatcgcg gcggtttgga
gaaagatgtt gttatgacag gtggcgtggc aaaaaatgca 660ggggtggtgc
gcgcggtggc gggcgttctg aagaccgatg ttatcgttgc tccgaatcct
720cagacgaccg gtgcactggg ggcagcgctg tatgcttatg aggccgccca gaagaagta
779531104DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 53atggccttca atagcgcaga tattaattct
ttccgcgata tttgggtgtt ttgtgaacag 60cgtgagggca aactgattaa caccgatttc
gaattaatta gcgaaggtcg taaactggct 120gacgaacgcg gaagcaaact
ggttggaatt ttgctggggc acgaagttga agaaatcgca 180aaagaattag
gcggctatgg tgcggacaag gtaattgtgt gcgatcatcc ggaacttaaa
240ttttacacta cggatgctta tgccaaagtt ttatgtgacg tcgtgatgga
agagaaaccg 300gaggtaattt tgatcggtgc caccaacatt ggccgtgatc
tcggaccgcg ttgtgctgca 360cgcttgcaca cggggctgac ggctgattgc
acgcacctgg atattgatat gaataaatat 420gtggactttc ttagcaccag
tagcaccttg gatatctcgt cgatgacttt ccctatggaa 480gatacaaacc
ttaaaatgac gcgccctgca tttggcggac atctgatggc aacgatcatt
540tgtccacgct tccgtccctg tatgagcaca gtgcgccccg gagtgatgaa
gaaagcggag 600ttctcgcagg agatggcgca agcatgtcaa gtagtgaccc
gtcacgtaaa tttgtcggat 660gaagacctta aaactaaagt aattaatatc
gtgaaggaaa cgaaaaagat tgtggatctg 720atcggcgcag aaattattgt
gtcagttggt cgtggtatct cgaaagatgt ccaaggtgga 780attgcactgg
ctgaaaaact tgcggacgca tttggtaacg gtgtcgtggg cggctcgcgc
840gcagtgattg attccggctg gttacctgcg gatcatcagg ttggacaaac
cggtaagacc 900gtgcacccga aagtctacgt ggcgctgggt attagtgggg
ctatccagca taaggctggg 960atgcaagact ctgaactgat cattgccgtc
aacaaagacg aaacggcgcc tatcttcgac 1020tgcgccgatt atggcatcac
cggtgattta tttaaaatcg taccgatgat gatcgacgcg 1080atcaaagagg
gtaaaaacgc atga 110454804DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 54atgcgcatct
atgtgtgtgt gaaacaagtc ccagatacga gcggcaaggt ggccgttaac 60cctgatggga
cccttaaccg tgcctcaatg gcagcgatta ttaacccgga cgatatgtcc
120gcgatcgaac aggcattaaa actgaaagat gaaaccggat gccaggttac
ggcgcttacg 180atgggtcctc ctcctgccga gggcatgttg cgcgaaatta
ttgcaatggg ggccgacgat 240ggtgtgctga tttcggcccg tgaatttggg
gggtccgata ccttcgcaac cagtcaaatt 300attagcgcgg caatccataa
attaggctta agcaatgaag acatgatctt ttgcggtcgt 360caggccattg
acggtgatac ggcccaagtc ggccctcaaa ttgccgaaaa actgagcatc
420ccacaggtaa cctatggcgc aggaatcaaa aaatctggtg atttagtgct
ggtgaagcgt 480atgttggagg atggttatat gatgatcgaa gtcgaaactc
catgtctgat tacctgcatt 540caggataaag cggtaaaacc acgttacatg
actctcaacg gtattatgga atgctactcc 600aagccgctcc tcgttctcga
ttacgaagca ctgaaagatg aaccgctgat cgaacttgat 660accattgggc
ttaaaggctc cccgacgaat atctttaaat cgtttacgcc gcctcagaaa
720ggcgttggtg tcatgctcca aggcaccgat aaggaaaaag tcgaggatct
ggtggataag 780ctgatgcaga aacatgtcat ctaa 804551185DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
55atgttcttac tgaagattaa aaaagaacgt atgaaacgca tggactttag tttaacgcgt
60gaacaggaga tgttaaaaaa actggcgcgt cagtttgctg agatcgagct ggaaccggtg
120gccgaagaga ttgatcgtga gcacgttttt cctgcagaaa actttaagaa
gatggcggaa 180attggcttaa ccggcattgg tatcccgaaa gaatttggtg
gctccggtgg aggcaccctg 240gagaaggtca ttgccgtgtc agaattcggc
aaaaagtgta tggcctcagc ttccatttta 300agcattcatc ttatcgcgcc
gcaggcaatc tacaaatatg ggaccaaaga acagaaagag 360acgtacctgc
cgcgtcttac caaaggtggt gaactgggcg cctttgcgct gacagaacca
420aacgccggaa gcgatgccgg cgcggtaaaa acgaccgcga ttctggacag
ccagacaaac 480gagtacgtgc tgaatggcac caaatgcttt atcagcgggg
gcgggcgcgc gggtgttctt 540gtaatttttg cgcttactga accgaaaaaa
ggtctgaaag ggatgagcgc gattatcgtg 600gagaaaggga ccccgggctt
cagcatcggc aaggtggaga gcaagatggg gatcgcaggt 660tcggaaaccg
cggaacttat cttcgaagat tgtcgcgttc cggctgccaa ccttttaggt
720aaagaaggca aaggctttaa aattgctatg gaagccctgg atggcgcccg
tattggcgtg 780ggcgctcaag caatcggaat tgccgagggg gcgatcgacc
tgagtgtgaa gtacgttcac 840gagcgcattc aatttggtaa accgatcgcg
aatctgcagg gaattcaatg gtatatcgcg 900gatatggcga ccaaaaccgc
cgcggcacgc gcacttgttg agtttgcagc gtatcttgaa 960gacgcgggta
aaccgttcac aaaggaatct gctatgtgca agctgaacgc ctccgaaaac
1020gcgcgttttg tgacaaattt agctctgcag attcacgggg gttacggtta
tatgaaagat 1080tatccgttag agcgtatgta tcgcgatgct aagattacgg
aaatttacga ggggacatca 1140gaaatccata aggtggtgat tgcgcgtgaa
gtaatgaaac gctaa 1185562463DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 56atgcgagtgt
tgaagttcgg cggtacatca gtggcaaatg cagaacgttt tctgcgtgtt 60gccgatattc
tggaaagcaa tgccaggcag gggcaggtgg ccaccgtcct ctctgccccc
120gccaaaatca ccaaccacct ggtggcgatg attgaaaaaa ccattagcgg
ccaggatgct 180ttacccaata tcagcgatgc cgaacgtatt tttgccgaac
ttttgacggg actcgccgcc 240gcccagccgg ggttcccgct ggcgcaattg
aaaactttcg tcgatcagga atttgcccaa 300ataaaacatg tcctgcatgg
cattagtttg ttggggcagt gcccggatag catcaacgct 360gcgctgattt
gccgtggcga gaaaatgtcg atcgccatta tggccggcgt attagaagcg
420cgcggtcaca acgttactgt tatcgatccg gtcgaaaaac tgctggcagt
ggggcattac 480ctcgaatcta ccgtcgatat tgctgagtcc acccgccgta
ttgcggcaag ccgcattccg 540gctgatcaca tggtgctgat ggcaggtttc
accgccggta atgaaaaagg cgaactggtg 600gtgcttggac gcaacggttc
cgactactct gctgcggtgc tggctgcctg tttacgcgcc 660gattgttgcg
agatttggac ggacgttgac ggggtctata cctgcgaccc gcgtcaggtg
720cccgatgcga ggttgttgaa gtcgatgtcc taccaggaag cgatggagct
ttcctacttc 780ggcgctaaag ttcttcaccc ccgcaccatt acccccatcg
cccagttcca gatcccttgc 840ctgattaaaa ataccggaaa tcctcaagca
ccaggtacgc tcattggtgc cagccgtgat 900gaagacgaat taccggtcaa
gggcatttcc aatctgaata acatggcaat gttcagcgtt
960tctggtccgg ggatgaaagg gatggtcggc atggcggcgc gcgtctttgc
agcgatgtca 1020cgcgcccgta tttccgtggt gctgattacg caatcatctt
ccgaatacag catcagtttc 1080tgcgttccac aaagcgactg tgtgcgagct
gaacgggcaa tgcaggaaga gttctacctg 1140gaactgaaag aaggcttact
ggagccgctg gcagtgacgg aacggctggc cattatctcg 1200gtggtaggtg
atggtatgcg caccttgcgt gggatctcgg cgaaattctt tgccgcactg
1260gcccgcgcca atatcaacat tgtcgccatt gctcagagat cttctgaacg
ctcaatctct 1320gtcgtggtaa ataacgatga tgcgaccact ggcgtgcgcg
ttactcatca gatgctgttc 1380aataccgatc aggttatcga agtgtttgtg
attggcgtcg gtggcgttgg cggtgcgctg 1440ctggagcaac tgaagcgtca
gcaaagctgg ctgaagaata aacatatcga cttacgtgtc 1500tgcggtgttg
ccaactcgaa ggctctgctc accaatgtac atggccttaa tctggaaaac
1560tggcaggaag aactggcgca agccaaagag ccgtttaatc tcgggcgctt
aattcgcctc 1620gtgaaagaat atcatctgct gaacccggtc attgttgact
gcacttccag ccaggcagtg 1680gcggatcaat atgccgactt cctgcgcgaa
ggtttccacg ttgtcacgcc gaacaaaaag 1740gccaacacct cgtcgatgga
ttactaccat cagttgcgtt atgcggcgga aaaatcgcgg 1800cgtaaattcc
tctatgacac caacgttggg gctggattac cggttattga gaacctgcaa
1860aatctgctca atgcaggtga tgaattgatg aagttctccg gcattctttc
tggttcgctt 1920tcttatatct tcggcaagtt agacgaaggc atgagtttct
ccgaggcgac cacgctggcg 1980cgggaaatgg gttataccga accggacccg
cgagatgatc tttctggtat ggatgtggcg 2040cgtaaactat tgattctcgc
tcgtgaaacg ggacgtgaac tggagctggc ggatattgaa 2100attgaacctg
tgctgcccgc agagtttaac gccgagggtg atgttgccgc ttttatggcg
2160aatctgtcac aactcgacga tctctttgcc gcgcgcgtgg cgaaggcccg
tgatgaagga 2220aaagttttgc gctatgttgg caatattgat gaagatggcg
tctgccgcgt gaagattgcc 2280gaagtggatg gtaatgatcc gctgttcaaa
gtgaaaaatg gcgaaaacgc cctggccttc 2340tatagccact attatcagcc
gctgccgttg gtactgcgcg gatatggtgc gggcaatgac 2400gttacagctg
ccggtgtctt tgctgatctg ctacgtaccc tctcatggaa gttaggagtc 2460tga
246357933DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 57atggttaaag tttatgcccc ggcttccagt
gccaatatga gcgtcgggtt tgatgtgctc 60ggggcggcgg tgacacctgt tgatggtgca
ttgctcggag atgtagtcac ggttgaggcg 120gcagagacat tcagtctcaa
caacctcgga cgctttgccg ataagctgcc gtcagaacca 180cgggaaaata
tcgtttatca gtgctgggag cgtttttgcc aggaactggg taagcaaatt
240ccagtggcga tgaccctgga aaagaatatg ccgatcggtt cgggcttagg
ctccagtgcc 300tgttcggtgg tcgcggcgct gatggcgatg aatgaacact
gcggcaagcc gcttaatgac 360actcgtttgc tggctttgat gggcgagctg
gaaggccgta tctccggcag cattcattac 420gacaacgtgg caccgtgttt
tctcggtggt atgcagttga tgatcgaaga aaacgacatc 480atcagccagc
aagtgccagg gtttgatgag tggctgtggg tgctggcgta tccggggatt
540aaagtctcga cggcagaagc cagggctatt ttaccggcgc agtatcgccg
ccaggattgc 600attgcgcacg ggcgacatct ggcaggcttc attcacgcct
gctattcccg tcagcctgag 660cttgccgcga agctgatgaa agatgttatc
gctgaaccct accgtgaacg gttactgcca 720ggcttccggc aggcgcggca
ggcggtcgcg gaaatcggcg cggtagcgag cggtatctcc 780ggctccggcc
cgaccttgtt cgctctgtgt gacaagccgg aaaccgccca gcgcgttgcc
840gactggttgg gtaagaacta cctgcaaaat caggaaggtt ttgttcatat
ttgccggctg 900gatacggcgg gcgcacgagt actggaaaac taa
933581287DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 58atgaaactct acaatctgaa agatcacaac
gagcaggtca gctttgcgca agccgtaacc 60caggggttgg gcaaaaatca ggggctgttt
tttccgcacg acctgccgga attcagcctg 120actgaaattg atgagatgct
gaagctggat tttgtcaccc gcagtgcgaa gatcctctcg 180gcgtttattg
gtgatgaaat cccacaggaa atcctggaag agcgcgtgcg cgcggcgttt
240gccttcccgg ctccggtcgc caatgttgaa agcgatgtcg gttgtctgga
attgttccac 300gggccaacgc tggcatttaa agatttcggc ggtcgcttta
tggcacaaat gctgacccat 360attgcgggtg ataagccagt gaccattctg
accgcgacct ccggtgatac cggagcggca 420gtggctcatg ctttctacgg
tttaccgaat gtgaaagtgg ttatcctcta tccacgaggc 480aaaatcagtc
cactgcaaga aaaactgttc tgtacattgg gcggcaatat cgaaactgtt
540gccatcgacg gcgatttcga tgcctgtcag gcgctggtga agcaggcgtt
tgatgatgaa 600gaactgaaag tggcgctagg gttaaactcg gctaactcga
ttaacatcag ccgtttgctg 660gcgcagattt gctactactt tgaagctgtt
gcgcagctgc cgcaggagac gcgcaaccag 720ctggttgtct cggtgccaag
cggaaacttc ggcgatttga cggcgggtct gctggcgaag 780tcactcggtc
tgccggtgaa acgttttatt gctgcgacca acgtgaacga taccgtgcca
840cgtttcctgc acgacggtca gtggtcaccc aaagcgactc aggcgacgtt
atccaacgcg 900atggacgtga gtcagccgaa caactggccg cgtgtggaag
agttgttccg ccgcaaaatc 960tggcaactga aagagctggg ttatgcagcc
gtggatgatg aaaccacgca acagacaatg 1020cgtgagttaa aagaactggg
ctacacttcg gagccgcacg ctgccgtagc ttatcgtgcg 1080ctgcgtgatc
agttgaatcc aggcgaatat ggcttgttcc tcggcaccgc gcatccggcg
1140aaatttaaag agagcgtgga agcgattctc ggtgaaacgt tggatctgcc
aaaagagctg 1200gcagaacgtg ctgatttacc cttgctttca cataatctgc
ccgccgattt tgctgcgttg 1260cgtaaattga tgatgaatca tcagtaa
1287591311DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 59atgagtgaaa catacgtgtc tgagaaaagt
ccaggagtga tggctagcgg agcggagctg 60attcgtgccg ccgacattca aacggcgcag
gcacgaattt cctccgtcat tgcaccaact 120ccattgcagt attgccctcg
tctttctgag gaaaccggag cggaaatcta ccttaagcgt 180gaggatctgc
aggatgttcg ttcctacaag atccgcggtg cgctgaactc tggagcgcag
240ctcacccaag agcagcgcga tgcaggtatc gttgccgcat ctgcaggtaa
ccatgcccag 300ggcgtggcct atgtgtgcaa gtccttgggc gttcagggac
gcatctatgt tcctgtgcag 360actccaaagc aaaagcgtga ccgcatcatg
gttcacggcg gagagtttgt ctccttggtg 420gtcactggca ataacttcga
cgaagcatcg gctgcagcgc atgaagatgc agagcgcacc 480ggcgcaacgc
tgatcgagcc tttcgatgct cgcaacaccg tcatcggtca gggcaccgtg
540gctgctgaga tcttgtcgca gctgacttcc atgggcaaga gtgcagatca
cgtgatggtt 600ccagtcggcg gtggcggact tcttgcaggt gtggtcagct
acatggctga tatggcacct 660cgcactgcga tcgttggtat cgaaccagcg
ggagcagcat ccatgcaggc tgcattgcac 720aatggtggac caatcacttt
ggagactgtt gatccctttg tggacggcgc agcagtcaaa 780cgtgtcggag
atctcaacta caccatcgtg gagaagaacc agggtcgcgt gcacatgatg
840agcgcgaccg agggcgctgt gtgtactgag atgctcgatc tttaccaaaa
cgaaggcatc 900atcgcggagc ctgctggcgc gctgtctatc gctgggttga
aggaaatgtc ctttgcacct 960ggttctgcag tggtgtgcat catctctggt
ggcaacaacg atgtgctgcg ttatgcggaa 1020atcgctgagc gctccttggt
gcaccgcggt ttgaagcact acttcttggt gaacttcccg 1080caaaagcctg
gtcagttgcg tcacttcctg gaagatatcc tgggaccgga tgatgacatc
1140acgctgtttg agtacctcaa gcgcaacaac cgtgagaccg gtactgcgtt
ggtgggtatt 1200cacttgagtg aagcatcagg attggattct ttgctggaac
gtatggagga atcggcaatt 1260gattcccgtc gcctcgagcc gggcacccct
gagtacgaat acttgaccta a 1311602664DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 60atgtcagaac
gtttcccaaa tgacgtggat ccgatcgaaa ctcgcgactg gctccaggcg 60atcgaatcgg
tcatccgtga agaaggtgtt gagcgtgctc agtatctgat cgaccaactg
120cttgctgaag cccgcaaagg cggtgtaaac gtagccgcag gcacaggtat
cagcaactac 180atcaacacca tccccgttga agaacaaccg gagtatccgg
gtaatctgga actggaacgc 240cgtattcgtt cagctatccg ctggaacgcc
atcatgacgg tgctgcgtgc gtcgaaaaaa 300gacctcgaac tgggcggcca
tatggcgtcc ttccagtctt ccgcaaccat ttatgatgtg 360tgctttaacc
acttcttccg tgcacgcaac gagcaggatg gcggcgacct ggtttacttc
420cagggccaca tctccccggg cgtgtacgct cgtgctttcc tggaaggtcg
tctgactcag 480gagcagctgg ataacttccg tcaggaagtt cacggcaatg
gcctctcttc ctatccgcac 540ccgaaactga tgccggaatt ctggcagttc
ccgaccgtat ctatgggtct gggtccgatt 600ggtgctattt accaggctaa
attcctgaaa tatctggaac accgtggcct gaaagatacc 660tctaaacaaa
ccgtttacgc gttcctcggt gacggtgaaa tggacgaacc ggaatccaaa
720ggtgcgatca ccatcgctac ccgtgaaaaa ctggataacc tggtcttcgt
tatcaactgt 780aacctgcagc gtcttgacgg cccggtcacc ggtaacggca
agatcatcaa cgaactggaa 840ggcatcttcg aaggtgctgg ctggaacgtg
atcaaagtga tgtggggtag ccgttgggat 900gaactgctgc gtaaggatac
cagcggtaaa ctgatccagc tgatgaacga aaccgttgac 960ggcgactacc
agaccttcaa atcgaaagat ggtgcgtacg ttcgtgaaca cttcttcggt
1020aaatatcctg aaaccgcagc actggttgca gactggactg acgagcagat
ctgggcactg 1080aaccgtggtg gtcacgatcc gaagaaaatc tacgctgcat
tcaagaaagc gcaggaaacc 1140aaaggcaaag cgacagtaat ccttgctcat
accattaaag gttacggcat gggcgacgcg 1200gctgaaggta aaaacatcgc
gcaccaggtt aagaaaatga acatggacgg tgtgcgtcat 1260atccgcgacc
gtttcaatgt gccggtgtct gatgcagata tcgaaaaact gccgtacatc
1320accttcccgg aaggttctga agagcatacc tatctgcacg ctcagcgtca
gaaactgcac 1380ggttatctgc caagccgtca gccgaacttc accgagaagc
ttgagctgcc gagcctgcaa 1440gacttcggcg cgctgttgga agagcagagc
aaagagatct ctaccactat cgctttcgtt 1500cgtgctctga acgtgatgct
gaagaacaag tcgatcaaag atcgtctggt accgatcatc 1560gccgacgaag
cgcgtacttt cggtatggaa ggtctgttcc gtcagattgg tatttacagc
1620ccgaacggtc agcagtacac cccgcaggac cgcgagcagg ttgcttacta
taaagaagac 1680gagaaaggtc agattctgca ggaagggatc aacgagctgg
gcgcaggttg ttcctggctg 1740gcagcggcga cctcttacag caccaacaat
ctgccgatga tcccgttcta catctattac 1800tcgatgttcg gcttccagcg
tattggcgat ctgtgctggg cggctggcga ccagcaagcg 1860cgtggcttcc
tgatcggcgg tacttccggt cgtaccaccc tgaacggcga aggtctgcag
1920cacgaagatg gtcacagcca cattcagtcg ctgactatcc cgaactgtat
ctcttacgac 1980ccggcttacg cttacgaagt tgctgtcatc atgcatgacg
gtctggagcg tatgtacggt 2040gaaaaacaag agaacgttta ctactacatc
actacgctga acgaaaacta ccacatgccg 2100gcaatgccgg aaggtgctga
ggaaggtatc cgtaaaggta tctacaaact cgaaactatt 2160gaaggtagca
aaggtaaagt tcagctgctc ggctccggtt ctatcctgcg tcacgtccgt
2220gaagcagctg agatcctggc gaaagattac ggcgtaggtt ctgacgttta
tagcgtgacc 2280tccttcaccg agctggcgcg tgatggtcag gattgtgaac
gctggaacat gctgcacccg 2340ctggaaactc cgcgcgttcc gtatatcgct
caggtgatga acgacgctcc ggcagtggca 2400tctaccgact atatgaaact
gttcgctgag caggtccgta cttacgtacc ggctgacgac 2460taccgcgtac
tgggtactga tggcttcggt cgttccgaca gccgtgagaa cctgcgtcac
2520cacttcgaag ttgatgcttc ttatgtcgtg gttgcggcgc tgggcgaact
ggctaaacgt 2580ggcgaaatcg ataagaaagt ggttgctgac gcaatcgcca
aattcaacat cgatgcagat 2640aaagttaacc cgcgtctggc gtaa
2664611893DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 61atggctatcg aaatcaaagt accggacatc
ggggctgatg aagttgaaat caccgagatc 60ctggtcaaag tgggcgacaa agttgaagcc
gaacagtcgc tgatcaccgt agaaggcgac 120aaagcctcta tggaagttcc
gtctccgcag gcgggtatcg ttaaagagat caaagtctct 180gttggcgata
aaacccagac cggcgcactg attatgattt tcgattccgc cgacggtgca
240gcagacgctg cacctgctca ggcagaagag aagaaagaag cagctccggc
agcagcacca 300gcggctgcgg cggcaaaaga cgttaacgtt ccggatatcg
gcagcgacga agttgaagtg 360accgaaatcc tggtgaaagt tggcgataaa
gttgaagctg aacagtcgct gatcaccgta 420gaaggcgaca aggcttctat
ggaagttccg gctccgtttg ctggcaccgt gaaagagatc 480aaagtgaacg
tgggtgacaa agtgtctacc ggctcgctga ttatggtctt cgaagtcgcg
540ggtgaagcag gcgcggcagc tccggccgct aaacaggaag cagctccggc
agcggcccct 600gcaccagcgg ctggcgtgaa agaagttaac gttccggata
tcggcggtga cgaagttgaa 660gtgactgaag tgatggtgaa agtgggcgac
aaagttgccg ctgaacagtc actgatcacc 720gtagaaggcg acaaagcttc
tatggaagtt ccggcgccgt ttgcaggcgt cgtgaaggaa 780ctgaaagtca
acgttggcga taaagtgaaa actggctcgc tgattatgat cttcgaagtt
840gaaggcgcag cgcctgcggc agctcctgcg aaacaggaag cggcagcgcc
ggcaccggca 900gcaaaagctg aagccccggc agcagcacca gctgcgaaag
cggaaggcaa atctgaattt 960gctgaaaacg acgcttatgt tcacgcgact
ccgctgatcc gccgtctggc acgcgagttt 1020ggtgttaacc ttgcgaaagt
gaagggcact ggccgtaaag gtcgtatcct gcgcgaagac 1080gttcaggctt
acgtgaaaga agctatcaaa cgtgcagaag cagctccggc agcgactggc
1140ggtggtatcc ctggcatgct gccgtggccg aaggtggact tcagcaagtt
tggtgaaatc 1200gaagaagtgg aactgggccg catccagaaa atctctggtg
cgaacctgag ccgtaactgg 1260gtaatgatcc cgcatgttac tcacttcgac
aaaaccgata tcaccgagtt ggaagcgttc 1320cgtaaacagc agaacgaaga
agcggcgaaa cgtaagctgg atgtgaagat caccccggtt 1380gtcttcatca
tgaaagccgt tgctgcagct cttgagcaga tgcctcgctt caatagttcg
1440ctgtcggaag acggtcagcg tctgaccctg aagaaataca tcaacatcgg
tgtggcggtg 1500gataccccga acggtctggt tgttccggta ttcaaagacg
tcaacaagaa aggcatcatc 1560gagctgtctc gcgagctgat gactatttct
aagaaagcgc gtgacggtaa gctgactgcg 1620ggcgaaatgc agggcggttg
cttcaccatc tccagcatcg gcggcctggg tactacccac 1680ttcgcgccga
ttgtgaacgc gccggaagtg gctatcctcg gcgtttccaa gtccgcgatg
1740gagccggtgt ggaatggtaa agagttcgtg ccgcgtctga tgctgccgat
ttctctctcc 1800ttcgaccacc gcgtgatcga cggtgctgat ggtgcccgtt
tcattaccat cattaacaac 1860acgctgtctg acattcgccg tctggtgatg taa
1893621425DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 62atgagtactg aaatcaaaac tcaggtcgtg
gtacttgggg caggccccgc aggttactcc 60gctgccttcc gttgcgctga tttaggtctg
gaaaccgtaa tcgtagaacg ttacaacacc 120cttggcggtg tttgcctgaa
cgtcggctgt atcccttcta aagcactgct gcacgtagca 180aaagttatcg
aagaagccaa agcgctggct gaacacggta tcgtcttcgg cgaaccgaaa
240accgatatcg acaagattcg tacctggaaa gagaaagtga tcaatcagct
gaccggtggt 300ctggctggta tggcgaaagg ccgcaaagtc aaagtggtca
acggtctggg taaattcacc 360ggggctaaca ccctggaagt tgaaggtgag
aacggcaaaa ccgtgatcaa cttcgacaac 420gcgatcattg cagcgggttc
tcgcccgatc caactgccgt ttattccgca tgaagatccg 480cgtatctggg
actccactga cgcgctggaa ctgaaagaag taccagaacg cctgctggta
540atgggtggcg gtatcatcgg tctggaaatg ggcaccgttt accacgcgct
gggttcacag 600attgacgtgg ttgaaatgtt cgaccaggtt atcccggcag
ctgacaaaga catcgttaaa 660gtcttcacca agcgtatcag caagaaattc
aacctgatgc tggaaaccaa agttaccgcc 720gttgaagcga aagaagacgg
catttatgtg acgatggaag gcaaaaaagc acccgctgaa 780ccgcagcgtt
acgacgccgt gctggtagcg attggtcgtg tgccgaacgg taaaaacctc
840gacgcaggca aagcaggcgt ggaagttgac gaccgtggtt tcatccgcgt
tgacaaacag 900ctgcgtacca acgtaccgca catctttgct atcggcgata
tcgtcggtca accgatgctg 960gcacacaaag gtgttcacga aggtcacgtt
gccgctgaag ttatcgccgg taagaaacac 1020tacttcgatc cgaaagttat
cccgtccatc gcctatacca aaccagaagt tgcatgggtg 1080ggtctgactg
agaaagaagc gaaagagaaa ggcatcagct atgaaaccgc caccttcccg
1140tgggctgctt ctggtcgtgc tatcgcttcc gactgcgcag acggtatgac
caagctgatt 1200ttcgacaaag aatctcaccg tgtgatcggt ggtgcgattg
tcggtactaa cggcggcgag 1260ctgctgggtg aaatcggcct ggcaatcgaa
atgggttgtg atgctgaaga catcgcactg 1320accatccacg cgcacccgac
tctgcacgag tctgtgggcc tggcggcaga agtgttcgaa 1380ggtagcatta
ccgacctgcc gaacccgaaa gcgaagaaga agtaa 142563355DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
63tgtggctttt atgaaaatca cacagtgatc acaaatttta aacagagcac aaaatgctgc
60ctcgaaatga gggcgggaaa ataaggttat cagccttgtt ttctccctca ttacttgaag
120gatatgaagc taaaaccctt ttttataaag catttgtccg aattcggaca
taatcaaaaa 180agcttaatta agatcaattt gatctacatc tctttaacca
acaatatgta agatctcaac 240tatcgcatcc gtggattaat tcaattataa
cttctctcta acgctgtgta tcgtaacggt 300aacactgtag aggggagcac
attgatgcga attcattaaa gaggagaaag gtacc 35564228DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
64ttccgaaaat tcctggcgag cagataaata agaattgttc ttatcaatat atctaactca
60ttgaatcttt attagttttg tttttcacgc ttgttaccac tattagtgtg ataggaacag
120ccagaatagc ggaacacata gccggtgcta tacttaatct cgttaattac
tgggacataa 180catcaagagg atatgaaatt cgaattcatt aaagaggaga aaggtacc
22865334DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 65gcttagatca ggtgattgcc ctttgtttat
gagggtgttg taatccatgt cgttgttgca 60tttgtaaggg caacacctca gcctgcaggc
aggcactgaa gataccaaag ggtagttcag 120attacacggt cacctggaaa
gggggccatt ttacttttta tcgccgctgg cggtgcaaag 180ttcacaaagt
tgtcttacga aggttgtaag gtaaaactta tcgatttgat aatggaaacg
240cattagccga atcggcaaaa attggttacc ttacatctca tcgaaaacac
ggaggaagta 300tagatgcgaa ttcattaaag aggagaaagg tacc
33466134DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 66ctcgagttca ttatccatcc tccatcgcca
cgatagttca tggcgatagg tagaatagca 60atgaacgatt atccctatca agcattctga
ctgataattg ctcacacgaa ttcattaaag 120aggagaaagg tacc
134673518DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 67cgacggtggc gataggcatc cgggtggtgc
tcaaaagcag cttcgcctga ctgatgcgct 60ggtcctcgcg ccagcttaat acgctaatcc
ctaactgctg gcggaacaaa tgcgacagac 120gcgacggcga caggcagaca
tgctgtgcga cgctggcgat atcaaaatta ctgtctgcca 180ggtgatcgct
gatgtactga caagcctcgc gtacccgatt atccatcggt ggatggagcg
240actcgttaat cgcttccatg cgccgcagta acaattgctc aagcagattt
atcgccagca 300attccgaata gcgcccttcc ccttgtccgg cattaatgat
ttgcccaaac aggtcgctga 360aatgcggctg gtgcgcttca tccgggcgaa
agaaaccggt attggcaaat atcgacggcc 420agttaagcca ttcatgccag
taggcgcgcg gacgaaagta aacccactgg tgataccatt 480cgtgagcctc
cggatgacga ccgtagtgat gaatctctcc aggcgggaac agcaaaatat
540cacccggtcg gcagacaaat tctcgtccct gatttttcac caccccctga
ccgcgaatgg 600tgagattgag aatataacct ttcattccca gcggtcggtc
gataaaaaaa tcgagataac 660cgttggcctc aatcggcgtt aaacccgcca
ccagatgggc gttaaacgag tatcccggca 720gcaggggatc attttgcgct
tcagccatac ttttcatact cccgccattc agagaagaaa 780ccaattgtcc
atattgcatc agacattgcc gtcactgcgt cttttactgg ctcttctcgc
840taacccaacc ggtaaccccg cttattaaaa gcattctgta acaaagcggg
accaaagcca 900tgacaaaaac gcgtaacaaa agtgtctata atcacggcag
aaaagtccac attgattatt 960tgcacggcgt cacactttgc tatgccatag
catttttatc cataagatta gcggatccag 1020cctgacgctt tttttcgcaa
ctctctactg tttctccata cccgtttttt tggatggagt 1080gaaacgatgg
taaaggaacg taaaaccgag ttggtcgagg gattccgcca ttcggttccc
1140tgtatcaata cccaccgggg aaaaacgttt gtcatcatgc tcggcggtga
agccattgag 1200catgagaatt tctccagtat cgttaatgat atcgggttgt
tgcacagcct cggcatccgt 1260ctggtggtgg tctatggcgc acgtccgcag
atcgacgcaa atctggctgc gcatcaccac 1320gaaccgctgt atcacaagaa
tatacgtgtg accgacgcca aaacactgga actggtgaag 1380caggctgcgg
gaacattgca actggatatt actgctcgcc tgtcgatgag tctcaataac
1440acgccgctgc agggcgcgca tatcaacgtc gtcagtggca attttattat
tgcccagccg 1500ctgggcgtcg atgacggcgt ggattactgc catagcgggc
gtatccggcg gattgatgaa 1560gacgcgatcc atcgtcaact ggacagcggt
gcaatagtgc taatggggcc ggtcgctgtt 1620tcagtcactg gcgagagctt
taacctgacc tcggaagaga ttgccactca actggccatc 1680aaactgaaag
ctgaaaagat gattggtttt
tgctcttccc agggcgtcac taatgacgac 1740ggtgatattg tctccgaact
tttccctaac gaagcgcaag cgcgggtaga agcccaggaa 1800gagaaaggcg
attacaactc cggtacggtg cgctttttgc gtggcgcagt gaaagcctgc
1860cgcagcggcg tgcgtcgctg tcatttaatc agttatcagg aagatggcgc
gctgttgcaa 1920gagttgttct cacgcgacgg tatcggtacg cagattgtga
tggaaagcgc cgagcagatt 1980cgtcgcgcaa caatcaacga tattggcggt
attctggagt tgattcgccc actggagcag 2040caaggtattc tggtacgccg
ttctcgcgag cagctggaga tggaaatcga caaattcacc 2100attattcagc
gcgataacac gactattgcc tgcgccgcgc tctatccgtt cccggaagag
2160aagattgggg aaatggcctg tgtggcagtt cacccggatt accgcagttc
atcaaggggt 2220gaagttctgc tggaacgcat tgccgctcag gctaagcaga
gcggcttaag caaattgttt 2280gtgctgacca cgcgcagtat tcactggttc
caggaacgtg gatttacccc agtggatatt 2340gatttactgc ccgagagcaa
aaagcagttg tacaactacc agcgtaaatc caaagtgttg 2400atggcggatt
tagggtaatg ggaattagcc atggtccata tgaatatcct ccttagttcc
2460tattccgaag ttcctattcc gaagttccta ttctctagaa agtataggaa
cttcgaagca 2520gctccagcct acacaatcgc tcaagacgtg taatgctgca
atctgcatgc aagcttggca 2580ctggccacgc aaaaaggcca tccgtcagga
tggccttctg cttaatttga tgcctggcag 2640tttatggcgg gcgtcctgcc
cgccaccctc cgggccgttg cttcgcaacg ttcaaatccg 2700ctcccggcgg
atttgtccta ctcaggagag cgttcaccga caaacaacag ataaaacgaa
2760aggcccagtc tttcgactga gcctttcgtt ttatttgatg cctggcagtt
ccctactctc 2820gcatgctcga gccatgggac gtccaggtat tagaagccaa
cctggcgctg ccaaaacaca 2880acctggtcac gctcacctgg ggcaatgtca
gcgccgttga tcgcgggcgc ggcgtcctgg 2940tgatcaaacc ttccggcgtc
gactacagca tcatgaccgc tgacgatatg gtcgtggtca 3000gcatcgaaac
cggtgaagtg gttgaaggta cgaaaaagcc ctcctccgac acgccaactc
3060accggctgct ctatcaggca ttcccgtcta ttggcggcat tgtgcacaca
cactcgcgcc 3120acgccaccat ctgggcgcag gcgggccagt cgattccagc
agccggcacc acccacgccg 3180actatttcta cggcaccatt ccctgcaccc
gcaaaatgac cgacgcagaa atcaacggtg 3240aatatgagtg ggaaaccggt
aacgtcatcg tagaaacctt cgaaaaacag ggtatcaatg 3300cagcgcaaat
gcccggcgtg ctggtccatt ctcacggccc atttgcatgg ggaaaaaacg
3360ccgaagatgc ggtgcataac gccatcgtgc tggaagaagt cgcttatatg
gggatattct 3420gccgtcagtt agcgccgcag ttaccggata tgcagcaaac
gctgctggat aaacactatc 3480tgcgtaagca tggcgcgaag gcatattacg ggcagtaa
35186860DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 68tagaactgat gcaaaaagtg ctcgacgaag gcacacagat
gtgtaggctg gagctgcttc 6069471DNAEscherichia coli 69atgcgaagct
cggctaagca agaagaacta gttaaagcat ttaaagcatt acttaaagaa 60gagaaattta
gctcccaggg cgaaatcgtc gccgcgttgc aggagcaagg ctttgacaat
120attaatcagt ctaaagtctc gcggatgttg accaagtttg gtgctgtacg
tacacgcaat 180gccaaaatgg aaatggttta ctgcctgcca gctgaactgg
gtgtaccaac cacctccagt 240ccattgaaga atctggtact ggatatcgac
tacaacgatg cagttgtcgt gattcatacc 300agccctggtg cggcgcagtt
aattgctcgc ctgctggact cactgggcaa agcagaaggt 360attctgggca
ccatcgctgg cgatgacacc atctttacta cccctgctaa cggtttcacc
420gtcaaagagc tgtacgaagc gattttagag ctgttcgacc aggagcttta a
4717052DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 70caacacgttt cctgaggaac catgaaacag tatttagaac
tgatgcaaaa ag 527146DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 71cgcacactgg cgtcggctct ggcaggatgt
ttcgtaatta gatagc 467236DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 72atatcgtcgc agcccacagc
aacacgtttc ctgagg 367347DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 73aagaatttaa cggagggcaa
aaaaaaccga cgcacactgg cgtcggc 477421DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
74gcaactggcc cgtaattatc c 217519DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 75acgcatcgca cgtaggttt
197621DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 76ggcaggccta acacatgcaa g 217722DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
77gtcgcctagg tgagccttta cc 2278191DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 78gcaactggcc
cgtaattatc catagctgta gtgatcactc ggtccgaatt aaacgcaatg 60atggcgagct
gagaacgatt agcatcaaac gctttaacga agattttgaa cgagtggagc
120atgatgagta tcgcaaaata tgtgccgaaa tagagcagga aacaaacctg
aaaaacctac 180gtgcgatgcg t 191798575DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
79ttattatcgc accgcaatcg ggattttcga ttcataaagc aggtcgtagg tcggcttgtt
60gagcaggtct tgcagcgtga aaccgtccag atacgtgaaa aacgacttca ttgcaccgcc
120gagtatgccc gtcagccggc aggacggcgt aatcaggcat tcgttgttcg
ggcccataca 180ctcgaccagc tgcatcggtt cgaggtggcg gacgaccgcg
ccgatattga tgcgttcggg 240cggcgcggcc agcctcagcc cgccgccttt
cccgcgtacg ctgtgcaaga acccgccttt 300gaccagcgcg gtaaccactt
tcatcaaatg gcttttggaa atgccgtagg tcgaggcgat 360ggtggcgata
ttgaccagcg cgtcgtcgtt gacggcggtg tagatgagga cgcgcagccc
420gtagtcggta tgttgggtca gatacataca acctccttag tacatgcaaa
attatttcta 480gagcaacata cgagccggaa gcataaagtg taaagcctgg
ggtgcctaat gagttgagtt 540gaggaattat aacaggaaga aatattcctc
atacgcttgt aattcctcta tggttgttga 600caattaatca tcggctcgta
taatgtataa cattcatatt ttgtgaattt taaactctag 660aaataatttt
gtttaacttt aagaaggaga tatacatatg gatttaaatt ctaaaaaata
720tcagatgctt aaagagctat atgtaagctt cgctgaaaat gaagttaaac
ctttagcaac 780agaacttgat gaagaagaaa gatttcctta tgaaacagtg
gaaaaaatgg caaaagcagg 840aatgatgggt ataccatatc caaaagaata
tggtggagaa ggtggagaca ctgtaggata 900tataatggca gttgaagaat
tgtctagagt ttgtggtact acaggagtta tattatcagc 960tcatacatct
cttggctcat ggcctatata tcaatatggt aatgaagaac aaaaacaaaa
1020attcttaaga ccactagcaa gtggagaaaa attaggagca tttggtctta
ctgagcctaa 1080tgctggtaca gatgcgtctg gccaacaaac aactgctgtt
ttagacgggg atgaatacat 1140acttaatggc tcaaaaatat ttataacaaa
cgcaatagct ggtgacatat atgtagtaat 1200ggcaatgact gataaatcta
aggggaacaa aggaatatca gcatttatag ttgaaaaagg 1260aactcctggg
tttagctttg gagttaaaga aaagaaaatg ggtataagag gttcagctac
1320gagtgaatta atatttgagg attgcagaat acctaaagaa aatttacttg
gaaaagaagg 1380tcaaggattt aagatagcaa tgtctactct tgatggtggt
agaattggta tagctgcaca 1440agctttaggt ttagcacaag gtgctcttga
tgaaactgtt aaatatgtaa aagaaagagt 1500acaatttggt agaccattat
caaaattcca aaatacacaa ttccaattag ctgatatgga 1560agttaaggta
caagcggcta gacaccttgt atatcaagca gctataaata aagacttagg
1620aaaaccttat ggagtagaag cagcaatggc aaaattattt gcagctgaaa
cagctatgga 1680agttactaca aaagctgtac aacttcatgg aggatatgga
tacactcgtg actatccagt 1740agaaagaatg atgagagatg ctaagataac
tgaaatatat gaaggaacta gtgaagttca 1800aagaatggtt atttcaggaa
aactattaaa atagtaagaa ggagatatac atatggagga 1860aggatttatg
aatatagtcg tttgtataaa acaagttcca gatacaacag aagttaaact
1920agatcctaat acaggtactt taattagaga tggagtacca agtataataa
accctgatga 1980taaagcaggt ttagaagaag ctataaaatt aaaagaagaa
atgggtgctc atgtaactgt 2040tataacaatg ggacctcctc aagcagatat
ggctttaaaa gaagctttag caatgggtgc 2100agatagaggt atattattaa
cagatagagc atttgcgggt gctgatactt gggcaacttc 2160atcagcatta
gcaggagcat taaaaaatat agattttgat attataatag ctggaagaca
2220ggcgatagat ggagatactg cacaagttgg acctcaaata gctgaacatt
taaatcttcc 2280atcaataaca tatgctgaag aaataaaaac tgaaggtgaa
tatgtattag taaaaagaca 2340atttgaagat tgttgccatg acttaaaagt
taaaatgcca tgccttataa caactcttaa 2400agatatgaac acaccaagat
acatgaaagt tggaagaata tatgatgctt tcgaaaatga 2460tgtagtagaa
acatggactg taaaagatat agaagttgac ccttctaatt taggtcttaa
2520aggttctcca actagtgtat ttaaatcatt tacaaaatca gttaaaccag
ctggtacaat 2580atacaatgaa gatgcgaaaa catcagctgg aattatcata
gataaattaa aagagaagta 2640tatcatataa taagaaggag atatacatat
gggtaacgtt ttagtagtaa tagaacaaag 2700agaaaatgta attcaaactg
tttctttaga attactagga aaggctacag aaatagcaaa 2760agattatgat
acaaaagttt ctgcattact tttaggtagt aaggtagaag gtttaataga
2820tacattagca cactatggtg cagatgaggt aatagtagta gatgatgaag
ctttagcagt 2880gtatacaact gaaccatata caaaagcagc ttatgaagca
ataaaagcag ctgaccctat 2940agttgtatta tttggtgcaa cttcaatagg
tagagattta gcgcctagag tttctgctag 3000aatacataca ggtcttactg
ctgactgtac aggtcttgca gtagctgaag atacaaaatt 3060attattaatg
acaagacctg cctttggtgg aaatataatg gcaacaatag tttgtaaaga
3120tttcagacct caaatgtcta cagttagacc aggggttatg aagaaaaatg
aacctgatga 3180aactaaagaa gctgtaatta accgtttcaa ggtagaattt
aatgatgctg ataaattagt 3240tcaagttgta caagtaataa aagaagctaa
aaaacaagtt aaaatagaag atgctaagat 3300attagtttct gctggacgtg
gaatgggtgg aaaagaaaac ttagacatac tttatgaatt 3360agctgaaatt
ataggtggag aagtttctgg ttctcgtgcc actatagatg caggttggtt
3420agataaagca agacaagttg gtcaaactgg taaaactgta agaccagacc
tttatatagc 3480atgtggtata tctggagcaa tacaacatat agctggtatg
gaagatgctg agtttatagt 3540tgctataaat aaaaatccag aagctccaat
atttaaatat gctgatgttg gtatagttgg 3600agatgttcat aaagtgcttc
cagaacttat cagtcagtta agtgttgcaa aagaaaaagg 3660tgaagtttta
gctaactaat aagaaggaga tatacatatg agagaagtag taattgccag
3720tgcagctaga acagcagtag gaagttttgg aggagcattt aaatcagttt
cagcggtaga 3780gttaggggta acagcagcta aagaagctat aaaaagagct
aacataactc cagatatgat 3840agatgaatct cttttagggg gagtacttac
agcaggtctt ggacaaaata tagcaagaca 3900aatagcatta ggagcaggaa
taccagtaga aaaaccagct atgactataa atatagtttg 3960tggttctgga
ttaagatctg tttcaatggc atctcaactt atagcattag gtgatgctga
4020tataatgtta gttggtggag ctgaaaacat gagtatgtct ccttatttag
taccaagtgc 4080gagatatggt gcaagaatgg gtgatgctgc ttttgttgat
tcaatgataa aagatggatt 4140atcagacata tttaataact atcacatggg
tattactgct gaaaacatag cagagcaatg 4200gaatataact agagaagaac
aagatgaatt agctcttgca agtcaaaata aagctgaaaa 4260agctcaagct
gaaggaaaat ttgatgaaga aatagttcct gttgttataa aaggaagaaa
4320aggtgacact gtagtagata aagatgaata tattaagcct ggcactacaa
tggagaaact 4380tgctaagtta agacctgcat ttaaaaaaga tggaacagtt
actgctggta atgcatcagg 4440aataaatgat ggtgctgcta tgttagtagt
aatggctaaa gaaaaagctg aagaactagg 4500aatagagcct cttgcaacta
tagtttctta tggaacagct ggtgttgacc ctaaaataat 4560gggatatgga
ccagttccag caactaaaaa agctttagaa gctgctaata tgactattga
4620agatatagat ttagttgaag ctaatgaggc atttgctgcc caatctgtag
ctgtaataag 4680agacttaaat atagatatga ataaagttaa tgttaatggt
ggagcaatag ctataggaca 4740tccaatagga tgctcaggag caagaatact
tactacactt ttatatgaaa tgaagagaag 4800agatgctaaa actggtcttg
ctacactttg tataggcggt ggaatgggaa ctactttaat 4860agttaagaga
tagtaagaag gagatataca tatgaaatta gctgtaatag gtagtggaac
4920tatgggaagt ggtattgtac aaacttttgc aagttgtgga catgatgtat
gtttaaagag 4980tagaactcaa ggtgctatag ataaatgttt agctttatta
gataaaaatt taactaagtt 5040agttactaag ggaaaaatgg atgaagctac
aaaagcagaa atattaagtc atgttagttc 5100aactactaat tatgaagatt
taaaagatat ggatttaata atagaagcat ctgtagaaga 5160catgaatata
aagaaagatg ttttcaagtt actagatgaa ttatgtaaag aagatactat
5220cttggcaaca aatacttcat cattatctat aacagaaata gcttcttcta
ctaagcgccc 5280agataaagtt ataggaatgc atttctttaa tccagttcct
atgatgaaat tagttgaagt 5340tataagtggt cagttaacat caaaagttac
ttttgataca gtatttgaat tatctaagag 5400tatcaataaa gtaccagtag
atgtatctga atctcctgga tttgtagtaa atagaatact 5460tatacctatg
ataaatgaag ctgttggtat atatgcagat ggtgttgcaa gtaaagaaga
5520aatagatgaa gctatgaaat taggagcaaa ccatccaatg ggaccactag
cattaggtga 5580tttaatcgga ttagatgttg ttttagctat aatgaacgtt
ttatatactg aatttggaga 5640tactaaatat agacctcatc cacttttagc
taaaatggtt agagctaatc aattaggaag 5700aaaaactaag ataggattct
atgattataa taaataataa gaaggagata tacatatgag 5760tacaagtgat
gttaaagttt atgagaatgt agctgttgaa gtagatggaa atatatgtac
5820agtgaaaatg aatagaccta aagcccttaa tgcaataaat tcaaagactt
tagaagaact 5880ttatgaagta tttgtagata ttaataatga tgaaactatt
gatgttgtaa tattgacagg 5940ggaaggaaag gcatttgtag ctggagcaga
tattgcatac atgaaagatt tagatgctgt 6000agctgctaaa gattttagta
tcttaggagc aaaagctttt ggagaaatag aaaatagtaa 6060aaaagtagtg
atagctgctg taaacggatt tgctttaggt ggaggatgtg aacttgcaat
6120ggcatgtgat ataagaattg catctgctaa agctaaattt ggtcagccag
aagtaactct 6180tggaataact ccaggatatg gaggaactca aaggcttaca
agattggttg gaatggcaaa 6240agcaaaagaa ttaatcttta caggtcaagt
tataaaagct gatgaagctg aaaaaatagg 6300gctagtaaat agagtcgttg
agccagacat tttaatagaa gaagttgaga aattagctaa 6360gataatagct
aaaaatgctc agcttgcagt tagatactct aaagaagcaa tacaacttgg
6420tgctcaaact gatataaata ctggaataga tatagaatct aatttatttg
gtctttgttt 6480ttcaactaaa gaccaaaaag aaggaatgtc agctttcgtt
gaaaagagag aagctaactt 6540tataaaaggg taataagaag gagatataca
tatgagaagt tttgaagaag taattaagtt 6600tgcaaaagaa agaggaccta
aaactatatc agtagcatgt tgccaagata aagaagtttt 6660aatggcagtt
gaaatggcta gaaaagaaaa aatagcaaat gccattttag taggagatat
6720agaaaagact aaagaaattg caaaaagcat agacatggat atcgaaaatt
atgaactgat 6780agatataaaa gatttagcag aagcatctct aaaatctgtt
gaattagttt cacaaggaaa 6840agccgacatg gtaatgaaag gcttagtaga
cacatcaata atactaaaag cagttttaaa 6900taaagaagta ggtcttagaa
ctggaaatgt attaagtcac gtagcagtat ttgatgtaga 6960gggatatgat
agattatttt tcgtaactga cgcagctatg aacttagctc ctgatacaaa
7020tactaaaaag caaatcatag aaaatgcttg cacagtagca cattcattag
atataagtga 7080accaaaagtt gctgcaatat gcgcaaaaga aaaagtaaat
ccaaaaatga aagatacagt 7140tgaagctaaa gaactagaag aaatgtatga
aagaggagaa atcaaaggtt gtatggttgg 7200tgggcctttt gcaattgata
atgcagtatc tttagaagca gctaaacata aaggtataaa 7260tcatcctgta
gcaggacgag ctgatatatt attagcccca gatattgaag gtggtaacat
7320attatataaa gctttggtat tcttctcaaa atcaaaaaat gcaggagtta
tagttggggc 7380taaagcacca ataatattaa cttctagagc agacagtgaa
gaaactaaac taaactcaat 7440agctttaggt gttttaatgg cagcaaaggc
ataataagaa ggagatatac atatgagcaa 7500aatatttaaa atcttaacaa
taaatcctgg ttcgacatca actaaaatag ctgtatttga 7560taatgaggat
ttagtatttg aaaaaacttt aagacattct tcagaagaaa taggaaaata
7620tgagaaggtg tctgaccaat ttgaatttcg taaacaagta atagaagaag
ctctaaaaga 7680aggtggagta aaaacatctg aattagatgc tgtagtaggt
agaggaggac ttcttaaacc 7740tataaaaggt ggtacttatt cagtaagtgc
tgctatgatt gaagatttaa aagtgggagt 7800tttaggagaa cacgcttcaa
acctaggtgg aataatagca aaacaaatag gtgaagaagt 7860aaatgttcct
tcatacatag tagaccctgt tgttgtagat gaattagaag atgttgctag
7920aatttctggt atgcctgaaa taagtagagc aagtgtagta catgctttaa
atcaaaaggc 7980aatagcaaga agatatgcta gagaaataaa caagaaatat
gaagatataa atcttatagt 8040tgcacacatg ggtggaggag tttctgttgg
agctcataaa aatggtaaaa tagtagatgt 8100tgcaaacgca ttagatggag
aaggaccttt ctctccagaa agaagtggtg gactaccagt 8160aggtgcatta
gtaaaaatgt gctttagtgg aaaatatact caagatgaaa ttaaaaagaa
8220aataaaaggt aatggcggac tagttgcata cttaaacact aatgatgcta
gagaagttga 8280agaaagaatt gaagctggtg atgaaaaagc taaattagta
tatgaagcta tggcatatca 8340aatctctaaa gaaataggag ctagtgctgc
agttcttaag ggagatgtaa aagcaatatt 8400attaactggt ggaatcgcat
attcaaaaat gtttacagaa atgattgcag atagagttaa 8460atttatagca
gatgtaaaag tttatccagg tgaagatgaa atgattgcat tagctcaagg
8520tggacttaga gttttaactg gtgaagaaga ggctcaagtt tatgataact aataa
8575806787DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 80ttattatcgc accgcaatcg ggattttcga
ttcataaagc aggtcgtagg tcggcttgtt 60gagcaggtct tgcagcgtga aaccgtccag
atacgtgaaa aacgacttca ttgcaccgcc 120gagtatgccc gtcagccggc
aggacggcgt aatcaggcat tcgttgttcg ggcccataca 180ctcgaccagc
tgcatcggtt cgaggtggcg gacgaccgcg ccgatattga tgcgttcggg
240cggcgcggcc agcctcagcc cgccgccttt cccgcgtacg ctgtgcaaga
acccgccttt 300gaccagcgcg gtaaccactt tcatcaaatg gcttttggaa
atgccgtagg tcgaggcgat 360ggtggcgata ttgaccagcg cgtcgtcgtt
gacggcggtg tagatgagga cgcgcagccc 420gtagtcggta tgttgggtca
gatacataca acctccttag tacatgcaaa attatttcta 480gagcaacata
cgagccggaa gcataaagtg taaagcctgg ggtgcctaat gagttgagtt
540gaggaattat aacaggaaga aatattcctc atacgcttgt aattcctcta
tggttgttga 600caattaatca tcggctcgta taatgtataa cattcatatt
ttgtgaattt taaactctag 660aaataatttt gtttaacttt aagaaggaga
tatacatatg atcgtaaaac ctatggtacg 720caacaatatc tgcctgaacg
cccatcctca gggctgcaag aagggagtgg aagatcagat 780tgaatatacc
aagaaacgca ttaccgcaga agtcaaagct ggcgcaaaag ctccaaaaaa
840cgttctggtg cttggctgct caaatggtta cggcctggcg agccgcatta
ctgctgcgtt 900cggatacggg gctgcgacca tcggcgtgtc ctttgaaaaa
gcgggttcag aaaccaaata 960tggtacaccg ggatggtaca ataatttggc
atttgatgaa gcggcaaaac gcgagggtct 1020ttatagcgtg acgatcgacg
gcgatgcgtt ttcagacgag atcaaggccc aggtaattga 1080ggaagccaaa
aaaaaaggta tcaaatttga tctgatcgta tacagcttgg ccagcccagt
1140acgtactgat cctgatacag gtatcatgca caaaagcgtt ttgaaaccct
ttggaaaaac 1200gttcacaggc aaaacagtag atccgtttac tggcgagctg
aaggaaatct ccgcggaacc 1260agcaaatgac gaggaagcag ccgccactgt
taaagttatg gggggtgaag attgggaacg 1320ttggattaag cagctgtcga
aggaaggcct cttagaagaa ggctgtatta ccttggccta 1380tagttatatt
ggccctgaag ctacccaagc tttgtaccgt aaaggcacaa tcggcaaggc
1440caaagaacac ctggaggcca cagcacaccg tctcaacaaa gagaacccgt
caatccgtgc 1500cttcgtgagc gtgaataaag gcctggtaac ccgcgcaagc
gccgtaatcc cggtaatccc 1560tctgtatctc gccagcttgt tcaaagtaat
gaaagagaag ggcaatcatg aaggttgtat 1620tgaacagatc acgcgtctgt
acgccgagcg cctgtaccgt aaagatggta caattccagt 1680tgatgaggaa
aatcgcattc gcattgatga ttgggagtta gaagaagacg tccagaaagc
1740ggtatccgcg ttgatggaga aagtcacggg tgaaaacgca gaatctctca
ctgacttagc 1800ggggtaccgc catgatttct tagctagtaa cggctttgat
gtagaaggta ttaattatga 1860agcggaagtt gaacgcttcg accgtatctg
ataagaagga gatatacata tgagagaagt 1920agtaattgcc agtgcagcta
gaacagcagt aggaagtttt ggaggagcat ttaaatcagt 1980ttcagcggta
gagttagggg taacagcagc taaagaagct ataaaaagag ctaacataac
2040tccagatatg atagatgaat ctcttttagg gggagtactt acagcaggtc
ttggacaaaa 2100tatagcaaga caaatagcat taggagcagg aataccagta
gaaaaaccag ctatgactat 2160aaatatagtt tgtggttctg gattaagatc
tgtttcaatg gcatctcaac ttatagcatt 2220aggtgatgct gatataatgt
tagttggtgg agctgaaaac atgagtatgt ctccttattt 2280agtaccaagt
gcgagatatg gtgcaagaat gggtgatgct gcttttgttg attcaatgat
2340aaaagatgga ttatcagaca tatttaataa ctatcacatg ggtattactg
ctgaaaacat 2400agcagagcaa tggaatataa ctagagaaga
acaagatgaa ttagctcttg caagtcaaaa 2460taaagctgaa aaagctcaag
ctgaaggaaa atttgatgaa gaaatagttc ctgttgttat 2520aaaaggaaga
aaaggtgaca ctgtagtaga taaagatgaa tatattaagc ctggcactac
2580aatggagaaa cttgctaagt taagacctgc atttaaaaaa gatggaacag
ttactgctgg 2640taatgcatca ggaataaatg atggtgctgc tatgttagta
gtaatggcta aagaaaaagc 2700tgaagaacta ggaatagagc ctcttgcaac
tatagtttct tatggaacag ctggtgttga 2760ccctaaaata atgggatatg
gaccagttcc agcaactaaa aaagctttag aagctgctaa 2820tatgactatt
gaagatatag atttagttga agctaatgag gcatttgctg cccaatctgt
2880agctgtaata agagacttaa atatagatat gaataaagtt aatgttaatg
gtggagcaat 2940agctatagga catccaatag gatgctcagg agcaagaata
cttactacac ttttatatga 3000aatgaagaga agagatgcta aaactggtct
tgctacactt tgtataggcg gtggaatggg 3060aactacttta atagttaaga
gatagtaaga aggagatata catatgaaat tagctgtaat 3120aggtagtgga
actatgggaa gtggtattgt acaaactttt gcaagttgtg gacatgatgt
3180atgtttaaag agtagaactc aaggtgctat agataaatgt ttagctttat
tagataaaaa 3240tttaactaag ttagttacta agggaaaaat ggatgaagct
acaaaagcag aaatattaag 3300tcatgttagt tcaactacta attatgaaga
tttaaaagat atggatttaa taatagaagc 3360atctgtagaa gacatgaata
taaagaaaga tgttttcaag ttactagatg aattatgtaa 3420agaagatact
atcttggcaa caaatacttc atcattatct ataacagaaa tagcttcttc
3480tactaagcgc ccagataaag ttataggaat gcatttcttt aatccagttc
ctatgatgaa 3540attagttgaa gttataagtg gtcagttaac atcaaaagtt
acttttgata cagtatttga 3600attatctaag agtatcaata aagtaccagt
agatgtatct gaatctcctg gatttgtagt 3660aaatagaata cttataccta
tgataaatga agctgttggt atatatgcag atggtgttgc 3720aagtaaagaa
gaaatagatg aagctatgaa attaggagca aaccatccaa tgggaccact
3780agcattaggt gatttaatcg gattagatgt tgttttagct ataatgaacg
ttttatatac 3840tgaatttgga gatactaaat atagacctca tccactttta
gctaaaatgg ttagagctaa 3900tcaattagga agaaaaacta agataggatt
ctatgattat aataaataat aagaaggaga 3960tatacatatg agtacaagtg
atgttaaagt ttatgagaat gtagctgttg aagtagatgg 4020aaatatatgt
acagtgaaaa tgaatagacc taaagccctt aatgcaataa attcaaagac
4080tttagaagaa ctttatgaag tatttgtaga tattaataat gatgaaacta
ttgatgttgt 4140aatattgaca ggggaaggaa aggcatttgt agctggagca
gatattgcat acatgaaaga 4200tttagatgct gtagctgcta aagattttag
tatcttagga gcaaaagctt ttggagaaat 4260agaaaatagt aaaaaagtag
tgatagctgc tgtaaacgga tttgctttag gtggaggatg 4320tgaacttgca
atggcatgtg atataagaat tgcatctgct aaagctaaat ttggtcagcc
4380agaagtaact cttggaataa ctccaggata tggaggaact caaaggctta
caagattggt 4440tggaatggca aaagcaaaag aattaatctt tacaggtcaa
gttataaaag ctgatgaagc 4500tgaaaaaata gggctagtaa atagagtcgt
tgagccagac attttaatag aagaagttga 4560gaaattagct aagataatag
ctaaaaatgc tcagcttgca gttagatact ctaaagaagc 4620aatacaactt
ggtgctcaaa ctgatataaa tactggaata gatatagaat ctaatttatt
4680tggtctttgt ttttcaacta aagaccaaaa agaaggaatg tcagctttcg
ttgaaaagag 4740agaagctaac tttataaaag ggtaataaga aggagatata
catatgagaa gttttgaaga 4800agtaattaag tttgcaaaag aaagaggacc
taaaactata tcagtagcat gttgccaaga 4860taaagaagtt ttaatggcag
ttgaaatggc tagaaaagaa aaaatagcaa atgccatttt 4920agtaggagat
atagaaaaga ctaaagaaat tgcaaaaagc atagacatgg atatcgaaaa
4980ttatgaactg atagatataa aagatttagc agaagcatct ctaaaatctg
ttgaattagt 5040ttcacaagga aaagccgaca tggtaatgaa aggcttagta
gacacatcaa taatactaaa 5100agcagtttta aataaagaag taggtcttag
aactggaaat gtattaagtc acgtagcagt 5160atttgatgta gagggatatg
atagattatt tttcgtaact gacgcagcta tgaacttagc 5220tcctgataca
aatactaaaa agcaaatcat agaaaatgct tgcacagtag cacattcatt
5280agatataagt gaaccaaaag ttgctgcaat atgcgcaaaa gaaaaagtaa
atccaaaaat 5340gaaagataca gttgaagcta aagaactaga agaaatgtat
gaaagaggag aaatcaaagg 5400ttgtatggtt ggtgggcctt ttgcaattga
taatgcagta tctttagaag cagctaaaca 5460taaaggtata aatcatcctg
tagcaggacg agctgatata ttattagccc cagatattga 5520aggtggtaac
atattatata aagctttggt attcttctca aaatcaaaaa atgcaggagt
5580tatagttggg gctaaagcac caataatatt aacttctaga gcagacagtg
aagaaactaa 5640actaaactca atagctttag gtgttttaat ggcagcaaag
gcataataag aaggagatat 5700acatatgagc aaaatattta aaatcttaac
aataaatcct ggttcgacat caactaaaat 5760agctgtattt gataatgagg
atttagtatt tgaaaaaact ttaagacatt cttcagaaga 5820aataggaaaa
tatgagaagg tgtctgacca atttgaattt cgtaaacaag taatagaaga
5880agctctaaaa gaaggtggag taaaaacatc tgaattagat gctgtagtag
gtagaggagg 5940acttcttaaa cctataaaag gtggtactta ttcagtaagt
gctgctatga ttgaagattt 6000aaaagtggga gttttaggag aacacgcttc
aaacctaggt ggaataatag caaaacaaat 6060aggtgaagaa gtaaatgttc
cttcatacat agtagaccct gttgttgtag atgaattaga 6120agatgttgct
agaatttctg gtatgcctga aataagtaga gcaagtgtag tacatgcttt
6180aaatcaaaag gcaatagcaa gaagatatgc tagagaaata aacaagaaat
atgaagatat 6240aaatcttata gttgcacaca tgggtggagg agtttctgtt
ggagctcata aaaatggtaa 6300aatagtagat gttgcaaacg cattagatgg
agaaggacct ttctctccag aaagaagtgg 6360tggactacca gtaggtgcat
tagtaaaaat gtgctttagt ggaaaatata ctcaagatga 6420aattaaaaag
aaaataaaag gtaatggcgg actagttgca tacttaaaca ctaatgatgc
6480tagagaagtt gaagaaagaa ttgaagctgg tgatgaaaaa gctaaattag
tatatgaagc 6540tatggcatat caaatctcta aagaaatagg agctagtgct
gcagttctta agggagatgt 6600aaaagcaata ttattaactg gtggaatcgc
atattcaaaa atgtttacag aaatgattgc 6660agatagagtt aaatttatag
cagatgtaaa agtttatcca ggtgaagatg aaatgattgc 6720attagctcaa
ggtggactta gagttttaac tggtgaagaa gaggctcaag tttatgataa 6780ctaataa
6787818012DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 81ctcgagttca ttatccatcc tccatcgcca
cgatagttca tggcgatagg tagaatagca 60atgaacgatt atccctatca agcattctga
ctgataattg ctcacacgaa ttcattaaag 120aggagaaagg taccatggat
ttaaattcta aaaaatatca gatgcttaaa gagctatatg 180taagcttcgc
tgaaaatgaa gttaaacctt tagcaacaga acttgatgaa gaagaaagat
240ttccttatga aacagtggaa aaaatggcaa aagcaggaat gatgggtata
ccatatccaa 300aagaatatgg tggagaaggt ggagacactg taggatatat
aatggcagtt gaagaattgt 360ctagagtttg tggtactaca ggagttatat
tatcagctca tacatctctt ggctcatggc 420ctatatatca atatggtaat
gaagaacaaa aacaaaaatt cttaagacca ctagcaagtg 480gagaaaaatt
aggagcattt ggtcttactg agcctaatgc tggtacagat gcgtctggcc
540aacaaacaac tgctgtttta gacggggatg aatacatact taatggctca
aaaatattta 600taacaaacgc aatagctggt gacatatatg tagtaatggc
aatgactgat aaatctaagg 660ggaacaaagg aatatcagca tttatagttg
aaaaaggaac tcctgggttt agctttggag 720ttaaagaaaa gaaaatgggt
ataagaggtt cagctacgag tgaattaata tttgaggatt 780gcagaatacc
taaagaaaat ttacttggaa aagaaggtca aggatttaag atagcaatgt
840ctactcttga tggtggtaga attggtatag ctgcacaagc tttaggttta
gcacaaggtg 900ctcttgatga aactgttaaa tatgtaaaag aaagagtaca
atttggtaga ccattatcaa 960aattccaaaa tacacaattc caattagctg
atatggaagt taaggtacaa gcggctagac 1020accttgtata tcaagcagct
ataaataaag acttaggaaa accttatgga gtagaagcag 1080caatggcaaa
attatttgca gctgaaacag ctatggaagt tactacaaaa gctgtacaac
1140ttcatggagg atatggatac actcgtgact atccagtaga aagaatgatg
agagatgcta 1200agataactga aatatatgaa ggaactagtg aagttcaaag
aatggttatt tcaggaaaac 1260tattaaaata gtaagaagga gatatacata
tggaggaagg atttatgaat atagtcgttt 1320gtataaaaca agttccagat
acaacagaag ttaaactaga tcctaataca ggtactttaa 1380ttagagatgg
agtaccaagt ataataaacc ctgatgataa agcaggttta gaagaagcta
1440taaaattaaa agaagaaatg ggtgctcatg taactgttat aacaatggga
cctcctcaag 1500cagatatggc tttaaaagaa gctttagcaa tgggtgcaga
tagaggtata ttattaacag 1560atagagcatt tgcgggtgct gatacttggg
caacttcatc agcattagca ggagcattaa 1620aaaatataga ttttgatatt
ataatagctg gaagacaggc gatagatgga gatactgcac 1680aagttggacc
tcaaatagct gaacatttaa atcttccatc aataacatat gctgaagaaa
1740taaaaactga aggtgaatat gtattagtaa aaagacaatt tgaagattgt
tgccatgact 1800taaaagttaa aatgccatgc cttataacaa ctcttaaaga
tatgaacaca ccaagataca 1860tgaaagttgg aagaatatat gatgctttcg
aaaatgatgt agtagaaaca tggactgtaa 1920aagatataga agttgaccct
tctaatttag gtcttaaagg ttctccaact agtgtattta 1980aatcatttac
aaaatcagtt aaaccagctg gtacaatata caatgaagat gcgaaaacat
2040cagctggaat tatcatagat aaattaaaag agaagtatat catataataa
gaaggagata 2100tacatatggg taacgtttta gtagtaatag aacaaagaga
aaatgtaatt caaactgttt 2160ctttagaatt actaggaaag gctacagaaa
tagcaaaaga ttatgataca aaagtttctg 2220cattactttt aggtagtaag
gtagaaggtt taatagatac attagcacac tatggtgcag 2280atgaggtaat
agtagtagat gatgaagctt tagcagtgta tacaactgaa ccatatacaa
2340aagcagctta tgaagcaata aaagcagctg accctatagt tgtattattt
ggtgcaactt 2400caataggtag agatttagcg cctagagttt ctgctagaat
acatacaggt cttactgctg 2460actgtacagg tcttgcagta gctgaagata
caaaattatt attaatgaca agacctgcct 2520ttggtggaaa tataatggca
acaatagttt gtaaagattt cagacctcaa atgtctacag 2580ttagaccagg
ggttatgaag aaaaatgaac ctgatgaaac taaagaagct gtaattaacc
2640gtttcaaggt agaatttaat gatgctgata aattagttca agttgtacaa
gtaataaaag 2700aagctaaaaa acaagttaaa atagaagatg ctaagatatt
agtttctgct ggacgtggaa 2760tgggtggaaa agaaaactta gacatacttt
atgaattagc tgaaattata ggtggagaag 2820tttctggttc tcgtgccact
atagatgcag gttggttaga taaagcaaga caagttggtc 2880aaactggtaa
aactgtaaga ccagaccttt atatagcatg tggtatatct ggagcaatac
2940aacatatagc tggtatggaa gatgctgagt ttatagttgc tataaataaa
aatccagaag 3000ctccaatatt taaatatgct gatgttggta tagttggaga
tgttcataaa gtgcttccag 3060aacttatcag tcagttaagt gttgcaaaag
aaaaaggtga agttttagct aactaataag 3120aaggagatat acatatgaga
gaagtagtaa ttgccagtgc agctagaaca gcagtaggaa 3180gttttggagg
agcatttaaa tcagtttcag cggtagagtt aggggtaaca gcagctaaag
3240aagctataaa aagagctaac ataactccag atatgataga tgaatctctt
ttagggggag 3300tacttacagc aggtcttgga caaaatatag caagacaaat
agcattagga gcaggaatac 3360cagtagaaaa accagctatg actataaata
tagtttgtgg ttctggatta agatctgttt 3420caatggcatc tcaacttata
gcattaggtg atgctgatat aatgttagtt ggtggagctg 3480aaaacatgag
tatgtctcct tatttagtac caagtgcgag atatggtgca agaatgggtg
3540atgctgcttt tgttgattca atgataaaag atggattatc agacatattt
aataactatc 3600acatgggtat tactgctgaa aacatagcag agcaatggaa
tataactaga gaagaacaag 3660atgaattagc tcttgcaagt caaaataaag
ctgaaaaagc tcaagctgaa ggaaaatttg 3720atgaagaaat agttcctgtt
gttataaaag gaagaaaagg tgacactgta gtagataaag 3780atgaatatat
taagcctggc actacaatgg agaaacttgc taagttaaga cctgcattta
3840aaaaagatgg aacagttact gctggtaatg catcaggaat aaatgatggt
gctgctatgt 3900tagtagtaat ggctaaagaa aaagctgaag aactaggaat
agagcctctt gcaactatag 3960tttcttatgg aacagctggt gttgacccta
aaataatggg atatggacca gttccagcaa 4020ctaaaaaagc tttagaagct
gctaatatga ctattgaaga tatagattta gttgaagcta 4080atgaggcatt
tgctgcccaa tctgtagctg taataagaga cttaaatata gatatgaata
4140aagttaatgt taatggtgga gcaatagcta taggacatcc aataggatgc
tcaggagcaa 4200gaatacttac tacactttta tatgaaatga agagaagaga
tgctaaaact ggtcttgcta 4260cactttgtat aggcggtgga atgggaacta
ctttaatagt taagagatag taagaaggag 4320atatacatat gaaattagct
gtaataggta gtggaactat gggaagtggt attgtacaaa 4380cttttgcaag
ttgtggacat gatgtatgtt taaagagtag aactcaaggt gctatagata
4440aatgtttagc tttattagat aaaaatttaa ctaagttagt tactaaggga
aaaatggatg 4500aagctacaaa agcagaaata ttaagtcatg ttagttcaac
tactaattat gaagatttaa 4560aagatatgga tttaataata gaagcatctg
tagaagacat gaatataaag aaagatgttt 4620tcaagttact agatgaatta
tgtaaagaag atactatctt ggcaacaaat acttcatcat 4680tatctataac
agaaatagct tcttctacta agcgcccaga taaagttata ggaatgcatt
4740tctttaatcc agttcctatg atgaaattag ttgaagttat aagtggtcag
ttaacatcaa 4800aagttacttt tgatacagta tttgaattat ctaagagtat
caataaagta ccagtagatg 4860tatctgaatc tcctggattt gtagtaaata
gaatacttat acctatgata aatgaagctg 4920ttggtatata tgcagatggt
gttgcaagta aagaagaaat agatgaagct atgaaattag 4980gagcaaacca
tccaatggga ccactagcat taggtgattt aatcggatta gatgttgttt
5040tagctataat gaacgtttta tatactgaat ttggagatac taaatataga
cctcatccac 5100ttttagctaa aatggttaga gctaatcaat taggaagaaa
aactaagata ggattctatg 5160attataataa ataataagaa ggagatatac
atatgagtac aagtgatgtt aaagtttatg 5220agaatgtagc tgttgaagta
gatggaaata tatgtacagt gaaaatgaat agacctaaag 5280cccttaatgc
aataaattca aagactttag aagaacttta tgaagtattt gtagatatta
5340ataatgatga aactattgat gttgtaatat tgacagggga aggaaaggca
tttgtagctg 5400gagcagatat tgcatacatg aaagatttag atgctgtagc
tgctaaagat tttagtatct 5460taggagcaaa agcttttgga gaaatagaaa
atagtaaaaa agtagtgata gctgctgtaa 5520acggatttgc tttaggtgga
ggatgtgaac ttgcaatggc atgtgatata agaattgcat 5580ctgctaaagc
taaatttggt cagccagaag taactcttgg aataactcca ggatatggag
5640gaactcaaag gcttacaaga ttggttggaa tggcaaaagc aaaagaatta
atctttacag 5700gtcaagttat aaaagctgat gaagctgaaa aaatagggct
agtaaataga gtcgttgagc 5760cagacatttt aatagaagaa gttgagaaat
tagctaagat aatagctaaa aatgctcagc 5820ttgcagttag atactctaaa
gaagcaatac aacttggtgc tcaaactgat ataaatactg 5880gaatagatat
agaatctaat ttatttggtc tttgtttttc aactaaagac caaaaagaag
5940gaatgtcagc tttcgttgaa aagagagaag ctaactttat aaaagggtaa
taagaaggag 6000atatacatat gagaagtttt gaagaagtaa ttaagtttgc
aaaagaaaga ggacctaaaa 6060ctatatcagt agcatgttgc caagataaag
aagttttaat ggcagttgaa atggctagaa 6120aagaaaaaat agcaaatgcc
attttagtag gagatataga aaagactaaa gaaattgcaa 6180aaagcataga
catggatatc gaaaattatg aactgataga tataaaagat ttagcagaag
6240catctctaaa atctgttgaa ttagtttcac aaggaaaagc cgacatggta
atgaaaggct 6300tagtagacac atcaataata ctaaaagcag ttttaaataa
agaagtaggt cttagaactg 6360gaaatgtatt aagtcacgta gcagtatttg
atgtagaggg atatgataga ttatttttcg 6420taactgacgc agctatgaac
ttagctcctg atacaaatac taaaaagcaa atcatagaaa 6480atgcttgcac
agtagcacat tcattagata taagtgaacc aaaagttgct gcaatatgcg
6540caaaagaaaa agtaaatcca aaaatgaaag atacagttga agctaaagaa
ctagaagaaa 6600tgtatgaaag aggagaaatc aaaggttgta tggttggtgg
gccttttgca attgataatg 6660cagtatcttt agaagcagct aaacataaag
gtataaatca tcctgtagca ggacgagctg 6720atatattatt agccccagat
attgaaggtg gtaacatatt atataaagct ttggtattct 6780tctcaaaatc
aaaaaatgca ggagttatag ttggggctaa agcaccaata atattaactt
6840ctagagcaga cagtgaagaa actaaactaa actcaatagc tttaggtgtt
ttaatggcag 6900caaaggcata ataagaagga gatatacata tgagcaaaat
atttaaaatc ttaacaataa 6960atcctggttc gacatcaact aaaatagctg
tatttgataa tgaggattta gtatttgaaa 7020aaactttaag acattcttca
gaagaaatag gaaaatatga gaaggtgtct gaccaatttg 7080aatttcgtaa
acaagtaata gaagaagctc taaaagaagg tggagtaaaa acatctgaat
7140tagatgctgt agtaggtaga ggaggacttc ttaaacctat aaaaggtggt
acttattcag 7200taagtgctgc tatgattgaa gatttaaaag tgggagtttt
aggagaacac gcttcaaacc 7260taggtggaat aatagcaaaa caaataggtg
aagaagtaaa tgttccttca tacatagtag 7320accctgttgt tgtagatgaa
ttagaagatg ttgctagaat ttctggtatg cctgaaataa 7380gtagagcaag
tgtagtacat gctttaaatc aaaaggcaat agcaagaaga tatgctagag
7440aaataaacaa gaaatatgaa gatataaatc ttatagttgc acacatgggt
ggaggagttt 7500ctgttggagc tcataaaaat ggtaaaatag tagatgttgc
aaacgcatta gatggagaag 7560gacctttctc tccagaaaga agtggtggac
taccagtagg tgcattagta aaaatgtgct 7620ttagtggaaa atatactcaa
gatgaaatta aaaagaaaat aaaaggtaat ggcggactag 7680ttgcatactt
aaacactaat gatgctagag aagttgaaga aagaattgaa gctggtgatg
7740aaaaagctaa attagtatat gaagctatgg catatcaaat ctctaaagaa
ataggagcta 7800gtgctgcagt tcttaaggga gatgtaaaag caatattatt
aactggtgga atcgcatatt 7860caaaaatgtt tacagaaatg attgcagata
gagttaaatt tatagcagat gtaaaagttt 7920atccaggtga agatgaaatg
attgcattag ctcaaggtgg acttagagtt ttaactggtg 7980aagaagaggc
tcaagtttat gataactaat aa 8012826224DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
82ctcgagttca ttatccatcc tccatcgcca cgatagttca tggcgatagg tagaatagca
60atgaacgatt atccctatca agcattctga ctgataattg ctcacacgaa ttcattaaag
120aggagaaagg taccatgatc gtaaaaccta tggtacgcaa caatatctgc
ctgaacgccc 180atcctcaggg ctgcaagaag ggagtggaag atcagattga
atataccaag aaacgcatta 240ccgcagaagt caaagctggc gcaaaagctc
caaaaaacgt tctggtgctt ggctgctcaa 300atggttacgg cctggcgagc
cgcattactg ctgcgttcgg atacggggct gcgaccatcg 360gcgtgtcctt
tgaaaaagcg ggttcagaaa ccaaatatgg tacaccggga tggtacaata
420atttggcatt tgatgaagcg gcaaaacgcg agggtcttta tagcgtgacg
atcgacggcg 480atgcgttttc agacgagatc aaggcccagg taattgagga
agccaaaaaa aaaggtatca 540aatttgatct gatcgtatac agcttggcca
gcccagtacg tactgatcct gatacaggta 600tcatgcacaa aagcgttttg
aaaccctttg gaaaaacgtt cacaggcaaa acagtagatc 660cgtttactgg
cgagctgaag gaaatctccg cggaaccagc aaatgacgag gaagcagccg
720ccactgttaa agttatgggg ggtgaagatt gggaacgttg gattaagcag
ctgtcgaagg 780aaggcctctt agaagaaggc tgtattacct tggcctatag
ttatattggc cctgaagcta 840cccaagcttt gtaccgtaaa ggcacaatcg
gcaaggccaa agaacacctg gaggccacag 900cacaccgtct caacaaagag
aacccgtcaa tccgtgcctt cgtgagcgtg aataaaggcc 960tggtaacccg
cgcaagcgcc gtaatcccgg taatccctct gtatctcgcc agcttgttca
1020aagtaatgaa agagaagggc aatcatgaag gttgtattga acagatcacg
cgtctgtacg 1080ccgagcgcct gtaccgtaaa gatggtacaa ttccagttga
tgaggaaaat cgcattcgca 1140ttgatgattg ggagttagaa gaagacgtcc
agaaagcggt atccgcgttg atggagaaag 1200tcacgggtga aaacgcagaa
tctctcactg acttagcggg gtaccgccat gatttcttag 1260ctagtaacgg
ctttgatgta gaaggtatta attatgaagc ggaagttgaa cgcttcgacc
1320gtatctgata agaaggagat atacatatga gagaagtagt aattgccagt
gcagctagaa 1380cagcagtagg aagttttgga ggagcattta aatcagtttc
agcggtagag ttaggggtaa 1440cagcagctaa agaagctata aaaagagcta
acataactcc agatatgata gatgaatctc 1500ttttaggggg agtacttaca
gcaggtcttg gacaaaatat agcaagacaa atagcattag 1560gagcaggaat
accagtagaa aaaccagcta tgactataaa tatagtttgt ggttctggat
1620taagatctgt ttcaatggca tctcaactta tagcattagg tgatgctgat
ataatgttag 1680ttggtggagc tgaaaacatg agtatgtctc cttatttagt
accaagtgcg agatatggtg 1740caagaatggg tgatgctgct tttgttgatt
caatgataaa agatggatta tcagacatat 1800ttaataacta tcacatgggt
attactgctg aaaacatagc agagcaatgg aatataacta 1860gagaagaaca
agatgaatta gctcttgcaa gtcaaaataa agctgaaaaa gctcaagctg
1920aaggaaaatt tgatgaagaa atagttcctg ttgttataaa aggaagaaaa
ggtgacactg 1980tagtagataa agatgaatat attaagcctg gcactacaat
ggagaaactt gctaagttaa 2040gacctgcatt taaaaaagat ggaacagtta
ctgctggtaa tgcatcagga ataaatgatg 2100gtgctgctat gttagtagta
atggctaaag aaaaagctga agaactagga atagagcctc 2160ttgcaactat
agtttcttat ggaacagctg gtgttgaccc taaaataatg ggatatggac
2220cagttccagc aactaaaaaa gctttagaag ctgctaatat gactattgaa
gatatagatt 2280tagttgaagc taatgaggca tttgctgccc aatctgtagc
tgtaataaga gacttaaata 2340tagatatgaa taaagttaat gttaatggtg
gagcaatagc tataggacat ccaataggat 2400gctcaggagc aagaatactt
actacacttt
tatatgaaat gaagagaaga gatgctaaaa 2460ctggtcttgc tacactttgt
ataggcggtg gaatgggaac tactttaata gttaagagat 2520agtaagaagg
agatatacat atgaaattag ctgtaatagg tagtggaact atgggaagtg
2580gtattgtaca aacttttgca agttgtggac atgatgtatg tttaaagagt
agaactcaag 2640gtgctataga taaatgttta gctttattag ataaaaattt
aactaagtta gttactaagg 2700gaaaaatgga tgaagctaca aaagcagaaa
tattaagtca tgttagttca actactaatt 2760atgaagattt aaaagatatg
gatttaataa tagaagcatc tgtagaagac atgaatataa 2820agaaagatgt
tttcaagtta ctagatgaat tatgtaaaga agatactatc ttggcaacaa
2880atacttcatc attatctata acagaaatag cttcttctac taagcgccca
gataaagtta 2940taggaatgca tttctttaat ccagttccta tgatgaaatt
agttgaagtt ataagtggtc 3000agttaacatc aaaagttact tttgatacag
tatttgaatt atctaagagt atcaataaag 3060taccagtaga tgtatctgaa
tctcctggat ttgtagtaaa tagaatactt atacctatga 3120taaatgaagc
tgttggtata tatgcagatg gtgttgcaag taaagaagaa atagatgaag
3180ctatgaaatt aggagcaaac catccaatgg gaccactagc attaggtgat
ttaatcggat 3240tagatgttgt tttagctata atgaacgttt tatatactga
atttggagat actaaatata 3300gacctcatcc acttttagct aaaatggtta
gagctaatca attaggaaga aaaactaaga 3360taggattcta tgattataat
aaataataag aaggagatat acatatgagt acaagtgatg 3420ttaaagttta
tgagaatgta gctgttgaag tagatggaaa tatatgtaca gtgaaaatga
3480atagacctaa agcccttaat gcaataaatt caaagacttt agaagaactt
tatgaagtat 3540ttgtagatat taataatgat gaaactattg atgttgtaat
attgacaggg gaaggaaagg 3600catttgtagc tggagcagat attgcataca
tgaaagattt agatgctgta gctgctaaag 3660attttagtat cttaggagca
aaagcttttg gagaaataga aaatagtaaa aaagtagtga 3720tagctgctgt
aaacggattt gctttaggtg gaggatgtga acttgcaatg gcatgtgata
3780taagaattgc atctgctaaa gctaaatttg gtcagccaga agtaactctt
ggaataactc 3840caggatatgg aggaactcaa aggcttacaa gattggttgg
aatggcaaaa gcaaaagaat 3900taatctttac aggtcaagtt ataaaagctg
atgaagctga aaaaataggg ctagtaaata 3960gagtcgttga gccagacatt
ttaatagaag aagttgagaa attagctaag ataatagcta 4020aaaatgctca
gcttgcagtt agatactcta aagaagcaat acaacttggt gctcaaactg
4080atataaatac tggaatagat atagaatcta atttatttgg tctttgtttt
tcaactaaag 4140accaaaaaga aggaatgtca gctttcgttg aaaagagaga
agctaacttt ataaaagggt 4200aataagaagg agatatacat atgagaagtt
ttgaagaagt aattaagttt gcaaaagaaa 4260gaggacctaa aactatatca
gtagcatgtt gccaagataa agaagtttta atggcagttg 4320aaatggctag
aaaagaaaaa atagcaaatg ccattttagt aggagatata gaaaagacta
4380aagaaattgc aaaaagcata gacatggata tcgaaaatta tgaactgata
gatataaaag 4440atttagcaga agcatctcta aaatctgttg aattagtttc
acaaggaaaa gccgacatgg 4500taatgaaagg cttagtagac acatcaataa
tactaaaagc agttttaaat aaagaagtag 4560gtcttagaac tggaaatgta
ttaagtcacg tagcagtatt tgatgtagag ggatatgata 4620gattattttt
cgtaactgac gcagctatga acttagctcc tgatacaaat actaaaaagc
4680aaatcataga aaatgcttgc acagtagcac attcattaga tataagtgaa
ccaaaagttg 4740ctgcaatatg cgcaaaagaa aaagtaaatc caaaaatgaa
agatacagtt gaagctaaag 4800aactagaaga aatgtatgaa agaggagaaa
tcaaaggttg tatggttggt gggccttttg 4860caattgataa tgcagtatct
ttagaagcag ctaaacataa aggtataaat catcctgtag 4920caggacgagc
tgatatatta ttagccccag atattgaagg tggtaacata ttatataaag
4980ctttggtatt cttctcaaaa tcaaaaaatg caggagttat agttggggct
aaagcaccaa 5040taatattaac ttctagagca gacagtgaag aaactaaact
aaactcaata gctttaggtg 5100ttttaatggc agcaaaggca taataagaag
gagatataca tatgagcaaa atatttaaaa 5160tcttaacaat aaatcctggt
tcgacatcaa ctaaaatagc tgtatttgat aatgaggatt 5220tagtatttga
aaaaacttta agacattctt cagaagaaat aggaaaatat gagaaggtgt
5280ctgaccaatt tgaatttcgt aaacaagtaa tagaagaagc tctaaaagaa
ggtggagtaa 5340aaacatctga attagatgct gtagtaggta gaggaggact
tcttaaacct ataaaaggtg 5400gtacttattc agtaagtgct gctatgattg
aagatttaaa agtgggagtt ttaggagaac 5460acgcttcaaa cctaggtgga
ataatagcaa aacaaatagg tgaagaagta aatgttcctt 5520catacatagt
agaccctgtt gttgtagatg aattagaaga tgttgctaga atttctggta
5580tgcctgaaat aagtagagca agtgtagtac atgctttaaa tcaaaaggca
atagcaagaa 5640gatatgctag agaaataaac aagaaatatg aagatataaa
tcttatagtt gcacacatgg 5700gtggaggagt ttctgttgga gctcataaaa
atggtaaaat agtagatgtt gcaaacgcat 5760tagatggaga aggacctttc
tctccagaaa gaagtggtgg actaccagta ggtgcattag 5820taaaaatgtg
ctttagtgga aaatatactc aagatgaaat taaaaagaaa ataaaaggta
5880atggcggact agttgcatac ttaaacacta atgatgctag agaagttgaa
gaaagaattg 5940aagctggtga tgaaaaagct aaattagtat atgaagctat
ggcatatcaa atctctaaag 6000aaataggagc tagtgctgca gttcttaagg
gagatgtaaa agcaatatta ttaactggtg 6060gaatcgcata ttcaaaaatg
tttacagaaa tgattgcaga tagagttaaa tttatagcag 6120atgtaaaagt
ttatccaggt gaagatgaaa tgattgcatt agctcaaggt ggacttagag
6180ttttaactgg tgaagaagag gctcaagttt atgataacta ataa
6224833118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 83ctcgagatgc tagcaattgt gagcggataa
caattgacat tgtgagcgga taacaagata 60ctgagcacat cagcaggacg cactgacctt
aattaaaaga attcattaaa gaggagaaag 120gtaccatgaa tattcgtgat
cttgagtacc tggtggcatt ggctgaacac cgccattttc 180ggcgtgcggc
agattcctgc cacgttagcc agccgacgct tagcgggcaa attcgtaagc
240tggaagatga gctgggcgtg atgttgctgg agcggaccag ccgtaaagtg
ttgttcaccc 300aggcgggaat gctgctggtg gatcaggcgc gtaccgtgct
gcgtgaggtg aaagtcctta 360aagagatggc aagccagcag ggcgagacga
tgtccggacc gctgcacatt ggtttgattc 420ccacagttgg accgtacctg
ctaccgcata ttatccctat gctgcaccag acctttccaa 480agctggaaat
gtatctgcat gaagcacaga cccaccagtt actggcgcaa ctggacagcg
540gcaaactcga ttgcgtgatc ctcgcgctgg tgaaagagag cgaagcattc
attgaagtgc 600cgttgtttga tgagccaatg ttgctggcta tctatgaaga
tcacccgtgg gcgaaccgcg 660aatgcgtacc gatggccgat ctggcagggg
aaaaactgct gatgctggaa gatggtcact 720gtttgcgcga tcaggcaatg
ggtttctgtt ttgaagccgg ggcggatgaa gatacacact 780tccgcgcgac
cagcctggaa actctgcgca acatggtggc ggcaggtagc gggatcactt
840tactgccagc gctggctgtg ccgccggagc gcaaacgcga tggggttgtt
tatctgccgt 900gcattaagcc ggaaccacgc cgcactattg gcctggttta
tcgtcctggc tcaccgctgc 960gcagccgcta tgagcagctg gcagaggcca
tccgcgcaag aatggatggc catttcgata 1020aagttttaaa acaggcggtt
taaggatccc atggtacgcg tgctagaggc atcaaataaa 1080acgaaaggct
cagtcgaaag actgggcctt tcgttttatc tgttgtttgt cggtgaacgc
1140tctcctgagt aggacaaatc cgccgcccta gacctagggg atatattccg
cttcctcgct 1200cactgactcg ctacgctcgg tcgttcgact gcggcgagcg
gaaatggctt acgaacgggg 1260cggagatttc ctggaagatg ccaggaagat
acttaacagg gaagtgagag ggccgcggca 1320aagccgtttt tccataggct
ccgcccccct gacaagcatc acgaaatctg acgctcaaat 1380cagtggtggc
gaaacccgac aggactataa agataccagg cgtttccccc tggcggctcc
1440ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg tcattccgct
gttatggccg 1500cgtttgtctc attccacgcc tgacactcag ttccgggtag
gcagttcgct ccaagctgga 1560ctgtatgcac gaaccccccg ttcagtccga
ccgctgcgcc ttatccggta actatcgtct 1620tgagtccaac ccggaaagac
atgcaaaagc accactggca gcagccactg gtaattgatt 1680tagaggagtt
agtcttgaag tcatgcgccg gttaaggcta aactgaaagg acaagttttg
1740gtgactgcgc tcctccaagc cagttacctc ggttcaaaga gttggtagct
cagagaacct 1800tcgaaaaacc gccctgcaag gcggtttttt cgttttcaga
gcaagagatt acgcgcagac 1860caaaacgatc tcaagaagat catcttatta
atcagataaa atatttctag atttcagtgc 1920aatttatctc ttcaaatgta
gcacctgaag tcagccccat acgatataag ttgttactag 1980tgcttggatt
ctcaccaata aaaaacgccc ggcggcaacc gagcgttctg aacaaatcca
2040gatggagttc tgaggtcatt actggatcta tcaacaggag tccaagcgag
ctctcgaacc 2100ccagagtccc gctcagaaga actcgtcaag aaggcgatag
aaggcgatgc gctgcgaatc 2160gggagcggcg ataccgtaaa gcacgaggaa
gcggtcagcc cattcgccgc caagctcttc 2220agcaatatca cgggtagcca
acgctatgtc ctgatagcgg tccgccacac ccagccggcc 2280acagtcgatg
aatccagaaa agcggccatt ttccaccatg atattcggca agcaggcatc
2340gccatgggtc acgacgagat cctcgccgtc gggcatgcgc gccttgagcc
tggcgaacag 2400ttcggctggc gcgagcccct gatgctcttc gtccagatca
tcctgatcga caagaccggc 2460ttccatccga gtacgtgctc gctcgatgcg
atgtttcgct tggtggtcga atgggcaggt 2520agccggatca agcgtatgca
gccgccgcat tgcatcagcc atgatggata ctttctcggc 2580aggagcaagg
tgagatgaca ggagatcctg ccccggcact tcgcccaata gcagccagtc
2640ccttcccgct tcagtgacaa cgtcgagcac agctgcgcaa ggaacgcccg
tcgtggccag 2700ccacgatagc cgcgctgcct cgtcctgcag ttcattcagg
gcaccggaca ggtcggtctt 2760gacaaaaaga accgggcgcc cctgcgctga
cagccggaac acggcggcat cagagcagcc 2820gattgtctgt tgtgcccagt
catagccgaa tagcctctcc acccaagcgg ccggagaacc 2880tgcgtgcaat
ccatcttgtt caatcatgcg aaacgatcct catcctgtct cttgatcaga
2940tcttgatccc ctgcgccatc agatccttgg cggcaagaaa gccatccagt
ttactttgca 3000gggcttccca accttaccag agggcgcccc agctggcaat
tccgacgtct aagaaaccat 3060tattatcatg acattaacct ataaaaatag
gcgtatcacg aggccctttc gtcttcac 3118848650DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
84gtaaaacgac ggccagtgaa ttcgttaaga cccactttca catttaagtt gtttttctaa
60tccgcatatg atcaattcaa ggccgaataa gaaggctggc tctgcacctt ggtgatcaaa
120taattcgata gcttgtcgta ataatggcgg catactatca gtagtaggtg
tttccctttc 180ttctttagcg acttgatgct cttgatcttc caatacgcaa
cctaaagtaa aatgccccac 240agcgctgagt gcatataatg cattctctag
tgaaaaacct tgttggcata aaaaggctaa 300ttgattttcg agagtttcat
actgtttttc tgtaggccgt gtacctaaat gtacttttgc 360tccatcgcga
tgacttagta aagcacatct aaaactttta gcgttattac gtaaaaaatc
420ttgccagctt tccccttcta aagggcaaaa gtgagtatgg tgcctatcta
acatctcaat 480ggctaaggcg tcgagcaaag cccgcttatt ttttacatgc
caatacaatg taggctgctc 540tacacctagc ttctgggcga gtttacgggt
tgttaaacct tcgattccga cctcattaag 600cagctctaat gcgctgttaa
tcactttact tttatctaat ctagacatca ttaattccta 660atttttgttg
acactctatc attgatagag ttattttacc actccctatc agtgatagag
720aaaagtgaac tctagaaata attttgttta actttaagaa ggagatatac
atatggattt 780aaattctaaa aaatatcaga tgcttaaaga gctatatgta
agcttcgctg aaaatgaagt 840taaaccttta gcaacagaac ttgatgaaga
agaaagattt ccttatgaaa cagtggaaaa 900aatggcaaaa gcaggaatga
tgggtatacc atatccaaaa gaatatggtg gagaaggtgg 960agacactgta
ggatatataa tggcagttga agaattgtct agagtttgtg gtactacagg
1020agttatatta tcagctcata catctcttgg ctcatggcct atatatcaat
atggtaatga 1080agaacaaaaa caaaaattct taagaccact agcaagtgga
gaaaaattag gagcatttgg 1140tcttactgag cctaatgctg gtacagatgc
gtctggccaa caaacaactg ctgttttaga 1200cggggatgaa tacatactta
atggctcaaa aatatttata acaaacgcaa tagctggtga 1260catatatgta
gtaatggcaa tgactgataa atctaagggg aacaaaggaa tatcagcatt
1320tatagttgaa aaaggaactc ctgggtttag ctttggagtt aaagaaaaga
aaatgggtat 1380aagaggttca gctacgagtg aattaatatt tgaggattgc
agaataccta aagaaaattt 1440acttggaaaa gaaggtcaag gatttaagat
agcaatgtct actcttgatg gtggtagaat 1500tggtatagct gcacaagctt
taggtttagc acaaggtgct cttgatgaaa ctgttaaata 1560tgtaaaagaa
agagtacaat ttggtagacc attatcaaaa ttccaaaata cacaattcca
1620attagctgat atggaagtta aggtacaagc ggctagacac cttgtatatc
aagcagctat 1680aaataaagac ttaggaaaac cttatggagt agaagcagca
atggcaaaat tatttgcagc 1740tgaaacagct atggaagtta ctacaaaagc
tgtacaactt catggaggat atggatacac 1800tcgtgactat ccagtagaaa
gaatgatgag agatgctaag ataactgaaa tatatgaagg 1860aactagtgaa
gttcaaagaa tggttatttc aggaaaacta ttaaaatagt aagaaggaga
1920tatacatatg gaggaaggat ttatgaatat agtcgtttgt ataaaacaag
ttccagatac 1980aacagaagtt aaactagatc ctaatacagg tactttaatt
agagatggag taccaagtat 2040aataaaccct gatgataaag caggtttaga
agaagctata aaattaaaag aagaaatggg 2100tgctcatgta actgttataa
caatgggacc tcctcaagca gatatggctt taaaagaagc 2160tttagcaatg
ggtgcagata gaggtatatt attaacagat agagcatttg cgggtgctga
2220tacttgggca acttcatcag cattagcagg agcattaaaa aatatagatt
ttgatattat 2280aatagctgga agacaggcga tagatggaga tactgcacaa
gttggacctc aaatagctga 2340acatttaaat cttccatcaa taacatatgc
tgaagaaata aaaactgaag gtgaatatgt 2400attagtaaaa agacaatttg
aagattgttg ccatgactta aaagttaaaa tgccatgcct 2460tataacaact
cttaaagata tgaacacacc aagatacatg aaagttggaa gaatatatga
2520tgctttcgaa aatgatgtag tagaaacatg gactgtaaaa gatatagaag
ttgacccttc 2580taatttaggt cttaaaggtt ctccaactag tgtatttaaa
tcatttacaa aatcagttaa 2640accagctggt acaatataca atgaagatgc
gaaaacatca gctggaatta tcatagataa 2700attaaaagag aagtatatca
tataataaga aggagatata catatgggta acgttttagt 2760agtaatagaa
caaagagaaa atgtaattca aactgtttct ttagaattac taggaaaggc
2820tacagaaata gcaaaagatt atgatacaaa agtttctgca ttacttttag
gtagtaaggt 2880agaaggttta atagatacat tagcacacta tggtgcagat
gaggtaatag tagtagatga 2940tgaagcttta gcagtgtata caactgaacc
atatacaaaa gcagcttatg aagcaataaa 3000agcagctgac cctatagttg
tattatttgg tgcaacttca ataggtagag atttagcgcc 3060tagagtttct
gctagaatac atacaggtct tactgctgac tgtacaggtc ttgcagtagc
3120tgaagataca aaattattat taatgacaag acctgccttt ggtggaaata
taatggcaac 3180aatagtttgt aaagatttca gacctcaaat gtctacagtt
agaccagggg ttatgaagaa 3240aaatgaacct gatgaaacta aagaagctgt
aattaaccgt ttcaaggtag aatttaatga 3300tgctgataaa ttagttcaag
ttgtacaagt aataaaagaa gctaaaaaac aagttaaaat 3360agaagatgct
aagatattag tttctgctgg acgtggaatg ggtggaaaag aaaacttaga
3420catactttat gaattagctg aaattatagg tggagaagtt tctggttctc
gtgccactat 3480agatgcaggt tggttagata aagcaagaca agttggtcaa
actggtaaaa ctgtaagacc 3540agacctttat atagcatgtg gtatatctgg
agcaatacaa catatagctg gtatggaaga 3600tgctgagttt atagttgcta
taaataaaaa tccagaagct ccaatattta aatatgctga 3660tgttggtata
gttggagatg ttcataaagt gcttccagaa cttatcagtc agttaagtgt
3720tgcaaaagaa aaaggtgaag ttttagctaa ctaataagaa ggagatatac
atatgagaga 3780agtagtaatt gccagtgcag ctagaacagc agtaggaagt
tttggaggag catttaaatc 3840agtttcagcg gtagagttag gggtaacagc
agctaaagaa gctataaaaa gagctaacat 3900aactccagat atgatagatg
aatctctttt agggggagta cttacagcag gtcttggaca 3960aaatatagca
agacaaatag cattaggagc aggaatacca gtagaaaaac cagctatgac
4020tataaatata gtttgtggtt ctggattaag atctgtttca atggcatctc
aacttatagc 4080attaggtgat gctgatataa tgttagttgg tggagctgaa
aacatgagta tgtctcctta 4140tttagtacca agtgcgagat atggtgcaag
aatgggtgat gctgcttttg ttgattcaat 4200gataaaagat ggattatcag
acatatttaa taactatcac atgggtatta ctgctgaaaa 4260catagcagag
caatggaata taactagaga agaacaagat gaattagctc ttgcaagtca
4320aaataaagct gaaaaagctc aagctgaagg aaaatttgat gaagaaatag
ttcctgttgt 4380tataaaagga agaaaaggtg acactgtagt agataaagat
gaatatatta agcctggcac 4440tacaatggag aaacttgcta agttaagacc
tgcatttaaa aaagatggaa cagttactgc 4500tggtaatgca tcaggaataa
atgatggtgc tgctatgtta gtagtaatgg ctaaagaaaa 4560agctgaagaa
ctaggaatag agcctcttgc aactatagtt tcttatggaa cagctggtgt
4620tgaccctaaa ataatgggat atggaccagt tccagcaact aaaaaagctt
tagaagctgc 4680taatatgact attgaagata tagatttagt tgaagctaat
gaggcatttg ctgcccaatc 4740tgtagctgta ataagagact taaatataga
tatgaataaa gttaatgtta atggtggagc 4800aatagctata ggacatccaa
taggatgctc aggagcaaga atacttacta cacttttata 4860tgaaatgaag
agaagagatg ctaaaactgg tcttgctaca ctttgtatag gcggtggaat
4920gggaactact ttaatagtta agagatagta agaaggagat atacatatga
aattagctgt 4980aataggtagt ggaactatgg gaagtggtat tgtacaaact
tttgcaagtt gtggacatga 5040tgtatgttta aagagtagaa ctcaaggtgc
tatagataaa tgtttagctt tattagataa 5100aaatttaact aagttagtta
ctaagggaaa aatggatgaa gctacaaaag cagaaatatt 5160aagtcatgtt
agttcaacta ctaattatga agatttaaaa gatatggatt taataataga
5220agcatctgta gaagacatga atataaagaa agatgttttc aagttactag
atgaattatg 5280taaagaagat actatcttgg caacaaatac ttcatcatta
tctataacag aaatagcttc 5340ttctactaag cgcccagata aagttatagg
aatgcatttc tttaatccag ttcctatgat 5400gaaattagtt gaagttataa
gtggtcagtt aacatcaaaa gttacttttg atacagtatt 5460tgaattatct
aagagtatca ataaagtacc agtagatgta tctgaatctc ctggatttgt
5520agtaaataga atacttatac ctatgataaa tgaagctgtt ggtatatatg
cagatggtgt 5580tgcaagtaaa gaagaaatag atgaagctat gaaattagga
gcaaaccatc caatgggacc 5640actagcatta ggtgatttaa tcggattaga
tgttgtttta gctataatga acgttttata 5700tactgaattt ggagatacta
aatatagacc tcatccactt ttagctaaaa tggttagagc 5760taatcaatta
ggaagaaaaa ctaagatagg attctatgat tataataaat aataagaagg
5820agatatacat atgagtacaa gtgatgttaa agtttatgag aatgtagctg
ttgaagtaga 5880tggaaatata tgtacagtga aaatgaatag acctaaagcc
cttaatgcaa taaattcaaa 5940gactttagaa gaactttatg aagtatttgt
agatattaat aatgatgaaa ctattgatgt 6000tgtaatattg acaggggaag
gaaaggcatt tgtagctgga gcagatattg catacatgaa 6060agatttagat
gctgtagctg ctaaagattt tagtatctta ggagcaaaag cttttggaga
6120aatagaaaat agtaaaaaag tagtgatagc tgctgtaaac ggatttgctt
taggtggagg 6180atgtgaactt gcaatggcat gtgatataag aattgcatct
gctaaagcta aatttggtca 6240gccagaagta actcttggaa taactccagg
atatggagga actcaaaggc ttacaagatt 6300ggttggaatg gcaaaagcaa
aagaattaat ctttacaggt caagttataa aagctgatga 6360agctgaaaaa
atagggctag taaatagagt cgttgagcca gacattttaa tagaagaagt
6420tgagaaatta gctaagataa tagctaaaaa tgctcagctt gcagttagat
actctaaaga 6480agcaatacaa cttggtgctc aaactgatat aaatactgga
atagatatag aatctaattt 6540atttggtctt tgtttttcaa ctaaagacca
aaaagaagga atgtcagctt tcgttgaaaa 6600gagagaagct aactttataa
aagggtaata agaaggagat atacatatga gaagttttga 6660agaagtaatt
aagtttgcaa aagaaagagg acctaaaact atatcagtag catgttgcca
6720agataaagaa gttttaatgg cagttgaaat ggctagaaaa gaaaaaatag
caaatgccat 6780tttagtagga gatatagaaa agactaaaga aattgcaaaa
agcatagaca tggatatcga 6840aaattatgaa ctgatagata taaaagattt
agcagaagca tctctaaaat ctgttgaatt 6900agtttcacaa ggaaaagccg
acatggtaat gaaaggctta gtagacacat caataatact 6960aaaagcagtt
ttaaataaag aagtaggtct tagaactgga aatgtattaa gtcacgtagc
7020agtatttgat gtagagggat atgatagatt atttttcgta actgacgcag
ctatgaactt 7080agctcctgat acaaatacta aaaagcaaat catagaaaat
gcttgcacag tagcacattc 7140attagatata agtgaaccaa aagttgctgc
aatatgcgca aaagaaaaag taaatccaaa 7200aatgaaagat acagttgaag
ctaaagaact agaagaaatg tatgaaagag gagaaatcaa 7260aggttgtatg
gttggtgggc cttttgcaat tgataatgca gtatctttag aagcagctaa
7320acataaaggt ataaatcatc ctgtagcagg acgagctgat atattattag
ccccagatat 7380tgaaggtggt aacatattat ataaagcttt ggtattcttc
tcaaaatcaa aaaatgcagg 7440agttatagtt ggggctaaag caccaataat
attaacttct agagcagaca gtgaagaaac 7500taaactaaac tcaatagctt
taggtgtttt aatggcagca aaggcataat aagaaggaga 7560tatacatatg
agcaaaatat ttaaaatctt aacaataaat cctggttcga catcaactaa
7620aatagctgta tttgataatg aggatttagt atttgaaaaa actttaagac
attcttcaga 7680agaaatagga aaatatgaga aggtgtctga ccaatttgaa
tttcgtaaac aagtaataga 7740agaagctcta aaagaaggtg gagtaaaaac
atctgaatta gatgctgtag taggtagagg 7800aggacttctt aaacctataa
aaggtggtac ttattcagta agtgctgcta tgattgaaga 7860tttaaaagtg
ggagttttag gagaacacgc ttcaaaccta ggtggaataa tagcaaaaca
7920aataggtgaa gaagtaaatg ttccttcata
catagtagac cctgttgttg tagatgaatt 7980agaagatgtt gctagaattt
ctggtatgcc tgaaataagt agagcaagtg tagtacatgc 8040tttaaatcaa
aaggcaatag caagaagata tgctagagaa ataaacaaga aatatgaaga
8100tataaatctt atagttgcac acatgggtgg aggagtttct gttggagctc
ataaaaatgg 8160taaaatagta gatgttgcaa acgcattaga tggagaagga
cctttctctc cagaaagaag 8220tggtggacta ccagtaggtg cattagtaaa
aatgtgcttt agtggaaaat atactcaaga 8280tgaaattaaa aagaaaataa
aaggtaatgg cggactagtt gcatacttaa acactaatga 8340tgctagagaa
gttgaagaaa gaattgaagc tggtgatgaa aaagctaaat tagtatatga
8400agctatggca tatcaaatct ctaaagaaat aggagctagt gctgcagttc
ttaagggaga 8460tgtaaaagca atattattaa ctggtggaat cgcatattca
aaaatgttta cagaaatgat 8520tgcagataga gttaaattta tagcagatgt
aaaagtttat ccaggtgaag atgaaatgat 8580tgcattagct caaggtggac
ttagagtttt aactggtgaa gaagaggctc aagtttatga 8640taactaataa
8650856862DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 85gtaaaacgac ggccagtgaa ttcgttaaga
cccactttca catttaagtt gtttttctaa 60tccgcatatg atcaattcaa ggccgaataa
gaaggctggc tctgcacctt ggtgatcaaa 120taattcgata gcttgtcgta
ataatggcgg catactatca gtagtaggtg tttccctttc 180ttctttagcg
acttgatgct cttgatcttc caatacgcaa cctaaagtaa aatgccccac
240agcgctgagt gcatataatg cattctctag tgaaaaacct tgttggcata
aaaaggctaa 300ttgattttcg agagtttcat actgtttttc tgtaggccgt
gtacctaaat gtacttttgc 360tccatcgcga tgacttagta aagcacatct
aaaactttta gcgttattac gtaaaaaatc 420ttgccagctt tccccttcta
aagggcaaaa gtgagtatgg tgcctatcta acatctcaat 480ggctaaggcg
tcgagcaaag cccgcttatt ttttacatgc caatacaatg taggctgctc
540tacacctagc ttctgggcga gtttacgggt tgttaaacct tcgattccga
cctcattaag 600cagctctaat gcgctgttaa tcactttact tttatctaat
ctagacatca ttaattccta 660atttttgttg acactctatc attgatagag
ttattttacc actccctatc agtgatagag 720aaaagtgaac tctagaaata
attttgttta actttaagaa ggagatatac atatgatcgt 780aaaacctatg
gtacgcaaca atatctgcct gaacgcccat cctcagggct gcaagaaggg
840agtggaagat cagattgaat ataccaagaa acgcattacc gcagaagtca
aagctggcgc 900aaaagctcca aaaaacgttc tggtgcttgg ctgctcaaat
ggttacggcc tggcgagccg 960cattactgct gcgttcggat acggggctgc
gaccatcggc gtgtcctttg aaaaagcggg 1020ttcagaaacc aaatatggta
caccgggatg gtacaataat ttggcatttg atgaagcggc 1080aaaacgcgag
ggtctttata gcgtgacgat cgacggcgat gcgttttcag acgagatcaa
1140ggcccaggta attgaggaag ccaaaaaaaa aggtatcaaa tttgatctga
tcgtatacag 1200cttggccagc ccagtacgta ctgatcctga tacaggtatc
atgcacaaaa gcgttttgaa 1260accctttgga aaaacgttca caggcaaaac
agtagatccg tttactggcg agctgaagga 1320aatctccgcg gaaccagcaa
atgacgagga agcagccgcc actgttaaag ttatgggggg 1380tgaagattgg
gaacgttgga ttaagcagct gtcgaaggaa ggcctcttag aagaaggctg
1440tattaccttg gcctatagtt atattggccc tgaagctacc caagctttgt
accgtaaagg 1500cacaatcggc aaggccaaag aacacctgga ggccacagca
caccgtctca acaaagagaa 1560cccgtcaatc cgtgccttcg tgagcgtgaa
taaaggcctg gtaacccgcg caagcgccgt 1620aatcccggta atccctctgt
atctcgccag cttgttcaaa gtaatgaaag agaagggcaa 1680tcatgaaggt
tgtattgaac agatcacgcg tctgtacgcc gagcgcctgt accgtaaaga
1740tggtacaatt ccagttgatg aggaaaatcg cattcgcatt gatgattggg
agttagaaga 1800agacgtccag aaagcggtat ccgcgttgat ggagaaagtc
acgggtgaaa acgcagaatc 1860tctcactgac ttagcggggt accgccatga
tttcttagct agtaacggct ttgatgtaga 1920aggtattaat tatgaagcgg
aagttgaacg cttcgaccgt atctgataag aaggagatat 1980acatatgaga
gaagtagtaa ttgccagtgc agctagaaca gcagtaggaa gttttggagg
2040agcatttaaa tcagtttcag cggtagagtt aggggtaaca gcagctaaag
aagctataaa 2100aagagctaac ataactccag atatgataga tgaatctctt
ttagggggag tacttacagc 2160aggtcttgga caaaatatag caagacaaat
agcattagga gcaggaatac cagtagaaaa 2220accagctatg actataaata
tagtttgtgg ttctggatta agatctgttt caatggcatc 2280tcaacttata
gcattaggtg atgctgatat aatgttagtt ggtggagctg aaaacatgag
2340tatgtctcct tatttagtac caagtgcgag atatggtgca agaatgggtg
atgctgcttt 2400tgttgattca atgataaaag atggattatc agacatattt
aataactatc acatgggtat 2460tactgctgaa aacatagcag agcaatggaa
tataactaga gaagaacaag atgaattagc 2520tcttgcaagt caaaataaag
ctgaaaaagc tcaagctgaa ggaaaatttg atgaagaaat 2580agttcctgtt
gttataaaag gaagaaaagg tgacactgta gtagataaag atgaatatat
2640taagcctggc actacaatgg agaaacttgc taagttaaga cctgcattta
aaaaagatgg 2700aacagttact gctggtaatg catcaggaat aaatgatggt
gctgctatgt tagtagtaat 2760ggctaaagaa aaagctgaag aactaggaat
agagcctctt gcaactatag tttcttatgg 2820aacagctggt gttgacccta
aaataatggg atatggacca gttccagcaa ctaaaaaagc 2880tttagaagct
gctaatatga ctattgaaga tatagattta gttgaagcta atgaggcatt
2940tgctgcccaa tctgtagctg taataagaga cttaaatata gatatgaata
aagttaatgt 3000taatggtgga gcaatagcta taggacatcc aataggatgc
tcaggagcaa gaatacttac 3060tacactttta tatgaaatga agagaagaga
tgctaaaact ggtcttgcta cactttgtat 3120aggcggtgga atgggaacta
ctttaatagt taagagatag taagaaggag atatacatat 3180gaaattagct
gtaataggta gtggaactat gggaagtggt attgtacaaa cttttgcaag
3240ttgtggacat gatgtatgtt taaagagtag aactcaaggt gctatagata
aatgtttagc 3300tttattagat aaaaatttaa ctaagttagt tactaaggga
aaaatggatg aagctacaaa 3360agcagaaata ttaagtcatg ttagttcaac
tactaattat gaagatttaa aagatatgga 3420tttaataata gaagcatctg
tagaagacat gaatataaag aaagatgttt tcaagttact 3480agatgaatta
tgtaaagaag atactatctt ggcaacaaat acttcatcat tatctataac
3540agaaatagct tcttctacta agcgcccaga taaagttata ggaatgcatt
tctttaatcc 3600agttcctatg atgaaattag ttgaagttat aagtggtcag
ttaacatcaa aagttacttt 3660tgatacagta tttgaattat ctaagagtat
caataaagta ccagtagatg tatctgaatc 3720tcctggattt gtagtaaata
gaatacttat acctatgata aatgaagctg ttggtatata 3780tgcagatggt
gttgcaagta aagaagaaat agatgaagct atgaaattag gagcaaacca
3840tccaatggga ccactagcat taggtgattt aatcggatta gatgttgttt
tagctataat 3900gaacgtttta tatactgaat ttggagatac taaatataga
cctcatccac ttttagctaa 3960aatggttaga gctaatcaat taggaagaaa
aactaagata ggattctatg attataataa 4020ataataagaa ggagatatac
atatgagtac aagtgatgtt aaagtttatg agaatgtagc 4080tgttgaagta
gatggaaata tatgtacagt gaaaatgaat agacctaaag cccttaatgc
4140aataaattca aagactttag aagaacttta tgaagtattt gtagatatta
ataatgatga 4200aactattgat gttgtaatat tgacagggga aggaaaggca
tttgtagctg gagcagatat 4260tgcatacatg aaagatttag atgctgtagc
tgctaaagat tttagtatct taggagcaaa 4320agcttttgga gaaatagaaa
atagtaaaaa agtagtgata gctgctgtaa acggatttgc 4380tttaggtgga
ggatgtgaac ttgcaatggc atgtgatata agaattgcat ctgctaaagc
4440taaatttggt cagccagaag taactcttgg aataactcca ggatatggag
gaactcaaag 4500gcttacaaga ttggttggaa tggcaaaagc aaaagaatta
atctttacag gtcaagttat 4560aaaagctgat gaagctgaaa aaatagggct
agtaaataga gtcgttgagc cagacatttt 4620aatagaagaa gttgagaaat
tagctaagat aatagctaaa aatgctcagc ttgcagttag 4680atactctaaa
gaagcaatac aacttggtgc tcaaactgat ataaatactg gaatagatat
4740agaatctaat ttatttggtc tttgtttttc aactaaagac caaaaagaag
gaatgtcagc 4800tttcgttgaa aagagagaag ctaactttat aaaagggtaa
taagaaggag atatacatat 4860gagaagtttt gaagaagtaa ttaagtttgc
aaaagaaaga ggacctaaaa ctatatcagt 4920agcatgttgc caagataaag
aagttttaat ggcagttgaa atggctagaa aagaaaaaat 4980agcaaatgcc
attttagtag gagatataga aaagactaaa gaaattgcaa aaagcataga
5040catggatatc gaaaattatg aactgataga tataaaagat ttagcagaag
catctctaaa 5100atctgttgaa ttagtttcac aaggaaaagc cgacatggta
atgaaaggct tagtagacac 5160atcaataata ctaaaagcag ttttaaataa
agaagtaggt cttagaactg gaaatgtatt 5220aagtcacgta gcagtatttg
atgtagaggg atatgataga ttatttttcg taactgacgc 5280agctatgaac
ttagctcctg atacaaatac taaaaagcaa atcatagaaa atgcttgcac
5340agtagcacat tcattagata taagtgaacc aaaagttgct gcaatatgcg
caaaagaaaa 5400agtaaatcca aaaatgaaag atacagttga agctaaagaa
ctagaagaaa tgtatgaaag 5460aggagaaatc aaaggttgta tggttggtgg
gccttttgca attgataatg cagtatcttt 5520agaagcagct aaacataaag
gtataaatca tcctgtagca ggacgagctg atatattatt 5580agccccagat
attgaaggtg gtaacatatt atataaagct ttggtattct tctcaaaatc
5640aaaaaatgca ggagttatag ttggggctaa agcaccaata atattaactt
ctagagcaga 5700cagtgaagaa actaaactaa actcaatagc tttaggtgtt
ttaatggcag caaaggcata 5760ataagaagga gatatacata tgagcaaaat
atttaaaatc ttaacaataa atcctggttc 5820gacatcaact aaaatagctg
tatttgataa tgaggattta gtatttgaaa aaactttaag 5880acattcttca
gaagaaatag gaaaatatga gaaggtgtct gaccaatttg aatttcgtaa
5940acaagtaata gaagaagctc taaaagaagg tggagtaaaa acatctgaat
tagatgctgt 6000agtaggtaga ggaggacttc ttaaacctat aaaaggtggt
acttattcag taagtgctgc 6060tatgattgaa gatttaaaag tgggagtttt
aggagaacac gcttcaaacc taggtggaat 6120aatagcaaaa caaataggtg
aagaagtaaa tgttccttca tacatagtag accctgttgt 6180tgtagatgaa
ttagaagatg ttgctagaat ttctggtatg cctgaaataa gtagagcaag
6240tgtagtacat gctttaaatc aaaaggcaat agcaagaaga tatgctagag
aaataaacaa 6300gaaatatgaa gatataaatc ttatagttgc acacatgggt
ggaggagttt ctgttggagc 6360tcataaaaat ggtaaaatag tagatgttgc
aaacgcatta gatggagaag gacctttctc 6420tccagaaaga agtggtggac
taccagtagg tgcattagta aaaatgtgct ttagtggaaa 6480atatactcaa
gatgaaatta aaaagaaaat aaaaggtaat ggcggactag ttgcatactt
6540aaacactaat gatgctagag aagttgaaga aagaattgaa gctggtgatg
aaaaagctaa 6600attagtatat gaagctatgg catatcaaat ctctaaagaa
ataggagcta gtgctgcagt 6660tcttaaggga gatgtaaaag caatattatt
aactggtgga atcgcatatt caaaaatgtt 6720tacagaaatg attgcagata
gagttaaatt tatagcagat gtaaaagttt atccaggtga 6780agatgaaatg
attgcattag ctcaaggtgg acttagagtt ttaactggtg aagaagaggc
6840tcaagtttat gataactaat aa 6862865644DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
86ttattatcgc accgcaatcg ggattttcga ttcataaagc aggtcgtagg tcggcttgtt
60gagcaggtct tgcagcgtga aaccgtccag atacgtgaaa aacgacttca ttgcaccgcc
120gagtatgccc gtcagccggc aggacggcgt aatcaggcat tcgttgttcg
ggcccataca 180ctcgaccagc tgcatcggtt cgaggtggcg gacgaccgcg
ccgatattga tgcgttcggg 240cggcgcggcc agcctcagcc cgccgccttt
cccgcgtacg ctgtgcaaga acccgccttt 300gaccagcgcg gtaaccactt
tcatcaaatg gcttttggaa atgccgtagg tcgaggcgat 360ggtggcgata
ttgaccagcg cgtcgtcgtt gacggcggtg tagatgagga cgcgcagccc
420gtagtcggta tgttgggtca gatacataca acctccttag tacatgcaaa
attatttcta 480gagcaacata cgagccggaa gcataaagtg taaagcctgg
ggtgcctaat gagttgagtt 540gaggaattat aacaggaaga aatattcctc
atacgcttgt aattcctcta tggttgttga 600caattaatca tcggctcgta
taatgtataa cattcatatt ttgtgaattt taaactctag 660aaataatttt
gtttaacttt aagaaggaga tatacatatg atcgtaaaac ctatggtacg
720caacaatatc tgcctgaacg cccatcctca gggctgcaag aagggagtgg
aagatcagat 780tgaatatacc aagaaacgca ttaccgcaga agtcaaagct
ggcgcaaaag ctccaaaaaa 840cgttctggtg cttggctgct caaatggtta
cggcctggcg agccgcatta ctgctgcgtt 900cggatacggg gctgcgacca
tcggcgtgtc ctttgaaaaa gcgggttcag aaaccaaata 960tggtacaccg
ggatggtaca ataatttggc atttgatgaa gcggcaaaac gcgagggtct
1020ttatagcgtg acgatcgacg gcgatgcgtt ttcagacgag atcaaggccc
aggtaattga 1080ggaagccaaa aaaaaaggta tcaaatttga tctgatcgta
tacagcttgg ccagcccagt 1140acgtactgat cctgatacag gtatcatgca
caaaagcgtt ttgaaaccct ttggaaaaac 1200gttcacaggc aaaacagtag
atccgtttac tggcgagctg aaggaaatct ccgcggaacc 1260agcaaatgac
gaggaagcag ccgccactgt taaagttatg gggggtgaag attgggaacg
1320ttggattaag cagctgtcga aggaaggcct cttagaagaa ggctgtatta
ccttggccta 1380tagttatatt ggccctgaag ctacccaagc tttgtaccgt
aaaggcacaa tcggcaaggc 1440caaagaacac ctggaggcca cagcacaccg
tctcaacaaa gagaacccgt caatccgtgc 1500cttcgtgagc gtgaataaag
gcctggtaac ccgcgcaagc gccgtaatcc cggtaatccc 1560tctgtatctc
gccagcttgt tcaaagtaat gaaagagaag ggcaatcatg aaggttgtat
1620tgaacagatc acgcgtctgt acgccgagcg cctgtaccgt aaagatggta
caattccagt 1680tgatgaggaa aatcgcattc gcattgatga ttgggagtta
gaagaagacg tccagaaagc 1740ggtatccgcg ttgatggaga aagtcacggg
tgaaaacgca gaatctctca ctgacttagc 1800ggggtaccgc catgatttct
tagctagtaa cggctttgat gtagaaggta ttaattatga 1860agcggaagtt
gaacgcttcg accgtatctg ataagaagga gatatacata tgagagaagt
1920agtaattgcc agtgcagcta gaacagcagt aggaagtttt ggaggagcat
ttaaatcagt 1980ttcagcggta gagttagggg taacagcagc taaagaagct
ataaaaagag ctaacataac 2040tccagatatg atagatgaat ctcttttagg
gggagtactt acagcaggtc ttggacaaaa 2100tatagcaaga caaatagcat
taggagcagg aataccagta gaaaaaccag ctatgactat 2160aaatatagtt
tgtggttctg gattaagatc tgtttcaatg gcatctcaac ttatagcatt
2220aggtgatgct gatataatgt tagttggtgg agctgaaaac atgagtatgt
ctccttattt 2280agtaccaagt gcgagatatg gtgcaagaat gggtgatgct
gcttttgttg attcaatgat 2340aaaagatgga ttatcagaca tatttaataa
ctatcacatg ggtattactg ctgaaaacat 2400agcagagcaa tggaatataa
ctagagaaga acaagatgaa ttagctcttg caagtcaaaa 2460taaagctgaa
aaagctcaag ctgaaggaaa atttgatgaa gaaatagttc ctgttgttat
2520aaaaggaaga aaaggtgaca ctgtagtaga taaagatgaa tatattaagc
ctggcactac 2580aatggagaaa cttgctaagt taagacctgc atttaaaaaa
gatggaacag ttactgctgg 2640taatgcatca ggaataaatg atggtgctgc
tatgttagta gtaatggcta aagaaaaagc 2700tgaagaacta ggaatagagc
ctcttgcaac tatagtttct tatggaacag ctggtgttga 2760ccctaaaata
atgggatatg gaccagttcc agcaactaaa aaagctttag aagctgctaa
2820tatgactatt gaagatatag atttagttga agctaatgag gcatttgctg
cccaatctgt 2880agctgtaata agagacttaa atatagatat gaataaagtt
aatgttaatg gtggagcaat 2940agctatagga catccaatag gatgctcagg
agcaagaata cttactacac ttttatatga 3000aatgaagaga agagatgcta
aaactggtct tgctacactt tgtataggcg gtggaatggg 3060aactacttta
atagttaaga gatagtaaga aggagatata catatgaaat tagctgtaat
3120aggtagtgga actatgggaa gtggtattgt acaaactttt gcaagttgtg
gacatgatgt 3180atgtttaaag agtagaactc aaggtgctat agataaatgt
ttagctttat tagataaaaa 3240tttaactaag ttagttacta agggaaaaat
ggatgaagct acaaaagcag aaatattaag 3300tcatgttagt tcaactacta
attatgaaga tttaaaagat atggatttaa taatagaagc 3360atctgtagaa
gacatgaata taaagaaaga tgttttcaag ttactagatg aattatgtaa
3420agaagatact atcttggcaa caaatacttc atcattatct ataacagaaa
tagcttcttc 3480tactaagcgc ccagataaag ttataggaat gcatttcttt
aatccagttc ctatgatgaa 3540attagttgaa gttataagtg gtcagttaac
atcaaaagtt acttttgata cagtatttga 3600attatctaag agtatcaata
aagtaccagt agatgtatct gaatctcctg gatttgtagt 3660aaatagaata
cttataccta tgataaatga agctgttggt atatatgcag atggtgttgc
3720aagtaaagaa gaaatagatg aagctatgaa attaggagca aaccatccaa
tgggaccact 3780agcattaggt gatttaatcg gattagatgt tgttttagct
ataatgaacg ttttatatac 3840tgaatttgga gatactaaat atagacctca
tccactttta gctaaaatgg ttagagctaa 3900tcaattagga agaaaaacta
agataggatt ctatgattat aataaataat aagaaggaga 3960tatacatatg
agtacaagtg atgttaaagt ttatgagaat gtagctgttg aagtagatgg
4020aaatatatgt acagtgaaaa tgaatagacc taaagccctt aatgcaataa
attcaaagac 4080tttagaagaa ctttatgaag tatttgtaga tattaataat
gatgaaacta ttgatgttgt 4140aatattgaca ggggaaggaa aggcatttgt
agctggagca gatattgcat acatgaaaga 4200tttagatgct gtagctgcta
aagattttag tatcttagga gcaaaagctt ttggagaaat 4260agaaaatagt
aaaaaagtag tgatagctgc tgtaaacgga tttgctttag gtggaggatg
4320tgaacttgca atggcatgtg atataagaat tgcatctgct aaagctaaat
ttggtcagcc 4380agaagtaact cttggaataa ctccaggata tggaggaact
caaaggctta caagattggt 4440tggaatggca aaagcaaaag aattaatctt
tacaggtcaa gttataaaag ctgatgaagc 4500tgaaaaaata gggctagtaa
atagagtcgt tgagccagac attttaatag aagaagttga 4560gaaattagct
aagataatag ctaaaaatgc tcagcttgca gttagatact ctaaagaagc
4620aatacaactt ggtgctcaaa ctgatataaa tactggaata gatatagaat
ctaatttatt 4680tggtctttgt ttttcaacta aagaccaaaa agaaggaatg
tcagctttcg ttgaaaagag 4740agaagctaac tttataaaag ggtaataaga
aggagatata catatgagtc aggcgctaaa 4800aaatttactg acattgttaa
atctggaaaa aattgaggaa ggactctttc gcggccagag 4860tgaagattta
ggtttacgcc aggtgtttgg cggccaggtc gtgggtcagg ccttgtatgc
4920tgcaaaagag accgtccctg aagagcggct ggtacattcg tttcacagct
actttcttcg 4980ccctggcgat agtaagaagc cgattattta tgatgtcgaa
acgctgcgtg acggtaacag 5040cttcagcgcc cgccgggttg ctgctattca
aaacggcaaa ccgatttttt atatgactgc 5100ctctttccag gcaccagaag
cgggtttcga acatcaaaaa acaatgccgt ccgcgccagc 5160gcctgatggc
ctcccttcgg aaacgcaaat cgcccaatcg ctggcgcacc tgctgccgcc
5220agtgctgaaa gataaattca tctgcgatcg tccgctggaa gtccgtccgg
tggagtttca 5280taacccactg aaaggtcacg tcgcagaacc acatcgtcag
gtgtggatcc gcgcaaatgg 5340tagcgtgccg gatgacctgc gcgttcatca
gtatctgctc ggttacgctt ctgatcttaa 5400cttcctgccg gtagctctac
agccgcacgg catcggtttt ctcgaaccgg ggattcagat 5460tgccaccatt
gaccattcca tgtggttcca tcgcccgttt aatttgaatg aatggctgct
5520gtatagcgtg gagagcacct cggcgtccag cgcacgtggc tttgtgcgcg
gtgagtttta 5580tacccaagac ggcgtactgg ttgcctcgac cgttcaggaa
ggggtgatgc gtaatcacaa 5640ttaa 5644875719DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
87gtaaaacgac ggccagtgaa ttcgttaaga cccactttca catttaagtt gtttttctaa
60tccgcatatg atcaattcaa ggccgaataa gaaggctggc tctgcacctt ggtgatcaaa
120taattcgata gcttgtcgta ataatggcgg catactatca gtagtaggtg
tttccctttc 180ttctttagcg acttgatgct cttgatcttc caatacgcaa
cctaaagtaa aatgccccac 240agcgctgagt gcatataatg cattctctag
tgaaaaacct tgttggcata aaaaggctaa 300ttgattttcg agagtttcat
actgtttttc tgtaggccgt gtacctaaat gtacttttgc 360tccatcgcga
tgacttagta aagcacatct aaaactttta gcgttattac gtaaaaaatc
420ttgccagctt tccccttcta aagggcaaaa gtgagtatgg tgcctatcta
acatctcaat 480ggctaaggcg tcgagcaaag cccgcttatt ttttacatgc
caatacaatg taggctgctc 540tacacctagc ttctgggcga gtttacgggt
tgttaaacct tcgattccga cctcattaag 600cagctctaat gcgctgttaa
tcactttact tttatctaat ctagacatca ttaattccta 660atttttgttg
acactctatc attgatagag ttattttacc actccctatc agtgatagag
720aaaagtgaac tctagaaata attttgttta actttaagaa ggagatatac
atatgatcgt 780aaaacctatg gtacgcaaca atatctgcct gaacgcccat
cctcagggct gcaagaaggg 840agtggaagat cagattgaat ataccaagaa
acgcattacc gcagaagtca aagctggcgc 900aaaagctcca aaaaacgttc
tggtgcttgg ctgctcaaat ggttacggcc tggcgagccg 960cattactgct
gcgttcggat acggggctgc gaccatcggc gtgtcctttg aaaaagcggg
1020ttcagaaacc aaatatggta caccgggatg gtacaataat ttggcatttg
atgaagcggc 1080aaaacgcgag ggtctttata gcgtgacgat cgacggcgat
gcgttttcag acgagatcaa 1140ggcccaggta attgaggaag ccaaaaaaaa
aggtatcaaa tttgatctga tcgtatacag 1200cttggccagc ccagtacgta
ctgatcctga tacaggtatc atgcacaaaa gcgttttgaa 1260accctttgga
aaaacgttca caggcaaaac agtagatccg tttactggcg agctgaagga
1320aatctccgcg gaaccagcaa atgacgagga agcagccgcc actgttaaag
ttatgggggg 1380tgaagattgg gaacgttgga ttaagcagct gtcgaaggaa
ggcctcttag aagaaggctg
1440tattaccttg gcctatagtt atattggccc tgaagctacc caagctttgt
accgtaaagg 1500cacaatcggc aaggccaaag aacacctgga ggccacagca
caccgtctca acaaagagaa 1560cccgtcaatc cgtgccttcg tgagcgtgaa
taaaggcctg gtaacccgcg caagcgccgt 1620aatcccggta atccctctgt
atctcgccag cttgttcaaa gtaatgaaag agaagggcaa 1680tcatgaaggt
tgtattgaac agatcacgcg tctgtacgcc gagcgcctgt accgtaaaga
1740tggtacaatt ccagttgatg aggaaaatcg cattcgcatt gatgattggg
agttagaaga 1800agacgtccag aaagcggtat ccgcgttgat ggagaaagtc
acgggtgaaa acgcagaatc 1860tctcactgac ttagcggggt accgccatga
tttcttagct agtaacggct ttgatgtaga 1920aggtattaat tatgaagcgg
aagttgaacg cttcgaccgt atctgataag aaggagatat 1980acatatgaga
gaagtagtaa ttgccagtgc agctagaaca gcagtaggaa gttttggagg
2040agcatttaaa tcagtttcag cggtagagtt aggggtaaca gcagctaaag
aagctataaa 2100aagagctaac ataactccag atatgataga tgaatctctt
ttagggggag tacttacagc 2160aggtcttgga caaaatatag caagacaaat
agcattagga gcaggaatac cagtagaaaa 2220accagctatg actataaata
tagtttgtgg ttctggatta agatctgttt caatggcatc 2280tcaacttata
gcattaggtg atgctgatat aatgttagtt ggtggagctg aaaacatgag
2340tatgtctcct tatttagtac caagtgcgag atatggtgca agaatgggtg
atgctgcttt 2400tgttgattca atgataaaag atggattatc agacatattt
aataactatc acatgggtat 2460tactgctgaa aacatagcag agcaatggaa
tataactaga gaagaacaag atgaattagc 2520tcttgcaagt caaaataaag
ctgaaaaagc tcaagctgaa ggaaaatttg atgaagaaat 2580agttcctgtt
gttataaaag gaagaaaagg tgacactgta gtagataaag atgaatatat
2640taagcctggc actacaatgg agaaacttgc taagttaaga cctgcattta
aaaaagatgg 2700aacagttact gctggtaatg catcaggaat aaatgatggt
gctgctatgt tagtagtaat 2760ggctaaagaa aaagctgaag aactaggaat
agagcctctt gcaactatag tttcttatgg 2820aacagctggt gttgacccta
aaataatggg atatggacca gttccagcaa ctaaaaaagc 2880tttagaagct
gctaatatga ctattgaaga tatagattta gttgaagcta atgaggcatt
2940tgctgcccaa tctgtagctg taataagaga cttaaatata gatatgaata
aagttaatgt 3000taatggtgga gcaatagcta taggacatcc aataggatgc
tcaggagcaa gaatacttac 3060tacactttta tatgaaatga agagaagaga
tgctaaaact ggtcttgcta cactttgtat 3120aggcggtgga atgggaacta
ctttaatagt taagagatag taagaaggag atatacatat 3180gaaattagct
gtaataggta gtggaactat gggaagtggt attgtacaaa cttttgcaag
3240ttgtggacat gatgtatgtt taaagagtag aactcaaggt gctatagata
aatgtttagc 3300tttattagat aaaaatttaa ctaagttagt tactaaggga
aaaatggatg aagctacaaa 3360agcagaaata ttaagtcatg ttagttcaac
tactaattat gaagatttaa aagatatgga 3420tttaataata gaagcatctg
tagaagacat gaatataaag aaagatgttt tcaagttact 3480agatgaatta
tgtaaagaag atactatctt ggcaacaaat acttcatcat tatctataac
3540agaaatagct tcttctacta agcgcccaga taaagttata ggaatgcatt
tctttaatcc 3600agttcctatg atgaaattag ttgaagttat aagtggtcag
ttaacatcaa aagttacttt 3660tgatacagta tttgaattat ctaagagtat
caataaagta ccagtagatg tatctgaatc 3720tcctggattt gtagtaaata
gaatacttat acctatgata aatgaagctg ttggtatata 3780tgcagatggt
gttgcaagta aagaagaaat agatgaagct atgaaattag gagcaaacca
3840tccaatggga ccactagcat taggtgattt aatcggatta gatgttgttt
tagctataat 3900gaacgtttta tatactgaat ttggagatac taaatataga
cctcatccac ttttagctaa 3960aatggttaga gctaatcaat taggaagaaa
aactaagata ggattctatg attataataa 4020ataataagaa ggagatatac
atatgagtac aagtgatgtt aaagtttatg agaatgtagc 4080tgttgaagta
gatggaaata tatgtacagt gaaaatgaat agacctaaag cccttaatgc
4140aataaattca aagactttag aagaacttta tgaagtattt gtagatatta
ataatgatga 4200aactattgat gttgtaatat tgacagggga aggaaaggca
tttgtagctg gagcagatat 4260tgcatacatg aaagatttag atgctgtagc
tgctaaagat tttagtatct taggagcaaa 4320agcttttgga gaaatagaaa
atagtaaaaa agtagtgata gctgctgtaa acggatttgc 4380tttaggtgga
ggatgtgaac ttgcaatggc atgtgatata agaattgcat ctgctaaagc
4440taaatttggt cagccagaag taactcttgg aataactcca ggatatggag
gaactcaaag 4500gcttacaaga ttggttggaa tggcaaaagc aaaagaatta
atctttacag gtcaagttat 4560aaaagctgat gaagctgaaa aaatagggct
agtaaataga gtcgttgagc cagacatttt 4620aatagaagaa gttgagaaat
tagctaagat aatagctaaa aatgctcagc ttgcagttag 4680atactctaaa
gaagcaatac aacttggtgc tcaaactgat ataaatactg gaatagatat
4740agaatctaat ttatttggtc tttgtttttc aactaaagac caaaaagaag
gaatgtcagc 4800tttcgttgaa aagagagaag ctaactttat aaaagggtaa
taagaaggag atatacatat 4860gagtcaggcg ctaaaaaatt tactgacatt
gttaaatctg gaaaaaattg aggaaggact 4920ctttcgcggc cagagtgaag
atttaggttt acgccaggtg tttggcggcc aggtcgtggg 4980tcaggccttg
tatgctgcaa aagagaccgt ccctgaagag cggctggtac attcgtttca
5040cagctacttt cttcgccctg gcgatagtaa gaagccgatt atttatgatg
tcgaaacgct 5100gcgtgacggt aacagcttca gcgcccgccg ggttgctgct
attcaaaacg gcaaaccgat 5160tttttatatg actgcctctt tccaggcacc
agaagcgggt ttcgaacatc aaaaaacaat 5220gccgtccgcg ccagcgcctg
atggcctccc ttcggaaacg caaatcgccc aatcgctggc 5280gcacctgctg
ccgccagtgc tgaaagataa attcatctgc gatcgtccgc tggaagtccg
5340tccggtggag tttcataacc cactgaaagg tcacgtcgca gaaccacatc
gtcaggtgtg 5400gatccgcgca aatggtagcg tgccggatga cctgcgcgtt
catcagtatc tgctcggtta 5460cgcttctgat cttaacttcc tgccggtagc
tctacagccg cacggcatcg gttttctcga 5520accggggatt cagattgcca
ccattgacca ttccatgtgg ttccatcgcc cgtttaattt 5580gaatgaatgg
ctgctgtata gcgtggagag cacctcggcg tccagcgcac gtggctttgt
5640gcgcggtgag ttttataccc aagacggcgt actggttgcc tcgaccgttc
aggaaggggt 5700gatgcgtaat cacaattaa 5719885719DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
88gtaaaacgac ggccagtgaa ttcgttaaga cccactttca catttaagtt gtttttctaa
60tccgcatatg atcaattcaa ggccgaataa gaaggctggc tctgcacctt ggtgatcaaa
120taattcgata gcttgtcgta ataatggcgg catactatca gtagtaggtg
tttccctttc 180ttctttagcg acttgatgct cttgatcttc caatacgcaa
cctaaagtaa aatgccccac 240agcgctgagt gcatataatg cattctctag
tgaaaaacct tgttggcata aaaaggctaa 300ttgattttcg agagtttcat
actgtttttc tgtaggccgt gtacctaaat gtacttttgc 360tccatcgcga
tgacttagta aagcacatct aaaactttta gcgttattac gtaaaaaatc
420ttgccagctt tccccttcta aagggcaaaa gtgagtatgg tgcctatcta
acatctcaat 480ggctaaggcg tcgagcaaag cccgcttatt ttttacatgc
caatacaatg taggctgctc 540tacacctagc ttctgggcga gtttacgggt
tgttaaacct tcgattccga cctcattaag 600cagctctaat gcgctgttaa
tcactttact tttatctaat ctagacatca ttaattccta 660atttttgttg
acactctatc attgatagag ttattttacc actccctatc agtgatagag
720aaaagtgaac tctagaaata attttgttta actttaagaa ggagatatac
atatgatcgt 780aaaacctatg gtacgcaaca atatctgcct gaacgcccat
cctcagggct gcaagaaggg 840agtggaagat cagattgaat ataccaagaa
acgcattacc gcagaagtca aagctggcgc 900aaaagctcca aaaaacgttc
tggtgcttgg ctgctcaaat ggttacggcc tggcgagccg 960cattactgct
gcgttcggat acggggctgc gaccatcggc gtgtcctttg aaaaagcggg
1020ttcagaaacc aaatatggta caccgggatg gtacaataat ttggcatttg
atgaagcggc 1080aaaacgcgag ggtctttata gcgtgacgat cgacggcgat
gcgttttcag acgagatcaa 1140ggcccaggta attgaggaag ccaaaaaaaa
aggtatcaaa tttgatctga tcgtatacag 1200cttggccagc ccagtacgta
ctgatcctga tacaggtatc atgcacaaaa gcgttttgaa 1260accctttgga
aaaacgttca caggcaaaac agtagatccg tttactggcg agctgaagga
1320aatctccgcg gaaccagcaa atgacgagga agcagccgcc actgttaaag
ttatgggggg 1380tgaagattgg gaacgttgga ttaagcagct gtcgaaggaa
ggcctcttag aagaaggctg 1440tattaccttg gcctatagtt atattggccc
tgaagctacc caagctttgt accgtaaagg 1500cacaatcggc aaggccaaag
aacacctgga ggccacagca caccgtctca acaaagagaa 1560cccgtcaatc
cgtgccttcg tgagcgtgaa taaaggcctg gtaacccgcg caagcgccgt
1620aatcccggta atccctctgt atctcgccag cttgttcaaa gtaatgaaag
agaagggcaa 1680tcatgaaggt tgtattgaac agatcacgcg tctgtacgcc
gagcgcctgt accgtaaaga 1740tggtacaatt ccagttgatg aggaaaatcg
cattcgcatt gatgattggg agttagaaga 1800agacgtccag aaagcggtat
ccgcgttgat ggagaaagtc acgggtgaaa acgcagaatc 1860tctcactgac
ttagcggggt accgccatga tttcttagct agtaacggct ttgatgtaga
1920aggtattaat tatgaagcgg aagttgaacg cttcgaccgt atctgataag
aaggagatat 1980acatatgaga gaagtagtaa ttgccagtgc agctagaaca
gcagtaggaa gttttggagg 2040agcatttaaa tcagtttcag cggtagagtt
aggggtaaca gcagctaaag aagctataaa 2100aagagctaac ataactccag
atatgataga tgaatctctt ttagggggag tacttacagc 2160aggtcttgga
caaaatatag caagacaaat agcattagga gcaggaatac cagtagaaaa
2220accagctatg actataaata tagtttgtgg ttctggatta agatctgttt
caatggcatc 2280tcaacttata gcattaggtg atgctgatat aatgttagtt
ggtggagctg aaaacatgag 2340tatgtctcct tatttagtac caagtgcgag
atatggtgca agaatgggtg atgctgcttt 2400tgttgattca atgataaaag
atggattatc agacatattt aataactatc acatgggtat 2460tactgctgaa
aacatagcag agcaatggaa tataactaga gaagaacaag atgaattagc
2520tcttgcaagt caaaataaag ctgaaaaagc tcaagctgaa ggaaaatttg
atgaagaaat 2580agttcctgtt gttataaaag gaagaaaagg tgacactgta
gtagataaag atgaatatat 2640taagcctggc actacaatgg agaaacttgc
taagttaaga cctgcattta aaaaagatgg 2700aacagttact gctggtaatg
catcaggaat aaatgatggt gctgctatgt tagtagtaat 2760ggctaaagaa
aaagctgaag aactaggaat agagcctctt gcaactatag tttcttatgg
2820aacagctggt gttgacccta aaataatggg atatggacca gttccagcaa
ctaaaaaagc 2880tttagaagct gctaatatga ctattgaaga tatagattta
gttgaagcta atgaggcatt 2940tgctgcccaa tctgtagctg taataagaga
cttaaatata gatatgaata aagttaatgt 3000taatggtgga gcaatagcta
taggacatcc aataggatgc tcaggagcaa gaatacttac 3060tacactttta
tatgaaatga agagaagaga tgctaaaact ggtcttgcta cactttgtat
3120aggcggtgga atgggaacta ctttaatagt taagagatag taagaaggag
atatacatat 3180gaaattagct gtaataggta gtggaactat gggaagtggt
attgtacaaa cttttgcaag 3240ttgtggacat gatgtatgtt taaagagtag
aactcaaggt gctatagata aatgtttagc 3300tttattagat aaaaatttaa
ctaagttagt tactaaggga aaaatggatg aagctacaaa 3360agcagaaata
ttaagtcatg ttagttcaac tactaattat gaagatttaa aagatatgga
3420tttaataata gaagcatctg tagaagacat gaatataaag aaagatgttt
tcaagttact 3480agatgaatta tgtaaagaag atactatctt ggcaacaaat
acttcatcat tatctataac 3540agaaatagct tcttctacta agcgcccaga
taaagttata ggaatgcatt tctttaatcc 3600agttcctatg atgaaattag
ttgaagttat aagtggtcag ttaacatcaa aagttacttt 3660tgatacagta
tttgaattat ctaagagtat caataaagta ccagtagatg tatctgaatc
3720tcctggattt gtagtaaata gaatacttat acctatgata aatgaagctg
ttggtatata 3780tgcagatggt gttgcaagta aagaagaaat agatgaagct
atgaaattag gagcaaacca 3840tccaatggga ccactagcat taggtgattt
aatcggatta gatgttgttt tagctataat 3900gaacgtttta tatactgaat
ttggagatac taaatataga cctcatccac ttttagctaa 3960aatggttaga
gctaatcaat taggaagaaa aactaagata ggattctatg attataataa
4020ataataagaa ggagatatac atatgagtac aagtgatgtt aaagtttatg
agaatgtagc 4080tgttgaagta gatggaaata tatgtacagt gaaaatgaat
agacctaaag cccttaatgc 4140aataaattca aagactttag aagaacttta
tgaagtattt gtagatatta ataatgatga 4200aactattgat gttgtaatat
tgacagggga aggaaaggca tttgtagctg gagcagatat 4260tgcatacatg
aaagatttag atgctgtagc tgctaaagat tttagtatct taggagcaaa
4320agcttttgga gaaatagaaa atagtaaaaa agtagtgata gctgctgtaa
acggatttgc 4380tttaggtgga ggatgtgaac ttgcaatggc atgtgatata
agaattgcat ctgctaaagc 4440taaatttggt cagccagaag taactcttgg
aataactcca ggatatggag gaactcaaag 4500gcttacaaga ttggttggaa
tggcaaaagc aaaagaatta atctttacag gtcaagttat 4560aaaagctgat
gaagctgaaa aaatagggct agtaaataga gtcgttgagc cagacatttt
4620aatagaagaa gttgagaaat tagctaagat aatagctaaa aatgctcagc
ttgcagttag 4680atactctaaa gaagcaatac aacttggtgc tcaaactgat
ataaatactg gaatagatat 4740agaatctaat ttatttggtc tttgtttttc
aactaaagac caaaaagaag gaatgtcagc 4800tttcgttgaa aagagagaag
ctaactttat aaaagggtaa taagaaggag atatacatat 4860gagtcaggcg
ctaaaaaatt tactgacatt gttaaatctg gaaaaaattg aggaaggact
4920ctttcgcggc cagagtgaag atttaggttt acgccaggtg tttggcggcc
aggtcgtggg 4980tcaggccttg tatgctgcaa aagagaccgt ccctgaagag
cggctggtac attcgtttca 5040cagctacttt cttcgccctg gcgatagtaa
gaagccgatt atttatgatg tcgaaacgct 5100gcgtgacggt aacagcttca
gcgcccgccg ggttgctgct attcaaaacg gcaaaccgat 5160tttttatatg
actgcctctt tccaggcacc agaagcgggt ttcgaacatc aaaaaacaat
5220gccgtccgcg ccagcgcctg atggcctccc ttcggaaacg caaatcgccc
aatcgctggc 5280gcacctgctg ccgccagtgc tgaaagataa attcatctgc
gatcgtccgc tggaagtccg 5340tccggtggag tttcataacc cactgaaagg
tcacgtcgca gaaccacatc gtcaggtgtg 5400gatccgcgca aatggtagcg
tgccggatga cctgcgcgtt catcagtatc tgctcggtta 5460cgcttctgat
cttaacttcc tgccggtagc tctacagccg cacggcatcg gttttctcga
5520accggggatt cagattgcca ccattgacca ttccatgtgg ttccatcgcc
cgtttaattt 5580gaatgaatgg ctgctgtata gcgtggagag cacctcggcg
tccagcgcac gtggctttgt 5640gcgcggtgag ttttataccc aagacggcgt
actggttgcc tcgaccgttc aggaaggggt 5700gatgcgtaat cacaattaa
571989180DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 89catttcctct catcccatcc ggggtgagag
tcttttcccc cgacttatgg ctcatgcatg 60catcaaaaaa gatgtgagct tgatcaaaaa
caaaaaatat ttcactcgac aggagtattt 120atattgcgcc cggatccctc
tagaaataat tttgtttaac tttaagaagg agatatacat 180901194DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
90atgatcgtaa aacctatggt acgcaacaat atctgcctga acgcccatcc tcagggctgc
60aagaagggag tggaagatca gattgaatat accaagaaac gcattaccgc agaagtcaaa
120gctggcgcaa aagctccaaa aaacgttctg gtgcttggct gctcaaatgg
ttacggcctg 180gcgagccgca ttactgctgc gttcggatac ggggctgcga
ccatcggcgt gtcctttgaa 240aaagcgggtt cagaaaccaa atatggtaca
ccgggatggt acaataattt ggcatttgat 300gaagcggcaa aacgcgaggg
tctttatagc gtgacgatcg acggcgatgc gttttcagac 360gagatcaagg
cccaggtaat tgaggaagcc aaaaaaaaag gtatcaaatt tgatctgatc
420gtatacagct tggccagccc agtacgtact gatcctgata caggtatcat
gcacaaaagc 480gttttgaaac cctttggaaa aacgttcaca ggcaaaacag
tagatccgtt tactggcgag 540ctgaaggaaa tctccgcgga accagcaaat
gacgaggaag cagccgccac tgttaaagtt 600atggggggtg aagattggga
acgttggatt aagcagctgt cgaaggaagg cctcttagaa 660gaaggctgta
ttaccttggc ctatagttat attggccctg aagctaccca agctttgtac
720cgtaaaggca caatcggcaa ggccaaagaa cacctggagg ccacagcaca
ccgtctcaac 780aaagagaacc cgtcaatccg tgccttcgtg agcgtgaata
aaggcctggt aacccgcgca 840agcgccgtaa tcccggtaat ccctctgtat
ctcgccagct tgttcaaagt aatgaaagag 900aagggcaatc atgaaggttg
tattgaacag atcacgcgtc tgtacgccga gcgcctgtac 960cgtaaagatg
gtacaattcc agttgatgag gaaaatcgca ttcgcattga tgattgggag
1020ttagaagaag acgtccagaa agcggtatcc gcgttgatgg agaaagtcac
gggtgaaaac 1080gcagaatctc tcactgactt agcggggtac cgccatgatt
tcttagctag taacggcttt 1140gatgtagaag gtattaatta tgaagcggaa
gttgaacgct tcgaccgtat ctga 119491397PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
91Met Ile Val Lys Pro Met Val Arg Asn Asn Ile Cys Leu Asn Ala His 1
5 10 15 Pro Gln Gly Cys Lys Lys Gly Val Glu Asp Gln Ile Glu Tyr Thr
Lys 20 25 30 Lys Arg Ile Thr Ala Glu Val Lys Ala Gly Ala Lys Ala
Pro Lys Asn 35 40 45 Val Leu Val Leu Gly Cys Ser Asn Gly Tyr Gly
Leu Ala Ser Arg Ile 50 55 60 Thr Ala Ala Phe Gly Tyr Gly Ala Ala
Thr Ile Gly Val Ser Phe Glu 65 70 75 80 Lys Ala Gly Ser Glu Thr Lys
Tyr Gly Thr Pro Gly Trp Tyr Asn Asn 85 90 95 Leu Ala Phe Asp Glu
Ala Ala Lys Arg Glu Gly Leu Tyr Ser Val Thr 100 105 110 Ile Asp Gly
Asp Ala Phe Ser Asp Glu Ile Lys Ala Gln Val Ile Glu 115 120 125 Glu
Ala Lys Lys Lys Gly Ile Lys Phe Asp Leu Ile Val Tyr Ser Leu 130 135
140 Ala Ser Pro Val Arg Thr Asp Pro Asp Thr Gly Ile Met His Lys Ser
145 150 155 160 Val Leu Lys Pro Phe Gly Lys Thr Phe Thr Gly Lys Thr
Val Asp Pro 165 170 175 Phe Thr Gly Glu Leu Lys Glu Ile Ser Ala Glu
Pro Ala Asn Asp Glu 180 185 190 Glu Ala Ala Ala Thr Val Lys Val Met
Gly Gly Glu Asp Trp Glu Arg 195 200 205 Trp Ile Lys Gln Leu Ser Lys
Glu Gly Leu Leu Glu Glu Gly Cys Ile 210 215 220 Thr Leu Ala Tyr Ser
Tyr Ile Gly Pro Glu Ala Thr Gln Ala Leu Tyr 225 230 235 240 Arg Lys
Gly Thr Ile Gly Lys Ala Lys Glu His Leu Glu Ala Thr Ala 245 250 255
His Arg Leu Asn Lys Glu Asn Pro Ser Ile Arg Ala Phe Val Ser Val 260
265 270 Asn Lys Gly Leu Val Thr Arg Ala Ser Ala Val Ile Pro Val Ile
Pro 275 280 285 Leu Tyr Leu Ala Ser Leu Phe Lys Val Met Lys Glu Lys
Gly Asn His 290 295 300 Glu Gly Cys Ile Glu Gln Ile Thr Arg Leu Tyr
Ala Glu Arg Leu Tyr 305 310 315 320 Arg Lys Asp Gly Thr Ile Pro Val
Asp Glu Glu Asn Arg Ile Arg Ile 325 330 335 Asp Asp Trp Glu Leu Glu
Glu Asp Val Gln Lys Ala Val Ser Ala Leu 340 345 350 Met Glu Lys Val
Thr Gly Glu Asn Ala Glu Ser Leu Thr Asp Leu Ala 355 360 365 Gly Tyr
Arg His Asp Phe Leu Ala Ser Asn Gly Phe Asp Val Glu Gly 370 375 380
Ile Asn Tyr Glu Ala Glu Val Glu Arg Phe Asp Arg Ile 385 390 395
921176DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 92atgagagaag tagtaattgc cagtgcagct
agaacagcag taggaagttt tggaggagca 60tttaaatcag tttcagcggt agagttaggg
gtaacagcag ctaaagaagc tataaaaaga 120gctaacataa ctccagatat
gatagatgaa tctcttttag ggggagtact tacagcaggt 180cttggacaaa
atatagcaag acaaatagca ttaggagcag gaataccagt agaaaaacca
240gctatgacta taaatatagt ttgtggttct ggattaagat ctgtttcaat
ggcatctcaa 300cttatagcat taggtgatgc tgatataatg ttagttggtg
gagctgaaaa catgagtatg 360tctccttatt tagtaccaag tgcgagatat
ggtgcaagaa tgggtgatgc tgcttttgtt 420gattcaatga taaaagatgg
attatcagac atatttaata actatcacat gggtattact 480gctgaaaaca
tagcagagca atggaatata actagagaag aacaagatga attagctctt
540gcaagtcaaa ataaagctga aaaagctcaa
gctgaaggaa aatttgatga agaaatagtt 600cctgttgtta taaaaggaag
aaaaggtgac actgtagtag ataaagatga atatattaag 660cctggcacta
caatggagaa acttgctaag ttaagacctg catttaaaaa agatggaaca
720gttactgctg gtaatgcatc aggaataaat gatggtgctg ctatgttagt
agtaatggct 780aaagaaaaag ctgaagaact aggaatagag cctcttgcaa
ctatagtttc ttatggaaca 840gctggtgttg accctaaaat aatgggatat
ggaccagttc cagcaactaa aaaagcttta 900gaagctgcta atatgactat
tgaagatata gatttagttg aagctaatga ggcatttgct 960gcccaatctg
tagctgtaat aagagactta aatatagata tgaataaagt taatgttaat
1020ggtggagcaa tagctatagg acatccaata ggatgctcag gagcaagaat
acttactaca 1080cttttatatg aaatgaagag aagagatgct aaaactggtc
ttgctacact ttgtataggc 1140ggtggaatgg gaactacttt aatagttaag agatag
117693391PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 93Met Arg Glu Val Val Ile Ala Ser Ala Ala Arg
Thr Ala Val Gly Ser 1 5 10 15 Phe Gly Gly Ala Phe Lys Ser Val Ser
Ala Val Glu Leu Gly Val Thr 20 25 30 Ala Ala Lys Glu Ala Ile Lys
Arg Ala Asn Ile Thr Pro Asp Met Ile 35 40 45 Asp Glu Ser Leu Leu
Gly Gly Val Leu Thr Ala Gly Leu Gly Gln Asn 50 55 60 Ile Ala Arg
Gln Ile Ala Leu Gly Ala Gly Ile Pro Val Glu Lys Pro 65 70 75 80 Ala
Met Thr Ile Asn Ile Val Cys Gly Ser Gly Leu Arg Ser Val Ser 85 90
95 Met Ala Ser Gln Leu Ile Ala Leu Gly Asp Ala Asp Ile Met Leu Val
100 105 110 Gly Gly Ala Glu Asn Met Ser Met Ser Pro Tyr Leu Val Pro
Ser Ala 115 120 125 Arg Tyr Gly Ala Arg Met Gly Asp Ala Ala Phe Val
Asp Ser Met Ile 130 135 140 Lys Asp Gly Leu Ser Asp Ile Phe Asn Asn
Tyr His Met Gly Ile Thr 145 150 155 160 Ala Glu Asn Ile Ala Glu Gln
Trp Asn Ile Thr Arg Glu Glu Gln Asp 165 170 175 Glu Leu Ala Leu Ala
Ser Gln Asn Lys Ala Glu Lys Ala Gln Ala Glu 180 185 190 Gly Lys Phe
Asp Glu Glu Ile Val Pro Val Val Ile Lys Gly Arg Lys 195 200 205 Gly
Asp Thr Val Val Asp Lys Asp Glu Tyr Ile Lys Pro Gly Thr Thr 210 215
220 Met Glu Lys Leu Ala Lys Leu Arg Pro Ala Phe Lys Lys Asp Gly Thr
225 230 235 240 Val Thr Ala Gly Asn Ala Ser Gly Ile Asn Asp Gly Ala
Ala Met Leu 245 250 255 Val Val Met Ala Lys Glu Lys Ala Glu Glu Leu
Gly Ile Glu Pro Leu 260 265 270 Ala Thr Ile Val Ser Tyr Gly Thr Ala
Gly Val Asp Pro Lys Ile Met 275 280 285 Gly Tyr Gly Pro Val Pro Ala
Thr Lys Lys Ala Leu Glu Ala Ala Asn 290 295 300 Met Thr Ile Glu Asp
Ile Asp Leu Val Glu Ala Asn Glu Ala Phe Ala 305 310 315 320 Ala Gln
Ser Val Ala Val Ile Arg Asp Leu Asn Ile Asp Met Asn Lys 325 330 335
Val Asn Val Asn Gly Gly Ala Ile Ala Ile Gly His Pro Ile Gly Cys 340
345 350 Ser Gly Ala Arg Ile Leu Thr Thr Leu Leu Tyr Glu Met Lys Arg
Arg 355 360 365 Asp Ala Lys Thr Gly Leu Ala Thr Leu Cys Ile Gly Gly
Gly Met Gly 370 375 380 Thr Thr Leu Ile Val Lys Arg 385 390
94846DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 94atgaaattag ctgtaatagg tagtggaact
atgggaagtg gtattgtaca aacttttgca 60agttgtggac atgatgtatg tttaaagagt
agaactcaag gtgctataga taaatgttta 120gctttattag ataaaaattt
aactaagtta gttactaagg gaaaaatgga tgaagctaca 180aaagcagaaa
tattaagtca tgttagttca actactaatt atgaagattt aaaagatatg
240gatttaataa tagaagcatc tgtagaagac atgaatataa agaaagatgt
tttcaagtta 300ctagatgaat tatgtaaaga agatactatc ttggcaacaa
atacttcatc attatctata 360acagaaatag cttcttctac taagcgccca
gataaagtta taggaatgca tttctttaat 420ccagttccta tgatgaaatt
agttgaagtt ataagtggtc agttaacatc aaaagttact 480tttgatacag
tatttgaatt atctaagagt atcaataaag taccagtaga tgtatctgaa
540tctcctggat ttgtagtaaa tagaatactt atacctatga taaatgaagc
tgttggtata 600tatgcagatg gtgttgcaag taaagaagaa atagatgaag
ctatgaaatt aggagcaaac 660catccaatgg gaccactagc attaggtgat
ttaatcggat tagatgttgt tttagctata 720atgaacgttt tatatactga
atttggagat actaaatata gacctcatcc acttttagct 780aaaatggtta
gagctaatca attaggaaga aaaactaaga taggattcta tgattataat 840aaataa
84695281PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 95Met Lys Leu Ala Val Ile Gly Ser Gly Thr Met
Gly Ser Gly Ile Val 1 5 10 15 Gln Thr Phe Ala Ser Cys Gly His Asp
Val Cys Leu Lys Ser Arg Thr 20 25 30 Gln Gly Ala Ile Asp Lys Cys
Leu Ala Leu Leu Asp Lys Asn Leu Thr 35 40 45 Lys Leu Val Thr Lys
Gly Lys Met Asp Glu Ala Thr Lys Ala Glu Ile 50 55 60 Leu Ser His
Val Ser Ser Thr Thr Asn Tyr Glu Asp Leu Lys Asp Met 65 70 75 80 Asp
Leu Ile Ile Glu Ala Ser Val Glu Asp Met Asn Ile Lys Lys Asp 85 90
95 Val Phe Lys Leu Leu Asp Glu Leu Cys Lys Glu Asp Thr Ile Leu Ala
100 105 110 Thr Asn Thr Ser Ser Leu Ser Ile Thr Glu Ile Ala Ser Ser
Thr Lys 115 120 125 Arg Pro Asp Lys Val Ile Gly Met His Phe Phe Asn
Pro Val Pro Met 130 135 140 Met Lys Leu Val Glu Val Ile Ser Gly Gln
Leu Thr Ser Lys Val Thr 145 150 155 160 Phe Asp Thr Val Phe Glu Leu
Ser Lys Ser Ile Asn Lys Val Pro Val 165 170 175 Asp Val Ser Glu Ser
Pro Gly Phe Val Val Asn Arg Ile Leu Ile Pro 180 185 190 Met Ile Asn
Glu Ala Val Gly Ile Tyr Ala Asp Gly Val Ala Ser Lys 195 200 205 Glu
Glu Ile Asp Glu Ala Met Lys Leu Gly Ala Asn His Pro Met Gly 210 215
220 Pro Leu Ala Leu Gly Asp Leu Ile Gly Leu Asp Val Val Leu Ala Ile
225 230 235 240 Met Asn Val Leu Tyr Thr Glu Phe Gly Asp Thr Lys Tyr
Arg Pro His 245 250 255 Pro Leu Leu Ala Lys Met Val Arg Ala Asn Gln
Leu Gly Arg Lys Thr 260 265 270 Lys Ile Gly Phe Tyr Asp Tyr Asn Lys
275 280 96798DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 96atgagtacaa gtgatgttaa
agtttatgag aatgtagctg ttgaagtaga tggaaatata 60tgtacagtga aaatgaatag
acctaaagcc cttaatgcaa taaattcaaa gactttagaa 120gaactttatg
aagtatttgt agatattaat aatgatgaaa ctattgatgt tgtaatattg
180acaggggaag gaaaggcatt tgtagctgga gcagatattg catacatgaa
agatttagat 240gctgtagctg ctaaagattt tagtatctta ggagcaaaag
cttttggaga aatagaaaat 300agtaaaaaag tagtgatagc tgctgtaaac
ggatttgctt taggtggagg atgtgaactt 360gcaatggcat gtgatataag
aattgcatct gctaaagcta aatttggtca gccagaagta 420actcttggaa
taactccagg atatggagga actcaaaggc ttacaagatt ggttggaatg
480gcaaaagcaa aagaattaat ctttacaggt caagttataa aagctgatga
agctgaaaaa 540atagggctag taaatagagt cgttgagcca gacattttaa
tagaagaagt tgagaaatta 600gctaagataa tagctaaaaa tgctcagctt
gcagttagat actctaaaga agcaatacaa 660cttggtgctc aaactgatat
aaatactgga atagatatag aatctaattt atttggtctt 720tgtttttcaa
ctaaagacca aaaagaagga atgtcagctt tcgttgaaaa gagagaagct
780aactttataa aagggtaa 79897265PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 97Met Ser Thr Ser Asp Val
Lys Val Tyr Glu Asn Val Ala Val Glu Val 1 5 10 15 Asp Gly Asn Ile
Cys Thr Val Lys Met Asn Arg Pro Lys Ala Leu Asn 20 25 30 Ala Ile
Asn Ser Lys Thr Leu Glu Glu Leu Tyr Glu Val Phe Val Asp 35 40 45
Ile Asn Asn Asp Glu Thr Ile Asp Val Val Ile Leu Thr Gly Glu Gly 50
55 60 Lys Ala Phe Val Ala Gly Ala Asp Ile Ala Tyr Met Lys Asp Leu
Asp 65 70 75 80 Ala Val Ala Ala Lys Asp Phe Ser Ile Leu Gly Ala Lys
Ala Phe Gly 85 90 95 Glu Ile Glu Asn Ser Lys Lys Val Val Ile Ala
Ala Val Asn Gly Phe 100 105 110 Ala Leu Gly Gly Gly Cys Glu Leu Ala
Met Ala Cys Asp Ile Arg Ile 115 120 125 Ala Ser Ala Lys Ala Lys Phe
Gly Gln Pro Glu Val Thr Leu Gly Ile 130 135 140 Thr Pro Gly Tyr Gly
Gly Thr Gln Arg Leu Thr Arg Leu Val Gly Met 145 150 155 160 Ala Lys
Ala Lys Glu Leu Ile Phe Thr Gly Gln Val Ile Lys Ala Asp 165 170 175
Glu Ala Glu Lys Ile Gly Leu Val Asn Arg Val Val Glu Pro Asp Ile 180
185 190 Leu Ile Glu Glu Val Glu Lys Leu Ala Lys Ile Ile Ala Lys Asn
Ala 195 200 205 Gln Leu Ala Val Arg Tyr Ser Lys Glu Ala Ile Gln Leu
Gly Ala Gln 210 215 220 Thr Asp Ile Asn Thr Gly Ile Asp Ile Glu Ser
Asn Leu Phe Gly Leu 225 230 235 240 Cys Phe Ser Thr Lys Asp Gln Lys
Glu Gly Met Ser Ala Phe Val Glu 245 250 255 Lys Arg Glu Ala Asn Phe
Ile Lys Gly 260 265 98903DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 98atgagaagtt
ttgaagaagt aattaagttt gcaaaagaaa gaggacctaa aactatatca 60gtagcatgtt
gccaagataa agaagtttta atggcagttg aaatggctag aaaagaaaaa
120atagcaaatg ccattttagt aggagatata gaaaagacta aagaaattgc
aaaaagcata 180gacatggata tcgaaaatta tgaactgata gatataaaag
atttagcaga agcatctcta 240aaatctgttg aattagtttc acaaggaaaa
gccgacatgg taatgaaagg cttagtagac 300acatcaataa tactaaaagc
agttttaaat aaagaagtag gtcttagaac tggaaatgta 360ttaagtcacg
tagcagtatt tgatgtagag ggatatgata gattattttt cgtaactgac
420gcagctatga acttagctcc tgatacaaat actaaaaagc aaatcataga
aaatgcttgc 480acagtagcac attcattaga tataagtgaa ccaaaagttg
ctgcaatatg cgcaaaagaa 540aaagtaaatc caaaaatgaa agatacagtt
gaagctaaag aactagaaga aatgtatgaa 600agaggagaaa tcaaaggttg
tatggttggt gggccttttg caattgataa tgcagtatct 660ttagaagcag
ctaaacataa aggtataaat catcctgtag caggacgagc tgatatatta
720ttagccccag atattgaagg tggtaacata ttatataaag ctttggtatt
cttctcaaaa 780tcaaaaaatg caggagttat agttggggct aaagcaccaa
taatattaac ttctagagca 840gacagtgaag aaactaaact aaactcaata
gctttaggtg ttttaatggc agcaaaggca 900taa 90399300PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
99Met Arg Ser Phe Glu Glu Val Ile Lys Phe Ala Lys Glu Arg Gly Pro 1
5 10 15 Lys Thr Ile Ser Val Ala Cys Cys Gln Asp Lys Glu Val Leu Met
Ala 20 25 30 Val Glu Met Ala Arg Lys Glu Lys Ile Ala Asn Ala Ile
Leu Val Gly 35 40 45 Asp Ile Glu Lys Thr Lys Glu Ile Ala Lys Ser
Ile Asp Met Asp Ile 50 55 60 Glu Asn Tyr Glu Leu Ile Asp Ile Lys
Asp Leu Ala Glu Ala Ser Leu 65 70 75 80 Lys Ser Val Glu Leu Val Ser
Gln Gly Lys Ala Asp Met Val Met Lys 85 90 95 Gly Leu Val Asp Thr
Ser Ile Ile Leu Lys Ala Val Leu Asn Lys Glu 100 105 110 Val Gly Leu
Arg Thr Gly Asn Val Leu Ser His Val Ala Val Phe Asp 115 120 125 Val
Glu Gly Tyr Asp Arg Leu Phe Phe Val Thr Asp Ala Ala Met Asn 130 135
140 Leu Ala Pro Asp Thr Asn Thr Lys Lys Gln Ile Ile Glu Asn Ala Cys
145 150 155 160 Thr Val Ala His Ser Leu Asp Ile Ser Glu Pro Lys Val
Ala Ala Ile 165 170 175 Cys Ala Lys Glu Lys Val Asn Pro Lys Met Lys
Asp Thr Val Glu Ala 180 185 190 Lys Glu Leu Glu Glu Met Tyr Glu Arg
Gly Glu Ile Lys Gly Cys Met 195 200 205 Val Gly Gly Pro Phe Ala Ile
Asp Asn Ala Val Ser Leu Glu Ala Ala 210 215 220 Lys His Lys Gly Ile
Asn His Pro Val Ala Gly Arg Ala Asp Ile Leu 225 230 235 240 Leu Ala
Pro Asp Ile Glu Gly Gly Asn Ile Leu Tyr Lys Ala Leu Val 245 250 255
Phe Phe Ser Lys Ser Lys Asn Ala Gly Val Ile Val Gly Ala Lys Ala 260
265 270 Pro Ile Ile Leu Thr Ser Arg Ala Asp Ser Glu Glu Thr Lys Leu
Asn 275 280 285 Ser Ile Ala Leu Gly Val Leu Met Ala Ala Lys Ala 290
295 300 1001080DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 100atgagcaaaa tatttaaaat
cttaacaata aatcctggtt cgacatcaac taaaatagct 60gtatttgata atgaggattt
agtatttgaa aaaactttaa gacattcttc agaagaaata 120ggaaaatatg
agaaggtgtc tgaccaattt gaatttcgta aacaagtaat agaagaagct
180ctaaaagaag gtggagtaaa aacatctgaa ttagatgctg tagtaggtag
aggaggactt 240cttaaaccta taaaaggtgg tacttattca gtaagtgctg
ctatgattga agatttaaaa 300gtgggagttt taggagaaca cgcttcaaac
ctaggtggaa taatagcaaa acaaataggt 360gaagaagtaa atgttccttc
atacatagta gaccctgttg ttgtagatga attagaagat 420gttgctagaa
tttctggtat gcctgaaata agtagagcaa gtgtagtaca tgctttaaat
480caaaaggcaa tagcaagaag atatgctaga gaaataaaca agaaatatga
agatataaat 540cttatagttg cacacatggg tggaggagtt tctgttggag
ctcataaaaa tggtaaaata 600gtagatgttg caaacgcatt agatggagaa
ggacctttct ctccagaaag aagtggtgga 660ctaccagtag gtgcattagt
aaaaatgtgc tttagtggaa aatatactca agatgaaatt 720aaaaagaaaa
taaaaggtaa tggcggacta gttgcatact taaacactaa tgatgctaga
780gaagttgaag aaagaattga agctggtgat gaaaaagcta aattagtata
tgaagctatg 840gcatatcaaa tctctaaaga aataggagct agtgctgcag
ttcttaaggg agatgtaaaa 900gcaatattat taactggtgg aatcgcatat
tcaaaaatgt ttacagaaat gattgcagat 960agagttaaat ttatagcaga
tgtaaaagtt tatccaggtg aagatgaaat gattgcatta 1020gctcaaggtg
gacttagagt tttaactggt gaagaagagg ctcaagttta tgataactaa
1080101359PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 101Met Ser Lys Ile Phe Lys Ile Leu Thr Ile
Asn Pro Gly Ser Thr Ser 1 5 10 15 Thr Lys Ile Ala Val Phe Asp Asn
Glu Asp Leu Val Phe Glu Lys Thr 20 25 30 Leu Arg His Ser Ser Glu
Glu Ile Gly Lys Tyr Glu Lys Val Ser Asp 35 40 45 Gln Phe Glu Phe
Arg Lys Gln Val Ile Glu Glu Ala Leu Lys Glu Gly 50 55 60 Gly Val
Lys Thr Ser Glu Leu Asp Ala Val Val Gly Arg Gly Gly Leu 65 70 75 80
Leu Lys Pro Ile Lys Gly Gly Thr Tyr Ser Val Ser Ala Ala Met Ile 85
90 95 Glu Asp Leu Lys Val Gly Val Leu Gly Glu His Ala Ser Asn Leu
Gly 100 105 110 Gly Ile Ile Ala Lys Gln Ile Gly Glu Glu Val Asn Val
Pro Ser Tyr 115 120 125 Ile Val Asp Pro Val Val Val Asp Glu Leu Glu
Asp Val Ala Arg Ile 130 135 140 Ser Gly Met Pro Glu Ile Ser Arg Ala
Ser Val Val His Ala Leu Asn 145 150 155 160 Gln Lys Ala Ile Ala Arg
Arg Tyr Ala Arg Glu Ile Asn Lys Lys Tyr 165 170 175 Glu Asp Ile Asn
Leu Ile Val Ala His Met Gly Gly Gly Val Ser Val 180 185 190 Gly Ala
His Lys Asn Gly Lys Ile Val Asp Val Ala Asn Ala Leu Asp 195 200 205
Gly Glu Gly Pro Phe Ser Pro Glu Arg Ser Gly Gly Leu Pro Val Gly 210
215 220 Ala Leu Val Lys Met Cys Phe Ser Gly Lys Tyr Thr Gln Asp Glu
Ile 225 230 235 240 Lys Lys Lys Ile Lys Gly Asn Gly Gly Leu Val Ala
Tyr Leu Asn Thr 245 250 255 Asn Asp Ala Arg Glu Val Glu Glu Arg Ile
Glu Ala Gly Asp Glu Lys 260 265 270 Ala Lys Leu Val Tyr Glu Ala Met
Ala Tyr Gln Ile Ser Lys
Glu Ile 275 280 285 Gly Ala Ser Ala Ala Val Leu Lys Gly Asp Val Lys
Ala Ile Leu Leu 290 295 300 Thr Gly Gly Ile Ala Tyr Ser Lys Met Phe
Thr Glu Met Ile Ala Asp 305 310 315 320 Arg Val Lys Phe Ile Ala Asp
Val Lys Val Tyr Pro Gly Glu Asp Glu 325 330 335 Met Ile Ala Leu Ala
Gln Gly Gly Leu Arg Val Leu Thr Gly Glu Glu 340 345 350 Glu Ala Gln
Val Tyr Asp Asn 355 10223DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 102tttgtttaac
tttaagaagg aga 2310318DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 103taagaaggag
atatacat 181046270DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 104catttcctct catcccatcc
ggggtgagag tcttttcccc cgacttatgg ctcatgcatg 60catcaaaaaa gatgtgagct
tgatcaaaaa caaaaaatat ttcactcgac aggagtattt 120atattgcgcc
cggatccctc tagaaataat tttgtttaac tttaagaagg agatatacat
180atgatcgtaa aacctatggt acgcaacaat atctgcctga acgcccatcc
tcagggctgc 240aagaagggag tggaagatca gattgaatat accaagaaac
gcattaccgc agaagtcaaa 300gctggcgcaa aagctccaaa aaacgttctg
gtgcttggct gctcaaatgg ttacggcctg 360gcgagccgca ttactgctgc
gttcggatac ggggctgcga ccatcggcgt gtcctttgaa 420aaagcgggtt
cagaaaccaa atatggtaca ccgggatggt acaataattt ggcatttgat
480gaagcggcaa aacgcgaggg tctttatagc gtgacgatcg acggcgatgc
gttttcagac 540gagatcaagg cccaggtaat tgaggaagcc aaaaaaaaag
gtatcaaatt tgatctgatc 600gtatacagct tggccagccc agtacgtact
gatcctgata caggtatcat gcacaaaagc 660gttttgaaac cctttggaaa
aacgttcaca ggcaaaacag tagatccgtt tactggcgag 720ctgaaggaaa
tctccgcgga accagcaaat gacgaggaag cagccgccac tgttaaagtt
780atggggggtg aagattggga acgttggatt aagcagctgt cgaaggaagg
cctcttagaa 840gaaggctgta ttaccttggc ctatagttat attggccctg
aagctaccca agctttgtac 900cgtaaaggca caatcggcaa ggccaaagaa
cacctggagg ccacagcaca ccgtctcaac 960aaagagaacc cgtcaatccg
tgccttcgtg agcgtgaata aaggcctggt aacccgcgca 1020agcgccgtaa
tcccggtaat ccctctgtat ctcgccagct tgttcaaagt aatgaaagag
1080aagggcaatc atgaaggttg tattgaacag atcacgcgtc tgtacgccga
gcgcctgtac 1140cgtaaagatg gtacaattcc agttgatgag gaaaatcgca
ttcgcattga tgattgggag 1200ttagaagaag acgtccagaa agcggtatcc
gcgttgatgg agaaagtcac gggtgaaaac 1260gcagaatctc tcactgactt
agcggggtac cgccatgatt tcttagctag taacggcttt 1320gatgtagaag
gtattaatta tgaagcggaa gttgaacgct tcgaccgtat ctgataagaa
1380ggagatatac atatgagaga agtagtaatt gccagtgcag ctagaacagc
agtaggaagt 1440tttggaggag catttaaatc agtttcagcg gtagagttag
gggtaacagc agctaaagaa 1500gctataaaaa gagctaacat aactccagat
atgatagatg aatctctttt agggggagta 1560cttacagcag gtcttggaca
aaatatagca agacaaatag cattaggagc aggaatacca 1620gtagaaaaac
cagctatgac tataaatata gtttgtggtt ctggattaag atctgtttca
1680atggcatctc aacttatagc attaggtgat gctgatataa tgttagttgg
tggagctgaa 1740aacatgagta tgtctcctta tttagtacca agtgcgagat
atggtgcaag aatgggtgat 1800gctgcttttg ttgattcaat gataaaagat
ggattatcag acatatttaa taactatcac 1860atgggtatta ctgctgaaaa
catagcagag caatggaata taactagaga agaacaagat 1920gaattagctc
ttgcaagtca aaataaagct gaaaaagctc aagctgaagg aaaatttgat
1980gaagaaatag ttcctgttgt tataaaagga agaaaaggtg acactgtagt
agataaagat 2040gaatatatta agcctggcac tacaatggag aaacttgcta
agttaagacc tgcatttaaa 2100aaagatggaa cagttactgc tggtaatgca
tcaggaataa atgatggtgc tgctatgtta 2160gtagtaatgg ctaaagaaaa
agctgaagaa ctaggaatag agcctcttgc aactatagtt 2220tcttatggaa
cagctggtgt tgaccctaaa ataatgggat atggaccagt tccagcaact
2280aaaaaagctt tagaagctgc taatatgact attgaagata tagatttagt
tgaagctaat 2340gaggcatttg ctgcccaatc tgtagctgta ataagagact
taaatataga tatgaataaa 2400gttaatgtta atggtggagc aatagctata
ggacatccaa taggatgctc aggagcaaga 2460atacttacta cacttttata
tgaaatgaag agaagagatg ctaaaactgg tcttgctaca 2520ctttgtatag
gcggtggaat gggaactact ttaatagtta agagatagta agaaggagat
2580atacatatga aattagctgt aataggtagt ggaactatgg gaagtggtat
tgtacaaact 2640tttgcaagtt gtggacatga tgtatgttta aagagtagaa
ctcaaggtgc tatagataaa 2700tgtttagctt tattagataa aaatttaact
aagttagtta ctaagggaaa aatggatgaa 2760gctacaaaag cagaaatatt
aagtcatgtt agttcaacta ctaattatga agatttaaaa 2820gatatggatt
taataataga agcatctgta gaagacatga atataaagaa agatgttttc
2880aagttactag atgaattatg taaagaagat actatcttgg caacaaatac
ttcatcatta 2940tctataacag aaatagcttc ttctactaag cgcccagata
aagttatagg aatgcatttc 3000tttaatccag ttcctatgat gaaattagtt
gaagttataa gtggtcagtt aacatcaaaa 3060gttacttttg atacagtatt
tgaattatct aagagtatca ataaagtacc agtagatgta 3120tctgaatctc
ctggatttgt agtaaataga atacttatac ctatgataaa tgaagctgtt
3180ggtatatatg cagatggtgt tgcaagtaaa gaagaaatag atgaagctat
gaaattagga 3240gcaaaccatc caatgggacc actagcatta ggtgatttaa
tcggattaga tgttgtttta 3300gctataatga acgttttata tactgaattt
ggagatacta aatatagacc tcatccactt 3360ttagctaaaa tggttagagc
taatcaatta ggaagaaaaa ctaagatagg attctatgat 3420tataataaat
aataagaagg agatatacat atgagtacaa gtgatgttaa agtttatgag
3480aatgtagctg ttgaagtaga tggaaatata tgtacagtga aaatgaatag
acctaaagcc 3540cttaatgcaa taaattcaaa gactttagaa gaactttatg
aagtatttgt agatattaat 3600aatgatgaaa ctattgatgt tgtaatattg
acaggggaag gaaaggcatt tgtagctgga 3660gcagatattg catacatgaa
agatttagat gctgtagctg ctaaagattt tagtatctta 3720ggagcaaaag
cttttggaga aatagaaaat agtaaaaaag tagtgatagc tgctgtaaac
3780ggatttgctt taggtggagg atgtgaactt gcaatggcat gtgatataag
aattgcatct 3840gctaaagcta aatttggtca gccagaagta actcttggaa
taactccagg atatggagga 3900actcaaaggc ttacaagatt ggttggaatg
gcaaaagcaa aagaattaat ctttacaggt 3960caagttataa aagctgatga
agctgaaaaa atagggctag taaatagagt cgttgagcca 4020gacattttaa
tagaagaagt tgagaaatta gctaagataa tagctaaaaa tgctcagctt
4080gcagttagat actctaaaga agcaatacaa cttggtgctc aaactgatat
aaatactgga 4140atagatatag aatctaattt atttggtctt tgtttttcaa
ctaaagacca aaaagaagga 4200atgtcagctt tcgttgaaaa gagagaagct
aactttataa aagggtaata agaaggagat 4260atacatatga gaagttttga
agaagtaatt aagtttgcaa aagaaagagg acctaaaact 4320atatcagtag
catgttgcca agataaagaa gttttaatgg cagttgaaat ggctagaaaa
4380gaaaaaatag caaatgccat tttagtagga gatatagaaa agactaaaga
aattgcaaaa 4440agcatagaca tggatatcga aaattatgaa ctgatagata
taaaagattt agcagaagca 4500tctctaaaat ctgttgaatt agtttcacaa
ggaaaagccg acatggtaat gaaaggctta 4560gtagacacat caataatact
aaaagcagtt ttaaataaag aagtaggtct tagaactgga 4620aatgtattaa
gtcacgtagc agtatttgat gtagagggat atgatagatt atttttcgta
4680actgacgcag ctatgaactt agctcctgat acaaatacta aaaagcaaat
catagaaaat 4740gcttgcacag tagcacattc attagatata agtgaaccaa
aagttgctgc aatatgcgca 4800aaagaaaaag taaatccaaa aatgaaagat
acagttgaag ctaaagaact agaagaaatg 4860tatgaaagag gagaaatcaa
aggttgtatg gttggtgggc cttttgcaat tgataatgca 4920gtatctttag
aagcagctaa acataaaggt ataaatcatc ctgtagcagg acgagctgat
4980atattattag ccccagatat tgaaggtggt aacatattat ataaagcttt
ggtattcttc 5040tcaaaatcaa aaaatgcagg agttatagtt ggggctaaag
caccaataat attaacttct 5100agagcagaca gtgaagaaac taaactaaac
tcaatagctt taggtgtttt aatggcagca 5160aaggcataat aagaaggaga
tatacatatg agcaaaatat ttaaaatctt aacaataaat 5220cctggttcga
catcaactaa aatagctgta tttgataatg aggatttagt atttgaaaaa
5280actttaagac attcttcaga agaaatagga aaatatgaga aggtgtctga
ccaatttgaa 5340tttcgtaaac aagtaataga agaagctcta aaagaaggtg
gagtaaaaac atctgaatta 5400gatgctgtag taggtagagg aggacttctt
aaacctataa aaggtggtac ttattcagta 5460agtgctgcta tgattgaaga
tttaaaagtg ggagttttag gagaacacgc ttcaaaccta 5520ggtggaataa
tagcaaaaca aataggtgaa gaagtaaatg ttccttcata catagtagac
5580cctgttgttg tagatgaatt agaagatgtt gctagaattt ctggtatgcc
tgaaataagt 5640agagcaagtg tagtacatgc tttaaatcaa aaggcaatag
caagaagata tgctagagaa 5700ataaacaaga aatatgaaga tataaatctt
atagttgcac acatgggtgg aggagtttct 5760gttggagctc ataaaaatgg
taaaatagta gatgttgcaa acgcattaga tggagaagga 5820cctttctctc
cagaaagaag tggtggacta ccagtaggtg cattagtaaa aatgtgcttt
5880agtggaaaat atactcaaga tgaaattaaa aagaaaataa aaggtaatgg
cggactagtt 5940gcatacttaa acactaatga tgctagagaa gttgaagaaa
gaattgaagc tggtgatgaa 6000aaagctaaat tagtatatga agctatggca
tatcaaatct ctaaagaaat aggagctagt 6060gctgcagttc ttaagggaga
tgtaaaagca atattattaa ctggtggaat cgcatattca 6120aaaatgttta
cagaaatgat tgcagataga gttaaattta tagcagatgt aaaagtttat
6180ccaggtgaag atgaaatgat tgcattagct caaggtggac ttagagtttt
aactggtgaa 6240gaagaggctc aagtttatga taactaataa
6270105466PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 105Met Gly Gln Ser Ser Gln Pro His Glu Leu
Gly Gly Gly Leu Lys Ser 1 5 10 15 Arg His Val Thr Met Leu Ser Ile
Ala Gly Val Ile Gly Ala Ser Leu 20 25 30 Phe Val Gly Ser Ser Val
Ala Ile Ala Glu Ala Gly Pro Ala Val Leu 35 40 45 Leu Ala Tyr Leu
Phe Ala Gly Leu Leu Val Val Met Ile Met Arg Met 50 55 60 Leu Ala
Glu Met Ala Val Ala Thr Pro Asp Thr Gly Ser Phe Ser Thr 65 70 75 80
Tyr Ala Asp Lys Ala Ile Gly Arg Trp Ala Gly Tyr Thr Ile Gly Trp 85
90 95 Leu Tyr Trp Trp Phe Trp Val Leu Val Ile Pro Leu Glu Ala Asn
Ile 100 105 110 Ala Ala Met Ile Leu His Ser Trp Val Pro Gly Ile Pro
Ile Trp Leu 115 120 125 Phe Ser Leu Val Ile Thr Leu Ala Leu Thr Gly
Ser Asn Leu Leu Ser 130 135 140 Val Lys Asn Tyr Gly Glu Phe Glu Phe
Trp Leu Ala Leu Cys Lys Val 145 150 155 160 Ile Ala Ile Leu Ala Phe
Ile Phe Leu Gly Ala Val Ala Ile Ser Gly 165 170 175 Phe Tyr Pro Tyr
Ala Glu Val Ser Gly Ile Ser Arg Leu Trp Asp Ser 180 185 190 Gly Gly
Phe Met Pro Asn Gly Phe Gly Ala Val Leu Ser Ala Met Leu 195 200 205
Ile Thr Met Phe Ser Phe Met Gly Ala Glu Ile Val Thr Ile Ala Ala 210
215 220 Ala Glu Ser Asp Thr Pro Glu Lys His Ile Val Arg Ala Thr Asn
Ser 225 230 235 240 Val Ile Trp Arg Ile Ser Ile Phe Tyr Leu Cys Ser
Ile Phe Val Val 245 250 255 Val Ala Leu Ile Pro Trp Asn Met Pro Gly
Leu Lys Ala Val Gly Ser 260 265 270 Tyr Arg Ser Val Leu Glu Leu Leu
Asn Ile Pro His Ala Lys Leu Ile 275 280 285 Met Asp Cys Val Ile Leu
Leu Ser Val Thr Ser Cys Leu Asn Ser Ala 290 295 300 Leu Tyr Thr Ala
Ser Arg Met Leu Tyr Ser Leu Ser Arg Arg Gly Asp 305 310 315 320 Ala
Pro Ala Val Met Gly Lys Ile Asn Arg Ser Lys Thr Pro Tyr Val 325 330
335 Ala Val Leu Leu Ser Thr Gly Ala Ala Phe Leu Thr Val Val Val Asn
340 345 350 Tyr Tyr Ala Pro Ala Lys Val Phe Lys Phe Leu Ile Asp Ser
Ser Gly 355 360 365 Ala Ile Ala Leu Leu Val Tyr Leu Val Ile Ala Val
Ser Gln Leu Arg 370 375 380 Met Arg Lys Ile Leu Arg Ala Glu Gly Ser
Glu Ile Arg Leu Arg Met 385 390 395 400 Trp Leu Tyr Pro Trp Leu Thr
Trp Leu Val Ile Gly Phe Ile Thr Phe 405 410 415 Val Leu Val Val Met
Leu Phe Arg Pro Ala Gln Gln Leu Glu Val Ile 420 425 430 Ser Thr Gly
Leu Leu Ala Ile Gly Ile Ile Cys Thr Val Pro Ile Met 435 440 445 Ala
Arg Trp Lys Lys Leu Val Leu Trp Gln Lys Thr Pro Val His Asn 450 455
460 Thr Arg 465 1061398DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 106atgggacagt
cttcacaacc acacgaactt gggggtggat tgaaatcgcg ccatgtgacc 60atgttaagta
tcgcaggcgt gattggcgcc tccttatttg tggggtcctc cgtggcgatt
120gcagaggcgg gtccggctgt acttttggca tatctttttg cgggtttact
ggttgtgatg 180atcatgcgca tgcttgccga aatggctgtg gccacgccgg
acacggggtc attttccact 240tatgcggaca aggcgattgg ccgctgggcc
gggtacacaa tcgggtggct gtattggtgg 300ttctgggtgt tagttatccc
cttggaggcc aacatcgccg caatgattct gcactcctgg 360gttccgggta
tcccgatctg gctgttcagc ttggtgatca ccctggcact gacgggcagc
420aacttattga gtgtgaaaaa ctatggagag tttgaatttt ggctggccct
gtgtaaagtc 480attgctatct tggcattcat ttttttagga gcggtagcaa
tcagtggctt ctacccttat 540gcagaagttt cggggatttc ccgtctttgg
gatagtggcg gattcatgcc aaacgggttt 600ggagctgtac tgtcagccat
gttgattacc atgtttagct ttatgggtgc cgagatcgtg 660acaatcgccg
cagccgagag tgataccccg gaaaagcaca ttgttcgtgc gacgaattcg
720gtaatttggc gtatttcgat tttttactta tgctccattt tcgttgtggt
cgcccttatc 780ccctggaaca tgccaggctt aaaagcagta ggcagctacc
gctcagtcct ggaattactg 840aacattcctc acgcgaagtt aattatggat
tgcgtaatcc tgttatcggt aacgagctgc 900cttaacagtg ctctgtacac
ggcttcacgt atgctgtact ctttaagtcg ccgtggcgat 960gcacctgccg
ttatgggcaa gattaaccgc agtaagacgc cgtatgtagc tgttttgctg
1020tcgactggag ctgcgtttct tacagtcgta gtaaactatt acgcaccagc
taaagttttc 1080aaattcctta ttgattcgtc tggggcaatc gcacttctgg
tgtacctggt catcgcggtg 1140tcacaacttc gcatgcgcaa gatcttgcgt
gcggagggca gtgagattcg tttgcgtatg 1200tggctgtatc cgtggctgac
gtggcttgtt attggtttca ttacttttgt gttggtagtg 1260atgctgtttc
gtccagcgca acagctggag gtgatttcta ccggactgtt ggcaatcggc
1320atcatctgta ccgtcccaat catggctcgc tggaaaaagt tggtcttatg
gcagaagacc 1380cctgtacaca acacccgt 1398107412PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
107Met Thr Asn Tyr Arg Val Glu Ser Ser Ser Gly Arg Ala Ala Arg Lys
1 5 10 15 Met Arg Leu Ala Leu Met Gly Pro Ala Phe Ile Ala Ala Ile
Gly Tyr 20 25 30 Ile Asp Pro Gly Asn Phe Ala Thr Asn Ile Gln Ala
Gly Ala Ser Phe 35 40 45 Gly Tyr Gln Leu Leu Trp Val Val Val Trp
Ala Asn Leu Met Ala Met 50 55 60 Leu Ile Gln Ile Leu Ser Ala Lys
Leu Gly Ile Ala Thr Gly Lys Asn 65 70 75 80 Leu Ala Glu Gln Ile Arg
Asp His Tyr Pro Arg Pro Val Val Trp Phe 85 90 95 Tyr Trp Val Gln
Ala Glu Ile Ile Ala Met Ala Thr Asp Leu Ala Glu 100 105 110 Phe Ile
Gly Ala Ala Ile Gly Phe Lys Leu Ile Leu Gly Val Ser Leu 115 120 125
Leu Gln Gly Ala Val Leu Thr Gly Ile Ala Thr Phe Leu Ile Leu Met 130
135 140 Leu Gln Arg Arg Gly Gln Lys Pro Leu Glu Lys Val Ile Gly Gly
Leu 145 150 155 160 Leu Leu Phe Val Ala Ala Ala Tyr Ile Val Glu Leu
Ile Phe Ser Gln 165 170 175 Pro Asn Leu Ala Gln Leu Gly Lys Gly Met
Val Ile Pro Ser Leu Pro 180 185 190 Thr Ser Glu Ala Val Phe Leu Ala
Ala Gly Val Leu Gly Ala Thr Ile 195 200 205 Met Pro His Val Ile Tyr
Leu His Ser Ser Leu Thr Gln His Leu His 210 215 220 Gly Gly Ser Arg
Gln Gln Arg Tyr Ser Ala Thr Lys Trp Asp Val Ala 225 230 235 240 Ile
Ala Met Thr Ile Ala Gly Phe Val Asn Leu Ala Met Met Ala Thr 245 250
255 Ala Ala Ala Ala Phe His Phe Ser Gly His Thr Gly Val Ala Asp Leu
260 265 270 Asp Glu Ala Tyr Leu Thr Leu Gln Pro Leu Leu Ser His Ala
Ala Ala 275 280 285 Thr Val Phe Gly Leu Ser Leu Val Ala Ala Gly Leu
Ser Ser Thr Val 290 295 300 Val Gly Thr Leu Ala Gly Gln Val Val Met
Gln Gly Phe Ile Arg Phe 305 310 315 320 His Ile Pro Leu Trp Val Arg
Arg Thr Val Thr Met Leu Pro Ser Phe 325 330 335 Ile Val Ile Leu Met
Gly Leu Asp Pro Thr Arg Ile Leu Val Met Ser 340 345 350 Gln Val Leu
Leu Ser Phe Gly Ile Ala Leu Ala Leu Val Pro Leu Leu 355 360 365 Ile
Phe Thr Ser Asp Ser Lys Leu Met Gly Asp Leu Val Asn Ser Lys 370 375
380 Arg Val Lys Gln Thr Gly Trp Val Ile Val Val Leu Val Val Ala Leu
385 390 395 400 Asn Ile Trp Leu Leu Val Gly Thr Ala Leu Gly Leu 405
410 1081236DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 108atgaccaatt atcgtgttga aagtagtagt
ggccgcgcgg ctcgtaaaat gcgtctggcc 60ttaatgggcc cggcgtttat tgctgcgatt
ggatacattg atccgggcaa tttcgctaca 120aacatccaag caggtgcatc
cttcggttac cagcttctgt gggtagtggt atgggctaac 180ctgatggcca
tgcttattca aattctttca gctaagcttg gtattgccac aggaaagaat
240ttagccgagc agattcgtga ccactatccc cgccccgtgg tctggttcta
ttgggtccag 300gcagagatta tcgcgatggc gactgattta gccgaattta
ttggggcagc tattggattt 360aagctgatcc
ttggcgtatc tctgttgcaa ggcgcggtat tgaccggaat tgcaaccttt
420ttgattctta tgttgcaacg tcgtgggcag aagcctctgg aaaaagtcat
cggcgggtta 480ttgctttttg ttgccgcggc ctacattgtg gaactgatct
tttctcaacc taacctggcg 540cagcttggta aaggcatggt aatcccgtca
cttcctacat ctgaggcagt attcttagca 600gccggcgtct tgggcgcaac
tatcatgccc catgtcatct acttacacag ttctctgact 660cagcacttac
acggtgggtc gcgccaacag cgttactccg caacaaagtg ggacgttgca
720attgccatga ccattgccgg ttttgttaac ctggcgatga tggccacggc
tgctgccgcc 780tttcatttca gtggccacac tggtgtagcc gatctggatg
aggcatacct gaccttgcag 840cctctgttgt ctcatgcagc cgccaccgtt
tttggtttaa gcttagtagc cgccggcttg 900agtagcacgg tggtaggcac
attggctgga caggtcgtga tgcaaggttt cattcgtttc 960catattccgt
tatgggtacg tcgcacggta acgatgctgc cgtcatttat cgtcatcctg
1020atgggattag acccgacgcg catcctggta atgtcgcaag ttttactgag
ctttggaatc 1080gcgttggccc tggtgccatt acttatcttc actagcgata
gtaagttgat gggtgatctt 1140gtcaatagca aacgtgtgaa gcaaacaggc
tgggtcattg tggtactggt tgtggcctta 1200aacatttggt tgttagtggg
cacggccctt ggcttg 1236109286PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 109Met Ser Gln Ala Leu
Lys Asn Leu Leu Thr Leu Leu Asn Leu Glu Lys 1 5 10 15 Ile Glu Glu
Gly Leu Phe Arg Gly Gln Ser Glu Asp Leu Gly Leu Arg 20 25 30 Gln
Val Phe Gly Gly Gln Val Val Gly Gln Ala Leu Tyr Ala Ala Lys 35 40
45 Glu Thr Val Pro Glu Glu Arg Leu Val His Ser Phe His Ser Tyr Phe
50 55 60 Leu Arg Pro Gly Asp Ser Lys Lys Pro Ile Ile Tyr Asp Val
Glu Thr 65 70 75 80 Leu Arg Asp Gly Asn Ser Phe Ser Ala Arg Arg Val
Ala Ala Ile Gln 85 90 95 Asn Gly Lys Pro Ile Phe Tyr Met Thr Ala
Ser Phe Gln Ala Pro Glu 100 105 110 Ala Gly Phe Glu His Gln Lys Thr
Met Pro Ser Ala Pro Ala Pro Asp 115 120 125 Gly Leu Pro Ser Glu Thr
Gln Ile Ala Gln Ser Leu Ala His Leu Leu 130 135 140 Pro Pro Val Leu
Lys Asp Lys Phe Ile Cys Asp Arg Pro Leu Glu Val 145 150 155 160 Arg
Pro Val Glu Phe His Asn Pro Leu Lys Gly His Val Ala Glu Pro 165 170
175 His Arg Gln Val Trp Ile Arg Ala Asn Gly Ser Val Pro Asp Asp Leu
180 185 190 Arg Val His Gln Tyr Leu Leu Gly Tyr Ala Ser Asp Leu Asn
Phe Leu 195 200 205 Pro Val Ala Leu Gln Pro His Gly Ile Gly Phe Leu
Glu Pro Gly Ile 210 215 220 Gln Ile Ala Thr Ile Asp His Ser Met Trp
Phe His Arg Pro Phe Asn 225 230 235 240 Leu Asn Glu Trp Leu Leu Tyr
Ser Val Glu Ser Thr Ser Ala Ser Ser 245 250 255 Ala Arg Gly Phe Val
Arg Gly Glu Phe Tyr Thr Gln Asp Gly Val Leu 260 265 270 Val Ala Ser
Thr Val Gln Glu Gly Val Met Arg Asn His Asn 275 280 285
11087DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 110caaataaaat gaaaggctca gtcgaaagac
tgggcctttc gttttatctg ttgtttgtcg 60gtgaacgctc tcctgagtag gacaaat
8711128DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 111agaaggccat cctgacggat ggcctttt
2811247DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 112gaagttccta tactttctag agaataggaa
cttcggaata ggaacta 47113161DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 113gtaccagttg
ttcttattgg tggtgttgct ttatggttgc atcgtagtaa atggttgtaa 60caaaagcaat
ttttccggct gtctgtatac aaaaacgccg taaagtttga gcgaagtcaa
120taaactctct acccattcag ggcaatatct ctcttggatc c
1611141332DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 114atggtaaagg aacgtaaaac cgagttggtc
gagggattcc gccattcggt tccctgtatc 60aatacccacc ggggaaaaac gtttgtcatc
atgctcggcg gtgaagccat tgagcatgag 120aatttctcca gtatcgttaa
tgatatcggg ttgttgcaca gcctcggcat ccgtctggtg 180gtggtctatg
gcgcacgtcc gcagatcgac gcaaatctgg ctgcgcatca ccacgaaccg
240ctgtatcaca agaatatacg tgtgaccgac gccaaaacac tggaactggt
gaagcaggct 300gcgggaacat tgcaactgga tattactgct cgcctgtcga
tgagtctcaa taacacgccg 360ctgcagggcg cgcatatcaa cgtcgtcagt
ggcaatttta ttattgccca gccgctgggc 420gtcgatgacg gcgtggatta
ctgccatagc gggcgtatcc ggcggattga tgaagacgcg 480atccatcgtc
aactggacag cggtgcaata gtgctaatgg ggccggtcgc tgtttcagtc
540actggcgaga gctttaacct gacctcggaa gagattgcca ctcaactggc
catcaaactg 600aaagctgaaa agatgattgg tttttgctct tcccagggcg
tcactaatga cgacggtgat 660attgtctccg aacttttccc taacgaagcg
caagcgcggg tagaagccca ggaagagaaa 720ggcgattaca actccggtac
ggtgcgcttt ttgcgtggcg cagtgaaagc ctgccgcagc 780ggcgtgcgtc
gctgtcattt aatcagttat caggaagatg gcgcgctgtt gcaagagttg
840ttctcacgcg acggtatcgg tacgcagatt gtgatggaaa gcgccgagca
gattcgtcgc 900gcaacaatca acgatattgg cggtattctg gagttgattc
gcccactgga gcagcaaggt 960attctggtac gccgttctcg cgagcagctg
gagatggaaa tcgacaaatt caccattatt 1020cagcgcgata acacgactat
tgcctgcgcc gcgctctatc cgttcccgga agagaagatt 1080ggggaaatgg
cctgtgtggc agttcacccg gattaccgca gttcatcaag gggtgaagtt
1140ctgctggaac gcattgccgc tcaggctaag cagagcggct taagcaaatt
gtttgtgctg 1200accacgcgca gtattcactg gttccaggaa cgtggattta
ccccagtgga tattgattta 1260ctgcccgaga gcaaaaagca gttgtacaac
taccagcgta aatccaaagt gttgatggcg 1320gatttagggt aa
133211548DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 115gaagttccta tactttctag agaataggaa
cttcggaata ggaacttc 48116985DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 116atgattgaac
aagatggatt gcacgcaggt tctccggccg cttgggtgga gaggctattc 60ggctatgact
gggcacaaca gacaatcggc tgctctgatg ccgccgtgtt ccggctgtca
120gcgcaggggc gcccggttct ttttgtcaag accgacctgt ccggtgccct
gaatgaactg 180caggacgagg cagcgcggct atcgtggctg gccacgacgg
gcgttccttg cgcagctgtg 240ctcgacgttg tcactgaagc gggaagggac
tggctgctat tgggcgaagt gccggggcag 300gatctcctgt catctcacct
tgctcctgcc gagaaagtat ccatcatggc tgatgcaatg 360cggcggctgc
atacgcttga tccggctacc tgcccattcg accaccaagc gaaacatcgc
420atcgagcgag cacgtactcg gatggaagcc ggtcttgtcg atcaggatga
tctggacgaa 480gagcatcagg ggctcgcgcc agccgaactg ttcgccaggc
tcaaggcgcg catgcccgac 540ggcgaggatc tcgtcgtgac ccatggcgat
gcctgcttgc cgaatatcat ggtggaaaat 600ggccgctttt ctggattcat
cgactgtggc cggctgggtg tggcggaccg ctatcaggac 660atagcgttgg
ctacccgtga tattgctgaa gagcttggcg gcgaatgggc tgaccgcttc
720ctcgtgcttt acggtatcgc cgctcccgat tcgcagcgca tcgccttcta
tcgccttctt 780gacgagttct tctgagcggg actctggggt tcgaaatgac
cgaccaagcg acgcccaacc 840tgccatcacg agatttcgat tccaccgccg
ccttctatga aaggttgggc ttcggaatcg 900ttttccggga cgccggctgg
atgatcctcc agcgcgggga tctcatgctg gagttcttcg 960cccaccccag
cttcaaaagc gctct 985117106DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 117ggttgggaag
ccctgcaaag taaactggat ggctttcttg ccgccaagga tctgatggcg 60caggggatca
agatctgatc aagagacagg atgaggatcg tttcgc 106118639DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
118tcatcgcagt actgttgtat tcattaagca tctgccgaca tggaagccat
cacaaacggc 60atgatgaacc tgaatcgcca gcggcatcag caccttgtcg ccttgcgtat
aatatttgcc 120catggtgaaa acgggggcga agaagttgtc catattggcc
acgtttaaat caaaactggt 180gaaactcacc cagggattgg ctgagacgaa
aaacatattc tcaataaacc ctttagggaa 240ataggccagg ttttcaccgt
aacacgccac atcttgcgaa tatatgtgta gaaactgccg 300gaaatcgtcg
tggtattcac tccagagcga tgaaaacgtt tcagtttgct catggaaaac
360ggtgtaacaa gggtgaacac tatcccatat caccagctca ccgtctttca
ttgccatacg 420taattccgga tgagcattca tcaggcgggc aagaatgtga
ataaaggccg gataaaactt 480gtgcttattt ttctttacgg tctttaaaaa
ggccgtaata tccagctgaa cggtctggtt 540ataggtacat tgagcaactg
actgaaatgc ctcaaaatgt tctttacgat gccattggga 600tatatcaacg
gtggtatatc cagtgatttt tttctccat 639119209DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
119tttagcttcc ttagctcctg aaaatctcga caactcaaaa aatacgcccg
gtagtgatct 60tatttcatta tggtgaaagt tggaacctct tacgtgccga tcaacgtctc
attttcgcca 120aaagttggcc cagggcttcc cggtatcaac agggacacca
ggatttattt attctgcgaa 180gtgatcttcc gtcacaggta ggcgcgccg
20912018DNAArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 120wntgaatwww wattcanw
1812114DNAArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 121ttgatnnnna tcaa
1412218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 122ttgttgayry rtcaacwa
1812315DNAArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 123ttataatnat tataa
1512450DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 124atgcgaagct cggctaagca agaagagagc
tgttcgacca ggagctttaa 5012560DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 125gtttcgtaat tagatagcca
ccggcgcttt aatgcccgga catatgaata tcctccttag 60
* * * * *
References