U.S. patent application number 17/350690 was filed with the patent office on 2021-12-02 for methods and compositions for improved production of fatty acids and derivatives thereof.
The applicant listed for this patent is Genomatica, Inc.. Invention is credited to Vikranth ARLAGADDA, Scott A. FRYKMAN, Derek L. GREENFIELD, Eli S. GROBAN, Louis G. HOM, Zhihao HU, Fernando A. SANCHEZ-RIERA.
Application Number | 20210371889 17/350690 |
Document ID | / |
Family ID | 1000005782971 |
Filed Date | 2021-12-02 |
United States Patent
Application |
20210371889 |
Kind Code |
A1 |
GREENFIELD; Derek L. ; et
al. |
December 2, 2021 |
Methods And Compositions For Improved Production Of Fatty Acids And
Derivatives Thereof
Abstract
The invention relates to compositions and methods, including
polynucleotide sequences, amino acid sequences, and engineered host
cells for producing fatty acids and derivates of fatty acids such
as acyl-CoA, terminal olefins, fatty aldehydes, fatty alcohols,
alkanes, alkenes, wax esters, ketones and internal olefins through
altered expression of the transcription factor, fadR.
Inventors: |
GREENFIELD; Derek L.; (South
San Francisco, CA) ; HOM; Louis G.; (San Carlos,
CA) ; SANCHEZ-RIERA; Fernando A.; (South San
Francisco, CA) ; HU; Zhihao; (Castro Valley, CA)
; ARLAGADDA; Vikranth; (San Bruno, CA) ; GROBAN;
Eli S.; (San Francisco, CA) ; FRYKMAN; Scott A.;
(San Francisco, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Genomatica, Inc. |
San Diego |
CA |
US |
|
|
Family ID: |
1000005782971 |
Appl. No.: |
17/350690 |
Filed: |
June 17, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14007857 |
Jan 22, 2014 |
11066682 |
|
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PCT/US12/31881 |
Apr 2, 2012 |
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17350690 |
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61470989 |
Apr 1, 2011 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07C 33/02 20130101;
C07C 31/125 20130101; Y02E 50/10 20130101; C12P 7/6409 20130101;
C07K 14/195 20130101; C07K 14/245 20130101; C07C 53/126
20130101 |
International
Class: |
C12P 7/64 20060101
C12P007/64; C07K 14/245 20060101 C07K014/245; C07K 14/195 20060101
C07K014/195; C07C 31/125 20060101 C07C031/125; C07C 33/02 20060101
C07C033/02; C07C 53/126 20060101 C07C053/126 |
Claims
1.-46. (canceled)
47. A recombinant host cell which is genetically engineered to
overexpress a FadR polypeptide and to overexpress a
phosphopantetheinyl transferase (PPTase), wherein the recombinant
host cell produces a fatty aldehyde, a fatty alcohol, a fatty acid
or a fatty ester when cultured in a culture medium under conditions
permissive for the production thereof.
48. The recombinant host cell of claim 47, wherein the FadR
polypeptide is encoded by a fadR gene obtained from Escherichia,
Salmonella, Citrobacter, Enterobacter, Klebsiella, Cronobacter,
Yersinia, Serratia, Erwinia, Pectobacterium, Photorhabdus,
Edwardsiella, Shewanella, or Vibrio.
49. The recombinant host cell of claim 47, wherein the FadR
polypeptide comprises an amino acid sequence having at least 80%
sequence identity to the amino acid sequence of SEQ ID NO: 1.
50. The recombinant host cell of claim 49, wherein the FadR
polypeptide comprises a mutation at amino acid 219 of SEQ ID NO:
1.
51. The recombinant host cell of claim 50, wherein the mutation is
a substitution of the amino acid 219 of SEQ ID NO: 1 with an
asparagine residue.
52. The recombinant host cell of claim 47, wherein the
overexpression of the FadR polypeptide is caused by a heterologous
promoter and/or a ribosome binding site operably linked to a
polynucleotide sequence which encodes the FadR polypeptide.
53. The recombinant host cell of claim 47, wherein the host cell is
further engineered to overexpress (a) a carboxylic acid reductase,
(b) a thioesterase, and (c) an alcohol dehydrogenase.
54. The recombinant host cell of claim 53, wherein the carboxylic
acid reductase is carB (SEQ ID NO: 8); the thioesterase is tesA
(SEQ ID NO: 11); and the alcohol dehydrogenase is YjgB (SEQ ID NO:
10) or AlrAadp1 (SEQ ID NO: 9).
55. The recombinant host cell of claim 47, wherein the PPTase is
EntD from E. coli MG1655 (SEQ ID NO: 12).
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 14/007,857 filed Jan. 22, 2014 which is a national phase
application of PCT Application No.: PCT/US2012/031881 filed 2 Apr.
2012 which claims priority benefit to U.S. Application Ser. No.
61/470,989, filed Apr. 1, 2011, which is expressly incorporated by
reference herein in its entirety.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY
[0002] The instant application contains a Sequence Listing which
has been submitted in ASCII format via EFS-Web and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Mar. 28, 2012, is named LS034PCT.txt and is 104,756 bytes in
size.
BACKGROUND OF THE INVENTION
[0003] Crude petroleum is a limited, natural resource found in the
Earth in liquid, gaseous, and solid forms. Although crude petroleum
is a valuable resource, it is discovered and extracted from the
Earth at considerable financial and environmental costs. Moreover,
in its natural form, crude petroleum extracted from the Earth has
few commercial uses. Crude petroleum is a mixture of hydrocarbons
(e.g., paraffins (or alkanes), olefins (or alkenes), alkynes,
napthenes (or cycloalkanes), aliphatic compounds, aromatic
compounds, etc.) of varying length and complexity. In addition,
crude petroleum contains other organic compounds (e.g., organic
compounds containing nitrogen, oxygen, sulfur, etc.) and impurities
(e.g., sulfur, salt, acid, metals, etc.). Hence, crude petroleum
must be refined and purified at considerable cost before it can be
used commercially.
[0004] Crude petroleum is also a primary source of raw materials
for producing petrochemicals. The two main classes of raw materials
derived from petroleum are short chain olefins (e.g., ethylene and
propylene) and aromatics (e.g., benzene and xylene isomers). These
raw materials are derived from longer chain hydrocarbons in crude
petroleum by cracking it at considerable expense using a variety of
methods, such as catalytic cracking, steam cracking, or catalytic
reforming. These raw materials can be used to make petrochemicals
such as monomers, solvents, detergents, and adhesives, which
otherwise cannot be directly refined from crude petroleum.
[0005] Petrochemicals, in turn, can be used to make specialty
chemicals, such as plastics, resins, fibers, elastomers,
pharmaceuticals, lubricants, and gels. Particular specialty
chemicals that can be produced from petrochemical raw materials
include fatty acids, hydrocarbons (e.g., long chain, branched
chain, saturated, unsaturated, etc.), fatty aldehydes, fatty
alcohols, esters, ketones, lubricants, etc.
[0006] Due to the inherent challenges posed by petroleum, there is
a need for a renewable petroleum source that does not need to be
explored, extracted, transported over long distances, or
substantially refined like crude petroleum. There is also a need
for a renewable petroleum source which can be produced economically
without creating the type of environmental damage produced by the
petroleum industry and the burning of petroleum-based fuels. For
similar reasons, there is also a need for a renewable source of
chemicals which are typically derived from petroleum.
[0007] One method of producing renewable petroleum is by
engineering microorganisms to produce renewable petroleum products.
Some microorganisms have long been known to possess a natural
ability to produce petroleum products (e.g., yeast to produce
ethanol). More recently, the development of advanced
biotechnologies has made it possible to metabolically engineer an
organism to produce bioproducts and biofuels. Bioproducts (e.g.,
chemicals) and biofuels (e.g., biodiesel) are renewable
alternatives to petroleum-based chemicals and fuels, respectively.
Bioproducts and biofuels can be derived from renewable sources,
such as plant matter, animal matter, and organic waste matter,
which are collectively known as biomass.
[0008] Biofuels can be substituted for any petroleum-based fuel
(e.g., gasoline, diesel, aviation fuel, heating oil, etc.), and
offer several advantages over petroleum-based fuels. Biofuels do
not require expensive and risky exploration or extraction. Biofuels
can be produced locally and therefore do not require transportation
over long distances. In addition, biofuels can be made directly and
require little or no additional refining. Furthermore, the
combustion of biofuels causes less of a burden on the environment
since the amount of harmful emissions (e.g., green house gases, air
pollution, etc.) released during combustion is reduced as compared
to the combustion of petroleum-based fuels. Moreover, biofuels
maintain a balanced carbon cycle because biofuels are produced from
biomass, a renewable, natural resource. Although combustion of
biofuels releases carbon (e.g., as carbon dioxide), this carbon
will be recycled during the production of biomass (e.g., the
cultivation of crops), thereby balancing the carbon cycle, which is
not achieved with the use of petroleum based fuels.
[0009] Biologically derived chemicals offer similar advantages over
petrochemicals that biofuels offer over petroleum-based fuels. In
particular, biologically derived chemicals can be converted from
biomass to the desired chemical product directly without extensive
refining, unlike petrochemicals, which must be produced by refining
crude petroleum to recover raw materials which are then processed
further into the desired petrochemical.
[0010] Hydrocarbons have many commercial uses. For example, shorter
chain alkanes are used as fuels. Methane and ethane are the main
constituents of natural gas. Longer chain alkanes (e.g., from five
to sixteen carbons) are used as transportation fuels (e.g.,
gasoline, diesel, or aviation fuel). Alkanes having more than
sixteen carbon atoms are important components of fuel oils and
lubricating oils. Even longer alkanes, which are solid at room
temperature, can be used, for example, as a paraffin wax. Alkanes
that contain approximately thirty-five carbons are found in
bitumen, which is used for road surfacing. In addition, longer
chain alkanes can be cracked to produce commercially useful shorter
chain hydrocarbons.
[0011] Like short chain alkanes, short chain alkenes are used in
transportation fuels. Longer chain alkenes are used in plastics,
lubricants, and synthetic lubricants. In addition, alkenes are used
as a feedstock to produce alcohols, esters, plasticizers,
surfactants, tertiary amines, enhanced oil recovery agents, fatty
acids, thiols, alkenylsuccinic anhydrides, epoxides, chlorinated
alkanes, chlorinated alkenes, waxes, fuel additives, and drag flow
reducers.
[0012] Esters have many commercial uses. For example, biodiesel, an
alternative fuel, is comprised of esters (e.g., fatty acid methyl
ester, fatty acid ethyl esters, etc.). Some low molecular weight
esters are volatile with a pleasant odor which makes them useful as
fragrances or flavoring agents. In addition, esters are used as
solvents for lacquers, paints, and varnishes. Furthermore, some
naturally occurring substances, such as waxes, fats, and oils are
comprised of esters. Esters are also used as softening agents in
resins and plastics, plasticizers, flame retardants, and additives
in gasoline and oil. In addition, esters can be used in the
manufacture of polymers, films, textiles, dyes, and
pharmaceuticals.
[0013] Aldehydes are used to produce many specialty chemicals. For
example, aldehydes are used to produce polymers, resins (e.g.,
Bakelite), dyes, flavorings, plasticizers, perfumes,
pharmaceuticals, and other chemicals, some of which may be used as
solvents, preservatives, or disinfectants. In addition, certain
natural and synthetic compounds, such as vitamins and hormones, are
aldehydes, and many sugars contain aldehyde groups. Fatty aldehydes
can be converted to fatty alcohols by chemical or enzymatic
reduction.
[0014] Fatty alcohols have many commercial uses. Worldwide annual
sales of fatty alcohols and their derivatives are in excess of U.S.
$1 billion. The shorter chain fatty alcohols are used in the
cosmetic and food industries as emulsifiers, emollients, and
thickeners. Due to their amphiphilic nature, fatty alcohols behave
as nonionic surfactants, which are useful in personal care and
household products, such as, for example, detergents. In addition,
fatty alcohols are used in waxes, gums, resins, pharmaceutical
salves and lotions, lubricating oil additives, textile antistatic
and finishing agents, plasticizers, cosmetics, industrial solvents,
and solvents for fats.
[0015] Acyl-CoA synthase (ACS) esterifies free fatty acids to
acyl-CoA by a two-step mechanism. The free fatty acid first is
converted to an acyl-AMP intermediate (an adenylate) through the
pyrophosphorolysis of ATP. The activated carbonyl carbon of the
adenylate is then coupled to the thiol group of CoA, releasing AMP
and the acyl-CoA final product (Shockey et al., Plant. Physiol.,
129: 1710-1722 (2002)).
[0016] FadR is a key regulatory factor involved in fatty acid
degradation and fatty acid biosynthesis pathways (Cronan et al.,
Mol. Microbiol., 29(4): 937-943 (1998)). The E. coli ACS enzyme
FadD and the fatty acid transport protein FadL are essential
components of a fatty acid uptake system. FadL mediates transport
of fatty acids into the bacterial cell, and FadD mediates formation
of acyl-CoA esters. When no other carbon source is available,
exogenous fatty acids are taken up by bacteria and converted to
acyl-CoA esters, which can bind to the transcription factor FadR
and derepress the expression of the fad genes that encode proteins
responsible for fatty acid transport (FadL), activation (FadD), and
.beta.-oxidation (FadA, FadB, FadE, and FadH). When alternative
sources of carbon are available, bacteria synthesize fatty acids as
acyl-ACPs, which are used for phospholipid synthesis, but are not
substrates for .beta.-oxidation. Thus, acyl-CoA and acyl-ACP are
both independent sources of fatty acids that can result in
different end-products (Caviglia et al., J. Biol. Chem., 279(12):
1163-1169 (2004)).
[0017] There remains a need for methods and compositions for
enhancing the production of biologically derived chemicals, such as
fatty acids and fatty acid derivatives. This invention provides
such methods and compositions. The invention further provides
products derived from the fatty acids and derivatives thereof
produced by the methods described herein, such as fuels,
surfactants, and detergents.
BRIEF SUMMARY OF THE INVENTION
[0018] The invention provides improved methods of producing a fatty
acid or a fatty acid derivative in a host cell. The method
comprises (a) providing a host cell which is genetically engineered
to have an altered level of expression of a FadR polypeptide as
compared to the level of expression of the FadR polypeptide in a
corresponding wild-type host cell, (b) culturing the engineered
host cell in a culture medium under conditions permissive for the
production of a fatty acid or a fatty acid derivative, and (c)
isolating the fatty acid or fatty acid derivative from the
engineered host cell. As a result of this method, one or more of
the titer, yield, or productivity of the fatty acid or fatty acid
derivative produced by the engineered host cell is increased
relative to that of the corresponding wild-type host cell.
[0019] Also provided are fatty acids and fatty acid derivatives,
such as an acyl-CoA, a fatty aldehyde, a short chain alcohol, a
long chain alcohol, a fatty alcohol, a hydrocarbon, or an ester,
produced by the methods of the invention. Further provided are
biofuel compositions and surfactant compositions comprising a fatty
acid or a fatty acid derivative produced by the methods of the
invention.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)
[0020] FIG. 1A-FIG. 1T is a chart of exemplary genes suitable for
use in practicing the invention. Polypeptide and/or polynucleotide
accession numbers are from the National Center for Biotechnology
Information (NCBI) database, and enzyme EC numbers are from the
Nomenclature Committee of the International Union of Biochemistry
and Molecular Biology (NC-IUBMB).
[0021] FIG. 2 is a graph of fatty species production in a control
E. coli strain (ALC310) or the transposon insertion strain,
D288.
[0022] FIG. 3 is a diagram depicting the location of the transposon
insertion in the D288 strain.
[0023] FIG. 4 is a bar graph of total fatty species (FA) titers in
expression library E. coli strains having altered expression of
wild-type FadR or mutant FadR[S219N] as compared to FA titers in
the control E. coli strain (ALC487).
[0024] FIG. 5 is a bar graph of total fatty species (FA) titers in
three separate shake flask (SF) fermentations of E. coli strain
D512 having altered expression of wild-type FadR as compared to FA
titers in the control ALC487 strain.
[0025] FIG. 6 is a bar graph of total fatty species yield on carbon
in shake flask fermentations of the control ALC487 strain or E.
coli strain D512 having altered expression of wild-type FadR.
[0026] FIG. 7 is a graph of fatty acid and fatty alcohol production
and total fatty species yield in 5 L bioreactor fermentations of
the control ALC487 strain fed at a glucose rate of 10 g/L/hr or the
D512 strain having altered expression of wild-type FadR fed at a
glucose rate of 10 g/L/hr or 15 g/L/hr. The bars represent fatty
alcohol or fatty acid titer, and the circles represent total fatty
species yield on carbon.
[0027] FIG. 8 is a graph of fatty acid and fatty alcohol production
and total fatty species yield in shake flask fermentations of the
D512 strain or a D512 strain in which the entD gene was deleted.
The bars represent fatty acid or fatty alcohol titer, and the
circles represent fatty acid yield.
[0028] FIG. 9 is a graph of total fatty species (fatty acids and
fatty acid methyl ester (FAME)) titers and yields in two ribosome
binding site (RBS) library E. coli strains having altered
expression of mutant FadR[S219N] (i.e., P1A4 and P1G7) as compared
to the total fatty species titers and yields in the parental E.
coli strain (DAM1-pDS57) in shake flask (SF) fermentations at
32.degree. C. The bars represent total fatty species titers after
56 hours of culture, and the squares represent total fatty species
yield after 56 hours of culture.
[0029] FIG. 10 is a line graph of combined FAME and free fatty acid
(FFA) titers in the parental DAM1 pDS57 strain, or RBS library
strains P1A4 or P1G7 in bioreactor fermentations at several
timepoints following induction of FAME and FFA production, wherein
DAM1 P1A4 and DAM1 P1G7 express FadR and DAM1 pDS57 does not
express FadR.
[0030] FIG. 11 is a line graph of combined FAME and FFA yields in
the parental DAM1 pDS57 strain, or RBS library strains P1A4 or P1G7
in bioreactor fermentations at several time points following
induction of FAME and FFA production, wherein DAM1 P1A4 and DAM1
P1G7 express FadR and DAM1 pDS57 does not express FadR.
DETAILED DESCRIPTION OF THE INVENTION
[0031] The invention is based, at least in part, on the discovery
that altering the level of expression of FadR in a host cell
facilitates enhanced production of fatty acids and fatty acid
derivatives by the host cell.
[0032] The invention provides improved methods of producing a fatty
acid or a fatty acid derivative in a host cell. The method
comprises (a) providing a host cell which is genetically engineered
to have an altered level of expression of a FadR polypeptide as
compared to the level of expression of the FadR polypeptide in a
corresponding wild-type host cell, (b) culturing the engineered
host cell in a culture medium under conditions permissive for the
production of a fatty acid or a fatty acid derivative, and (c)
isolating the fatty acid or fatty acid derivative from the
engineered host cell. As a result of this method, one or more of
the titer, yield, or productivity of the fatty acid or fatty acid
derivative produced by the engineered host cell is increased
relative to that of the corresponding wild-type host cell.
Definitions
[0033] As used in this specification and the appended claims, the
singular forms "a," "an" and "the" include plural referents unless
the context clearly dictates otherwise. Thus, for example,
reference to "a recombinant host cell" includes two or more such
recombinant host cells, reference to "a fatty alcohol" includes one
or more fatty alcohols, or mixtures of fatty alcohols, reference to
"a nucleic acid coding sequence" includes one or more nucleic acid
coding sequences, reference to "an enzyme" includes one or more
enzymes, and the like.
[0034] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which the invention pertains. Although
other methods and materials similar, or equivalent, to those
described herein can be used in the practice of the present
invention, the preferred materials and methods are described
herein.
[0035] In describing and claiming the present invention, the
following terminology will be used in accordance with the
definitions set out below.
[0036] Accession Numbers: Sequence Accession numbers throughout
this description were obtained from databases provided by the NCBI
(National Center for Biotechnology Information) maintained by the
National Institutes of Health, U.S.A. (which are identified herein
as "NCBI Accession Numbers" or alternatively as "GenBank Accession
Numbers"), and from the UniProt Knowledgebase (UniProtKB) and
Swiss-Prot databases provided by the Swiss Institute of
Bioinformatics (which are identified herein as "UniProtKB Accession
Numbers").
[0037] Enzyme Classification (EC) Numbers: EC numbers are
established by the Nomenclature Committee of the International
Union of Biochemistry and Molecular Biology (IUBMB), description of
which is available on the IUBMB Enzyme Nomenclature website on the
World Wide Web. EC numbers classify enzymes according to the
reaction catalyzed.
[0038] The term "FadR polypeptide" refers to a polypeptide having
biological activity corresponding to that of FadR derived from E.
coli MG1655 (SEQ ID NO: 1).
[0039] As used herein, the term "fatty acid or derivative thereof"
means a "fatty acid" or a "fatty acid derivative." The term "fatty
acid" means a carboxylic acid having the formula RCOOH. R
represents an aliphatic group, preferably an alkyl group. R can
comprise between about 4 and about 22 carbon atoms. Fatty acids can
be saturated, monounsaturated, or polyunsaturated. In a preferred
embodiment, the fatty acid is made from a fatty acid biosynthetic
pathway. A "fatty acid derivative" is a product made in part from
the fatty acid biosynthetic pathway of the production host
organism. "Fatty acid derivatives" includes products made in part
from acyl-ACP or acyl-ACP derivatives. Exemplary fatty acid
derivatives include, for example, acyl-CoA, fatty acids, fatty
aldehydes, short and long chain alcohols, hydrocarbons, fatty
alcohols, esters (e.g., waxes, fatty acid esters, or fatty esters),
terminal olefins, internal olefins, and ketones.
[0040] A "fatty acid derivative composition" as referred to herein
is produced by a recombinant host cell and typically comprises a
mixture of fatty acid derivative. In some cases, the mixture
includes more than one type of product (e.g., fatty acids and fatty
alcohols, fatty acids and fatty acid esters or alkanes and
olefins). In other cases, the fatty acid derivative compositions
may comprise, for example, a mixture of fatty alcohols (or another
fatty acid derivative) with various chain lengths and saturation or
branching characteristics. In still other cases, the fatty acid
derivative composition comprises a mixture of both more than one
type of product and products with various chain lengths and
saturation or branching characteristics.
[0041] As used herein "acyl-CoA" refers to an acyl thioester formed
between the carbonyl carbon of alkyl chain and the sulfhydryl group
of the 4'-phosphopantethionyl moiety of coenzyme A (CoA), which has
the formula R--C(O)S-CoA, where R is any alkyl group having at
least 4 carbon atoms.
[0042] As used herein "acyl-ACP" refers to an acyl thioester formed
between the carbonyl carbon of alkyl chain and the sulfhydryl group
of the phosphopantetheinyl moiety of an acyl carrier protein (ACP).
The phosphopantetheinyl moiety is post-translationally attached to
a conserved serine residue on the ACP by the action of holo-acyl
carrier protein synthase (ACPS), a phosphopantetheinyl transferase.
In some embodiments an acyl-ACP is an intermediate in the synthesis
of fully saturated acyl-ACPs. In other embodiments an acyl-ACP is
an intermediate in the synthesis of unsaturated acyl-ACPs. In some
embodiments, the carbon chain will have about 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26
carbons. Each of these acyl-ACPs are substrates for enzymes that
convert them to fatty acid derivatives.
[0043] As used herein, the term "fatty acid biosynthetic pathway"
means a biosynthetic pathway that produces fatty acids. The fatty
acid biosynthetic pathway includes fatty acid synthases that can be
engineered to produce fatty acids, and in some embodiments can be
expressed with additional enzymes to produce fatty acids having
desired carbon chain characteristics.
[0044] As used herein, "fatty aldehyde" means an aldehyde having
the formula RCHO characterized by a carbonyl group (C.dbd.O). In
some embodiments, the fatty aldehyde is any aldehyde made from a
fatty acid or fatty acid derivative.
[0045] As used herein, "fatty alcohol" means an alcohol having the
formula ROH. In some embodiments, the fatty alcohol is any alcohol
made from a fatty acid or fatty acid derivative.
[0046] In certain embodiments, the R group of a fatty acid, fatty
aldehyde, or fatty alcohol is at least 5, at least 6, at least 7,
at least 8, at least 9, at least 10, at least 11, at least 12, at
least 13, at least 14, at least 15, at least 16, at least 17, at
least 18, or at least 19, carbons in length. Alternatively, or in
addition, the R group is 20 or less, 19 or less, 18 or less, 17 or
less, 16 or less, 15 or less, 14 or less, 13 or less, 12 or less,
11 or less, 10 or less, 9 or less, 8 or less, 7 or less, or 6 or
less carbons in length. Thus, the R group can have an R group
bounded by any two of the above endpoints. For example, the R group
can be 6-16 carbons in length, 10-14 carbons in length, or 12-18
carbons in length. In some embodiments, the fatty acid, fatty
aldehyde, or fatty alcohol is a C.sub.6, C.sub.7, C.sub.8, C.sub.9,
C.sub.10, C.sub.11, C.sub.12, C.sub.13, C.sub.14, C.sub.15,
C.sub.16, C.sub.17, C.sub.18, C.sub.19, C.sub.20, C.sub.21,
C.sub.22, C.sub.23, C.sub.24, C.sub.25, or a C.sub.26 fatty acid,
fatty aldehyde, or fatty alcohol. In certain embodiments, the fatty
acid, fatty aldehyde, or fatty alcohol is a C.sub.6, C.sub.8,
C.sub.10, C.sub.12, C.sub.13, C.sub.14, C.sub.15, C.sub.16,
C.sub.17, or C.sub.18 fatty acid, fatty aldehyde, or fatty
alcohol.
[0047] The R group of a fatty acid, fatty aldehyde, or fatty
alcohol can be a straight chain or a branched chain. Branched
chains may have more than one point of branching and may include
cyclic branches. In some embodiments, the branched fatty acid,
branched fatty aldehyde, or branched fatty alcohol is a C.sub.6,
C.sub.7, C.sub.8, C.sub.9, C.sub.10, C.sub.11, C.sub.12, C.sub.13,
C.sub.14, C.sub.15, C.sub.16, C.sub.17, C.sub.18, C.sub.19,
C.sub.20, C.sub.21, C.sub.22, C.sub.23, C.sub.24, C.sub.25, Or a
C.sub.26 branched fatty acid, branched fatty aldehyde, or branched
fatty alcohol. In particular embodiments, the branched fatty acid,
branched fatty aldehyde, or branched fatty alcohol is a C.sub.6,
C.sub.8, C.sub.10, C.sub.12, C.sub.13, C.sub.14, C.sub.15,
C.sub.16, C.sub.17, or C.sub.18 branched fatty acid, branched fatty
aldehyde, or branched fatty alcohol. In certain embodiments, the
hydroxyl group of the branched fatty acid, branched fatty aldehyde,
or branched fatty alcohol is in the primary (CO position.
[0048] In certain embodiments, the branched fatty acid, branched
fatty aldehyde, or branched fatty alcohol is an iso-fatty acid,
iso-fatty aldehyde, or iso-fatty alcohol, or an antesio-fatty acid,
an anteiso-fatty aldehyde, or anteiso-fatty alcohol. In exemplary
embodiments, the branched fatty acid, branched fatty aldehyde, or
branched fatty alcohol is selected from iso-C.sub.7:0,
iso-C.sub.8:0, iso-C.sub.9:0, iso-C.sub.10:0, iso-C.sub.11:0,
iso-C.sub.12:0, iso-C.sub.13:0, iso-C.sub.14:0, iso-C.sub.15:0,
iso-C.sub.16:0, iso-C.sub.17:0, iso-C.sub.18:0, iso-C.sub.19:0,
anteiso-C.sub.7:0, anteiso-C.sub.8:0, anteiso-C.sub.9:0,
anteiso-C.sub.10:0, anteiso-C.sub.11:0, anteiso-C.sub.12:0,
anteiso-C.sub.13:0, anteiso-C.sub.14:0, anteiso-C.sub.15:0,
anteiso-C.sub.16:0, anteiso-C.sub.17:0, anteiso-C.sub.18:0, and
anteiso-C.sub.19:0 branched fatty acid, branched fatty aldehyde or
branched fatty alcohol.
[0049] The R group of a branched or unbranched fatty acid, branched
or unbranched fatty aldehyde, or branched or unbranched fatty
alcohol can be saturated or unsaturated. If unsaturated, the R
group can have one or more than one point of unsaturation. In some
embodiments, the unsaturated fatty acid, unsaturated fatty
aldehyde, or unsaturated fatty alcohol is a monounsaturated fatty
acid, monounsaturated fatty aldehyde, or monounsaturated fatty
alcohol. In certain embodiments, the unsaturated fatty acid,
unsaturated fatty aldehyde, or unsaturated fatty alcohol is a C6:1,
C7:1, C8:1, C9:1, C10:1, C11:1, C12:1, C13:1, C14:1, C15:1, C16:1,
C17:1, C18:1, C19:1, C20:1, C21:1, C22:1, C23:1, C24:1, C25:1, or a
C26:1 unsaturated fatty acid, unsaturated fatty aldehyde, or
unsaturated fatty alcohol. In certain preferred embodiments, the
unsaturated fatty acid, unsaturated fatty aldehyde, or unsaturated
fatty alcohol is C10:1, C12:1, C14:1, C16:1, or C18:1. In yet other
embodiments, the unsaturated fatty acid, unsaturated fatty
aldehyde, or unsaturated fatty alcohol is unsaturated at the
omega-7 position. In certain embodiments, the unsaturated fatty
acid, unsaturated fatty aldehyde, or unsaturated fatty alcohol
comprises a cis double bond.
[0050] As used herein, the term "alkane" means saturated
hydrocarbons or compounds that consist only of carbon (C) and
hydrogen (H), wherein these atoms are linked together by single
bonds (i.e., they are saturated compounds).
[0051] The terms "olefin" and "alkene" are used interchangeably
herein, and refer to hydrocarbons containing at least one
carbon-to-carbon double bond (i.e., they are unsaturated
compounds).
[0052] The terms "terminal olefin," ".alpha.-olefin", "terminal
alkene" and "1-alkene" are used interchangeably herein with
reference to .alpha.-olefins or alkenes with a chemical formula
C.sub.xH.sub.2x, distinguished from other olefins with a similar
molecular formula by linearity of the hydrocarbon chain and the
position of the double bond at the primary or alpha position.
[0053] As used herein, the term "fatty ester" may be used in
reference to an ester. In a preferred embodiment, a fatty ester is
any ester made from a fatty acid, for example a fatty acid ester.
In some embodiments, a fatty ester contains an A side and a B side.
As used herein, an "A side" of an ester refers to the carbon chain
attached to the carboxylate oxygen of the ester. As used herein, a
"B side" of an ester refers to the carbon chain comprising the
parent carboxylate of the ester. In embodiments where the fatty
ester is derived from the fatty acid biosynthetic pathway, the A
side is contributed by an alcohol, and the B side is contributed by
a fatty acid.
[0054] Any alcohol can be used to form the A side of the fatty
esters. For example, the alcohol can be derived from the fatty acid
biosynthetic pathway. Alternatively, the alcohol can be produced
through non-fatty acid biosynthetic pathways. Moreover, the alcohol
can be provided exogenously. For example, the alcohol can be
supplied in the fermentation broth in instances where the fatty
ester is produced by an organism. Alternatively, a carboxylic acid,
such as a fatty acid or acetic acid, can be supplied exogenously in
instances where the fatty ester is produced by an organism that can
also produce alcohol.
[0055] The carbon chains comprising the A side or B side can be of
any length. In one embodiment, the A side of the ester is at least
about 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, or 18 carbons in
length. When the fatty ester is a fatty acid methyl ester, the A
side of the ester is 1 carbon in length. When the fatty ester is a
fatty acid ethyl ester, the A side of the ester is 2 carbons in
length. The B side of the ester can be at least about 4, 6, 8, 10,
12, 14, 16, 18, 20, 22, 24, or 26 carbons in length. The A side
and/or the B side can be straight or branched chain. The branched
chains can have one or more points of branching. In addition, the
branched chains can include cyclic branches. Furthermore, the A
side and/or B side can be saturated or unsaturated. If unsaturated,
the A side and/or B side can have one or more points of
unsaturation.
[0056] In some embodiments, the fatty acid ester is a fatty acid
methyl ester (FAME) or a fatty acid ethyl ester (FAEE). In certain
embodiments, the FAME is a beta-hydroxy (B-OH) FAME. In one
embodiment, the fatty ester is produced biosynthetically. In this
embodiment, first the fatty acid is "activated." Non-limiting
examples of "activated" fatty acids are acyl-CoA, acyl ACP, and
acyl phosphate. Acyl-CoA can be a direct product of fatty acid
biosynthesis or degradation. In addition, acyl-CoA can be
synthesized from a free fatty acid, a CoA, and an adenosine
nucleotide triphosphate (ATP). An example of an enzyme which
produces acyl-CoA is acyl-CoA synthase.
[0057] After a fatty acid is activated, it can be readily
transferred to a recipient nucleophile. Exemplary nucleophiles are
alcohols, thiols, or phosphates.
[0058] In one embodiment, the fatty ester is a wax. The wax can be
derived from a long chain alcohol and a long chain fatty acid. In
another embodiment, the fatty ester is a fatty acid thioester, for
example, fatty acyl Coenzyme A (CoA). In other embodiments, the
fatty ester is a fatty acyl pantothenate, an acyl carrier protein
(ACP), or a fatty phosphate ester.
[0059] As used herein "acyl CoA" refers to an acyl thioester formed
between the carbonyl carbon of alkyl chain and the sulfydryl group
of the 4'-phosphopantethionyl moiety of coenzyme A (CoA), which has
the formula R--C(O)S-CoA, where R is any alkyl group having at
least 4 carbon atoms. In some instances an acyl CoA will be an
intermediate in the synthesis of fully saturated acyl CoAs,
including, but not limited to 3-keto-acyl CoA, a 3-hydroxy acyl
CoA, a delta-2-trans-enoyl-CoA, or an alkyl acyl CoA. In some
embodiments, the carbon chain will have about 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26
carbons. In other embodiments the acyl CoA will be branched. In one
embodiment the branched acyl CoA is an isoacyl CoA, in another it
is an anti-isoacyl CoA. Each of these "acyl CoAs" are substrates
for enzymes that convert them to fatty acid derivatives such as
those described herein.
[0060] The terms "altered level of expression" and "modified level
of expression" are used interchangeably and mean that a
polynucleotide, polypeptide, or hydrocarbon is present in a
different concentration in an engineered host cell as compared to
its concentration in a corresponding wild-type cell under the same
conditions.
[0061] "Polynucleotide" refers to a polymer of DNA or RNA, which
can be single-stranded or double-stranded and which can contain
non-natural or altered nucleotides. The terms "polynucleotide,"
"nucleic acid," and "nucleic acid molecule" are used herein
interchangeably to refer to a polymeric form of nucleotides of any
length, either ribonucleotides (RNA) or deoxyribonucleotides (DNA).
These terms refer to the primary structure of the molecule, and
thus include double- and single-stranded DNA, and double- and
single-stranded RNA. The terms include, as equivalents, analogs of
either RNA or DNA made from nucleotide analogs and modified
polynucleotides such as, though not limited to methylated and/or
capped polynucleotides. The polynucleotide can be in any form,
including but not limited to plasmid, viral, chromosomal, EST,
cDNA, mRNA, and rRNA.
[0062] The term "nucleotide" as used herein refers to a monomeric
unit of a polynucleotide that consists of a heterocyclic base, a
sugar, and one or more phosphate groups. The naturally occurring
bases (guanine, (G), adenine, (A), cytosine, (C), thymine, (T), and
uracil (U)) are typically derivatives of purine or pyrimidine,
though it should be understood that naturally and non-naturally
occurring base analogs are also included. The naturally occurring
sugar is the pentose (five-carbon sugar) deoxyribose (which forms
DNA) or ribose (which forms RNA), though it should be understood
that naturally and non-naturally occurring sugar analogs are also
included. Nucleic acids are typically linked via phosphate bonds to
form nucleic acids or polynucleotides, though many other linkages
are known in the art (e.g., phosphorothioates, boranophosphates,
and the like).
[0063] Polynucleotides described herein may comprise degenerate
nucleotides which are defined according to the IUPAC code for
nucleotide degeneracy wherein B is C, G, or T; D is A, G, or T; H
is A, C, or T; K is G or T; M is A or C; N is A, C, G, or T; R is A
or G; S is C or G; V is A, C, or G; W is A or T; and Y is C or
T.
[0064] The terms "polypeptide" and "protein" refer to a polymer of
amino acid residues. The term "recombinant polypeptide" refers to a
polypeptide that is produced by recombinant DNA techniques, wherein
generally DNA encoding the expressed protein or RNA is inserted
into a suitable expression vector that is in turn used to transform
a host cell to produce the polypeptide or RNA.
[0065] In some embodiments, the polypeptide, polynucleotide, or
hydrocarbon having an altered or modified level of expression is
"overexpressed" or has an "increased level of expression." As used
herein, "overexpress" and "increasing the level of expression" mean
to express or cause to be expressed a polynucleotide, polypeptide,
or hydrocarbon in a cell at a greater concentration than is
normally expressed in a corresponding wild-type cell under the same
conditions. For example, a polypeptide can be "overexpressed" in an
engineered host cell when the polypeptide is present in a greater
concentration in the engineered host cell as compared to its
concentration in a non-engineered host cell of the same species
under the same conditions.
[0066] In other embodiments, the polypeptide, polynucleotide, or
hydrocarbon having an altered level of expression is "attenuated"
or has a "decreased level of expression." As used herein,
"attenuate" and "decreasing the level of expression" mean to
express or cause to be expressed a polynucleotide, polypeptide, or
hydrocarbon in a cell at a lesser concentration than is normally
expressed in a corresponding wild-type cell under the same
conditions.
[0067] The degree of overexpression or attenuation can be 1.5-fold
or more, e.g., 2-fold or more, 3-fold or more, 5-fold or more,
10-fold or more, or 15-fold or more. Alternatively, or in addition,
the degree of overexpression or attenuation can be 500-fold or
less, e.g., 100-fold or less, 50-fold or less, 25-fold or less, or
20-fold or less. Thus, the degree of overexpression or attenuation
can be bounded by any two of the above endpoints. For example, the
degree of overexpression or attenuation can be 1.5-500-fold,
2-50-fold, 10-25-fold, or 15-20-fold.
[0068] In some embodiments, a polypeptide described herein has
"increased level of activity." By "increased level of activity" is
meant that a polypeptide has a higher level of biochemical or
biological function (e.g., DNA binding or enzymatic activity) in an
engineered host cell as compared to its level of biochemical and/or
biological function in a corresponding wild-type host cell under
the same conditions. The degree of enhanced activity can be about
10% or more, about 20% or more, about 50% or more, about 75% or
more, about 100% or more, about 200% or more, about 500% or more,
about 1000% or more, or any range therein.
[0069] A polynucleotide or polypeptide can be attenuated using
methods known in the art. In some embodiments, the expression of a
gene or polypeptide encoded by the gene is attenuated by mutating
the regulatory polynucleotide sequences which control expression of
the gene. In other embodiments, the expression of a gene or
polypeptide encoded by the gene is attenuated by overexpressing a
repressor protein, or by providing an exogenous regulatory element
that activates a repressor protein. In still yet other embodiments,
DNA- or RNA-based gene silencing methods are used to attenuate the
expression of a gene or polynucleotide. In some embodiments, the
expression of a gene or polypeptide is completely attenuated, e.g.,
by deleting all or a portion of the polynucleotide sequence of a
gene.
[0070] A polynucleotide or polypeptide can be overexpressed using
methods known in the art. In some embodiments, overexpression of a
polypeptide is achieved by the use of an exogenous regulatory
element. The term "exogenous regulatory element" generally refers
to a regulatory element originating outside of the host cell.
However, in certain embodiments, the term "exogenous regulatory
element" can refer to a regulatory element derived from the host
cell whose function is replicated or usurped for the purpose of
controlling the expression of an endogenous polypeptide. For
example, if the host cell is an E. coli cell, and the FadR
polypeptide is a encoded by an endogenous fadR gene, then
expression of the endogenous fadR can be controlled by a promoter
derived from another E. coli gene.
[0071] In some embodiments, the exogenous regulatory element is a
chemical compound, such as a small molecule. As used herein, the
term "small molecule" refers to a substance or compound having a
molecular weight of less than about 1,000 g/mol.
[0072] In some embodiments, the exogenous regulatory element which
controls the expression of an endogenous fadR gene is an expression
control sequence which is operably linked to the endogenous fadR
gene by recombinant integration into the genome of the host cell.
In certain embodiments, the expression control sequence is
integrated into a host cell chromosome by homologous recombination
using methods known in the art (e.g., Datsenko et al., Proc. Natl.
Acad. Sci. U.S.A., 97(12): 6640-6645 (2000)).
[0073] Expression control sequences are known in the art and
include, for example, promoters, enhancers, polyadenylation
signals, transcription terminators, internal ribosome entry sites
(IRES), ribosome binding sites (RBS) and the like, that provide for
the expression of the polynucleotide sequence in a host cell.
Expression control sequences interact specifically with cellular
proteins involved in transcription (Maniatis et al., Science, 236:
1237-1245 (1987)). Exemplary expression control sequences are
described in, for example, Goeddel, Gene Expression Technology:
Methods in Enzymology, Vol. 185, Academic Press, San Diego, Calif.
(1990).
[0074] In the methods of the invention, an expression control
sequence is operably linked to a polynucleotide sequence. By
"operably linked" is meant that a polynucleotide sequence and an
expression control sequence(s) are connected in such a way as to
permit gene expression when the appropriate molecules (e.g.,
transcriptional activator proteins) are bound to the expression
control sequence(s). Operably linked promoters are located upstream
of the selected polynucleotide sequence in terms of the direction
of transcription and translation. Operably linked enhancers can be
located upstream, within, or downstream of the selected
polynucleotide.
[0075] In some embodiments, the polynucleotide sequence is provided
to the host cell by way of a recombinant vector, which comprises a
promoter operably linked to the polynucleotide sequence. In certain
embodiments, the promoter is a developmentally-regulated, an
organelle-specific, a tissue-specific, an inducible, a
constitutive, or a cell-specific promoter.
[0076] As used herein, the term "vector" refers to a nucleic acid
molecule capable of transporting another nucleic acid, i.e., a
polynucleotide sequence, to which it has been linked. One type of
useful vector is an episome (i.e., a nucleic acid capable of
extra-chromosomal replication). Useful vectors are those capable of
autonomous replication and/or expression of nucleic acids to which
they are linked. Vectors capable of directing the expression of
genes to which they are operatively linked are referred to herein
as "expression vectors." In general, expression vectors of utility
in recombinant DNA techniques are often in the form of "plasmids,"
which refer generally to circular double stranded DNA loops that,
in their vector form, are not bound to the chromosome. The terms
"plasmid" and "vector" are used interchangeably herein, inasmuch as
a plasmid is the most commonly used form of vector. However, also
included are such other forms of expression vectors that serve
equivalent functions and that become known in the art subsequently
hereto.
[0077] The term "regulatory sequences" as used herein typically
refers to a sequence of bases in DNA, operably-linked to DNA
sequences encoding a protein that ultimately controls the
expression of the protein. Examples of regulatory sequences
include, but are not limited to, RNA promoter sequences,
transcription factor binding sequences, transcription termination
sequences, modulators of transcription (such as enhancer elements),
nucleotide sequences that affect RNA stability, and translational
regulatory sequences (such as, ribosome binding sites (e.g.,
Shine-Dalgarno sequences in prokaryotes or Kozak sequences in
eukaryotes), initiation codons, termination codons).
[0078] As used herein, the phrase "the expression of said
nucleotide sequence is modified relative to the wild type
nucleotide sequence," means an increase or decrease in the level of
expression and/or activity of an endogenous nucleotide sequence or
the expression and/or activity of a heterologous or non-native
polypeptide-encoding nucleotide sequence.
[0079] As used herein, the term "express" with respect to a
polynucleotide is to cause it to function. A polynucleotide which
encodes a polypeptide (or protein) will, when expressed, be
transcribed and translated to produce that polypeptide (or
protein). As used herein, the term "overexpress" means to express
or cause to be expressed a polynucleotide or polypeptide in a cell
at a greater concentration than is normally expressed in a
corresponding wild-type cell under the same conditions.
[0080] In some embodiments, the recombinant vector comprises at
least one sequence selected from the group consisting of (a) an
expression control sequence operatively coupled to the
polynucleotide sequence; (b) a selection marker operatively coupled
to the polynucleotide sequence; (c) a marker sequence operatively
coupled to the polynucleotide sequence; (d) a purification moiety
operatively coupled to the polynucleotide sequence; (e) a secretion
sequence operatively coupled to the polynucleotide sequence; and
(f) a targeting sequence operatively coupled to the polynucleotide
sequence.
[0081] The expression vectors described herein include a
polynucleotide sequence described herein in a form suitable for
expression of the polynucleotide sequence in a host cell. It will
be appreciated by those skilled in the art that the design of the
expression vector can depend on such factors as the choice of the
host cell to be transformed, the level of expression of polypeptide
desired, etc. The expression vectors described herein can be
introduced into host cells to produce polypeptides, including
fusion polypeptides, encoded by the polynucleotide sequences as
described herein.
[0082] Expression of genes encoding polypeptides in prokaryotes,
for example, E. coli, is most often carried out with vectors
containing constitutive or inducible promoters directing the
expression of either fusion or non-fusion polypeptides. Fusion
vectors add a number of amino acids to a polypeptide encoded
therein, usually to the amino- or carboxy-terminus of the
recombinant polypeptide. Such fusion vectors typically serve one or
more of the following three purposes: (1) to increase expression of
the recombinant polypeptide; (2) to increase the solubility of the
recombinant polypeptide; and (3) to aid in the purification of the
recombinant polypeptide by acting as a ligand in affinity
purification. Often, in fusion expression vectors, a proteolytic
cleavage site is introduced at the junction of the fusion moiety
and the recombinant polypeptide. This enables separation of the
recombinant polypeptide from the fusion moiety after purification
of the fusion polypeptide. Examples of such enzymes, and their
cognate recognition sequences, include Factor Xa, thrombin, and
enterokinase. Exemplary fusion expression vectors include pGEX
(Pharmacia Biotech, Inc., Piscataway, N.J.; Smith et al., Gene, 67:
31-40 (1988)), pMAL (New England Biolabs, Beverly, Mass.), and
pRITS (Pharmacia Biotech, Inc., Piscataway, N.J.), which fuse
glutathione S-transferase (GST), maltose E binding protein, or
protein A, respectively, to the target recombinant polypeptide.
[0083] Suitable expression systems for both prokaryotic and
eukaryotic cells are well known in the art; see, e.g., Sambrook et
al., "Molecular Cloning: A Laboratory Manual," second edition, Cold
Spring Harbor Laboratory (1989). Examples of inducible, non-fusion
E. coli expression vectors include pTrc (Amann et al., Gene, 69:
301-315 (1988)) and PET 11d (Studier et al., Gene Expression
Technology: Methods in Enzymology 185, Academic Press, San Diego,
Calif., pp. 60-89 (1990)). In certain embodiments, a polynucleotide
sequence of the invention is operably linked to a promoter derived
from bacteriophage T5. Examples of vectors for expression in yeast
include pYepSec1 (Baldari et al., EMBO J., 6: 229-234 (1987)), pMFa
(Kurjan et al., Cell, 30: 933-943 (1982)), pJRY88 (Schultz et al.,
Gene, 54: 113-123 (1987)), pYES2 (Invitrogen Corp., San Diego,
Calif.), and picZ (Invitrogen Corp., San Diego, Calif.).
Baculovirus vectors available for expression of proteins in
cultured insect cells (e.g., Sf9 cells) include, for example, the
pAc series (Smith et al., Mol. Cell Biol., 3: 2156-2165 (1983)) and
the pVL series (Lucklow et al., Virology, 170: 31-39 (1989)).
Examples of mammalian expression vectors include pCDM8 (Seed,
Nature, 329: 840 (1987)) and pMT2PC (Kaufman et al., EMBO J., 6:
187-195 (1987)).
[0084] Vectors can be introduced into prokaryotic or eukaryotic
cells via conventional transformation or transfection techniques.
As used herein, the terms "transformation" and "transfection" refer
to a variety of art-recognized techniques for introducing foreign
nucleic acid (e.g., DNA) into a host cell, including calcium
phosphate or calcium chloride co-precipitation,
DEAE-dextran-mediated transfection, lipofection, or
electroporation. Suitable methods for transforming or transfecting
host cells can be found in, for example, Sambrook et al.
(supra).
[0085] For stable transformation of bacterial cells, it is known
that, depending upon the expression vector and transformation
technique used, only a small fraction of cells will take-up and
replicate the expression vector. In order to identify and select
these transformants, a gene that encodes a selectable marker (e.g.,
resistance to an antibiotic) can be introduced into the host cells
along with the gene of interest. Selectable markers include those
that confer resistance to drugs such as, but not limited to,
ampicillin, kanamycin, chloramphenicol, or tetracycline. Nucleic
acids encoding a selectable marker can be introduced into a host
cell on the same vector as that encoding a polypeptide described
herein or can be introduced on a separate vector. Cells stably
transformed with the introduced nucleic acid can be identified by
growth in the presence of an appropriate selection drug.
[0086] Similarly, for stable transfection of mammalian cells, it is
known that, depending upon the expression vector and transfection
technique used, only a small fraction of cells may integrate the
foreign DNA into their genome. In order to identify and select
these integrants, a gene that encodes a selectable marker (e.g.,
resistance to an antibiotic) can be introduced into the host cells
along with the gene of interest. Preferred selectable markers
include those which confer resistance to drugs, such as G418,
hygromycin, and methotrexate. Nucleic acids encoding a selectable
marker can be introduced into a host cell on the same vector as
that encoding a polypeptide described herein or can be introduced
on a separate vector. Cells stably transfected with the introduced
nucleic acid can be identified by growth in the presence of an
appropriate selection drug.
[0087] In some embodiments, the FadR polypeptide has the amino acid
sequence of SEQ ID NO: 1.
[0088] In other embodiments, the FadR polypeptide is encoded by a
fadR gene obtained from microorganisms of the genera Escherichia,
Salmonella, Citrobacter, Enterobacter, Klebsiella, Cronobacter,
Yersinia, Serratia, Erwinia, Pectobacterium, Photorhabdus,
Edwardsiella, Shewanella, or Vibrio.
[0089] In other embodiments, the FadR polypeptide is a homologue of
FadR having an amino acid sequence that is at least 80%, at least
85%, at least 90%, at least 91%, at least 92%, at least 93%, at
least 94%, at least 95%, at least 96%, at least 97%, at least 98%,
or at least 99% identical to the amino acid sequence of SEQ ID NO:
1.
[0090] The identity of a FadR polypeptide having at least 80%
identity to the amino acid sequence of SEQ ID NO: 1 is not
particularly limited, and one of ordinary skill in the art can
readily identify homologues of E. coli MG1655 derived-FadR using
the methods described herein as well as methods known in the
art.
[0091] As used herein, the terms "homolog," and "homologous" refer
to a polynucleotide or a polypeptide comprising a sequence that is
at least about 50% identical to the corresponding polynucleotide or
polypeptide sequence. Preferably homologous polynucleotides or
polypeptides have polynucleotide sequences or amino acid sequences
that have at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,
88%, 89%, 90%, 91%, 2%, 93%, 94%, 95%, 96%, 97%, 98% or at least
about 99% homology to the corresponding amino acid sequence or
polynucleotide sequence. As used herein the terms sequence
"homology" and sequence "identity" are used interchangeably.
[0092] Briefly, calculations of "homology" between two sequences
can be performed as follows. The sequences are aligned for optimal
comparison purposes (e.g., gaps can be introduced in one or both of
a first and a second amino acid or nucleic acid sequence for
optimal alignment and non-homologous sequences can be disregarded
for comparison purposes. The amino acid residues or nucleotides at
corresponding amino acid positions or nucleotide positions of the
first and second sequences are then compared. When a position in
the first sequence is occupied by the same amino acid residue or
nucleotide as the corresponding position in the second sequence,
then the molecules are identical at that position (as used herein,
amino acid or nucleic acid "identity" is equivalent to amino acid
or nucleic acid "homology"). The percent identity between the two
sequences is a function of the number of identical positions shared
by the sequences, taking into account the number of gaps and the
length of each gap, which need to be introduced for optimal
alignment of the two sequences.
[0093] The comparison of sequences and determination of percent
homology between two sequences can be accomplished using a
mathematical algorithm, such as BLAST (Altschul et al., J. Mol.
Biol., 215(3): 403-410 (1990)). The percent homology between two
amino acid sequences also can be determined using the Needleman and
Wunsch algorithm that has been incorporated into the GAP program in
the GCG software package, using either a Blossum 62 matrix or a
PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a
length weight of 1, 2, 3, 4, 5, or 6 (Needleman and Wunsch, J. Mol.
Biol., 48: 444-453 (1970)). The percent homology between two
nucleotide sequences also can be determined using the GAP program
in the GCG software package, using a NWSgapdna.CMP matrix and a gap
weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4,
5, or 6. One of ordinary skill in the art can perform initial
homology calculations and adjust the algorithm parameters
accordingly. A preferred set of parameters (and the one that should
be used if a practitioner is uncertain about which parameters
should be applied to determine if a molecule is within a homology
limitation of the claims) are a Blossum 62 scoring matrix with a
gap penalty of 12, a gap extend penalty of 4, and a frameshift gap
penalty of 5. Additional methods of sequence alignment are known in
the biotechnology arts (see, e.g., Rosenberg, BMC Bioinformatics,
6: 278 (2005); Altschul et al., FEBS J., 272(20): 5101-5109
(2005)).
[0094] As used herein, the term "hybridizes under low stringency,
medium stringency, high stringency, or very high stringency
conditions" describes conditions for hybridization and washing.
Guidance for performing hybridization reactions can be found in
Current Protocols in Molecular Biology, John Wiley & Sons, N.Y.
(1989), 6.3.1-6.3.6. Aqueous and nonaqueous methods are described
in that reference and either method can be used. Specific
hybridization conditions referred to herein are as follows: 1) low
stringency hybridization conditions in 6.times. sodium
chloride/sodium citrate (SSC) at about 45.degree. C., followed by
two washes in 0.2.times.SSC, 0.1% SDS at least at 50.degree. C.
(the temperature of the washes can be increased to 55.degree. C.
for low stringency conditions); 2) medium stringency hybridization
conditions in 6.times.SSC at about 45.degree. C., followed by one
or more washes in 0.2.times.SSC, 0.1% SDS at 60.degree. C.; 3) high
stringency hybridization conditions in 6.times.SSC at about
45.degree. C., followed by one or more washes in 0.2..times.SSC,
0.1% SDS at 65.degree. C.; and preferably 4) very high stringency
hybridization conditions are 0.5M sodium phosphate, 7% SDS at
65.degree. C., followed by one or more washes at 0.2.times.SSC, 1%
SDS at 65.degree. C. Very high stringency conditions (4) are the
preferred conditions unless otherwise specified.
[0095] In some embodiments, the polypeptide is a fragment of any of
the polypeptides described herein. The term "fragment" refers to a
shorter portion of a full-length polypeptide or protein ranging in
size from four amino acid residues to the entire amino acid
sequence minus one amino acid residue. In certain embodiments of
the invention, a fragment refers to the entire amino acid sequence
of a domain of a polypeptide or protein (e.g., a substrate binding
domain or a catalytic domain).
[0096] An "endogenous" polypeptide refers to a polypeptide encoded
by the genome of the parental microbial cell (also termed "host
cell") from which the recombinant cell is engineered (or
"derived").
[0097] An "exogenous" polypeptide refers to a polypeptide which is
not encoded by the genome of the parental microbial cell. A variant
(i.e., mutant) polypeptide is an example of an exogenous
polypeptide.
[0098] The term "heterologous" as used herein typically refers to a
nucleotide sequence or a protein not naturally present in an
organism. For example, a polynucleotide sequence endogenous to a
plant can be introduced into a host cell by recombinant methods,
and the plant polynucleotide is then a heterologous polynucleotide
in a recombinant host cell.
[0099] In some embodiments, the polypeptide is a mutant or a
variant of any of the polypeptides described herein. The terms
"mutant" and "variant" as used herein refer to a polypeptide having
an amino acid sequence that differs from a wild-type polypeptide by
at least one amino acid. For example, the mutant can comprise one
or more of the following conservative amino acid substitutions:
replacement of an aliphatic amino acid, such as alanine, valine,
leucine, and isoleucine, with another aliphatic amino acid;
replacement of a serine with a threonine; replacement of a
threonine with a serine; replacement of an acidic residue, such as
aspartic acid and glutamic acid, with another acidic residue;
replacement of a residue bearing an amide group, such as asparagine
and glutamine, with another residue bearing an amide group;
exchange of a basic residue, such as lysine and arginine, with
another basic residue; and replacement of an aromatic residue, such
as phenylalanine and tyrosine, with another aromatic residue. In
some embodiments, the mutant polypeptide has about 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, or more
amino acid substitutions, additions, insertions, or deletions.
[0100] As used herein, the term "mutagenesis" refers to a process
by which the genetic information of an organism is changed in a
stable manner Mutagenesis of a protein coding nucleic acid sequence
produces a mutant protein. Mutagenesis also refers to changes in
non-coding nucleic acid sequences that result in modified protein
activity.
[0101] As used herein, the term "gene" refers to nucleic acid
sequences encoding either an RNA product or a protein product, as
well as operably-linked nucleic acid sequences affecting the
expression of the RNA or protein (e.g., such sequences include but
are not limited to promoter or enhancer sequences) or
operably-linked nucleic acid sequences encoding sequences that
affect the expression of the RNA or protein (e.g., such sequences
include but are not limited to ribosome binding sites or
translational control sequences).
[0102] In certain embodiments, the FadR polypeptide comprises a
mutation at an amino acid residue corresponding to amino acid 219
of SEQ ID NO: 1. In certain embodiments, the mutation results in a
substitution of the amino acid residue corresponding to amino acid
219 of SEQ ID NO: 1 with an asparagine residue. The FadR(S219N)
mutation has been previously described (Raman et al., J. Biol.
Chem., 270: 1092-1097 (1995)).
[0103] Preferred fragments or mutants of a polypeptide retain some
or all of the biological function (e.g., enzymatic activity) of the
corresponding wild-type polypeptide. In some embodiments, the
fragment or mutant retains at least 75%, at least 80%, at least
90%, at least 95%, or at least 98% or more of the biological
function of the corresponding wild-type polypeptide. In other
embodiments, the fragment or mutant retains about 100% of the
biological function of the corresponding wild-type polypeptide.
Guidance in determining which amino acid residues may be
substituted, inserted, or deleted without affecting biological
activity may be found using computer programs well known in the
art, for example, LASERGENE.TM. software (DNASTAR, Inc., Madison,
Wis.).
[0104] In yet other embodiments, a fragment or mutant exhibits
increased biological function as compared to a corresponding
wild-type polypeptide. For example, a fragment or mutant may
display at least a 10%, at least a 25%, at least a 50%, at least a
75%, or at least a 90% improvement in enzymatic activity as
compared to the corresponding wild-type polypeptide. In other
embodiments, the fragment or mutant displays at least 100% (e.g.,
at least 200%, or at least 500%) improvement in enzymatic activity
as compared to the corresponding wild-type polypeptide.
[0105] It is understood that the polypeptides described herein may
have additional conservative or non-essential amino acid
substitutions, which do not have a substantial effect on the
polypeptide function. Whether or not a particular substitution will
be tolerated (i.e., will not adversely affect desired biological
function, such as DNA binding or enzyme activity) can be determined
as described in Bowie et al. (Science, 247: 1306-1310 (1990)).
[0106] A "conservative amino acid substitution" is one in which the
amino acid residue is replaced with an amino acid residue having a
similar side chain. Families of amino acid residues having similar
side chains have been defined in the art. These families include
amino acids with basic side chains (e.g., lysine, arginine,
histidine), acidic side chains (e.g., aspartic acid, glutamic
acid), uncharged polar side chains (e.g., glycine, asparagine,
glutamine, serine, threonine, tyrosine, cysteine), nonpolar side
chains (e.g., alanine, valine, leucine, isoleucine, proline,
phenylalanine, methionine, tryptophan), beta-branched side chains
(e.g., threonine, valine, isoleucine), and aromatic side chains
(e.g., tyrosine, phenylalanine, tryptophan, histidine).
[0107] Variants can be naturally occurring or created in vitro. In
particular, such variants can be created using genetic engineering
techniques, such as site directed mutagenesis, random chemical
mutagenesis, Exonuclease III deletion procedures, or standard
cloning techniques. Alternatively, such variants, fragments,
analogs, or derivatives can be created using chemical synthesis or
modification procedures.
[0108] Methods of making variants are well known in the art. These
include procedures in which nucleic acid sequences obtained from
natural isolates are modified to generate nucleic acids that encode
polypeptides having characteristics that enhance their value in
industrial or laboratory applications. In such procedures, a large
number of variant sequences having one or more nucleotide
differences with respect to the sequence obtained from the natural
isolate are generated and characterized. Typically, these
nucleotide differences result in amino acid changes with respect to
the polypeptides encoded by the nucleic acids from the natural
isolates.
[0109] For example, variants can be prepared by using random and
site-directed mutagenesis (see, e.g., Arnold, Curr. Opin. Biotech.,
4: 450-455 (1993)). Random mutagenesis can be achieved using error
prone PCR (see, e.g., Leung et al., Technique, 1: 11-15 (1989); and
Caldwell et al., PCR Methods Applic., 2: 28-33 (1992)).
Site-directed mutagenesis can be achieved using
oligonucleotide-directed mutagenesis to generate site-specific
mutations in any cloned DNA of interest (see, e.g., Reidhaar-Olson
et al., Science, 241: 53-57 (1988)). Other methods for generating
variants include, e.g., assembly PCR (see, e.g., U.S. Pat. No.
5,965,408), sexual PCR mutagenesis (see, e.g., Stemmer, Proc. Natl.
Acad. Sci., U.S.A., 91: 10747-10751 (1994) and U.S. Pat. Nos.
5,965,408 and 5,939,250), recursive ensemble mutagenesis (see,
e.g., Arkin et al., Proc. Natl. Acad. Sci., U.S.A., 89: 7811-7815
(1992)), and exponential ensemble mutagenesis (see, e.g., Delegrave
et al., Biotech. Res, 11: 1548-1552 (1993).
[0110] Variants can also be created by in vivo mutagenesis. In some
embodiments, random mutations in a nucleic acid sequence are
generated by propagating the sequence in a bacterial strain, such
as an E. coli strain, which carries mutations in one or more of the
DNA repair pathways. Such "mutator" strains have a higher random
mutation rate than that of a wild-type strain. Propagating a DNA
sequence (e.g., a polynucleotide sequence encoding a PPTase) in one
of these strains will eventually generate random mutations within
the DNA. Mutator strains suitable for use for in vivo mutagenesis
are described in, for example, International Patent Application
Publication No. WO 1991/016427.
[0111] Variants can also be generated using cassette mutagenesis.
In cassette mutagenesis, a small region of a double-stranded DNA
molecule is replaced with a synthetic oligonucleotide "cassette"
that differs from the native sequence. The oligonucleotide often
contains a completely and/or partially randomized native
sequence.
[0112] As used herein, a "host cell" is a cell used to produce a
product described herein (e.g., a fatty aldehyde or a fatty
alcohol). In any of the aspects of the invention described herein,
the host cell can be selected from the group consisting of a
mammalian cell, plant cell, insect cell, fungus cell (e.g., a
filamentous fungus cell or a yeast cell), and bacterial cell. A
host cell is referred to as an "engineered host cell" or a
"recombinant host cell" if the expression of one or more
polynucleotides or polypeptides in the host cell are altered or
modified as compared to their expression in a corresponding
wild-type host cell under the same conditions.
[0113] In some embodiments, the host cell is a Gram-positive
bacterial cell. In other embodiments, the host cell is a
Gram-negative bacterial cell.
[0114] In some embodiments, the host cell is selected from the
genus Escherichia, Bacillus, Lactobacillus, Rhodococcus,
Pseudomonas, Aspergillus, Trichoderma, Neurospora, Fusarium,
Humicola, Rhizomucor, Kluyveromyces, Pichia, Mucor, Myceliophtora,
Penicillium, Phanerochaete, Pleurotus, Trametes, Chrysosporium,
Saccharomyces, Stenotrophamonas, Schizosaccharomyces, Yarrowia, or
Streptomyces.
[0115] In other embodiments, the host cell is a Bacillus lentus
cell, a Bacillus brevis cell, a Bacillus stearothermophilus cell, a
Bacillus lichen formis cell, a Bacillus alkalophilus cell, a
Bacillus coagulans cell, a Bacillus circulars cell, a Bacillus
pumilis cell, a Bacillus thuringiensis cell, a Bacillus clausii
cell, a Bacillus megaterium cell, a Bacillus subtilis cell, or a
Bacillus amyloliquefaciens cell.
[0116] In other embodiments, the host cell is a Trichoderma
koningii cell, a Trichoderma viride cell, a Trichoderma reesei
cell, a Trichoderma longibrachiatum cell, an Aspergillus awamori
cell, an Aspergillus fumigates cell, an Aspergillus foetidus cell,
an Aspergillus nidulans cell, an Aspergillus niger cell, an
Aspergillus oryzae cell, a Humicola insolens cell, a Humicola
lanuginose cell, a Rhodococcus opacus cell, a Rhizomucor miehei
cell, or a Mucor michei cell.
[0117] In yet other embodiments, the host cell is a Streptomyces
lividans cell or a Streptomyces murinus cell.
[0118] In yet other embodiments, the host cell is an Actinomycetes
cell.
[0119] In some embodiments, the host cell is a Saccharomyces
cerevisiae cell. In some embodiments, the host cell is a
Saccharomyces cerevisiae cell.
[0120] In still other embodiments, the host cell is a CHO cell, a
COS cell, a VERO cell, a BHK cell, a HeLa cell, a Cvl cell, an MDCK
cell, a 293 cell, a 3T3 cell, or a PC12 cell.
[0121] In other embodiments, the host cell is a cell from a
eukaryotic plant, algae, cyanobacterium, green-sulfur bacterium,
green non-sulfur bacterium, purple sulfur bacterium, purple
non-sulfur bacterium, extremophile, yeast, fungus, an engineered
organism thereof, or a synthetic organism. In some embodiments, the
host cell is light-dependent or fixes carbon. In some embodiments,
the host cell is light-dependent or fixes carbon. In some
embodiments, the host cell has autotrophic activity. In some
embodiments, the host cell has photoautotrophic activity, such as
in the presence of light. In some embodiments, the host cell is
heterotrophic or mixotrophic in the absence of light. In certain
embodiments, the host cell is a cell from Avabidopsis thaliana,
Panicum virgatum, Miscanthus giganteus, Zea mays, Botryococcuse
braunii, Chlamydomonas reinhardtii, Dunaliela saliva, Synechococcus
Sp. PCC 7002, Synechococcus Sp. PCC 7942, Synechocystis Sp. PCC
6803, Thermosynechococcus elongates BP-1, Chlorobium tepidum,
Chlorojlexus auranticus, Chromatiumm vinosum, Rhodospirillum
rubrum, Rhodobacter capsulatus, Rhodopseudomonas palusris,
Clostridium ljungdahlii, Clostridiuthermocellum, Penicillium
chrysogenum, Pichia pastoris, Saccharomyces cerevisiae,
Schizosaccharomyces pombe, Pseudomonasjluorescens, or Zymomonas
mobilis.
[0122] In certain preferred embodiments, the host cell is an E.
coli cell. In some embodiments, the E. coli cell is a strain B, a
strain C, a strain K, or a strain W E. coli cell.
[0123] In other embodiments, the host cell is a Pantoea citrea
cell.
[0124] As used herein, the term "conditions permissive for the
production" means any conditions that allow a host cell to produce
a desired product, such as a fatty acid or a fatty acid derivative.
Similarly, the term "conditions in which the polynucleotide
sequence of a vector is expressed" means any conditions that allow
a host cell to synthesize a polypeptide. Suitable conditions
include, for example, fermentation conditions. Fermentation
conditions can comprise many parameters, such as temperature
ranges, levels of aeration, and media composition. Each of these
conditions, individually and in combination, allows the host cell
to grow. Exemplary culture media include broths or gels. Generally,
the medium includes a carbon source that can be metabolized by a
host cell directly. In addition, enzymes can be used in the medium
to facilitate the mobilization (e.g., the depolymerization of
starch or cellulose to fermentable sugars) and subsequent
metabolism of the carbon source.
[0125] As used herein, the phrase "carbon source" refers to a
substrate or compound suitable to be used as a source of carbon for
prokaryotic or simple eukaryotic cell growth. Carbon sources can be
in various forms, including, but not limited to polymers,
carbohydrates, acids, alcohols, aldehydes, ketones, amino acids,
peptides, and gases (e.g., CO and CO.sub.2). Exemplary carbon
sources include, but are not limited to, monosaccharides, such as
glucose, fructose, mannose, galactose, xylose, and arabinose;
oligosaccharides, such as fructo-oligosaccharide and
galacto-oligosaccharide; polysaccharides such as starch, cellulose,
pectin, and xylan; disaccharides, such as sucrose, maltose, and
turanose; cellulosic material and variants such as methyl cellulose
and sodium carboxymethyl cellulose; saturated or unsaturated fatty
acid esters, succinate, lactate, and acetate; alcohols, such as
ethanol, methanol, and glycerol, or mixtures thereof. The carbon
source can also be a product of photosynthesis, such as glucose. In
certain preferred embodiments, the carbon source is biomass. In
other preferred embodiments, the carbon source is glucose. In still
other preferred embodiments, the carbon source is sucrose.
[0126] As used herein, the term "biomass" refers to any biological
material from which a carbon source is derived. In some
embodiments, a biomass is processed into a carbon source, which is
suitable for bioconversion. In other embodiments, the biomass does
not require further processing into a carbon source. The carbon
source can be converted into a biofuel. An exemplary source of
biomass is plant matter or vegetation, such as corn, sugar cane, or
switchgrass. Another exemplary source of biomass is metabolic waste
products, such as animal matter (e.g., cow manure). Further
exemplary sources of biomass include algae and other marine plants.
Biomass also includes waste products from industry, agriculture,
forestry, and households, including, but not limited to,
fermentation waste, ensilage, straw, lumber, sewage, garbage,
cellulosic urban waste, and food leftovers. The term "biomass" also
can refer to sources of carbon, such as carbohydrates (e.g.,
monosaccharides, disaccharides, or polysaccharides).
[0127] As used herein, the term "clone" typically refers to a cell
or group of cells descended from and essentially genetically
identical to a single common ancestor, for example, the bacteria of
a cloned bacterial colony arose from a single bacterial cell.
[0128] As used herein, the term "culture" typical refers to a
liquid media comprising viable cells. In one embodiment, a culture
comprises cells reproducing in a predetermined culture media under
controlled conditions, for example, a culture of recombinant host
cells grown in liquid media comprising a selected carbon source and
nitrogen.
[0129] "Culturing" or "cultivation" refers to growing a population
of recombinant host cells under suitable conditions in a liquid or
solid medium. In particular embodiments, culturing refers to the
fermentative bioconversion of a substrate to an end-product.
Culturing media are well known and individual components of such
culture media are available from commercial sources, e.g., under
the Difco.TM. and BBL.TM. trademarks. In one non-limiting example,
the aqueous nutrient medium is a "rich medium" comprising complex
sources of nitrogen, salts, and carbon, such as YP medium,
comprising 10 g/L of peptone and 10 g/L yeast extract of such a
medium.
[0130] To determine if conditions are sufficient to allow
production of a product or expression of a polypeptide, a host cell
can be cultured, for example, for about 4, 8, 12, 24, 36, 48, 72,
or more hours. During and/or after culturing, samples can be
obtained and analyzed to determine if the conditions allow
production or expression. For example, the host cells in the sample
or the medium in which the host cells were grown can be tested for
the presence of a desired product. When testing for the presence of
a fatty acid or fatty acid derivative, assays, such as, but not
limited to, mass spectrometry (MS), thin layer chromatography
(TLC), high-performance liquid chromatography (HPLC), liquid
chromatography (LC), GC coupled with a flame ionization detector
(FID), GC-MS, and liquid chromatography-mass spectrometry (LC-MS)
can be used. When testing for the expression of a polypeptide,
techniques such as, but not limited to, Western blotting and dot
blotting may be used.
[0131] In the compositions and methods of the invention, the
production and isolation of fatty acids and fatty acid derivatives
can be enhanced by optimizing fermentation conditions. In some
embodiments, fermentation conditions are optimized to increase the
percentage of the carbon source that is converted to hydrocarbon
products. During normal cellular lifecycles, carbon is used in
cellular functions, such as producing lipids, saccharides,
proteins, organic acids, and nucleic acids. Reducing the amount of
carbon necessary for growth-related activities can increase the
efficiency of carbon source conversion to product. This can be
achieved by, for example, first growing host cells to a desired
density (for example, a density achieved at the peak of the log
phase of growth). At such a point, replication checkpoint genes can
be harnessed to stop the growth of cells. Specifically, quorum
sensing mechanisms (reviewed in Camilli et al., Science 311: 1113
(2006); Venturi, FEMS Microbiol. Rev., 30: 274-291 (2006); and
Reading et al., FEMS Microbiol. Lett., 254: 1-11 (2006)) can be
used to activate checkpoint genes, such as p53, p21, or other
checkpoint genes.
[0132] Genes that can be activated to stop cell replication and
growth in E. coli include umuDC genes. The overexpression of umuDC
genes stops the progression from stationary phase to exponential
growth (Murli et al., J. Bacteriol., 182: 1127-1135 (2000)). UmuC
is a DNA polymerase that can carry out translesion synthesis over
non-coding lesions which commonly result from ultraviolet (UV) and
chemical mutagenesis. The umuDC gene products are involved in the
process of translesion synthesis and also serve as a DNA sequence
damage checkpoint. The umuDC gene products include UmuC, UmuD,
umuD', UmuD'.sub.2C, UmuD'.sub.2, and UmuD.sub.2. Simultaneously,
product-producing genes can be activated, thereby minimizing the
need for replication and maintenance pathways to be used while a
fatty aldehyde or fatty alcohol is being made. Host cells can also
be engineered to express umuC and umuD from E. coli in pBAD24 under
the prpBCDE promoter system through de novo synthesis of this gene
with the appropriate end-product production genes.
[0133] The host cell can be additionally engineered to express a
recombinant cellulosome, which can allow the host cell to use
cellulosic material as a carbon source. Exemplary cellulosomes
suitable for use in the methods of the invention include, e.g, the
cellulosomes described in International Patent Application
Publication WO 2008/100251. The host cell also can be engineered to
assimilate carbon efficiently and use cellulosic materials as
carbon sources according to methods described in U.S. Pat. Nos.
5,000,000; 5,028,539; 5,424,202; 5,482,846; and 5,602,030. In
addition, the host cell can be engineered to express an invertase
so that sucrose can be used as a carbon source.
[0134] In some embodiments of the fermentation methods of the
invention, the fermentation chamber encloses a fermentation that is
undergoing a continuous reduction, thereby creating a stable
reductive environment. The electron balance can be maintained by
the release of carbon dioxide (in gaseous form). Efforts to augment
the NAD/H and NADP/H balance can also facilitate in stabilizing the
electron balance. The availability of intracellular NADPH can also
be enhanced by engineering the host cell to express an NADH:NADPH
transhydrogenase. The expression of one or more NADH:NADPH
transhydrogenases converts the NADH produced in glycolysis to
NADPH, which can enhance the production of fatty aldehydes and
fatty alcohols.
[0135] For small scale production, the engineered host cells can be
grown in batches of, for example, about 100 mL, 500 mL, 1 L, 2 L, 5
L, or 10 L; fermented; and induced to express a desired
polynucleotide sequence, such as a polynucleotide sequence encoding
a PPTase. For large scale production, the engineered host cells can
be grown in batches of about 10 L, 100 L, 1000 L, 10,000 L, 100,000
L, 1,000,000 L or larger; fermented; and induced to express a
desired polynucleotide sequence.
[0136] The fatty acids and derivatives thereof produced by the
methods of invention generally are isolated from the host cell. The
term "isolated" as used herein with respect to products, such as
fatty acids and derivatives thereof, refers to products that are
separated from cellular components, cell culture media, or chemical
or synthetic precursors. The fatty acids and derivatives thereof
produced by the methods described herein can be relatively
immiscible in the fermentation broth, as well as in the cytoplasm.
Therefore, the fatty acids and derivatives thereof can collect in
an organic phase either intracellularly or extracellularly. The
collection of the products in the organic phase can lessen the
impact of the fatty acid or fatty acid derivative on cellular
function and can allow the host cell to produce more product.
[0137] In some embodiments, the fatty acids and fatty acid
derivatives produced by the methods of invention are purified. As
used herein, the term "purify," "purified," or "purification" means
the removal or isolation of a molecule from its environment by, for
example, isolation or separation. "Substantially purified"
molecules are at least about 60% free (e.g., at least about 70%
free, at least about 75% free, at least about 85% free, at least
about 90% free, at least about 95% free, at least about 97% free,
at least about 99% free) from other components with which they are
associated. As used herein, these terms also refer to the removal
of contaminants from a sample. For example, the removal of
contaminants can result in an increase in the percentage of a fatty
aldehyde or a fatty alcohol in a sample. For example, when a fatty
aldehyde or a fatty alcohol is produced in a host cell, the fatty
aldehyde or fatty alcohol can be purified by the removal of host
cell proteins. After purification, the percentage of a fatty acid
or derivative thereof in the sample is increased.
[0138] As used herein, the terms "purify," "purified," and
"purification" are relative terms which do not require absolute
purity. Thus, for example, when a fatty acid or derivative thereof
is produced in host cells, a purified fatty acid or derivative
thereof is a fatty acid or derivative thereof that is substantially
separated from other cellular components (e.g., nucleic acids,
polypeptides, lipids, carbohydrates, or other hydrocarbons).
[0139] Additionally, a purified fatty acid preparation or a
purified fatty acid derivative preparation is a fatty acid
preparation or a fatty acid derivative preparation in which the
fatty acid or derivative thereof is substantially free from
contaminants, such as those that might be present following
fermentation. In some embodiments, a fatty acid or derivative
thereof is purified when at least about 50% by weight of a sample
is composed of the fatty acid or fatty acid derivative. In other
embodiments, a fatty acid or derivative thereof is purified when at
least about 60%, e.g., at least about 70%, at least about 80%, at
least about 85%, at least about 90%, at least about 92% or more by
weight of a sample is composed of the fatty acid or derivative
thereof. Alternatively, or in addition, a fatty acid or derivative
thereof is purified when less than about 100%, e.g., less than
about 99%, less than about 98%, less than about 95%, less than
about 90%, or less than about 80% by weight of a sample is composed
of the fatty acid or derivative thereof. Thus, a purified fatty
acid or derivative thereof can have a purity level bounded by any
two of the above endpoints. For example, a fatty acid or derivative
thereof can be purified when at least about 80%-95%, at least about
85%-99%, or at least about 90%-98% of a sample is composed of the
fatty acid or fatty acid derivative.
[0140] The fatty acid or derivative thereof may be present in the
extracellular environment, or it may be isolated from the
extracellular environment of the host cell. In certain embodiments,
a fatty acid or derivative thereof is secreted from the host cell.
In other embodiments, a fatty acid or derivative thereof is
transported into the extracellular environment. In yet other
embodiments, the fatty acid or derivative thereof is passively
transported into the extracellular environment. A fatty acid or
derivative thereof can be isolated from a host cell using methods
known in the art, such as those disclosed in International Patent
Application Publications WO 2010/042664 and WO 2010/062480.
[0141] The methods described herein can result in the production of
homogeneous compounds wherein at least about 60%, at least about
70%, at least about 80%, at least about 90%, or at least about 95%,
of the fatty acids or fatty acid derivatives produced will have
carbon chain lengths that vary by less than 6 carbons, less than 5
carbons, less than 4 carbons, less than 3 carbons, or less than
about 2 carbons. Alternatively, or in addition, the methods
described herein can result in the production of homogeneous
compounds wherein less than about 98%, less than about 95%, less
than about 90%, less than about 80%, or less than about 70% of the
fatty acids or fatty acid derivatives produced will have carbon
chain lengths that vary by less than 6 carbons, less than 5
carbons, less than 4 carbons, less than 3 carbons, or less than
about 2 carbons. Thus, the fatty acids or fatty acid derivatives
can have a degree of homogeneity bounded by any two of the above
endpoints. For example, the fatty acid or fatty acid derivative can
have a degree of homogeneity wherein about 70%-95%, about 80%-98%,
or about 90%-95% of the fatty acids or fatty acid derivatives
produced will have carbon chain lengths that vary by less than 6
carbons, less than 5 carbons, less than 4 carbons, less than 3
carbons, or less than about 2 carbons. These compounds can also be
produced with a relatively uniform degree of saturation.
[0142] As a result of the methods of the present invention, one or
more of the titer, yield, or productivity of the fatty acid or
derivative thereof produced by the engineered host cell having an
altered level of expression of a FadR polypeptide is increased
relative to that of the corresponding wild-type host cell.
[0143] The term "titer" refers to the quantity of fatty acid or
fatty acid derivative produced per unit volume of host cell
culture. In any aspect of the compositions and methods described
herein, a fatty acid or a fatty acid derivative such as a terminal
olefin, a fatty aldehyde, a fatty alcohol, an alkane, a fatty
ester, a ketone or an internal olefins is produced at a titer of
about 25 mg/L, about 50 mg/L, about 75 mg/L, about 100 mg/L, about
125 mg/L, about 150 mg/L, about 175 mg/L, about 200 mg/L, about 225
mg/L, about 250 mg/L, about 275 mg/L, about 300 mg/L, about 325
mg/L, about 350 mg/L, about 375 mg/L, about 400 mg/L, about 425
mg/L, about 450 mg/L, about 475 mg/L, about 500 mg/L, about 525
mg/L, about 550 mg/L, about 575 mg/L, about 600 mg/L, about 625
mg/L, about 650 mg/L, about 675 mg/L, about 700 mg/L, about 725
mg/L, about 750 mg/L, about 775 mg/L, about 800 mg/L, about 825
mg/L, about 850 mg/L, about 875 mg/L, about 900 mg/L, about 925
mg/L, about 950 mg/L, about 975 mg/L, about 1000 g/L, about 1050
mg/L, about 1075 mg/L, about 1100 mg/L, about 1125 mg/L, about 1150
mg/L, about 1175 mg/L, about 1200 mg/L, about 1225 mg/L, about 1250
mg/L, about 1275 mg/L, about 1300 mg/L, about 1325 mg/L, about 1350
mg/L, about 1375 mg/L, about 1400 mg/L, about 1425 mg/L, about 1450
mg/L, about 1475 mg/L, about 1500 mg/L, about 1525 mg/L, about 1550
mg/L, about 1575 mg/L, about 1600 mg/L, about 1625 mg/L, about 1650
mg/L, about 1675 mg/L, about 1700 mg/L, about 1725 mg/L, about 1750
mg/L, about 1775 mg/L, about 1800 mg/L, about 1825 mg/L, about 1850
mg/L, about 1875 mg/L, about 1900 mg/L, about 1925 mg/L, about 1950
mg/L, about 1975 mg/L, about 2000 mg/L, or a range bounded by any
two of the foregoing values. In other embodiments, a fatty acid or
fatty acid derivative is produced at a titer of more than 2000
mg/L, more than 5000 mg/L, more than 10,000 mg/L, or higher, such
as 50 g/L, 70 g/L, 100 g/L, 120 g/L, 150 g/L, or 200 g/L.
[0144] As used herein, the "yield of fatty acid derivative produced
by a host cell" refers to the efficiency by which an input carbon
source is converted to product (i.e., fatty alcohol or fatty
aldehyde) in a host cell. Host cells engineered to produce fatty
acid derivatives according to the methods of the invention have a
yield of at least 3%, at least 4%, at least 5%, at least 6%, at
least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at
least 12%, at least 13%, at least 14%, at least 15%, at least 16%,
at least 17%, at least 18%, at least 19%, at least 20%, at least
21%, at least 22%, at least 23%, at least 24%, at least 25%, at
least 26%, at least 27%, at least 28%, at least 29%, or at least
30% or a range bounded by any two of the foregoing values. In other
embodiments, a fatty acid derivative or derivatives is produced at
a yield of more than 30%, 40%, 50%, 60%, 70%, 80%, 90% or more.
Alternatively, or in addition, the yield is about 30% or less,
about 27% or less, about 25% or less, or about 22% or less. Thus,
the yield can be bounded by any two of the above endpoints. For
example, the yield of a fatty acid derivative or derivatives
produced by the recombinant host cell according to the methods of
the invention can be 5% to 15%, 10% to 25%, 10% to 22%, 15% to 27%,
18% to 22%, 20% to 28%, or 20% to 30%. The yield may refer to a
particular fatty acid derivative or a combination of fatty acid
derivatives produced by a given recombinant host cell culture.
[0145] In one approach, the term "productivity of the fatty acid or
derivative thereof produced by a host cell" refers to the quantity
of fatty acid or fatty acid derivative produced per unit volume of
host cell culture per unit density of host cell culture. In any
aspect of the compositions and methods described herein, the
productivity of a fatty acid or a fatty acid derivative such as an
olefin, a fatty aldehyde, a fatty alcohol, an alkane, a fatty
ester, or a ketone produced by an engineered host cells is at least
about at least about 3 mg/L/OD.sub.600, at least about 6
mg/L/OD.sub.600, at least about 9 mg/L/OD.sub.600, at least about
12 mg/L/OD.sub.600, or at least about 15 mg/L/OD.sub.600.
Alternatively, or in addition, the productivity is about 50
mg/L/OD.sub.600 or less, about 40 mg/L/OD.sub.600 or less, about 30
mg/L/OD.sub.600 or less, or about 20 mg/L/OD.sub.600 or less. Thus,
the productivity can be bounded by any two of the above endpoints.
For example, the productivity can be about 3 to about 30
mg/L/OD.sub.600, about 6 to about 20 mg/L/OD.sub.600, or about 15
to about 30 mg/L/OD.sub.600.
[0146] In another approach, the term "productivity" refers to the
quantity of a fatty acid derivative or derivatives produced per
unit volume of host cell culture per unit time. In any aspect of
the compositions and methods described herein, the productivity of
a fatty acid derivative or derivatives produced by a recombinant
host cell is at least 100 mg/L/hour, at least 200 mg/L/hour, at
least 300 mg/L/hour, at least 400 mg/L/hour, at least 500
mg/L/hour, at least 600 mg/L/hour, at least 700 mg/L/hour, at least
800 mg/L/hour, at least 900 mg/L/hour, at least 1000 mg/L/hour, at
least 1100 mg/L/hour, at least 1200 mg/L/hour, at least 1300
mg/L/hour, at least 1400 mg/L/hour, at least 1500 mg/L/hour, at
least 1600 mg/L/hour, at least 1700 mg/L/hour, at least 1800
mg/L/hour, at least 1900 mg/L/hour, at least 2000 mg/L/hour, at
least 2100 mg/L/hour, at least 2200 mg/L/hour, at least 2300
mg/L/hour, at least 2400 mg/L/hour, or at least 2500 mg/L/hour.
Alternatively, or in addition, the productivity is 2500 mg/L/hour
or less, 2000 mg/L/OD600 or less, 1500 mg/L/OD600 or less, 120
mg/L/hour, or less, 1000 mg/L/hour or less, 800 mg/L/hour, or less,
or 600 mg/L/hour or less. Thus, the productivity can be bounded by
any two of the above endpoints. For example, the productivity can
be 3 to 30 mg/L/hour, 6 to 20 mg/L/hour, or 15 to 30 mg/L/hour. For
example, the productivity of a fatty acid derivative or derivatives
produced by a recombinant host cell according to the methods of the
may be from 500 mg/L/hour to 2500 mg/L/hour, or from 700 mg/L/hour
to 2000 mg/L/hour. The productivity may refer to a particular fatty
acid derivative or a combination of fatty acid derivatives produced
by a given recombinant host cell culture.
[0147] In the compositions and methods of the invention, the
production and isolation of a desired fatty acid or derivative
thereof (e.g., acyl-CoA, fatty acids, terminal olefins, fatty
aldehydes, fatty alcohols, alkanes, alkenes, wax esters, ketones
and internal olefins) can be enhanced by altering the expression of
one or more genes involved in the regulation of fatty acid, fatty
ester, alkane, alkene, olefin fatty alcohol production, degradation
and/or secretion in the engineered host cell.
[0148] FadR is known to modulate the expression and/or activity of
numerous genes, including fabA, fabB, iclR, fadA, fadB, fadD, fadE,
fadI, fadf, fadL, fadM, uspA, aceA, aceB, and aceK. In some
embodiments of the methods described herein, the engineered host
cell further comprises an altered level of expression of one or
more genes selected from the group consisting of fabA, fabB, iclR,
fadA, fadB, fadD, fadE, fadI, fadf, fadL, fadM, uspA, aceA, aceB,
and aceK as compared to the level of expression of the selected
gene(s) in a corresponding wild-type host cell. Exemplary accession
numbers for polypeptides encoded by the FadR target genes include
fabA (NP_415474), fabB (BAA16180), (NP_418442), fadA (YP_026272.1),
fadB (NP_418288.1), fadD (AP_002424), fadE (NP_414756.2), fadI
(NP_416844.1), fadJ (NP_416843.1), fadL (AAC75404), fadM
(NP_414977.1), uspA (AAC76520), aceA (AAC76985.1), aceB
(AAC76984.1), and aceK (AAC76986.1).
[0149] Exemplary enzymes and polypeptides for use in practicing the
invention are listed in FIG. 1. One of ordinary skill in the art
will understand that depending upon the purpose (e.g., desired
fatty acid or fatty acid derivative product), specific genes (or
combinations of genes) listed in FIG. 1 may be overexpressed,
modified, attenuated or deleted in an engineered host cell which
has an altered level of expression of a FadR polypeptide.
[0150] In some embodiments, the method comprises modifying the
expression of a gene encoding one or more of a thioesterase (e.g.,
TesA), a decarboxylase, a carboxylic acid reductase (CAR; e.g.,
CarB), an alcohol dehydrogenase (aldehyde reductase); an aldehyde
decarbonylase, a fatty alcohol forming acyl-CoA reductase (FAR), an
acyl ACP reductase (AAR), an ester synthase, an acyl-CoA reductase
(ACR1), OleA, OleCD and OleBCD.
[0151] In certain embodiments of the invention, the engineered host
cell having an altered level of expression of a FadR polypeptide
may be engineered to further comprise a polynucleotide sequence
encoding a polypeptide: (1) having thioesterase activity (EC
3.1.2.14), wherein the engineered host cell synthesizes fatty
acids; (2) having decarboxylase activity, wherein the engineered
host cell synthesizes terminal olefins; (3) having carboxylic acid
reductase activity, wherein the engineered host cell synthesizes
fatty aldehydes; (4) having carboxylic acid reductase and alcohol
dehydrogenase activity (EC 1.1.1.1), wherein the engineered host
cell synthesizes fatty alcohols; (5) having carboxylic acid
reductase and aldehyde decarbonylase activity (EC 4.1.99.5),
wherein the engineered host cell synthesizes alkanes; (6) having
acyl-CoA reductase activity (EC 1.2.1.50), wherein microorganism
synthesizes fatty aldehydes; (7) having acyl-CoA reductase activity
(EC 1.2.1.50) and alcohol dehydrogenase activity (EC 1.1.1.1),
wherein the engineered host cell synthesizes fatty alcohols; (8)
having acyl-CoA reductase activity (EC 1.2.1.50) and aldehyde
decarbonylase activity (EC 4.1.99.5), wherein the engineered host
cell synthesizes alkanes; (9) having alcohol forming acyl CoA
reductase activity wherein the engineered host cell synthesizes
fatty aldehydes and fatty alcohols; (10) having carboxylic acid
reductase activity, wherein the engineered host cell synthesizes
fatty aldehydes; (11) having acyl ACP reductase activity, wherein
the engineered host cell synthesizes fatty aldehydes; (12) having
acyl ACP reductase activity and alcohol dehydrogenase activity(EC
1.1.1.1), wherein engineered host cell synthesizes fatty alcohols;
(13) having acyl ACP reductase activity and aldehyde decarbonylase
activity (EC 4.1.99.5), wherein engineered host cell synthesizes
alkanes; (14) having ester synthase activity (EC 3.1.1.67), wherein
the engineered host cell synthesizes fatty esters; (15) having
ester synthase activity (EC 3.1.1.67) and (a) carboxylic acid
reductase activity, (b) acyl-CoA reductase activity, (c) acyl ACP
reductase activity, or (d) alcohol dehydrogenase activity(EC
1.1.1.1), wherein the engineered host cell synthesizes wax esters;
(16) having OleA activity, wherein the engineered host cell
synthesizes 2-alkyl-3-keto-acyl CoA and ketones; or (17) having
OleCD or OleBCD activity, wherein the engineered host cell
synthesizes internal olefins.
[0152] In some embodiments, the method further comprises modifying
the expression of a gene encoding a fatty acid synthase in the host
cell. As used herein, "fatty acid synthase" means any enzyme
involved in fatty acid biosynthesis. In certain embodiments,
modifying the expression of a gene encoding a fatty acid synthase
includes expressing a gene encoding a fatty acid synthase in the
host cell and/or increasing the expression or activity of an
endogenous fatty acid synthase in the host cell. In alternate
embodiments, modifying the expression of a gene encoding a fatty
acid synthase includes attenuating a gene encoding a fatty acid
synthase in the host cell and/or decreasing the expression or
activity of an endogenous fatty acid synthase in the host cell. In
some embodiments, the fatty acid synthase is a thioesterase (EC
3.1.1.5 or EC 3.1.2.14). In particular embodiments, the
thioesterase is encoded by tesA, tesA without leader sequence,
tesB, fatB, fatB2, fatB3, fatA, or fatA1.
[0153] In other embodiments, the host cell is genetically
engineered to express an attenuated level of a fatty acid
degradation enzyme relative to a wild-type host cell. As used
herein, the term "fatty acid degradation enzyme" means an enzyme
involved in the breakdown or conversion of a fatty acid or fatty
acid derivative into another product, such as, but not limited to,
an acyl-CoA synthase. In some embodiments, the host cell is
genetically engineered to express an attenuated level of an
acyl-CoA synthase relative to a wild-type host cell. In particular
embodiments, the host cell expresses an attenuated level of an
acyl-CoA synthase encoded by fadD, fadK, BH3103, yhfl, PJI-4354,
EAV15023, fadD1, fadD2, RPC_4074, fadDD35, fadDD22, faa3p, or the
gene encoding the protein YP_002028218. In certain embodiments, the
genetically engineered host cell comprises a knockout of one or
more genes encoding a fatty acid degradation enzyme, such as the
aforementioned acyl-CoA synthase genes.
[0154] The fatty acid biosynthetic pathway in host cells uses the
precursors acetyl-CoA and malonyl-CoA. The steps in this pathway
are catalyzed by enzymes of the fatty acid biosynthesis (fab) and
acetyl-CoA carboxylase (acc) gene families (see, e.g., Heath et
al., Prog. Lipid Res. 40(6): 467-97 (2001)). Acetyl-CoA is
carboxylated by acetyl-CoA carboxylase (EC 6.4.1.2), which is a
multisubunit enzyme encoded by four separate genes (accA, accB,
accC, and accD) in most prokaryotes, to form malonyl-CoA. In some
bacteria, such as Corynebacterium glutamicus, acetyl-CoA
carboxylase is consisted two subunits, AccDA [YP_225123.1] and
AccBC [YP_224991], encoded by accDA and accBC, respectively.
Depending upon the desired fatty acid or fatty acid derivative
product, specific fab and/or acc genes (or combinations thereof)
may be overexpressed, modified, attenuated or deleted in an
engineered host cell.
[0155] In some embodiments, an acetyl-CoA carboxylase complex is
overexpressed in the engineered host cell. In certain embodiments,
the acetyl-CoA carboxylase subunit genes are obtained from one or
more of Corynebacterium glutamicum, Escherichia coli, Lactococcus
lactis, Kineococcus radiotolerans, Desulfovibrio desulfuricans,
Erwinia amylovora, Rhodospirillum rubrum, Vibrio furnissii,
Stenotrophomonas maltophilia, Synechocystis sp. PCC6803, and
Synechococcus elongatus.
[0156] Biotin protein ligase (EC 6.3.4.15) is an enzyme that
catalyzes the covalent attachment of biotin to the biotin carboxyl
carrier protein (BCCP) subunit of acetyl-CoA carboxylase. In some
embodiments of the present invention, a biotin protein ligase is
expressed or overexpressed in the engineered host cell. In certain
embodiments, the biotin protein ligase is birA from Corynebacterium
glutamicum (YP_225000) or bpl1 from Saccharomyces cerevisiae
(NP_010140).
[0157] The production of fatty acid esters such as FAMEs or FAEEs
in a host cell can be facilitated by expression or overexpression
of an ester synthase (EC 2.3.1.75 or EC 3.1.1.67) in an engineered
host cell. In some embodiments, the ester synthase is ES9 from
Marinobacter hydrocarbonoclasticus (SEQ ID NO: 2), ES8 from
Marinobacter hydrocarbonoclasticus (SEQ ID NO: 3), AtfA1 from
Alcanivorax borkumensis SK2 (SEQ ID NO: 4), AtfA2 from Alcanivorax
borkumensis SK2 (SEQ ID NO: 5), diacylglycerol O-acyltransferase
from Marinobacter aquaeolei VT8 (SEQ ID NO: 6 or SEQ ID NO: 7), a
wax synthase, or a bifunctional wax ester
synthase/acyl-CoA:diacylglycerol acyltransferase (wax-dgaT).
[0158] In certain embodiments, a gene encoding a fatty aldehyde
biosynthetic polypeptide is expressed or overexpressed in the host
cell. Exemplary fatty aldehyde biosynthetic polypeptides suitable
for use in the methods of the invention are disclosed, for example,
in International Patent Application Publication WO 2010/042664. In
preferred embodiments, the fatty aldehyde biosynthetic polypeptide
has carboxylic acid reductase (EC 6.2.1.3 or EC 1.2.1.42) activity,
e.g., fatty acid reductase activity.
[0159] In the methods of the invention, the polypeptide having
carboxylic acid reductase activity is not particularly limited.
Exemplary polypeptides having carboxylic acid reductase activity
which are suitable for use in the methods of the present invention
are disclosed, for example, in International Patent Application
Publications WO 2010/062480 and WO 2010/042664. In some
embodiments, the polypeptide having carboxylic acid reductase
activity is CarB from M. smegmatis (YP_889972) (SEQ ID NO: 8). In
other embodiments, the polypeptide having carboxylic acid reductase
activity is CarA [ABK75684] from M. smegmatis, FadD9 [AAK46980]
from M. tuberculosis, CAR [AAR91681] from Nocardia sp. NRRL 5646,
CAR [YP-001070587] from Mycobacterium sp. JLS, or CAR [YP-118225]
from Streptomyces griseus. The terms "carboxylic acid reductase,"
"CAR," and "fatty aldehyde biosynthetic polypeptide" are used
interchangeably herein.
[0160] In certain embodiments, a thioesterase and a carboxylic acid
reductase are expressed or overexpressed in the engineered host
cell.
[0161] In some embodiments, a gene encoding a fatty alcohol
biosynthetic polypeptide is expressed or overexpressed in the host
cell. Exemplary fatty alcohol biosynthetic polypeptides suitable
for use in the methods of the invention are disclosed, for example,
in International Patent Application Publication WO 2010/062480. In
certain embodiments, the fatty alcohol biosynthetic polypeptide has
aldehyde reductase or alcohol dehydrogenase activity (EC 1.1.1.1).
Exemplary fatty alcohol biosynthetic polypeptides include, but are
not limited to AlrA of Acenitobacter sp. M-1 (SEQ ID NO: 9) or AlrA
homologs and endogenous E. coli alcohol dehydrogenases such as
YjgB, (AAC77226) (SEQ ID NO: 10), DkgA (NP_417485), DkgB
(NP_414743), YdjL (AAC74846), YdjJ (NP_416288), AdhP (NP_415995),
YhdH (NP_417719), YahK (NP_414859), YphC (AAC75598), YqhD (446856)
and YbbO [AAC73595.1].
[0162] As used herein, the term "alcohol dehydrogenase" is a
peptide capable of catalyzing the conversion of a fatty aldehyde to
an alcohol (e.g., fatty alcohol). One of ordinary skill in the art
will appreciate that certain alcohol dehydrogenases are capable of
catalyzing other reactions as well. For example, certain alcohol
dehydrogenases will accept other substrates in addition to fatty
aldehydes, and these non-specific alcohol dehydrogenases also are
encompassed by the term "alcohol dehydrogenase." Exemplary alcohol
dehydrogenases suitable for use in the methods of the invention are
disclosed, for example, in International Patent Application
Publication WO 2010/062480.
[0163] In some embodiments, a thioesterase, a carboxylic acid
reductase, and an alcohol dehydrogenase are expressed or
overexpressed in the engineered host cell. In certain embodiments,
the thioesterase is tesA (SEQ ID NO: 11), the carboxylic acid
reductase is carB (SEQ ID NO: 8), and the alcohol dehydrogenase is
YjgB (SEQ ID NO: 10) or AlrAadp1 (SEQ ID NO: 9).
[0164] Phosphopantetheine transferases (PPTases) (EC 2.7.8.7)
catalyze the transfer of 4'-phosphopantetheine from CoA to a
substrate. Nocardia CAR and several of its homologues contain a
putative attachment site for 4'-phosphopantetheine (PPT) (He et
al., Appl. Environ. Microbiol., 70(3): 1874-1881 (2004)). In some
embodiments of the invention, a PPTase is expressed or
overexpressed in an engineered host cell. In certain embodiments,
the PPTase is EntD from E. coli MG1655 (SEQ ID NO: 12).
[0165] In some embodiments, a thioesterase, a carboxylic acid
reductase, a PPTase, and an alcohol dehydrogenase are expressed or
overexpressed in the engineered host cell. In certain embodiments,
the thioesterase is tesA (SEQ ID NO: 11), the carboxylic acid
reductase is carB (SEQ ID NO: 8), the PPTase is entD (SEQ ID NO:
12), and the alcohol dehydrogenase is yjgB (SEQ ID NO: 10) or
alrAadp1 (SEQ ID NO: 9).
[0166] The invention also provides a fatty acid or a fatty
derivative produced by any of the methods described herein. A fatty
acid or derivative thereof produced by any of the methods described
herein can be used directly as fuels, fuel additives, starting
materials for production of other chemical compounds (e.g.,
polymers, surfactants, plastics, textiles, solvents, adhesives,
etc.), or personal care additives. These compounds can also be used
as feedstock for subsequent reactions, for example, hydrogenation,
catalytic cracking (e.g., via hydrogenation, pyrolisis, or both),
to make other products.
[0167] In some embodiments, the invention provides a biofuel
composition comprising the fatty acid or derivative thereof
produced by the methods described herein. As used herein, the term
"biofuel" refers to any fuel derived from biomass. Biofuels can be
substituted for petroleum-based fuels. For example, biofuels are
inclusive of transportation fuels (e.g., gasoline, diesel, jet
fuel, etc.), heating fuels, and electricity-generating fuels.
Biofuels are a renewable energy source. As used herein, the term
"biodiesel" means a biofuel that can be a substitute of diesel,
which is derived from petroleum. Biodiesel can be used in internal
combustion diesel engines in either a pure form, which is referred
to as "neat" biodiesel, or as a mixture in any concentration with
petroleum-based diesel. Biodiesel can include esters or
hydrocarbons, such as alcohols. In certain embodiments, the biofuel
is selected from the group consisting of a biodiesel, a fatty
alcohol, a fatty ester, a triacylglyceride, a gasoline, or a jet
fuel.
[0168] Fuel additives are used to enhance the performance of a fuel
or engine. For example, fuel additives can be used to alter the
freezing/gelling point, cloud point, lubricity, viscosity,
oxidative stability, ignition quality, octane level, and/or flash
point of a fuel. In the United States, all fuel additives must be
registered with Environmental Protection Agency (EPA). The names of
fuel additives and the companies that sell the fuel additives are
publicly available by contacting the EPA or by viewing the EPA's
website. One of ordinary skill in the art will appreciate that a
biofuel produced according to the methods described herein can be
mixed with one or more fuel additives to impart a desired
quality.
[0169] The invention also provides a surfactant composition or a
detergent composition comprising a fatty alcohol produced by any of
the methods described herein. One of ordinary skill in the art will
appreciate that, depending upon the intended purpose of the
surfactant or detergent composition, different fatty alcohols can
be produced and used. For example, when the fatty alcohols
described herein are used as a feedstock for surfactant or
detergent production, one of ordinary skill in the art will
appreciate that the characteristics of the fatty alcohol feedstock
will affect the characteristics of the surfactant or detergent
composition produced. Hence, the characteristics of the surfactant
or detergent composition can be selected for by producing
particular fatty alcohols for use as a feedstock.
[0170] A fatty alcohol-based surfactant and/or detergent
composition described herein can be mixed with other surfactants
and/or detergents well known in the art. In some embodiments, the
mixture can include at least about 10%, at least about 15%, at
least about 20%, at least about 30%, at least about 40%, at least
about 50%, at least about 60%, or a range bounded by any two of the
foregoing values, by weight of the fatty alcohol. In other
examples, a surfactant or detergent composition can be made that
includes at least about 5%, at least about 10%, at least about 20%,
at least about 30%, at least about 40%, at least about 50%, at
least about 60%, at least about 70%, at least about 80%, at least
about 85%, at least about 90%, at least about 95%, or a range
bounded by any two of the foregoing values, by weight of a fatty
alcohol that includes a carbon chain that is 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, or 22 carbons in length. Such
surfactant or detergent compositions also can include at least one
additive, such as a microemulsion or a surfactant or detergent from
nonmicrobial sources such as plant oils or petroleum, which can be
present in the amount of at least about 5%, at least about 10%, at
least about 15%, at least about 20%, at least about 30%, at least
about 40%, at least about 50%, at least about 60%, at least about
70%, at least about 80%, at least about 85%, at least about 90%, at
least about 95%, or a range bounded by any two of the foregoing
values, by weight of the fatty alcohol.
[0171] Bioproducts (e.g., fatty acids, acyl-CoAs, hydrocarbons,
fatty aldehydes, fatty alcohols, fatty esters, surfactant
compositions, and biofuel compositions) produced according to the
methods of the invention can be distinguished from organic
compounds derived from petrochemical carbon on the basis of dual
carbon-isotopic fingerprinting or .sup.14C dating. Additionally,
the specific source of biosourced carbon (e.g., glucose vs.
glycerol) can be determined by dual carbon-isotopic fingerprinting
(see, e.g., U.S. Pat. No. 7,169,588).
[0172] The ability to distinguish bioproducts from petroleum-based
organic compounds is beneficial in tracking these materials in
commerce. For example, organic compounds or chemicals comprising
both biologically-based and petroleum-based carbon isotope profiles
may be distinguished from organic compounds and chemicals made only
of petroleum-based materials. Hence, the materials prepared in
accordance with the inventive methods may be followed in commerce
on the basis of their unique carbon isotope profile.
[0173] Bioproducts can be distinguished from petroleum-based
organic compounds by comparing the stable carbon isotope ratio
(.sup.13C/.sup.12C) in each fuel. The .sup.13C/.sup.12C ratio in a
given bioproduct is a consequence of the .sup.13C/.sup.12C ratio in
atmospheric carbon dioxide at the time the carbon dioxide is fixed.
It also reflects the precise metabolic pathway. Regional variations
also occur. Petroleum, C.sub.3 plants (the broadleaf), C.sub.4
plants (the grasses), and marine carbonates all show significant
differences in .sup.13C/.sup.12C and the corresponding
.delta..sup.13C values. Furthermore, lipid matter of C.sub.3 and
C.sub.4 plants analyze differently than materials derived from the
carbohydrate components of the same plants as a consequence of the
metabolic pathway.
[0174] The .sup.13C measurement scale was originally defined by a
zero set by Pee Dee Belemnite (PDB) limestone, where values are
given in parts per thousand deviations from this material. The
".delta..sup.13C" values are expressed in parts per thousand (per
mil), abbreviated, % o, and are calculated as follows:
.delta..sup.13C (%
o)=[(.sup.13C/.sup.12C).sub.sample-(.sup.13C/.sup.12C).sub.standard]/(.su-
p.13C/.sup.12C)standard.times.1000
[0175] In some embodiments, a bioproduct produced according to the
methods of the invention has a .delta..sup.13C of about -30 or
greater, about -28 or greater, about -27 or greater, about -20 or
greater, about -18 or greater, about -15 or greater, about -13 or
greater, or about -10 or greater. Alternatively, or in addition, a
bioproduct has a .delta..sup.13C of about -4 or less, about -5 or
less, about -8 or less, about -10 or less, about -13 or less, about
-15 or less, about -18 or less, or about -20 or less. Thus, the
bioproduct can have a .delta..sup.13C bounded by any two of the
above endpoints. For example, the bioproduct can have a
.delta..sup.13C of about -30 to about -15, about -27 to about -19,
about -25 to about -21, about -15 to about -5, about -13 to about
-7, or about -13 to about -10. In some embodiments, the bioproduct
can have a .delta..sup.13C of about -10, -11, -12, or -12.3. In
other embodiments, the bioproduct has a .delta..sup.13C of about
-15.4 or greater. In yet other embodiments, the bioproduct has a
.delta..sup.13C of about -15.4 to about -10.9, or a .delta..sup.13C
of about -13.92 to about -13.84.
[0176] Bioproducts can also be distinguished from petroleum-based
organic compounds by comparing the amount of .sup.14C in each
compound. Because .sup.14C has a nuclear half life of 5730 years,
petroleum based fuels containing "older" carbon can be
distinguished from bioproducts which contain "newer" carbon (see,
e.g., Currie, "Source Apportionment of Atmospheric Particles",
Characterization of Environmental Particles, J. Buffle and H. P.
van Leeuwen, Eds., Vol. I of the IUPAC Environmental Analytical
Chemistry Series, Lewis Publishers, Inc., pp. 3-74 (1992)).
[0177] .sup.14C can be measured by accelerator mass spectrometry
(AMS), with results given in units of "fraction of modern carbon"
(f.sub.M). f.sub.M is defined by National Institute of Standards
and Technology (NIST) Standard Reference Materials (SRMs) 4990B and
4990C. As used herein, "fraction of modem carbon" or f.sub.M has
the same meaning as defined by National Institute of Standards and
Technology (NIST) Standard Reference Materials (SRMs) 4990B and
4990C, known as oxalic acids standards HOxI and HOxII,
respectively. The fundamental definition relates to 0.95 times the
.sup.14C/.sup.12C isotope ratio HOxI (referenced to AD 1950). This
is roughly equivalent to decay-corrected pre-Industrial Revolution
wood. For the current living biosphere (plant material), f.sub.M is
approximately 1.1.
[0178] In some embodiments, a bioproduct produced according to the
methods of the invention has a f.sub.M.sup.14C of at least about 1,
e.g., at least about 1.003, at least about 1.01, at least about
1.04, at least about 1.111, at least about 1.18, or at least about
1.124. Alternatively, or in addition, the bioproduct has an
f.sub.M.sup.14C of about 1.130 or less, e.g., about 1.124 or less,
about 1.18 or less, about 1.111 or less, or about 1.04 or less.
Thus, the bioproduct can have a f.sub.M.sup.14C bounded by any two
of the above endpoints. For example, the bioproduct can have a
f.sub.M.sup.14C of about 1.003 to about 1.124, a f.sub.M.sup.14C of
about 1.04 to about 1.18, or a f.sub.M.sup.14C of about 1.111 to
about 1.124.
[0179] Another measurement of .sup.14C is known as the percent of
modem carbon, i.e., pMC. For an archaeologist or geologist using
.sup.14C dates, AD 1950 equals "zero years old." This also
represents 100 pMC. "Bomb carbon" in the atmosphere reached almost
twice the normal level in 1963 at the peak of thermo-nuclear
weapons testing. Its distribution within the atmosphere has been
approximated since its appearance, showing values that are greater
than 100 pMC for plants and animals living since AD 1950. It has
gradually decreased over time with today's value being near 107.5
pMC. This means that a fresh biomass material, such as corn, would
give a .sup.14C signature near 107.5 pMC. Petroleum-based compounds
will have a pMC value of zero. Combining fossil carbon with present
day carbon will result in a dilution of the present day pMC
content. By presuming 107.5 pMC represents the .sup.14C content of
present day biomass materials and 0 pMC represents the .sup.14C
content of petroleum-based products, the measured pMC value for
that material will reflect the proportions of the two component
types. For example, a material derived 100% from present day
soybeans would have a radiocarbon signature near 107.5 pMC. If that
material was diluted 50% with petroleum-based products, the
resulting mixture would have a radiocarbon signature of
approximately 54 pMC.
[0180] A biologically-based carbon content is derived by assigning
"100%" equal to 107.5 pMC and "0%" equal to 0 pMC. For example, a
sample measuring 99 pMC will provide an equivalent
biologically-based carbon content of 93%. This value is referred to
as the mean biologically-based carbon result and assumes that all
of the components within the analyzed material originated either
from present day biological material or petroleum-based
material.
[0181] In some embodiments, a bioproduct produced according to the
methods of the invention has a pMC of at least about 50, at least
about 60, at least about 70, at least about 75, at least about 80,
at least about 85, at least about 90, at least about 95, at least
about 96, at least about 97, or at least about 98. Alternatively,
or in addition, the bioproduct has a pMC of about 100 or less,
about 99 or less, about 98 or less, about 96 or less, about 95 or
less, about 90 or less, about 85 or less, or about 80 or less.
Thus, the bioproduct can have a pMC bounded by any two of the above
endpoints. For example, a bioproduct can have a pMC of about 50 to
about 100; about 60 to about 100; about 70 to about 100; about 80
to about 100; about 85 to about 100; about 87 to about 98; or about
90 to about 95. In other embodiments, a bioproduct described herein
has a pMC of about 90, about 91, about 92, about 93, about 94, or
about 94.2.
[0182] The following examples further illustrate the invention but,
of course, should not be construed as in any way limiting its
scope.
Example 1
[0183] This example demonstrates a method to identify engineered
host cells which display enhanced production of fatty acids and
derivatives thereof.
[0184] ALC310 is a previously characterized E. coli strain having
the genotype MG1655 (.DELTA.fadE::FRT .DELTA.fhuA::FRT fabB[A329V]
.DELTA.entD::P.sub.T5-entD) which carries the plasmid ALC310
(pCL1920_P.sub.TRC_carBopt_13 G04_alrA_sthA) (SEQ ID NO: 13) and
produces fatty acids and derivatives thereof. To identify strains
which display an improved titer or yield of fatty acids or
derivatives thereof, transposon mutagenesis of ALC310 was performed
followed by high-throughput screening.
[0185] The transposon DNA was prepared by cloning a DNA fragment
into the plasmid EZ-Tn5.TM. pMOD.TM.<R6K ori/MCS> (Epicentre
Biotechnologies, Madison, Wis.). The DNA fragment contains a T5
promoter and a chloramphenicol resistance gene (cat) flanked by
loxP sites. The resulting plasmid was named p100.38 (SEQ ID NO:
14). The p100.38 plasmid was optionally digested with PshAI
restriction enzyme, incubated with EZ-Tn5.TM. Transposase enzyme
(Epicentre Biotechnologies, Madison, Wis.), and electroporated into
electrocompetent ALC310 cells as per the manufacturer's
instructions. The resulting colonies contained the transposon DNA
inserted randomly into the chromosome of ALC310.
[0186] Transposon clones were then subjected to high-throughput
screening to measure production of fatty alcohols. Briefly,
colonies were picked into deep-well plates containing Luria-Bertani
(LB) medium. After overnight growth, each culture was inoculated
into fresh LB. After 3 hours growth, each culture was inoculated
into fresh FA-2 media. Spectinomycin (100 .mu.g/mL) was included in
all media to maintain selection of the 7P36 plasmid. FA-2 medium is
M9 medium with 3% glucose supplemented with antibiotics, 10 .mu.g/L
iron citrate, 1 .mu.g/L thiamine, 0.1 M Bis-Tris buffer (pH 7.0),
and a 1:1000 dilution of the trace mineral solution described in
Table 1.
TABLE-US-00001 TABLE 1 Trace mineral solution (filter sterilized) 2
g/L ZnCl.cndot.4H.sub.2O 2 g/L CaCl.sub.2.cndot.6H.sub.2O 2 g/L
Na.sub.2MoO.sub.4.cndot.2H.sub.2O 1.9 g/L
CuSO.sub.4.cndot.5H.sub.2O 0.5 g/L H.sub.3BO.sub.3 100 mL/L
concentrated HCl q.s. Milli-Q water
[0187] After 20 hours growth in FA-2, the cultures were extracted
with butyl acetate. The crude extract was derivatized with BSTFA
(N,O-bis[Trimethylsilyl]trifluoroacetamide) and total fatty species
(e.g., fatty alcohols, fatty aldehydes, and fatty acids) were
measured with GC-FID as described in International Patent
Application Publication WO 2008/119082.
[0188] Clones that produced 15% more total fatty species than
ALC310 were subjected to further verification using a shake-flask
fermentation. Briefly, the clones were grown in 2 mL of LB medium
supplemented with spectinomycin (100 mg/L) at 37.degree. C. After
overnight growth, 100 .mu.L of culture was transferred into 2 mL of
fresh LB supplemented with antibiotics. After 3 hours growth, 2 mL
of culture was transferred into a 125 mL-flask containing 18 mL of
FA-2 medium supplemented with spectinomycin (100 mg/L). When the
OD.sub.600 of the culture reached 2.5, 1 mM of IPTG was added to
each flask. After 20 hours of growth at 37.degree. C., a 400 .mu.L
sample from each flask was removed, and total fatty species were
extracted with 400 .mu.L butyl acetate. The crude extracts were
analyzed directly with GC-FID as described above.
[0189] A transposon clone (termed D288) was identified which
displayed increased titers of total fatty species as compared to
the parental ALC310 strain (FIG. 2).
[0190] The results of this example demonstrate a method to identify
engineered host cells which display enhanced production of fatty
acids and derivatives thereof as compared to a corresponding
wild-type host cell.
Example 2
[0191] This example demonstrates that an engineered host cell with
a transposon insertion in the nhaB gene displays enhanced
production of fatty acids and derivatives thereof as compared to a
corresponding wild-type host cell.
[0192] Sequence analysis was performed to identify the location of
the transposon insertion in the D288 strain identified in Example
1. To do so, genomic DNA was purified from a 3-mL overnight LB
culture of D288 cells using the ZR Fungal/Bacterial DNA
MiniPrep.TM. kit (Zymo Research) according to the manufacturer's
instructions. The purified genomic DNA was sequenced outward from
the transposon using the primers DG150
(GCAGTTATTGGTGCCCTTAAACGCCTGGTTGCTACGCCTG) (SEQ ID NO: 15) and
DG153 (CCCAGGGCTTCCCGGTATCAACAGGGACACCAGG) (SEQ ID NO: 16),
internal to the transposon.
[0193] The D288 strain was determined to have a transposon
insertion in the nhaB gene (FIG. 3).
[0194] The results of this example demonstrate an engineered E.
coli host cell with a transposon insertion in the nhaB gene
displays enhanced production of fatty acids and derivatives thereof
as compared to a corresponding wild-type E. coli host cell.
Example 3
[0195] This example demonstrates that engineered host cells having
an altered level of production of FadR display enhanced production
of fatty acids and derivatives thereof.
[0196] The nhaB gene is proximal to the gene encoding the fatty
acid degradation regulator, FadR (FIG. 3). To determine if altering
the expression of FadR affects the production of fatty acids or
derivatives thereof in host cells, a FadR expression library was
cloned and screened.
[0197] To clone the expression library, the wild-type fadR gene was
amplified from genomic DNA of E. coli MG1655 by PCR using primers
DG191 (SEQ ID NO: 17) and DG192 (SEQ ID NO: 18). A mutant fadR gene
containing amino acid change S219N was also amplified from E. coli
MG1655 fadR[S219N] genomic DNA using the DG191 and DG192 primer
set. The primers used in this example are listed in Table 2.
TABLE-US-00002 TABLE 2 Sequence Primer Sequence Identifier DG191
ATGGTCATTAAGGCGCAAAGCCCGG SEQ ID NO: 17 DG192
GAGACCCCACACTACCATCCTCGAGTTATCGCCCCTGA SEQ ID NO: 18
ATGGCTAAATCACCC SL03 CTCGAGGATGGTAGTGTGGGGTCTCCC SEQ ID NO: 19 SL23
GAGACCGTTTCTCGAATTTAAATATGATACGCTCGAGCT SEQ ID NO: 20
TCGTCTGTTTCTACTGGTATTGGCACAAAC DG193
TGAAAGATTAAATTTNHHARNDDHDDNWAGGAGNNNN SEQ ID NO: 21
NNNATGGTCATTAAGGCGCAAAGCCCGG
[0198] A gene cassette encoding for kanamycin resistance (kan) was
PCR amplified from plasmid pKD13 using primers SL03 (SEQ ID NO: 19)
and SL23 (SEQ ID NO: 20). Each fadR cassette (i.e., wild-type and
S219N mutant) was separately joined with the kanamycin resistance
cassette using splicing by overlap extension (SOE) PCR using
primers SL23 and DG193 (SEQ ID NO: 21). The DG193 primer contained
degenerate nucleotides for the generation of expression
variants.
[0199] Plasmid p100.487 (pCL1920_P.sub.TRC_carBopt_13
G04_alrA_fabB[A329G]) (SEQ ID NO: 22) was linearized via
restriction digestion with enzymes SwaI and XhoI. Each of the two
SOE PCR fadR-kan products were separately cloned into linearized
plasmid p100.487 using the INFUSION.TM. system (Clontech, Mountain
View, Calif.), and then the plasmids were transformed into
chemically competent NEB TURBO' cells (New England Biolabs,
Ipswich, Mass.). Transformants were plated on LB agar containing 50
.mu.g/mL kanamycin.
[0200] Thousands of colonies were obtained for fadR and fadR
[S219N]. Colonies were scraped from plates and the plasmids were
isolated by miniprepping according to standard protocols. The
resulting pool of plasmids was transformed into an E. coli EG149
strain having a genotype of MG1655 (.DELTA.fadE::FRT
.DELTA.fhuA::FRT fabB[A329V] .DELTA.entD::P.sub.T5-entD)), and
selected on LB plates containing 100 .mu.g/mL spectinomycin.
[0201] Transformants were then screened for production of total
fatty species (e.g., fatty acids, fatty aldehydes, and fatty
alcohols) using the deep-well procedure described in Example 1.
Numerous strains were identified which displayed enhanced
production of total fatty species as compared to the control ALC487
strain (EG149 strain carrying plasmid p100.487) (FIG. 4). Strains
expressing either wild-type fadR or fadR [S219N] displayed enhanced
production of total fatty species as compared to the ALC487 strain,
although the highest titers were observed in strains expressing
wild-type FadR (FIG. 4).
[0202] Several of the top producing strains expressing wild-type
FadR identified in the initial screen were assigned strain IDs and
validated in a shake flask fermentation. Briefly, each strain was
streaked for single colonies, and three separate colonies from each
strain were grown in three separate flasks according to the shake
flask fermentation protocol described in Example 1. Total fatty
species were measured using GC-FID as described in Example 1. All
of the strains expressing wild-type FadR displayed higher total
fatty species titers as compared to the control ALC487 strain (FIG.
5).
[0203] Several of the top producing strains expressing wild-type
FadR were then further characterized in order to determine the
yield of fatty species. To do so, a shake flask fermentation was
performed as described above, except that (i) the temperature was
held at 32.degree. C., (ii) additional glucose was added after 18
hours and 43 hours, and (iii) extraction was performed at 68.5
hours. The total fatty species produced was divided by the total
glucose consumed to calculate the fatty species yield. All of the
strains expressing wild-type FadR displayed a higher yield of total
fatty species as compared to the control ALC487 strain (FIG.
6).
[0204] The D512 strain was then further characterized by evaluating
total fatty species titer and yield following fermentation in a 5 L
bioreactor. At a glucose feed rate of 10 g/L/hr glucose, the D512
strain produced higher titers of fatty acids and fatty alcohols as
compared to the control ALC487 strain (FIG. 7). In addition, the
total yield on all fatty species increased in the D512 strain as
compared to the ALC487 strain (FIG. 7). At a higher glucose feed
rate of 15 g/L/hr, the D512 strain produced approximately 68.5 g/L
total fatty species at a yield of approximately 20% (FIG. 7). The
D512 strain produced a higher total fatty species titer and yield
at 15 g/L/hr as compared to 10 g/L/hr (FIG. 7).
[0205] Plasmid DNA was isolated from the D512 strain and sequenced
according to standard protocols. The plasmid obtained from the D512
strain, termed pDG109, was determined to have the sequence
corresponding to SEQ ID NO: 23.
[0206] The results of this example demonstrate that engineered host
cells having an altered level of expression of FadR produce higher
titers and yields of fatty acids and derivatives thereof as
compared to corresponding wild-type host cells.
Example 4
[0207] This example demonstrates a method to produce high titers of
fatty acids in engineered host cells having an altered level of
expression of FadR.
[0208] The E. coli EG149 strain utilized in Example 3 overexpresses
the entD gene, which encodes a phosphopantetheine transferase
(PPTase) involved in the activation of the CarB enzyme that
catalyzes the reduction of fatty acids to fatty aldehydes and fatty
alcohols.
[0209] To assess the effect of entD expression on fatty acid and
fatty alcohol production in the D512 strain, a D512 variant was
generated which contained a deletion of the entD gene (D512
.DELTA.entD). Shake flask fermentations were performed with the
D512 strain and the D512 .DELTA.entD strain as described in Example
1. The D512 strain produced high titers of fatty alcohols and
comparatively lower titers and yields of fatty acids (FIG. 7). In
contrast, the D512 .DELTA.entD strain produced high titers and
yields of fatty acids, and relatively low titers of fatty alcohols
(FIG. 8). The titers of total fatty species were similar between
the D512 strain and the D512 .DELTA.entD strain (FIG. 8).
[0210] The results of this example demonstrate that engineered host
cells having an altered level of FadR expression produce high
titers of fatty acids when the entD gene is deleted.
Example 5
[0211] This example demonstrates a method to identify engineered
host cells which display enhanced production of fatty acids and
derivatives thereof.
[0212] To further assess the effect of altered FadR expression on
the production of fatty acids and derivatives thereof, ribosome
binding site (RBS) libraries of FadR (S219N) and wild-type FadR
were prepared and screened in E. coli host cells.
[0213] An RBS library was inserted upstream of the fadR (S219N)
gene in pDS57 as follows. The genomic DNA of a strain containing
the fadR(S219N) allele Moniker stEP005; id: s26z7 was amplified by
PCR using the DG191 (SEQ ID NO: 17) and fadR (S219N)_pme319rc (SEQ
ID NO: 24) primer set. The primers used in this example are listed
in Table 3.
TABLE-US-00003 TABLE 3 Sequence Primer Sequence Identifier DG191
ATGGTCATTAAGGCGCAAAGCCCGG SEQ ID NO: 17 fadR
CAAAACAGCCAAGCTGGAGACCGTTTTTATCGCC SEQ ID NO: 24 (S219N)_
CCTGAATGGCTAAATCACC pme319rc 377-rbs-fadR
GCCCGAACCCGCAAGTAANHHARNDDHDDNWAG SEQ ID NO: 25 (S219N)f
GARNNNNNNNATGGTCATTAAGGCGCAAAGCCC GG NH246
AAAAACGGTCTCCAGCTTGGCTGTTTTGGCGGAT SEQ ID NO: 26 GAGAGAAGATTTTC
377-3r TTACTTGCGGGTTCGGGCGC SEQ ID NO: 27
[0214] After the fadR (S219N) template was made, the RBS was added
by PCR using the 377-rbs-fadR (S219N)f (SEQ ID NO: 25) and fadR
(S219N)-pme319rc (SEQ ID NO: 24) primer set. The 377-rbs-fadR
(S219N)f primer contained degenerate nucleotides to introduce
variability into the RBS library. The RBS-fadR (S219N) was ligated
with a pDS57 vector backbone (described in Example 5), using the
commercial available CLONEZ.TM. kit from Genscript (Piscataway,
N.J.) with the NH246 (SEQ ID NO: 26) and 377-3r (SEQ ID NO: 27)
primer set.
[0215] An RBS library also was inserted upstream of the wild-type
fadR gene in pDS57 using s similar protocol, except that the
wild-type fadR gene was amplified by PCR using E. coli DV2 genomic
DNA.
[0216] The ligated pDS57-rbs-fadR (S219N) and pDS57-rbs-fadR
constructs were transformed separately into an E. coli DAM1 strain
by electroporation. Strain DAM1 was produced as a derivative of
strain DV2 (MG1655 .DELTA.fadE, .DELTA.fhuA), where the
lacI.sup.q-P.sub.Trc-tesA-fadD genes were integrated into the
chromosome using the Tn7-based delivery system present in plasmid
pGRG25 (described in McKenzie et al., BMC Microbiology 6: 39
(2006)). After transformation, the cells were recovered for 1 hour
at 37.degree. C. followed by plating on LB agar containing
spectinomycin. After overnight incubation at 37.degree. C., single
colonies were picked to screen in 96 deep well-plates containing
300 .mu.L/well LB with spectinomycin. The plates were incubated in
a 32.degree. C. shaker with 80% humidity and shaking at 250 RPM for
approximately 5 hours. After 5 hours of growth, 30 .mu.L/well of LB
culture was transferred to 300 .mu.L/well FA2 (2 g/L nitrogen)
medium containing spectinomycin. Plates were incubated again in a
32.degree. C. shaker with 80% humidity and shaking at 250 RPM
overnight. 30 .mu.L/well of the overnight culture was inoculated
into 300 .mu.L/well FA2 (1 g/L nitrogen) medium containing
spectinomycin, 1 mM IPTG, and 2% methanol. One replicate plate was
incubated in 32.degree. C. shaker and another was incubated in a
37.degree. C. shaker with 80% humidity and shaking at 250 RPM
overnight. The recipe for FA2 medium is listed in Table 4.
TABLE-US-00004 TABLE 4 Reagent mL Reagent per 1000 mL FA2 5.times.
Salt Solution 200 Thiamine (10 mg/mL) 0.1 1M MgSO.sub.4 1 1M
CaCl.sub.2 0.1 50% glucose 60 TM2 (trace minerals no iron) 1 10 g/L
ferric citrate 1 2M Bis-Tris buffer 50 NH.sub.4Cl* 10 Water q.s. to
1000 mL *eliminated for FA2 (1 g/L nitrogen) medium
[0217] After approximately 24 hours of incubation, the plates were
extracted by adding 40 .mu.L/well 1M HCl and 300 .mu.L/well butyl
acetate. The plates were shaken for 15 minutes at 2000 RPM, and
then centrifuged for 10 minutes at 4500 RPM at room temperature. 50
.mu.L of the organic layer per well was transferred to a shallow
well 96-well plate containing 50 .mu.L/well BSTFA (Sigma Aldrich,
St. Louis, Mo.), and the extracts were analyzed by GC-FID.
[0218] Several clones of E. coli DAM1 transformed with
pDS57-rbs-fadR were identified as producing substantially higher
titers of FAMEs and free fatty acids as compared to control E. coli
DAM1 transformed with pDS57 alone. In general, the FadR variants
produced low C14 to C16 ratios and displayed overall higher titers
at 32.degree. C. as compared to 37.degree. C.
[0219] Numerous clones of E. coli DAM1 transformed with
pDS57-rbs-FadR(S219N) also were identified as producing
substantially higher titers of FAMEs and free fatty acids as
compared to control E. coli DV2 or E. coli DAM1 transformed with
pDS57 alone.
[0220] Two of the clones transformed with pDS57-rbs-FadR(S219N)
identified in the initial screen (designated as P1A4 and P1G7) were
further characterized in shake flask fermentations. Briefly, each
colony was inoculated into 5 mL of LB containing spectinomycin and
incubated at 37.degree. C. with shaking at approximately 200 RPM
for about 5 hours. 1.5 mL of the LB culture was transferred into
13.5 mL FA2 (2 g/L nitrogen) medium containing 0.05% Triton X-100
and spectinomycin in a 125 mL baffled flask. The flask cultures
were incubated overnight at 32.degree. C., 80% humidity and 250
RPM. 1.5 mL of the overnight culture was transferred into a new 125
mL baffled flask that contained 13.5 mL FA2 (1 g/L nitrogen) medium
containing 0.05% Triton X-100, 1 mM IPTG, 2% methanol, and
spectinomycin. The flask cultures were then incubated at 32.degree.
C., 80% humidity and 250 RPM. After 56 hours of incubation, 500
.mu.L samples were taken out from each flask. 100 .mu.L of each
sample was diluted with 900 .mu.L water to measure the OD of the
culture, 100 .mu.L of each sample was diluted with 900 .mu.L water
to measure remaining glucose, and 300 .mu.L of each sample was
extracted and analyzed using GC-FID as described above.
[0221] Both of the two FadR variants (i.e., P1A4 and P1G7) produced
higher titers and yields of total fatty species as compared to the
control strain transformed with pDS57 alone in the shake flask
fermentation (FIG. 9).
[0222] Production of fatty species by P1A4 and P1G7 was also
measured in large scale fermentations. To do so, cells from a
frozen stock were grown in LB media for a few hours and then
transferred to a defined media consisting of 3 g/L
KH.sub.2PO.sub.4, 6 g/L Na.sub.2HPO.sub.4 dihydrate, 2 g/L
NH.sub.4Cl, 0.24 g/L MgSO.sub.4.times.7 H.sub.2O, 20 g/L glucose,
200 mM Bis-Tris buffer (pH 7.2), 1.0 ml/L trace metals solution,
and 1.0 mg/L thiamine, and cultured overnight. The trace metals
solution was composed of 27 g/L FeCl.sub.3.times.6 H.sub.2O, 2 g/L
ZnCl.sub.2.times.4H.sub.2O, 2 g/L CaCl.sub.2.times.6 H.sub.2O, 2
g/L Na.sub.2MoO.sub.4.times.2H.sub.2O, 1.9 g/L CuSO.sub.4.times.5
H.sub.2O, 0.5 g/L H.sub.3BO.sub.3, and 40 mL/L of concentrated
HCl.
[0223] 50 mL of each overnight culture was inoculated into 1 liter
of production medium in a fermentor with temperature, pH,
agitation, aeration and dissolved oxygen control. The medium
composition was as follows: 1 g/L KH.sub.2PO.sub.4, 0.5 g/L
(NH.sub.4).sub.2SO.sub.4, 0.5 g/L MgSO.sub.4.times.7 H.sub.2O, 5
g/L Bacto casaminoacids, 0.034 g/L ferric citrate, 0.12 ml/L 1M
HCl, 0.02 g/L ZnCl.sub.2.times.4 H.sub.2O, 0.02 g/L
CaCl.sub.2.times.2H.sub.2O, 0.02 g/L
Na.sub.2MoO.sub.4.times.2H.sub.2O, 0.019 g/L CuSO.sub.4.times.5
H.sub.2O, 0.005 g/L H.sub.3BO.sub.3 and 1.25 mL/L of a vitamin
solution. The vitamin solution contained 0.06 g/L riboflavina, 5.40
g/L pantothenic acid, 6.0 g/L niacine, 1.4 g/L piridoxine and 0.01
g/L folic acid.
[0224] The fermentations were performed at 32.degree. C., pH 6.8,
and dissolved oxygen (DO) equal to 25% of saturation. pH was
maintained by addition of NH.sub.4OH, which also served as nitrogen
source for cell growth. When the initial 5 g/L of glucose had been
almost consumed, a feed consisting of 500 g/L glucose, 1.6 g/L of
KH.sub.2PO.sub.4, 3.9 g/L MgSO.sub.4.7H.sub.2O, 0.13 g/L ferric
citrate, and 30 ml/L of methanol was supplied to the fermentor.
[0225] In the early phase of growth, the production of FAME was
induced by the addition of 1 mM IPTG and 20 ml/L of pure methanol.
After most of the cell growth was completed, the feed rate was
maintained at a rate of 7.5 g glucose/L/hour. After induction,
methanol was continuously supplied with the glucose feed. The
fermentation was continued for a period of 3 days, and samples were
taken at several timepoints for analysis of fatty species as
described above.
[0226] P1A4 and P1G7 produced higher titers of total fatty species
(FAMEs and free fatty acids) as compared to the control strain
transformed with pDS57 alone in the large scale fermentations (FIG.
10). In addition, P1A4 and P1G7 produced higher yields of total
fatty species as compared to the control strain in the large scale
fermentations (FIG. 11).
[0227] The results of this example demonstrate methods to produce
engineered host cells having altered FadR expression which display
enhanced titers and yields of FAMEs and fatty acids as compared to
corresponding wild-type cells.
[0228] All references, including publications, patent applications,
and patents, cited herein are hereby incorporated by reference to
the same extent as if each reference were individually and
specifically indicated to be incorporated by reference and were set
forth in its entirety herein.
[0229] The use of the terms "a" and "an" and "the" and similar
referents in the context of describing the invention (especially in
the context of the following claims) are to be construed to cover
both the singular and the plural, unless otherwise indicated herein
or clearly contradicted by context. The terms "comprising,"
"having," "including," and "containing" are to be construed as
open-ended terms (i.e., meaning "including, but not limited to,")
unless otherwise noted. Recitation of ranges of values herein are
merely intended to serve as a shorthand method of referring
individually to each separate value falling within the range,
unless otherwise indicated herein, and each separate value is
incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g., "such as") provided herein, is
intended merely to better illuminate the invention and does not
pose a limitation on the scope of the invention unless otherwise
claimed. No language in the specification should be construed as
indicating any non-claimed element as essential to the practice of
the invention.
[0230] Preferred embodiments of this invention are described
herein, including the best mode known to the inventors for carrying
out the invention. Variations of those preferred embodiments may
become apparent to those of ordinary skill in the art upon reading
the foregoing description. The inventors expect skilled artisans to
employ such variations as appropriate, and the inventors intend for
the invention to be practiced otherwise than as specifically
described herein. Accordingly, this invention includes all
modifications and equivalents of the subject matter recited in the
claims appended hereto as permitted by applicable law. Moreover,
any combination of the above-described elements in all possible
variations thereof is encompassed by the invention unless otherwise
indicated herein or otherwise clearly contradicted by context.
Sequence CWU 1
1
231239PRTEscherichia coli 1Met Val Ile Lys Ala Gln Ser Pro Ala Gly
Phe Ala Glu Glu Tyr Ile1 5 10 15Ile Glu Ser Ile Trp Asn Asn Arg Phe
Pro Pro Gly Thr Ile Leu Pro 20 25 30Ala Glu Arg Glu Leu Ser Glu Leu
Ile Gly Val Thr Arg Thr Thr Leu 35 40 45Arg Glu Val Leu Gln Arg Leu
Ala Arg Asp Gly Trp Leu Thr Ile Gln 50 55 60His Gly Lys Pro Thr Lys
Val Asn Asn Phe Trp Glu Thr Ser Gly Leu65 70 75 80Asn Ile Leu Glu
Thr Leu Ala Arg Leu Asp His Glu Ser Val Pro Gln 85 90 95Leu Ile Asp
Asn Leu Leu Ser Val Arg Thr Asn Ile Ser Thr Ile Phe 100 105 110Ile
Arg Thr Ala Phe Arg Gln His Pro Asp Lys Ala Gln Glu Val Leu 115 120
125Ala Thr Ala Asn Glu Val Ala Asp His Ala Asp Ala Phe Ala Glu Leu
130 135 140Asp Tyr Asn Ile Phe Arg Gly Leu Ala Phe Ala Ser Gly Asn
Pro Ile145 150 155 160Tyr Gly Leu Ile Leu Asn Gly Met Lys Gly Leu
Tyr Thr Arg Ile Gly 165 170 175Arg His Tyr Phe Ala Asn Pro Glu Ala
Arg Ser Leu Ala Leu Gly Phe 180 185 190Tyr His Lys Leu Ser Ala Leu
Cys Ser Glu Gly Ala His Asp Gln Val 195 200 205Tyr Glu Thr Val Arg
Arg Tyr Gly His Glu Ser Gly Glu Ile Trp His 210 215 220Arg Met Gln
Lys Asn Leu Pro Gly Asp Leu Ala Ile Gln Gly Arg225 230
2352473PRTMarinobacter hydrocarbonoclasticus 2Met Lys Arg Leu Gly
Thr Leu Asp Ala Ser Trp Leu Ala Val Glu Ser1 5 10 15Glu Asp Thr Pro
Met His Val Gly Thr Leu Gln Ile Phe Ser Leu Pro 20 25 30Glu Gly Ala
Pro Glu Thr Phe Leu Arg Asp Met Val Thr Arg Met Lys 35 40 45Glu Ala
Gly Asp Val Ala Pro Pro Trp Gly Tyr Lys Leu Ala Trp Ser 50 55 60Gly
Phe Leu Gly Arg Val Ile Ala Pro Ala Trp Lys Val Asp Lys Asp65 70 75
80Ile Asp Leu Asp Tyr His Val Arg His Ser Ala Leu Pro Arg Pro Gly
85 90 95Gly Glu Arg Glu Leu Gly Ile Leu Val Ser Arg Leu His Ser Asn
Pro 100 105 110Leu Asp Phe Ser Arg Pro Leu Trp Glu Cys His Val Ile
Glu Gly Leu 115 120 125Glu Asn Asn Arg Phe Ala Leu Tyr Thr Lys Met
His His Ser Met Ile 130 135 140Asp Gly Ile Ser Gly Val Arg Leu Met
Gln Arg Val Leu Thr Thr Asp145 150 155 160Pro Glu Arg Cys Asn Met
Pro Pro Pro Trp Thr Val Arg Pro His Gln 165 170 175Arg Arg Gly Ala
Lys Thr Asp Lys Glu Ala Ser Val Pro Ala Ala Val 180 185 190Ser Gln
Ala Met Asp Ala Leu Lys Leu Gln Ala Asp Met Ala Pro Arg 195 200
205Leu Trp Gln Ala Gly Asn Arg Leu Val His Ser Val Arg His Pro Glu
210 215 220Asp Gly Leu Thr Ala Pro Phe Thr Gly Pro Val Ser Val Leu
Asn His225 230 235 240Arg Val Thr Ala Gln Arg Arg Phe Ala Thr Gln
His Tyr Gln Leu Asp 245 250 255Arg Leu Lys Asn Leu Ala His Ala Ser
Gly Gly Ser Leu Asn Asp Ile 260 265 270Val Leu Tyr Leu Cys Gly Thr
Ala Leu Arg Arg Phe Leu Ala Glu Gln 275 280 285Asn Asn Leu Pro Asp
Thr Pro Leu Thr Ala Gly Ile Pro Val Asn Ile 290 295 300Arg Pro Ala
Asp Asp Glu Gly Thr Gly Thr Gln Ile Ser Phe Met Ile305 310 315
320Ala Ser Leu Ala Thr Asp Glu Ala Asp Pro Leu Asn Arg Leu Gln Gln
325 330 335Ile Lys Thr Ser Thr Arg Arg Ala Lys Glu His Leu Gln Lys
Leu Pro 340 345 350Lys Ser Ala Leu Thr Gln Tyr Thr Met Leu Leu Met
Ser Pro Tyr Ile 355 360 365Leu Gln Leu Met Ser Gly Leu Gly Gly Arg
Met Arg Pro Val Phe Asn 370 375 380Val Thr Ile Ser Asn Val Pro Gly
Pro Glu Gly Thr Leu Tyr Tyr Glu385 390 395 400Gly Ala Arg Leu Glu
Ala Met Tyr Pro Val Ser Leu Ile Ala His Gly 405 410 415Gly Ala Leu
Asn Ile Thr Cys Leu Ser Tyr Ala Gly Ser Leu Asn Phe 420 425 430Gly
Phe Thr Gly Cys Arg Asp Thr Leu Pro Ser Met Gln Lys Leu Ala 435 440
445Val Tyr Thr Gly Glu Ala Leu Asp Glu Leu Glu Ser Leu Ile Leu Pro
450 455 460Pro Lys Lys Arg Ala Arg Thr Arg Lys465
4703455PRTMarinobacter hydrocarbonoclasticus 3Met Thr Pro Leu Asn
Pro Thr Asp Gln Leu Phe Leu Trp Leu Glu Lys1 5 10 15Arg Gln Gln Pro
Met His Val Gly Gly Leu Gln Leu Phe Ser Phe Pro 20 25 30Glu Gly Ala
Pro Asp Asp Tyr Val Ala Gln Leu Ala Asp Gln Leu Arg 35 40 45Gln Lys
Thr Glu Val Thr Ala Pro Phe Asn Gln Arg Leu Ser Tyr Arg 50 55 60Leu
Gly Gln Pro Val Trp Val Glu Asp Glu His Leu Asp Leu Glu His65 70 75
80His Phe Arg Phe Glu Ala Leu Pro Thr Pro Gly Arg Ile Arg Glu Leu
85 90 95Leu Ser Phe Val Ser Ala Glu His Ser His Leu Met Asp Arg Glu
Arg 100 105 110Pro Met Trp Glu Val His Leu Ile Glu Gly Leu Lys Asp
Arg Gln Phe 115 120 125Ala Leu Tyr Thr Lys Val His His Ser Leu Val
Asp Gly Val Ser Ala 130 135 140Met Arg Met Ala Thr Arg Met Leu Ser
Glu Asn Pro Asp Glu His Gly145 150 155 160Met Pro Pro Ile Trp Asp
Leu Pro Cys Leu Ser Arg Asp Arg Gly Glu 165 170 175Ser Asp Gly His
Ser Leu Trp Arg Ser Val Thr His Leu Leu Gly Leu 180 185 190Ser Asp
Arg Gln Leu Gly Thr Ile Pro Thr Val Ala Lys Glu Leu Leu 195 200
205Lys Thr Ile Asn Gln Ala Arg Lys Asp Pro Ala Tyr Asp Ser Ile Phe
210 215 220His Ala Pro Arg Cys Met Leu Asn Gln Lys Ile Thr Gly Ser
Arg Arg225 230 235 240Phe Ala Ala Gln Ser Trp Cys Leu Lys Arg Ile
Arg Ala Val Cys Glu 245 250 255Ala Tyr Gly Thr Thr Val Asn Asp Val
Val Thr Ala Met Cys Ala Ala 260 265 270Ala Leu Arg Thr Tyr Leu Met
Asn Gln Asp Ala Leu Pro Glu Lys Pro 275 280 285Leu Val Ala Phe Val
Pro Val Ser Leu Arg Arg Asp Asp Ser Ser Gly 290 295 300Gly Asn Gln
Val Gly Val Ile Leu Ala Ser Leu His Thr Asp Val Gln305 310 315
320Asp Ala Gly Glu Arg Leu Leu Lys Ile His His Gly Met Glu Glu Ala
325 330 335Lys Gln Arg Tyr Arg His Met Ser Pro Glu Glu Ile Val Asn
Tyr Thr 340 345 350Ala Leu Thr Leu Ala Pro Ala Ala Phe His Leu Leu
Thr Gly Leu Ala 355 360 365Pro Lys Trp Gln Thr Phe Asn Val Val Ile
Ser Asn Val Pro Gly Pro 370 375 380Ser Arg Pro Leu Tyr Trp Asn Gly
Ala Lys Leu Glu Gly Met Tyr Pro385 390 395 400Val Ser Ile Asp Met
Asp Arg Leu Ala Leu Asn Met Thr Leu Thr Ser 405 410 415Tyr Asn Asp
Gln Val Glu Phe Gly Leu Ile Gly Cys Arg Arg Thr Leu 420 425 430Pro
Ser Leu Gln Arg Met Leu Asp Tyr Leu Glu Gln Gly Leu Ala Glu 435 440
445Leu Glu Leu Asn Ala Gly Leu 450 4554457PRTAlcanivorax
borkumensis 4Met Lys Ala Leu Ser Pro Val Asp Gln Leu Phe Leu Trp
Leu Glu Lys1 5 10 15Arg Gln Gln Pro Met His Val Gly Gly Leu Gln Leu
Phe Ser Phe Pro 20 25 30Glu Gly Ala Gly Pro Lys Tyr Val Ser Glu Leu
Ala Gln Gln Met Arg 35 40 45Asp Tyr Cys His Pro Val Ala Pro Phe Asn
Gln Arg Leu Thr Arg Arg 50 55 60Leu Gly Gln Tyr Tyr Trp Thr Arg Asp
Lys Gln Phe Asp Ile Asp His65 70 75 80His Phe Arg His Glu Ala Leu
Pro Lys Pro Gly Arg Ile Arg Glu Leu 85 90 95Leu Ser Leu Val Ser Ala
Glu His Ser Asn Leu Leu Asp Arg Glu Arg 100 105 110Pro Met Trp Glu
Ala His Leu Ile Glu Gly Ile Arg Gly Arg Gln Phe 115 120 125Ala Leu
Tyr Tyr Lys Ile His His Ser Val Met Asp Gly Ile Ser Ala 130 135
140Met Arg Ile Ala Ser Lys Thr Leu Ser Thr Asp Pro Ser Glu Arg
Glu145 150 155 160Met Ala Pro Ala Trp Ala Phe Asn Thr Lys Lys Arg
Ser Arg Ser Leu 165 170 175Pro Ser Asn Pro Val Asp Met Ala Ser Ser
Met Ala Arg Leu Thr Ala 180 185 190Ser Ile Ser Lys Gln Ala Ala Thr
Val Pro Gly Leu Ala Arg Glu Val 195 200 205Tyr Lys Val Thr Gln Lys
Ala Lys Lys Asp Glu Asn Tyr Val Ser Ile 210 215 220Phe Gln Ala Pro
Asp Thr Ile Leu Asn Asn Thr Ile Thr Gly Ser Arg225 230 235 240Arg
Phe Ala Ala Gln Ser Phe Pro Leu Pro Arg Leu Lys Val Ile Ala 245 250
255Lys Ala Tyr Asn Cys Thr Ile Asn Thr Val Val Leu Ser Met Cys Gly
260 265 270His Ala Leu Arg Glu Tyr Leu Ile Ser Gln His Ala Leu Pro
Asp Glu 275 280 285Pro Leu Ile Ala Met Val Pro Met Ser Leu Arg Gln
Asp Asp Ser Thr 290 295 300Gly Gly Asn Gln Ile Gly Met Ile Leu Ala
Asn Leu Gly Thr His Ile305 310 315 320Cys Asp Pro Ala Asn Arg Leu
Arg Val Ile His Asp Ser Val Glu Glu 325 330 335Ala Lys Ser Arg Phe
Ser Gln Met Ser Pro Glu Glu Ile Leu Asn Phe 340 345 350Thr Ala Leu
Thr Met Ala Pro Thr Gly Leu Asn Leu Leu Thr Gly Leu 355 360 365Ala
Pro Lys Trp Arg Ala Phe Asn Val Val Ile Ser Asn Ile Pro Gly 370 375
380Pro Lys Glu Pro Leu Tyr Trp Asn Gly Ala Gln Leu Gln Gly Val
Tyr385 390 395 400Pro Val Ser Ile Ala Leu Asp Arg Ile Ala Leu Asn
Ile Thr Leu Thr 405 410 415Ser Tyr Val Asp Gln Met Glu Phe Gly Leu
Ile Ala Cys Arg Arg Thr 420 425 430Leu Pro Ser Met Gln Arg Leu Leu
Asp Tyr Leu Glu Gln Ser Ile Arg 435 440 445Glu Leu Glu Ile Gly Ala
Gly Ile Lys 450 4555451PRTAlcanivorax borkumensis 5Met Ala Arg Lys
Leu Ser Ile Met Asp Ser Gly Trp Leu Met Met Glu1 5 10 15Thr Arg Glu
Thr Pro Met His Val Gly Gly Leu Ala Leu Phe Ala Ile 20 25 30Pro Glu
Gly Ala Pro Glu Asp Tyr Val Glu Ser Ile Tyr Arg Tyr Leu 35 40 45Val
Asp Val Asp Ser Ile Cys Arg Pro Phe Asn Gln Lys Ile Gln Ser 50 55
60His Leu Pro Leu Tyr Leu Asp Ala Thr Trp Val Glu Asp Lys Asn Phe65
70 75 80Asp Ile Asp Tyr His Val Arg His Ser Ala Leu Pro Arg Pro Gly
Arg 85 90 95Val Arg Glu Leu Leu Ala Leu Val Ser Arg Leu His Ala Gln
Arg Leu 100 105 110Asp Pro Ser Arg Pro Leu Trp Glu Ser Tyr Leu Ile
Glu Gly Leu Glu 115 120 125Gly Asn Arg Phe Ala Leu Tyr Thr Lys Met
His His Ser Met Val Asp 130 135 140Gly Val Ala Gly Met His Leu Met
Gln Ser Arg Leu Ala Thr Cys Ala145 150 155 160Glu Asp Arg Leu Pro
Ala Pro Trp Ser Gly Glu Trp Asp Ala Glu Lys 165 170 175Lys Pro Arg
Lys Ser Arg Gly Ala Ala Ala Ala Asn Ala Gly Met Lys 180 185 190Gly
Thr Met Asn Asn Leu Arg Arg Gly Gly Gly Gln Leu Val Asp Leu 195 200
205Leu Arg Gln Pro Lys Asp Gly Asn Val Lys Thr Ile Tyr Arg Ala Pro
210 215 220Lys Thr Gln Leu Asn Arg Arg Val Thr Gly Ala Arg Arg Phe
Ala Ala225 230 235 240Gln Ser Trp Ser Leu Ser Arg Ile Lys Ala Ala
Gly Lys Gln His Gly 245 250 255Gly Thr Val Asn Asp Ile Phe Leu Ala
Met Cys Gly Gly Ala Leu Arg 260 265 270Arg Tyr Leu Leu Ser Gln Asp
Ala Leu Ser Asp Gln Pro Leu Val Ala 275 280 285Gln Val Pro Val Ala
Leu Arg Ser Ala Asp Gln Ala Gly Glu Gly Gly 290 295 300Asn Ala Ile
Thr Thr Val Gln Val Ser Leu Gly Thr His Ile Ala Gln305 310 315
320Pro Leu Asn Arg Leu Ala Ala Ile Gln Asp Ser Met Lys Ala Val Lys
325 330 335Ser Arg Leu Gly Asp Met Gln Lys Ser Glu Ile Asp Val Tyr
Thr Val 340 345 350Leu Thr Asn Met Pro Leu Ser Leu Gly Gln Val Thr
Gly Leu Ser Gly 355 360 365Arg Val Ser Pro Met Phe Asn Leu Val Ile
Ser Asn Val Pro Gly Pro 370 375 380Lys Glu Thr Leu His Leu Asn Gly
Ala Glu Met Leu Ala Thr Tyr Pro385 390 395 400Val Ser Leu Val Leu
His Gly Tyr Ala Leu Asn Ile Thr Val Val Ser 405 410 415Tyr Lys Asn
Ser Leu Glu Phe Gly Val Ile Gly Cys Arg Asp Thr Leu 420 425 430Pro
His Ile Gln Arg Phe Leu Val Tyr Leu Glu Glu Ser Leu Val Glu 435 440
445Leu Glu Pro 4506455PRTMarinobacter aquaeolei 6Met Thr Pro Leu
Asn Pro Thr Asp Gln Leu Phe Leu Trp Leu Glu Lys1 5 10 15Arg Gln Gln
Pro Met His Val Gly Gly Leu Gln Leu Phe Ser Phe Pro 20 25 30Glu Gly
Ala Pro Asp Asp Tyr Val Ala Gln Leu Ala Asp Gln Leu Arg 35 40 45Gln
Lys Thr Glu Val Thr Ala Pro Phe Asn Gln Arg Leu Ser Tyr Arg 50 55
60Leu Gly Gln Pro Val Trp Val Glu Asp Glu His Leu Asp Leu Glu His65
70 75 80His Phe Arg Phe Glu Ala Leu Pro Thr Pro Gly Arg Ile Arg Glu
Leu 85 90 95Leu Ser Phe Val Ser Ala Glu His Ser His Leu Met Asp Arg
Glu Arg 100 105 110Pro Met Trp Glu Val His Leu Ile Glu Gly Leu Lys
Asp Arg Gln Phe 115 120 125Ala Leu Tyr Thr Lys Val His His Ser Leu
Val Asp Gly Val Ser Ala 130 135 140Met Arg Met Ala Thr Arg Met Leu
Ser Glu Asn Pro Asp Glu His Gly145 150 155 160Met Pro Pro Ile Trp
Asp Leu Pro Cys Leu Ser Arg Asp Arg Gly Glu 165 170 175Ser Asp Gly
His Ser Leu Trp Arg Ser Val Thr His Leu Leu Gly Leu 180 185 190Ser
Gly Arg Gln Leu Gly Thr Ile Pro Thr Val Ala Lys Glu Leu Leu 195 200
205Lys Thr Ile Asn Gln Ala Arg Lys Asp Pro Ala Tyr Asp Ser Ile Phe
210 215 220His Ala Pro Arg Cys Met Leu Asn Gln Lys Ile Thr Gly Ser
Arg Arg225 230 235 240Phe Ala Ala Gln Ser Trp Cys Leu Lys Arg Ile
Arg Ala Val Cys Glu 245 250 255Ala Tyr Gly Thr Thr Val Asn Asp Val
Val Thr Ala Met Cys Ala Ala 260 265 270Ala Leu Arg Thr Tyr Leu Met
Asn Gln Asp Ala Leu Pro Glu Lys Pro 275 280 285Leu Val Ala Phe Val
Pro Val Ser Leu Arg Arg Asp Asp Ser Ser Gly 290 295 300Gly Asn Gln
Val Gly Val Ile Leu Ala Ser Leu His Thr Asp Val Gln305 310 315
320Glu Ala Gly Glu Arg Leu Leu Lys Ile His His Gly Met Glu Glu Ala
325 330 335Lys Gln Arg Tyr Arg His Met Ser Pro Glu Glu Ile Val Asn
Tyr Thr 340 345 350Ala Leu Thr Leu Ala Pro Ala Ala Phe His Leu Leu
Thr Gly Leu Ala 355 360 365Pro Lys Trp Gln Thr Phe Asn Val Val Ile
Ser Asn Val Pro Gly Pro 370
375 380Ser Arg Pro Leu Tyr Trp Asn Gly Ala Lys Leu Glu Gly Met Tyr
Pro385 390 395 400Val Ser Ile Asp Met Asp Arg Leu Ala Leu Asn Met
Thr Leu Thr Ser 405 410 415Tyr Asn Asp Gln Val Glu Phe Gly Leu Ile
Gly Cys Arg Arg Thr Leu 420 425 430Pro Ser Leu Gln Arg Met Leu Asp
Tyr Leu Glu Gln Gly Leu Ala Glu 435 440 445Leu Glu Leu Asn Ala Gly
Leu 450 4557473PRTMarinobacter aquaeolei 7Met Lys Arg Leu Gly Thr
Leu Asp Ala Ser Trp Leu Ala Val Glu Ser1 5 10 15Glu Asp Thr Pro Met
His Val Gly Thr Leu Gln Ile Phe Ser Leu Pro 20 25 30Glu Gly Ala Pro
Glu Thr Phe Leu Arg Asp Met Val Thr Arg Met Lys 35 40 45Glu Ala Gly
Asp Val Ala Pro Pro Trp Gly Tyr Lys Leu Ala Trp Ser 50 55 60Gly Phe
Leu Gly Arg Val Ile Ala Pro Ala Trp Lys Val Asp Lys Asp65 70 75
80Ile Asp Leu Asp Tyr His Val Arg His Ser Ala Leu Pro Arg Pro Gly
85 90 95Gly Glu Arg Glu Leu Gly Ile Leu Val Ser Arg Leu His Ser Asn
Pro 100 105 110Leu Asp Phe Ser Arg Pro Leu Trp Glu Cys His Val Ile
Glu Gly Leu 115 120 125Glu Asn Asn Arg Phe Ala Leu Tyr Thr Lys Met
His His Ser Met Ile 130 135 140Asp Gly Ile Ser Gly Val Arg Leu Met
Gln Arg Val Leu Thr Thr Asp145 150 155 160Pro Glu Arg Cys Asn Met
Pro Pro Pro Trp Thr Val Arg Pro His Gln 165 170 175Arg Arg Gly Ala
Lys Thr Asp Lys Glu Ala Ser Val Pro Ala Ala Val 180 185 190Ser Gln
Ala Met Asp Ala Leu Lys Leu Gln Ala Asp Met Ala Pro Arg 195 200
205Leu Trp Gln Ala Gly Asn Arg Leu Val His Ser Val Arg His Pro Glu
210 215 220Asp Gly Leu Thr Ala Pro Phe Thr Gly Pro Val Ser Val Leu
Asn His225 230 235 240Arg Val Thr Ala Gln Arg Arg Phe Ala Thr Gln
His Tyr Gln Leu Asp 245 250 255Arg Leu Lys Asn Leu Ala His Ala Ser
Gly Gly Ser Leu Asn Asp Ile 260 265 270Val Leu Tyr Leu Cys Gly Thr
Ala Leu Arg Arg Phe Leu Ala Glu Gln 275 280 285Asn Asn Leu Pro Asp
Thr Pro Leu Thr Ala Gly Ile Pro Val Asn Ile 290 295 300Arg Pro Ala
Asp Asp Glu Gly Thr Gly Thr Gln Ile Ser Phe Met Ile305 310 315
320Ala Ser Leu Ala Thr Asp Glu Ala Asp Pro Leu Asn Arg Leu Gln Gln
325 330 335Ile Lys Thr Ser Thr Arg Arg Ala Lys Glu His Leu Gln Lys
Leu Pro 340 345 350Lys Ser Ala Leu Thr Gln Tyr Thr Met Leu Leu Met
Ser Pro Tyr Ile 355 360 365Leu Gln Leu Met Ser Gly Leu Gly Gly Arg
Met Arg Pro Val Phe Asn 370 375 380Val Thr Ile Ser Asn Val Pro Gly
Pro Glu Asp Thr Leu Tyr Tyr Glu385 390 395 400Gly Ala Arg Leu Glu
Ala Met Tyr Pro Val Ser Leu Ile Ala His Gly 405 410 415Gly Ala Leu
Asn Ile Thr Cys Leu Ser Tyr Ala Gly Ser Leu Asn Phe 420 425 430Gly
Phe Thr Gly Cys Arg Asp Thr Leu Pro Ser Met Gln Lys Leu Ala 435 440
445Val Tyr Thr Gly Glu Ala Leu Asp Glu Leu Glu Ser Leu Ile Leu Pro
450 455 460Pro Lys Lys Arg Ala Arg Thr Arg Lys465
47081173PRTMycobacterium smegmatis 8Met Thr Ser Asp Val His Asp Ala
Thr Asp Gly Val Thr Glu Thr Ala1 5 10 15Leu Asp Asp Glu Gln Ser Thr
Arg Arg Ile Ala Glu Leu Tyr Ala Thr 20 25 30Asp Pro Glu Phe Ala Ala
Ala Ala Pro Leu Pro Ala Val Val Asp Ala 35 40 45Ala His Lys Pro Gly
Leu Arg Leu Ala Glu Ile Leu Gln Thr Leu Phe 50 55 60Thr Gly Tyr Gly
Asp Arg Pro Ala Leu Gly Tyr Arg Ala Arg Glu Leu65 70 75 80Ala Thr
Asp Glu Gly Gly Arg Thr Val Thr Arg Leu Leu Pro Arg Phe 85 90 95Asp
Thr Leu Thr Tyr Ala Gln Val Trp Ser Arg Val Gln Ala Val Ala 100 105
110Ala Ala Leu Arg His Asn Phe Ala Gln Pro Ile Tyr Pro Gly Asp Ala
115 120 125Val Ala Thr Ile Gly Phe Ala Ser Pro Asp Tyr Leu Thr Leu
Asp Leu 130 135 140Val Cys Ala Tyr Leu Gly Leu Val Ser Val Pro Leu
Gln His Asn Ala145 150 155 160Pro Val Ser Arg Leu Ala Pro Ile Leu
Ala Glu Val Glu Pro Arg Ile 165 170 175Leu Thr Val Ser Ala Glu Tyr
Leu Asp Leu Ala Val Glu Ser Val Arg 180 185 190Asp Val Asn Ser Val
Ser Gln Leu Val Val Phe Asp His His Pro Glu 195 200 205Val Asp Asp
His Arg Asp Ala Leu Ala Arg Ala Arg Glu Gln Leu Ala 210 215 220Gly
Lys Gly Ile Ala Val Thr Thr Leu Asp Ala Ile Ala Asp Glu Gly225 230
235 240Ala Gly Leu Pro Ala Glu Pro Ile Tyr Thr Ala Asp His Asp Gln
Arg 245 250 255Leu Ala Met Ile Leu Tyr Thr Ser Gly Ser Thr Gly Ala
Pro Lys Gly 260 265 270Ala Met Tyr Thr Glu Ala Met Val Ala Arg Leu
Trp Thr Met Ser Phe 275 280 285Ile Thr Gly Asp Pro Thr Pro Val Ile
Asn Val Asn Phe Met Pro Leu 290 295 300Asn His Leu Gly Gly Arg Ile
Pro Ile Ser Thr Ala Val Gln Asn Gly305 310 315 320Gly Thr Ser Tyr
Phe Val Pro Glu Ser Asp Met Ser Thr Leu Phe Glu 325 330 335Asp Leu
Ala Leu Val Arg Pro Thr Glu Leu Gly Leu Val Pro Arg Val 340 345
350Ala Asp Met Leu Tyr Gln His His Leu Ala Thr Val Asp Arg Leu Val
355 360 365Thr Gln Gly Ala Asp Glu Leu Thr Ala Glu Lys Gln Ala Gly
Ala Glu 370 375 380Leu Arg Glu Gln Val Leu Gly Gly Arg Val Ile Thr
Gly Phe Val Ser385 390 395 400Thr Ala Pro Leu Ala Ala Glu Met Arg
Ala Phe Leu Asp Ile Thr Leu 405 410 415Gly Ala His Ile Val Asp Gly
Tyr Gly Leu Thr Glu Thr Gly Ala Val 420 425 430Thr Arg Asp Gly Val
Ile Val Arg Pro Pro Val Ile Asp Tyr Lys Leu 435 440 445Ile Asp Val
Pro Glu Leu Gly Tyr Phe Ser Thr Asp Lys Pro Tyr Pro 450 455 460Arg
Gly Glu Leu Leu Val Arg Ser Gln Thr Leu Thr Pro Gly Tyr Tyr465 470
475 480Lys Arg Pro Glu Val Thr Ala Ser Val Phe Asp Arg Asp Gly Tyr
Tyr 485 490 495His Thr Gly Asp Val Met Ala Glu Thr Ala Pro Asp His
Leu Val Tyr 500 505 510Val Asp Arg Arg Asn Asn Val Leu Lys Leu Ala
Gln Gly Glu Phe Val 515 520 525Ala Val Ala Asn Leu Glu Ala Val Phe
Ser Gly Ala Ala Leu Val Arg 530 535 540Gln Ile Phe Val Tyr Gly Asn
Ser Glu Arg Ser Phe Leu Leu Ala Val545 550 555 560Val Val Pro Thr
Pro Glu Ala Leu Glu Gln Tyr Asp Pro Ala Ala Leu 565 570 575Lys Ala
Ala Leu Ala Asp Ser Leu Gln Arg Thr Ala Arg Asp Ala Glu 580 585
590Leu Gln Ser Tyr Glu Val Pro Ala Asp Phe Ile Val Glu Thr Glu Pro
595 600 605Phe Ser Ala Ala Asn Gly Leu Leu Ser Gly Val Gly Lys Leu
Leu Arg 610 615 620Pro Asn Leu Lys Asp Arg Tyr Gly Gln Arg Leu Glu
Gln Met Tyr Ala625 630 635 640Asp Ile Ala Ala Thr Gln Ala Asn Gln
Leu Arg Glu Leu Arg Arg Ala 645 650 655Ala Ala Thr Gln Pro Val Ile
Asp Thr Leu Thr Gln Ala Ala Ala Thr 660 665 670Ile Leu Gly Thr Gly
Ser Glu Val Ala Ser Asp Ala His Phe Thr Asp 675 680 685Leu Gly Gly
Asp Ser Leu Ser Ala Leu Thr Leu Ser Asn Leu Leu Ser 690 695 700Asp
Phe Phe Gly Phe Glu Val Pro Val Gly Thr Ile Val Asn Pro Ala705 710
715 720Thr Asn Leu Ala Gln Leu Ala Gln His Ile Glu Ala Gln Arg Thr
Ala 725 730 735Gly Asp Arg Arg Pro Ser Phe Thr Thr Val His Gly Ala
Asp Ala Thr 740 745 750Glu Ile Arg Ala Ser Glu Leu Thr Leu Asp Lys
Phe Ile Asp Ala Glu 755 760 765Thr Leu Arg Ala Ala Pro Gly Leu Pro
Lys Val Thr Thr Glu Pro Arg 770 775 780Thr Val Leu Leu Ser Gly Ala
Asn Gly Trp Leu Gly Arg Phe Leu Thr785 790 795 800Leu Gln Trp Leu
Glu Arg Leu Ala Pro Val Gly Gly Thr Leu Ile Thr 805 810 815Ile Val
Arg Gly Arg Asp Asp Ala Ala Ala Arg Ala Arg Leu Thr Gln 820 825
830Ala Tyr Asp Thr Asp Pro Glu Leu Ser Arg Arg Phe Ala Glu Leu Ala
835 840 845Asp Arg His Leu Arg Val Val Ala Gly Asp Ile Gly Asp Pro
Asn Leu 850 855 860Gly Leu Thr Pro Glu Ile Trp His Arg Leu Ala Ala
Glu Val Asp Leu865 870 875 880Val Val His Pro Ala Ala Leu Val Asn
His Val Leu Pro Tyr Arg Gln 885 890 895Leu Phe Gly Pro Asn Val Val
Gly Thr Ala Glu Val Ile Lys Leu Ala 900 905 910Leu Thr Glu Arg Ile
Lys Pro Val Thr Tyr Leu Ser Thr Val Ser Val 915 920 925Ala Met Gly
Ile Pro Asp Phe Glu Glu Asp Gly Asp Ile Arg Thr Val 930 935 940Ser
Pro Val Arg Pro Leu Asp Gly Gly Tyr Ala Asn Gly Tyr Gly Asn945 950
955 960Ser Lys Trp Ala Gly Glu Val Leu Leu Arg Glu Ala His Asp Leu
Cys 965 970 975Gly Leu Pro Val Ala Thr Phe Arg Ser Asp Met Ile Leu
Ala His Pro 980 985 990Arg Tyr Arg Gly Gln Val Asn Val Pro Asp Met
Phe Thr Arg Leu Leu 995 1000 1005Leu Ser Leu Leu Ile Thr Gly Val
Ala Pro Arg Ser Phe Tyr Ile 1010 1015 1020Gly Asp Gly Glu Arg Pro
Arg Ala His Tyr Pro Gly Leu Thr Val 1025 1030 1035Asp Phe Val Ala
Glu Ala Val Thr Thr Leu Gly Ala Gln Gln Arg 1040 1045 1050Glu Gly
Tyr Val Ser Tyr Asp Val Met Asn Pro His Asp Asp Gly 1055 1060
1065Ile Ser Leu Asp Val Phe Val Asp Trp Leu Ile Arg Ala Gly His
1070 1075 1080Pro Ile Asp Arg Val Asp Asp Tyr Asp Asp Trp Val Arg
Arg Phe 1085 1090 1095Glu Thr Ala Leu Thr Ala Leu Pro Glu Lys Arg
Arg Ala Gln Thr 1100 1105 1110Val Leu Pro Leu Leu His Ala Phe Arg
Ala Pro Gln Ala Pro Leu 1115 1120 1125Arg Gly Ala Pro Glu Pro Thr
Glu Val Phe His Ala Ala Val Arg 1130 1135 1140Thr Ala Lys Val Gly
Pro Gly Asp Ile Pro His Leu Asp Glu Ala 1145 1150 1155Leu Ile Asp
Lys Tyr Ile Arg Asp Leu Arg Glu Phe Gly Leu Ile 1160 1165
11709341PRTAcinetobacter baylyi 9Met Ala Thr Thr Asn Val Ile His
Ala Tyr Ala Ala Met Gln Ala Gly1 5 10 15Glu Ala Leu Val Pro Tyr Ser
Phe Asp Ala Gly Glu Leu Gln Pro His 20 25 30Gln Val Glu Val Lys Val
Glu Tyr Cys Gly Leu Cys His Ser Asp Val 35 40 45Ser Val Leu Asn Asn
Glu Trp His Ser Ser Val Tyr Pro Val Val Ala 50 55 60Gly His Glu Val
Ile Gly Thr Ile Thr Gln Leu Gly Ser Glu Ala Lys65 70 75 80Gly Leu
Lys Ile Gly Gln Arg Val Gly Ile Gly Trp Thr Ala Glu Ser 85 90 95Cys
Gln Ala Cys Asp Gln Cys Ile Ser Gly Gln Gln Val Leu Cys Thr 100 105
110Gly Glu Asn Thr Ala Thr Ile Ile Gly His Ala Gly Gly Phe Ala Asp
115 120 125Lys Val Arg Ala Gly Trp Gln Trp Val Ile Pro Leu Pro Asp
Glu Leu 130 135 140Asp Pro Thr Ser Ala Gly Pro Leu Leu Cys Gly Gly
Ile Thr Val Phe145 150 155 160Asp Pro Ile Leu Lys His Gln Ile Gln
Ala Ile His His Val Ala Val 165 170 175Ile Gly Ile Gly Gly Leu Gly
His Met Ala Ile Lys Leu Leu Lys Ala 180 185 190Trp Gly Cys Glu Ile
Thr Ala Phe Ser Ser Asn Pro Asn Lys Thr Asp 195 200 205Glu Leu Lys
Ala Met Gly Ala Asp His Val Val Asn Ser Arg Asp Asp 210 215 220Ala
Glu Ile Lys Ser Gln Gln Gly Lys Phe Asp Leu Leu Leu Ser Thr225 230
235 240Val Asn Val Pro Leu Asn Trp Asn Ala Tyr Leu Asn Thr Leu Ala
Pro 245 250 255Asn Gly Thr Phe His Phe Leu Gly Val Val Met Glu Pro
Ile Pro Val 260 265 270Pro Val Gly Ala Leu Leu Gly Gly Ala Lys Ser
Leu Thr Ala Ser Pro 275 280 285Thr Gly Ser Pro Ala Ala Leu Arg Lys
Leu Leu Glu Phe Ala Ala Arg 290 295 300Lys Asn Ile Ala Pro Gln Ile
Glu Met Tyr Pro Met Ser Glu Leu Asn305 310 315 320Glu Ala Ile Glu
Arg Leu His Ser Gly Gln Ala Arg Tyr Arg Ile Val 325 330 335Leu Lys
Ala Asp Phe 34010339PRTEscherichia coli 10Met Ser Met Ile Lys Ser
Tyr Ala Ala Lys Glu Ala Gly Gly Glu Leu1 5 10 15Glu Val Tyr Glu Tyr
Asp Pro Gly Glu Leu Arg Pro Gln Asp Val Glu 20 25 30Val Gln Val Asp
Tyr Cys Gly Ile Cys His Ser Asp Leu Ser Met Ile 35 40 45Asp Asn Glu
Trp Gly Phe Ser Gln Tyr Pro Leu Val Ala Gly His Glu 50 55 60Val Ile
Gly Arg Val Val Ala Leu Gly Ser Ala Ala Gln Asp Lys Gly65 70 75
80Leu Gln Val Gly Gln Arg Val Gly Ile Gly Trp Thr Ala Arg Ser Cys
85 90 95Gly His Cys Asp Ala Cys Ile Ser Gly Asn Gln Ile Asn Cys Glu
Gln 100 105 110Gly Ala Val Pro Thr Ile Met Asn Arg Gly Gly Phe Ala
Glu Lys Leu 115 120 125Arg Ala Asp Trp Gln Trp Val Ile Pro Leu Pro
Glu Asn Ile Asp Ile 130 135 140Glu Ser Ala Gly Pro Leu Leu Cys Gly
Gly Ile Thr Val Phe Lys Pro145 150 155 160Leu Leu Met His His Ile
Thr Ala Thr Ser Arg Val Gly Val Ile Gly 165 170 175Ile Gly Gly Leu
Gly His Ile Ala Ile Lys Leu Leu His Ala Met Gly 180 185 190Cys Glu
Val Thr Ala Phe Ser Ser Asn Pro Ala Lys Glu Gln Glu Val 195 200
205Leu Ala Met Gly Ala Asp Lys Val Val Asn Ser Arg Asp Pro Gln Ala
210 215 220Leu Lys Ala Leu Ala Gly Gln Phe Asp Leu Ile Ile Asn Thr
Val Asn225 230 235 240Val Ser Leu Asp Trp Gln Pro Tyr Phe Glu Ala
Leu Thr Tyr Gly Gly 245 250 255Asn Phe His Thr Val Gly Ala Val Leu
Thr Pro Leu Ser Val Pro Ala 260 265 270Phe Thr Leu Ile Ala Gly Asp
Arg Ser Val Ser Gly Ser Ala Thr Gly 275 280 285Thr Pro Tyr Glu Leu
Arg Lys Leu Met Arg Phe Ala Ala Arg Ser Lys 290 295 300Val Ala Pro
Thr Thr Glu Leu Phe Pro Met Ser Lys Ile Asn Asp Ala305 310 315
320Ile Gln His Val Arg Asp Gly Lys Ala Arg Tyr Arg Val Val Leu Lys
325 330 335Ala Asp Phe11208PRTEscherichia coli 11Met Met Asn Phe
Asn Asn Val Phe Arg Trp His Leu Pro Phe Leu Phe1 5 10 15Leu Val Leu
Leu Thr Phe Arg Ala Ala Ala Ala Asp Thr Leu Leu Ile 20 25 30Leu Gly
Asp Ser Leu Ser Ala Gly Tyr Arg Met Ser Ala Ser Ala Ala 35 40 45Trp
Pro Ala Leu
Leu Asn Asp Lys Trp Gln Ser Lys Thr Ser Val Val 50 55 60Asn Ala Ser
Ile Ser Gly Asp Thr Ser Gln Gln Gly Leu Ala Arg Leu65 70 75 80Pro
Ala Leu Leu Lys Gln His Gln Pro Arg Trp Val Leu Val Glu Leu 85 90
95Gly Gly Asn Asp Gly Leu Arg Gly Phe Gln Pro Gln Gln Thr Glu Gln
100 105 110Thr Leu Arg Gln Ile Leu Gln Asp Val Lys Ala Ala Asn Ala
Glu Pro 115 120 125Leu Leu Met Gln Ile Arg Leu Pro Ala Asn Tyr Gly
Arg Arg Tyr Asn 130 135 140Glu Ala Phe Ser Ala Ile Tyr Pro Lys Leu
Ala Lys Glu Phe Asp Val145 150 155 160Pro Leu Leu Pro Phe Phe Met
Glu Glu Val Tyr Leu Lys Pro Gln Trp 165 170 175Met Gln Asp Asp Gly
Ile His Pro Asn Arg Asp Ala Gln Pro Phe Ile 180 185 190Ala Asp Trp
Met Ala Lys Gln Leu Gln Pro Leu Val Asn His Asp Ser 195 200
20512209PRTEscherichia coli 12Met Val Asp Met Lys Thr Thr His Thr
Ser Leu Pro Phe Ala Gly His1 5 10 15Thr Leu His Phe Val Glu Phe Asp
Pro Ala Asn Phe Cys Glu Gln Asp 20 25 30Leu Leu Trp Leu Pro His Tyr
Ala Gln Leu Gln His Ala Gly Arg Lys 35 40 45Arg Lys Thr Glu His Leu
Ala Gly Arg Ile Ala Ala Val Tyr Ala Leu 50 55 60Arg Glu Tyr Gly Tyr
Lys Cys Val Pro Ala Ile Gly Glu Leu Arg Gln65 70 75 80Pro Val Trp
Pro Ala Glu Val Tyr Gly Ser Ile Ser His Cys Gly Thr 85 90 95Thr Ala
Leu Ala Val Val Ser Arg Gln Pro Ile Gly Ile Asp Ile Glu 100 105
110Glu Ile Phe Ser Val Gln Thr Ala Arg Glu Leu Thr Asp Asn Ile Ile
115 120 125Thr Pro Ala Glu His Glu Arg Leu Ala Asp Cys Gly Leu Ala
Phe Ser 130 135 140Leu Ala Leu Thr Leu Ala Phe Ser Ala Lys Glu Ser
Ala Phe Lys Ala145 150 155 160Ser Glu Ile Gln Thr Asp Ala Gly Phe
Leu Asp Tyr Gln Ile Ile Ser 165 170 175Trp Asn Lys Gln Gln Val Ile
Ile His Arg Glu Asn Glu Met Phe Ala 180 185 190Val His Trp Gln Ile
Lys Glu Lys Ile Val Ile Thr Leu Cys Gln His 195 200
205Asp1312397DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 13cactatacca
attgagatgg gctagtcaat gataattact agtccttttc ctttgagttg 60tgggtatctg
taaattctgc tagacctttg ctggaaaact tgtaaattct gctagaccct
120ctgtaaattc cgctagacct ttgtgtgttt tttttgttta tattcaagtg
gttataattt 180atagaataaa gaaagaataa aaaaagataa aaagaataga
tcccagccct gtgtataact 240cactacttta gtcagttccg cagtattaca
aaaggatgtc gcaaacgctg tttgctcctc 300tacaaaacag accttaaaac
cctaaaggcg tcggcatccg cttacagaca agctgtgacc 360gtctccggga
gctgcatgtg tcagaggttt tcaccgtcat caccgaaacg cgcgaggcag
420cagatcaatt cgcgcgcgaa ggcgaagcgg catgcattta cgttgacacc
atcgaatggt 480gcaaaacctt tcgcggtatg gcatgatagc gcccggaaga
gagtcaattc agggtggtga 540atgtgaaacc agtaacgtta tacgatgtcg
cagagtatgc cggtgtctct tatcagaccg 600tttcccgcgt ggtgaaccag
gccagccacg tttctgcgaa aacgcgggaa aaagtggaag 660cggcgatggc
ggagctgaat tacattccca accgcgtggc acaacaactg gcgggcaaac
720agtcgttgct gattggcgtt gccacctcca gtctggccct gcacgcgccg
tcgcaaattg 780tcgcggcgat taaatctcgc gccgatcaac tgggtgccag
cgtggtggtg tcgatggtag 840aacgaagcgg cgtcgaagcc tgtaaagcgg
cggtgcacaa tcttctcgcg caacgcgtca 900gtgggctgat cattaactat
ccgctggatg accaggatgc cattgctgtg gaagctgcct 960gcactaatgt
tccggcgtta tttcttgatg tctctgacca gacacccatc aacagtatta
1020ttttctccca tgaagacggt acgcgactgg gcgtggagca tctggtcgca
ttgggtcacc 1080agcaaatcgc gctgttagcg ggcccattaa gttctgtctc
ggcgcgtctg cgtctggctg 1140gctggcataa atatctcact cgcaatcaaa
ttcagccgat agcggaacgg gaaggcgact 1200ggagtgccat gtccggtttt
caacaaacca tgcaaatgct gaatgagggc atcgttccca 1260ctgcgatgct
ggttgccaac gatcagatgg cgctgggcgc aatgcgcgcc attaccgagt
1320ccgggctgcg cgttggtgcg gatatctcgg tagtgggata cgacgatacc
gaagacagct 1380catgttatat cccgccgtta accaccatca aacaggattt
tcgcctgctg gggcaaacca 1440gcgtggaccg cttgctgcaa ctctctcagg
gccaggcggt gaagggcaat cagctgttgc 1500ccgtctcact ggtgaaaaga
aaaaccaccc tggcgcccaa tacgcaaacc gcctctcccc 1560gcgcgttggc
cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc
1620agtgagcgca acgcaattaa tgtaagttag cgcgaattga tctggtttga
cagcttatca 1680tcgactgcac ggtgcaccaa tgcttctggc gtcaggcagc
catcggaagc tgtggtatgg 1740ctgtgcaggt cgtaaatcac tgcataattc
gtgtcgctca aggcgcactc ccgttctgga 1800taatgttttt tgcgccgaca
tcataacggt tctggcaaat attctgaaat gagctgttga 1860caattaatca
tccggctcgt ataatgtgtg gaattgtgag cggataacaa tttcacacag
1920gaaacagcgc cgctgagaaa aagcgaagcg gcactgctct ttaacaattt
atcagacaat 1980ctgtgtgggc actcgaccgg aattatcgat taactttatt
attaaaaatt aaagaggtat 2040atattaatgt atcgattaaa taaggaggaa
taaaccatga cgagcgatgt tcacgacgcg 2100accgacggcg ttaccgagac
tgcactggat gatgagcaga gcactcgtcg tattgcagaa 2160ctgtacgcaa
cggacccaga gttcgcagca gcagctcctc tgccggccgt tgtcgatgcg
2220gcgcacaaac cgggcctgcg tctggcggaa atcctgcaga ccctgttcac
cggctacggc 2280gatcgtccgg cgctgggcta tcgtgcacgt gagctggcga
cggacgaagg cggtcgtacg 2340gtcacgcgtc tgctgccgcg cttcgatacc
ctgacctatg cacaggtgtg gagccgtgtt 2400caagcagtgg ctgcagcgtt
gcgtcacaat ttcgcacaac cgatttaccc gggcgacgcg 2460gtcgcgacta
tcggctttgc gagcccggac tatttgacgc tggatctggt gtgcgcgtat
2520ctgggcctgg tcagcgttcc tttgcagcat aacgctccgg tgtctcgcct
ggccccgatt 2580ctggccgagg tggaaccgcg tattctgacg gtgagcgcag
aatacctgga cctggcggtt 2640gaatccgtcc gtgatgtgaa ctccgtcagc
cagctggttg ttttcgacca tcatccggaa 2700gtggacgatc accgtgacgc
actggctcgc gcacgcgagc agctggccgg caaaggtatc 2760gcagttacga
ccctggatgc gatcgcagac gaaggcgcag gtttgccggc tgagccgatt
2820tacacggcgg atcacgatca gcgtctggcc atgattctgt ataccagcgg
ctctacgggt 2880gctccgaaag gcgcgatgta caccgaagcg atggtggctc
gcctgtggac tatgagcttt 2940atcacgggcg acccgacccc ggttatcaac
gtgaacttca tgccgctgaa ccatctgggc 3000ggtcgtatcc cgattagcac
cgccgtgcag aatggcggta ccagctactt cgttccggaa 3060agcgacatga
gcacgctgtt tgaggatctg gccctggtcc gccctaccga actgggtctg
3120gtgccgcgtg ttgcggacat gctgtaccag catcatctgg cgaccgtgga
tcgcctggtg 3180acccagggcg cggacgaact gactgcggaa aagcaggccg
gtgcggaact gcgtgaacag 3240gtcttgggcg gtcgtgttat caccggtttt
gtttccaccg cgccgttggc ggcagagatg 3300cgtgcttttc tggatatcac
cttgggtgca cacatcgttg acggttacgg tctgaccgaa 3360accggtgcgg
tcacccgtga tggtgtgatt gttcgtcctc cggtcattga ttacaagctg
3420atcgatgtgc cggagctggg ttacttctcc accgacaaac cgtacccgcg
tggcgagctg 3480ctggttcgta gccaaacgtt gactccgggt tactacaagc
gcccagaagt caccgcgtcc 3540gttttcgatc gcgacggcta ttaccacacc
ggcgacgtga tggcagaaac cgcgccagac 3600cacctggtgt atgtggaccg
ccgcaacaat gttctgaagc tggcgcaagg tgaatttgtc 3660gccgtggcta
acctggaggc cgttttcagc ggcgctgctc tggtccgcca gattttcgtg
3720tatggtaaca gcgagcgcag ctttctgttg gctgttgttg tccctacccc
ggaggcgctg 3780gagcaatacg accctgccgc attgaaagca gccctggcgg
attcgctgca gcgtacggcg 3840cgtgatgccg agctgcagag ctatgaagtg
ccggcggact tcattgttga gactgagcct 3900tttagcgctg cgaacggtct
gctgagcggt gttggcaagt tgctgcgtcc gaatttgaag 3960gatcgctacg
gtcagcgttt ggagcagatg tacgcggaca tcgcggctac gcaggcgaac
4020caattgcgtg aactgcgccg tgctgcggct actcaaccgg tgatcgacac
gctgacgcaa 4080gctgcggcga ccatcctggg taccggcagc gaggttgcaa
gcgacgcaca ctttactgat 4140ttgggcggtg attctctgag cgcgctgacg
ttgagcaact tgctgtctga cttctttggc 4200tttgaagtcc cggttggcac
gattgttaac ccagcgacta atctggcaca gctggcgcaa 4260catatcgagg
cgcagcgcac ggcgggtgac cgccgtccat cctttacgac ggtccacggt
4320gcggatgcta cggaaatccg tgcaagcgaa ctgactctgg acaaattcat
cgacgctgag 4380actctgcgcg cagcacctgg tttgccgaag gttacgactg
agccgcgtac ggtcctgttg 4440agcggtgcca atggttggtt gggccgcttc
ctgaccctgc agtggctgga acgtttggca 4500ccggttggcg gtaccctgat
caccattgtg cgcggtcgtg acgatgcagc ggcacgtgca 4560cgtttgactc
aggcttacga tacggaccca gagctgtccc gccgcttcgc tgagttggcg
4620gatcgccact tgcgtgtggt ggcaggtgat atcggcgatc cgaatctggg
cctgaccccg 4680gagatttggc accgtctggc agcagaggtc gatctggtcg
ttcatccagc ggccctggtc 4740aaccacgtcc tgccgtaccg ccagctgttt
ggtccgaatg ttgttggcac cgccgaagtt 4800atcaagttgg ctctgaccga
gcgcatcaag cctgttacct acctgtccac ggttagcgtc 4860gcgatgggta
ttcctgattt tgaggaggac ggtgacattc gtaccgtcag cccggttcgt
4920ccgctggatg gtggctatgc aaatggctat ggcaacagca agtgggctgg
cgaggtgctg 4980ctgcgcgagg cacatgacct gtgtggcctg ccggttgcga
cgtttcgtag cgacatgatt 5040ctggcccacc cgcgctaccg tggccaagtg
aatgtgccgg acatgttcac ccgtctgctg 5100ctgtccctgc tgatcacggg
tgtggcaccg cgttccttct acattggtga tggcgagcgt 5160ccgcgtgcac
actacccggg cctgaccgtc gattttgttg cggaagcggt tactaccctg
5220ggtgctcagc aacgtgaggg ttatgtctcg tatgacgtta tgaatccgca
cgatgacggt 5280attagcttgg atgtctttgt ggactggctg attcgtgcgg
gccacccaat tgaccgtgtt 5340gacgactatg atgactgggt gcgtcgtttt
gaaaccgcgt tgaccgcctt gccggagaaa 5400cgtcgtgcgc agaccgttct
gccgctgctg catgcctttc gcgcgccaca ggcgccgttg 5460cgtggcgccc
ctgaaccgac cgaagtgttt catgcagcgg tgcgtaccgc taaagtcggt
5520ccgggtgata ttccgcacct ggatgaagcc ctgatcgaca agtacatccg
tgacctgcgc 5580gagttcggtc tgatttagaa ttccataatt gctgttagga
gatatatatg gcggacacgt 5640tattgattct gggtgatagc ctgagcgccg
ggtatcgaat gtctgccagc gcggcctggc 5700ctgccttgtt gaatgataag
tggcagagta aaacgtcggt agttaatgcc agcatcagcg 5760gcgacacctc
gcaacaagga ctggcgcgcc ttccggctct gctgaaacag catcagccgc
5820gttgggtgct ggttgaactg ggcggctgtg acggtttgcg tggttttcag
ccacagcaaa 5880ccgagcaaac gctgcgccag attttgcagg atgtcaaagc
cgccaacgct cttccattgt 5940taatgcaaat acgtctgcct tacaactatg
gtcgtcgtta taatgaagcc tttagcgcca 6000tttaccccaa actcgccaaa
gagtttgatg ttccgctgct gccctttttt atggaagagg 6060tctgcctcaa
gccacaatgg atgcaggatg acggtattca tcccaaccgc gacgcccagc
6120cgtttattgc cgactggatg gcgaagcagt tgcagccttt aaccaatcat
gactcataag 6180cttctaagga aataatagga gattgaaaat ggcaacaact
aatgtgattc atgcttatgc 6240tgcaatgcag gcaggtgaag cactcgtgcc
ttattcgttt gatgcaggcg aactgcaacc 6300acatcaggtt gaagttaaag
tcgaatattg tgggctgtgc cattccgatg tctcggtact 6360caacaacgaa
tggcattctt cggtttatcc agtcgtggca ggtcatgaag tgattggtac
6420gattacccaa ctgggaagtg aagccaaagg actaaaaatt ggtcaacgtg
ttggtattgg 6480ctggacggca gaaagctgtc aggcctgtga ccaatgcatc
agtggtcagc aggtattgtg 6540cacgggcgaa aataccgcaa ctattattgg
tcatgctggt ggctttgcag ataaggttcg 6600tgcaggctgg caatgggtca
ttcccctgcc cgacgaactc gatccgacca gtgctggtcc 6660tttgctgtgt
ggcggaatca cagtatttga tccaatttta aaacatcaga ttcaggctat
6720tcatcatgtt gctgtgattg gtatcggtgg tttgggacat atggccatca
agctacttaa 6780agcatggggc tgtgaaatta ctgcgtttag ttcaaatcca
aacaaaaccg atgagctcaa 6840agctatgggg gccgatcacg tggtcaatag
ccgtgatgat gccgaaatta aatcgcaaca 6900gggtaaattt gatttactgc
tgagtacagt taatgtgcct ttaaactgga atgcgtatct 6960aaacacactg
gcacccaatg gcactttcca ttttttgggc gtggtgatgg aaccaatccc
7020tgtacctgtc ggtgcgctgc taggaggtgc caaatcgcta acagcatcac
caactggctc 7080gcctgctgcc ttacgtaagc tgctcgaatt tgcggcacgt
aagaatatcg cacctcaaat 7140cgagatgtat cctatgtcgg agctgaatga
ggccatcgaa cgcttacatt cgggtcaagc 7200acgttatcgg attgtactta
aagccgattt ttaacctagg gataatagag gttaagagcg 7260gccagatgcc
acattcctac gattacgatg ccatagtaat aggttccggc cccggcggcg
7320aaggcgctgc aatgggcctg gttaagcaag gtgcgcgcgt cgcagttatc
gagcgttatc 7380aaaatgttgg cggcggttgc acccactggg gcaccatccc
gtcgaaagct ctccgtcacg 7440ccgtcagccg cattatagaa ttcaatcaaa
acccacttta cagcgaccat tcccgactgc 7500tccgctcttc ttttgccgat
atccttaacc atgccgataa cgtgattaat caacaaacgc 7560gcatgcgtca
gggattttac gaacgtaatc actgtgaaat attgcaggga aacgctcgct
7620ttgttgacga gcatacgttg gcgctggatt gcccggacgg cagcgttgaa
acactaaccg 7680ctgaaaaatt tgttattgcc tgcggctctc gtccatatca
tccaacagat gttgatttca 7740cccatccacg catttacgac agcgactcaa
ttctcagcat gcaccacgaa ccgcgccatg 7800tacttatcta tggtgctgga
gtgatcggct gtgaatatgc gtcgatcttc cgcggtatgg 7860atgtaaaagt
ggatctgatc aacacccgcg atcgcctgct ggcatttctc gatcaagaga
7920tgtcagattc tctctcctat cacttctgga acagtggcgt agtgattcgt
cacaacgaag 7980agtacgagaa gatcgaaggc tgtgacgatg gtgtgatcat
gcatctgaag tcgggtaaaa 8040aactgaaagc tgactgcctg ctctatgcca
acggtcgcac cggtaatacc gattcgctgg 8100cgttacagaa cattgggcta
gaaactgaca gccgcggaca gctgaaggtc aacagcatgt 8160atcagaccgc
acagccacac gtttacgcgg tgggcgacgt gattggttat ccgagcctgg
8220cgtcggcggc ctatgaccag gggcgcattg ccgcgcaggc gctggtaaaa
ggcgaagcca 8280ccgcacatct gattgaagat atccctaccg gtatttacac
catcccggaa atcagctctg 8340tgggcaaaac cgaacagcag ctgaccgcaa
tgaaagtgcc atatgaagtg ggccgcgccc 8400agtttaaaca tctggcacgc
gcacaaatcg tcggcatgaa cgtgggcacg ctgaaaattt 8460tgttccatcg
ggaaacaaaa gagattctgg gtattcactg ctttggcgag cgcgctgccg
8520aaattattca tatcggtcag gcgattatgg aacagaaagg tggcggcaac
actattgagt 8580acttcgtcaa caccaccttt aactacccga cgatggcgga
agcctatcgg gtagctgcgt 8640taaacggttt aaaccgcctg ttttaaactt
tatcgaaatg gccatccatt cttggtttaa 8700acggtctcca gcttggctgt
tttggcggat gagagaagat tttcagcctg atacagatta 8760aatcagaacg
cagaagcggt ctgataaaac agaatttgcc tggcggcagt agcgcggtgg
8820tcccacctga ccccatgccg aactcagaag tgaaacgccg tagcgccgat
ggtagtgtgg 8880ggtctcccca tgcgagagta gggaactgcc aggcatcaaa
taaaacgaaa ggctcagtcg 8940aaagactggg cctttcgttt tatctgttgt
ttgtcggtga acgctctcct gacgcctgat 9000gcggtatttt ctccttacgc
atctgtgcgg tatttcacac cgcatatggt gcactctcag 9060tacaatctgc
tctgatgccg catagttaag ccagccccga cacccgccaa cacccgctga
9120cgagcttagt aaagccctcg ctagatttta atgcggatgt tgcgattact
tcgccaacta 9180ttgcgataac aagaaaaagc cagcctttca tgatatatct
cccaatttgt gtagggctta 9240ttatgcacgc ttaaaaataa taaaagcaga
cttgacctga tagtttggct gtgagcaatt 9300atgtgcttag tgcatctaac
gcttgagtta agccgcgccg cgaagcggcg tcggcttgaa 9360cgaattgtta
gacattattt gccgactacc ttggtgatct cgcctttcac gtagtggaca
9420aattcttcca actgatctgc gcgcgaggcc aagcgatctt cttcttgtcc
aagataagcc 9480tgtctagctt caagtatgac gggctgatac tgggccggca
ggcgctccat tgcccagtcg 9540gcagcgacat ccttcggcgc gattttgccg
gttactgcgc tgtaccaaat gcgggacaac 9600gtaagcacta catttcgctc
atcgccagcc cagtcgggcg gcgagttcca tagcgttaag 9660gtttcattta
gcgcctcaaa tagatcctgt tcaggaaccg gatcaaagag ttcctccgcc
9720gctggaccta ccaaggcaac gctatgttct cttgcttttg tcagcaagat
agccagatca 9780atgtcgatcg tggctggctc gaagatacct gcaagaatgt
cattgcgctg ccattctcca 9840aattgcagtt cgcgcttagc tggataacgc
cacggaatga tgtcgtcgtg cacaacaatg 9900gtgacttcta cagcgcggag
aatctcgctc tctccagggg aagccgaagt ttccaaaagg 9960tcgttgatca
aagctcgccg cgttgtttca tcaagcctta cggtcaccgt aaccagcaaa
10020tcaatatcac tgtgtggctt caggccgcca tccactgcgg agccgtacaa
atgtacggcc 10080agcaacgtcg gttcgagatg gcgctcgatg acgccaacta
cctctgatag ttgagtcgat 10140acttcggcga tcaccgcttc cctcatgatg
tttaactttg ttttagggcg actgccctgc 10200tgcgtaacat cgttgctgct
ccataacatc aaacatcgac ccacggcgta acgcgcttgc 10260tgcttggatg
cccgaggcat agactgtacc ccaaaaaaac agtcataaca agccatgaaa
10320accgccactg cgccgttacc accgctgcgt tcggtcaagg ttctggacca
gttgcgtgag 10380cgcatacgct acttgcatta cagcttacga accgaacagg
cttatgtcca ctgggttcgt 10440gccttcatcc gtttccacgg tgtgcgtcac
ccggcaacct tgggcagcag cgaagtcgag 10500gcatttctgt cctggctggc
gaacgagcgc aaggtttcgg tctccacgca tcgtcaggca 10560ttggcggcct
tgctgttctt ctacggcaag gtgctgtgca cggatctgcc ctggcttcag
10620gagatcggaa gacctcggcc gtcgcggcgc ttgccggtgg tgctgacccc
ggatgaagtg 10680gttcgcatcc tcggttttct ggaaggcgag catcgtttgt
tcgcccagct tctgtatgga 10740acgggcatgc ggatcagtga gggtttgcaa
ctgcgggtca aggatctgga tttcgatcac 10800ggcacgatca tcgtgcggga
gggcaagggc tccaaggatc gggccttgat gttacccgag 10860agcttggcac
ccagcctgcg cgagcagggg aattaattcc cacgggtttt gctgcccgca
10920aacgggctgt tctggtgttg ctagtttgtt atcagaatcg cagatccggc
ttcagccggt 10980ttgccggctg aaagcgctat ttcttccaga attgccatga
ttttttcccc acgggaggcg 11040tcactggctc ccgtgttgtc ggcagctttg
attcgataag cagcatcgcc tgtttcaggc 11100tgtctatgtg tgactgttga
gctgtaacaa gttgtctcag gtgttcaatt tcatgttcta 11160gttgctttgt
tttactggtt tcacctgttc tattaggtgt tacatgctgt tcatctgtta
11220cattgtcgat ctgttcatgg tgaacagctt tgaatgcacc aaaaactcgt
aaaagctctg 11280atgtatctat cttttttaca ccgttttcat ctgtgcatat
ggacagtttt ccctttgata 11340tgtaacggtg aacagttgtt ctacttttgt
ttgttagtct tgatgcttca ctgatagata 11400caagagccat aagaacctca
gatccttccg tatttagcca gtatgttctc tagtgtggtt 11460cgttgttttt
gcgtgagcca tgagaacgaa ccattgagat catacttact ttgcatgtca
11520ctcaaaaatt ttgcctcaaa actggtgagc tgaatttttg cagttaaagc
atcgtgtagt 11580gtttttctta gtccgttatg taggtaggaa tctgatgtaa
tggttgttgg tattttgtca 11640ccattcattt ttatctggtt gttctcaagt
tcggttacga gatccatttg tctatctagt 11700tcaacttgga aaatcaacgt
atcagtcggg cggcctcgct tatcaaccac caatttcata 11760ttgctgtaag
tgtttaaatc tttacttatt ggtttcaaaa cccattggtt aagcctttta
11820aactcatggt agttattttc aagcattaac atgaacttaa attcatcaag
gctaatctct 11880atatttgcct tgtgagtttt cttttgtgtt agttctttta
ataaccactc ataaatcctc 11940atagagtatt tgttttcaaa agacttaaca
tgttccagat tatattttat gaattttttt 12000aactggaaaa gataaggcaa
tatctcttca ctaaaaacta attctaattt ttcgcttgag 12060aacttggcat
agtttgtcca ctggaaaatc tcaaagcctt taaccaaagg attcctgatt
12120tccacagttc tcgtcatcag ctctctggtt gctttagcta atacaccata
agcattttcc 12180ctactgatgt tcatcatctg agcgtattgg ttataagtga
acgataccgt ccgttctttc 12240cttgtagggt tttcaatcgt ggggttgagt
agtgccacac agcataaaat tagcttggtt 12300tcatgctccg ttaagtcata
gcgactaatc gctagttcat ttgctttgaa aacaactaat 12360tcagacatac
atctcaattg gtctaggtga ttttaat 12397143227DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 14gacgaaaggg cctcgtgata cgcctatttt tataggttaa
tgtcatgata ataatggttt 60cttagacgtc aggtggcact tttcggggaa atgtgcgcgg
aacccctatt tgtttatttt 120tctaaataca ttcaaatatg tatccgctca
tgagacaata accctgataa atgcttcaat 180aatattgaaa
aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt
240ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa
gtaaaagatg 300ctgaagatca gttgggtgca cgagtgggtt acatcgaact
ggatctcaac agcggtaaga 360tccttgagag ttttcgcccc gaagaacgtt
ttccaatgat gagcactttt aaagttctgc 420tatgtggcgc ggtattatcc
cgtattgacg ccgggcaaga gcaactcggt cgccgcatac 480actattctca
gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg
540gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac
actgcggcca 600acttacttct gacaacgatc ggaggaccga aggagctaac
cgcttttttg cacaacatgg 660gggatcatgt aactcgcctt gatcgttggg
aaccggagct gaatgaagcc ataccaaacg 720acgagcgtga caccacgatg
cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg 780gcgaactact
tactctagct tcccggcaac aattaataga ctggatggag gcggataaag
840ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct
gataaatctg 900gagccggtga gcgtgggtct cgcggtatca ttgcagcact
ggggccagat ggtaagccct 960cccgtatcgt agttatctac acgacgggga
gtcaggcaac tatggatgaa cgaaatagac 1020agatcgctga gataggtgcc
tcactgatta agcattggta actgtcagac caagtttact 1080catatatact
ttagattgat ttaaaacttc atttttaatt tgtgcatccg aagatcagca
1140gttcaacctg ttgatagtac gtactaagct ctcatgtttc acgtactaag
ctctcatgtt 1200taacgtacta agctctcatg tttaacgaac taaaccctca
tggctaacgt actaagctct 1260catggctaac gtactaagct ctcatgtttg
aacaataaaa ttaatataaa tcagcaactt 1320aaatagcctc taaggtttta
agttttataa gaaaaaaaag aatatataag gcttttaaag 1380ctagctttta
aggtttcacc atgttctttc ctgcgttatc ccctgattct gtggataacc
1440gtattaccgc ctttgagtga gctgataccg ctcgccgcag ccgaacgacc
gagcgcagcg 1500agtcagtgag cgaggaagcg gaagagcgcc caatacgcaa
accgcctctc cccgcgcgtt 1560ggccgattca ttaagacagc tgtctcttat
acacatctca accctgaagc tcttgttggc 1620tagtgcgtag tcgttggcaa
gctttccgct gtttctgcat tcttacgttt taggatgcat 1680atggcggccg
cataacttcg tatagcatac attatacgaa gttatctaga gttgcatgcc
1740tgcaggtccg cttattatca cttattcagg cgtagcaacc aggcgtttaa
gggcaccaat 1800aactgcctta aaaaaattac gccccgccct gccactcatc
gcagtactgt tgtaattcat 1860taagcattct gccgacatgg aagccatcac
aaacggcatg atgaacctga atcgccagcg 1920gcatcagcac cttgtcgcct
tgcgtataat atttgcccat ggtgaaaacg ggggcgaaga 1980agttgtccat
attggccacg tttaaatcaa aactggtgaa actcacccag ggattggctg
2040agacgaaaaa catattctca ataaaccctt tagggaaata ggccaggttt
tcaccgtaac 2100acgccacatc ttgcgaatat atgtgtagaa actgccggaa
atcgtcgtgg tattcactcc 2160agagcgatga aaacgtttca gtttgctcat
ggaaaacggt gtaacaaggg tgaacactat 2220cccatatcac cagctcaccg
tctttcattg ccatacggaa ttccggatga gcattcatca 2280ggcgggcaag
aatgtgaata aaggccggat aaaacttgtg cttatttttc tttacggtct
2340ttaaaaaggc cgtaatatcc agctgaacgg tctggttata ggtacattga
gcaactgact 2400gaaatgcctc aaaatgttct ttacgatgcc attgggatat
atcaacggtg gtatatccag 2460tgattttttt ctccatttta gcttccttag
ctcctgaaaa tctcgataac tcaaaaaata 2520cgcccggtag tgatcttatt
tcattatggt gaaagttgga acctcttacg tgccgatcaa 2580cgtctcattt
tcgccaaaag ttggcccagg gcttcccggt atcaacaggg acaccaggat
2640ttatttattc tgcgaagtga tcttccgtca caggtattta ttcgactcta
gataacttcg 2700tatagcatac attatacgaa gttatggatc cagcttatcg
ataccgtcaa acaaatcata 2760aaaaatttat ttgctttcag gaaaattttt
ctgtataata gattcaattg cgatgacgac 2820gaacacgcat taaggaggtg
aagagctcga attcgagcca atatgcgaga acacccgaga 2880aaattcatcg
atgatggttg agatgtgtat aagagacagc tgtcgtaata gcgaagaggc
2940ccgcaccgat cgcccttccc aacagttgcg cagcctgaat ggcgaatggc
gcctgatgcg 3000gtattttctc cttacgcatc tgtgcggtat ttcacaccgc
atatggtgca ctctcagtac 3060aatctgctct gatgccgcat agttaagcca
gccccgacac ccgccaacac ccgctgacgc 3120gccctgacgg gcttgtctgc
tcccggcatc cgcttacaga caagctgtga ccgtctccgg 3180gagctgcatg
tgtcagaggt tttcaccgtc atcaccgaaa cgcgcga 32271540DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 15gcagttattg gtgcccttaa acgcctggtt gctacgcctg
401634DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 16cccagggctt cccggtatca acagggacac cagg
341725DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 17atggtcatta aggcgcaaag cccgg
251853DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 18gagaccccac actaccatcc tcgagttatc
gcccctgaat ggctaaatca ccc 531927DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 19ctcgaggatg gtagtgtggg gtctccc 272069DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 20gagaccgttt ctcgaattta aatatgatac gctcgagctt cgtctgtttc
tactggtatt 60ggcacaaac 692165DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer"modified_base(16)..(16)a, c, t, g, unknown or
othermodified_base(21)..(21)a, c, t, g, unknown or
othermodified_base(27)..(27)a, c, t, g, unknown or
othermodified_base(34)..(40)a, c, t, g, unknown or other
21tgaaagatta aatttnhhar nddhddnwag gagnnnnnnn atggtcatta aggcgcaaag
60cccgg 652212206DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 22cactatacca
attgagatgg gctagtcaat gataattact agtccttttc ctttgagttg 60tgggtatctg
taaattctgc tagacctttg ctggaaaact tgtaaattct gctagaccct
120ctgtaaattc cgctagacct ttgtgtgttt tttttgttta tattcaagtg
gttataattt 180atagaataaa gaaagaataa aaaaagataa aaagaataga
tcccagccct gtgtataact 240cactacttta gtcagttccg cagtattaca
aaaggatgtc gcaaacgctg tttgctcctc 300tacaaaacag accttaaaac
cctaaaggcg tcggcatccg cttacagaca agctgtgacc 360gtctccggga
gctgcatgtg tcagaggttt tcaccgtcat caccgaaacg cgcgaggcag
420cagatcaatt cgcgcgcgaa ggcgaagcgg catgcattta cgttgacacc
atcgaatggt 480gcaaaacctt tcgcggtatg gcatgatagc gcccggaaga
gagtcaattc agggtggtga 540atgtgaaacc agtaacgtta tacgatgtcg
cagagtatgc cggtgtctct tatcagaccg 600tttcccgcgt ggtgaaccag
gccagccacg tttctgcgaa aacgcgggaa aaagtggaag 660cggcgatggc
ggagctgaat tacattccca accgcgtggc acaacaactg gcgggcaaac
720agtcgttgct gattggcgtt gccacctcca gtctggccct gcacgcgccg
tcgcaaattg 780tcgcggcgat taaatctcgc gccgatcaac tgggtgccag
cgtggtggtg tcgatggtag 840aacgaagcgg cgtcgaagcc tgtaaagcgg
cggtgcacaa tcttctcgcg caacgcgtca 900gtgggctgat cattaactat
ccgctggatg accaggatgc cattgctgtg gaagctgcct 960gcactaatgt
tccggcgtta tttcttgatg tctctgacca gacacccatc aacagtatta
1020ttttctccca tgaagacggt acgcgactgg gcgtggagca tctggtcgca
ttgggtcacc 1080agcaaatcgc gctgttagcg ggcccattaa gttctgtctc
ggcgcgtctg cgtctggctg 1140gctggcataa atatctcact cgcaatcaaa
ttcagccgat agcggaacgg gaaggcgact 1200ggagtgccat gtccggtttt
caacaaacca tgcaaatgct gaatgagggc atcgttccca 1260ctgcgatgct
ggttgccaac gatcagatgg cgctgggcgc aatgcgcgcc attaccgagt
1320ccgggctgcg cgttggtgcg gatatctcgg tagtgggata cgacgatacc
gaagacagct 1380catgttatat cccgccgtta accaccatca aacaggattt
tcgcctgctg gggcaaacca 1440gcgtggaccg cttgctgcaa ctctctcagg
gccaggcggt gaagggcaat cagctgttgc 1500ccgtctcact ggtgaaaaga
aaaaccaccc tggcgcccaa tacgcaaacc gcctctcccc 1560gcgcgttggc
cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc
1620agtgagcgca acgcaattaa tgtaagttag cgcgaattga tctggtttga
cagcttatca 1680tcgactgcac ggtgcaccaa tgcttctggc gtcaggcagc
catcggaagc tgtggtatgg 1740ctgtgcaggt cgtaaatcac tgcataattc
gtgtcgctca aggcgcactc ccgttctgga 1800taatgttttt tgcgccgaca
tcataacggt tctggcaaat attctgaaat gagctgttga 1860caattaatca
tccggctcgt ataatgtgtg gaattgtgag cggataacaa tttcacacag
1920gaaacagcgc cgctgagaaa aagcgaagcg gcactgctct ttaacaattt
atcagacaat 1980ctgtgtgggc actcgaccgg aattatcgat taactttatt
attaaaaatt aaagaggtat 2040atattaatgt atcgattaaa taaggaggaa
taaaccatga cgagcgatgt tcacgacgcg 2100accgacggcg ttaccgagac
tgcactggat gatgagcaga gcactcgtcg tattgcagaa 2160ctgtacgcaa
cggacccaga gttcgcagca gcagctcctc tgccggccgt tgtcgatgcg
2220gcgcacaaac cgggcctgcg tctggcggaa atcctgcaga ccctgttcac
cggctacggc 2280gatcgtccgg cgctgggcta tcgtgcacgt gagctggcga
cggacgaagg cggtcgtacg 2340gtcacgcgtc tgctgccgcg cttcgatacc
ctgacctatg cacaggtgtg gagccgtgtt 2400caagcagtgg ctgcagcgtt
gcgtcacaat ttcgcacaac cgatttaccc gggcgacgcg 2460gtcgcgacta
tcggctttgc gagcccggac tatttgacgc tggatctggt gtgcgcgtat
2520ctgggcctgg tcagcgttcc tttgcagcat aacgctccgg tgtctcgcct
ggccccgatt 2580ctggccgagg tggaaccgcg tattctgacg gtgagcgcag
aatacctgga cctggcggtt 2640gaatccgtcc gtgatgtgaa ctccgtcagc
cagctggttg ttttcgacca tcatccggaa 2700gtggacgatc accgtgacgc
actggctcgc gcacgcgagc agctggccgg caaaggtatc 2760gcagttacga
ccctggatgc gatcgcagac gaaggcgcag gtttgccggc tgagccgatt
2820tacacggcgg atcacgatca gcgtctggcc atgattctgt ataccagcgg
ctctacgggt 2880gctccgaaag gcgcgatgta caccgaagcg atggtggctc
gcctgtggac tatgagcttt 2940atcacgggcg acccgacccc ggttatcaac
gtgaacttca tgccgctgaa ccatctgggc 3000ggtcgtatcc cgattagcac
cgccgtgcag aatggcggta ccagctactt cgttccggaa 3060agcgacatga
gcacgctgtt tgaggatctg gccctggtcc gccctaccga actgggtctg
3120gtgccgcgtg ttgcggacat gctgtaccag catcatctgg cgaccgtgga
tcgcctggtg 3180acccagggcg cggacgaact gactgcggaa aagcaggccg
gtgcggaact gcgtgaacag 3240gtcttgggcg gtcgtgttat caccggtttt
gtttccaccg cgccgttggc ggcagagatg 3300cgtgcttttc tggatatcac
cttgggtgca cacatcgttg acggttacgg tctgaccgaa 3360accggtgcgg
tcacccgtga tggtgtgatt gttcgtcctc cggtcattga ttacaagctg
3420atcgatgtgc cggagctggg ttacttctcc accgacaaac cgtacccgcg
tggcgagctg 3480ctggttcgta gccaaacgtt gactccgggt tactacaagc
gcccagaagt caccgcgtcc 3540gttttcgatc gcgacggcta ttaccacacc
ggcgacgtga tggcagaaac cgcgccagac 3600cacctggtgt atgtggaccg
ccgcaacaat gttctgaagc tggcgcaagg tgaatttgtc 3660gccgtggcta
acctggaggc cgttttcagc ggcgctgctc tggtccgcca gattttcgtg
3720tatggtaaca gcgagcgcag ctttctgttg gctgttgttg tccctacccc
ggaggcgctg 3780gagcaatacg accctgccgc attgaaagca gccctggcgg
attcgctgca gcgtacggcg 3840cgtgatgccg agctgcagag ctatgaagtg
ccggcggact tcattgttga gactgagcct 3900tttagcgctg cgaacggtct
gctgagcggt gttggcaagt tgctgcgtcc gaatttgaag 3960gatcgctacg
gtcagcgttt ggagcagatg tacgcggaca tcgcggctac gcaggcgaac
4020caattgcgtg aactgcgccg tgctgcggct actcaaccgg tgatcgacac
gctgacgcaa 4080gctgcggcga ccatcctggg taccggcagc gaggttgcaa
gcgacgcaca ctttactgat 4140ttgggcggtg attctctgag cgcgctgacg
ttgagcaact tgctgtctga cttctttggc 4200tttgaagtcc cggttggcac
gattgttaac ccagcgacta atctggcaca gctggcgcaa 4260catatcgagg
cgcagcgcac ggcgggtgac cgccgtccat cctttacgac ggtccacggt
4320gcggatgcta cggaaatccg tgcaagcgaa ctgactctgg acaaattcat
cgacgctgag 4380actctgcgcg cagcacctgg tttgccgaag gttacgactg
agccgcgtac ggtcctgttg 4440agcggtgcca atggttggtt gggccgcttc
ctgaccctgc agtggctgga acgtttggca 4500ccggttggcg gtaccctgat
caccattgtg cgcggtcgtg acgatgcagc ggcacgtgca 4560cgtttgactc
aggcttacga tacggaccca gagctgtccc gccgcttcgc tgagttggcg
4620gatcgccact tgcgtgtggt ggcaggtgat atcggcgatc cgaatctggg
cctgaccccg 4680gagatttggc accgtctggc agcagaggtc gatctggtcg
ttcatccagc ggccctggtc 4740aaccacgtcc tgccgtaccg ccagctgttt
ggtccgaatg ttgttggcac cgccgaagtt 4800atcaagttgg ctctgaccga
gcgcatcaag cctgttacct acctgtccac ggttagcgtc 4860gcgatgggta
ttcctgattt tgaggaggac ggtgacattc gtaccgtcag cccggttcgt
4920ccgctggatg gtggctatgc aaatggctat ggcaacagca agtgggctgg
cgaggtgctg 4980ctgcgcgagg cacatgacct gtgtggcctg ccggttgcga
cgtttcgtag cgacatgatt 5040ctggcccacc cgcgctaccg tggccaagtg
aatgtgccgg acatgttcac ccgtctgctg 5100ctgtccctgc tgatcacggg
tgtggcaccg cgttccttct acattggtga tggcgagcgt 5160ccgcgtgcac
actacccggg cctgaccgtc gattttgttg cggaagcggt tactaccctg
5220ggtgctcagc aacgtgaggg ttatgtctcg tatgacgtta tgaatccgca
cgatgacggt 5280attagcttgg atgtctttgt ggactggctg attcgtgcgg
gccacccaat tgaccgtgtt 5340gacgactatg atgactgggt gcgtcgtttt
gaaaccgcgt tgaccgcctt gccggagaaa 5400cgtcgtgcgc agaccgttct
gccgctgctg catgcctttc gcgcgccaca ggcgccgttg 5460cgtggcgccc
ctgaaccgac cgaagtgttt catgcagcgg tgcgtaccgc taaagtcggt
5520ccgggtgata ttccgcacct ggatgaagcc ctgatcgaca agtacatccg
tgacctgcgc 5580gagttcggtc tgatttagaa ttctttagcg ttaagaagga
gatatatatg gcggacacgt 5640tattgattct gggtgatagc ctgagcgccg
ggtatcgaat gtctgccagc gcggcctggc 5700ctgccttgtt gaatgataag
tggcagagta aaacgtcggt agttaatgcc agcatcagcg 5760gcgacacctc
gcaacaagga ctggcgcgcc ttccggctct gctgaaacag catcagccgc
5820gttgggtgct ggttgaactg ggcggcaatg acggtttgcg tggttttcag
ccacagcaaa 5880ccgagcaaac gctgcgccag attttgcagg atgtcaaagc
cgccaacgct gaaccattgt 5940taatgcaaat acgtctgcct tacaactatg
gtcgtcgtta taatgaagcc tttagcgcca 6000tttaccccaa actcgccaaa
gagtttgatg ttccgctgct gccctttttt atggaagagg 6060tctgcctcaa
gccacaatgg atgcaggatg acggtattca tcccaaccgc gacgcccagc
6120cgtttattgc cgactggatg gcgaagcagt tgcagccttt agtaaatcat
gactcataag 6180cttctaagga aataatagga gattgaaaat ggcaacaact
aatgtgattc atgcttatgc 6240tgcaatgcag gcaggtgaag cactcgtgcc
ttattcgttt gatgcaggcg aactgcaacc 6300acatcaggtt gaagttaaag
tcgaatattg tgggctgtgc cattccgatg tctcggtact 6360caacaacgaa
tggcattctt cggtttatcc agtcgtggca ggtcatgaag tgattggtac
6420gattacccaa ctgggaagtg aagccaaagg actaaaaatt ggtcaacgtg
ttggtattgg 6480ctggacggca gaaagctgtc aggcctgtga ccaatgcatc
agtggtcagc aggtattgtg 6540cacgggcgaa aataccgcaa ctattattgg
tcatgctggt ggctttgcag ataaggttcg 6600tgcaggctgg caatgggtca
ttcccctgcc cgacgaactc gatccgacca gtgctggtcc 6660tttgctgtgt
ggcggaatca cagtatttga tccaatttta aaacatcaga ttcaggctat
6720tcatcatgtt gctgtgattg gtatcggtgg tttgggacat atggccatca
agctacttaa 6780agcatggggc tgtgaaatta ctgcgtttag ttcaaatcca
aacaaaaccg atgagctcaa 6840agctatgggg gccgatcacg tggtcaatag
ccgtgatgat gccgaaatta aatcgcaaca 6900gggtaaattt gatttactgc
tgagtacagt taatgtgcct ttaaactgga atgcgtatct 6960aaacacactg
gcacccaatg gcactttcca ttttttgggc gtggtgatgg aaccaatccc
7020tgtacctgtc ggtgcgctgc taggaggtgc caaatcgcta acagcatcac
caactggctc 7080gcctgctgcc ttacgtaagc tgctcgaatt tgcggcacgt
aagaatatcg cacctcaaat 7140cgagatgtat cctatgtcgg agctgaatga
ggccatcgaa cgcttacatt cgggtcaagc 7200acgttatcgg attgtactta
aagccgattt ttaacctagg atcagtatct ggtaggagat 7260cacggatgaa
acgtgcagtg attactggcc tgggcattgt ttccagcatc ggtaataacc
7320agcaggaagt cctggcatct ctgcgtgaag gacgttcagg gatcactttc
tctcaggagc 7380tgaaggattc cggcatgcgt agccacgtct ggggcaacgt
aaaactggat accactggcc 7440tcattgaccg caaagttgtg cgctttatga
gcgacgcatc catttatgca ttcctttcta 7500tggagcaggc aatcgctgat
gcgggcctct ctccggaagc ttaccagaat aacccgcgcg 7560ttggcctgat
tgcaggttcc ggcggcggct ccccgcgttt ccaggtgttc ggcgctgacg
7620caatgcgcgg cccgcgcggc ctgaaagcgg ttggcccgta tgtggtcacc
aaagcgatgg 7680catccggcgt ttctgcctgc ctcgccaccc cgtttaaaat
tcatggcgtt aactactcca 7740tcagctccgc gtgtgcgact tccgcacact
gtatcggtaa cgcagtagag cagatccaac 7800tgggcaaaca ggacatcgtg
tttgctggcg gcggcgaaga gctgtgctgg gaaatggctt 7860gcgaattcga
cgcaatgggt gcgctgtcta ctaaatacaa cgacaccccg gaaaaagcct
7920cccgtactta cgacgctcac cgtgacggtt tcgttatcgc tggcggcggc
ggtatggtag 7980tggttgaaga gctggaacac gcgctggcgc gtggtgctca
catctatgct gaaatcgttg 8040gctacggcgc aacctctgat ggtgcagaca
tggttgctcc gtctggcgaa ggcgcagtac 8100gctgcatgaa gatggcgatg
catggcgttg ataccccaat cgattacctg aactcccacg 8160gtacttcgac
tccggttggc gacgtgaaag agctggcagc tatccgtgaa gtgttcggcg
8220ataagagccc ggcgatttct gcaaccaaag ggatgaccgg tcactctctg
ggcgctgctg 8280gcgtacagga agctatctac tctctgctga tgctggaaca
cggctttatc gccccgagca 8340tcaacattga agagctggac gagcaggctg
cgggtctgaa catcgtgacc gaaacgaccg 8400atcgcgaact gaccaccgtt
atgtctaaca gcttcggctt cggcggcacc aacgccacgc 8460tggtaatgcg
caagctgaaa gattaaattt aaatgctatg tctcgagaaa cggtctccag
8520cttggctgtt ttggcggatg agagaagatt ttcagcctga tacagattaa
atcagaacgc 8580agaagcggtc tgataaaaca gaatttgcct ggcggcagta
gcgcggtggt cccacctgac 8640cccatgccga actcagaagt gaaacgccgt
agcgccgatg gtagtgtggg gtctccccat 8700gcgagagtag ggaactgcca
ggcatcaaat aaaacgaaag gctcagtcga aagactgggc 8760ctttcgtttt
atctgttgtt tgtcggtgaa cgctctcctg acgcctgatg cggtattttc
8820tccttacgca tctgtgcggt atttcacacc gcatatggtg cactctcagt
acaatctgct 8880ctgatgccgc atagttaagc cagccccgac acccgccaac
acccgctgac gagcttagta 8940aagccctcgc tagattttaa tgcggatgtt
gcgattactt cgccaactat tgcgataaca 9000agaaaaagcc agcctttcat
gatatatctc ccaatttgtg tagggcttat tatgcacgct 9060taaaaataat
aaaagcagac ttgacctgat agtttggctg tgagcaatta tgtgcttagt
9120gcatctaacg cttgagttaa gccgcgccgc gaagcggcgt cggcttgaac
gaattgttag 9180acattatttg ccgactacct tggtgatctc gcctttcacg
tagtggacaa attcttccaa 9240ctgatctgcg cgcgaggcca agcgatcttc
ttcttgtcca agataagcct gtctagcttc 9300aagtatgacg ggctgatact
gggccggcag gcgctccatt gcccagtcgg cagcgacatc 9360cttcggcgcg
attttgccgg ttactgcgct gtaccaaatg cgggacaacg taagcactac
9420atttcgctca tcgccagccc agtcgggcgg cgagttccat agcgttaagg
tttcatttag 9480cgcctcaaat agatcctgtt caggaaccgg atcaaagagt
tcctccgccg ctggacctac 9540caaggcaacg ctatgttctc ttgcttttgt
cagcaagata gccagatcaa tgtcgatcgt 9600ggctggctcg aagatacctg
caagaatgtc attgcgctgc cattctccaa attgcagttc 9660gcgcttagct
ggataacgcc acggaatgat gtcgtcgtgc acaacaatgg tgacttctac
9720agcgcggaga atctcgctct ctccagggga agccgaagtt tccaaaaggt
cgttgatcaa 9780agctcgccgc gttgtttcat caagccttac ggtcaccgta
accagcaaat caatatcact 9840gtgtggcttc aggccgccat ccactgcgga
gccgtacaaa tgtacggcca gcaacgtcgg 9900ttcgagatgg cgctcgatga
cgccaactac ctctgatagt tgagtcgata cttcggcgat 9960caccgcttcc
ctcatgatgt ttaactttgt tttagggcga ctgccctgct gcgtaacatc
10020gttgctgctc cataacatca aacatcgacc cacggcgtaa cgcgcttgct
gcttggatgc 10080ccgaggcata gactgtaccc caaaaaaaca gtcataacaa
gccatgaaaa ccgccactgc 10140gccgttacca ccgctgcgtt cggtcaaggt
tctggaccag ttgcgtgagc gcatacgcta 10200cttgcattac agcttacgaa
ccgaacaggc ttatgtccac tgggttcgtg ccttcatccg 10260tttccacggt
gtgcgtcacc cggcaacctt gggcagcagc gaagtcgagg catttctgtc
10320ctggctggcg aacgagcgca aggtttcggt ctccacgcat cgtcaggcat
tggcggcctt 10380gctgttcttc tacggcaagg tgctgtgcac ggatctgccc
tggcttcagg agatcggaag 10440acctcggccg tcgcggcgct tgccggtggt
gctgaccccg gatgaagtgg ttcgcatcct 10500cggttttctg gaaggcgagc
atcgtttgtt cgcccagctt ctgtatggaa cgggcatgcg 10560gatcagtgag
ggtttgcaac tgcgggtcaa ggatctggat ttcgatcacg gcacgatcat
10620cgtgcgggag ggcaagggct ccaaggatcg ggccttgatg ttacccgaga
gcttggcacc 10680cagcctgcgc gagcagggga attaattccc acgggttttg
ctgcccgcaa acgggctgtt 10740ctggtgttgc tagtttgtta tcagaatcgc
agatccggct tcagccggtt tgccggctga 10800aagcgctatt tcttccagaa
ttgccatgat tttttcccca cgggaggcgt cactggctcc 10860cgtgttgtcg
gcagctttga ttcgataagc agcatcgcct gtttcaggct gtctatgtgt
10920gactgttgag ctgtaacaag ttgtctcagg tgttcaattt catgttctag
ttgctttgtt 10980ttactggttt cacctgttct attaggtgtt acatgctgtt
catctgttac attgtcgatc 11040tgttcatggt gaacagcttt gaatgcacca
aaaactcgta aaagctctga tgtatctatc 11100ttttttacac cgttttcatc
tgtgcatatg gacagttttc cctttgatat gtaacggtga 11160acagttgttc
tacttttgtt tgttagtctt gatgcttcac tgatagatac aagagccata
11220agaacctcag atccttccgt atttagccag tatgttctct agtgtggttc
gttgtttttg 11280cgtgagccat gagaacgaac cattgagatc atacttactt
tgcatgtcac tcaaaaattt 11340tgcctcaaaa ctggtgagct gaatttttgc
agttaaagca tcgtgtagtg tttttcttag 11400tccgttatgt aggtaggaat
ctgatgtaat ggttgttggt attttgtcac cattcatttt 11460tatctggttg
ttctcaagtt cggttacgag atccatttgt ctatctagtt caacttggaa
11520aatcaacgta tcagtcgggc ggcctcgctt atcaaccacc aatttcatat
tgctgtaagt 11580gtttaaatct ttacttattg gtttcaaaac ccattggtta
agccttttaa actcatggta 11640gttattttca agcattaaca tgaacttaaa
ttcatcaagg ctaatctcta tatttgcctt 11700gtgagttttc ttttgtgtta
gttcttttaa taaccactca taaatcctca tagagtattt 11760gttttcaaaa
gacttaacat gttccagatt atattttatg aattttttta actggaaaag
11820ataaggcaat atctcttcac taaaaactaa ttctaatttt tcgcttgaga
acttggcata 11880gtttgtccac tggaaaatct caaagccttt aaccaaagga
ttcctgattt ccacagttct 11940cgtcatcagc tctctggttg ctttagctaa
tacaccataa gcattttccc tactgatgtt 12000catcatctga gcgtattggt
tataagtgaa cgataccgtc cgttctttcc ttgtagggtt 12060ttcaatcgtg
gggttgagta gtgccacaca gcataaaatt agcttggttt catgctccgt
12120taagtcatag cgactaatcg ctagttcatt tgctttgaaa acaactaatt
cagacataca 12180tctcaattgg tctaggtgat tttaat
122062314893DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 23cactatacca
attgagatgg gctagtcaat gataattact agtccttttc ctttgagttg 60tgggtatctg
taaattctgc tagacctttg ctggaaaact tgtaaattct gctagaccct
120ctgtaaattc cgctagacct ttgtgtgttt tttttgttta tattcaagtg
gttataattt 180atagaataaa gaaagaataa aaaaagataa aaagaataga
tcccagccct gtgtataact 240cactacttta gtcagttccg cagtattaca
aaaggatgtc gcaaacgctg tttgctcctc 300tacaaaacag accttaaaac
cctaaaggcg tcggcatccg cttacagaca agctgtgacc 360gtctccggga
gctgcatgtg tcagaggttt tcaccgtcat caccgaaacg cgcgaggcag
420cagatcaatt cgcgcgcgaa ggcgaagcgg catgcattta cgttgacacc
atcgaatggt 480gcaaaacctt tcgcggtatg gcatgatagc gcccggaaga
gagtcaattc agggtggtga 540atgtgaaacc agtaacgtta tacgatgtcg
cagagtatgc cggtgtctct tatcagaccg 600tttcccgcgt ggtgaaccag
gccagccacg tttctgcgaa aacgcgggaa aaagtggaag 660cggcgatggc
ggagctgaat tacattccca accgcgtggc acaacaactg gcgggcaaac
720agtcgttgct gattggcgtt gccacctcca gtctggccct gcacgcgccg
tcgcaaattg 780tcgcggcgat taaatctcgc gccgatcaac tgggtgccag
cgtggtggtg tcgatggtag 840aacgaagcgg cgtcgaagcc tgtaaagcgg
cggtgcacaa tcttctcgcg caacgcgtca 900gtgggctgat cattaactat
ccgctggatg accaggatgc cattgctgtg gaagctgcct 960gcactaatgt
tccggcgtta tttcttgatg tctctgacca gacacccatc aacagtatta
1020ttttctccca tgaagacggt acgcgactgg gcgtggagca tctggtcgca
ttgggtcacc 1080agcaaatcgc gctgttagcg ggcccattaa gttctgtctc
ggcgcgtctg cgtctggctg 1140gctggcataa atatctcact cgcaatcaaa
ttcagccgat agcggaacgg gaaggcgact 1200ggagtgccat gtccggtttt
caacaaacca tgcaaatgct gaatgagggc atcgttccca 1260ctgcgatgct
ggttgccaac gatcagatgg cgctgggcgc aatgcgcgcc attaccgagt
1320ccgggctgcg cgttggtgcg gatatctcgg tagtgggata cgacgatacc
gaagacagct 1380catgttatat cccgccgtta accaccatca aacaggattt
tcgcctgctg gggcaaacca 1440gcgtggaccg cttgctgcaa ctctctcagg
gccaggcggt gaagggcaat cagctgttgc 1500ccgtctcact ggtgaaaaga
aaaaccaccc tggcgcccaa tacgcaaacc gcctctcccc 1560gcgcgttggc
cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc
1620agtgagcgca acgcaattaa tgtaagttag cgcgaattga tctggtttga
cagcttatca 1680tcgactgcac ggtgcaccaa tgcttctggc gtcaggcagc
catcggaagc tgtggtatgg 1740ctgtgcaggt cgtaaatcac tgcataattc
gtgtcgctca aggcgcactc ccgttctgga 1800taatgttttt tgcgccgaca
tcataacggt tctggcaaat attctgaaat gagctgttga 1860caattaatca
tccggctcgt ataatgtgtg gaattgtgag cggataacaa tttcacacag
1920gaaacagcgc cgctgagaaa aagcgaagcg gcactgctct ttaacaattt
atcagacaat 1980ctgtgtgggc actcgaccgg aattatcgat taactttatt
attaaaaatt aaagaggtat 2040atattaatgt atcgattaaa taaggaggaa
taaaccatga cgagcgatgt tcacgacgcg 2100accgacggcg ttaccgagac
tgcactggat gatgagcaga gcactcgtcg tattgcagaa 2160ctgtacgcaa
cggacccaga gttcgcagca gcagctcctc tgccggccgt tgtcgatgcg
2220gcgcacaaac cgggcctgcg tctggcggaa atcctgcaga ccctgttcac
cggctacggc 2280gatcgtccgg cgctgggcta tcgtgcacgt gagctggcga
cggacgaagg cggtcgtacg 2340gtcacgcgtc tgctgccgcg cttcgatacc
ctgacctatg cacaggtgtg gagccgtgtt 2400caagcagtgg ctgcagcgtt
gcgtcacaat ttcgcacaac cgatttaccc gggcgacgcg 2460gtcgcgacta
tcggctttgc gagcccggac tatttgacgc tggatctggt gtgcgcgtat
2520ctgggcctgg tcagcgttcc tttgcagcat aacgctccgg tgtctcgcct
ggccccgatt 2580ctggccgagg tggaaccgcg tattctgacg gtgagcgcag
aatacctgga cctggcggtt 2640gaatccgtcc gtgatgtgaa ctccgtcagc
cagctggttg ttttcgacca tcatccggaa 2700gtggacgatc accgtgacgc
actggctcgc gcacgcgagc agctggccgg caaaggtatc 2760gcagttacga
ccctggatgc gatcgcagac gaaggcgcag gtttgccggc tgagccgatt
2820tacacggcgg atcacgatca gcgtctggcc atgattctgt ataccagcgg
ctctacgggt 2880gctccgaaag gcgcgatgta caccgaagcg atggtggctc
gcctgtggac tatgagcttt 2940atcacgggcg acccgacccc ggttatcaac
gtgaacttca tgccgctgaa ccatctgggc 3000ggtcgtatcc cgattagcac
cgccgtgcag aatggcggta ccagctactt cgttccggaa 3060agcgacatga
gcacgctgtt tgaggatctg gccctggtcc gccctaccga actgggtctg
3120gtgccgcgtg ttgcggacat gctgtaccag catcatctgg cgaccgtgga
tcgcctggtg 3180acccagggcg cggacgaact gactgcggaa aagcaggccg
gtgcggaact gcgtgaacag 3240gtcttgggcg gtcgtgttat caccggtttt
gtttccaccg cgccgttggc ggcagagatg 3300cgtgcttttc tggatatcac
cttgggtgca cacatcgttg acggttacgg tctgaccgaa 3360accggtgcgg
tcacccgtga tggtgtgatt gttcgtcctc cggtcattga ttacaagctg
3420atcgatgtgc cggagctggg ttacttctcc accgacaaac cgtacccgcg
tggcgagctg 3480ctggttcgta gccaaacgtt gactccgggt tactacaagc
gcccagaagt caccgcgtcc 3540gttttcgatc gcgacggcta ttaccacacc
ggcgacgtga tggcagaaac cgcgccagac 3600cacctggtgt atgtggaccg
ccgcaacaat gttctgaagc tggcgcaagg tgaatttgtc 3660gccgtggcta
acctggaggc cgttttcagc ggcgctgctc tggtccgcca gattttcgtg
3720tatggtaaca gcgagcgcag ctttctgttg gctgttgttg tccctacccc
ggaggcgctg 3780gagcaatacg accctgccgc attgaaagca gccctggcgg
attcgctgca gcgtacggcg 3840cgtgatgccg agctgcagag ctatgaagtg
ccggcggact tcattgttga gactgagcct 3900tttagcgctg cgaacggtct
gctgagcggt gttggcaagt tgctgcgtcc gaatttgaag 3960gatcgctacg
gtcagcgttt ggagcagatg tacgcggaca tcgcggctac gcaggcgaac
4020caattgcgtg aactgcgccg tgctgcggct actcaaccgg tgatcgacac
gctgacgcaa 4080gctgcggcga ccatcctggg taccggcagc gaggttgcaa
gcgacgcaca ctttactgat 4140ttgggcggtg attctctgag cgcgctgacg
ttgagcaact tgctgtctga cttctttggc 4200tttgaagtcc cggttggcac
gattgttaac ccagcgacta atctggcaca gctggcgcaa 4260catatcgagg
cgcagcgcac ggcgggtgac cgccgtccat cctttacgac ggtccacggt
4320gcggatgcta cggaaatccg tgcaagcgaa ctgactctgg acaaattcat
cgacgctgag 4380actctgcgcg cagcacctgg tttgccgaag gttacgactg
agccgcgtac ggtcctgttg 4440agcggtgcca atggttggtt gggccgcttc
ctgaccctgc agtggctgga acgtttggca 4500ccggttggcg gtaccctgat
caccattgtg cgcggtcgtg acgatgcagc ggcacgtgca 4560cgtttgactc
aggcttacga tacggaccca gagctgtccc gccgcttcgc tgagttggcg
4620gatcgccact tgcgtgtggt ggcaggtgat atcggcgatc cgaatctggg
cctgaccccg 4680gagatttggc accgtctggc agcagaggtc gatctggtcg
ttcatccagc ggccctggtc 4740aaccacgtcc tgccgtaccg ccagctgttt
ggtccgaatg ttgttggcac cgccgaagtt 4800atcaagttgg ctctgaccga
gcgcatcaag cctgttacct acctgtccac ggttagcgtc 4860gcgatgggta
ttcctgattt tgaggaggac ggtgacattc gtaccgtcag cccggttcgt
4920ccgctggatg gtggctatgc aaatggctat ggcaacagca agtgggctgg
cgaggtgctg 4980ctgcgcgagg cacatgacct gtgtggcctg ccggttgcga
cgtttcgtag cgacatgatt 5040ctggcccacc cgcgctaccg tggccaagtg
aatgtgccgg acatgttcac ccgtctgctg 5100ctgtccctgc tgatcacggg
tgtggcaccg cgttccttct acattggtga tggcgagcgt 5160ccgcgtgcac
actacccggg cctgaccgtc gattttgttg cggaagcggt tactaccctg
5220ggtgctcagc aacgtgaggg ttatgtctcg tatgacgtta tgaatccgca
cgatgacggt 5280attagcttgg atgtctttgt ggactggctg attcgtgcgg
gccacccaat tgaccgtgtt 5340gacgactatg atgactgggt gcgtcgtttt
gaaaccgcgt tgaccgcctt gccggagaaa 5400cgtcgtgcgc agaccgttct
gccgctgctg catgcctttc gcgcgccaca ggcgccgttg 5460cgtggcgccc
ctgaaccgac cgaagtgttt catgcagcgg tgcgtaccgc taaagtcggt
5520ccgggtgata ttccgcacct ggatgaagcc ctgatcgaca agtacatccg
tgacctgcgc 5580gagttcggtc tgatttagaa ttctttagcg ttaagaagga
gatatatatg gcggacacgt 5640tattgattct gggtgatagc ctgagcgccg
ggtatcgaat gtctgccagc gcggcctggc 5700ctgccttgtt gaatgataag
tggcagagta aaacgtcggt agttaatgcc agcatcagcg 5760gcgacacctc
gcaacaagga ctggcgcgcc ttccggctct gctgaaacag catcagccgc
5820gttgggtgct ggttgaactg ggcggcaatg acggtttgcg tggttttcag
ccacagcaaa 5880ccgagcaaac gctgcgccag attttgcagg atgtcaaagc
cgccaacgct gaaccattgt 5940taatgcaaat acgtctgcct tacaactatg
gtcgtcgtta taatgaagcc tttagcgcca 6000tttaccccaa actcgccaaa
gagtttgatg ttccgctgct gccctttttt atggaagagg 6060tctgcctcaa
gccacaatgg atgcaggatg acggtattca tcccaaccgc gacgcccagc
6120cgtttattgc cgactggatg gcgaagcagt tgcagccttt agtaaatcat
gactcataag 6180cttctaagga aataatagga gattgaaaat ggcaacaact
aatgtgattc atgcttatgc 6240tgcaatgcag gcaggtgaag cactcgtgcc
ttattcgttt gatgcaggcg aactgcaacc 6300acatcaggtt gaagttaaag
tcgaatattg tgggctgtgc cattccgatg tctcggtact 6360caacaacgaa
tggcattctt cggtttatcc agtcgtggca ggtcatgaag tgattggtac
6420gattacccaa ctgggaagtg aagccaaagg actaaaaatt ggtcaacgtg
ttggtattgg 6480ctggacggca gaaagctgtc aggcctgtga ccaatgcatc
agtggtcagc aggtattgtg 6540cacgggcgaa aataccgcaa ctattattgg
tcatgctggt ggctttgcag ataaggttcg 6600tgcaggctgg caatgggtca
ttcccctgcc cgacgaactc gatccgacca gtgctggtcc 6660tttgctgtgt
ggcggaatca cagtatttga tccaatttta aaacatcaga ttcaggctat
6720tcatcatgtt gctgtgattg gtatcggtgg tttgggacat atggccatca
agctacttaa 6780agcatggggc tgtgaaatta ctgcgtttag ttcaaatcca
aacaaaaccg atgagctcaa 6840agctatgggg gccgatcacg tggtcaatag
ccgtgatgat gccgaaatta aatcgcaaca 6900gggtaaattt gatttactgc
tgagtacagt taatgtgcct ttaaactgga atgcgtatct 6960aaacacactg
gcacccaatg gcactttcca ttttttgggc gtggtgatgg aaccaatccc
7020tgtacctgtc ggtgcgctgc taggaggtgc caaatcgcta acagcatcac
caactggctc 7080gcctgctgcc ttacgtaagc tgctcgaatt tgcggcacgt
aagaatatcg cacctcaaat 7140cgagatgtat cctatgtcgg agctgaatga
ggccatcgaa cgcttacatt cgggtcaagc 7200acgttatcgg attgtactta
aagccgattt ttaacctagg atcagtatct ggtaggagat 7260cacggatgaa
acgtgcagtg attactggcc tgggcattgt ttccagcatc ggtaataacc
7320agcaggaagt cctggcatct ctgcgtgaag gacgttcagg gatcactttc
tctcaggagc 7380tgaaggattc cggcatgcgt agccacgtct ggggcaacgt
aaaactggat accactggcc 7440tcattgaccg caaagttgtg cgctttatga
gcgacgcatc catttatgca ttcctttcta 7500tggagcaggc aatcgctgat
gcgggcctct ctccggaagc ttaccagaat aacccgcgcg 7560ttggcctgat
tgcaggttcc ggcggcggct ccccgcgttt ccaggtgttc ggcgctgacg
7620caatgcgcgg cccgcgcggc ctgaaagcgg ttggcccgta tgtggtcacc
aaagcgatgg 7680catccggcgt ttctgcctgc ctcgccaccc cgtttaaaat
tcatggcgtt aactactcca 7740tcagctccgc gtgtgcgact tccgcacact
gtatcggtaa cgcagtagag cagatccaac 7800tgggcaaaca ggacatcgtg
tttgctggcg gcggcgaaga gctgtgctgg gaaatggctt 7860gcgaattcga
cgcaatgggt gcgctgtcta ctaaatacaa cgacaccccg gaaaaagcct
7920cccgtactta cgacgctcac cgtgacggtt tcgttatcgc tggcggcggc
ggtatggtag 7980tggttgaaga gctggaacac gcgctggcgc gtggtgctca
catctatgct gaaatcgttg 8040gctacggcgc aacctctgat ggtgcagaca
tggttgctcc gtctggcgaa ggcgcagtac 8100gctgcatgaa gatggcgatg
catggcgttg ataccccaat cgattacctg aactcccacg 8160gtacttcgac
tccggttggc gacgtgaaag agctggcagc tatccgtgaa gtgttcggcg
8220ataagagccc ggcgatttct gcaaccaaag ggatgaccgg tcactctctg
ggcgctgctg 8280gcgtacagga agctatctac tctctgctga tgctggaaca
cggctttatc gccccgagca 8340tcaacattga agagctggac gagcaggctg
cgggtctgaa catcgtgacc gaaacgaccg 8400atcgcgaact gaccaccgtt
atgtctaaca gcttcggctt cggcggcacc aacgccacgc 8460tggtaatgcg
caagctgaaa gattaaattt ctaaaattca gttaggaggt atttgatggt
8520cattaaggcg caaagcccgg cgggtttcgc ggaagagtac attattgaaa
gtatctggaa 8580taaccgcttc cctcccggga ctattttgcc cgcagaacgt
gaactttcag aattaattgg 8640cgtaacgcgt actacgttac gtgaagtgtt
acagcgtctg gcacgagatg gctggttgac 8700cattcaacat ggcaagccga
cgaaggtgaa taatttctgg gaaacttccg gtttaaatat 8760ccttgaaaca
ctggcgcgac tggatcacga aagtgtgccg cagcttattg ataatttgct
8820gtcggtgcgt accaatattt ccactatttt tattcgcacc gcgtttcgtc
agcatcccga 8880taaagcgcag gaagtgctgg ctaccgctaa tgaagtggcc
gatcacgccg atgcctttgc 8940cgagctggat tacaacatat tccgcggcct
ggcgtttgct tccggcaacc cgatttacgg 9000tctgattctt aacgggatga
aagggctgta tacgcgtatt ggtcgtcact atttcgccaa 9060tccggaagcg
cgcagtctgg cgctgggctt ctaccacaaa ctgtcggcgt tgtgcagtga
9120aggcgcgcac gatcaggtgt acgaaacagt gcgtcgctat gggcatgaga
gtggcgagat 9180ttggcaccgg atgcagaaaa atctgccggg tgatttagcc
attcaggggc gataactcga 9240ggatggtagt gtggggtctc cccatgcgag
agtagggaac tgccaggcat caaataaaac 9300gaaaggctca gtcgaaagac
tgggcctttc gttttatctg ttgtttgtcg gtgaacgctc 9360tcctgagtag
gacaaatccg ccgggagcgg atttgaacgt tgcgaagcaa cggcccggag
9420ggtggcgggc aggacgcccg ccataaactg ccaggcatca aattaagcag
aaggccatcc 9480tgacggatgg cctttttgcg tggccagtgc caagcttgca
tgcagattgc agcattacac 9540gtcttgagcg attgtgtagg ctggagctgc
ttcgaagttc ctatactttc tagagaatag 9600gaacttcgga ataggaactt
caagatcccc ttattagaag aactcgtcaa gaaggcgata 9660gaaggcgatg
cgctgcgaat cgggagcggc gataccgtaa agcacgagga agcggtcagc
9720ccattcgccg ccaagctctt cagcaatatc acgggtagcc aacgctatgt
cctgatagcg 9780gtccgccaca cccagccggc cacagtcgat gaatccagaa
aagcggccat tttccaccat 9840gatattcggc aagcaggcat cgccatgggt
cacgacgaga tcctcgccgt cgggcatgcg 9900cgccttgagc ctggcgaaca
gttcggctgg cgcgagcccc tgatgctctt cgtccagatc 9960atcctgatcg
acaagaccgg cttccatccg agtacgtgct cgctcgatgc gatgtttcgc
10020ttggtggtcg aatgggcagg tagccggatc aagcgtatgc agccgccgca
ttgcatcagc 10080catgatggat actttctcgg caggagcaag gtgagatgac
aggagatcct gccccggcac 10140ttcgcccaat agcagccagt cccttcccgc
ttcagtgaca acgtcgagca cagctgcgca 10200aggaacgccc gtcgtggcca
gccacgatag ccgcgctgcc tcgtcctgca gttcattcag 10260ggcaccggac
aggtcggtct tgacaaaaag aaccgggcgc ccctgcgctg acagccggaa
10320cacggcggca tcagagcagc cgattgtctg ttgtgcccag tcatagccga
atagcctctc 10380cacccaagcg gccggagaac ctgcgtgcaa tccatcttgt
tcaatcatgc gaaacgatcc 10440tcatcctgtc tcttgatcag atcttgatcc
cctgcgccat cagatccttg gcggcaagaa 10500agccatccag tttactttgc
agggcttccc aaccttacca gagggcgccc cagctggcaa 10560ttccggttcg
cttgctgtcc ataaaaccgc ccagtctagc tatcgccatg taagcccact
10620gcaagctacc tgctttctct ttgcgcttgc gttttccctt gtccagatag
cccagtagct 10680gacattcatc cggggtcagc accgtttctg cggactggct
ttctacgtgt tccgcttcct 10740ttagcagccc ttgcgccctg agtgcttgcg
gcagcgtgag cttcaaaagc gctctgaagt 10800tcctatactt tctagagaat
aggaacttcg aactgcaggt cgacggatcc ccggaattaa 10860ttctcatgtt
tgacagctta tcactgatca gtgaattaat ggcgatgacg catcctcacg
10920ataatatccg ggtaggcgca atcactttcg tctctactcc gttacaaagc
gaggctgggt 10980atttcccggc ctttctgtta tccgaaatcc actgaaagca
cagcggctgg ctgaggagat 11040aaataataaa cgaggggctg tatgcacaaa
gcatcttctg ttgagttaag aacgagtatc 11100gagatggcac atagccttgc
tcaaattgga atcaggtttg tgccaatacc agtagaaaca 11160gacgaagctc
gagcgtatca tatttaaatt cgagaaacgg tctccagctt ggctgttttg
11220gcggatgaga gaagattttc agcctgatac agattaaatc agaacgcaga
agcggtctga 11280taaaacagaa tttgcctggc ggcagtagcg cggtggtccc
acctgacccc atgccgaact 11340cagaagtgaa acgccgtagc gccgatggta
gtgtggggtc tccccatgcg agagtaggga 11400actgccaggc atcaaataaa
acgaaaggct cagtcgaaag actgggcctt tcgttttatc 11460tgttgtttgt
cggtgaacgc tctcctgacg cctgatgcgg tattttctcc ttacgcatct
11520gtgcggtatt tcacaccgca tatggtgcac tctcagtaca atctgctctg
atgccgcata 11580gttaagccag ccccgacacc cgccaacacc cgctgacgag
cttagtaaag ccctcgctag 11640attttaatgc ggatgttgcg attacttcgc
caactattgc gataacaaga aaaagccagc 11700ctttcatgat atatctccca
atttgtgtag ggcttattat gcacgcttaa aaataataaa 11760agcagacttg
acctgatagt ttggctgtga gcaattatgt gcttagtgca tctaacgctt
11820gagttaagcc gcgccgcgaa gcggcgtcgg cttgaacgaa ttgttagaca
ttatttgccg 11880actaccttgg tgatctcgcc tttcacgtag tggacaaatt
cttccaactg atctgcgcgc 11940gaggccaagc gatcttcttc ttgtccaaga
taagcctgtc tagcttcaag tatgacgggc 12000tgatactggg ccggcaggcg
ctccattgcc cagtcggcag cgacatcctt cggcgcgatt 12060ttgccggtta
ctgcgctgta ccaaatgcgg gacaacgtaa gcactacatt tcgctcatcg
12120ccagcccagt cgggcggcga gttccatagc gttaaggttt catttagcgc
ctcaaataga 12180tcctgttcag gaaccggatc aaagagttcc tccgccgctg
gacctaccaa ggcaacgcta 12240tgttctcttg cttttgtcag caagatagcc
agatcaatgt cgatcgtggc tggctcgaag 12300atacctgcaa gaatgtcatt
gcgctgccat tctccaaatt gcagttcgcg cttagctgga 12360taacgccacg
gaatgatgtc gtcgtgcaca acaatggtga cttctacagc gcggagaatc
12420tcgctctctc caggggaagc cgaagtttcc aaaaggtcgt tgatcaaagc
tcgccgcgtt 12480gtttcatcaa gccttacggt caccgtaacc agcaaatcaa
tatcactgtg tggcttcagg 12540ccgccatcca ctgcggagcc gtacaaatgt
acggccagca acgtcggttc gagatggcgc 12600tcgatgacgc caactacctc
tgatagttga gtcgatactt cggcgatcac cgcttccctc 12660atgatgttta
actttgtttt agggcgactg ccctgctgcg taacatcgtt gctgctccat
12720aacatcaaac atcgacccac ggcgtaacgc gcttgctgct tggatgcccg
aggcatagac 12780tgtaccccaa aaaaacagtc ataacaagcc atgaaaaccg
ccactgcgcc gttaccaccg 12840ctgcgttcgg tcaaggttct ggaccagttg
cgtgagcgca tacgctactt gcattacagc 12900ttacgaaccg aacaggctta
tgtccactgg gttcgtgcct tcatccgttt ccacggtgtg 12960cgtcacccgg
caaccttggg cagcagcgaa gtcgaggcat ttctgtcctg gctggcgaac
13020gagcgcaagg tttcggtctc cacgcatcgt caggcattgg cggccttgct
gttcttctac 13080ggcaaggtgc tgtgcacgga tctgccctgg cttcaggaga
tcggaagacc tcggccgtcg 13140cggcgcttgc cggtggtgct gaccccggat
gaagtggttc gcatcctcgg ttttctggaa 13200ggcgagcatc gtttgttcgc
ccagcttctg tatggaacgg gcatgcggat
cagtgagggt 13260ttgcaactgc gggtcaagga tctggatttc gatcacggca
cgatcatcgt gcgggagggc 13320aagggctcca aggatcgggc cttgatgtta
cccgagagct tggcacccag cctgcgcgag 13380caggggaatt aattcccacg
ggttttgctg cccgcaaacg ggctgttctg gtgttgctag 13440tttgttatca
gaatcgcaga tccggcttca gccggtttgc cggctgaaag cgctatttct
13500tccagaattg ccatgatttt ttccccacgg gaggcgtcac tggctcccgt
gttgtcggca 13560gctttgattc gataagcagc atcgcctgtt tcaggctgtc
tatgtgtgac tgttgagctg 13620taacaagttg tctcaggtgt tcaatttcat
gttctagttg ctttgtttta ctggtttcac 13680ctgttctatt aggtgttaca
tgctgttcat ctgttacatt gtcgatctgt tcatggtgaa 13740cagctttgaa
tgcaccaaaa actcgtaaaa gctctgatgt atctatcttt tttacaccgt
13800tttcatctgt gcatatggac agttttccct ttgatatgta acggtgaaca
gttgttctac 13860ttttgtttgt tagtcttgat gcttcactga tagatacaag
agccataaga acctcagatc 13920cttccgtatt tagccagtat gttctctagt
gtggttcgtt gtttttgcgt gagccatgag 13980aacgaaccat tgagatcata
cttactttgc atgtcactca aaaattttgc ctcaaaactg 14040gtgagctgaa
tttttgcagt taaagcatcg tgtagtgttt ttcttagtcc gttatgtagg
14100taggaatctg atgtaatggt tgttggtatt ttgtcaccat tcatttttat
ctggttgttc 14160tcaagttcgg ttacgagatc catttgtcta tctagttcaa
cttggaaaat caacgtatca 14220gtcgggcggc ctcgcttatc aaccaccaat
ttcatattgc tgtaagtgtt taaatcttta 14280cttattggtt tcaaaaccca
ttggttaagc cttttaaact catggtagtt attttcaagc 14340attaacatga
acttaaattc atcaaggcta atctctatat ttgccttgtg agttttcttt
14400tgtgttagtt cttttaataa ccactcataa atcctcatag agtatttgtt
ttcaaaagac 14460ttaacatgtt ccagattata ttttatgaat ttttttaact
ggaaaagata aggcaatatc 14520tcttcactaa aaactaattc taatttttcg
cttgagaact tggcatagtt tgtccactgg 14580aaaatctcaa agcctttaac
caaaggattc ctgatttcca cagttctcgt catcagctct 14640ctggttgctt
tagctaatac accataagca ttttccctac tgatgttcat catctgagcg
14700tattggttat aagtgaacga taccgtccgt tctttccttg tagggttttc
aatcgtgggg 14760ttgagtagtg ccacacagca taaaattagc ttggtttcat
gctccgttaa gtcatagcga 14820ctaatcgcta gttcatttgc tttgaaaaca
actaattcag acatacatct caattggtct 14880aggtgatttt aat 14893
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