U.S. patent application number 13/380222 was filed with the patent office on 2012-06-21 for biological methods for preparing adipic acid.
This patent application is currently assigned to VERDEZYNE, INC.. Invention is credited to Tom Beardslee, Stephen Picataggio.
Application Number | 20120156761 13/380222 |
Document ID | / |
Family ID | 43411767 |
Filed Date | 2012-06-21 |
United States Patent
Application |
20120156761 |
Kind Code |
A1 |
Picataggio; Stephen ; et
al. |
June 21, 2012 |
BIOLOGICAL METHODS FOR PREPARING ADIPIC ACID
Abstract
The technology relates in part to biological methods for
producing adipic acid and engineered microorganisms capable of such
production.
Inventors: |
Picataggio; Stephen;
(Carlsbad, CA) ; Beardslee; Tom; (Carlsbad,
CA) |
Assignee: |
VERDEZYNE, INC.
Carlsbad
CA
|
Family ID: |
43411767 |
Appl. No.: |
13/380222 |
Filed: |
July 1, 2010 |
PCT Filed: |
July 1, 2010 |
PCT NO: |
PCT/US2010/040837 |
371 Date: |
March 2, 2012 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
61222902 |
Jul 2, 2009 |
|
|
|
Current U.S.
Class: |
435/254.22 ;
435/254.2 |
Current CPC
Class: |
C12N 15/815 20130101;
C12N 15/52 20130101; C12P 7/44 20130101; C12N 9/0006 20130101 |
Class at
Publication: |
435/254.22 ;
435/254.2 |
International
Class: |
C12N 1/19 20060101
C12N001/19 |
Claims
1-213. (canceled)
214. An engineered yeast comprising modifications that add or
increase a hexanoate synthase activity, a monooxygenase activity,
and a monooxygenase reductase activity, which yeast is capable of
producing a diacid from a sugar.
215. The engineered yeast of claim 214, which comprises increased
copies of a polynucleotide encoding a polypeptide having the
hexanoate synthase activity, the monooxygenase activity, or the
monooxygenase reductase activity.
216. The engineered yeast of claim 214, which comprises a
heterologous promoter and/or 5' UTR in genomic DNA in functional
connection with a polynucleotide encoding a polypeptide having the
hexanoate synthase activity, the monooxygenase activity, or the
monooxygenase reductase activity.
217. The engineered yeast of claim 214, wherein the hexanoate
synthase activity is provided by a heterologous polypeptide.
218. The engineered yeast of claim 217, wherein the heterologous
polypeptide is encoded by a hexonate synthase subunit alpha (HEXA)
gene, hexanoate synthase subunit beta (HEXB) gene, or a hexonate
synthase subunit alpha (HEXA) gene and hexanoate synthase subunit
beta (HEXB) gene.
219. The engineered yeast of claim 218, wherein the HEXA gene, HEXB
gene, or HEXA gene and HEXB gene are from an Aspergillus spp.
fungus.
220. The engineered yeast of claim 219, wherein the Aspergillus
spp. fungus is Aspergillus parasiticus.
221. The engineered yeast of claim 214, which includes an increased
number of copies of an endogenous polynucleotide that encodes a
polypeptide having the monooxygenase activity.
222. The engineered yeast of claim 221, wherein the endogenous
polynucleotide encodes a CYP52A15 polypeptide, CYP52A16 polypeptide
or CYP52A19 polypeptide.
223. The engineered yeast of claim 214, which comprises a
heterologous promoter in genomic DNA in functional connection with
an endogenous polynucleotide that encodes a polypeptide having the
monooxygenase activity.
224. The engineered yeast of claim 223, wherein the endogenous
polynucleotide encodes a CYP52A15 polypeptide, CYP52A16 polypeptide
or CYP52A19 polypeptide.
225. The engineered yeast of claim 214, which includes an increased
number of copies of an endogenous polynucleotide that encodes a
polypeptide having the monooxygenase reductase activity.
226. The engineered yeast of claim 225, wherein the endogenous
polynucleotide encodes a CPRA polypeptide or CPRB polypeptide.
227. The engineered yeast of claim 214, which comprises a
heterologous promoter in genomic DNA in functional connection with
an endogenous polynucleotide that encodes a polypeptide having the
monooxygenase reductase activity.
228. The engineered yeast of claim 227, wherein the endogenous
polynucleotide encodes a CPRA polypeptide or CPRB polypeptide.
229. The engineered yeast of claim 214, which is a Candida spp.
yeast.
230. The engineered yeast of claim 214, which is a Yarrowia spp.
yeast.
231. The engineered yeast of claim 230, wherein the Yarrowia spp.
yeast is Yarrowia lipolytica.
232. The engineered yeast of claim 214, wherein the diacid is
adipic acid.
Description
RELATED PATENT APPLICATIONS
[0001] This patent application is a national stage of international
patent application no. PCT/US2010/040837 filed on Jul. 1, 2010,
entitled BIOLOGICAL METHODS FOR PREPARING ADIPIC ACID, naming
Stephen Picataggio and Tom Beardslee as inventors, and designated
by Attorney Docket No. VRD-1001-PC, which claims the benefit of
U.S. provisional patent application No. 61/222,902 filed on Jul. 2,
2009, entitled BIOLOGICAL METHODS FOR PREPARING ADIPIC ACID, naming
Stephen Picataggio as inventor and designated by Attorney Docket
No. VRD-1001-PV. The entire contents of the foregoing patent
applications are incorporated herein by reference, including,
without limitation, all text, tables and drawings.
SEQUENCE LISTING
[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 Feb. 13, 2012, is named VRD1001US.txt and is 181,059 bytes in
size.
FIELD
[0003] The technology relates in part to biological methods for
producing adipic acid and engineered microorganisms capable of such
production.
BACKGROUND
[0004] Microorganisms employ various enzyme-driven biological
pathways to support their own metabolism and growth. A cell
synthesizes native proteins, including enzymes, in vivo from
deoxyribonucleic acid (DNA). DNA first is transcribed into a
complementary ribonucleic acid (RNA) that comprises a
ribonucleotide sequence encoding the protein. RNA then directs
translation of the encoded protein by interaction with various
cellular components, such as ribosomes. The resulting enzymes
participate as biological catalysts in pathways involved in
production of molecules by the organism.
[0005] These pathways can be exploited for the harvesting of the
naturally produced products. The pathways also can be altered to
increase production or to produce different products that may be
commercially valuable. Advances in recombinant molecular biology
methodology allow researchers to isolate DNA from one organism and
insert it into another organism, thus altering the cellular
synthesis of enzymes or other proteins. Such genetic engineering
can change the biological pathways within the host organism,
causing it to produce a desired product. Microorganic industrial
production can minimize the use of caustic chemicals and the
production of toxic byproducts, thus providing a "clean" source for
certain compounds.
SUMMARY
[0006] Provided herein are engineered microorganisms that produce
six-carbon organic molecules such as adipic acid, methods for
manufacturing such microorganisms and methods for using them to
produce adipic acid and other six-carbon organic molecules.
[0007] Thus, provided herein in some embodiments are engineered
microorganisms capable of producing adipic acid, or produce adipic
acid, which microorganisms comprise one or more altered activities
selected from the group consisting of aldehyde dehydrogenase
activity (e.g., 6-oxohexanoic acid dehydrogenase activity, omega
oxo fatty acid dehydrogenase activity), fatty alcohol oxidase
activity (e.g., 6-hydroxyhexanoic acid dehydrogenase activity,
omega hydroxyl fatty acid dehydrogenase activity), hexanoate
synthase activity and monooxygenase activity. In certain
embodiments, the microorganism comprises a genetic modification
that adds or increases the aldehyde dehydrogenase activity (e.g.,
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase activity), fatty alcohol oxidase activity (e.g.,
6-hydroxyhexanoic acid dehydrogenase activity, omega hydroxyl fatty
acid dehydrogenase activity), hexanoate synthase activity,
monooxygenase activity, monooxygenase reductase activity, fatty
alcohol oxidase activity, acyl-CoA ligase activity, acyl-CoA
oxidase activity, enoyl-CoA hydratase activity, 3-hydroxyacyl-CoA
dehydrogenase activity, and/or acetyl-CoA C-acyltransferase
activity. Also provided in some embodiments, are engineered
microorganisms that produce adipic acid, which microorganisms
comprise an altered monooxygenase activity. Provided also herein in
some embodiments are engineered microorganisms that include a
genetic modification that reduces the acyl-CoA oxidase
activity.
[0008] In some embodiments, an engineered microorganism includes a
genetic modification that includes multiple copies of a
polynucleotide that encodes a polypeptide having aldehyde
dehydrogenase activity (e.g., 6-oxohexanoic acid dehydrogenase
activity, omega oxo fatty acid dehydrogenase activity), fatty
alcohol oxidase activity (e.g., 6-hydroxyhexanoic acid
dehydrogenase activity, omega hydroxyl fatty acid dehydrogenase
activity), hexanoate synthase activity, monooxygenase activity,
monooxygenase reductase activity, fatty alcohol oxidase activity,
acyl-CoA ligase activity, acyl-CoA oxidase activity, enoyl-CoA
hydratase activity, 3-hydroxyacyl-CoA dehydrogenase activity,
and/or acetyl-CoA C-acyltransferase activity. In some embodiments,
2, 3, 4, 5, 6, 7, 8, 9 or 10 or more copies of the particular
polynucleotide are present in the microbe. In certain embodiments,
an engineered microorganism includes a heterologous promoter
(and/or 5'UTR) in functional connection with a polynucleotide that
encodes a polypeptide having aldehyde dehydrogenase activity (e.g.,
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase activity), fatty alcohol oxidase activity (e.g.,
6-hydroxyhexanoic acid dehydrogenase activity, omega hydroxyl fatty
acid dehydrogenase activity), hexanoate synthase activity,
monooxygenase activity, monooxygenase reductase activity, fatty
alcohol oxidase activity, acyl-CoA ligase activity, acyl-CoA
oxidase activity, enoyl-CoA hydratase activity, 3-hydroxyacyl-CoA
dehydrogenase activity, and/or acetyl-CoA C-acyltransferase
activity. In some embodiments, the promoter is a POX4 or POX5
promoter or monooxygenase promoter from a yeast (e.g., Candida
yeast strain (e.g., C. tropicalis strain)), or other promoter.
Examples of promoters that can be utilized are described herein.
The promoter sometimes is exogenous or endogenous with respect to
the microbe.
[0009] Also provided herein is an engineered microorganism that
produces adipic acid, where the microorganism includes an altered
monooxygenase activity. In certain embodiments, an engineered
microorganism comprises a genetic modification that alters a
monooxygenase activity. In some embodiments, an engineered
microorganism includes a genetic modification that alters a
monooxygenase activity selected from the group consisting of
CYP52A15 activity, CYP52A16 activity, or CYP52A15 activity and
CYP52A16 activity. In some embodiments, the monooxygenase activity
is encoded by a CYP52A15 polynucleotide, a CYP52A16 polynucleotide,
or CYP52A15 and CYP52A16 polynucleotides. In some embodiments, the
genetic modification increases monooxygenase activity. In certain
embodiments, the genetic modification increases the copy number of
an endogenous polynucleotide that encodes a polypeptide having the
monooxygenase activity (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more
copies of the polynucleotide). In certain embodiments, an
engineered microorganism comprises a polynucleotide that includes a
promoter (e.g., promoter and/or 5'UTR) and encodes a polypeptide
having a monooxygenase activity. The promoter may be exogenous or
endogenous with respect to the microbe. An engineered microorganism
in certain embodiments comprises a heterologous polynucleotide
encoding a polypeptide having monooxygenase activity. In related
embodiments, the heterologous polynucleotide is from a yeast, such
as a Candida yeast in certain embodiments (e.g., C.
tropicalis).
[0010] In certain embodiments, an engineered microorganism
comprises a genetic modification that alters monooxygenase
reductase activity. In some embodiments, the genetic modification
increases the copy number of an endogenous polynucleotide that
encodes a polypeptide having monooxygenase reductase activity
(e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more copies of the
polynucleotide). An engineered microorganism in certain embodiments
comprises a heterologous promoter (e.g., endogenous or exogenous
promoter with respect to the microbe) in functional connection with
a polynucleotide that encodes a polypeptide having monooxygenase
reductase activity. In some embodiments, the polynucleotide is from
a yeast, and in certain embodiments the yeast is a Candida yeast
(e.g., C. tropicalis).
[0011] An engineered microorganism in some embodiments comprises an
altered thioesterase activity. In some embodiments, an engineered
microorganism comprises a genetic modification that alters the
thioesterase activity, and in certain embodiments, the engineered
microorganism comprises a genetic alteration that adds or increases
a thioesterase activity. In some embodiments, the engineered
microorganism comprises a heterologous polynucleotide encoding a
polypeptide having thioesterase activity.
[0012] An engineered microorganism in some embodiments comprises an
altered fatty alcohol oxidase activity. In some embodiments, an
engineered microorganism comprises a genetic modification that
alters the fatty alcohol oxidase activity, and in certain
embodiments, the engineered microorganism comprises a genetic
alteration that adds or increases a fatty alcohol oxidase activity.
In some embodiments, the genetic modification increases the copy
number of an endogenous polynucleotide that encodes a polypeptide
having fatty alcohol oxidase activity (e.g., 2, 3, 4, 5, 6, 7, 8,
9, 10 or more copies of the polynucleotide). An engineered
microorganism in certain embodiments comprises a heterologous
promoter (e.g., endogenous or exogenous promoter with respect to
the microbe) in functional connection with a polynucleotide that
encodes a polypeptide having fatty alcohol oxidase activity. In
some embodiments, the engineered microorganism comprises a
heterologous polynucleotide encoding a polypeptide having fatty
alcohol oxidase activity. In some embodiments, the polynucleotide
is from a yeast, and in certain embodiments the yeast is Candida
(e.g., a C. tropicalis strain).
[0013] An engineered microorganism in some embodiments comprises an
altered 6-oxohexanoic acid dehydrogenase activity or an altered
omega oxo fatty acid dehydrogenase activity. In some embodiments,
an engineered microorganism comprises a genetic modification that
adds or increases 6-oxohexanoic acid dehydrogenase activity or
omega oxo fatty acid dehydrogenase activity, and in certain
embodiments, an engineered microorganism comprises a heterologous
polynucleotide encoding a polypeptide having 6-oxohexanoic acid
dehydrogenase activity or omega oxo fatty acid dehydrogenase
activity. In related embodiments, the heterologous polynucleotide
sometimes is from a bacterium, such as an Acinetobacter, Nocardia,
Pseudomonas or Xanthobacter bacterium in some embodiments.
[0014] An engineered microorganism in some embodiments comprises an
altered 6-hydroxyhexanoic acid dehydrogenase activity or an altered
omega hydroxyl fatty acid dehydrogenase activity. In some
embodiments, an engineered microorganism comprises a genetic
modification that adds or increases the 6-hydroxyhexanoic acid
dehydrogenase activity or omega hydroxyl fatty acid dehydrogenase
activity, and in certain embodiments, an engineered microorganism
comprises a heterologous polynucleotide encoding a polypeptide
having 6-hydroxyhexanoic acid dehydrogenase activity or omega
hydroxyl fatty acid dehydrogenase activity. In related embodiments,
the heterologous polynucleotide is from a bacterium, such as an
Acinetobacter, Nocardia, Pseudomonas or Xanthobacter bacterium in
some embodiments.
[0015] An engineered microorganism in some embodiments comprises an
altered hexanoate synthase activity. In some embodiments, an
engineered microorganism comprises a genetic modification that
alters hexanoate synthase activity. In certain embodiments, an
engineered microorganism includes a genetic alteration that adds or
increases hexanoate synthase activity. In some embodiments, an
engineered microorganism comprises a heterologous polynucleotide
encoding a polypeptide having hexanoate synthase activity. In
certain embodiments, the hexanoate synthase activity is provided by
a polypeptide having hexanoate synthase activity. In certain
embodiments, the hexanoate synthase activity is provided by a
polypeptide having hexanoate synthase subunit A activity, hexanoate
synthase subunit B activity, or hexanoate synthase subunit A
activity and hexanoate synthase subunit B activity. In some
embodiments, the heterologous polynucleotide is from a fungus, such
as an Aspergillus fungus in certain embodiments (e.g., A.
parasiticus, A. nidulans).
[0016] In certain embodiments, an engineered microorganism
comprises a genetic modification that results in substantial (e.g.,
primary) hexanoate usage by monooxygenase activity. In related
embodiments, the genetic modification reduces a polyketide synthase
activity.
[0017] An engineered microorganism in some embodiments is a
non-prokaryotic organism, and sometimes is a eukaryote. A eukaryote
can be a yeast in some embodiments, such as a Candida yeast (e.g.,
C. tropicalis), for example. In certain embodiments a eukaryote is
a fungus, such as a Yarrowia fungus (e.g., Y. lipolytica) or
Aspergillus fungus (e.g., A. parasiticus or A. nidulans), for
example.
[0018] In some embodiments, an engineered microorganism comprises a
genetic modification that reduces 6-hydroxyhexanoic acid
conversion. In related embodiments, the genetic modification
reduces 6-hydroxyhexanoic acid dehydrogenase activity or omega
hydroxyl fatty acid dehydrogenase activity.
[0019] In certain embodiments, an engineered microorganism
comprises a genetic modification that reduces beta-oxidation
activity, and in some embodiments, the genetic modification renders
beta-oxidation activity undetectable (e.g., completely blocked
beta-oxidation activity). In certain embodiments, the genetic
modification partially reduces beta-oxidation activity. In some
embodiments, an engineered microorganism comprises a genetic
modification that increases omega-oxidation activity. In some
embodiments, an engineered microorganism comprises one or more
genetic modifications that alter a reverse activity in a beta
oxidation pathway, an omega oxidation pathway, or a beta oxidation
and omega oxidation pathway, thereby increasing carbon flux through
the respective pathways, due to the reduction in one or more
reverse enzymatic activities.
[0020] A fatty acid-CoA derivative, or dicarboxylic acid-CoA
derivative, can be converted to a trans-2,3-dehydroacyl-CoA
derivative by the activity of acyl-CoA oxidase (e.g., also known as
or referred to as acyl-CoA oxidoreductase and fatty acyl-coenzyme A
oxidase), in many organisms. In some embodiments, an engineered
microorganism comprises a genetic modification that alters the
specificity of and/or reduces the activity of an acyl-CoA oxidase
activity. In certain embodiments, the genetic modification disrupts
an acyl-CoA oxidase activity. In some embodiments, the genetic
modification includes disrupting a polynucleotide that encodes a
polypeptide having an acyl-CoA oxidase activity. In certain
embodiments, the genetic modification includes disrupting a
promoter and/or 5'UTR in functional connection with a
polynucleotide that encodes a polypeptide having the acyl-CoA
oxidase activity. In some embodiments, the polypeptide having
acyl-CoA activity is a POX polypeptide. In certain embodiments, the
POX polypeptide is a POX4 polypeptide, a POX5 polypeptide, or a
POX4 polypeptide and POX5 polypeptide. In certain embodiments, the
genetic modification disrupts an acyl-CoA activity by disrupting a
POX4 nucleotide sequence, a POX5 nucleotide sequence, or a POX4 and
POX5 nucleotide sequence.
[0021] An engineered microorganism can include a heterologous
polynucleotide that encodes a polypeptide providing an activity
described above, and the heterologous polynucleotide can be from
any suitable microorganism. Examples of microorganisms are
described herein (e.g., Candida yeast, Saccharomyces yeast,
Yarrowia yeast, Pseudomonas bacteria, Bacillus bacteria,
Clostridium bacteria, Eubacterium bacteria and others include
Megasphaera bacteria.
[0022] Also provided in some embodiments are methods for
manufacturing adipic acid, which comprise culturing an engineered
microorganism described herein under culture conditions in which
the cultured microorganism produces adipic acid. In some
embodiments, the host microorganism from which the engineered
microorganism is generated does not produce a detectable amount of
adipic acid. In certain embodiments, the culture conditions
comprise fermentation conditions, introduction of biomass,
introduction of glucose, introduction of a paraffin (e.g., plant or
petroleum based, such as hexane or coconut oil, for example) and/or
combinations thereof. In some embodiments, the adipic acid is
produced with a yield of greater than about 0.3 grams per gram of
glucose added. In related embodiments, a method comprises purifying
the adipic acid from the cultured microorganisms and or modifying
the adipic acid, thereby producing modified adipic acid. In certain
embodiments, a method comprises placing the cultured
microorganisms, the adipic acid or the modified adipic acid in a
container, and optionally, shipping the container.
[0023] Provided also in certain embodiments are methods for
manufacturing 6-hydroxyhexanoic acid, which comprise culturing an
engineered microorganism described herein under culture conditions
in which the cultured microorganism produces 6-hydroxyhexanoic
acid. In some embodiments, the host microorganism from which the
engineered microorganism is generated does not produce a detectable
amount of 6-hydroxyhexanoic acid. In certain embodiments, the
culture conditions comprise fermentation conditions, introduction
of biomass, introduction of glucose, and/or introduction of hexane.
In some embodiments, the 6-hydroxyhexanoic acid is produced with a
yield of greater than about 0.3 grams per gram of glucose added. In
related embodiments, a method comprises purifying the
6-hydroxyhexanoic acid from the cultured microorganisms and or
modifying the 6-hydroxyhexanoic acid, thereby producing modified
6-hydroxyhexanoic acid. In certain embodiments, a method comprises
placing the cultured microorganisms, the 6-hydroxyhexanoic acid or
the modified 6-hydroxyhexanoic acid in a container, and optionally,
shipping the container.
[0024] Also provided in some embodiments are methods for preparing
an engineered microorganism that produces adipic acid, which
comprise: (a) introducing a genetic modification to a host organism
that adds or increases monooxygenase activity, thereby producing
engineered microorganisms having detectable and/or increased
monooxygenase activity; and (b) selecting for engineered
microorganisms that produce adipic acid. Provided also herein in
some embodiments are methods for preparing an engineered
microorganism that produces adipic acid, which comprise: (a)
culturing a host organism with hexane as a nutrient source, thereby
producing engineered microorganisms having detectable monooxygenase
activity; and (b) selecting for engineered microorganisms that
produce adipic acid. In some embodiments the monooxygenase activity
is incorporation of a hydroxyl moiety into a six-carbon molecule,
and in certain embodiments, the six-carbon molecule is hexanoate.
In related embodiments, a method comprises selecting the engineered
microorganisms that have a detectable amount of the monooxygenase
activity. In some embodiments, a method comprises introducing a
genetic modification that adds or increases a hexanoate synthase
activity, thereby producing engineered microorganisms, and
selecting for engineered microorganisms having detectable and/or
increased hexanoate synthase activity. In related embodiments, the
genetic modification encodes a polypeptide having a hexanoate
synthase subunit A activity, a hexanoate synthase subunit B
activity, or a hexanoate synthase subunit A activity and a
hexanoate synthase subunit B activity.
[0025] In some embodiments, a method comprises introducing a
genetic modification that adds or increases an aldehyde
dehydrogenase activity (e.g., 6-oxohexanoic acid dehydrogenase
activity, omega oxo fatty acid dehydrogenase), thereby producing
engineered microorganisms, and selecting for engineered
microorganisms having detectable and/or increased 6-oxohexanoic
acid dehydrogenase activity or omega oxo fatty acid dehydrogenase
relative to the host microorgansim. In certain embodiments, a
method for preparing microorganisms that produce adipic acid
includes selecting for engineered microorganisms having one or more
detectable and/or increased activities selected from the group
consisting of an aldehyde dehydrogenase activity (e.g.,
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase), fatty alcohol oxidase activity (e.g.,
6-hydroxyhexanoic acid dehydrogenase activity, omega hydroxyl-fatty
acid dehydrogenase), hexanoate synthase activity, monooxygenase
activity, monooxygenase reductase activity, fatty alcohol oxidase
activity, acyl-CoA ligase activity, acyl-CoA oxidase activity,
enoyl-CoA hydratase activity, 3-hydroxyacyl-CoA dehydrogenase
activity, and/or acetyl-CoA C-acyltransferase activity.
[0026] In certain embodiments, a method comprises introducing a
genetic modification that adds or increases a fatty alcohol oxidase
activity (e.g., 6-hydroxyhexanoic acid dehydrogenase activity,
omega hydroxyl fatty acid dehydrogenase activity) thereby producing
engineered microorganisms, and selecting for engineered
microorganisms having a detectable and/or increased
6-hydroxyhexanoic acid dehydrogenase activity or omega hydroxyl
fatty acid dehydrogenase activity relative to the host
microorganism. In some embodiments, a method comprises introducing
a genetic modification that adds or increases a thioesterase
activity, thereby producing engineered microorganisms, and
selecting for engineered microorganisms having a detectable and/or
increased thioesterase activity relative to the host
microorganism.
[0027] In certain embodiments, a method comprises introducing a
genetic modification that reduces 6-hydroxyhexanoic acid
conversion, thereby producing engineered microorganisms, and
selecting for engineered microorganisms having reduced
6-hydroxyhexanoic acid conversion relative to the host
microorganism. In some embodiments, a method comprises introducing
a genetic modification that reduces beta-oxidation activity,
thereby producing engineered microorganisms, and selecting for
engineered microorganisms having reduced beta-oxidation activity
relative to the host microorganism. In certain embodiments, a
method comprises introducing a genetic modification that results in
substantial hexanoate usage by the monooxygenase activity, thereby
producing engineered microorganisms, and selecting for engineered
microorganisms in which substantial hexanoate usage is by the
monooxygenase activity relative to the host microorganism. In some
embodiments, a method comprises introducing a genetic modification
that increases omega-oxidation activity, thereby producing
engineered microorganisms, and selecting for engineered
microorganisms having increased omega-oxidation activity relative
to the host microorganism.
[0028] Provided also herein in certain embodiments are methods for
preparing a microorganism that produces adipic acid, which
comprise: (a) introducing one or more genetic modifications to a
host organism that add or increase one or more activities selected
from the group consisting of 6-oxohexanoic acid dehydrogenase
activity, omega oxo fatty acid dehydrogenase activity,
6-hydroxyhexanoic acid dehydrogenase activity, omega hydroxyl fatty
acid dehydrogenase activity, hexanoate synthase activity,
monooxygenase activity, monooxygenase reductase activity, fatty
alcohol oxidase activity, acyl-CoA ligase activity, acyl-CoA
oxidase activity, enoyl-CoA hydratase activity, 3-hydroxyacyl-CoA
dehydrogenase activity, and/or acetyl-CoA C-acyltransferase
activity, thereby producing engineered microorganisms, and (b)
selecting for engineered microorganisms that produce adipic acid.
In some embodiments, a method comprises selecting for engineered
microorganisms having one or more detectable and/or increased
activities selected from the group consisting of 6-oxohexanoic acid
dehydrogenase activity, 6-hydroxyhexanoic acid dehydrogenase
activity, hexanoate synthase activity, monooxygenase activity,
monooxygenase reductase activity, fatty alcohol oxidase activity,
acyl-CoA ligase activity, acyl-CoA oxidase activity, enoyl-CoA
hydratase activity, 3-hydroxyacyl-CoA dehydrogenase activity,
and/or acetyl-CoA C-acyltransferase activity, relative to the host
microorganism.
[0029] In certain embodiments, a method comprises introducing a
genetic modification that reduces 6-hydroxyhexanoic acid
conversion, thereby producing engineered microorganisms, and
selecting for engineered microorganisms having reduced
6-hydroxyhexanoic acid conversion relative to the host
microorganism. In some embodiments, a method comprises introducing
a genetic modification that reduces beta-oxidation activity,
thereby producing engineered microorganisms, and selecting for
engineered microorganisms having reduced beta-oxidation activity
relative to the host microorganism. In certain embodiments, a
method comprises introducing a genetic modification that results in
substantial hexanoate usage by the monooxygenase activity, thereby
producing engineered microorganisms, and selecting for engineered
microorganisms in which substantial hexanoate usage is by the
monooxygenase activity relative to the host microorganism.
[0030] Also provided in some embodiments are methods for preparing
a microorganism that produces 6-hydroxyhexanoic acid, which
comprise: (a) introducing one or more genetic modifications to a
host organism that add or increase one or more activities selected
from the group consisting of 6-oxohexanoic acid dehydrogenase
activity, hexanoate synthase activity, monooxygenase activity,
monooxygenase reductase activity, fatty alcohol oxidase activity,
acyl-CoA ligase activity, acyl-CoA oxidase activity, enoyl-CoA
hydratase activity, 3-hydroxyacyl-CoA dehydrogenase activity,
and/or acetyl-CoA C-acyltransferase activity, thereby producing
engineered microorganisms, (b) introducing a genetic modification
to the host organism that reduces 6-hydroxyhexanoic acid
conversion, and (c) selecting for engineered microorganisms that
produce 6-hydroxyhexanoic acid. In certain embodiments, a method
comprises selecting for engineered microorganisms having reduced
6-hydroxyhexanoic acid conversion relative to the host
microorganism. In some embodiments, a method comprises selecting
for engineered microorganisms having one or more detectable and/or
increased activities selected from the group consisting of aldehyde
dehydrogenase activity (e.g., 6-oxohexanoic acid dehydrogenase
activity, omega oxo fatty acid dehydrogenase activity), fatty
alcohol oxidase activity (e.g., 6-hydroxyhexanoic acid
dehydrogenase activity, omega hydroxyl fatty acid dehydrogenase
activity), hexanoate synthase activity, monooxygenase activity,
monooxygenase reductase activity, fatty alcohol oxidase activity,
acyl-CoA ligase activity, acyl-CoA oxidase activity, enoyl-CoA
hydratase activity, 3-hydroxyacyl-CoA dehydrogenase activity,
and/or acetyl-CoA C-acyltransferase activity, relative to the host
microorganism. In certain embodiments, a method comprises
introducing a genetic modification that reduces beta-oxidation
activity, thereby producing engineered microorganisms, and
selecting for engineered microorganisms having reduced
beta-oxidation activity relative to the host microorganism. In some
embodiments, a method comprises introducing a genetic modification
that results in substantial hexanoate usage by the monooxygenase
activity, thereby producing engineered microorganisms, and
selecting for engineered microorganisms in which substantial
hexanoate usage is by the monooxygenase activity relative to the
host microorganism.
[0031] Also provided are methods that include contacting an
engineered microorganism with a feedstock including one or more
polysaccharides, wherein the engineered microorganism includes: (a)
a genetic alteration that blocks beta oxidation activity, and (b) a
genetic alteration that adds or increases a monooxygenase activity
or a genetic alteration that adds or increases a hexanoate
synthetase activity, and culturing the engineered microorganism
under conditions in which adipic acid is produced. In some
embodiments, the engineered microorganism comprises a genetic
alteration that adds or increases hexanoate synthetase activity. In
certain embodiments, the engineered microorganism comprises a
heterologous polynucleotide encoding a polypeptide having hexanoate
synthase subunit A activity, and in some embodiments the engineered
microorganism comprises a heterologous polynucleotide encoding a
polypeptide having hexanoate synthase subunit B activity. In
certain embodiments, the heterologous polynucleotide independently
is selected from a fungus. In some embodiments, the fungus is an
Aspergillus fungus, and in certain embodiments the Aspergillus
fungus is A. parasiticus. In some embodiments, wherein the
microorganism is a Candida yeast, and in certain embodiments, the
microorganism is a C. tropicalis strain.
[0032] Provided also are methods that include contacting an
engineered microorganism with a feedstock comprising one or more
paraffins, wherein the engineered microorganism comprises a genetic
alteration that partially blocks beta oxidation activity and
culturing the engineered microorganism under conditions in which
adipic acid is produced. In certain embodiments, the microorganism
comprises a genetic alteration that increases a monooxygenase
activity. In some embodiments, the microorganism is a Candida
yeast, and in certain embodiments, the microorganism is a C.
tropicalis strain.
[0033] In some embodiments, the genetic alteration that increases
monooxygenase activity comprises a genetic alteration that
increases Cytochrome P450 reductase activity. In certain
embodiments, the genetic alteration increases the number of copies
of a polynucleotide that encodes a polypeptide having the
Cytochrome P450 reductase activity. In some embodiments, the
genetic alteration places a promoter and/or 5'UTR in functional
connection with a polynucleotide that encodes a polypeptide having
the Cytochrome P450 reductase activity. In certain embodiments, the
monooxygenase activity is a CYP52A15 activity, CYP52A16 activity,
or a CYP52A15 activity and CYP52A16 activity. In some embodiments,
the genetic alteration increases the number of copies of a
polynucleotide that encodes a polypeptide having the monooxygenase
activity. In certain embodiments, the genetic alteration places a
promoter and/or 5'UTR in functional connection with a
polynucleotide that encodes a polypeptide having the monooxygenase
activity.
[0034] In certain embodiments, the genetic alteration that blocks
beta oxidation activity disrupts acyl-CoA oxidase activity. In some
embodiments, the genetic alteration disrupts POX4 and/or POXS
activity. In certain embodiments, the genetic alteration disrupts a
polynucleotide that encodes a polypeptide having the acyl-CoA
oxidase activity. In some embodiments, the genetic alteration
disrupts a promoter and/or 5'UTR in functional connection with a
polynucleotide that encodes a polypeptide having the acyl-CoA
oxidase activity.
[0035] In some embodiments, the feedstock comprises a 6-carbon
sugar. In certain embodiments, the feedstock comprises a 5-carbon
sugar. In certain embodiments, the adipic acid is produced at a
level of about 80% or more of theoretical yield. In some
embodiments, the amount of adipic acid produced is detected. In
certain embodiments, the adipic acid produced is isolated (e.g.,
partially or completely purified). In some embodiments, the culture
conditions comprise fermenting the engineered microorganism.
[0036] Provided also herein are engineered microorganisms in
contact with a feedstock. In some embodiments, the feedstock
includes a saccharide. In certain embodiments, the saccharide is a
monosaccharide, polysaccharide, or a mixture of a monosaccharide
and polysaccharide. In some embodiments, the feedstock includes a
paraffin. In certain embodiments, the paraffin is a saturated
paraffin, unsaturated paraffin, substituted paraffin, branched
paraffin, linear paraffin, or combination thereof.
[0037] In some embodiments, the paraffin includes about 1 to about
60 carbon atoms (e.g., between about 1 carbon atom, about 2 carbon
atoms, about 3 carbon atoms, about 4 carbon atoms, about 5 carbon
atoms, about 6 carbon atoms, about 7 carbon atoms, about 8 carbon
atoms, about 9 carbon atoms, about 10 carbon atoms, about 12 carbon
atoms, about 14 carbon atoms, about 16 carbon atoms, about 18
carbon atoms, about 20 carbon atoms, about 22 carbon atoms, about
24 carbon atoms, about 26 carbon atoms, about 28 carbon atoms,
about 30 carbon atoms, about 32 carbon atoms, about 34 carbon
atoms, about 36 carbon atoms, about 38 carbon atoms, about 40
carbon atoms, about 42 carbon atoms, about 44 carbon atoms, about
46 carbon atoms, about 48 carbon atoms, about 50 carbon atoms,
about 52 carbon atoms, about 54 carbon atoms, about 56 carbon
atoms, about 58 carbon atoms and about 60 carbon atoms). In certain
embodiments, the paraffin is in a mixture of paraffins. In some
embodiments, the paraffins in the mixture of paraffins have a mean
number of carbon atoms of about 8 carbon atoms to about 18 carbon
atoms (e.g., about 8 carbon atoms, about 9 carbon atoms, about 10
carbon atoms, about 11 carbon atoms, about 12 carbon atoms, about
13 carbon atoms, about 14 carbon atoms, about 15 carbon atoms,
about 16 carbon atoms, about 17 carbon atoms or about 18 carbon
atoms). In certain embodiments, the paraffin is in a wax, and in
some embodiments, the paraffin is in an oil. In certain
embodiments, the paraffin is from a petroleum product, and in some
embodiments, the petroleum product is a petroleum distillate. In
certain embodiments, the paraffin is from a plant or plant
product.
[0038] Also provided herein, is an isolated polynucleotide selected
from the group including a polynucleotide having a nucleotide
sequence 96% or more (e.g., 96% or more, 97% or more, 98% or more,
99% or more, or 100%) identical to the nucleotide sequence of SEQ
ID NO: 1, a polynucleotide having a nucleotide sequence that
encodes a polypeptide of SEQ ID NO: 8, and a polynucleotide having
a portion of a nucleotide sequence 96% or more identical to the
nucleotide sequence of SEQ ID NO: 1 and encodes a polypeptide
having fatty alcohol oxidase activity.
[0039] Also provided herein, is an isolated polynucleotide selected
from the group including a polynucleotide having a nucleotide
sequence 98% or more (e.g., 98% or more, 99% or more, or 100%)
identical to the nucleotide sequence of SEQ ID NO: 2, a
polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO:10, and a polynucleotide having a portion
of a nucleotide sequence 98% or more identical to the nucleotide
sequence of SEQ ID NO: 2 and encodes a polypeptide having fatty
alcohol oxidase activity.
[0040] Also provided herein, is an isolated polynucleotide selected
from the group including a polynucleotide having a nucleotide
sequence 95% or more (e.g., 95% or more, 96% or more, 97% or more,
98% or more, 99% or more, or 100%) identical to the nucleotide
sequence of SEQ ID NO: 3, a polynucleotide having a nucleotide
sequence that encodes a polypeptide of SEQ ID NO: 9, and a
polynucleotide having a portion of a nucleotide sequence 95% or
more identical to the nucleotide sequence of SEQ ID NO: 3 and
encodes a polypeptide having fatty alcohol oxidase activity.
[0041] Also provided herein, is an isolated polynucleotide selected
from the group including a polynucleotide having a nucleotide
sequence 83% or more (e.g., 83% or more, 84% or more, 85% or more,
86% or more, 87% or more, 88% or more, 89% or more, 90% or more,
91% or more, 92% or more, 93% or more, 94% or more, 95% or more,
96% or more, 97% or more, 98% or more, 99% or more, or 100%)
identical to the nucleotide sequence of SEQ ID NO: 4, a
polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 11, and a polynucleotide having a portion
of a nucleotide sequence 83% or more identical to the nucleotide
sequence of SEQ ID NO: 3 and encodes a polypeptide having fatty
alcohol oxidase activity.
[0042] Also provided herein, is an isolated polynucleotide selected
from the group including a polynucleotide having a nucleotide
sequence 82% or more (e.g., 82% or more, 83% or more, 84% or more,
85% or more, 86% or more, 87% or more, 88% or more, 89% or more,
90% or more, 91% or more, 92% or more, 93% or more, 94% or more,
95% or more, 96% or more, 97% or more, 98% or more, 99% or more, or
100%) identical to the nucleotide sequence of SEQ ID NO: 5, a
polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 12, and a polynucleotide having a portion
of a nucleotide sequence 82% or more identical to the nucleotide
sequence of SEQ ID NO: 3 and encodes a polypeptide having fatty
alcohol oxidase activity.
[0043] In certain embodiments, an expression vector includes a
polynucleotide sequence of SEQ ID NOs: 1 to 5. In some embodiments,
an integration vector includes a polynucleotide sequence of SEQ ID
NOs: 1 to 5. In certain embodiments, a microorganism includes an
expression vector, an integration vector, or an expression vector
and an integration vector that includes a polynucleotide sequence
of SEQ ID NOs: 1 to 5. In some embodiments, a culture includes a
microorganism that includes an expression vector, an integration
vector, or an expression vector and an integration vector that
includes a polynucleotide sequence of SEQ ID NOs: 1 to 5. In
certain embodiments, a fermentation device includes a microorganism
that includes an expression vector, an integration vector, or an
expression vector and an integration vector that includes a
polynucleotide sequence of SEQ ID NOs: 1 to 5. Also provided herein
is a polypeptide encoded by a polynucleotide sequence of SEQ ID
NOs: 1 to 5 or produced by an expression vector that includes a
polynucleotide sequence of SEQ ID NOs: 1 to 5. Provided also herein
is an antibody that specifically binds to a polypeptide encoded by
a polynucleotide sequence of SEQ ID NOs: 1 to 5 or produced by an
expression vector that includes a polynucleotide sequence of SEQ ID
NOs: 1 to 5.
[0044] Certain embodiments are described further in the following
description, examples, claims and drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0045] The drawings illustrate embodiments of the technology and
are not limiting. For clarity and ease of illustration, the
drawings are not made to scale and, in some instances, various
aspects may be shown exaggerated or enlarged to facilitate an
understanding of particular embodiments.
[0046] FIG. 1 depicts a metabolic pathway for making adipic acid.
The pathway can be engineered into a eukaryotic microorganism to
generate a microorganism capable of producing adipic acid.
[0047] FIG. 2 depicts an embodiment for a method of generating an
adipic acid producing microorganism. The method comprises
expressing one or more genes catalyzing the omega oxidation of
fatty acids to dicarboxylic acids in a host microorganism that
produces hexanoate. In the method depicted, the host organism, for
example A. parasiticus or A. nidulans, endogenously includes HEXA
and HEXB (or STCJ and STCK) genes. In one embodiment the method
comprises knocking out or otherwise disabling the gene coding for
diversion of hexanoate into an endogenous pathway such as mycotoxin
production. Certain embodiments of the method further comprise
inserting a heterologous cytochrome P450 gene. Some embodiments of
the method comprise growing the culture on hexane and screening for
increased P450 expression. The copy number of hexanoate induced
P450 may in certain embodiments be increased. In some embodiments
the microorganism may be altered to increase the flux of six carbon
substrate through the final two oxidation steps.
[0048] FIG. 3 depicts an embodiment for a method of generating an
adipic acid producing organism. The method comprises expressing one
or more genes encoding hexanoate synthase in a host microorganism
that produces dicarboxylic acids via an omega-oxidation pathway.
Such microorganisms may include, without limitation, C. tropicalis
and C. maltosa. As depicted, the method comprises inserting HEXA
and HEXB genes into the host microorganism. The genes may be
isolated from Aspergillus, or another appropriate organism. In some
embodiments, the genes are synthesized from an alternative sequence
as described herein to produce the amino acid sequence of the donor
mircroorganism enzyme through a non-standard translation mechanism
of C. tropicalis. In some embodiments the method comprises
inserting a heterologous cytochrome P450 gene into the host
organism. In certain embodiments the microorganism may be altered
to increase the flux of a six-carbon substrate through the final
two oxidation steps.
[0049] FIG. 4 depicts an embodiment of a method for generating an
adipic acid producing organism. The method comprises expressing one
or more genes encoding hexanoate synthase in a host microorganism
that produces dicarboxylic acids via an omega-oxidation pathway.
The microorganisms can include, without limitation, C. tropicalis
and C. maltosa. In some embodiments, the method comprises growing a
host microorganism on hexane and screening for increased P450
expression. In certain embodiments, copy number of hexane-induced
P450 may be increased. HEXA and HEXB genes may be inserted into the
host microorganism. In certain embodiments, the host microorganism
may be altered to increase the flux of a six-carbon substrate
through the final two oxidation steps.
[0050] FIG. 5 depicts a plasmid diagram for inserting Aspergillus
hexanoate synthase genes HEXA and HEXB into C. tropicalis or Y.
lipolytica.
[0051] FIG. 6 depicts a plasmid diagram for inserting a
heterologous cytochrome P450 monooxygenase gene and cytochrome P450
reductase gene into C. tropicalis or Y. lipolytica.
[0052] FIG. 7 depicts a plasmid diagram for inserting a
heterologous cytochrome P450 monooxygenase gene and cytochrome P450
reductase gene into A. parasiticus or A. nidulans.
[0053] FIG. 8 depicts a system for biological production of a
target product. As depicted, a fermenter is populated with
microorganisms engineered for target product production. A flexible
feedstock supplies the fermenter with an energy and nutrition
source for the microorganisms. In some embodiments the feedstock
comprises a sugar. In certain embodiments the feedstock comprises
fatty acids. The feedstock may also include biomass, industrial
waste products and other sources of carbon. Vitamins, minerals,
enzymes and other growth or production enhancers may be added to
the feedstock. In certain embodiments the fermentation produces
adipic acid. The fermentation process may produce other novel
chemicals.
[0054] FIG. 9 depicts a metabolic pathway for making adipic acid
from saccharide or polysaccharide carbon sources, similar to the
pathway depicted in FIG. 1, with additional activities that aid in
metabolism of, or enhance metabolism of, pathway intermediates,
thereby potentially increasing the yield of adipic acid. The
additional activities are a monooxygenase reductase activity
(cytochrome P450 reductase or CPR) and a fatty alcohol oxidase
activity (FAO). Part, or all, of the pathway can be engineered into
a eukaryotic microorganism to generate a microorganism capable of
producing adipic acid.
[0055] FIG. 10 depicts a non-limiting example of a metabolic
pathway for making adipic acid from paraffins, fats, oils, fatty
acids or dicarboxylic acids, as described in FIG. 2. Part, or all,
of the pathway can be engineered (e.g., added, altered to increase
or decrease copy number, or increase or decrease promoter activity,
depending on the desired effect) into a microorganism, depending on
the activities already present in the host organism, to generate a
microorganism capable of producing adipic acid.
[0056] FIGS. 11A and 11B depict omega and beta oxidation pathways
useful for producing adipic acid from various carbon sources.
Adipic acid can be produced from paraffins, fats, oils and
intermediates of sugar metabolism, using omega oxidation, as shown
in FIG. 11A. Adipic acid also can be produced from long chain fatty
acids or dicarboxylic acids using beta oxidation, as shown in FIG.
11A. FIG. 11B shows a common intermediate from the metabolism of
fats and sugars entering the omega oxidation pathway to ultimately
produce adipic acid.
[0057] FIG. 12 shows results of immunodetection of
6.times.His-tagged proteins (`6.times.His` disclosed as SEQ ID NO:
13) expressed in S. cerevisiae BY4742. Strains sAA061, sAA140,
sAA141, sAA142 contain 6.times.His-tagged HEXA and HEXB proteins
(`6.times.His` disclosed as SEQ ID NO: 13). Strain sAA144 contains
6.times.His-tagged STCJ and STCK proteins (`6.times.His` disclosed
as SEQ ID NO: 13). Strain sAA048 contains only vectors p425GPD and
p426GPD.
[0058] FIG. 13 shows results of immunodetection of
6.times.His-tagged proteins (`6.times.His` disclosed as SEQ ID NO:
13) expressed in either S. cerevisiae (sAA144) or in C. tropicalis
(sAA103, sAA270, sAA269). 6.times.His tagged HEXA and HEXB
(`6.times.His` disclosed as SEQ ID NO: 13) expressed in strains
sAA269 and sAA270 are indicated with arrows. 6.times.His tagged
STCJ and STCK (`6.times.His` disclosed as SEQ ID NO: 13) from
strain sAA144 were included as a positive control. Strain sAA103 is
the parent strain for sAA269 and sAA270 and does not contain
integrated vectors for the expression of 6.times.His-tagged HEXA
and HEXB (`6.times.His` disclosed as SEQ ID NO: 13).
[0059] FIG. 14 shows results of RT-PCR from cultures of C.
tropicalis strain sAA003 exposed to glucose only (Glc), hexane only
(Hex), or hexanoic acid only (HA). PCR products of A15 and A16
alleles show hexane and hexanoic acid specific induction.
[0060] FIGS. 15A-15C illustrate results of acyl-CoA oxidase (POX)
enzymatic activity assays on substrates of various carbon lengths,
using acyl-CoA enzyme preparations from Candida tropicalis strains
with no POX genes disrupted (see FIG. 15A), POX4 genes disrupted
(see FIG. 15C) or POX5 genes disrupted (see FIG. 15B). Experimental
results and conditions are given in the Detailed Description and
Examples sections.
[0061] FIGS. 16-34 illustrate various plasmids for cloning,
expression, or integration of various activities described herein,
into a host organism or engineered organism. FIG. 16 depicts a
plasmid diagram for inserting a heterologous HEXA gene into S.
cerevisiae. FIG. 17 depicts a plasmid diagram for inserting a
heterologous HEXB gene into S. cerevisiae. FIG. 18 depicts a
plasmid diagram for inserting a heterologous HEXA-6.times.His gene
(`6.times.His` disclosed as SEQ ID NO: 13) into S. cerevisiae. FIG.
19 depicts a plasmid diagram for inserting a heterologous
HEXB-6.times.His gene (`6.times.His` disclosed as SEQ ID NO: 13)
into S. cerevisiae.
[0062] FIG. 20 depicts a plasmid diagram for inserting a
heterologous STCJ gene into S. cerevisiae.
[0063] FIG. 21 depicts a plasmid diagram for inserting a
heterologous STCK gene into S. cerevisiae.
[0064] FIG. 22 depicts a plasmid diagram for inserting a
heterologous STCJ-6.times.His gene (`6.times.His` disclosed as SEQ
ID NO: 13) into S. cerevisiae. FIG. 23 depicts a plasmid diagram
for inserting a heterologous STCK-6.times.His gene (`6.times.His`
disclosed as SEQ ID NO: 13) into S. cerevisiae.
[0065] FIG. 24 depicts a plasmid diagram for inserting a
heterologous alternative genetic code (AGC) HEXA gene into C.
tropicalis. FIG. 25 depicts a plasmid diagram for inserting a
heterologous AGC-HEXB gene into C. tropicalis. FIG. 25 discloses
`6.times.His` as SEQ ID NO: 13. FIG. 26 depicts a plasmid diagram
for inserting a heterologous AGC-HEXA-6.times.His gene
(`6.times.His` disclosed as SEQ ID NO: 13) into C. tropicalis. FIG.
27 depicts a plasmid diagram for inserting a heterologous
AGC-HEXB-6.times.His gene (`6.times.His` disclosed as SEQ ID NO:
13) into C. tropicalis.
[0066] FIG. 28 depicts a diagram of a plasmid used for cloning the
POX5 gene from C. tropicalis.
[0067] FIG. 29 depicts a diagram of a plasmid used for cloning the
POX4 gene from C. tropicalis.
[0068] FIG. 30 illustrates a plasmid constructed for use of URA
selection in C. tropicalis. FIG. 31 depicts a plasmid containing
the PGK promoter and terminator from C. tropicalis. FIG. 32 depicts
a plasmid used for integration of the CPR gene in C. tropicalis.
FIG. 33 depicts a plasmid used for integration of the CYP52A15 gene
in C. tropicalis. FIG. 34 depicts a plasmid used for integration of
the CYP52A16 gene in C. tropicalis.
DETAILED DESCRIPTION
[0069] Adipic acid is a six-carbon organic molecule that is a
chemical intermediate in manufacturing processes used to make
certain polyamides, polyurethanes and plasticizers, all of which
have wide applications in producing items such as carpets,
coatings, adhesives, elastomers, food packaging, and lubricants,
for example. Some large-scale processes for making adipic acid
include (i) liquid phase oxidation of ketone alcohol oil (KA oil);
(ii) air oxidation/hydration of cyclohexane with boric acid to make
cyclohexanol, followed by oxidation with nitric acid; and (iii)
hydrocyanation of butadiene to a pentenenitrile mixture, followed
by hydroisomerization of adiponitrile, followed by hydrogenation.
Each of the latter processes requires use of noxious chemicals
and/or solvents, some require high temperatures, and all require
significant energy input. In addition, some of the processes emit
toxic byproducts (such as nitrous oxide) and give rise to
environmental concerns.
[0070] Provided herein are methods for producing adipic acid and
other organic chemical intermediates using biological systems. Such
production systems may have significantly less environmental impact
and could be economically competitive with current manufacturing
systems. Thus, provided herein are methods for manufacturing adipic
acid by engineered microorganisms. In some embodiments
microorganisms are engineered to contain at least one heterologous
gene encoding an enzyme, where the enzyme is a member of a novel
pathway engineered into the microorganism. In certain embodiments,
an organism may be selected for elevated activity of a native
enzyme.
Microorganisms
[0071] A microorganism selected often is suitable for genetic
manipulation and often can be cultured at cell densities useful for
industrial production of a target product. A microorganism selected
often can be maintained in a fermentation device.
[0072] The term "engineered microorganism" as used herein refers to
a modified microorganism that includes one or more activities
distinct from an activity present in a microorganism utilized as a
starting point (hereafter a "host microorganism"). An engineered
microorganism includes a heterologous polynucleotide in some
embodiments, and in certain embodiments, an engineered organism has
been subjected to selective conditions that alter an activity, or
introduce an activity, relative to the host microorganism. Thus, an
engineered microorganism has been altered directly or indirectly by
a human being. A host microorganism sometimes is a native
microorganism, and at times is a microorganism that has been
engineered to a certain point.
[0073] In some embodiments an engineered microorganism is a single
cell organism, often capable of dividing and proliferating. A
microorganism can include one or more of the following features:
aerobe, anaerobe, filamentous, non-filamentous, monoploid, dipoid,
auxotrophic and/or non-auxotrophic. In certain embodiments, an
engineered microorganism is a prokaryotic microorganism (e.g.,
bacterium), and in certain embodiments, an engineered microorganism
is a non-prokaryotic microorganism. In some embodiments, an
engineered microorganism is a eukaryotic microorganism (e.g.,
yeast, fungi, amoeba).
[0074] Any suitable yeast may be selected as a host microorganism,
engineered microorganism or source for a heterologous
polynucleotide. Yeast include, but are not limited to, Yarrowia
yeast (e.g., Y. lipolytica (formerly classified as Candida
lipolytica)), Candida yeast (e.g., C. revkaufi, C. pulcherrima, C.
tropicalis, C. utilis), Rhodotorula yeast (e.g., R. glutinus, R.
graminis), Rhodosporidium yeast (e.g., R. toruloides),
Saccharomyces yeast (e.g., S. cerevisiae, S. bayanus, S.
pastorianus, S. carlsbergensis), Cryptococcus yeast, Trichosporon
yeast (e.g., T. pullans, T. cutaneum), Pichia yeast (e.g., P.
pastoris) and Lipomyces yeast (e.g., L. starkeyii, L. lipoferus).
In some embodiments, a yeast is a Y. lipolytica strain that
includes, but is not limited to, ATCC20362, ATCC8862, ATCC18944,
ATCC20228, ATCC76982 and LGAM S(7)1 strains (Papanikolaou S., and
Aggelis G., Bioresour. Technol. 82(1):43-9 (2002)). In certain
embodiments, a yeast is a C. tropicalis strain that includes, but
is not limited to, ATCC20336, ATCC20913, SU-2 (ura3-/ura3-),
ATCC20962, H5343 (beta oxidation blocked; U.S. Pat. No. 5,648,247)
strains.
[0075] Any suitable fungus may be selected as a host microorganism,
engineered microorganism or source for a heterologous
polynucleotide. Non-limiting examples of fungi include, but are not
limited to, Aspergillus fungi (e.g., A. parasiticus, A. nidulans),
Thraustochytrium fungi, Schizochytrium fungi and Rhizopus fungi
(e.g., R. arrhizus, R. oryzae, R. nigricans). In some embodiments,
a fungus is an A. parasiticus strain that includes, but is not
limited to, strain ATCC24690, and in certain embodiments, a fungus
is an A. nidulans strain that includes, but is not limited to,
strain ATCC38163.
[0076] Any suitable prokaryote may be selected as a host
microorganism, engineered microorganism or source for a
heterologous polynucleotide. A Gram negative or Gram positive
bacteria may be selected. Examples of bacteria include, but are not
limited to, Bacillus bacteria (e.g., B. subtilis, B. megaterium),
Acinetobacter bacteria, Norcardia baceteria, Xanthobacter bacteria,
Escherichia bacteria (e.g., E. coli (e.g., strains DH10B, Stb12,
DH5-alpha, DB3, DB3.1), DB4, DB5, JDP682 and ccdA-over (e.g., U.S.
application Ser. No. 09/518,188))), Streptomyces bacteria, Erwinia
bacteria, Klebsiella bacteria, Serratia bacteria (e.g., S.
marcessans), Pseudomonas bacteria (e.g., P. aeruginosa), Salmonella
bacteria (e.g., S. typhimurium, S. typhi), Megasphaera bacteria
(e.g., Megasphaera elsdenii). Bacteria also include, but are not
limited to, photosynthetic bacteria (e.g., green non-sulfur
bacteria (e.g., Choroflexus bacteria (e.g., C. aurantiacus),
Chloronema bacteria (e.g., C. gigateum)), green sulfur bacteria
(e.g., Chlorobium bacteria (e.g., C. limicola), Pelodictyon
bacteria (e.g., P. luteolum), purple sulfur bacteria (e.g.,
Chromatium bacteria (e.g., C. okenii)), and purple non-sulfur
bacteria (e.g., Rhodospirillum bacteria (e.g., R. rubrum),
Rhodobacter bacteria (e.g., R. sphaeroides, R. capsulatus), and
Rhodomicrobium bacteria (e.g., R. vanellii)).
[0077] Cells from non-microbial organisms can be utilized as a host
microorganism, engineered microorganism or source for a
heterologous polynucleotide. Examples of such cells, include, but
are not limited to, insect cells (e.g., Drosophila (e.g., D.
melanogaster), Spodoptera (e.g., S. frugiperda Sf9 or Sf21 cells)
and Trichoplusa (e.g., High-Five cells); nematode cells (e.g., C.
elegans cells); avian cells; amphibian cells (e.g., Xenopus laevis
cells); reptilian cells; and mammalian cells (e.g., NIH3T3, 293,
CHO, COS, VERO, C127, BHK, Per-C6, Bowes melanoma and HeLa
cells).
[0078] Microorganisms or cells used as host organisms or source for
a heterologous polynucleotide are commercially available.
Microoganisms and cells described herein, and other suitable
microorganisms and cells are available, for example, from
Invitrogen Corporation, (Carlsbad, Calif.), American Type Culture
Collection (Manassas, Va.), and Agricultural Research Culture
Collection (NRRL; Peoria, Ill.).
[0079] Host microorganisms and engineered microorganisms may be
provided in any suitable form. For example, such microorganisms may
be provided in liquid culture or solid culture (e.g., agar-based
medium), which may be a primary culture or may have been passaged
(e.g., diluted and cultured) one or more times. Microorganisms also
may be provided in frozen form or dry form (e.g., lyophilized).
Microorganisms may be provided at any suitable concentration.
Carbon Processing Pathways and Activities
[0080] FIGS. 1 and 9 depict an embodiment of a biological pathway
for making adipic acid, using a sugar as the carbon source starting
material. Any suitable sugar can be used as the feedstock for the
organism, (e.g., 6-carbon sugars (e.g., glucose, fructose),
5-carbon sugars (e.g., xylose), the like or combinations thereof).
The sugars are initially metabolized using naturally occurring
and/or engineered pathways to yield malonyl CoA, which is depicted
as the molecule entering the omega oxidation pathway shown in FIG.
9. As depicted, the enzyme hexanoate synthase converts two
molecules of malonyl CoA and one molecule of acetyl CoA to one
molecule of hexanoic acid. In some embodiments a cytochrome P450
enzyme converts hexanoic acid to 6-hydroxyhexanoic acid, which may
be oxidized to 6-oxohexanoic acid via 6-hydroxyhexanoic acid
dehydrogenase, or fatty alcohol oxidase. 6-oxohexanoic acid may be
converted to adipic acid by 6-oxohexanoic acid dehydrogenase.
[0081] A hexanoate synthase enzyme (HexS) is coded by hexonate
synthase subunit alpha (HEXA) and hexanoate synthase subunit beta
(HEXB) genes. In some embodiments, the HexS enzyme is endogenous to
the host microorganism. In certain embodiments, HEXA and HEXB genes
may be isolated from a suitable organism (e.g., Aspergillus
parasiticus). In some embodiments, HEXA and HEXB orthologs, such as
STCJ and STCK, also may be isolated from suitable organisms (e.g.,
Aspergillus nidulans).
[0082] Hexanoate is omega-hydroxylated by the enzyme cytochrome
P450, thereby generating a six carbon alcohol, in some embodiments.
In certain embodiments, the cytochrome P450 enzyme is endogenous to
the host microorganism. In some embodiments the cytochrome P450
gene is isolated from Bacillus megaterium and codes for a single
subunit, soluble, cytoplasmic enzyme. Soluble or membrane bound
cytochrome P450 from certain host organisms is specific for
6-carbon substrates and may be used in some embodiments.
[0083] Cytochrome P450 is reduced by the activity of cytochrome
P450 reductase (CPR), thereby recycling cytochrome P450 to allow
further enzymatic activity. In certain embodiments, the CPR enzyme
is endogenous to the host microorganism. In some embodiments, host
CPR activity can be increased by increasing the number of copies of
a CPR gene (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more copies of the
gene), by increasing the activity of a promoter that regulates
transcription of a CPR gene, or by increasing the number of copies
of a CPR gene and increasing the activity of a promoter that
regulates transcription of a CPR gene, thereby increasing the
production of target product (e.g., adipic acid) via increased
recycling of cytochrome P450. In certain embodiments, the promoter
can be a heterologous promoter (e.g., endogenous or exogenous
promoter). In some embodiments, the CPR gene is heterologous and
exogenous and can be isolated from any suitable organism.
Non-limiting examples of organisms from which a CPR gene can be
isolated include C. tropicalis, S. cerevisiae and Bacillus
megaterium.
[0084] Oxidation of the alcohol to an aldehyde may be performed by
an enzyme in the fatty alcohol oxidase family (e.g.,
6-hydroxyhexanoic acid dehydrogenase, omega hydroxyl fatty acid
dehydrogenase), or an enzyme in the aldehyde dehydrogenase family
(e.g., 6-oxohexanoic acid dehydrogenase, omega oxo fatty acid
dehydrogenase). The enzyme 6-oxohexanoic acid dehydrogenase or
omega oxo fatty acid dehydrogenase may oxidize the aldehyde to the
carboxylic acid adipic acid. In some embodiments, the enzymes
6-hydroxyhexanoic acid dehydrogenase, omega hydroxyl fatty acid
dehydrogenase, fatty alcohol oxidase, 6-oxohexanoic acid
dehydrogenase, or omega oxo fatty acid dehydrogenase, exist in a
host organism. Flux through these two steps may sometimes be
augmented by increasing the copy number of the enzymes, or by
increasing the activity of the promoter transcribing the genes. In
some embodiments alcohol and aldehyde dehydrogenases specific for
six carbon substrates may be isolated from another organism, for
example Acinetobacter, Candida, Saccharomyces or Pseudomonas and
inserted into the host organism.
[0085] FIG. 10 depicts an embodiment of a biological pathway for
making adipic acid, using fats, oils, dicarboxylic acids, paraffins
(e.g., linear, branched, substituted, saturated, unsaturated, the
like and combinations thereof), fatty alcohols, fatty acids, or the
like, as the carbon source starting material. Any suitable fatty
alcohol, fatty acid, paraffin, dicarboxylic acid, fat or oil can be
used as the feedstock for the organism, (e.g., hexane, hexanoic
acid, oleic acid, coconut oil, the like or combinations thereof).
Carbon sources with longer chain lengths (e.g., 8 carbons or
greater in length) can be metabolized using naturally occurring
and/or engineered pathways to yield molecules that can be further
metabolized using the beta oxidation pathway shown in FIG. 10 and
the lower portion of FIG. 11A. In some embodiments, the activities
in the pathway shown in FIG. 10 also can be engineered (e.g., as
described herein) to enhance metabolism and target product
formation. The enzyme acyl-CoA ligase converts a long chain fatty
alcohol, fatty acid or dicarboxylic acid and 1 molecule of
acetyl-CoA into an acyl-CoA derivative of the long chain fatty
alcohol, fatty acid or dicarboxylic acid with the conversion of ATP
to AMP and inorganic phosphate, as depicted in the first step of
the reaction in FIG. 10. The term "beta oxidation pathway" as used
herein, refers to a series of enzymatic activities utilized to
metabolize fatty alcohols, fatty acids, or dicarboxylic acids. The
activities utilized to metabolize fatty alcohols, fatty acids, or
dicarboxylic acids include, but are not limited to, acyl-CoA ligase
activity, acyl-CoA oxidase activity, enoyl-CoA hydratase activity,
3-hydroxyacyl-CoA dehydrogenase activity and acetyl-CoA
C-acyltransferase activity. The term "beta oxidation activity"
refers to any of the activities in the beta oxidation pathway
utilized to metabolize fatty alcohols, fatty acids or dicarboxylic
acids. The term "omega oxidation activity" refers to any of the
activities in the omega oxidation pathway utilized to metabolize
fatty alcohols, fatty acids, dicarboxylic acids, or sugars.
[0086] In certain embodiments, an Acyl-CoA ligase enzyme converts a
long chain fatty alcohol, fatty acid or dicarboxylic acid into the
acyl-CoA derivative, which may be oxidized to yield a
trans-2,3-dehydroacyl-CoA derivative, by the activity of Acyl CoA
oxidase (e.g., also known as acyl-CoA oxidoreductase and fatty
acyl-coenzyme A oxidase). The trans-2,3-dehydroacyl-CoA derivative
long chain fatty alcohol, fatty acid or dicarboxylic acid may be
further converted to 3-hydroxyacyl-CoA by the activity of enoyl-CoA
hydratase. 3-hydroxyacyl-CoA can be converted to 3-oxoacyl-CoA by
the activity of 3-hydroxyacyl-CoA dehydrogenase. 3-oxoacyl-CoA may
be converted to an acyl-CoA molecule, shortened by 2 carbons and an
acetyl-CoA, by the activity of Acetyl-CoA C-acyltransferase (e.g.,
also known as beta-ketothiolase and .beta.-ketothiolase). In some
embodiments, acyl-CoA molecules may be repeatedly shortened by beta
oxidation until a desired carbon chain length is generated (e.g., 6
carbons, adipic acid). The shortened fatty acid can be further
processed using omega oxidation to yield adipic acid.
[0087] An acyl-CoA ligase enzyme sometimes is encoded by the host
organism and can be added to generate an engineered organism. In
some embodiments, host acyl-CoA ligase activity can be increased by
increasing the number of copies of an acyl-CoA ligase gene, by
increasing the activity of a promoter that regulates transcription
of an acyl-CoA ligase gene, or by increasing the number copies of
the gene and by increasing the activity of a promoter that
regulates transcription of the gene, thereby increasing production
of target product (e.g., adipic acid) due to increased carbon flux
through the pathway. In certain embodiments, the acyl-CoA ligase
gene can be isolated from any suitable organism. Non-limiting
examples of organisms that include, or can be used as donors for,
acyl-CoA ligase enzymes include Candida, Saccharomyces, or
Yarrowia.
[0088] An enoyl-CoA hydratase enzyme catalyzes the addition of a
hydroxyl group and a proton to the unsaturated .beta.-carbon on a
fatty-acyl CoA and sometimes is encoded by the host organism and
sometimes can be added to generate an engineered organism. In
certain embodiments, the enoyl-CoA hydratase activity is unchanged
in a host or engineered organism. In some embodiments, the host
enoyl-CoA hydratase activity can be increased by increasing the
number of copies of an enoyl-CoA hydratase gene, by increasing the
activity of a promoter that regulates transcription of an enoyl-CoA
hydratase gene, or by increasing the number copies of the gene and
by increasing the activity of a promoter that regulates
transcription of the gene, thereby increasing the production of
target product (e.g., adipic acid) due to increased carbon flux
through the pathway. In certain embodiments, the enoyl-CoA
hydratase gene can be isolated from any suitable organism.
Non-limiting examples of organisms that include, or can be used as
donors for, enoyl-CoA hydratase enzymes include Candida,
Saccharomyces, or Yarrowia.
[0089] 3-hydroxyacyl-CoA dehydrogenase enzyme catalyzes the
formation of a 3-ketoacyl-CoA by removal of a hydrogen from the
newly formed hydroxyl group created by the activity of enoyl-CoA
hydratase. In some embodiments, the activity is encoded by the host
organism and sometimes can be added or increased to generate an
engineered organism. In certain embodiments, the 3-hydroxyacyl-CoA
activity is unchanged in a host or engineered organism. In some
embodiments, the host 3-hydroxyacyl-CoA dehydrogenase activity can
be increased by increasing the number of copies of a
3-hydroxyacyl-CoA dehydrogenase gene, by increasing the activity of
a promoter that regulates transcription of a 3-hydroxyacyl-CoA
dehydrogenase gene, or by increasing the number copies of the gene
and by increasing the activity of a promoter that regulates
transcription of the gene, thereby increasing production of target
product (e.g., adipic acid) due to increased carbon flux through
the pathway. In certain embodiments, the 3-hydroxyacyl-CoA
dehydrogenase gene can be isolated from any suitable organism.
Non-limiting examples of organisms that include, or can be used as
donors for, 3-hydroxyacyl-CoA dehydrogenase enzymes include
Candida, Saccharomyces, or Yarrowia.
[0090] An Acetyl-CoA C-acyltransferase (e.g., .beta.-ketothiolase)
enzyme catalyzes the formation of a fatty acyl-CoA shortened by 2
carbons by cleavage of the 3-ketoacyl-CoA by the thiol group of
another molecule of CoA. The thiol is inserted between C-2 and C-3,
which yields an acetyl CoA molecule and an acyl CoA molecule that
is two carbons shorter. An Acetyl-CoA C-acyltransferase sometimes
is encoded by the host organism and sometimes can be added to
generate an engineered organism. In certain embodiments, the
acetyl-CoA C-acyltransferase activity is unchanged in a host or
engineered organism. In some embodiments, the host acetyl-CoA
C-acyltransferase activity can be increased by increasing the
number of copies of an acetyl-CoA C-acyltransferase gene, or by
increasing the activity of a promoter that regulates transcription
of an acetyl-CoA C-acyltransferase gene, thereby increasing the
production of target product (e.g., adipic acid) due to increased
carbon flux through the pathway. In certain embodiments, the
acetyl-CoA C-acyltransferase gene can be isolated from any suitable
organism. Non-limiting examples of organisms that include, or can
be used as donors for, acetyl-CoA C-acyltransferase enzymes include
Candida, Saccharomyces, or Yarrowia.
[0091] A microorganism may be modified and engineered to include or
regulate one or more activities in an adipic acid pathway. The term
"activity" as used herein refers to the functioning of a
microorganism's natural or engineered biological pathways to yield
various products including adipic acid and its precursors. Adipic
acid producing activity can be provided by any non-mammalian source
in certain embodiments. Such sources include, without limitation,
eukaryotes such as yeast and fungi and prokaryotes such as
bacteria. In some embodiments, a reverse activity in a pathway
described herein can be altered (e.g., disrupted, reduced) to
increase carbon flux through a beta oxidation pathway, an omega
oxidation pathway, or a beta oxidation and omega oxidation pathway,
towards the production of target product (e.g., adipic acid). In
some embodiments, a genetic modification disrupts an activity in
the beta oxidation pathway, or disrupts a polynucleotide that
encodes a polypeptide that carries out a forward reaction in the
beta oxidation pathway, which renders beta oxidation activity
undetectable. The term "undetectable" as used herein refers to an
amount of an analyte that is below the limits of detection, using
detection methods or assays known (e.g., described herein). In
certain embodiments, the genetic modification partially reduces
beta oxidation activity. The term "partially reduces beta oxidation
activity" as used here refers to a level of activity in an
engineered organism that is lower than the level of activity found
in the host or starting organism.
[0092] An activity within an engineered microorganism provided
herein can include one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
or all) of the following activities: 6-oxohexanoic acid
dehydrogenase activity; 6-hydroxyhexanoic acid dehydrogenase
activity; hexanoate synthase activity; cytochrome P450 activity;
cytochrome P450 reductase activity; fatty alcohol oxidase activity;
acyl-CoA ligase activity, acyl-CoA oxidase activity; enoyl-CoA
hydratase activity, 3-hydroxyacyl-CoA dehydrogenase activity, and
thioesterase activity (e.g., acetyl-CoA C-acyltransferase,
beta-ketothiolase). In certain embodiments, one or more (e.g., 1,
2, 3, 4, 5, 6, 7, 8, 9, 10 or all) of the foregoing activities is
altered by way of a genetic modification. In some embodiments, one
or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or all) of the
foregoing activities is altered by way of (i) adding a heterologous
polynucleotide that encodes a polypeptide having the activity,
and/or (ii) altering or adding a regulatory sequence that regulates
the expression of a polypeptide having the activity.
[0093] The term "6-oxohexanoic acid dehydrogenase activity" as used
herein refers to conversion of 6-oxohexanoic acid to adipic acid.
The 6-oxohexanoic acid dehydrogenase activity can be provided by a
polypeptide. In some embodiments, the polypeptide is encoded by a
heterologous nucleotide sequence introduced to a host
microorganism. In certain embodiments, an endogenous polypeptide
having the 6-oxohexanoic acid dehydrogenase activity is identified
in the host microorganism, and the host microorganism is
genetically altered to increase the amount of the polypeptide
produced (e.g., a heterologous promoter is introduced in operable
linkage with a polynucleotide that encodes the polypeptide; the
copy number of a polynucleotide that encodes the polypeptide is
increased (e.g., by introducing a plasmid that includes the
polynucleotide)). Nucleic acid sequences conferring 6-oxohexanoic
acid dehydrogenase activity can be obtained from a number of
sources, including Actinobacter, Norcardia, Pseudomonas and
Xanthobacter bacteria. Examples of an amino acid sequence of a
polypeptide having 6-oxohexanoic acid dehyrdogenase activity, and a
nucleotide sequence of a polynucleotide that encodes the
polypeptide, are presented herein. Presence, absence or amount of
6-oxohexanoic acid dehydrogenase activity can be detected by any
suitable method known in the art. For an example of a detection
method for alcohol oxidase or alcohol dehydrogenase activity (see
Appl Environ Microbiol 70: 4872). In some embodiments,
6-oxohexanoic acid dehydrogenase activity is not altered in a host
microorganism, and in certain embodiments, the activity is added or
increased in the engineered microorganism relative to the host
microorganism.
[0094] The term "omega oxo fatty acid dehydrogenase activity" as
used herein refers to conversion of an omega oxo fatty acid to a
dicarboxylic acid. The omega oxo fatty acid dehydrogenase activity
can be provided by a polypeptide. In some embodiments, the
polypeptide is encoded by a heterologous nucleotide sequence
introduced to a host microorganism. In certain embodiments, an
endogenous polypeptide having the omega oxo fatty acid
dehydrogenase activity is identified in the host microorganism, and
the host microorganism is genetically altered to increase the
amount of the polypeptide produced (e.g., a heterologous promoter
is introduced in operable linkage with a polynucleotide that
encodes the polypeptide; the copy number of a polynucleotide that
encodes the polypeptide is increased (e.g., by introducing a
plasmid that includes the polynucleotide)). Nucleic acid sequences
conferring omega oxo fatty acid dehydrogenase activity can be
obtained from a number of sources, including Actinobacter,
Norcardia, Pseudomonas and Xanthobacter bacteria. Examples of an
amino acid sequence of a polypeptide having omega oxo fatty acid
dehydrogenase activity and a nucleotide sequence of a
polynucleotide that encodes the polypeptide, are presented herein.
Presence, absence or amount of omega oxo fatty acid dehydrogenase
activity can be detected by any suitable method known in the art.
In some embodiments, omega oxo fatty acid dehydrogenase activity is
not altered in a host microorganism, and in certain embodiments,
the activity is added or increased in the engineered microorganism
relative to the host microorganism.
[0095] The term "6-hydroxyhexanoic acid dehydrogenase activity" as
used herein refers to conversion of 6-hydroxyhexanoic acid to
6-oxohexanoic acid. The 6-hydroxyhexanoic acid dehydrogenase
activity can be provided by a polypeptide. In some embodiments, the
polypeptide is encoded by a heterologous nucleotide sequence
introduced to a host microorganism. In certain embodiments, an
endogenous polypeptide having the 6-hydroxyhexanoic acid
dehydrogenase activity is identified in the host microorganism, and
the host microorganism is genetically altered to increase the
amount of the polypeptide produced (e.g., a heterologous promoter
is introduced in operable linkage with a polynucleotide that
encodes the polypeptide; the copy number of a polynucleotide that
encodes the polypeptide is increased (e.g., by introducing a
plasmid that includes the polynucleotide)). Nucleic acid sequences
conferring 6-hydroxohexanoic acid dehydrogenase activity can be
obtained from a number of sources, including Actinobacter,
Norcardia, Pseudomonas, and Xanthobacter. Examples of an amino acid
sequence of a polypeptide having 6-hydroxyhexanoic acid
dehydrogenase activity, and a nucleotide sequence of a
polynucleotide that encodes the polypeptide, are presented herein.
Presence, absence or amount of 6-hydroxyhexanoic acid dehydrogenase
activity can be detected by any suitable method known in the art.
An example of such a method is described in Methods in Enzymology,
188: 176. In some embodiments, 6-hydroxyhexanoic acid dehydrogenase
activity is not altered in a host microorganism, and in certain
embodiments, the activity is added or increased in the engineered
microorganism relative to the host microorganism.
[0096] The term "omega hydroxyl fatty acid dehydrogenase activity"
as used herein refers to conversion of an omega hydroxyl fatty acid
to an omega oxo fatty acid. The omega hydroxyl fatty acid
dehydrogenase activity can be provided by a polypeptide. In some
embodiments, the polypeptide is encoded by a heterologous
nucleotide sequence introduced to a host microorganism. In certain
embodiments, an endogenous polypeptide having the omega hydroxyl
fatty acid dehydrogenase activity is identified in the host
microorganism, and the host microorganism is genetically altered to
increase the amount of the polypeptide produced (e.g., a
heterologous promoter is introduced in operable linkage with a
polynucleotide that encodes the polypeptide; the copy number of a
polynucleotide that encodes the polypeptide is increased (e.g., by
introducing a plasmid that includes the polynucleotide)). Nucleic
acid sequences conferring omega hydroxyl fatty acid dehydrogenase
activity can be obtained from a number of sources, including
Actinobacter, Norcardia, Pseudomonas and Xanthobacter bacteria.
Examples of an amino acid sequence of a polypeptide having omega
hydroxyl fatty acid dehydrogenase activity and a nucleotide
sequence of a polynucleotide that encodes the polypeptide, are
presented herein. Presence, absence or amount of omega hydroxyl
fatty acid dehydrogenase activity can be detected by any suitable
method known in the art. In some embodiments, omega hydroxyl fatty
acid dehydrogenase activity is not altered in a host microorganism,
and in certain embodiments, the activity is added or increased in
the engineered microorganism relative to the host
microorganism.
[0097] The term "hexanoate synthase activity" as used herein refers
to conversion of acetyl-CoA and malonyl-CoA to hexanoic acid.
Hexanoate synthase activity may be provided by an enzyme that
includes one or two subunits (referred to hereafter as "subunit A"
and/or "subunit B"). The hexanoate synthase activity can be
provided by a polypeptide. In some embodiments, the polypeptide is
encoded by a heterologous nucleotide sequence introduced to a host
microorganism. Nucleic acid sequences conferring hexonate synthase
activity can be obtained from a number of sources, including
Aspergillus parisiticus, for example. Examples of an amino acid
sequence of a polypeptide having hexanoate synthase activity, and a
nucleotide sequence of a polynucleotide that encodes the
polypeptide, are presented herein. In some embodiments, hexanoate
synthase activity is not altered in a host microorganism, and in
certain embodiments, the activity is added or increased in the
engineered microorganism relative to the host microorganism.
[0098] Presence, absence or amount of hexanoate synthase activity
can be detected by any suitable method known in the art. An example
of such a method is described in Hexanoate synthase+thioesterase
(Chemistry and Biology 9: 981-988). Briefly, an indicator strain
may be prepared. An indicator strain may be Bacillus subtilis
containing a reporter gene (beta-galactosidase, green fluorescent
protein, etc.) under control of the promoter regulated by LiaR, for
example. An indicator strain also may be Candida tropicalis
containing either the LiaR regulatable promoter from Bacillus
subtilis or the alkane inducible promoter for the native gene for
the peroxisomal 3-ketoacyl coenzyme A thiolase gene (CT-T3A), for
example. Mutants with an improved functionality of HexS, thereby
producing more hexanoic acid, can be plated onto a lawn of
indicator strain. Upon incubation and growth of both the test
mutant and the indicator strain, the appearance of a larger halo,
which correlates to the induction of the reporter strain compared
to control strains, indicates a mutant with improved activity. In
alternative approach, mutants are grown in conditions favoring
production of hexanoyl CoA or hexanoic acid and lysed. Cell lysates
are treated with proteases which may release hexanoic acid from the
PKS. Clarified lysates may be spotted onto lawns of indicator
strains to assess improved production. In another alternative
approach, indicator strains are grown under conditions suitable to
support expression of the reporter gene when induced by hexanoic
acid. Dilutions of a known concentration of hexanoic acid are used
to determine a standard curve. Lysates of the test strain grown
under conditions favoring production of hexanoic acid are prepared
and dilutions of the lysate added to the indicator strain.
Indicator strains with lysates are placed under identical
conditions as used to determine the standard curve. The lysate
dilutions that minimally support induction can be used to
determine, quantitatively, the amount produced when compared to the
standard curve.
[0099] The term "monooxygenase activity" as used herein refers to
inserting one atom of oxygen from O.sub.2 into an organic substrate
(RH) and reducing the other oxygen atom to water. In some
embodiments, monooxygenase activity refers to incorporation of an
oxygen atom onto a six-carbon organic substrate. In certain
embodiments, monooxygenase activity refers to conversion of
hexanoate to 6-hydroxyhexanoic acid. Monooxygenase activity can be
provided by any suitable polypeptide, such as a cytochrome P450
polypeptide (hereafter "CYP450") in certain embodiments. Nucleic
acid sequences conferring CYP450 activity can be obtained from a
number of sources, including Bacillus megaterium and may be induced
in organisms including but not limited to Candida tropicalis,
Yarrowia lipolytica, Aspergillus nidulans, and Aspergillus
parasiticus. Examples of oligonucleotide sequences utilized to
isolate a polynucleotide sequence encoding a polypeptide having
CYP450 activity (e.g., CYP52A15 activity, CYP52A16 activity, or
CYP52A15 activity and CYP52A16 activity) are presented herein. In
some embodiments, monooxygenase activity is not altered in a host
microorganism, and in certain embodiments, the activity is added or
increased in the engineered microorganism relative to the host
microorganism.
[0100] Presence, absence or amount of cytochrome P450 activity can
be detected by any suitable method known in the art. For example,
detection can be performed by assaying a reaction containing
cytochrome P450 (CYP52A family) and NADPH--cytochrome P450
reductase (see Appl Environ Microbiol 69: 5983 and 5992). Briefly,
cells are grown under standard conditions and harvested for
production of microsomes, which are used to detect CYP activity.
Microsomes are prepared by lysing cells in Tris-buffered sucrose
(10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.25M sucrose). Differential
centrifugation is performed first at 25,000.times.g then at
100,000.times.g to pellet cell debris then microsomes,
respectively. The microsome pellet is resuspended in 0.1 M
phosphate buffer (pH 7.5), 1 mM EDTA to a final concentration of
approximately 10 mg protein/mL. A reaction mixture containing
approximately 0.3 mg microsomes, 0.1 mM sodium hexanoate, 0.7 mM
NADPH, 50 mM Tris-HCl pH 7.5 in 1 mL is initiated by the addition
of NADPH and incubated at 37.degree. C. for 10 minutes. The
reaction is terminated by addition of 0.25 mL 5M HCl and 0.25 mL
2.5 ug/mL 10-hydroxydecanoic acid is added as an internal standard
(3.3 nmol). The mixture is extracted with 4.5 mL diethyl ether
under NaCl-saturated conditions. The organic phase is transferred
to a new tube and evaporated to dryness. The residue is dissolved
in acetonitrile containing 10 mM
3-bromomethyl-7-methoxy-1,4-benzoxazin-2-one (BrMB) and 0.1 mL of
15 mg/mL 18-crown-6 in acetonitril saturated with K.sub.2CO.sub.3.
The solution is incubated at 40.degree. C. for 30 minutes before
addition of 0.05 mL 2% acetic acid. The fluorescently labeled
omega-hydroxy fatty acids are resolved via HPLC with detection at
430 nm and excitation at 355 nm (Yamada et al., 1991, AnalBiochem
199: 132-136). Optionally, specifically induced CYP gene(s) may be
detected by Northern blotting and/or quantitative RT-PCR. (Craft et
al., 2003, AppEnvironMicro 69: 5983-5991).
[0101] The term "monooxygenase reductase activity" as used herein
refers to the transfer of an electron from NAD(P)H, FMN, or FAD by
way of an electron transfer chain, reducing the ferric heme iron of
cytochrome P450 to the ferrous state. The term "monooxygenase
reductase activity" as used herein also can refer to the transfer
of a second electron via the electron transport system, reducing a
dioxygen adduct to a negatively charged peroxo group. In some
embodiments, a monooxygenase activity can donate electrons from the
two-electron donor NAD(P)H to the heme of cytochrome P450 (e.g.,
monooxygenase activity) in a coupled two-step reaction in which
NAD(P)H can bind to the NAD(P)H-binding domain of the polypeptide
having the monooxygenase reductase activity and electrons are
shuttled from NAD(P)H through FAD and FMN to the heme of the
monooxygenase activity, thereby regenerating an active
monooxygenase activity (e.g., cytochrome P450). Monooxygenase
reductase activity can be provided by any suitable polypeptide,
such as a cytochrome P450 reductase polypeptide (hereafter "CPR")
in certain embodiments. Nucleic acid sequences conferring CPR
activity can be obtained from and/or induced in a number of
sources, including but not limited to Bacillus megaterium, Candida
tropicalis, Yarrowia lipolytica, Aspergillus nidulans, and
Aspergillus parasiticus. Examples of oligonucleotide sequences
utilized to isolate a polynucleotide sequence encoding a
polypeptide having CPR activity are presented herein. In some
embodiments, monooxygenase reductase activity is not altered in a
host microorganism, and in certain embodiments, the activity is
added or increased in the engineered microorganism relative to the
host microorganism.
[0102] Presence, absence or amount of CPR activity can be detected
by any suitable method known in the art. For example, an engineered
microorganism having an increased number of genes encoding a CPR
activity, relative to the host microorganism, could be detected
using quantitative nucleic acid detection methods (e.g., southern
blotting, PCR, primer extension, the like and combinations
thereof). An engineered microorganism having increased expression
of genes encoding a CPR activity, relative to the host
microorganism, could be detected using quantitative expression
based analysis (e.g., RT-PCR, western blot analysis, northern blot
analysis, the like and combinations thereof). Alternately, an
enzymatic assay can be used to detect Cytochrome P450 reductase
activity, where the enzyme activity alters the optical absorbance
at 550 nanometers of a substrate solution (Masters, B. S. S.,
Williams, C. H., Kamin, H. (1967) Methods in Enzymology, X,
565-573).
[0103] The term "fatty alcohol oxidase activity" as used herein
refers to inserting one atom of oxygen from O.sub.2 into an organic
substrate and reducing the other oxygen atom to peroxide. Fatty
alcohol oxidase activity sometimes also is referred to as
"long-chain-alcohol oxidase activity", "long-chain-alcohol:oxygen
oxidoreductase activity", "fatty alcohol:oxygen oxidoreductase
activity" and "long-chain fatty acid oxidase activity". In some
embodiments, fatty alcohol oxidase activity refers to incorporation
of an oxygen atom onto a six-carbon organic substrate. In certain
embodiments, fatty alcohol oxidase activity refers to the
conversion of 6-hydroxyhexanoic acid into 6-oxohexanoic acid. In
some embodiments, fatty alcohol oxidase activity refers to the
conversion of an omega hydroxyl fatty acid into an omega oxo fatty
acid. A Fatty alcohol oxidase (FAO) activity can be provided by any
suitable polypeptide, such as a fatty alcohol oxidase peptide, a
long-chain-alcohol oxidase peptide, a long-chain-alcohol:oxygen
oxidoreductase peptide, a fatty alcohol:oxygen oxidoreductase
peptide and a long-chain fatty acid oxidase peptide. Nucleic acid
sequences conferring FAO activity can be obtained from a number of
sources, including but not limited to Candida tropicalis, Candida
cloacae, Yarrowia lipolytica, and Arabidopsis thaliana. Examples of
amino acid sequences of polypeptides having FAO activity, and
nucleotide sequences of polynucleotides that encode the
polypeptides, are presented herein. In some embodiments, fatty
alcohol oxidase activity is not altered in a host microorganism,
and in certain embodiments, the activity is added or increased in
the engineered microorganism relative to the host
microorganism.
[0104] Presence, absence or amount of FAO activity can be detected
by any suitable method known in the art. For example, an engineered
microorganism having an increased number of genes encoding an FAO
activity, relative to the host microorganism, could be detected
using quantitative nucleic acid detection methods (e.g., southern
blotting, PCR, primer extension, the like and combinations
thereof). An engineered microorganism having increased expression
of genes encoding an FAO activity, relative to the host
microorganism, could be detected using quantitative expression
based analysis (e.g., RT-PCR, western blot analysis, northern blot
analysis, the like and combinations thereof). Alternately, an
enzymatic assay can be used to detect fatty alcohol oxidase
activity as described in Eirich et al, 2004, or as modified in the
Examples herein.
[0105] The term "acyl-CoA oxidase activity" as used herein refers
to the oxidation of a long chain fatty-acyl-CoA to a
trans-2,3-dehydroacyl-CoA fatty alcohol. In some embodiments, the
acyl-CoA activity is from a peroxisome. In certain embodiments, the
acyl-CoA oxidase activity is a peroxisomal acyl-CoA oxidase (POX)
activity, carried out by a POX polypeptide. In some embodiments the
acyl-CoA oxidase activity is encoded by the host organism and
sometimes can be altered to generate an engineered organism.
Acyl-CoA oxidase activity is encoded by the POX4 and POX5 genes of
C. tropicalis. In certain embodiments, endogenous acyl-CoA oxidase
activity can be increased. In some embodiments, acyl-CoA oxidase
activity of the POX4 polypeptide or the POX5 polypeptide can be
altered independently of each other (e.g., increase activity of
POX4 alone, POX5 alone, increase one and disrupt the other, and the
like). Increasing the activity of one POX activity, while
disrupting the activity of another POX activity, may alter the
specific activity of acyl-CoA oxidase with respect to carbon chain
length, while maintaining or increasing overall flux through the
beta oxidation pathway, in certain embodiments.
[0106] FIGS. 15A-15C graphically illustrate the units of acyl-CoA
oxidase activity expressed as units (U) per milligram of protein (Y
axis) in various strains of Candida tropicalis induced by
feedstocks of specific chain length (Picataggio et al. 1991
Molecular and Cellular Biology 11: 4333-4339). Isolated protein was
assayed for acyl-CoA oxidase activity using carbon chains of
various length (X axis). The X and Y axes in FIGS. 15A-15C
represent substantially similar data. FIG. 15A illustrates acyl-CoA
oxidase activity as measured in a strain having a full complement
of POX genes (e.g., POX4 and POXS are active). FIG. 15B illustrates
acyl-CoA oxidase activity as measured in a strain having a
disrupted POXS gene. The activity encoded by the functional POX4
gene exhibits a higher specific activity for acyl-CoA molecules
with shorter carbon chain lengths (e.g., less than 10 carbons). The
results of the POXS disrupted strain also are presented numerically
in the table in FIG. 15B. FIG. 15C illustrates acyl-CoA oxidase
activity as measured in a strain having a disrupted POX4 gene. The
activity encoded by the functional POXS gene exhibits a narrow peak
of high specific activity for acyl-CoA molecules 12 carbons in
length, with a lower specific activity for molecules 10 carbons in
length. The results of the POX4 disrupted strain are presented
numerically in the table in FIG. 15C.
[0107] In certain embodiments, host acyl-CoA oxidase activity of
one of the POX genes can be increased by genetically altering
(e.g., increasing) the amount of the polypeptide produced (e.g., a
strongly transcribed or constitutively expressed heterologous
promoter is introduced in operable linkage with a polynucleotide
that encodes the polypeptide; the copy number of a polynucleotide
that encodes the polypeptide is increased (e.g., by introducing a
plasmid that includes the polynucleotide, integration of additional
copies in the host genome)). In some embodiments, the host acyl-CoA
oxidase activity can be decreased by disruption (e.g., knockout,
insertion mutagenesis, the like and combinations thereof) of an
acyl-CoA oxidase gene, or by decreasing the activity of the
promoter (e.g., addition of repressor sequences to the promoter or
5'UTR) which transcribes an acyl-CoA oxidase gene.
[0108] A noted above, disruption of nucleotide sequences encoding
POX4, POX 5, or POX4 and POX5 sometimes can alter pathway
efficiency, specificity and/or specific activity with respect to
metabolism of carbon chains of different lengths (e.g., carbon
chains including fatty alcohols, fatty acids, paraffins,
dicarboxylic acids of between about 1 and about 60 carbons in
length). In some embodiments, the nucleotide sequence of POX4,
POX5, or POX4 and POX5 is disrupted with a URA3 nucleotide sequence
encoding a selectable marker, and introduced to a host
microorganism, thereby generating an engineered organism deficient
in POX4, POX5 or POX4 and
[0109] POX5 activity. Nucleic acid sequences encoding POX4 and POX5
can be obtained from a number of sources, including Candida
tropicalis, for example. Examples of POX4 and POX5 amino acid
sequences and nucleotide sequences of polynucleotides that encode
the polypeptides, are presented herein.
[0110] Presence, absence or amount of POX4 and/or POX5 activity can
be detected by any suitable method known in the art. For example,
using enzymatic assays as described in Shimizu et al, 1979, and as
described herein in the Examples. Alternatively, nucleic acid
sequences representing native and/or disrupted POX4 and POX5
sequences also can be detected using nucleic acid detection methods
(e.g., PCR, primer extension, nucleic acid hybridization, the like
and combinations thereof), or quantitative expression based
analysis (e.g., RT-PCR, western blot analysis, northern blot
analysis, the like and combinations thereof), where the engineered
organism exhibits decreased RNA and/or polypeptide levels as
compared to the host organism.
[0111] The term "thioesterase activity" as used herein refers to
removal of Coenzyme A from hexanoate.
[0112] The thioesterase activity can be provided by a polypeptide.
In some embodiments, the polypeptide is encoded by a heterologous
nucleotide sequence introduced to a host microorganism. Nucleic
acid sequences conferring thioesterase activity can be obtained
from a number of sources, including Cuphea lanceolata. Examples of
such polypeptides include, without limitation, acyl-(ACP)
thioesterase type B from Cuphea lanceolata, encoded by the
nucleotide sequences referenced by accession number CAB60830 at the
World Wide Web Uniform Resource Locator (URL) ncbi.nlm.nih.gov of
the National Center for Biotechnology Information (NCBI).
[0113] Presence, absence or amount of thioesterase activity can be
detected by any suitable method known in the art. An example of
such a method is described Chemistry and Biology 9: 981-988. In
some embodiments, thioesterase activity is not altered in a host
microorganism, and in certain embodiments, the activity is added or
increased in the engineered microorganism relative to the host
microorganism. In some embodiments, a polypeptide having
thioesterase activity is linked to another polypeptide (e.g., a
hexanoate synthase A or hexanoate synthase B polypeptide). A
non-limiting example of an amino acid sequence (one letter code
sequence) for a polypeptide having thioesterase activity is
provided hereafter:
TABLE-US-00001 (SEQ ID NO: 14)
MVAAAATSAFFPVPAPGTSPKPGKSGNWPSSLSPTFKPKSIPNAGFQVKA
NASAHPKANGSAVNLKSGSLNTQEDTSSSPPPRAFLNQLPDWSMLLTAIT
TVFVAAEKQWTMLDRKSKRPDMLVDSVGLKSIVRDGLVSRQSFLIRSYEI
GADRTASIETLMNHLQETSINHCKSLGLLNDGFGRTPGMCKNDLIWVLTK
MQIMVNRYPTWGDTVEINTWFSQSGKIGMASDWLISDCNTGEILIRATSV
WAMMNQKTRRFSRLPYEVRQELTPHFVDSPHVIEDNDQKLHKFDVKTGDS
IRKGLTPRWNDLDVNQHVSNVKYIGWILESMPIEVLETQELCSLTVEYRR
ECGMDSVLESVTAVDPSENGGRSQYKHLLRLEDGTDIVKSRTEWRPKNAG
TNGAISTSTAKTSNGNSAS
[0114] The term "a genetic modification that results in substantial
hexanoate usage by monooxygenase activity" as used herein refers to
a genetic alteration of a host microorganism that reduces an
endogenous activity that converts hexanoate to another product. In
some embodiments, an endogenous activity that converts hexanoate to
a toxin (e.g., in fungus) is reduced. In certain embodiments, a
polyketide synthase activity is reduced. Such alterations can
advantageously increase yields of end products, such as adipic
acid.
[0115] The term "polyketide synthase activity" as used herein
refers to the alteration of hexanoic acid by the polyketide
synthase enzyme (PKS) as a step in the production of other products
including mycotoxin. The PKS activity can be provided by a
polypeptide. Examples of such polypeptides include, without
limitation, an Aspergillus parasiticus enzyme referenced by
accession number AAS66004 at the World Wide Web Uniform Resource
Locator (URL) ncbi.nlm.nih.gov of the National Center for
Biotechnology Information (NCBI). In certain embodiments, a PKS
enzyme uses hexanoic acid generated by hexanoate synthase as a
substrate and a component of the Aspergillus N or S multienzyme
complex, a closely associated gene cluster involved in the
synthesis of various products including mytoxin. Accordingly, a PKS
activity sometimes is altered to free hexanoic acid for an
engineered adipic acid pathway. In some embodiments PKS activity is
diminished or blocked. In certain embodiments the PKS enzyme is
engineered to substitute thioesterase activity for PKS activity.
Presence, absence, or amount of PKS activity can be detected by any
suitable method known in the art, such as that described in
Watanabe C and Townsend C (2002) Initial characterization of a type
I fatty acid synthase and polyketide synthase multienzyme complex N
or S in the biosynthesis of aflatoxin B1. Chemistry and Biology 9:
981-988. A non-limiting example of an amino acid sequence (one
letter code sequence) of a polypeptide having polyketide synthase
activity is provided hereafter:
TABLE-US-00002 (SEQ ID NO: 15)
MAQSRQLFLFGDQTADFVPKLRSLLSVQDSPILAAFLDQSHYVVRAQMLQ
SMNTVDHKLARTADLRQMVQKYVDGKLTPAFRTALVCLCQLGCFIREYEE
SGNMYPQPSDSYVLGFCMGSLAAVAVSCSRSLSELLPIAVQTVLIAFRLG
LCALEMRDRVDGCSDDRGDPWSTIVWGLDPQQARDQIEVFCRTTNVPQTR
RPWISCISKNAITLSGSPSTLRAFCAMPQMAQHRTAPIPICLPAHNGALF
TQADITTILDTTPTTPWEQLPGQIPYISHVTGNVVQTSNYRDLIEVALSE
TLLEQVRLDLVETGLPRLLQSRQVKSVTIVPFLTRMNETMSNILPDSFIS
TETRTDTGRAIPASGRPGAGKCKLAIVSMSGRFPESPTTESFWDLLYKGL
DVCKEVPRRRWDINTHVDPSGKARNKGATKWGCWLDFSGDFDPRFFGISP
KEAPQMDPAQRMALMSTYEAMERAGLVPDTTPSTQRDRIGVFHGVTSNDW
METNTAQNIDTYFITGGNRGFIPGRINFCFEFAGPSYTNDTACSSSLAAI
HLACNSLWRGDCDTAVAGGTNMIYTPDGHTGLDKGFFLSRTGNCKPYDDK
ADGYCRAEGVGTVFIKRLEDALADNDPILGVILDAKTNHSAMSESMTRPH
VGAQIDNMTAALNTTGLHPNDFSYIEMHGTGTQVGDAVEMESVLSVFAPS
ETARKADQPLFVGSAKANVGHGEGVSGVTSLIKVLMMMQHDTIPPHCGIK
PGSKINRNFPDLGARNVHIAFEPKPWPRTHTPRRVLINNFSAAGGNTALI
VEDAPERHWPTEKDPRSSHIVALSAHVGASMKTNLERLHQYLLKNPHTDL
AQLSYTTTARRWHYLHRVSVTGASVEEVTRKLEMAIQNGDGVSRPKSKPK
ILFAFTGQGSQYATMGKQVYDAYPSFREDLEKFDRLAQSHGFPSFLHVCT
SPKGDVEEMAPVVVQLAITCLQMALTNLMTSFGIRPDVTVGHSLGEFAAL
YAAGVLSASDVVYLVGQRAELLQERCQRGTHAMLAVKATPEALSQWIQDH
DCEVACINGPEDTVLSGTTKNVAEVQRAMTDNGIKCTLLKLPFAFHSAQV
QPILDDFEALAQGATFAKPQLLILSPLLRTEIHEQGVVTPSYVAQHCRHT
VDMAQALRSAREKGLIDDKTLVIELGPKPLISGMVKMTLGDKISTLPTLA
PNKAIWPSLQKILTSVYTGGWDINWKKYHAPFASSQKVVDLPSYGWDLKD
YYIPYQGDWCLHRHQQDCKCAAPGHEIKTADYQVPPESTPHRPSKLDPSK
EAFPEIKTTTTLHRVVEETTKPLGATLVVETDISRKDVNGLARGHLVDGI
PLCTPSFYADIAMQVGQYSMQRLRAGHPGAGAIDGLVDVSDMVVDKALVP
HGKGPQLLRTTLTMEWPPKAAATTRSAKVKFATYFADGKLDTEHASCTVR
FTSDAQLKSLRRSVSEYKTHIRQLHDGHAKGQFMRYNRKTGYKLMSSMAR
FNPDYMLLDYLVLNEAENEAASGVDFSLGSSEGTFAAHPAHVDAITQVAG
FAMNANDNVDIEKQVYVNHGWDSFQIYQPLDNSKSYQVYTKMGQAKENDL
VHGDVVVLDGEQIVAFFRGLTLRSVPRGALRVVLQTTVKKADRQLGFKTM
PSPPPPTTTMPISPYKPANTQVSSQAIPAEATHSHTPPQPKHSPVPETAG
SAPAAKGVGVSNEKLDAVMRVVSEESGIALEELTDDSNFADMGIDSLSSM
VIGSRFREDLGLDLGPEFSLFIDCTTVRALKDFMLGSGDAGSGSNVEDPP
PSATPGINPETDWSSSASDSIFASEDHGHSSESGADTGSPPALDLKPYCR
PSTSVVLQGLPMVARKTLFMLPDGGGSAFSYASLPRLKSDTAVVGLNCPY
ARDPENMNCTHGAMIESFCNEIRRRQPRGPYHLGGWSSGGAFAYVVAEAL
VNQGEEVHSLIIIDAPIPQAMEQLPRAFYEHCNSIGLFATQPGASPDGST
EPPSYLIPHFTAVVDVMLDYKLAPLHARRMPKVGIVWAADTVMDERDAPK
MKGMHFMIQKRTEFGPDGWDTIMPGASFDIVRADGANHFTLMQKEHVSII SDLIDRVMA
[0116] The terms "a genetic modification that reduces
6-hydroxyhexanoic acid conversion" or "a genetic modification that
reduces omega hydroxyl fatty acid conversion" as used herein refer
to genetic alterations of a host microorganism that reduce an
endogenous activity that converts 6-hydroxyhexanoic acid to another
product. In some embodiments, an endogenous 6-hydroxyhexanoic acid
dehydrogenase activity is reduced. Such alterations can
advantageously increase the amount of 6-hydroxyhexanoic acid, which
can be purified and further processed.
[0117] The term "a genetic modification that reduces beta-oxidation
activity" as used herein refers to a genetic alteration of a host
microorganism that reduces an endogenous activity that oxidizes a
beta carbon of carboxylic acid containing organic molecules. In
certain embodiments, the organic molecule is a six carbon molecule,
and sometimes contains one or two carboxylic acid moieties located
at a terminus of the molecule (e.g., adipic acid). Such alterations
can advantageously increase yields of end products, such as adipic
acid.
Polynucleotides and Polypeptides
[0118] A nucleic acid (e.g., also referred to herein as nucleic
acid reagent, target nucleic acid, target nucleotide sequence,
nucleic acid sequence of interest or nucleic acid region of
interest) can be from any source or composition, such as DNA, cDNA,
gDNA (genomic DNA), RNA, siRNA (short inhibitory RNA), RNAi, tRNA
or mRNA, for example, and can be in any form (e.g., linear,
circular, supercoiled, single-stranded, double-stranded, and the
like). A nucleic acid can also comprise DNA or RNA analogs (e.g.,
containing base analogs, sugar analogs and/or a non-native backbone
and the like). It is understood that the term "nucleic acid" does
not refer to or infer a specific length of the polynucleotide
chain, thus polynucleotides and oligonucleotides are also included
in the definition. Deoxyribonucleotides include deoxyadenosine,
deoxycytidine, deoxyguanosine and deoxythymidine. For RNA, the
uracil base is uridine.
[0119] A nucleic acid sometimes is a plasmid, phage, autonomously
replicating sequence (ARS), centromere, artificial chromosome,
yeast artificial chromosome (e.g., YAC) or other nucleic acid able
to replicate or be replicated in a host cell. In certain
embodiments a nucleic acid can be from a library or can be obtained
from enzymatically digested, sheared or sonicated genomic DNA
(e.g., fragmented) from an organism of interest. In some
embodiments, nucleic acid subjected to fragmentation or cleavage
may have a nominal, average or mean length of about 5 to about
10,000 base pairs, about 100 to about 1,000 base pairs, about 100
to about 500 base pairs, or about 10, 15, 20, 25, 30, 35, 40, 45,
50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500,
600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000,
9000 or 10000 base pairs. Fragments can be generated by any
suitable method in the art, and the average, mean or nominal length
of nucleic acid fragments can be controlled by selecting an
appropriate fragment-generating procedure by the person of ordinary
skill. In some embodiments, the fragmented DNA can be size selected
to obtain nucleic acid fragments of a particular size range.
[0120] Nucleic acid can be fragmented by various methods known to
the person of ordinary skill, which include without limitation,
physical, chemical and enzymic processes. Examples of such
processes are described in U.S. Patent Application Publication No.
20050112590 (published on May 26, 2005, entitled
"Fragmentation-based methods and systems for sequence variation
detection and discovery," naming Van Den Boom et al.). Certain
processes can be selected by the person of ordinary skill to
generate non-specifically cleaved fragments or specifically cleaved
fragments. Examples of processes that can generate non-specifically
cleaved fragment sample nucleic acid include, without limitation,
contacting sample nucleic acid with apparatus that expose nucleic
acid to shearing force (e.g., passing nucleic acid through a
syringe needle; use of a French press); exposing sample nucleic
acid to irradiation (e.g., gamma, x-ray, UV irradiation; fragment
sizes can be controlled by irradiation intensity); boiling nucleic
acid in water (e.g., yields about 500 base pair fragments) and
exposing nucleic acid to an acid and base hydrolysis process.
[0121] Nucleic acid may be specifically cleaved by contacting the
nucleic acid with one or more specific cleavage agents. The term
"specific cleavage agent" as used herein refers to an agent,
sometimes a chemical or an enzyme that can cleave a nucleic acid at
one or more specific sites. Specific cleavage agents often will
cleave specifically according to a particular nucleotide sequence
at a particular site. Examples of enzymic specific cleavage agents
include without limitation endonucleases (e.g., DNase (e.g., DNase
I, II); RNase (e.g., RNase E, F, H, P); Cleavase.TM. enzyme; Taq
DNA polymerase; E. coli DNA polymerase I and eukaryotic
structure-specific endonucleases; murine FEN-1 endonucleases; type
I, II or III restriction endonucleases such as Acc I, Afl III, Alu
I, Alw44 I, Apa I, Asn I, Ava I, Ava II, BamH I, Ban II, Bcl I, Bgl
I. Bgl II, Bln I, Bsm I, BssH II, BstE II, Cfo I, Cla I, Dde I, Dpn
I, Dra I, EcIX I, EcoR I, EcoR I, EcoR II, EcoR V, Hae II, Hae II,
Hind III, Hind III, Hpa I, Hpa II, Kpn I, Ksp I, Mlu I, MIuN I, Msp
I, Nci I, Nco I, Nde I, Nde II, Nhe I, Not I, Nru I, Nsi I, Pst I,
Pvu I, Pvu II, Rsa I, Sac I, Sal I, Sau3A I, Sca I, ScrF I, Sfi I,
Sma I, Spe I, Sph I, Ssp I, Stu I, Sty I, Swa I, Taq I, Xba I, Xho
I); glycosylases (e.g., uracil-DNA glycolsylase (UDG),
3-methyladenine DNA glycosylase, 3-methyladenine DNA glycosylase
II, pyrimidine hydrate-DNA glycosylase, FaPy-DNA glycosylase,
thymine mismatch-DNA glycosylase, hypoxanthine-DNA glycosylase,
5-Hydroxymethyluracil DNA glycosylase (HmUDG),
5-Hydroxymethylcytosine DNA glycosylase, or 1,N6-etheno-adenine DNA
glycosylase); exonucleases (e.g., exonuclease III); ribozymes, and
DNAzymes. Sample nucleic acid may be treated with a chemical agent,
or synthesized using modified nucleotides, and the modified nucleic
acid may be cleaved. In non-limiting examples, sample nucleic acid
may be treated with (i) alkylating agents such as methylnitrosourea
that generate several alkylated bases, including N3-methyladenine
and N3-methylguanine, which are recognized and cleaved by alkyl
purine DNA-glycosylase; (ii) sodium bisulfite, which causes
deamination of cytosine residues in DNA to form uracil residues
that can be cleaved by uracil N-glycosylase; and (iii) a chemical
agent that converts guanine to its oxidized form, 8-hydroxyguanine,
which can be cleaved by formamidopyrimidine DNA N-glycosylase.
Examples of chemical cleavage processes include without limitation
alkylation, (e.g., alkylation of phosphorothioate-modified nucleic
acid); cleavage of acid lability of
P3'-N5'-phosphoroamidate-containing nucleic acid; and osmium
tetroxide and piperidine treatment of nucleic acid.
[0122] As used herein, the term "complementary cleavage reactions"
refers to cleavage reactions that are carried out on the same
nucleic acid using different cleavage reagents or by altering the
cleavage specificity of the same cleavage reagent such that
alternate cleavage patterns of the same target or reference nucleic
acid or protein are generated. In certain embodiments, nucleic
acids of interest may be treated with one or more specific cleavage
agents (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more specific
cleavage agents) in one or more reaction vessels (e.g., nucleic
acid of interest is treated with each specific cleavage agent in a
separate vessel).
[0123] A nucleic acid suitable for use in the embodiments described
herein sometimes is amplified by any amplification process known in
the art (e.g., PCR, RT-PCR and the like). Nucleic acid
amplification may be particularly beneficial when using organisms
that are typically difficult to culture (e.g., slow growing,
require specialize culture conditions and the like). The terms
"amplify", "amplification", "amplification reaction", or
"amplifying" as used herein refer to any in vitro processes for
multiplying the copies of a target sequence of nucleic acid.
Amplification sometimes refers to an "exponential" increase in
target nucleic acid. However, "amplifying" as used herein can also
refer to linear increases in the numbers of a select target
sequence of nucleic acid, but is different than a one-time, single
primer extension step. In some embodiments, a limited amplification
reaction, also known as pre-amplification, can be performed.
Pre-amplification is a method in which a limited amount of
amplification occurs due to a small number of cycles, for example
10 cycles, being performed. Pre-amplification can allow some
amplification, but stops amplification prior to the exponential
phase, and typically produces about 500 copies of the desired
nucleotide sequence(s). Use of pre-amplification may also limit
inaccuracies associated with depleted reactants in standard PCR
reactions.
[0124] In some embodiments, a nucleic acid reagent sometimes is
stably integrated into the chromosome of the host organism, or a
nucleic acid reagent can be a deletion of a portion of the host
chromosome, in certain embodiments (e.g., genetically modified
organisms, where alteration of the host genome confers the ability
to selectively or preferentially maintain the desired organism
carrying the genetic modification). Such nucleic acid reagents
(e.g., nucleic acids or genetically modified organisms whose
altered genome confers a selectable trait to the organism) can be
selected for their ability to guide production of a desired protein
or nucleic acid molecule. When desired, the nucleic acid reagent
can be altered such that codons encode for (i) the same amino acid,
using a different tRNA than that specified in the native sequence,
or (ii) a different amino acid than is normal, including
unconventional or unnatural amino acids (including detectably
labeled amino acids). As described herein, the term "native
sequence" refers to an unmodified nucleotide sequence as found in
its natural setting (e.g., a nucleotide sequence as found in an
organism).
[0125] A nucleic acid or nucleic acid reagent can comprise certain
elements often selected according to the intended use of the
nucleic acid. Any of the following elements can be included in or
excluded from a nucleic acid reagent. A nucleic acid reagent, for
example, may include one or more or all of the following nucleotide
elements: one or more promoter elements, one or more 5'
untranslated regions (5'UTRs), one or more regions into which a
target nucleotide sequence may be inserted (an "insertion
element"), one or more target nucleotide sequences, one or more 3'
untranslated regions (3'UTRs), and one or more selection elements.
A nucleic acid reagent can be provided with one or more of such
elements and other elements may be inserted into the nucleic acid
before the nucleic acid is introduced into the desired organism. In
some embodiments, a provided nucleic acid reagent comprises a
promoter, 5'UTR, optional 3'UTR and insertion element(s) by which a
target nucleotide sequence is inserted (i.e., cloned) into the
nucleotide acid reagent. In certain embodiments, a provided nucleic
acid reagent comprises a promoter, insertion element(s) and
optional 3'UTR, and a 5' UTR/target nucleotide sequence is inserted
with an optional 3'UTR. The elements can be arranged in any order
suitable for expression in the chosen expression system (e.g.,
expression in a chosen organism, or expression in a cell free
system, for example), and in some embodiments a nucleic acid
reagent comprises the following elements in the 5' to 3' direction:
(1) promoter element, 5'UTR, and insertion element(s); (2) promoter
element, 5'UTR, and target nucleotide sequence; (3) promoter
element, 5'UTR, insertion element(s) and 3'UTR; and (4) promoter
element, 5'UTR, target nucleotide sequence and 3'UTR.
[0126] A promoter element typically is required for DNA synthesis
and/or RNA synthesis. A promoter element often comprises a region
of DNA that can facilitate the transcription of a particular gene,
by providing a start site for the synthesis of RNA corresponding to
a gene. Promoters generally are located near the genes they
regulate, are located upstream of the gene (e.g., 5' of the gene),
and are on the same strand of DNA as the sense strand of the gene,
in some embodiments. In some embodiments, a promoter element can be
isolated from a gene or organism and inserted in functional
connection with a polynucleotide sequence to allow altered and/or
regulated expression. A non-native promoter (e.g., promoter not
normally associated with a given nucleic acid sequence) used for
expression of a nucleic acid often is referred to as a heterologous
promoter. In certain embodiments, a heterologous promoter and/or a
5'UTR can be inserted in functional connection with a
polynucleotide that encodes a polypeptide having a desired activity
as described herein. The terms "operably linked" and "in functional
connection with" as used herein with respect to promoters, refer to
a relationship between a coding sequence and a promoter element.
The promoter is operably linked or in functional connection with
the coding sequence when expression from the coding sequence via
transcription is regulated, or controlled by, the promoter element.
The terms "operably linked" and "in functional connection with" are
utilized interchangeably herein with respect to promoter
elements.
[0127] A promoter often interacts with a RNA polymerase. A
polymerase is an enzyme that catalyses synthesis of nucleic acids
using a preexisting nucleic acid reagent. When the template is a
DNA template, an RNA molecule is transcribed before protein is
synthesized. Enzymes having polymerase activity suitable for use in
the present methods include any polymerase that is active in the
chosen system with the chosen template to synthesize protein. In
some embodiments, a promoter (e.g., a heterologous promoter) also
referred to herein as a promoter element, can be operably linked to
a nucleotide sequence or an open reading frame (ORF). Transcription
from the promoter element can catalyze the synthesis of an RNA
corresponding to the nucleotide sequence or ORF sequence operably
linked to the promoter, which in turn leads to synthesis of a
desired peptide, polypeptide or protein.
[0128] Promoter elements sometimes exhibit responsiveness to
regulatory control. Promoter elements also sometimes can be
regulated by a selective agent. That is, transcription from
promoter elements sometimes can be turned on, turned off,
up-regulated or down-regulated, in response to a change in
environmental, nutritional or internal conditions or signals (e.g.,
heat inducible promoters, light regulated promoters, feedback
regulated promoters, hormone influenced promoters, tissue specific
promoters, oxygen and pH influenced promoters, promoters that are
responsive to selective agents (e.g., kanamycin) and the like, for
example). Promoters influenced by environmental, nutritional or
internal signals frequently are influenced by a signal (direct or
indirect) that binds at or near the promoter and increases or
decreases expression of the target sequence under certain
conditions.
[0129] Non-limiting examples of selective or regulatory agents that
can influence transcription from a promoter element used in
embodiments described herein include, without limitation, (1)
nucleic acid segments that encode products that provide resistance
against otherwise toxic compounds (e.g., antibiotics); (2) nucleic
acid segments that encode products that are otherwise lacking in
the recipient cell (e.g., essential products, tRNA genes,
auxotrophic markers); (3) nucleic acid segments that encode
products that suppress the activity of a gene product; (4) nucleic
acid segments that encode products that can be readily identified
(e.g., phenotypic markers such as antibiotics (e.g.,
.beta.-lactamase), .beta.-galactosidase, green fluorescent protein
(GFP), yellow fluorescent protein (YFP), red fluorescent protein
(RFP), cyan fluorescent protein (CFP), and cell surface proteins);
(5) nucleic acid segments that bind products that are otherwise
detrimental to cell survival and/or function; (6) nucleic acid
segments that otherwise inhibit the activity of any of the nucleic
acid segments described in Nos. 1-5 above (e.g., antisense
oligonucleotides); (7) nucleic acid segments that bind products
that modify a substrate (e.g., restriction endonucleases); (8)
nucleic acid segments that can be used to isolate or identify a
desired molecule (e.g., specific protein binding sites); (9)
nucleic acid segments that encode a specific nucleotide sequence
that can be otherwise non-functional (e.g., for PCR amplification
of subpopulations of molecules); (10) nucleic acid segments that,
when absent, directly or indirectly confer resistance or
sensitivity to particular compounds; (11) nucleic acid segments
that encode products that either are toxic or convert a relatively
non-toxic compound to a toxic compound (e.g., Herpes simplex
thymidine kinase, cytosine deaminase) in recipient cells; (12)
nucleic acid segments that inhibit replication, partition or
heritability of nucleic acid molecules that contain them; and/or
(13) nucleic acid segments that encode conditional replication
functions, e.g., replication in certain hosts or host cell strains
or under certain environmental conditions (e.g., temperature,
nutritional conditions, and the like). In some embodiments, the
regulatory or selective agent can be added to change the existing
growth conditions to which the organism is subjected (e.g., growth
in liquid culture, growth in a fermentor, growth on solid nutrient
plates and the like for example).
[0130] In some embodiments, regulation of a promoter element can be
used to alter (e.g., increase, add, decrease or substantially
eliminate) the activity of a peptide, polypeptide or protein (e.g.,
enzyme activity for example). For example, a microorganism can be
engineered by genetic modification to express a nucleic acid
reagent that can add a novel activity (e.g., an activity not
normally found in the host organism) or increase the expression of
an existing activity by increasing transcription from a homologous
or heterologous promoter operably linked to a nucleotide sequence
of interest (e.g., homologous or heterologous nucleotide sequence
of interest), in certain embodiments. In some embodiments, a
microorganism can be engineered by genetic modification to express
a nucleic acid reagent that can decrease expression of an activity
by decreasing or substantially eliminating transcription from a
homologous or heterologous promoter operably linked to a nucleotide
sequence of interest, in certain embodiments.
[0131] In some embodiments the activity can be altered using
recombinant DNA and genetic techniques known to the artisan.
Methods for engineering microorganisms are further described
herein. Tables herein provide non-limiting lists of yeast promoters
that are up-regulated by oxygen, yeast promoters that are
down-regulated by oxygen, yeast transcriptional repressors and
their associated genes, DNA binding motifs as determined using the
MEME sequence analysis software. Potential regulator binding motifs
can be identified using the program MEME to search intergenic
regions bound by regulators for overrepresented sequences. For each
regulator, the sequences of intergenic regions bound with p-values
less than 0.001 were extracted to use as input for motif discovery.
The MEME software was run using the following settings: a motif
width ranging from 6 to 18 bases, the "zoops" distribution model, a
6.sup.th order Markov background model and a discovery limit of 20
motifs. The discovered sequence motifs were scored for significance
by two criteria: an E-value calculated by MEME and a specificity
score. The motif with the best score using each metric is shown for
each regulator. All motifs presented are derived from datasets
generated in rich growth conditions with the exception of a
previously published dataset for epitope-tagged Gal4 grown in
galactose.
[0132] In some embodiments, the altered activity can be found by
screening the organism under conditions that select for the desired
change in activity. For example, certain microorganisms can be
adapted to increase or decrease an activity by selecting or
screening the organism in question on a media containing substances
that are poorly metabolized or even toxic. An increase in the
ability of an organism to grow a substance that is normally poorly
metabolized would result in an increase in the growth rate on that
substance, for example. A decrease in the sensitivity to a toxic
substance might be manifested by growth on higher concentrations of
the toxic substance, for example. Genetic modifications that are
identified in this manner sometimes are referred to as naturally
occurring mutations or the organisms that carry them can sometimes
be referred to as naturally occurring mutants. Modifications
obtained in this manner are not limited to alterations in promoter
sequences. That is, screening microorganisms by selective pressure,
as described above, can yield genetic alterations that can occur in
non-promoter sequences, and sometimes also can occur in sequences
that are not in the nucleotide sequence of interest, but in a
related nucleotide sequences (e.g., a gene involved in a different
step of the same pathway, a transport gene, and the like).
Naturally occurring mutants sometimes can be found by isolating
naturally occurring variants from unique environments, in some
embodiments.
[0133] In addition to the regulated promoter sequences, regulatory
sequences, and coding polynucleotides provided herein, a nucleic
acid reagent may include a polynucleotide sequence 80% or more
identical to the foregoing (or to the complementary sequences).
That is, a nucleotide sequence that is at least 80% or more, 81% or
more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or
more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or
more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or
more, 97% or more, 98% or more, or 99% or more identical to a
nucleotide sequence described herein can be utilized. The term
"identical" as used herein refers to two or more nucleotide
sequences having substantially the same nucleotide sequence when
compared to each other. One test for determining whether two
nucleotide sequences or amino acids sequences are substantially
identical is to determine the percent of identical nucleotide
sequences or amino acid sequences shared.
[0134] Calculations of sequence identity can be performed as
follows. 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 length of a reference sequence aligned for
comparison purposes is sometimes 30% or more, 40% or more, 50% or
more, often 60% or more, and more often 70% or more, 80% or more,
90% or more, or 100% of the length of the reference sequence. The
nucleotides or amino acids at corresponding nucleotide or
polypeptide positions, respectively, are then compared among the
two sequences. When a position in the first sequence is occupied by
the same nucleotide or amino acid as the corresponding position in
the second sequence, the nucleotides or amino acids are deemed to
be identical at that position. 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, introduced for optimal alignment of the two
sequences.
[0135] Comparison of sequences and determination of percent
identity between two sequences can be accomplished using a
mathematical algorithm. Percent identity between two amino acid or
nucleotide sequences can be determined using the algorithm of
Meyers & Miller, CABIOS 4: 11-17 (1989), which has been
incorporated into the ALIGN program (version 2.0), using a PAM120
weight residue table, a gap length penalty of 12 and a gap penalty
of 4. Also, percent identity between two amino acid sequences can
be determined using the Needleman & Wunsch, J. Mol. Biol. 48:
444-453 (1970) algorithm which has been incorporated into the GAP
program in the GCG software package (available at the http address
www.gcg.com), 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. Percent identity between two nucleotide
sequences can be determined using the GAP program in the GCG
software package (available at http address www.gcg.com), 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. A set of parameters often
used is a Blossum 62 scoring matrix with a gap open penalty of 12,
a gap extend penalty of 4, and a frameshift gap penalty of 5.
[0136] Sequence identity can also be determined by hybridization
assays conducted under stringent conditions. As use herein, the
term "stringent conditions" refers to conditions for hybridization
and washing. Stringent conditions are known to those skilled in the
art and can be found in Current Protocols in Molecular Biology,
John Wiley & Sons, N.Y., 6.3.1-6.3.6 (1989). Aqueous and
non-aqueous methods are described in that reference and either can
be used. An example of stringent hybridization conditions is
hybridization in 6.times. sodium chloride/sodium citrate (SSC) at
about 45.degree. C., followed by one or more washes in
0.2.times.SSC, 0.1% SDS at 50.degree. C. Another example of
stringent hybridization conditions are hybridization in 6.times.
sodium chloride/sodium citrate (SSC) at about 45.degree. C.,
followed by one or more washes in 0.2.times.SSC, 0.1% SDS at
55.degree. C. A further example of stringent hybridization
conditions is hybridization in 6.times. sodium chloride/sodium
citrate (SSC) at about 45.degree. C., followed by one or more
washes in 0.2.times.SSC, 0.1% SDS at 60.degree. C. Often, stringent
hybridization conditions are hybridization in 6.times. sodium
chloride/sodium citrate (SSC) at about 45.degree. C., followed by
one or more washes in 0.2.times.SSC, 0.1% SDS at 65.degree. C. More
often, stringency 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.
[0137] As noted above, nucleic acid reagents may also comprise one
or more 5' UTR's, and one or more 3'UTR's. A 5' UTR may comprise
one or more elements endogenous to the nucleotide sequence from
which it originates, and sometimes includes one or more exogenous
elements. A 5' UTR can originate from any suitable nucleic acid,
such as genomic DNA, plasmid DNA, RNA or mRNA, for example, from
any suitable organism (e.g., virus, bacterium, yeast, fungi, plant,
insect or mammal). The artisan may select appropriate elements for
the 5' UTR based upon the chosen expression system (e.g.,
expression in a chosen organism, or expression in a cell free
system, for example). A 5' UTR sometimes comprises one or more of
the following elements known to the artisan: enhancer sequences
(e.g., transcriptional or translational), transcription initiation
site, transcription factor binding site, translation regulation
site, translation initiation site, translation factor binding site,
accessory protein binding site, feedback regulation agent binding
sites, Pribnow box, TATA box, -35 element, E-box (helix-loop-helix
binding element), ribosome binding site, replicon, internal
ribosome entry site (IRES), silencer element and the like. In some
embodiments, a promoter element may be isolated such that all 5'
UTR elements necessary for proper conditional regulation are
contained in the promoter element fragment, or within a functional
subsequence of a promoter element fragment.
[0138] A 5'UTR in the nucleic acid reagent can comprise a
translational enhancer nucleotide sequence. A translational
enhancer nucleotide sequence often is located between the promoter
and the target nucleotide sequence in a nucleic acid reagent. A
translational enhancer sequence often binds to a ribosome,
sometimes is an 18S rRNA-binding ribonucleotide sequence (i.e., a
40S ribosome binding sequence) and sometimes is an internal
ribosome entry sequence (IRES). An IRES generally forms an RNA
scaffold with precisely placed RNA tertiary structures that contact
a 40S ribosomal subunit via a number of specific intermolecular
interactions. Examples of ribosomal enhancer sequences are known
and can be identified by the artisan (e.g., Mignone et al., Nucleic
Acids Research 33: D141-D146 (2005); Paulous et al., Nucleic Acids
Research 31: 722-733 (2003); Akbergenov et al., Nucleic Acids
Research 32: 239-247 (2004); Mignone et al., Genome Biology 3(3):
reviews0004.1-0001.10 (2002); Gallie, Nucleic Acids Research 30:
3401-3411 (2002); Shaloiko et al., http address
www.interscience.wiley.com, DOI: 10.1002/bit.20267; and Gallie et
al., Nucleic Acids Research 15: 3257-3273 (1987)).
[0139] A translational enhancer sequence sometimes is a eukaryotic
sequence, such as a Kozak consensus sequence or other sequence
(e.g., hydroid polyp sequence, GenBank accession no. U07128). A
translational enhancer sequence sometimes is a prokaryotic
sequence, such as a Shine-Dalgarno consensus sequence. In certain
embodiments, the translational enhancer sequence is a viral
nucleotide sequence. A translational enhancer sequence sometimes is
from a 5' UTR of a plant virus, such as Tobacco Mosaic Virus (TMV),
Alfalfa Mosaic Virus (AMV); Tobacco Etch Virus (ETV); Potato Virus
Y (PVY); Turnip Mosaic (poty) Virus and Pea Seed Borne Mosaic
Virus, for example. In certain embodiments, an omega sequence about
67 bases in length from TMV is included in the nucleic acid reagent
as a translational enhancer sequence (e.g., devoid of guanosine
nucleotides and includes a 25 nucleotide long poly (CAA) central
region).
[0140] A 3' UTR may comprise one or more elements endogenous to the
nucleotide sequence from which it originates and sometimes includes
one or more exogenous elements. A 3' UTR may originate from any
suitable nucleic acid, such as genomic DNA, plasmid DNA, RNA or
mRNA, for example, from any suitable organism (e.g., a virus,
bacterium, yeast, fungi, plant, insect or mammal). The artisan can
select appropriate elements for the 3' UTR based upon the chosen
expression system (e.g., expression in a chosen organism, for
example). A 3' UTR sometimes comprises one or more of the following
elements known to the artisan: transcription regulation site,
transcription initiation site, transcription termination site,
transcription factor binding site, translation regulation site,
translation termination site, translation initiation site,
translation factor binding site, ribosome binding site, replicon,
enhancer element, silencer element and polyadenosine tail. A 3' UTR
often includes a polyadenosine tail and sometimes does not, and if
a polyadenosine tail is present, one or more adenosine moieties may
be added or deleted from it (e.g., about 5, about 10, about 15,
about 20, about 25, about 30, about 35, about 40, about 45 or about
50 adenosine moieties may be added or subtracted).
[0141] In some embodiments, modification of a 5' UTR and/or a 3'
UTR can be used to alter (e.g., increase, add, decrease or
substantially eliminate) the activity of a promoter. Alteration of
the promoter activity can in turn alter the activity of a peptide,
polypeptide or protein (e.g., enzyme activity for example), by a
change in transcription of the nucleotide sequence(s) of interest
from an operably linked promoter element comprising the modified 5'
or 3' UTR. For example, a microorganism can be engineered by
genetic modification to express a nucleic acid reagent comprising a
modified 5' or 3' UTR that can add a novel activity (e.g., an
activity not normally found in the host organism) or increase the
expression of an existing activity by increasing transcription from
a homologous or heterologous promoter operably linked to a
nucleotide sequence of interest (e.g., homologous or heterologous
nucleotide sequence of interest), in certain embodiments. In some
embodiments, a microorganism can be engineered by genetic
modification to express a nucleic acid reagent comprising a
modified 5' or 3' UTR that can decrease the expression of an
activity by decreasing or substantially eliminating transcription
from a homologous or heterologous promoter operably linked to a
nucleotide sequence of interest, in certain embodiments.
[0142] A nucleotide reagent sometimes can comprise a target
nucleotide sequence. A "target nucleotide sequence" as used herein
encodes a nucleic acid, peptide, polypeptide or protein of
interest, and may be a ribonucleotide sequence or a
deoxyribonucleotide sequence. A target nucleic acid sometimes is an
untranslated ribonucleic acid and sometimes is a translated
ribonucleic acid. An untranslated ribonucleic acid may include, but
is not limited to, a small interfering ribonucleic acid (siRNA), a
short hairpin ribonucleic acid (shRNA), other ribonucleic acid
capable of RNA interference (RNAi), an antisense ribonucleic acid,
or a ribozyme. A translatable target nucleotide sequence (e.g., a
target ribonucleotide sequence) sometimes encodes a peptide,
polypeptide or protein, which are sometimes referred to herein as
"target peptides," "target polypeptides" or "target proteins."
[0143] Any peptides, polypeptides or proteins, or an activity
catalyzed by one or more peptides, polypeptides or proteins may be
encoded by a target nucleotide sequence and may be selected by a
user. Representative proteins include enzymes (e.g., hexanoate
synthase, thioesterase, monooxygenase, monooxygenase reductase,
fatty alcohol oxidase, 6-oxohexanoic acid deydrogenase,
6-hydroxyhexanoic acid dehydrogenase and the like, for example),
antibodies, serum proteins (e.g., albumin), membrane bound
proteins, hormones (e.g., growth hormone, erythropoietin, insulin,
etc.), cytokines, etc., and include both naturally occurring and
exogenously expressed polypeptides. Representative activities
(e.g., enzymes or combinations of enzymes which are functionally
associated to provide an activity) include hexanoate synthase
activity, thioesterase activity, monooxygenase activity,
6-oxohexanoic acid deydrogenase activity, 6-hydroxyhexanoic acid
dehydrogenase activity, beta-oxidation activity and the like, for
example. The term "enzyme" as used herein refers to a protein which
can act as a catalyst to induce a chemical change in other
compounds, thereby producing one or more products from one or more
substrates.
[0144] Specific polypeptides (e.g., enzymes) useful for embodiments
described herein are listed herein. The term "protein" as used
herein refers to a molecule having a sequence of amino acids linked
by peptide bonds. This term includes fusion proteins,
oligopeptides, peptides, cyclic peptides, polypeptides and
polypeptide derivatives, whether native or recombinant, and also
includes fragments, derivatives, homologs, and variants thereof. A
protein or polypeptide sometimes is of intracellular origin (e.g.,
located in the nucleus, cytosol, or interstitial space of host
cells in vivo) and sometimes is a cell membrane protein in vivo. In
some embodiments (described above, and in further detail hereafter
in Engineering and Alteration Methods), a genetic modification can
result in a modification (e.g., increase, substantially increase,
decrease or substantially decrease) of a target activity.
[0145] A translatable nucleotide sequence generally is located
between a start codon (AUG in ribonucleic acids and ATG in
deoxyribonucleic acids) and a stop codon (e.g., UAA (ochre), UAG
(amber) or UGA (opal) in ribonucleic acids and TAA, TAG or TGA in
deoxyribonucleic acids), and sometimes is referred to herein as an
"open reading frame" (ORF). A translatable nucleotide sequence
(e.g., ORF) sometimes is encoded differently in one organism (e.g.,
most organisms encode CTG as leucine) than in another organism
(e.g., C. tropicalis encodes CTG as serine). In some embodiments, a
translatable nucleotide sequence is altered to correct alternate
genetic code (e.g., codon usage) differences between a nucleotide
donor organism and an nucleotide recipient organism (e.g.,
engineered organism). In certain embodiments, a translatable
nucleotide sequence is altered to improve; (i) codon usage, (ii)
transcriptional efficiency, (iii) translational efficiency, (iv)
the like, and combinations thereof.
[0146] A nucleic acid reagent sometimes comprises one or more ORFs.
An ORF may be from any suitable source, sometimes from genomic DNA,
mRNA, reverse transcribed RNA or complementary DNA (cDNA) or a
nucleic acid library comprising one or more of the foregoing, and
is from any organism species that contains a nucleic acid sequence
of interest, protein of interest, or activity of interest.
Non-limiting examples of organisms from which an ORF can be
obtained include bacteria, yeast, fungi, human, insect, nematode,
bovine, equine, canine, feline, rat or mouse, for example.
[0147] A nucleic acid reagent sometimes comprises a nucleotide
sequence adjacent to an ORF that is translated in conjunction with
the ORF and encodes an amino acid tag. The tag-encoding nucleotide
sequence is located 3' and/or 5' of an ORF in the nucleic acid
reagent, thereby encoding a tag at the C-terminus or N-terminus of
the protein or peptide encoded by the ORF. Any tag that does not
abrogate in vitro transcription and/or translation may be utilized
and may be appropriately selected by the artisan. Tags may
facilitate isolation and/or purification of the desired ORF product
from culture or fermentation media.
[0148] A tag sometimes specifically binds a molecule or moiety of a
solid phase or a detectable label, for example, thereby having
utility for isolating, purifying and/or detecting a protein or
peptide encoded by the ORF. In some embodiments, a tag comprises
one or more of the following elements: FLAG (e.g., DYKDDDDKG (SEQ
ID NO: 16)), V5 (e.g., GKPIPNPLLGLDST (SEQ ID NO: 17)), c-MYC
(e.g., EQKLISEEDL (SEQ ID NO: 18)), HSV (e.g., QPELAPEDPED (SEQ ID
NO: 19)), influenza hemaglutinin, HA (e.g., YPYDVPDYA (SEQ ID NO:
20)), VSV-G (e.g., YTDIEMNRLGK (SEQ ID NO: 21)), bacterial
glutathione-5-transferase, maltose binding protein, a streptavidin-
or avidin-binding tag (e.g., pcDNA.TM.6 BioEase.TM. Gateway.RTM.
Biotinylation System (Invitrogen)), thioredoxin, 3-galactosidase,
VSV-glycoprotein, a fluorescent protein (e.g., green fluorescent
protein or one of its many color variants (e.g., yellow, red,
blue)), a polylysine or polyarginine sequence, a polyhistidine
sequence (e.g., His6 (SEQ ID NO:13)) or other sequence that
chelates a metal (e.g., cobalt, zinc, copper), and/or a
cysteine-rich sequence that binds to an arsenic-containing
molecule.
[0149] In certain embodiments, a cysteine-rich tag comprises the
amino acid sequence CC-Xn-CC (SEQ ID NO: 22), wherein X is any
amino acid and n is 1 to 3, and the cysteine-rich sequence
sometimes is CCPGCC (SEQ ID NO: 23). In certain embodiments, the
tag comprises a cysteine-rich element and a polyhistidine element
(e.g., CCPGCC (SEQ ID NO: 23) and His6 (SEQ ID NO: 13)).
[0150] A tag often conveniently binds to a binding partner. For
example, some tags bind to an antibody (e.g., FLAG) and sometimes
specifically bind to a small molecule. For example, a polyhistidine
tag specifically chelates a bivalent metal, such as copper, zinc
and cobalt; a polylysine or polyarginine tag specifically binds to
a zinc finger; a glutathione S-transferase tag binds to
glutathione; and a cysteine-rich tag specifically binds to an
arsenic-containing molecule. Arsenic-containing molecules include
LUMIO.TM. agents (Invitrogen, California), such as FLAsH.TM.
(EDT2[4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein-(1,2-ethan-
edithiol)2]) and ReAsH reagents (e.g., U.S. Pat. No. 5,932,474 to
Tsien et al., entitled "Target Sequences for Synthetic Molecules;"
U.S. Pat. No. 6,054,271 to Tsien et al., entitled "Methods of Using
Synthetic Molecules and Target Sequences;" U.S. Pat. Nos. 6,451,569
and 6,008,378; published U.S. Patent Application 2003/0083373, and
published PCT Patent Application WO 99/21013, all to Tsien et al.
and all entitled "Synthetic Molecules that Specifically React with
Target Sequences"). Such antibodies and small molecules sometimes
are linked to a solid phase for convenient isolation of the target
protein or target peptide.
[0151] A tag sometimes comprises a sequence that localizes a
translated protein or peptide to a component in a system, which is
referred to as a "signal sequence" or "localization signal
sequence" herein. A signal sequence often is incorporated at the
N-terminus of a target protein or target peptide, and sometimes is
incorporated at the C-terminus. Examples of signal sequences are
known to the artisan, are readily incorporated into a nucleic acid
reagent, and often are selected according to the organism in which
expression of the nucleic acid reagent is performed. A signal
sequence in some embodiments localizes a translated protein or
peptide to a cell membrane. Examples of signal sequences include,
but are not limited to, a nucleus targeting signal (e.g., steroid
receptor sequence and N-terminal sequence of SV40 virus large T
antigen); mitochondrial targeting signal (e.g., amino acid sequence
that forms an amphipathic helix); peroxisome targeting signal
(e.g., C-terminal sequence in YFG from S.cerevisiae); and a
secretion signal (e.g., N-terminal sequences from invertase, mating
factor alpha, PHO5 and SUC2 in S.cerevisiae; multiple N-terminal
sequences of B. subtilis proteins (e.g., Tjalsma et al.,
Microbiol.Molec. Biol. Rev. 64: 515-547 (2000)); alpha amylase
signal sequence (e.g., U.S. Pat. No. 6,288,302); pectate lyase
signal sequence (e.g., U.S. Pat. No. 5,846,818); precollagen signal
sequence (e.g., U.S. Pat. No. 5,712,114); OmpA signal sequence
(e.g., U.S. Pat. No. 5,470,719); lam beta signal sequence (e.g.,
U.S. Pat. No. 5,389,529); B. brevis signal sequence (e.g., U.S.
Pat. No. 5,232,841); and P. pastoris signal sequence (e.g., U.S.
Pat. No. 5,268,273)).
[0152] A tag sometimes is directly adjacent to the amino acid
sequence encoded by an ORF (i.e., there is no intervening sequence)
and sometimes a tag is substantially adjacent to an ORF encoded
amino acid sequence (e.g., an intervening sequence is present). An
intervening sequence sometimes includes a recognition site for a
protease, which is useful for cleaving a tag from a target protein
or peptide. In some embodiments, the intervening sequence is
cleaved by Factor Xa (e.g., recognition site I (E/D)GR), thrombin
(e.g., recognition site LVPRGS (SEQ ID NO: 24)), enterokinase
(e.g., recognition site DDDDK (SEQ ID NO: 25)), TEV protease (e.g.,
recognition site ENLYFQG (SEQ ID NO: 26)) or PreScission.TM.
protease (e.g., recognition site LEVLFQGP (SEQ ID NO: 27)), for
example.
[0153] An intervening sequence sometimes is referred to herein as a
"linker sequence," and may be of any suitable length selected by
the artisan. A linker sequence sometimes is about 1 to about 20
amino acids in length, and sometimes about 5 to about 10 amino
acids in length. The artisan may select the linker length to
substantially preserve target protein or peptide function (e.g., a
tag may reduce target protein or peptide function unless separated
by a linker), to enhance disassociation of a tag from a target
protein or peptide when a protease cleavage site is present (e.g.,
cleavage may be enhanced when a linker is present), and to enhance
interaction of a tag/target protein product with a solid phase. A
linker can be of any suitable amino acid content, and often
comprises a higher proportion of amino acids having relatively
short side chains (e.g., glycine, alanine, serine and
threonine).
[0154] A nucleic acid reagent sometimes includes a stop codon
between a tag element and an insertion element or ORF, which can be
useful for translating an ORF with or without the tag. Mutant tRNA
molecules that recognize stop codons (described above) suppress
translation termination and thereby are designated "suppressor
tRNAs." Suppressor tRNAs can result in the insertion of amino acids
and continuation of translation past stop codons (e.g., U.S. Patent
Application No. 60/587,583, filed Jul. 14, 2004, entitled
"Production of Fusion Proteins by Cell-Free Protein Synthesis,";
Eggertsson, et al., (1988) Microbiological Review 52(3):354-374,
and Engleerg-Kukla, et al. (1996) in Escherichia coli and
Salmonella Cellular and Molecular Biology, Chapter 60, pps 909-921,
Neidhardt, et al. eds., ASM Press, Washington, D.C.). A number of
suppressor tRNAs are known, including but not limited to, supE,
supP, supD, supF and supZ suppressors, which suppress the
termination of translation of the amber stop codon; supB, gIT,
supL, supN, supC and supM suppressors, which suppress the function
of the ochre stop codon and glyT, trpT and Su-9 suppressors, which
suppress the function of the opal stop codon. In general,
suppressor tRNAs contain one or more mutations in the anti-codon
loop of the tRNA that allows the tRNA to base pair with a codon
that ordinarily functions as a stop codon. The mutant tRNA is
charged with its cognate amino acid residue and the cognate amino
acid residue is inserted into the translating polypeptide when the
stop codon is encountered. Mutations that enhance the efficiency of
termination suppressors (i.e., increase stop codon read-through)
have been identified. These include, but are not limited to,
mutations in the uar gene (also known as the prfA gene), mutations
in the ups gene, mutations in the sueA, sueB and sueC genes,
mutations in the rpsD (ramA) and rpsE (spcA) genes and mutations in
the rpIL gene.
[0155] Thus, a nucleic acid reagent comprising a stop codon located
between an ORF and a tag can yield a translated ORF alone when no
suppressor tRNA is present in the translation system, and can yield
a translated ORF-tag fusion when a suppressor tRNA is present in
the system. Suppressor tRNA can be generated in cells transfected
with a nucleic acid encoding the tRNA (e.g., a replication
incompetent adenovirus containing the human tRNA-Ser suppressor
gene can be transfected into cells, or a YAC containing a yeast or
bacterial tRNA suppressor gene can be transfected into yeast cells,
for example). Vectors for synthesizing suppressor tRNA and for
translating ORFs with or without a tag are available to the artisan
(e.g., Tag-On-Demand.TM. kit (Invitrogen Corporation, California);
Tag-On-Demand.TM. Suppressor Supernatant Instruction Manual,
Version B, 6 Jun. 2003, at http address
www.invitrogen.com/content/sfs/manuals/tagondemand supernatant
man.pdf; Tag-On-Demand.TM. Gateway.RTM. Vector Instruction Manual,
Version B, 20 Jun., 2003 at http address
www.invitrogen.com/content/sfs/manuals/tagondemand vectors man.pdf;
and Capone et al., Amber, ochre and opal suppressor tRNA genes
derived from a human serine tRNA gene. EMBO J. 4:213, 1985).
[0156] Any convenient cloning strategy known in the art may be
utilized to incorporate an element, such as an ORF, into a nucleic
acid reagent. Known methods can be utilized to insert an element
into the template independent of an insertion element, such as (1)
cleaving the template at one or more existing restriction enzyme
sites and ligating an element of interest and (2) adding
restriction enzyme sites to the template by hybridizing
oligonucleotide primers that include one or more suitable
restriction enzyme sites and amplifying by polymerase chain
reaction (described in greater detail herein). Other cloning
strategies take advantage of one or more insertion sites present or
inserted into the nucleic acid reagent, such as an oligonucleotide
primer hybridization site for PCR, for example, and others
described herein. In some embodiments, a cloning strategy can be
combined with genetic manipulation such as recombination (e.g.,
recombination of a nucleic acid reagent with a nucleic acid
sequence of interest into the genome of the organism to be
modified, as described further herein). In some embodiments, the
cloned ORF(s) can produce (directly or indirectly) adipic acid, by
engineering a microorganism with one or more ORFs of interest,
which microorganism comprises one or more altered activities
selected from the group consisting of 6-oxohexanoic acid
dehydrogenase activity, 6-hydroxyhexanoic acid dehydrogenase
activity, hexanoate synthase activity and monooxygenase
activity.
[0157] In some embodiments, the nucleic acid reagent includes one
or more recombinase insertion sites. A recombinase insertion site
is a recognition sequence on a nucleic acid molecule that
participates in an integration/recombination reaction by
recombination proteins. For example, the recombination site for Cre
recombinase is loxP, which is a 34 base pair sequence comprised of
two 13 base pair inverted repeats (serving as the recombinase
binding sites) flanking an 8 base pair core sequence (e.g., FIG. 1
of Sauer, B., Curr. Opin. Biotech. 5:521-527 (1994)). Other
examples of recombination sites include attB, attP, attL, and attR
sequences, and mutants, fragments, variants and derivatives
thereof, which are recognized by the recombination protein A Int
and by the auxiliary proteins integration host factor (IHF), FIS
and excisionase (Xis) (e.g., U.S. Pat. Nos. 5,888,732; 6,143,557;
6,171,861; 6,270,969; 6,277,608; and 6,720,140; U.S. patent
application Ser. Nos. 09/517,466, filed Mar. 2, 2000, and
09/732,914, filed Aug. 14, 2003, and in U.S. patent publication no.
2002-0007051-A1; Landy, Curr. Opin. Biotech. 3:699-707 (1993)).
[0158] Examples of recombinase cloning nucleic acids are in
Gateway.RTM. systems (Invitrogen, California), which include at
least one recombination site for cloning a desired nucleic acid
molecules in vivo or in vitro. In some embodiments, the system
utilizes vectors that contain at least two different site-specific
recombination sites, often based on the bacteriophage lambda system
(e.g., att1 and att2), and are mutated from the wild-type (att0)
sites. Each mutated site has a unique specificity for its cognate
partner att site (i.e., its binding partner recombination site) of
the same type (for example attB1 with attP1, or attL1 with attR1)
and will not cross-react with recombination sites of the other
mutant type or with the wild-type att0 site. Different site
specificities allow directional cloning or linkage of desired
molecules thus providing desired orientation of the cloned
molecules. Nucleic acid fragments flanked by recombination sites
are cloned and subcloned using the Gateway.RTM. system by replacing
a selectable marker (for example, ccdB) flanked by att sites on the
recipient plasmid molecule, sometimes termed the Destination
Vector. Desired clones are then selected by transformation of a
ccdB sensitive host strain and positive selection for a marker on
the recipient molecule. Similar strategies for negative selection
(e.g., use of toxic genes) can be used in other organisms such as
thymidine kinase (TK) in mammals and insects.
[0159] A recombination system useful for engineering yeast is
outlined briefly. The system makes use of the URA3 gene (e.g., for
S. cerevisieae and C. albicans, for example) or URA4 and URA5 genes
(e.g., for S. pombe, for example) and toxicity of the nucleotide
analogue 5-Fluoroorotic acid (5-FOA). The URA3 or URA4 and URA5
genes encode orotine-5'-monophosphate (OMP) dicarboxylase. Yeast
with an active URA3 or URA4 and URA5 gene (phenotypically Ura+)
convert 5-FOA to fluorodeoxyuridine, which is toxic to yeast cells.
Yeast carrying a mutation in the appropriate gene(s) or having a
knock out of the appropriate gene(s) can grow in the presence of
5-FOA, if the media is also supplemented with uracil.
[0160] A nucleic acid engineering construct can be made which may
comprise the URA3 gene or cassette (for S. cerevisieae), flanked on
either side by the same nucleotide sequence in the same
orientation. The URA3 cassette comprises a promoter, the URA3 gene
and a functional transcription terminator. Target sequences which
direct the construct to a particular nucleic acid region of
interest in the organism to be engineered are added such that the
target sequences are adjacent to and abut the flanking sequences on
either side of the URA3 cassette. Yeast can be transformed with the
engineering construct and plated on minimal media without uracil.
Colonies can be screened by PCR to determine those transformants
that have the engineering construct inserted in the proper location
in the genome. Checking insertion location prior to selecting for
recombination of the ura3 cassette may reduce the number of
incorrect clones carried through to later stages of the procedure.
Correctly inserted transformants can then be replica plated on
minimal media containing 5-FOA to select for recombination of the
URA3 cassette out of the construct, leaving a disrupted gene and an
identifiable footprint (e.g., nucleic acid sequence) that can be
use to verify the presence of the disrupted gene. The technique
described is useful for disrupting or "knocking out" gene function,
but also can be used to insert genes or constructs into a host
organisms genome in a targeted, sequence specific manner.
[0161] In certain embodiments, a nucleic acid reagent includes one
or more topoisomerase insertion sites. A topoisomerase insertion
site is a defined nucleotide sequence recognized and bound by a
site-specific topoisomerase. For example, the nucleotide sequence
5'-(C/T)CCTT-3' is a topoisomerase recognition site bound
specifically by most poxvirus topoisomerases, including vaccinia
virus DNA topoisomerase I. After binding to the recognition
sequence, the topoisomerase cleaves the strand at the 3'-most
thymidine of the recognition site to produce a nucleotide sequence
comprising 5'-(C/T)CCTT-PO4-TOPO, a complex of the topoisomerase
covalently bound to the 3' phosphate via a tyrosine in the
topoisomerase (e.g., Shuman, J. Biol. Chem. 266:11372-11379, 1991;
Sekiguchi and Shuman, Nucl. Acids Res. 22:5360-5365, 1994; U.S.
Pat. No. 5,766,891; PCT/US95/16099; and PCT/US98/12372). In
comparison, the nucleotide sequence 5'-GCAACTT-3' is a
topoisomerase recognition site for type IA E. coli topoisomerase
III. An element to be inserted often is combined with
topoisomerase-reacted template and thereby incorporated into the
nucleic acid reagent (e.g., World Wide Web URL
invitrogen.com/downloads/F-13512_Topo_Flyer.pdf; World Wide Web URL
invitrogen.com/content/sfs/brochures/710.sub.--021849%/20_B_TOPOCloning_b-
ro.pdf; TOPO TA Cloning.RTM. Kit and Zero Blunt.RTM. TOPO.RTM.
Cloning Kit product information).
[0162] A nucleic acid reagent sometimes contains one or more origin
of replication (ORI) elements. In some embodiments, a template
comprises two or more ORIs, where one functions efficiently in one
organism (e.g., a bacterium) and another functions efficiently in
another organism (e.g., a eukaryote, like yeast for example). In
some embodiments, an ORI may function efficiently in one species
(e.g., S. cerevisieae, for example) and another ORI may function
efficiently in a different species (e.g., S. pombe, for example). A
nucleic acid reagent also sometimes includes one or more
transcription regulation sites.
[0163] A nucleic acid reagent can include one or more selection
elements (e.g., elements for selection of the presence of the
nucleic acid reagent, and not for activation of a promoter element
which can be selectively regulated). Selection elements often are
utilized using known processes to determine whether a nucleic acid
reagent is included in a cell. In some embodiments, a nucleic acid
reagent includes two or more selection elements, where one
functions efficiently in one organism and another functions
efficiently in another organism. Examples of selection elements
include, but are not limited to, (1) nucleic acid segments that
encode products that provide resistance against otherwise toxic
compounds (e.g., antibiotics); (2) nucleic acid segments that
encode products that are otherwise lacking in the recipient cell
(e.g., essential products, tRNA genes, auxotrophic markers); (3)
nucleic acid segments that encode products that suppress the
activity of a gene product; (4) nucleic acid segments that encode
products that can be readily identified (e.g., phenotypic markers
such as antibiotics (e.g., .beta.-lactamase), .beta.-galactosidase,
green fluorescent protein (GFP), yellow fluorescent protein (YFP),
red fluorescent protein (RFP), cyan fluorescent protein (CFP), and
cell surface proteins); (5) nucleic acid segments that bind
products that are otherwise detrimental to cell survival and/or
function; (6) nucleic acid segments that otherwise inhibit the
activity of any of the nucleic acid segments described in Nos. 1-5
above (e.g., antisense oligonucleotides); (7) nucleic acid segments
that bind products that modify a substrate (e.g., restriction
endonucleases); (8) nucleic acid segments that can be used to
isolate or identify a desired molecule (e.g., specific protein
binding sites); (9) nucleic acid segments that encode a specific
nucleotide sequence that can be otherwise non-functional (e.g., for
PCR amplification of subpopulations of molecules); (10) nucleic
acid segments that, when absent, directly or indirectly confer
resistance or sensitivity to particular compounds; (11) nucleic
acid segments that encode products that either are toxic or convert
a relatively non-toxic compound to a toxic compound (e.g., Herpes
simplex thymidine kinase, cytosine deaminase) in recipient cells;
(12) nucleic acid segments that inhibit replication, partition or
heritability of nucleic acid molecules that contain them; and/or
(13) nucleic acid segments that encode conditional replication
functions, e.g., replication in certain hosts or host cell strains
or under certain environmental conditions (e.g., temperature,
nutritional conditions, and the like).
[0164] A nucleic acid reagent is of any form useful for in vivo
transcription and/or translation. A nucleic acid sometimes is a
plasmid, such as a supercoiled plasmid, sometimes is a yeast
artificial chromosome (e.g., YAC), sometimes is a linear nucleic
acid (e.g., a linear nucleic acid produced by PCR or by restriction
digest), sometimes is single-stranded and sometimes is
double-stranded. A nucleic acid reagent sometimes is prepared by an
amplification process, such as a polymerase chain reaction (PCR)
process or transcription-mediated amplification process (TMA). In
TMA, two enzymes are used in an isothermal reaction to produce
amplification products detected by light emission (see, e.g.,
Biochemistry 1996 Jun. 25; 35(25):8429-38 and http address
www.devicelink.com/ivdt/archive/00/11/007.html). Standard PCR
processes are known (e.g., U.S. Pat. Nos. 4,683,202; 4,683,195;
4,965,188; and 5,656,493), and generally are performed in cycles.
Each cycle includes heat denaturation, in which hybrid nucleic
acids dissociate; cooling, in which primer oligonucleotides
hybridize; and extension of the oligonucleotides by a polymerase
(i.e., Taq polymerase). An example of a PCR cyclical process is
treating the sample at 95.degree. C. for 5 minutes; repeating
forty-five cycles of 95.degree. C. for 1 minute, 59.degree. C. for
1 minute, 10 seconds, and 72.degree. C. for 1 minute 30 seconds;
and then treating the sample at 72.degree. C. for 5 minutes.
Multiple cycles frequently are performed using a commercially
available thermal cycler. PCR amplification products sometimes are
stored for a time at a lower temperature (e.g., at 4.degree. C.)
and sometimes are frozen (e.g., at -20.degree. C.) before
analysis.
[0165] In some embodiments, a nucleic acid reagent, protein
reagent, protein fragment reagent or other reagent described herein
is isolated or purified. The term "isolated" as used herein refers
to material removed from its original environment (e.g., the
natural environment if it is naturally occurring, or a host cell if
expressed exogenously), and thus is altered "by the hand of man"
from its original environment. The term "purified" as used herein
with reference to molecules does not refer to absolute purity.
Rather, "purified" refers to a substance in a composition that
contains fewer substance species in the same class (e.g., nucleic
acid or protein species) other than the substance of interest in
comparison to the sample from which it originated. "Purified," if a
nucleic acid or protein for example, refers to a substance in a
composition that contains fewer nucleic acid species or protein
species other than the nucleic acid or protein of interest in
comparison to the sample from which it originated. Sometimes, a
protein or nucleic acid is "substantially pure," indicating that
the protein or nucleic acid represents at least 50% of protein or
nucleic acid on a mass basis of the composition. Often, a
substantially pure protein or nucleic acid is at least 75% on a
mass basis of the composition, and sometimes at least 95% on a mass
basis of the composition.
Engineering and Alteration Methods
[0166] Methods and compositions (e.g., nucleic acid reagents)
described herein can be used to generate engineered microorganisms.
As noted above, the term "engineered microorganism" as used herein
refers to a modified organism that includes one or more activities
distinct from an activity present in a microorganism utilized as a
starting point for modification (e.g., host microorganism or
unmodified organism). Engineered microorganisms typically arise as
a result of a genetic modification, usually introduced or selected
for, by one of skill in the art using readily available techniques.
Non-limiting examples of methods useful for generating an altered
activity include, introducing a heterologous polynucleotide (e.g.,
nucleic acid or gene integration, also referred to as "knock in"),
removing an endogenous polynucleotide, altering the sequence of an
existing endogenous nucleic acid sequence (e.g., site-directed
mutagenesis), disruption of an existing endogenous nucleic acid
sequence (e.g., knock outs and transposon or insertion element
mediated mutagenesis), selection for an altered activity where the
selection causes a change in a naturally occurring activity that
can be stably inherited (e.g., causes a change in a nucleic acid
sequence in the genome of the organism or in an epigenetic nucleic
acid that is replicated and passed on to daughter cells), PCR-based
mutagenesis, and the like. The term "mutagenesis" as used herein
refers to any modification to a nucleic acid (e.g., nucleic acid
reagent, or host chromosome, for example) that is subsequently used
to generate a product in a host or modified organism. Non-limiting
examples of mutagenesis include, deletion, insertion, substitution,
rearrangement, point mutations, suppressor mutations and the like.
Mutagenesis methods are known in the art and are readily available
to the artisan. Non-limiting examples of mutagenesis methods are
described herein and can also be found in Maniatis, T., E. F.
Fritsch and J. Sambrook (1982) Molecular Cloning: a Laboratory
Manual; Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
Another non-limiting example of mutagenesis can be conducted using
a Stratagene (San Diego, Calif.) "QuickChange" kit according to the
manufacturer's instructions.
[0167] The term "genetic modification" as used herein refers to any
suitable nucleic acid addition, removal or alteration that
facilitates production of a target product (e.g., adipic acid,
6-hydroxyhexanoic acid) in an engineered microorganism. Genetic
modifications include, without limitation, insertion of one or more
nucleotides in a native nucleic acid of a host organism in one or
more locations, deletion of one or more nucleotides in a native
nucleic acid of a host organism in one or more locations,
modification or substitution of one or more nucleotides in a native
nucleic acid of a host organism in one or more locations, insertion
of a non-native nucleic acid into a host organism (e.g., insertion
of an autonomously replicating vector), and removal of a non-native
nucleic acid in a host organism (e.g., removal of a vector).
[0168] The term "heterologous polynucleotide" as used herein refers
to a nucleotide sequence not present in a host microorganism in
some embodiments. In certain embodiments, a heterologous
polynucleotide is present in a different amount (e.g., different
copy number) than in a host microorganism, which can be
accomplished, for example, by introducing more copies of a
particular nucleotide sequence to a host microorganism (e.g., the
particular nucleotide sequence may be in a nucleic acid autonomous
of the host chromosome or may be inserted into a chromosome). A
heterologous polynucleotide is from a different organism in some
embodiments, and in certain embodiments, is from the same type of
organism but from an outside source (e.g., a recombinant
source).
[0169] In some embodiments, an organism engineered using the
methods and nucleic acid reagents described herein can produce
adipic acid. In certain embodiments, an engineered microorganism
described herein that produces adipic acid may comprise one or more
altered activities selected from the group consisting of
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase activity, 6-hydroxyhexanoic acid dehydrogenase
activity, omega hydroxyl fatty acid dehydrogenase activity,
hexanoate synthase activity and monooxygenase activity. In some
embodiments, an engineered microorganism as described herein may
comprise a genetic modification that adds or increases the
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase activity, 6-hydroxyhexanoic acid dehydrogenase
activity, omega hydroxyl fatty acid dehydrogenase activity,
hexanoate synthase activity and monooxygenase activity.
[0170] In certain embodiments, an engineered microorganism
described herein can comprise an altered thioesterase activity. In
some embodiments, the engineered microorganism may comprise a
genetic alteration that adds or increases a thioesterase activity.
In some embodiments, the engineered microorganism comprising a
genetic alteration that adds or increases a thioesterase activity,
may further comprise a heterologous polynucleotide encoding a
polypeptide having thioesterase activity.
[0171] The term "altered activity" as used herein refers to an
activity in an engineered microorganism that is added or modified
relative to the host microorganism (e.g., added, increased,
reduced, inhibited or removed activity). An activity can be altered
by introducing a genetic modification to a host microorganism that
yields an engineered microorganism having added, increased,
reduced, inhibited or removed activity.
[0172] An added activity often is an activity not detectable in a
host microorganism. An increased activity generally is an activity
detectable in a host microorganism that has been increased in an
engineered microorganism. An activity can be increased to any
suitable level for production of a target product (e.g., adipic
acid, 6-hydroxyhexanoic acid), including but not limited to less
than 2-fold (e.g., about 10% increase to about 99% increase; about
20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% increase), 2-fold, 3-fold,
4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, of 10-fold
increase, or greater than about 10-fold increase. A reduced or
inhibited activity generally is an activity detectable in a host
microorganism that has been reduced or inhibited in an engineered
microorganism. An activity can be reduced to undetectable levels in
some embodiments, or detectable levels in certain embodiments. An
activity can be decreased to any suitable level for production of a
target product (e.g., adipic acid, 6-hydroxyhexanoic acid),
including but not limited to less than 2-fold (e.g., about 10%
decrease to about 99% decrease; about 20%, 30%, 40%, 50%, 60%, 70%,
80%, 90% decrease), 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold,
8-fold, 9-fold, of 10-fold decrease, or greater than about 10-fold
decrease.
[0173] An altered activity sometimes is an activity not detectable
in a host organism and is added to an engineered organism. An
altered activity also may be an activity detectable in a host
organism and is increased in an engineered organism. An activity
may be added or increased by increasing the number of copies of a
polynucleotide that encodes a polypeptide having a target activity,
in some embodiments. In certain embodiments an activity can be
added or increased by inserting into a host microorganism a
heterologous polynucleotide that encodes a polypeptide having the
added activity. In certain embodiments, an activity can be added or
increased by inserting into a host microorganism a heterologous
polynucleotide that is (i) operably linked to another
polynucleotide that encodes a polypeptide having the added
activity, and (ii) up regulates production of the polynucleotide.
Thus, an activity can be added or increased by inserting or
modifying a regulatory polynucleotide operably linked to another
polynucleotide that encodes a polypeptide having the target
activity. In certain embodiments, an activity can be added or
increased by subjecting a host microorganism to a selective
environment and screening for microorganisms that have a detectable
level of the target activity. Examples of a selective environment
include, without limitation, a medium containing a substrate that a
host organism can process and a medium lacking a substrate that a
host organism can process.
[0174] An altered activity sometimes is an activity detectable in a
host organism and is reduced, inhibited or removed (i.e., not
detectable) in an engineered organism. An activity may be reduced
or removed by decreasing the number of copies of a polynucleotide
that encodes a polypeptide having a target activity, in some
embodiments. In some embodiments, an activity can be reduced or
removed by (i) inserting a polynucleotide within a polynucleotide
that encodes a polypeptide having the target activity (disruptive
insertion), and/or (ii) removing a portion of or all of a
polynucleotide that encodes a polypeptide having the target
activity (deletion or knock out, respectively). In certain
embodiments, an activity can be reduced or removed by inserting
into a host microorganism a heterologous polynucleotide that is (i)
operably linked to another polynucleotide that encodes a
polypeptide having the target activity, and (ii) down regulates
production of the polynucleotide. Thus, an activity can be reduced
or removed by inserting or modifying a regulatory polynucleotide
operably linked to another polynucleotide that encodes a
polypeptide having the target activity.
[0175] An activity also can be reduced or removed by (i) inhibiting
a polynucleotide that encodes a polypeptide having the activity or
(ii) inhibiting a polynucleotide operably linked to another
polynucleotide that encodes a polypeptide having the activity. A
polynucleotide can be inhibited by a suitable technique known in
the art, such as by contacting an RNA encoded by the polynucleotide
with a specific inhibitory RNA (e.g., RNAi, siRNA, ribozyme). An
activity also can be reduced or removed by contacting a polypeptide
having the activity with a molecule that specifically inhibits the
activity (e.g., enzyme inhibitor, antibody). In certain
embodiments, an activity can be reduced or removed by subjecting a
host microorganism to a selective environment and screening for
microorganisms that have a reduced level or removal of the target
activity.
[0176] In some embodiments, an untranslated ribonucleic acid, or a
cDNA can be used to reduce the expression of a particular activity
or enzyme. For example, a microorganism can be engineered by
genetic modification to express a nucleic acid reagent that reduces
the expression of an activity by producing an RNA molecule that is
partially or substantially homologous to a nucleic acid sequence of
interest which encodes the activity of interest. The RNA molecule
can bind to the nucleic acid sequence of interest and inhibit the
nucleic acid sequence from performing its natural function, in
certain embodiments. In some embodiments, the RNA may alter the
nucleic acid sequence of interest which encodes the activity of
interest in a manner that the nucleic acid sequence of interest is
no longer capable of performing its natural function (e.g., the
action of a ribozyme for example).
[0177] In certain embodiments, nucleotide sequences sometimes are
added to, modified or removed from one or more of the nucleic acid
reagent elements, such as the promoter, 5'UTR, target sequence, or
3'UTR elements, to enhance, potentially enhance, reduce, or
potentially reduce transcription and/or translation before or after
such elements are incorporated in a nucleic acid reagent. In some
embodiments, one or more of the following sequences may be modified
or removed if they are present in a 5'UTR: a sequence that forms a
stable secondary structure (e.g., quadruplex structure or stem loop
stem structure (e.g., EMBL sequences X12949, AF274954, AF139980,
AF152961, S95936, U194144, AF116649 or substantially identical
sequences that form such stem loop stem structures)); a translation
initiation codon upstream of the target nucleotide sequence start
codon; a stop codon upstream of the target nucleotide sequence
translation initiation codon; an ORF upstream of the target
nucleotide sequence translation initiation codon; an iron
responsive element (IRE) or like sequence; and a 5' terminal
oligopyrimidine tract (TOP, e.g., consisting of 5-15 pyrimidines
adjacent to the cap). A translational enhancer sequence and/or an
internal ribosome entry site (IRES) sometimes is inserted into a
5'UTR (e.g., EMBL nucleotide sequences J04513, X87949, M95825,
M12783, AF025841, AF013263, AF006822, M17169, M13440, M22427,
D14838 and M17446 and substantially identical nucleotide
sequences).
[0178] An AU-rich element (ARE, e.g., AUUUA repeats) and/or
splicing junction that follows a non-sense codon sometimes is
removed from or modified in a 3'UTR. A polyadenosine tail sometimes
is inserted into a 3'UTR if none is present, sometimes is removed
if it is present, and adenosine moieties sometimes are added to or
removed from a polyadenosine tail present in a 3'UTR. Thus, some
embodiments are directed to a process comprising: determining
whether any nucleotide sequences that increase, potentially
increase, reduce or potentially reduce translation efficiency are
present in the elements, and adding, removing or modifying one or
more of such sequences if they are identified. Certain embodiments
are directed to a process comprising: determining whether any
nucleotide sequences that increase or potentially increase
translation efficiency are not present in the elements, and
incorporating such sequences into the nucleic acid reagent.
[0179] In some embodiments, an activity can be altered by modifying
the nucleotide sequence of an ORF. An ORF sometimes is mutated or
modified (for example, by point mutation, deletion mutation,
insertion mutation, PCR based mutagenesis and the like) to alter,
enhance or increase, reduce, substantially reduce or eliminate the
activity of the encoded protein or peptide. The protein or peptide
encoded by a modified ORF sometimes is produced in a lower amount
or may not be produced at detectable levels, and in other
embodiments, the product or protein encoded by the modified ORF is
produced at a higher level (e.g., codons sometimes are modified so
they are compatible with tRNA's preferentially used in the host
organism or engineered organism). To determine the relative
activity, the activity from the product of the mutated ORF (or cell
containing it) can be compared to the activity of the product or
protein encoded by the unmodified ORF (or cell containing it).
[0180] In some embodiments, an ORF nucleotide sequence sometimes is
mutated or modified to alter the triplet nucleotide sequences used
to encode amino acids (e.g., amino acid codon triplets, for
example). Modification of the nucleotide sequence of an ORF to
alter codon triplets sometimes is used to change the codon found in
the original sequence to better match the preferred codon usage of
the organism in which the ORF or nucleic acid reagent will be
expressed. The codon usage, and therefore the codon triplets
encoded by a nucleic acid sequence, in bacteria may be different
from the preferred codon usage in eukaryotes, like yeast or plants
for example. Preferred codon usage also may be different between
bacterial species. In certain embodiments an ORF nucleotide
sequences sometimes is modified to eliminate codon pairs and/or
eliminate mRNA secondary structures that can cause pauses during
translation of the mRNA encoded by the ORF nucleotide sequence.
Translational pausing sometimes occurs when nucleic acid secondary
structures exist in an mRNA, and sometimes occurs due to the
presence of codon pairs that slow the rate of translation by
causing ribosomes to pause. In some embodiments, the use of lower
abundance codon triplets can reduce translational pausing due to a
decrease in the pause time needed to load a charged tRNA into the
ribosome translation machinery. Therefore, to increase
transcriptional and translational efficiency in bacteria (e.g.,
where transcription and translation are concurrent, for example) or
to increase translational efficiency in eukaryotes (e.g., where
transcription and translation are functionally separated), the
nucleotide sequence of a nucleotide sequence of interest can be
altered to better suit the transcription and/or translational
machinery of the host and/or genetically modified microorganism. In
certain embodiments, slowing the rate of translation by the use of
lower abundance codons, which slow or pause the ribosome, can lead
to higher yields of the desired product due to an increase in
correctly folded proteins and a reduction in the formation of
inclusion bodies.
[0181] Codons can be altered and optimized according to the
preferred usage by a given organism by determining the codon
distribution of the nucleotide sequence donor organism and
comparing the distribution of codons to the distribution of codons
in the recipient or host organism. Techniques described herein
(e.g., site directed mutagenesis and the like) can then be used to
alter the codons accordingly. Comparisons of codon usage can be
done by hand, or using nucleic acid analysis software commercially
available to the artisan.
[0182] Modification of the nucleotide sequence of an ORF also can
be used to correct codon triplet sequences that have diverged in
different organisms. For example, certain yeast (e.g., C.
tropicalis and C. maltosa) use the amino acid triplet CUG (e.g.,
CTG in the DNA sequence) to encode serine. CUG typically encodes
leucine in most organisms. In order to maintain the correct amino
acid in the resultant polypeptide or protein, the CUG codon must be
altered to reflect the organism in which the nucleic acid reagent
will be expressed. Thus, if an ORF from a bacterial donor is to be
expressed in either Candida yeast strain mentioned above, the
heterologous nucleotide sequence must first be altered or modified
to the appropriate leucine codon. Therefore, in some embodiments,
the nucleotide sequence of an ORF sometimes is altered or modified
to correct for differences that have occurred in the evolution of
the amino acid codon triplets between different organisms. In some
embodiments, the nucleotide sequence can be left unchanged at a
particular amino acid codon, if the amino acid encoded is a
conservative or neutral change in amino acid when compared to the
originally encoded amino acid.
[0183] In some embodiments, an activity can be altered by modifying
translational regulation signals, like a stop codon for example. A
stop codon at the end of an ORF sometimes is modified to another
stop codon, such as an amber stop codon described above. In some
embodiments, a stop codon is introduced within an ORF, sometimes by
insertion or mutation of an existing codon. An ORF comprising a
modified terminal stop codon and/or internal stop codon often is
translated in a system comprising a suppressor tRNA that recognizes
the stop codon. An ORF comprising a stop codon sometimes is
translated in a system comprising a suppressor tRNA that
incorporates an unnatural amino acid during translation of the
target protein or target peptide. Methods for incorporating
unnatural amino acids into a target protein or peptide are known,
which include, for example, processes utilizing a heterologous
tRNA/synthetase pair, where the tRNA recognizes an amber stop codon
and is loaded with an unnatural amino acid (e.g., World Wide Web
URL iupac.org/news/prize/2003/wang.pdf).
[0184] Depending on the portion of a nucleic acid reagent (e.g.,
Promoter, 5' or 3' UTR, ORI, ORF, and the like) chosen for
alteration (e.g., by mutagenesis, introduction or deletion, for
example) the modifications described above can alter a given
activity by (i) increasing or decreasing feedback inhibition
mechanisms, (ii) increasing or decreasing promoter initiation,
(iii) increasing or decreasing translation initiation, (iv)
increasing or decreasing translational efficiency, (v) modifying
localization of peptides or products expressed from nucleic acid
reagents described herein, or (vi) increasing or decreasing the
copy number of a nucleotide sequence of interest, (vii) expression
of an anti-sense RNA, RNAi, siRNA, ribozyme and the like. In some
embodiments, alteration of a nucleic acid reagent or nucleotide
sequence can alter a region involved in feedback inhibition (e.g.,
5' UTR, promoter and the like). A modification sometimes is made
that can add or enhance binding of a feedback regulator and
sometimes a modification is made that can reduce, inhibit or
eliminate binding of a feedback regulator.
[0185] In certain embodiments, alteration of a nucleic acid reagent
or nucleotide sequence can alter sequences involved in
transcription initiation (e.g., promoters, 5' UTR, and the like). A
modification sometimes can be made that can enhance or increase
initiation from an endogenous or heterologous promoter element. A
modification sometimes can be made that removes or disrupts
sequences that increase or enhance transcription initiation,
resulting in a decrease or elimination of transcription from an
endogenous or heterologous promoter element.
[0186] In some embodiments, alteration of a nucleic acid reagent or
nucleotide sequence can alter sequences involved in translational
initiation or translational efficiency (e.g., 5' UTR, 3' UTR, codon
triplets of higher or lower abundance, translational terminator
sequences and the like, for example). A modification sometimes can
be made that can increase or decrease translational initiation,
modifying a ribosome binding site for example. A modification
sometimes can be made that can increase or decrease translational
efficiency. Removing or adding sequences that form hairpins and
changing codon triplets to a more or less preferred codon are
non-limiting examples of genetic modifications that can be made to
alter translation initiation and translation efficiency.
[0187] In certain embodiments, alteration of a nucleic acid reagent
or nucleotide sequence can alter sequences involved in localization
of peptides, proteins or other desired products (e.g., adipic acid,
for example). A modification sometimes can be made that can alter,
add or remove sequences responsible for targeting a polypeptide,
protein or product to an intracellular organelle, the periplasm,
cellular membranes, or extracellularly. Transport of a heterologous
product to a different intracellular space or extracellularly
sometimes can reduce or eliminate the formation of inclusion bodies
(e.g., insoluble aggregates of the desired product).
[0188] In some embodiments, alteration of a nucleic acid reagent or
nucleotide sequence can alter sequences involved in increasing or
decreasing the copy number of a nucleotide sequence of interest. A
modification sometimes can be made that increases or decreases the
number of copies of an ORF stably integrated into the genome of an
organism or on an epigenetic nucleic acid reagent. Non-limiting
examples of alterations that can increase the number of copies of a
sequence of interest include, adding copies of the sequence of
interest by duplication of regions in the genome (e.g., adding
additional copies by recombination or by causing gene amplification
of the host genome, for example), cloning additional copies of a
sequence onto a nucleic acid reagent, or altering an ORI to
increase the number of copies of an epigenetic nucleic acid
reagent. Non-limiting examples of alterations that can decrease the
number of copies of a sequence of interest include, removing copies
of the sequence of interest by deletion or disruption of regions in
the genome, removing additional copies of the sequence from
epigenetic nucleic acid reagents, or altering an ORI to decrease
the number of copies of an epigenetic nucleic acid reagent.
[0189] In certain embodiments, increasing or decreasing the
expression of a nucleotide sequence of interest can also be
accomplished by altering, adding or removing sequences involved in
the expression of an anti-sense RNA, RNAi, siRNA, ribozyme and the
like. The methods described above can be used to modify expression
of anti-sense RNA, RNAi, siRNA, ribozyme and the like.
[0190] The methods and nucleic acid reagents described herein can
be used to generate genetically modified microorganisms with
altered activities in cellular processes involved in adipic acid
synthesis. In some embodiments, an engineered microorganism
described herein may comprise a heterologous polynucleotide
encoding a polypeptide having 6-oxohexanoic acid dehydrogenase
activity, and in certain embodiments, an engineered microorganism
described herein may comprise a heterologous polynucleotide
encoding a polypeptide having omega oxo fatty acid dehydrogenase
activity. In some embodiments, an engineered microorganism
described herein may comprise a heterologous polynucleotide
encoding a polypeptide having 6-hydroxyhexanoic acid dehydrogenase
activity, and in certain embodiments, an engineered microorganism
described herein may comprise a heterologous polynucleotide
encoding a polypeptide having omega hydroxyl fatty acid
dehydrogenase activity. In some embodiments, the heterologous
polynucleotide can be from a bacterium. In some embodiments, the
bacterium can be an Acinetobacter, Nocardia, Pseudomonas or
Xanthobacter bacterium.
[0191] In certain embodiments, an engineered microorganism
described herein may comprise a heterologous polynucleotide
encoding a polypeptide having hexanoate synthase subunit A
activity. In some embodiments, an engineered microorganism
described herein may comprise a heterologous polynucleotide
encoding a polypeptide having hexanoate synthase subunit B
activity. In certain embodiments, the heterologous polynucleotide
independently is selected from a fungus.
[0192] In some embodiments, the fungus can be an Aspergillus
fungus. In certain embodiments, the Aspergillus fungus is A.
parasiticus.
[0193] In some embodiments, an engineered microorganism described
herein may comprise a heterologous polynucleotide encoding a
polypeptide having monooxygenase activity. In certain embodiments,
the heterologous polynucleotide can be from a bacterium. In some
embodiments, the bacterium can be a Bacillus bacterium. In certain
embodiments, the Bacillus bacterium is B. megaterium.
[0194] In some embodiments, an engineered microorganism described
herein may comprise a genetic modification that results in primary
hexanoate usage by monooxygenase activity. In certain embodiments,
the genetic modification can reduce a polyketide synthase activity.
In some embodiments, the engineered microorganism can be a
eukaryote. In certain embodiments, the eukaryote can be a yeast. In
some embodiments, the eukaryote may be a fungus. In certain
embodiments, the yeast can be a Candida yeast. In some embodiments,
the Candida yeast may be C. troplicalis. In certain embodiments,
the fungus can be a Yarrowia fungus. In some embodiments the
Yarrowia fungus may be Y. lipolytica. In certain embodiments, the
fungus can be an Aspergillus fungus. In some embodiments, the
Aspergillus fungus may be A. parasiticus or A. nidulans.
[0195] In certain embodiments, an engineered microorganism
described herein may comprise a genetic modification that reduces
6-hydroxyhexanoic acid conversion. In some embodiments, the genetic
modification can reduce 6-hydroxyhexanoic acid dehydrogenase
activity. In certain embodiments, an engineered microorganism
described herein may comprise a genetic modification that reduces
beta-oxidation activity. In some embodiments, the genetic
modification can reduce a target activity described herein.
[0196] Engineered microorganisms that produce adipic acid, as
described herein, can comprise an altered monooxygenase activity,
in certain embodiments. In some embodiments, the engineered
microorganism described herein may comprise a genetic modification
that alters the monooxygenase activity. In certain embodiments, the
genetic modification can result in substantial hexanoate usage by
the monooxygenase activity. In some embodiments, the genetic
modification can reduce a polyketide synthase activity. In certain
embodiments, the engineered microorganism described herein can
comprise a heterologous polynucleotide encoding a polypeptide
having monooxygenase activity. In certain embodiments, the
heterologous polynucleotide can be from a bacterium. In some
embodiments, the bacterium can be a Bacillus bacterium. In certain
embodiments, the Bacillus bacterium is B. megaterium.
[0197] In some embodiments, the engineered microorganism described
herein may comprise an altered hexanoate synthase activity. In
certain embodiments, the altered hexanoate synthase activity is an
altered hexanoate synthase subunit A activity, altered hexanoate
synthase subunit B activity, or altered hexanoate synthase subunit
A activity and altered hexanoate synthase subunit B activity. In
some embodiments, the engineered microorganism may comprise a
genetic alteration that adds or increases hexanoate synthase
activity. In certain embodiments, the engineered microorganism may
comprise a heterologous polynucleotide encoding a polypeptide
having hexanoate synthase activity. In some embodiments, the
heterologous polynucleotide can be from a fungus. In certain
embodiments, the fungus can be an Aspergillus fungus. In some
embodiments, the Aspergillus fungus is A. parasiticus.
[0198] Engineered microorganisms that produce adipic acid, as
described herein, can comprise an altered thioesterase activity, in
certain embodiments. In some embodiments, the engineered
microorganism may comprise a genetic modification that adds or
increases the thioesterase activity. In certain embodiments, the
engineered microorganism may comprise a heterologous polynucleotide
encoding a polypeptide having thioesterase activity.
[0199] In some embodiments, the engineered microorganism with an
altered thioesterase activity may comprise an altered 6-oxohexanoic
acid dehydrogenase activity, or an altered omega oxo fatty acid
dehydrogenase activity. In certain embodiments, the engineered
microorganism with an altered thioesterase activity may comprise a
genetic modification that adds or increases 6-oxohexanoic acid
dehydrogenase activity, or a genetic modification that adds or
increases omega oxo fatty acid dehydrogenase activity. In some
embodiments, the engineered microorganism may comprise a
heterologous polynucleotide encoding a polypeptide having altered
6-oxohexanoic acid dehydrogenase activity, and in some embodiments,
the engineered microorganism may comprise a heterologous
polynucleotide encoding a polypeptide having altered omega oxo
fatty acid dehydrogenase activity. In certain embodiments, the
heterologous polynucleotide can be from a bacterium. In some
embodiments, the bacterium can be an Acinetobacter, Nocardia,
Pseudomonas or Xanthobacter bacterium.
[0200] Engineered microorganisms that produce adipic acid, as
described herein, can comprise an altered 6-hydroxyhexanoic acid
dehydrogenase activity, in certain embodiments, and in some
embodiments, can comprise an altered omega hydroxyl fatty acid
dehydrogenase activity. In certain embodiments, the engineered
microorganism may comprise a genetic modification that adds or
increases the 6-hydroxyhexanoic acid dehydrogenase activity and in
some embodiments the engineered microorganism may comprise a
genetic modification that adds or increases the omega hydroxyl
fatty acid dehydrogenase activity. In certain embodiments, the
engineered microorganism may comprise a heterologous polynucleotide
encoding a polypeptide having altered 6-hydroxyhexanoic acid
dehydrogenase activity, and in some embodiments, the engineered
microorganism may comprise a heterologous polynucleotide encoding a
polypeptide having altered omega hydroxyl fatty acid dehydrogenase
activity. In some embodiments, the heterologous polynucleotide is
from a bacterium. In certain embodiments, the bacterium can be an
Acinetobacter, Nocardia, Pseudomonas or Xanthobacter bacterium. In
some embodiments, the engineered microorganism can be a eukaryote.
In certain embodiments, the eukaryote can be a yeast. In some
embodiments, the eukaryote may be a fungus. In certain embodiments,
the yeast can be a Candida yeast. In some embodiments, the Candida
yeast may be C. troplicalis. In certain embodiments, the fungus can
be a Yarrowia fungus. In some embodiments the Yarrowia fungus may
be Y. lipolytica. In certain embodiments, the fungus can be an
Aspergillus fungus. In some embodiments, the Aspergillus fungus may
be A. parasiticus or A. nidulans.
[0201] In some embodiments, an engineered microorganism as
described above may comprise a genetic modification that reduces
6-hydroxyhexanoic acid conversion. In certain embodiments, the
genetic modification can reduce 6-hydroxyhexanoic acid
dehydrogenase activity. In some embodiments the genetic may reduce
beta-oxidation activity. In certain embodiments, the genetic
modification may reduce a target activity described herein.
[0202] Engineered microorganisms can be prepared by altering,
introducing or removing nucleotide sequences in the host genome or
in stably maintained epigenetic nucleic acid reagents, as noted
above. The nucleic acid reagents use to alter, introduce or remove
nucleotide sequences in the host genome or epigenetic nucleic acids
can be prepared using the methods described herein or available to
the artisan.
[0203] Nucleic acid sequences having a desired activity can be
isolated from cells of a suitable organism using lysis and nucleic
acid purification procedures described in a known reference manual
(e.g., Maniatis, T., E. F. Fritsch and J. Sambrook (1982) Molecular
Cloning: a Laboratory Manual; Cold Spring Harbor Laboratory, Cold
Spring Harbor, N.Y.) or using commercially available cell lysis and
DNA purification reagents and kits. In some embodiments, nucleic
acids used to engineer microorganisms can be provided for
conducting methods described herein after processing of the
organism containing the nucleic acid. For example, the nucleic acid
of interest may be extracted, isolated, purified or amplified from
a sample (e.g., from an organism of interest or culture containing
a plurality of organisms of interest, like yeast or bacteria for
example). The term "isolated" as used herein refers to nucleic acid
removed from its original environment (e.g., the natural
environment if it is naturally occurring, or a host cell if
expressed exogenously), and thus is altered "by the hand of man"
from its original environment. An isolated nucleic acid generally
is provided with fewer non-nucleic acid components (e.g., protein,
lipid) than the amount of components present in a source sample. A
composition comprising isolated sample nucleic acid can be
substantially isolated (e.g., about 90%, 91%, 92%, 93%, 94%, 95%,
96%, 97%, 98%, 99% or greater than 99% free of non-nucleic acid
components). The term "purified" as used herein refers to sample
nucleic acid provided that contains fewer nucleic acid species than
in the sample source from which the sample nucleic acid is derived.
A composition comprising sample nucleic acid may be substantially
purified (e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99% or greater than 99% free of other nucleic acid species). The
term "amplified" as used herein refers to subjecting nucleic acid
of a cell, organism or sample to a process that linearly or
exponentially generates amplicon nucleic acids having the same or
substantially the same nucleotide sequence as the nucleotide
sequence of the nucleic acid in the sample, or portion thereof. As
noted above, the nucleic acids used to prepare nucleic acid
reagents as described herein can be subjected to fragmentation or
cleavage.
[0204] Amplification of nucleic acids is sometimes necessary when
dealing with organisms that are difficult to culture. Where
amplification may be desired, any suitable amplification technique
can be utilized. Non-limiting examples of methods for amplification
of polynucleotides include, polymerase chain reaction (PCR);
ligation amplification (or ligase chain reaction (LCR));
amplification methods based on the use of Q-beta replicase or
template-dependent polymerase (see US Patent Publication Number
US20050287592); helicase-dependant isothermal amplification
(Vincent et al., "Helicase-dependent isothermal DNA amplification".
EMBO reports 5 (8): 795-800 (2004)); strand displacement
amplification (SDA); thermophilic SDA nucleic acid sequence based
amplification (3SR or NASBA) and transcription-associated
amplification (TAA). Non-limiting examples of PCR amplification
methods include standard PCR, AFLP-PCR, Allele-specific PCR,
Alu-PCR, Asymmetric PCR, Colony PCR, Hot start PCR, Inverse PCR
(IPCR), In situ PCR (ISH), Intersequence-specific PCR (ISSR-PCR),
Long PCR, Multiplex PCR, Nested PCR, Quantitative PCR, Reverse
Transcriptase PCR(RT-PCR), Real Time PCR, Single cell PCR, Solid
phase PCR, combinations thereof, and the like. Reagents and
hardware for conducting PCR are commercially available.
[0205] Protocols for conducting the various type of PCR listed
above are readily available to the artisan. PCR conditions can be
dependent upon primer sequences, target abundance, and the desired
amount of amplification, and therefore, one of skill in the art may
choose from a number of PCR protocols available (see, e.g., U.S.
Pat. Nos. 4,683,195 and 4,683,202; and PCR Protocols: A Guide to
Methods and Applications, Innis et al., eds, 1990. PCR often is
carried out as an automated process with a thermostable enzyme. In
this process, the temperature of the reaction mixture is cycled
through a denaturing region, a primer-annealing region, and an
extension reaction region automatically. Machines specifically
adapted for this purpose are commercially available. A non-limiting
example of a PCR protocol that may be suitable for embodiments
described herein is, treating the sample at 95.degree. C. for 5
minutes; repeating forty-five cycles of 95.degree. C. for 1 minute,
59.degree. C. for 1 minute, 10 seconds, and 72.degree. C. for 1
minute 30 seconds; and then treating the sample at 72.degree. C.
for 5 minutes. Additional PCR protocols are described in the
example section. Multiple cycles frequently are performed using a
commercially available thermal cycler. Suitable isothermal
amplification processes known and selected by the person of
ordinary skill in the art also may be applied, in certain
embodiments. In some embodiments, nucleic acids encoding
polypeptides with a desired activity can be isolated by amplifying
the desired sequence from an organism having the desired activity
using oligonucleotides or primers designed based on sequences
described herein.
[0206] Amplified, isolated and/or purified nucleic acids can be
cloned into the recombinant DNA vectors described in Figures herein
or into suitable commercially available recombinant DNA vectors.
Cloning of nucleic acid sequences of interest into recombinant DNA
vectors can facilitate further manipulations of the nucleic acids
for preparation of nucleic acid reagents, (e.g., alteration of
nucleotide sequences by mutagenesis, homologous recombination,
amplification and the like, for example). Standard cloning
procedures (e.g., enzymic digestion, ligation, and the like) are
known (e.g., described in Maniatis, T., E. F. Fritsch and J.
Sambrook (1982) Molecular Cloning: a Laboratory Manual; Cold Spring
Harbor Laboratory, Cold Spring Harbor, N.Y.).
[0207] In some embodiments, nucleic acid sequences prepared by
isolation or amplification can be used, without any further
modification, to add an activity to a microorganism and thereby
create a genetically modified or engineered microorganism. In
certain embodiments, nucleic acid sequences prepared by isolation
or amplification can be genetically modified to alter (e.g.,
increase or decrease, for example) a desired activity. In some
embodiments, nucleic acids, used to add an activity to an organism,
sometimes are genetically modified to optimize the heterologous
polynucleotide sequence encoding the desired activity (e.g.,
polypeptide or protein, for example). The term "optimize" as used
herein can refer to alteration to increase or enhance expression by
preferred codon usage. The term optimize can also refer to
modifications to the amino acid sequence to increase the activity
of a polypeptide or protein, such that the activity exhibits a
higher catalytic activity as compared to the "natural" version of
the polypeptide or protein.
[0208] Nucleic acid sequences of interest can be genetically
modified using methods known in the art. Mutagenesis techniques are
particularly useful for small scale (e.g., 1, 2, 5, 10 or more
nucleotides) or large scale (e.g., 50, 100, 150, 200, 500, or more
nucleotides) genetic modification. Mutagenesis allows the artisan
to alter the genetic information of an organism in a stable manner,
either naturally (e.g., isolation using selection and screening) or
experimentally by the use of chemicals, radiation or inaccurate DNA
replication (e.g., PCR mutagenesis). In some embodiments, genetic
modification can be performed by whole scale synthetic synthesis of
nucleic acids, using a native nucleotide sequence as the reference
sequence, and modifying nucleotides that can result in the desired
alteration of activity. Mutagenesis methods sometimes are specific
or targeted to specific regions or nucleotides (e.g., site-directed
mutagenesis, PCR-based site-directed mutagenesis, and in vitro
mutagenesis techniques such as transplacement and in vivo
oligonucleotide site-directed mutagenesis, for example).
Mutagenesis methods sometimes are non-specific or random with
respect to the placement of genetic modifications (e.g., chemical
mutagenesis, insertion element (e.g., insertion or transposon
elements) and inaccurate PCR based methods, for example).
[0209] Site directed mutagenesis is a procedure in which a specific
nucleotide or specific nucleotides in a DNA molecule are mutated or
altered. Site directed mutagenesis typically is performed using a
nucleic acid sequence of interest cloned into a circular plasmid
vector. Site-directed mutagenesis requires that the wild type
sequence be known and used a platform for the genetic alteration.
Site-directed mutagenesis sometimes is referred to as
oligonucleotide-directed mutagenesis because the technique can be
performed using oligonucleotides which have the desired genetic
modification incorporated into the complement a nucleotide sequence
of interest. The wild type sequence and the altered nucleotide are
allowed to hybridize and the hybridized nucleic acids are extended
and replicated using a DNA polymerase. The double stranded nucleic
acids are introduced into a host (e.g., E. coli, for example) and
further rounds of replication are carried out in vivo. The
transformed cells carrying the mutated nucleic acid sequence are
then selected and/or screened for those cells carrying the
correctly mutagenized sequence. Cassette mutagenesis and PCR-based
site-directed mutagenesis are further modifications of the
site-directed mutagenesis technique. Site-directed mutagenesis can
also be performed in vivo (e.g., transplacement "pop-in pop-out",
In vivo site-directed mutagenesis with synthetic oligonucleotides
and the like, for example).
[0210] PCR-based mutagenesis can be performed using PCR with
oligonucleotide primers that contain the desired mutation or
mutations. The technique functions in a manner similar to standard
site-directed mutagenesis, with the exception that a thermocycler
and PCR conditions are used to replace replication and selection of
the clones in a microorganism host. As PCR-based mutagenesis also
uses a circular plasmid vector, the amplified fragment (e.g.,
linear nucleic acid molecule) containing the incorporated genetic
modifications can be separated from the plasmid containing the
template sequence after a sufficient number of rounds of
thermocycler amplification, using standard electrophorectic
procedures. A modification of this method uses linear amplification
methods and a pair of mutagenic primers that amplify the entire
plasmid. The procedure takes advantage of the E. coli Dam methylase
system which causes DNA replicated in vivo to be sensitive to the
restriction endonucleases DpnI. PCR synthesized DNA is not
methylated and is therefore resistant to DpnI. This approach allows
the template plasmid to be digested, leaving the genetically
modified, PCR synthesized plasmids to be isolated and transformed
into a host bacteria for DNA repair and replication, thereby
facilitating subsequent cloning and identification steps. A certain
amount of randomness can be added to PCR-based sited directed
mutagenesis by using partially degenerate primers.
[0211] Recombination sometimes can be used as a tool for
mutagenesis. Homologous recombination allows the artisan to
specifically target regions of known sequence for insertion of
heterologous nucleotide sequences using the host organisms natural
DNA replication and repair enzymes. Homologous recombination
methods sometimes are referred to as "pop in pop out" mutagenesis,
transplacement, knock out mutagenesis or knock in mutagenesis.
Integration of a nucleic acid sequence into a host genome is a
single cross over event, which inserts the entire nucleic acid
reagent (e.g., pop in). A second cross over event excises all but a
portion of the nucleic acid reagent, leaving behind a heterologous
sequence, often referred to as a "footprint" (e.g., pop out).
Mutagenesis by insertion (e.g., knock in) or by double
recombination leaving behind a disrupting heterologous nucleic acid
(e.g., knock out) both server to disrupt or "knock out" the
function of the gene or nucleic acid sequence in which insertion
occurs. By combining selectable markers and/or auxotrophic markers
with nucleic acid reagents designed to provide the appropriate
nucleic acid target sequences, the artisan can target a selectable
nucleic acid reagent to a specific region, and then select for
recombination events that "pop out" a portion of the inserted
(e.g., "pop in") nucleic acid reagent.
[0212] Such methods take advantage of nucleic acid reagents that
have been specifically designed with known target nucleic acid
sequences at or near a nucleic acid or genomic region of interest.
Popping out typically leaves a "foot print" of left over sequences
that remain after the recombination event. The left over sequence
can disrupt a gene and thereby reduce or eliminate expression of
that gene. In some embodiments, the method can be used to insert
sequences, upstream or downstream of genes that can result in an
enhancement or reduction in expression of the gene. In certain
embodiments, new genes can be introduced into the genome of a host
organism using similar recombination or "pop in" methods. An
example of a yeast recombination system using the ura3 gene and
5-FOA were described briefly above and further detail is presented
herein.
[0213] A method for modification is described in Alani et al., "A
method for gene disruption that allows repeated use of URA3
selection in the construction of multiply disrupted yeast strains",
Genetics 116(4):541-545 August 1987. The original method uses a
Ura3 cassette with 1000 base pairs (bp) of the same nucleotide
sequence cloned in the same orientation on either side of the URA3
cassette. Targeting sequences of about 50 bp are added to each side
of the construct. The double stranded targeting sequences are
complementary to sequences in the genome of the host organism. The
targeting sequences allow site-specific recombination in a region
of interest. The modification of the original technique replaces
the two 1000 bp sequence direct repeats with two 200 bp direct
repeats. The modified method also uses 50 bp targeting sequences.
The modification reduces or eliminates recombination of a second
knock out into the 1000 bp repeat left behind in a first
mutagenesis, therefore allowing multiply knocked out yeast.
Additionally, the 200 bp sequences used herein are uniquely
designed, self-assembling sequences that leave behind identifiable
footprints. The technique used to design the sequences incorporate
design features such as low identity to the yeast genome, and low
identity to each other. Therefore a library of the self-assembling
sequences can be generated to allow multiple knockouts in the same
organism, while reducing or eliminating the potential for
integration into a previous knockout.
[0214] As noted above, the URA3 cassette makes use of the toxicity
of 5-FOA in yeast carrying a functional URA3 gene. Uracil synthesis
deficient yeast are transformed with the modified URA3 cassette,
using standard yeast transformation protocols, and the transformed
cells are plated on minimal media minus uracil. In some
embodiments, PCR can be used to verify correct insertion into the
region of interest in the host genome, and certain embodiments the
PCR step can be omitted. Inclusion of the PCR step can reduce the
number of transformants that need to be counter selected to "pop
out" the URA3 cassette. The transformants (e.g., all or the ones
determined to be correct by PCR, for example) can then be
counter-selected on media containing 5-FOA, which will select for
recombination out (e.g., popping out) of the URA3 cassette, thus
rendering the yeast ura3 deficient again, and resistant to 5-FOA
toxicity. Targeting sequences used to direct recombination events
to specific regions are presented herein. A modification of the
method described above can be used to integrate genes in to the
chromosome, where after recombination a functional gene is left in
the chromosome next to the 200 bp footprint.
[0215] In some embodiments, other auxotrophic or dominant selection
markers can be used in place of URA3 (e.g., an auxotrophic
selectable marker), with the appropriate change in selection media
and selection agents. Auxotrophic selectable markers are used in
strains deficient for synthesis of a required biological molecule
(e.g., amino acid or nucleoside, for example). Non-limiting
examples of additional auxotrophic markers include; HIS3, TRP1,
LEU2, LEU2-d, and LYS2. Certain auxotrophic markers (e.g., URA3 and
LYS2) allow counter selection to select for the second
recombination event that pops out all but one of the direct repeats
of the recombination construct. HIS3 encodes an activity involved
in histidine synthesis. TRP1 encodes an activity involved in
tryptophan synthesis. LEU2 encodes an activity involved in leucine
synthesis. LEU2-d is a low expression version of LEU2 that selects
for increased copy number (e.g., gene or plasmid copy number, for
example) to allow survival on minimal media without leucine. LYS2
encodes an activity involved in lysine synthesis, and allows
counter selection for recombination out of the LYS2 gene using
alpha-amino adipate (.alpha.-amino adipate).
[0216] Dominant selectable markers are useful because they also
allow industrial and/or prototrophic strains to be used for genetic
manipulations. Additionally, dominant selectable markers provide
the advantage that rich medium can be used for plating and culture
growth, and thus growth rates are markedly increased. Non-limiting
examples of dominant selectable markers include; Tn903 kan.sup.r,
Cm.sup.r, Hyg.sup.r, CUP1, and DHFR. Tn903 kan.sup.r encodes an
activity involved in kanamycin antibiotic resistance (e.g.,
typically neomycin phosphotransferase II or NPTII, for example).
Cmr encodes an activity involved in chloramphenicol antibiotic
resistance (e.g., typically chloramphenicol acetyl transferase or
CAT, for example). Hygr encodes an activity involved in hygromycin
resistance by phosphorylation of hygromycin B (e.g., hygromycin
phosphotransferase, or HPT). CUP1 encodes an activity involved in
resistance to heavy metal (e.g., copper, for example) toxicity.
DHFR encodes a dihydrofolate reductase activity which confers
resistance to methotrexate and sulfanilamde compounds.
[0217] In contrast to site-directed or specific mutagenesis, random
mutagenesis does not require any sequence information and can be
accomplished by a number of widely different methods. Random
mutagenesis often is used to create mutant libraries that can be
used to screen for the desired genotype or phenotype. Non-limiting
examples of random mutagenesis include; chemical mutagenesis,
UV-induced mutagenesis, insertion element or transposon-mediated
mutagenesis, DNA shuffling, error-prone PCR mutagenesis, and the
like.
[0218] Chemical mutagenesis often involves chemicals like ethyl
methanesulfonate (EMS), nitrous acid, mitomycin C,
N-methyl-N-nitrosourea (MNU), diepoxybutane (DEB),
1,2,7,8-diepoxyoctane (DEO), methyl methane sulfonate (MMS),
N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), 4-nitroquinoline
1-oxide (4-NQO),
2-methyloxy-6-chloro-9(3-[ethyl-2-chloroethyl]-aminopropylamino)-acridine-
dihydrochloride (ICR-170), 2-amino purine (2AP), and hydroxylamine
(HA), provided herein as non-limiting examples. These chemicals can
cause base-pair substitutions, frameshift mutations, deletions,
transversion mutations, transition mutations, incorrect
replication, and the like. In some embodiments, the mutagenesis can
be carried out in vivo. Sometimes the mutagenic process involves
the use of the host organisms DNA replication and repair mechanisms
to incorporate and replicate the mutagenized base or bases. Another
type of chemical mutagenesis involves the use of base-analogs. The
use of base-analogs cause incorrect base pairing which in the
following round of replication is corrected to a mismatched
nucleotide when compared to the starting sequence. Base analog
mutagenesis introduces a small amount of non-randomness to random
mutagenesis, because specific base analogs can be chose which can
be incorporated at certain nucleotides in the starting sequence.
Correction of the mispairing typically yields a known substitution.
For example, Bromo-deoxyuridine (BrdU) can be incorporated into DNA
and replaces T in the sequence. The host DNA repair and replication
machinery can sometime correct the defect, but sometimes will
mispair the BrdU with a G. The next round of replication then
causes a G-C transversion from the original A-T in the native
sequence.
[0219] Ultra violet (UV) induced mutagenesis is caused by the
formation of thymidine dimers when UV light irradiates chemical
bonds between two adjacent thymine residues. Excision repair
mechanism of the host organism correct the lesion in the DNA, but
occasionally the lesion is incorrectly repaired typically resulting
in a C to T transition.
[0220] Insertion element or transposon-mediated mutagenesis makes
use of naturally occurring or modified naturally occurring mobile
genetic elements. Transposons often encode accessory activities in
addition to the activities necessary for transposition (e.g.,
movement using a transposase activity, for example). In many
examples, transposon accessory activities are antibiotic resistance
markers (e.g., see Tn903 kan.sup.r described above, for example).
Insertion elements typically only encode the activities necessary
for movement of the nucleic acid sequence. Insertion element and
transposon mediated mutagenesis often can occur randomly, however
specific target sequences are known for some transposons. Mobile
genetic elements like IS elements or Transposons (Tn) often have
inverted repeats, direct repeats or both inverted and direct
repeats flanking the region coding for the transposition genes.
Recombination events catalyzed by the transposase cause the element
to remove itself from the genome and move to a new location,
leaving behind a portion of an inverted or direct repeat. Classic
examples of transposons are the "mobile genetic elements"
discovered in maize. Transposon mutagenesis kits are commercially
available which are designed to leave behind a 5 codon insert
(e.g., Mutation Generation System kit, Finnzymes, World Wide Web
URL finnzymes.us, for example). This allows the artisan to identify
the insertion site, without fully disrupting the function of most
genes.
[0221] DNA shuffling is a method which uses DNA fragments from
members of a mutant library and reshuffles the fragments randomly
to generate new mutant sequence combinations. The fragments are
typically generated using DNasel, followed by random annealing and
re-joining using self priming PCR. The DNA overhanging ends, from
annealing of random fragments, provide "primer" sequences for the
PCR process. Shuffling can be applied to libraries generated by any
of the above mutagenesis methods.
[0222] Error prone PCR and its derivative rolling circle error
prone PCR uses increased magnesium and manganese concentrations in
conjunction with limiting amounts of one or two nucleotides to
reduce the fidelity of the Taq polymerase. The error rate can be as
high as 2% under appropriate conditions, when the resultant mutant
sequence is compared to the wild type starting sequence. After
amplification, the library of mutant coding sequences must be
cloned into a suitable plasmid. Although point mutations are the
most common types of mutation in error prone PCR, deletions and
frameshift mutations are also possible. There are a number of
commercial error-prone PCR kits available, including those from
Stratagene and Clontech (e.g., World Wide Web URL strategene.com
and World Wide Web URL clontech.com, respectively, for example).
Rolling circle error-prone PCR is a variant of error-prone PCR in
which wild-type sequence is first cloned into a plasmid, then the
whole plasmid is amplified under error-prone conditions.
[0223] As noted above, organisms with altered activities can also
be isolated using genetic selection and screening of organisms
challenged on selective media or by identifying naturally occurring
variants from unique environments. For example, 2-Deoxy-D-glucose
is a toxic glucose analog. Growth of yeast on this substance yields
mutants that are glucose-deregulated. A number of mutants have been
isolated using 2-Deoxy-D-glucose including transport mutants, and
mutants that ferment glucose and galactose simultaneously instead
of glucose first then galactose when glucose is depleted. Similar
techniques have been used to isolate mutant microorganisms that can
metabolize plastics (e.g., from landfills), petrochemicals (e.g.,
from oil spills), and the like, either in a laboratory setting or
from unique environments.
[0224] Similar methods can be used to isolate naturally occurring
mutations in a desired activity when the activity exists at a
relatively low or nearly undetectable level in the organism of
choice, in some embodiments. The method generally consists of
growing the organism to a specific density in liquid culture,
concentrating the cells, and plating the cells on various
concentrations of the substance to which an increase in metabolic
activity is desired. The cells are incubated at a moderate growth
temperature, for 5 to 10 days. To enhance the selection process,
the plates can be stored for another 5 to 10 days at a low
temperature. The low temperature sometimes can allow strains that
have gained or increased an activity to continue growing while
other strains are inhibited for growth at the low temperature.
Following the initial selection and secondary growth at low
temperature, the plates can be replica plated on higher or lower
concentrations of the selection substance to further select for the
desired activity.
[0225] A native, heterologous or mutagenized polynucleotide can be
introduced into a nucleic acid reagent for introduction into a host
organism, thereby generating an engineered microorganism. Standard
recombinant DNA techniques (restriction enzyme digests, ligation,
and the like) can be used by the artisan to combine the mutagenized
nucleic acid of interest into a suitable nucleic acid reagent
capable of (i) being stably maintained by selection in the host
organism, or (ii) being integrating into the genome of the host
organism. As noted above, sometimes nucleic acid reagents comprise
two replication origins to allow the same nucleic acid reagent to
be manipulated in bacterial before final introduction of the final
product into the host organism (e.g., yeast or fungus for example).
Standard molecular biology and recombinant DNA methods are known
(e.g., described in Maniatis, T., E. F. Fritsch and J. Sambrook
(1982) Molecular Cloning: a Laboratory Manual; Cold Spring Harbor
Laboratory, Cold Spring Harbor, N.Y.).
[0226] Nucleic acid reagents can be introduced into microorganisms
using various techniques. Non-limiting examples of methods used to
introduce heterologous nucleic acids into various organisms
include; transformation, transfection, transduction,
electroporation, ultrasound-mediated transformation, particle
bombardment and the like. In some instances the addition of carrier
molecules (e.g., bis-benzimdazolyl compounds, for example, see U.S.
Pat. No. 5,595,899) can increase the uptake of DNA in cells
typically though to be difficult to transform by conventional
methods. Conventional methods of transformation are known (e.g.,
described in Maniatis, T., E. F. Fritsch and J. Sambrook (1982)
Molecular Cloning: a Laboratory Manual; Cold Spring Harbor
Laboratory, Cold Spring Harbor, N.Y.).
Culture, Production and Process Methods
[0227] Engineered microorganisms often are cultured under
conditions that optimize yield of a target molecule (e.g.,
six-carbon target molecule). Non-limiting examples of such target
molecules are adipic acid and 6-hydroxyhexanoic acid. Culture
conditions often optimize activity of one or more of the following
activities: 6-oxohexanoic acid dehydrogenase activity, omega oxo
fatty acid dehydrogenase activity, 6-hydroxyhexanoic acid
dehydrogenase activity, omega hydroxyl fatty acid dehydrogenase
activity, hexanoate synthase, monooxygenase, monooxygenase
reductase, fatty alcohol oxidase, acyl-CoA ligase, acyl-CoA
oxidase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase,
and/or acetyl-CoA C-acyltransferase activities. In general,
non-limiting examples of conditions that may be optimized include
the type and amount of carbon source, the type and amount of
nitrogen source, the carbon-to-nitrogen ratio, the oxygen level,
growth temperature, pH, length of the biomass production phase,
length of target product accumulation phase, and time of cell
harvest.
[0228] Culture media generally contain a suitable carbon source.
Carbon sources useful for culturing microorganisms and/or
fermentation processes sometimes are referred to as feedstocks. The
term "feedstock" as used herein refers to a composition containing
a carbon source that is provided to an organism, which is used by
the organism to produce energy and metabolic products useful for
growth. A feedstock may be a natural substance, a "man-made
substance," a purified or isolated substance, a mixture of purified
substances, a mixture of unpurified substances or combinations
thereof. A feedstock often is prepared by and/or provided to an
organism by a person, and a feedstock often is formulated prior to
administration to the organism. A carbon source may include, but is
not limited to including, one or more of the following substances:
monosaccharides (e.g., also referred to as "saccharides," which
include 6-carbon sugars (e.g., glucose, fructose), 5-carbon sugars
(e.g., xylose and other pentoses) and the like), disaccharides
(e.g., lactose, sucrose), oligosaccharides (e.g., glycans,
homopolymers of a monosaccharide), polysaccharides (e.g., starch,
cellulose, heteropolymers of monosaccharides or mixtures thereof),
sugar alcohols (e.g., glycerol), and renewable feedstocks (e.g.,
cheese whey permeate, cornsteep liquor, sugar beet molasses, barley
malt). Carbon sources also can be selected from one or more of the
following non-limiting examples: paraffin (e.g., saturated
paraffin, unsaturated paraffin, substituted paraffin, linear
paraffin, branched paraffin, or combinations thereof); alkanes
(e.g., hexane), alkenes or alkynes, each of which may be linear,
branched, saturated, unsaturated, substituted or combinations
thereof (described in greater detail below); linear or branched
alcohols (e.g., hexanol); fatty acids (e.g., about 1 carbon to
about 60 carbons, including free fatty acids, soap stock, for
example); esters of fatty acids; monoglycerides; diglycerides;
triglycerides, phospholipids. Non-limiting commercial sources of
products for preparing feedstocks include plants or plant products
(e.g., vegetable oils (e.g., almond oil, canola oil, cocoa butter,
coconut oil, corn oil, cottonseed oil, flaxseed oil, grape seed
oil, illipe, olive oil, palm oil, palm olein, palm kernel oil,
safflower oil, peanut oil, soybean oil, sesame oil, shea nut oil,
sunflower oil walnut oil, the like and combinations thereof) and
animal fats (e.g., beef tallow, butterfat, lard, cod liver oil). A
carbon source may include a petroleum product and/or a petroleum
distillate (e.g., diesel, fuel oils, gasoline, kerosene, paraffin
wax, paraffin oil, petrochemicals).
[0229] The term "paraffin" as used herein refers to the common name
for alkane hydrocarbons, independent of the source (e.g., plant
derived, petroleum derived, chemically synthesized, fermented by a
microorganism), or carbon chain length. A carbon source sometimes
comprises a paraffin, and in some embodiments, a paraffin is
predominant in a carbon source (e.g., about 75%, 80%, 85%, 90% or
95% paraffin). A paraffin sometimes is saturated (e.g., fully
saturated), sometimes includes one or more unsaturations (e.g.,
about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 unsaturations) and sometimes is
substituted with one or more non-hydrogen substituents.
Non-limiting examples of non-hydrogen substituents include halo,
acetyl, .dbd.O, .dbd.N--CN, .dbd.N--OR, .dbd.NR, OR, NR.sub.2, SR,
SO.sub.2R, SO.sub.2NR.sub.2, NRSO.sub.2R, NRCONR.sub.2, NRCOOR,
NRCOR, CN, COOR, CONR.sub.2, OOCR, COR, and NO.sub.2, where each R
is independently H, C1-C8 alkyl, C2-C8 heteroalkyl, C1-C8 acyl,
C2-C8 heteroacyl, C2-C8 alkenyl, C2-C8 heteroalkenyl, C2-C8
alkynyl, C2-C8 heteroalkynyl, C6-C10 aryl, or C5-C10 heteroaryl,
and each R is optionally substituted with halo, .dbd.O, .dbd.N--CN,
.dbd.N--OR', .dbd.NR', OR', NR'.sub.2, SR', SO.sub.2R',
SO.sub.2NR'.sub.2, NR'SO.sub.2R', NR'CONR'.sub.2, NR'COOR',
NR'COR', CN, COOR', CONR'.sub.2, OOCR', COR', and NO.sub.2, where
each R' is independently H, C1-C8 alkyl, C2-C8 heteroalkyl, C1-C8
acyl, C2-C8 heteroacyl, C6-C10 aryl or C5-C10 heteroaryl.
[0230] In some embodiments a feedstock is selected according to the
genotype and/or phenotype of the engineered microorganism to be
cultured. For example, a feedstock rich in 12-carbon fatty acids,
12-carbon dicarboxylic acids or 12-carbon paraffins, or a mixture
of 10-carbon and 12-carbon compounds can be useful for culturing
yeast strains harboring an alteration that partially blocks beta
oxidation by disrupting POX4 activity, as described herein.
Non-limiting examples of carbon sources having 10 and/or 12 carbons
include fats (e.g., coconut oil, palm kernel oil), paraffins (e.g.,
alkanes, alkenes, or alkynes) having 10 or 12 carbons, (e.g.,
decane, dodecane (also referred to as adakanel2, bihexyl, dihexyl
and duodecane), alkene and alkyne derivatives), fatty acids
(decanoic acid, dodecanoic acid), fatty alcohols (decanol,
dodecanol), the like, non-toxic substituted derivatives or
combinations thereof.
[0231] A carbon source sometimes comprises an alkyl, alkenyl or
alkynyl compound or molecule (e.g., a compound that includes an
alkyl, alkenyl or alkynyl moiety (e.g., alkane, alkene, alkyne)).
In certain embodiments, an alkyl, alkenyl or alkynyl molecule, or
combination thereof, is predominant in a carbon source (e.g., about
75%, 80%, 85%, 90% or 95% of such molecules). As used herein, the
terms "alkyl," "alkenyl" and "alkynyl" include straight-chain
(referred to herein as "linear"), branched-chain (referred to
herein as "non-linear"), cyclic monovalent hydrocarbyl radicals,
and combinations of these, which contain only C and H atoms when
they are unsubstituted. Non-limiting examples of alkyl moieties
include methyl, ethyl, isobutyl, cyclohexyl, cyclopentylethyl,
2-propenyl, 3-butynyl, and the like. An alkyl that contains only C
and H atoms and is unsubstituted sometimes is referred to as
"saturated." An alkenyl or alkynyl generally is "unsaturated" as it
contains one or more double bonds or triple bonds, respectively. An
alkenyl can include any number of double bonds, such as 1, 2, 3, 4
or 5 double bonds, for example. An alkynyl can include any number
of triple bonds, such as 1, 2, 3, 4 or 5 triple bonds, for example.
Alkyl, alkenyl and alkynyl molecules sometimes contain between
about 2 to about 60 carbon atoms (C). For example, an alkyl,
alkenyl and alkynyl molecule can include about 1 carbon atom, about
2 carbon atoms, about 3 carbon atoms, about 4 carbon atoms, about 5
carbon atoms, about 6 carbon atoms, about 7 carbon atoms, about 8
carbon atoms, about 9 carbon atoms, about 10 carbon atoms, about 12
carbon atoms, about 14 carbon atoms, about 16 carbon atoms, about
18 carbon atoms, about 20 carbon atoms, about 22 carbon atoms,
about 24 carbon atoms, about 26 carbon atoms, about 28 carbon
atoms, about 30 carbon atoms, about 32 carbon atoms, about 34
carbon atoms, about 36 carbon atoms, about 38 carbon atoms, about
40 carbon atoms, about 42 carbon atoms, about 44 carbon atoms,
about 46 carbon atoms, about 48 carbon atoms, about 50 carbon
atoms, about 52 carbon atoms, about 54 carbon atoms, about 56
carbon atoms, about 58 carbon atoms or about 60 carbon atoms. In
some embodiments, paraffins can have a mean number of carbon atoms
of between about 8 to about 18 carbon atoms (e.g., about 8 carbon
atoms, about 9 carbon atoms, about 10 carbon atoms, about 11 carbon
atoms, about 12 carbon atoms, about 13 carbon atoms, about 14
carbon atoms, about 15 carbon atoms, about 16 carbon atoms, about
17 carbon atoms and about 18 carbon atoms). A single group can
include more than one type of multiple bond, or more than one
multiple bond. Such groups are included within the definition of
the term "alkenyl" when they contain at least one carbon-carbon
double bond, and are included within the term "alkynyl" when they
contain at least one carbon-carbon triple bond. Alkyl, alkenyl and
alkynyl molecules include molecules that comprise an alkyl, alkenyl
and/or alkynyl moiety, and include molecules that consist of an
alkyl, alkenyl or alkynyl moiety (i.e., alkane, alkene and alkyne
molecules).
[0232] Alkyl, alkenyl and alkynyl substituents sometimes contain
1-20C (alkyl) or 2-20C (alkenyl or alkynyl). They can contain about
8-14C or about 10-14C in some embodiments. A single group can
include more than one type of multiple bond, or more than one
multiple bond. Such groups are included within the definition of
the term "alkenyl" when they contain at least one carbon-carbon
double bond, and are included within the term "alkynyl" when they
contain at least one carbon-carbon triple bond.
[0233] Alkyl, alkenyl and alkynyl groups or compounds sometimes are
substituted to the extent that such substitution can be synthesized
and can exist. Typical substituents include, but are not limited
to, halo, acetyl, .dbd.O, .dbd.N--CN, .dbd.N--OR, .dbd.NR, OR,
NR.sub.2, SR, SO.sub.2R, SO.sub.2NR.sub.2, NRSO.sub.2R,
NRCONR.sub.2, NRCOOR, NRCOR, CN, COOR, CONR.sub.2, OOCR, COR, and
NO.sub.2, where each R is independently H, C1-C8 alkyl, C2-C8
heteroalkyl, C1-C8 acyl, C2-C8 heteroacyl, C2-C8 alkenyl, C2-C8
heteroalkenyl, C2-C8 alkynyl, C2-C8 heteroalkynyl, C6-C11 aryl, or
C5-C11 heteroaryl, and each R is optionally substituted with halo,
.dbd.O, .dbd.N--CN, .dbd.N--OR', .dbd.NR', OR', NR'.sub.2, SR',
SO.sub.2R', SO.sub.2NR'.sub.2, NR'SO.sub.2R', NR'CONR'.sub.2,
NR'COOR', NR'COR', CN, COOR', CONR'.sub.2, OOCR', COR', and
NO.sub.2, where each R' is independently H, C1-C8 alkyl, C2-C8
heteroalkyl, C1-C8 acyl, C2-C8 heteroacyl, C6-C10 aryl or C5-C10
heteroaryl. Alkyl, alkenyl and alkynyl groups can also be
substituted by C1-C8 acyl, C2-C8 heteroacyl, C6-C10 aryl or C5-C10
heteroaryl, each of which can be substituted by the substituents
that are appropriate for the particular group.
[0234] "Acetylene" or "acetyl" substituents are 2-10C alkynyl
groups that are optionally substituted, and are of the formula
--C.ident.C--R1, where R1 is H or C1-C8 alkyl, C2-C8 heteroalkyl,
C2-C8 alkenyl, C2-C8 heteroalkenyl, C2-C8 alkynyl, C2-C8
heteroalkynyl, C1-C8 acyl, C2-C8 heteroacyl, C6-C10 aryl, C5-C10
heteroaryl, C7-C12 arylalkyl, or C6-C12 heteroarylalkyl, and each
Ri group is optionally substituted with one or more substituents
selected from halo, .dbd.O, .dbd.N--CN, .dbd.N--OR', .dbd.NR', OR',
NR'2, SR', SO.sub.2R', SO.sub.2NR'.sub.2, NR'SO.sub.2R',
NR'CONR'.sub.2, NR'COOR', NR'COR', CN, COOR', CONR.sub.2, OOCR',
COR', and NO.sub.2, where each R' is independently H, C1-C6 alkyl,
C2-C6 heteroalkyl, C1-C6 acyl, C2-C6 heteroacyl, C6-C10 aryl,
C5-C10 heteroaryl, C7-12 arylalkyl, or C6-12 heteroarylalkyl, each
of which is optionally substituted with one or more groups selected
from halo, C1-C4 alkyl, C1-C4 heteroalkyl, C1-C6 acyl, C1-C6
heteroacyl, hydroxy, amino, and .dbd.O; and where two R' can be
linked to form a 3-7 membered ring optionally containing up to
three heteroatoms selected from N, O and S. In some embodiments, R1
of --C.ident.C--Ri is H or Me.
[0235] A carbon source sometimes comprises a heteroalkyl,
heteroalkenyl and/or heteroalkynyl molecule or compound (e.g.,
comprises heteroalkyl, heteroalkenyl and/or heteroalkynyl moiety
(e.g., heteroalkane, heteroalkene or heteroalkyne)). "Heteroalkyl",
"heteroalkenyl", and "heteroalkynyl" and the like are defined
similarly to the corresponding hydrocarbyl (alkyl, alkenyl and
alkynyl) groups, but the `hetero` terms refer to groups that
contain one to three O, S or N heteroatoms or combinations thereof
within the backbone; thus at least one carbon atom of a
corresponding alkyl, alkenyl, or alkynyl group is replaced by one
of the specified heteroatoms to form a heteroalkyl, heteroalkenyl,
or heteroalkynyl group. The typical and sizes for heteroforms of
alkyl, alkenyl and alkynyl groups are generally the same as for the
corresponding hydrocarbyl groups, and the substituents that may be
present on the heteroforms are the same as those described above
for the hydrocarbyl groups. For reasons of chemical stability, it
is also understood that, unless otherwise specified, such groups do
not include more than two contiguous heteroatoms except where an
oxo group is present on N or S as in a nitro or sulfonyl group.
[0236] The term "alkyl" as used herein includes cycloalkyl and
cycloalkylalkyl groups and compounds, the term "cycloalkyl" may be
used herein to describe a carbocyclic non-aromatic compound or
group that is connected via a ring carbon atom, and
"cycloalkylalkyl" may be used to describe a carbocyclic
non-aromatic compound or group that is connected to a molecule
through an alkyl linker. Similarly, "heterocyclyl" may be used to
describe a non-aromatic cyclic group that contains at least one
heteroatom as a ring member and that is connected to the molecule
via a ring atom, which may be C or N; and "heterocyclylalkyl" may
be used to describe such a group that is connected to another
molecule through a linker. The sizes and substituents that are
suitable for the cycloalkyl, cycloalkylalkyl, heterocyclyl, and
heterocyclylalkyl groups are the same as those described above for
alkyl groups. As used herein, these terms also include rings that
contain a double bond or two, as long as the ring is not
aromatic.
[0237] A carbon source sometimes comprises an acyl compound or
moiety (e.g., compound comprising an acyl moiety). As used herein,
"acyl" encompasses groups comprising an alkyl, alkenyl, alkynyl,
aryl or arylalkyl radical attached at one of the two available
valence positions of a carbonyl carbon atom, and heteroacyl refers
to the corresponding groups where at least one carbon other than
the carbonyl carbon has been replaced by a heteroatom chosen from
N, O and S. Thus heteroacyl includes, for example, --C(.dbd.O)OR
and --C(.dbd.O)NR.sub.2 as well as --C(.dbd.O)-heteroaryl.
[0238] Acyl and heteroacyl groups are bonded to any group or
molecule to which they are attached through the open valence of the
carbonyl carbon atom. Typically, they are C1-C8 acyl groups, which
include formyl, acetyl, pivaloyl, and benzoyl, and C2-C8 heteroacyl
groups, which include methoxyacetyl, ethoxycarbonyl, and
4-pyridinoyl. The hydrocarbyl groups, aryl groups, and heteroforms
of such groups that comprise an acyl or heteroacyl group can be
substituted with the substituents described herein as generally
suitable substituents for each of the corresponding component of
the acyl or heteroacyl group.
[0239] A carbon source sometimes comprises one or more aromatic
moieties and/or heteroaromatic moieties. "Aromatic" moiety or
"aryl" moiety refers to a monocyclic or fused bicyclic moiety
having the well-known characteristics of aromaticity; examples
include phenyl and naphthyl. Similarly, "heteroaromatic" and
"heteroaryl" refer to such monocyclic or fused bicyclic ring
systems which contain as ring members one or more heteroatoms
selected from O, S and N. The inclusion of a heteroatom permits
aromaticity in 5 membered rings as well as 6 membered rings.
Typical heteroaromatic systems include monocyclic C5-C6 aromatic
groups such as pyridyl, pyrimidyl, pyrazinyl, thienyl, furanyl,
pyrrolyl, pyrazolyl, thiazolyl, oxazolyl, and imidazolyl and the
fused bicyclic moieties formed by fusing one of these monocyclic
groups with a phenyl ring or with any of the heteroaromatic
monocyclic groups to form a C8-C10 bicyclic group such as indolyl,
benzimidazolyl, indazolyl, benzotriazolyl, isoquinolyl, quinolyl,
benzothiazolyl, benzofuranyl, pyrazolopyridyl, quinazolinyl,
quinoxalinyl, cinnolinyl, and the like. Any monocyclic or fused
ring bicyclic system which has the characteristics of aromaticity
in terms of electron distribution throughout the ring system is
included in this definition. It also includes bicyclic groups where
at least the ring which is directly attached to the remainder of
the molecule has the characteristics of aromaticity. Typically, the
ring systems contain 5-12 ring member atoms. The monocyclic
heteroaryls sometimes contain 5-6 ring members, and the bicyclic
heteroaryls sometimes contain 8-10 ring members.
[0240] Aryl and heteroaryl moieties may be substituted with a
variety of substituents including C1-C8 alkyl, C2-C8 alkenyl, C2-C8
alkynyl, C5-C12 aryl, C1-C8 acyl, and heteroforms of these, each of
which can itself be further substituted; other substituents for
aryl and heteroaryl moieties include halo, OR, NR.sub.2, SR,
SO.sub.2R, SO.sub.2NR.sub.2, NRSO.sub.2R, NRCONR.sub.2, NRCOOR,
NRCOR, CN, COOR, CONR.sub.2, OOCR, COR, and NO.sub.2, where each R
is independently H, C1-C8 alkyl, C2-C8 heteroalkyl, C2-C8 alkenyl,
C2-C8 heteroalkenyl, C2-C8 alkynyl, C2-C8 heteroalkynyl, C6-C10
aryl, C5-C10 heteroaryl, C7-C12 arylalkyl, or C6-C12
heteroarylalkyl, and each R is optionally substituted as described
above for alkyl groups. The substituent groups on an aryl or
heteroaryl group may be further substituted with the groups
described herein as suitable for each type of such substituents or
for each component of the substituent. Thus, for example, an
arylalkyl substituent may be substituted on the aryl portion with
substituents typical for aryl groups, and it may be further
substituted on the alkyl portion with substituents as typical or
suitable for alkyl groups.
[0241] Similarly, "arylalkyl" and "heteroarylalkyl" refer to
aromatic and heteroaromatic ring systems, which are stand-alone
molecules (e.g., benzene or substituted benzene, pyridine or
substituted pyridine), or which are bonded to an attachment point
through a linking group such as an alkylene, including substituted
or unsubstituted, saturated or unsaturated, cyclic or acyclic
linkers. A linker often is C1-C8 alkyl or a hetero form thereof.
These linkers also may include a carbonyl group, thus making them
able to provide substituents as an acyl or heteroacyl moiety. An
aryl or heteroaryl ring in an arylalkyl or heteroarylalkyl group
may be substituted with the same substituents described above for
aryl groups. An arylalkyl group sometimes includes a phenyl ring
optionally substituted with the groups defined above for aryl
groups and a C1-C4 alkylene that is unsubstituted or is substituted
with one or two C1-C4 alkyl groups or heteroalkyl groups, where the
alkyl or heteroalkyl groups can optionally cyclize to form a ring
such as cyclopropane, dioxolane, or oxacyclopentane. Similarly, a
heteroarylalkyl group often includes a C5-C6 monocyclic heteroaryl
group optionally substituted with one or more of the groups
described above as substituents typical on aryl groups and a C1-C4
alkylene that is unsubstituted. A heteroarylalkyl group sometimes
is substituted with one or two C1-C4 alkyl groups or heteroalkyl
groups, or includes an optionally substituted phenyl ring or C5-C6
monocyclic heteroaryl and a C1-C4 heteroalkylene that is
unsubstituted or is substituted with one or two C1-C4 alkyl or
heteroalkyl groups, where the alkyl or heteroalkyl groups can
optionally cyclize to form a ring such as cyclopropane, dioxolane,
or oxacyclopentane.
[0242] Where an arylalkyl or heteroarylalkyl group is described as
optionally substituted, the substituents may be on the alkyl or
heteroalkyl portion or on the aryl or heteroaryl portion of the
group. The substituents optionally present on the alkyl or
heteroalkyl portion sometimes are the same as those described above
for alkyl groups, and the substituents optionally present on the
aryl or heteroaryl portion often are the same as those described
above for aryl groups generally.
[0243] "Arylalkyl" groups as used herein are hydrocarbyl groups if
they are unsubstituted, and are described by the total number of
carbon atoms in the ring and alkylene or similar linker. Thus a
benzyl group is a C7-arylalkyl group, and phenylethyl is a
C8-arylalkyl.
[0244] "Heteroarylalkyl" as described above refers to a moiety
comprising an aryl group that is attached through a linking group,
and differs from "arylalkyl" in that at least one ring atom of the
aryl moiety or one atom in the linking group is a heteroatom
selected from N, O and S. The heteroarylalkyl groups are described
herein according to the total number of atoms in the ring and
linker combined, and they include aryl groups linked through a
heteroalkyl linker; heteroaryl groups linked through a hydrocarbyl
linker such as an alkylene; and heteroaryl groups linked through a
heteroalkyl linker. Thus, for example, C7-heteroarylalkyl includes
pyridylmethyl, phenoxy, and N-pyrrolylmethoxy.
[0245] "Alkylene" as used herein refers to a divalent hydrocarbyl
group. Because an alkylene is divalent, it can link two other
groups together. An alkylene often is referred to as
--(CH.sub.2).sub.n-- where n can be 1-20, 1-10, 1-8, or 1-4, though
where specified, an alkylene can also be substituted by other
groups, and can be of other lengths, and the open valences need not
be at opposite ends of a chain. Thus --CH(Me)-- and --C(Me).sub.2--
may also be referred to as alkylenes, as can a cyclic group such as
cyclopropan-1,1-diyl. Where an alkylene group is substituted, the
substituents include those typically present on alkyl groups as
described herein.
[0246] Nitrogen may be supplied from an inorganic (e.g.,
(NH.sub.4).sub.2SO.sub.4) or organic source (e.g., urea or
glutamate). In addition to appropriate carbon and nitrogen sources,
culture media also can contain suitable minerals, salts, cofactors,
buffers, vitamins, metal ions (e.g., Mn.sup.+2, Co.sup.+2,
Zn.sup.+2, Mg.sup.+2) and other components suitable for culture of
microorganisms.
[0247] Engineered microorganisms sometimes are cultured in complex
media (e.g., yeast extract-peptone-dextrose broth (YPD)). In some
embodiments, engineered microorganisms are cultured in a defined
minimal media that lacks a component necessary for growth and
thereby forces selection of a desired expression cassette (e.g.,
Yeast Nitrogen Base (DIFCO Laboratories, Detroit, Mich.)). Culture
media in some embodiments are common commercially prepared media,
such as Yeast Nitrogen Base (DIFCO Laboratories, Detroit, Mich.).
Other defined or synthetic growth media may also be used and the
appropriate medium for growth of the particular microorganism are
known. A variety of host organisms can be selected for the
production of engineered microorganisms. Non-limiting examples
include yeast (e.g., Candida tropicalis (e.g., ATCC20336,
ATCC20913, ATCC20962), Yarrowia lipolytica (e.g., ATCC20228)) and
filamentous fungi (e.g., Aspergillus nidulans (e.g., ATCC38164) and
Aspergillus parasiticus (e.g., ATCC 24690)). In specific
embodiments, yeast are cultured in YPD media (10 g/L Bacto Yeast
Extract, 20 g/L Bacto Peptone, and 20 g/L Dextrose). Filamentous
fungi, in particular embodiments, are grown in CM (Complete Medium)
containing 10 g/L Dextrose, 2 g/L Bacto Peptone, 1 g/L Bacto Yeast
Extract, 1 g/L Casamino acids, 50 mL/L 20.times. Nitrate Salts (120
g/L NaNO.sub.3, 10.4 g/L KCl, 10.4 g/L MgSO.sub.4.7 H.sub.2O), 1
mL/L 1000.times. Trace Elements (22 g/L ZnSO.sub.4.7 H.sub.2O, 11
g/L H.sub.3BO.sub.3, 5 g/L MnCl.sub.2.7 H.sub.2O, 5 g/L
FeSO.sub.4.7 H.sub.2O, 1.7 g/L CoCl.sub.2.6 H.sub.2O, 1.6 g/L
CuSO.sub.4.5 H.sub.2O, 1.5 g/L Na.sub.2MoO.sub.4.2 H.sub.2O, and 50
g/L Na.sub.4EDTA), and 1 mL/L Vitamin Solution (100 mg each of
Biotin, pyridoxine, thiamine, riboflavin, p-aminobenzoic acid, and
nicotinic acid in 100 mL water).
[0248] A suitable pH range for the fermentation often is between
about pH 4.0 to about pH 8.0, where a pH in the range of about pH
5.5 to about pH 7.0 sometimes is utilized for initial culture
conditions. Depending on the host organism, culturing may be
conducted under aerobic or anaerobic conditions, where microaerobic
conditions sometimes are maintained. A two-stage process may be
utilized, where one stage promotes microorganism proliferation and
another state promotes production of target molecule. In a
two-stage process, the first stage may be conducted under aerobic
conditions (e.g., introduction of air and/or oxygen) and the second
stage may be conducted under anaerobic conditions (e.g., air or
oxygen are not introduced to the culture conditions). In some
embodiments, the first stage may be conducted under anaerobic
conditions and the second stage may be conducted under aerobic
conditions. In certain embodiments, a two-stage process may include
two more organisms, where one organism generates an intermediate
product (e.g., hexanoic acid produced by Megasphera spp.) in one
stage and another organism processes the intermediate product into
a target product (e.g., adipic acid) in another stage, for
example.
[0249] A variety of fermentation processes may be applied for
commercial biological production of a target product. In some
embodiments, commercial production of a target product from a
recombinant microbial host is conducted using a batch, fed-batch or
continuous fermentation process, for example.
[0250] A batch fermentation process often is a closed system where
the media composition is fixed at the beginning of the process and
not subject to further additions beyond those required for
maintenance of pH and oxygen level during the process. At the
beginning of the culturing process the media is inoculated with the
desired organism and growth or metabolic activity is permitted to
occur without adding additional sources (i.e., carbon and nitrogen
sources) to the medium. In batch processes the metabolite and
biomass compositions of the system change constantly up to the time
the culture is terminated. In a typical batch process, cells
proceed through a static lag phase to a high-growth log phase and
finally to a stationary phase, wherein the growth rate is
diminished or halted. Left untreated, cells in the stationary phase
will eventually die.
[0251] A variation of the standard batch process is the fed-batch
process, where the carbon source is continually added to the
fermentor over the course of the fermentation process. Fed-batch
processes are useful when catabolite repression is apt to inhibit
the metabolism of the cells or where it is desirable to have
limited amounts of carbon source in the media at any one time.
[0252] Measurement of the carbon source concentration in fed-batch
systems may be estimated on the basis of the changes of measurable
factors such as pH, dissolved oxygen and the partial pressure of
waste gases (e.g., CO.sub.2).
[0253] Batch and fed-batch culturing methods are known in the art.
Examples of such methods may be found in Thomas D. Brock in
Biotechnology: A Textbook of Industrial Microbiology, 2.sup.nd ed.,
(1989) Sinauer Associates Sunderland, Mass. and Deshpande, Mukund
V., Appl. Biochem. Biotechnol., 36:227 (1992).
[0254] In continuous fermentation process a defined media often is
continuously added to a bioreactor while an equal amount of culture
volume is removed simultaneously for product recovery. Continuous
cultures generally maintain cells in the log phase of growth at a
constant cell density. Continuous or semi-continuous culture
methods permit the modulation of one factor or any number of
factors that affect cell growth or end product concentration. For
example, an approach may limit the carbon source and allow all
other parameters to moderate metabolism. In some systems, a number
of factors affecting growth may be altered continuously while the
cell concentration, measured by media turbidity, is kept constant.
Continuous systems often maintain steady state growth and thus the
cell growth rate often is balanced against cell loss due to media
being drawn off the culture. Methods of modulating nutrients and
growth factors for continuous culture processes, as well as
techniques for maximizing the rate of product formation, are known
and a variety of methods are detailed by Brock, supra.
[0255] In some embodiments involving fermentation, the fermentation
can be carried out using two or more microorganisms (e.g., host
microorganism, engineered microorganism, isolated naturally
occurring microorganism, the like and combinations thereof), where
a feedstock is partially or completely utilized by one or more
organisms in the fermentation (e.g., mixed fermentation), and the
products of cellular respiration or metabolism of one or more
organisms can be further metabolized by one or more other organisms
to produce a desired target product (e.g., adipic acid, hexanoic
acid). In certain embodiments, each organism can be fermented
independently and the products of cellular respiration or
metabolism purified and contacted with another organism to produce
a desired target product. In some embodiments, one or more
organisms are partially or completely blocked in a metabolic
pathway (e.g., beta oxidation, omega oxidation, the like or
combinations thereof), thereby producing a desired product that can
be used as a feedstock for one or more other organisms. Any
suitable combination of microorganisms can be utilized to carry out
mixed fermentation or sequential fermentation. A non-limiting
example of an organism combination and feedstock suitable for use
in mixed fermentations or sequential fermentations where the
fermented media from a first organism is used as a feedstock for a
second organism is the use of long chain dicarboxylic acids as a
fermentation media for Megasphaera elsdenii to produce hexanoic
acid, and Candida tropicalis engineered as described herein to
produce adipic acid from the hexanoic acid produced by Megasphaera
elsdenii. Megasphaera elsdenii is a facultative anaerobe. Without
being limited by theory, it is believe that Megasphaera elsdenii
naturally accumulates hexanoic acid as a result of anaerobic
respiration. Candida tropicalis can grow aerobically and
anaerobically. In some embodiments, the hexanoic acid produced by
Megasphaera elsdenii can be utilized as a feedstock for Candida
tropicalis to produce adipic acid. In certain embodiments, the
Megasphaera produced hexanoic acid is purified (e.g., partially,
completely) prior to being used as a feedstock for C.
tropicalis.
[0256] In various embodiments adipic acid is isolated or purified
from the culture media or extracted from the engineered
microorganisms. In some embodiments, fermentation of feedstocks by
methods described herein can produce a target product (e.g., adipic
acid) at a level of about 80% or more of theoretical yield (e.g.,
80% or more, 81% or more, 82% or more, 83% or more, 84% or more,
85% or more, 86% or more, 87% or more, 88% or more, 89% or more,
90% or more, 91% or more, 92% or more, 93% or more, 94% or more,
95% or more, 96% or more, 97% or more, 98% or more, or 99% or more
of theoretical yield). The term "theoretical yield" as used herein
refers to the amount of product that could be made from a starting
material if the reaction is 100% complete. Theoretical yield is
based on the stoichiometry of a reaction and ideal conditions in
which starting material is completely consumed, undesired side
reactions do not occur, the reverse reaction does not occur, and
there are no losses in the work-up procedure. Culture media may be
tested for target product (e.g., adipic acid) concentration and
drawn off when the concentration reaches a predetermined level.
Detection methods are known in the art, including but not limited
to those set forth in B Stieglitz and P J Weimer, Novel microbial
screen for detection of 1,4-butanediol, ethylene glycol, and adipic
acid, Appl Environ Microbiol. 198. Target product (e.g., adipic
acid) may be present at a range of levels as described herein.
[0257] A target product sometimes is retained within an engineered
microorganism after a culture process is completed, and in certain
embodiments, the target product is secreted out of the
microorganism into the culture medium. For the latter embodiments,
(i) culture media may be drawn from the culture system and fresh
medium may be supplemented, and/or (ii) target product may be
extracted from the culture media during or after the culture
process is completed. Engineered microorganisms may be cultured on
or in solid, semi-solid or liquid media. In some embodiments media
is drained from cells adhering to a plate. In certain embodiments,
a liquid-cell mixture is centrifuged at a speed sufficient to
pellet the cells but not disrupt the cells and allow extraction of
the media, as known in the art. The cells may then be resuspended
in fresh media. Target product may be purified from culture media
according to known methods, such as those described in U.S. Pat.
No. 6,787,669 and U.S. Pat. No. 5,296,639, for example.
[0258] In certain embodiments, target product is extracted from the
cultured engineered microorganisms. The micoorganism cells may be
concentrated through centrifugation at a speed sufficient to shear
the cell membranes. In some embodiments, the cells may be
physically disrupted (e.g., shear force, sonication) or chemically
disrupted (e.g., contacted with detergent or other lysing agent).
The phases may be separated by centrifugation or other method known
in the art and target product may be isolated according to known
methods.
[0259] Commercial grade target product sometimes is provided in
substantially pure form (e.g., 90% pure or greater, 95% pure or
greater, 99% pure or greater or 99.5% pure or greater). In some
embodiments, target product may be modified into any one of a
number of downstream products. For example, adipic acid may be
polycondensed with hexamethylenediamine to produce nylon. Nylon may
be further processed into fibers for applications in carpeting,
automobile tire cord and clothing. Adipic acid is also used for
manufacturing plasticizers, lubricant components and polyester
polyols for polyurethane systems. Food grade adipic acid is used as
a gelling aid, acidulant, leavening and buffering agent. Adipic
acid has two carboxylic acid (--COOH) groups, which can yield two
kinds of salts. Its derivatives, acyl halides, anhydrides, esters,
amides and nitriles, are used in making downstream products such as
flavoring agents, internal plasticizers, pesticides, dyes, textile
treatment agents, fungicides, and pharmaceuticals through further
reactions of substitution, catalytic reduction, metal hydride
reduction, diborane reduction, keto formation with organometallic
reagents, electrophile bonding at oxygen, and condensation.
[0260] Target product may be provided within cultured microbes
containing target product, and cultured microbes may be supplied
fresh or frozen in a liquid media or dried. Fresh or frozen
microbes may be contained in appropriate moisture-proof containers
that may also be temperature controlled as necessary. Target
product sometimes is provided in culture medium that is
substantially cell-free. In some embodiments target product or
modified target product purified from microbes is provided, and
target product sometimes is provided in substantially pure form. In
certain embodiments crystallized or powdered target product is
provided. Crystalline adipic acid is a white powder with a melting
point of 360.degree. F. and may be transported in a variety of
containers including one ton cartons, drums, 50 pound bags and the
like.
[0261] In certain embodiments, a target product (e.g., adipic acid,
6-hydroxyhexanoic acid) is produced with a yield of about 0.30
grams of target product, or greater, per gram of glucose added
during a fermentation process (e.g., about 0.31 grams of target
product per gram of glucose added, or greater; about 0.32 grams of
target product per gram of glucose added, or greater; about 0.33
grams of target product per gram of glucose added, or greater;
about 0.34 grams of target product per gram of glucose added, or
greater; about 0.35 grams of target product per gram of glucose
added, or greater; about 0.36 grams of target product per gram of
glucose added, or greater; about 0.37 grams of target product per
gram of glucose added, or greater; about 0.38 grams of target
product per gram of glucose added, or greater; about 0.39 grams of
target product per gram of glucose added, or greater; about 0.40
grams of target product per gram of glucose added, or greater;
about 0.41 grams of target product per gram of glucose added, or
greater; 0.42 grams of target product per gram of glucose added, or
greater; 0.43 grams of target product per gram of glucose added, or
greater; 0.44 grams of target product per gram of glucose added, or
greater; 0.45 grams of target product per gram of glucose added, or
greater; 0.46 grams of target product per gram of glucose added, or
greater; 0.47 grams of target product per gram of glucose added, or
greater; 0.48 grams of target product per gram of glucose added, or
greater; 0.49 grams of target product per gram of glucose added, or
greater; 0.50 grams of target product per gram of glucose added, or
greater; 0.51 grams of target product per gram of glucose added, or
greater; 0.52 grams of target product per gram of glucose added, or
greater; 0.53 grams of target product per gram of glucose added, or
greater; 0.54 grams of target product per gram of glucose added, or
greater; 0.55 grams of target product per gram of glucose added, or
greater; 0.56 grams of target product per gram of glucose added, or
greater; 0.57 grams of target product per gram of glucose added, or
greater; 0.58 grams of target product per gram of glucose added, or
greater; 0.59 grams of target product per gram of glucose added, or
greater; 0.60 grams of target product per gram of glucose added, or
greater; 0.61 grams of target product per gram of glucose added, or
greater; 0.62 grams of target product per gram of glucose added, or
greater; 0.63 grams of target product per gram of glucose added, or
greater; 0.64 grams of target product per gram of glucose added, or
greater; 0.65 grams of target product per gram of glucose added, or
greater; 0.66 grams of target product per gram of glucose added, or
greater; 0.67 grams of target product per gram of glucose added, or
greater; 0.68 grams of target product per gram of glucose added, or
greater; 0.69 or 0.70 grams of target product per gram of glucose
added or greater).
EXAMPLES
[0262] The examples set forth below illustrate certain embodiments
and do not limit the technology. Certain examples set forth below
utilize standard recombinant DNA and other biotechnology protocols
known in the art. Many such techniques are described in detail in
Maniatis, T., E. F. Fritsch and J. Sambrook (1982) Molecular
Cloning: a Laboratory Manual; Cold Spring Harbor Laboratory, Cold
Spring Harbor, N.Y. DNA mutagenesis can be accomplished using the
Stratagene (San Diego, Calif.) "QuickChange" kit according to the
manufacturer's instructions.
Example 1
Cloning Hexanoate Synthase ("HexS") Subunit Genes
[0263] Total RNA from Aspergillus parasiticus was prepared using
the RiboPure.TM. (Ambion, Austin, Tex.) kit for yeast. The genes
encoding the two subunits of hexanoate synthase (referred to as
"hexA" and "hex B" were isolated from this total RNA using the
2-step RT-PCR method with Superscript III reverse transcriptase
(Life Technologies, Carlsbad, Calif.) and the fragments were gel
purified. The primers used for each RT-PCR reaction are as
follows:
TABLE-US-00003 SEQ ID HexA Aspergillus parasiticus primers NO:
SP_HexA_Apar_1_1149 ATGGTCATCCAAGGGAAGAGATTGGCCGCCTCCTCTATTCAGC 28
ASP_HexA_Apar_1_1149 GTAGGCGTCACAGGAAAGACTGCGTACCA 29
SP_HexA_Apar_941_2270 TATCACCAATGCTGGATGTAAAGAAGTCGCG 30
ASP_HexA_Apar_941_2270 AATTGGGCTAGGAAACCGGGGATGC 31
SP_HexA_Apar_2067_3016 CGGTCTAATGACGGCGCATGATATCATAGCCGAAACGGTCGAG
32 ASP_HexA_Apar_2067_3016 ACTTGGCTGGAGTCCATCCCTTCGGCA 33
SP_HexA_Apar_2812_4181 CTGCCCGAGTTTGAAGTATCTCAACTTACCGCCGACGCCATG
34 ASP_HexA_Apar_2812_4181 TGAGACGCGCTGCGCAGGGC 35
SP_HexA_Apar_3975_5016 CGAGGTGATCGAGACGCAGATGC 36
ASP_HexA_Apar_3975_5016 TTATGAAGCACCAGACATCAGCCCCAGC 37
TABLE-US-00004 SEQ ID HexB Aspergillus parasiticus primers NO:
SP_HexB_Apar_1_1166 ATGGGTTCCGTTAGTAGGGAACATGAGTCAATC 38
ASP_HexB_Apar_1_1166 GTTCCTTGTGTGAGCTCCTGAATAAGACTGCATG 39
SP_HexB_Apar_962_2042 CCATCAAAATCCCCCTCTATCACACGGGCACTGGGAGCAAC 40
ASP_HexB_Apar_962_2042 CCCACGCCTTGCGCATCTATAATCAGG 41
SP_HexB_Apar_1837_3527 TGTCCGAATATTCTCCTCGTTGTAGGTAGTGGATT 42
ASP_HexB_Apar_1837_3527 GCAGTAGTCGATAGGTACACATCCTTGGGGGTTCCATGACTGC
43 SP_HexB_Apar_3322_4460
AGAGGATCAAGGCATTATACATGAGTCTGTGGAACTTGGGCTTTCC 44
ASP_HexB_Apar_3322_4460 TTCCCCGTCCTCCATGGCCTTATGC 45
SP_HexB_Apar_4256_5667 GGCCTTTGCGCGATACGCTGGTCTCTCGGGTCCCAT 46
ASP_HexB_Apar_4256_5667 TCACGCCATTTGTTGAAGCAGGGAATG 47
[0264] Each of the fragments was inserted separately into the
plasmid pCRBlunt II (Life Technologies, Carlsbad, Calif.) such that
there were four hexA plasmids, each with a different hexA gene
fragment, and five hex B plasmids each with a different hexB gene
fragment. Each hexA and hexB fragment was sequence verified, after
which the fragments were PCR cloned from each plasmid. Overlap PCR
was then used to create the full length hexA and hexB genes. The
hexA gene was inserted into the vector p425GPD which has a LEU2
selectable marker and a glyceraldehyde 3-phosphate dehydrogenase
promoter (American Type Culture Collection) and the hexB full
length gene was inserted into p426GPD which has a URA3 selectable
marker and a glyceraldehyde 3-phosphate dehydrogenase promoter
(American Type Culture Collection).
Example 2
Transformation of Saccharomyces Cerevisiae with HexA and HexB
Genes
[0265] Saccharomyces cereviseae cells (strain BY4742, ATCC
Accession Number 201389) were grown in standard YPD (10 g Yeast
Extract, 20 g Bacto-Peptone, 20 g Glucose, 1 L total) media at
about 30 degrees Celsius for about 3 days. The plasmids containing
the hexA and hexB genes were co-transformed into the Saccharomyces
cerevisiae. Transformation was accomplished using the Zymo kit
(Catalog number T2001; Zymo Research Corp., Orange, Calif. 92867)
using 1 .mu.g plasmid DNA and cultured on SC drop out media with
glucose (minus uracil and minus leucine) (20 g glucose; 2.21 g SC
(-URA,-LEU) dry mix, 6.7 g Yeast Nitrogen Base, 1 L total) for 2-3
days at about 30.degree. C.
SC(-URA) Mix Contains:
TABLE-US-00005 [0266] 0.4 g Adenine hemisulfate 3.5 g Arginine 1 g
Glutamic Acid 0.433 g Histidine 0.4 g Myo-Inositol 5.2 g Isoleucine
0.9 g Lysine 1.5 g Methionine 0.8 g Phenylalanine 1.1 g Serine 1.2
g Threonine 0.8 g Tryptophan 0.2 g Tyrosine 1.2 g Valine
[0267] When needed:
TABLE-US-00006 0.263 g Leucine 0.2 g Uracil
[0268] Co-transformants were selected and established as liquid
cultures in YPD media under standard conditions.
Example 3
Production of Synthetic HexA and HexB Genes
[0269] Synthetic hexaonoate synthase subunit genes were designed
for use in Candida tropicalis. This organism uses an alternate
genetic code in which the codon "CTG" encodes serine instead of
leucine. Therefore, all "CTG" codons were replaced with the codon
"TTG" to ensure that these genes, when translated by C. tropicalis,
would generate polypeptides with amino acid sequences identical to
the wild type polypeptides found in A. parasiticus. Due to the
large size of each subunit, each was synthesized as four fragments,
and each fragment was inserted into the vector pUC57. PCR was used
to clone each fragment, and overlap extension PCR was then used to
generate each full length gene.
[0270] The sequence of the synthetic gene for each hexanoate
synthase subunit is set forth below. The synthetic gene encoding
the hexA subunit is referred to as hexA-AGC ("Alternate Genetic
Code") and the synthetic gene encoding the hexB subunit is referred
to as hexB-AGC.
TABLE-US-00007 >hexA-AGC for Candida tropicalis (SEQ ID NO: 48)
atggtcatccaagggaagagattggccgcctcctctattcagcttctcgc
aagctcgttagacgcgaagaagctttgttatgagtatgacgagaggcaag
ccccaggtgtaacccaaatcaccgaggaggcgcctacagagcaaccgcct
ctctctacccctccctcgctaccccaaacgcccaatatttcgcctataag
tgcttcaaagatcgtgatcgacgatgtggcgctatctcgagtgcaaattg
ttcaggctcttgttgccagaaagttgaagacggcaattgctcagcttcct
acatcaaagtcaatcaaagagttgtcgggtggtcggtcttctttgcagaa
cgagctcgtgggggatatacacaacgagttcagctccatcccggatgcac
cagagcagatcttgttgcgggactttggcgacgccaacccaacagtgcaa
ttggggaaaacgtcctccgcggcagttgccaaactaatctcgtccaagat
gcctagtgacttcaacgccaacgctattcgagcccacctagcaaacaagt
ggggtctaggacccttgcgacaaacagcggtgttgctctacgccattgcg
tcagaacccccatcgcgtttagcttcatcgagcgcagcggaagagtactg
ggacaacgtgtcatccatgtacgccgaatcgtgtggcatcaccctccgcc
cgagacaagacactatgaatgaagatgctatggcatcgtcggcgattgat
ccggctgtggtagccgagttttccaaggggcaccgtaggctcggagttca
acagttccaagcgctagcagaatacttacaaattgatttgtcggggtctc
aagcctctcagtcggatgctttggtggcggaacttcagcagaaagtcgat
ctctggacggccgaaatgacccccgagtttctcgccgggatatcaccaat
gttggatgtaaagaagtcgcgacgctatggctcgtggtggaacatggcac
ggcaggatgtcttggccttctatcgccgtccttcctacagtgaattcgtg
gacgacgccttggccttcaaagtttttctcaatcgtctctgtaaccgagc
tgatgaggccctcctcaacatggtacgcagtctttcctgtgacgcctact
tcaagcaaggttctttgcccggatatcatgccgcctcgcgactccttgag
caggccatcacatccacagtggcggattgcccgaaggcacgcctcattct
cccggcggtgggcccccacaccaccattacaaaggacggcacgattgaat
acgcggaggcaccgcgccagggagtgagtggtcccactgcgtacatccag
tctctccgccaaggcgcatctttcattggtctcaagtcagccgacgtcga
tactcagagcaacttgaccgacgctttgcttgacgccatgtgcttagcac
tccataatggaatctcgtttgttggtaaaacctttttggtgacgggagcg
ggtcaggggtcaataggagcgggagtggtgcgtctattgttagagggagg
agcccgagtattggtgacgacgagcagggagccggcgacgacatccagat
acttccagcagatgtacgataatcacggtgcgaagttctccgagttgcgg
gtagttccttgcaatctagccagcgcccaagattgcgaagggttgatccg
gcacgtctacgatccccgtgggctaaattgggatttggatgccatccttc
ccttcgctgccgcgtccgactacagcaccgagatgcatgacattcgggga
cagagcgagttgggccaccggctaatgttggtcaatgtcttccgcgtgtt
ggggcatatcgtccactgtaaacgagatgccggggttgactgccatccga
cgcaggtgttgttgccattgtcgccaaatcacggcatcttcggtggcgat
gggatgtatccggagtcaaagctagcccttgagagcttgttccatcgcat
ccgatcagagtcttggtcagaccagttatctatatgcggcgttcgtatcg
gttggacccggtcgaccggtctaatgacggcgcatgatatcatagccgaa
acggtcgaggaacacggaatacgcacattttccgtggccgagatggcact
caacatagccatgttgttaacccccgactttgtggcccattgtgaagatg
gacctttggatgccgatttcaccggcagcttgggaacattgggtagcatc
cccggtttcctagcccaattgcaccagaaagtccagttggcagccgaggt
gatccgtgccgtgcaggccgaggatgagcatgagagattcttgtctccgg
gaacaaaacctaccttgcaagcacccgtggccccaatgcacccccgcagt
agccttcgtgtaggctatccccgtctccccgattatgagcaagagattcg
cccgttgtccccacggttggaaaggttgcaagatccggccaatgctgtgg
tggtggtcgggtactcggagttggggccatggggtagcgcgcgattacgg
tgggaaatagagagccagggccagtggacttcagccggttatgtcgaact
tgcctggttgatgaacctcatccgccacgtcaacgatgaatcctacgtcg
gctgggtggatactcagaccggaaagccagtgcgggatggcgagatccag
gcattgtacggggaccacattgacaaccacaccggtatccgtcctatcca
gtccacctcgtacaacccagagcgcatggaggtcttgcaggaggtcgctg
tcgaggaggatttgcccgagtttgaagtatctcaacttaccgccgacgcc
atgcgtctccgccatggagctaacgtttccatccgccccagtggaaatcc
cgacgcatgccacgtgaagcttaaacgaggcgctgttatccttgttccca
agacagttccctttgtttggggatcgtgtgccggtgagttgccgaaggga
tggactccagccaagtacggcatccctgagaacctaattcatcaggtcga
ccccgtcacgctctatacaatttgctgcgtggcggaggcattttacagtg
ccggtataactcaccctcttgaggtctttcgacacattcacctctcggaa
ctaggcaactttatcggatcctccatgggtgggccgacgaagactcgtca
gctctaccgagatgtctacttcgaccatgagattccgtcggatgttttgc
aagacacttatctcaacacacctgctgcctgggttaatatgctactcctt
ggctgcacggggccgatcaaaactcccgtcggcgcatgtgccaccggggt
cgagtcgatcgattccggctacgagtcaatcatggcgggcaagacaaaga
tgtgtcttgtgggtggctacgacgatttgcaggaggaggcatcgtatgga
ttcgcacaacttaaggccacggtcaacgttgaagaggagatcgcctgcgg
tcgacagccctcggagatgtcgcgccccatggctgagagtcgtgctggct
ttgtcgaggcgcatggctgcggtgtacagttgttgtgtcgaggtgacatc
gccttgcaaatgggtcttcctatctatgcggtcattgccagctcagccat
ggccgccgacaagatcggttcctcggtgccagcaccgggccagggcattc
taagcttctcccgtgagcgcgctcgatccagtatgatatccgtcacgtcg
cgcccgagtagccgtagcagcacatcatctgaagtctcggacaaatcatc
cttgacctcaatcacctcaatcagcaatcccgctcctcgtgcacaacgcg
cccgatccaccactgatatggctccgttgcgagcagcgcttgcgacttgg
gggttgactatcgacgacttggatgtggcctcattgcacggcacctcgac
gcgcggtaacgatctcaatgagcccgaggtgatcgagacgcagatgcgcc
atttaggtcgcactcctggccgccccttgtgggccatctgccaaaagtca
gtgacgggacaccctaaagccccagcggccgcatggatgctcaatggatg
cttgcaagtattggactcggggttggtgccgggcaaccgcaatcttgaca
cgttggacgaggccttgcgcagcgcgtctcatctctgcttccctacgcgc
accgtgcagctacgtgaggtcaaggcattcttgttgacctcatttggctt
cggacagaaggggggccaagtcgtcggcgttgcccccaagtacttctttg
ctacgctcccccgccccgaggttgagggctactatcgcaaggtgagggtt
cgaaccgaggcgggtgatcgcgcctacgccgcggcggtcatgtcgcaggc
ggtggtgaagatccagacgcaaaacccgtacgacgagccggatgcccccc
gcatttttctcgatcccttggcacgtatctcccaggatccgtcgacgggc
cagtatcggtttcgttccgatgccactcccgccctcgatgatgatgcttt
gccacctcccggcgaacccaccgagctagtgaagggcatctcctccgcct
ggatcgaggagaaggtgcgaccgcatatgtctcccggcggcacggtgggc
gtggacttggttcctctcgcctccttcgacgcatacaagaatgccatctt
tgttgagcgcaattatacggtaagggagcgcgattgggctgaaaagagtg
cggatgtgcgcgcggcctatgccagtcggtggtgtgcaaaagaggcggtg
ttcaaatgtctccagacacattcacagggcgcgggggcagccatgaaaga
gattgagatcgagcatggaggtaacggcgcaccgaaagtcaagctccggg
gtgctgcgcaaacagcggcgcggcaacgaggattggaaggagtgcaattg
agcatcagctatggcgacgatgcggtgatagcggtggcgttggggttgat gtctggtgcttcataa
>hexB-AGC for Candida tropicalis (SEQ ID NO: 49)
atgggttccgttagtagggaacatgagtcaatccccatccaggccgccca
gagaggcgctgcccggatctgcgctgcttttggaggtcaagggtctaaca
atttggacgtgttaaaaggtctattggagttatacaagcggtatggccca
gatttggatgagctactagacgtggcatccaacacgctttcgcagttggc
atcttcccctgctgcaatagacgtccacgaaccctggggtttcgacctcc
gacaatggttgaccacaccggaggttgctcctagcaaagaaattcttgcc
ttgccaccacgaagctttcccttaaatacgttacttagcttggcgctcta
ttgtgcaacttgtcgagagcttgaacttgatcctgggcaatttcgatccc
tccttcatagttccacggggcattcccaaggcatattggcggcggtggcc
atcacccaagccgagagctggccaaccttttatgacgcctgcaggacggt
gctccagatctctttctggattggactcgaggcttacctcttcactccat
cctccgccgcctcggatgccatgatccaagattgcatcgaacatggcgag
ggccttctttcctcaatgctaagtgtctccgggctctcccgctcccaagt
tgagcgagtaattgagcacgtcaataaagggctcggagaatgcaaccgat
gggttcacttggccttggttaactcccacgaaaagttcgtcttagcggga
ccacctcaatccttatgggccgtttgtcttcatgtccgacggatcagagc
agacaatgacctcgaccagtcgcgtatcttgttccgcaaccgaaagccta
tagtggatatattatttcttcccatatccgcaccatttcacacaccgtac
ttggacggtgttcaagatcgcgttatcgaggctttgagctctgcttcgtt
ggctctccattccatcaaaatccccctctatcacacgggcactgggagca
acctacaagaactacaaccacatcagctaatcccgactcttatccgcgcc
attaccgtggaccaattggactggccgttggtttgccggggcttgaacgc
aacgcacgtgttggactttggacctggacaaacatgcagtcttattcagg
agctcacacaaggaacaggtgtatcagtgatccagttgactactcaatcg
ggaccaaaacccgttggaggccatttggcggcagtgaactgggaggccga
gtttggcttacgacttcatgccaatgtccacggtgcagctaaattgcaca
accgtatgacaacattgcttgggaagcctcctgtgatggtagccggaatg
acacctactacggtgcgctgggactttgtcgctgccgttgctcaagctgg
ataccacgtcgaattggctggtggtggctaccacgcagagcgccagttcg
aggccgagattcggcgcttggcaactgccatcccagcagatcatggcatc
acctgcaatctcctctacgccaagcctacgactttttcctggcagatctc
tgtcatcaaggatttggtgcgccagggagttcccgtggaaggaatcacca
tcggcgccggcatcccttctccggaggtcgtccaagaatgtgtacagtcc
atcggactcaagcacatctcattcaagcctgggtctttcgaagccattca
ccaagtcatacagatcgcgcgtacccatcctaactttttgatcgggttgc
aatggaccgcaggacgagggggaggacatcattcctgggaagacttccat
ggacctattttggcaacctacgctcaaatccgatcatgtccgaatattct
cctcgttgtaggtagtggattcggtggaggcccggacacgtttccctacc
tcacgggccaatgggcccaggcctttggctatccatgcatgcccttcgac
ggagtgttgctcggcagtcgcatgatggtggctcgggaagcccatacgtc
agcccaggcaaaacgcttgattatagatgcgcaaggcgtgggagatgcag
attggcacaagtctttcgatgagcctaccggcggcgtagtgacggtcaac
tcggaattcggtcaacctatccacgttctagctactcgcggagtgatgtt
gtggaaagaactcgacaaccgggtcttttcaatcaaagacacttctaagc
gcttagaatatttgcgcaaccaccggcaagaaattgtgagccgtcttaac
gcagactttgcccgtccctggtttgccgttgacggacacggacagaatgt
ggagttggaggacatgacctacctcgaggttctccgccgtttgtgcgatc
tcacgtatgtttcccaccagaagcgatgggtagatccatcatatcgaata
ttattgttggacttcgttcatttgcttcgagaacgattccaatgcgctat
tgacaaccccggcgaatatccactcgacatcatcgtccgggtggaagaga
gcttgaaggataaagcataccgcacgctttatccagaagatgtctctctt
ctaatgcatttgttcagccgacgtgacatcaagcccgtaccattcatccc
caggttggatgagcgttttgagacctggtttaaaaaagactcattgtggc
aatccgaagatgtggaggcggtaattggacaggacgtccagcgaatcttc
atcattcaagggcctatggccgttcagtactcaatatccgacgatgagtc
tgttaaagacattttacacaatatttgtaatcattacgtggaggctctac
aggctgattcaagagaaacttctatcggcgatgtacactcgatcacgcaa
aaacctctcagcgcgtttcctgggctcaaagtgacgacaaatagggtcca
agggctctataagttcgagaaagtaggagcagtccccgaaatggacgttc
tttttgagcatattgtcggattgtcgaagtcatgggctcggacatgtttg
atgagtaaatcggtctttagggacggttctcgtttgcataaccccattcg
cgccgcactccagctccagcgcggcgacaccatcgaggtgcttttaacag
cagactcggaaattcgcaagattcgacttatttcacccacgggggatggt
ggatccacttctaaggtcgtattagagatagtctctaacgacggacaaag
agttttcgccaccttggcccctaacatcccactcagccccgagcccagcg
tcgtcttttgcttcaaggtcgaccagaagccgaatgagtggacccttgag
gaggatgcgtctggccgggcagagaggatcaaggcattatacatgagttt
gtggaacttgggctttccgaacaaggcctctgttttgggtcttaattcgc
aattcacgggagaagaattgatgatcacaacggacaagattcgtgatttc
gaaagggtattgcggcaaaccagtcctcttcagttgcagtcatggaaccc
ccaaggatgtgtacctatcgactactgcgtggtcatcgcctggtctgctc
ttaccaagcctttgatggtctcctctttgaaatgcgacctcttggatttg
ctccacagcgctataagcttccactatgctccatctgtcaaaccattgcg
ggtgggcgatattgtcaaaacctcatcccgtatcctagcggtctcggtga
gacctaggggaactatgttgacggtgtcggcggacattcagcgccaggga
caacatgtagtcactgtcaaatcagatttctttctcggaggccccgtttt
ggcatgtgaaacccctttcgaactcactgaggagcctgaaatggttgtcc
atgtcgactctgaagtgcgccgtgctattttacacagccgcaagtggctc
atgcgagaagatcgcgcgctagatttgctagggaggcagctcctcttcag
attaaagagcgaaaaattgttcaggccagacggccagctagcattgttac
aggtaacaggttccgtgttcagctacagccccgatgggtcaacgacagca
ttcggtcgcgtatacttcgaaagcgagtcttgtacagggaacgtggtgat
ggacttcttgcaccgctacggtgcacctcgggcgcagttgttggagttgc
aacatcccgggtggacgggcacctctactgtggcagtaagaggtcctcga
cgcagccaatcctacgcacgcgtctccctcgatcataatcccatccatgt
ttgtccggcctttgcgcgatacgctggtctctcgggtcccattgtccatg
ggatggaaacctctgccatgatgcgcagaattgccgaatgggccatcgga
gatgcagaccggtctcggttccggagctggcatatcaccttgcaagcacc
cgtccaccccaacgaccctttgcgggtggagttgcagcataaggccatgg
aggacggggaaatggttttgaaagtacaagcatttaacgaaaggacggaa
gaacgcgtagcggaggcagatgcccatgttgagcaggaaactacggctta
cgtcttctgtggccagggcagtcaacgacaggggatgggaatggacttgt
acgtcaactgtccggaggctaaagcgttgtgggctcgcgccgacaagcat
ttgtgggagaaatatgggttctccatcttgcacattgtgcaaaacaaccc
tccagccctcactgttcactttggcagccagcgagggcgccgtattcgtg
ccaactatttgcgcatgatgggacagccaccgatagatggtagacatccg
cccatattgaagggattgacgcggaattcgacctcgtacaccttctccta
ttcccaggggttgttgatgtccacccagttcgcccagcccgcattggcgt
tgatggaaatggctcagttcgaatggctcaaagcccagggagtcgttcag
aagggtgcgcggttcgcgggacattcgttgggagaatatgccgcccttgg
agcttgtgcttccttcctctcatttgaagatctcatatctctcatctttt
atcggggcttgaagatgcagaatgcgttgccgcgcgatgccaacggccac
accgactatggaatgttggctgccgatccatcgcggataggaaaaggttt
cgaggaagcgagtttgaaatgtcttgtccatatcattcaacaggagaccg
gctggttcgtggaagtcgtcaactacaacatcaactcgcagcaatacgtc
tgtgcaggccatttccgagccctttggatgttgggtaagatatgcgatga
cctttcatgccaccctcaaccggagactgttgaaggccaagagctacggg
ccatggtctggaagcatgtcccgacggtggagcaggtgccccgcgaggat
cgcatggaacgaggtcgagcgaccattccgttgccggggatcgatatccc
ataccattcgaccatgttacgaggggagattgagccttatcgtgaatatt
tgtctgaacgtatcaaggtgggggatgtgaagccgtgcgaattggtggga
cgctggatccctaatgttgttggccagcctttctccgtcgataagtctta
cgttcagttggtgcacggcatcacaggtagtcctcggcttcattccttgc
ttcaacaaatggcgtga
Example 4
Transformation of C. Tropicalis with the Synthetic Hexanoate
Synthase Subunit Genes
[0271] Candida tropicalis cells (ATCC number 20962) and cultured
under standard conditions in YPD medium at 30 degrees Celsius. The
synthetic genes encoding hexA and hexB are amplified using standard
PCR amplification techniques. A linear DNA construct comprising,
from 5' to 3', the TEF (transcription elongation factor) promoter,
the hexA-AGC gene, the TEF promoter, the hexB-AGC gene, and the
URA3 marker. Each end of this construct is designed to contain a
mini-URA-Blaster for integration of the construct into C.
tropicalis genomic DNA (Alani E, Cao L, Kleckner N. A method for
gene disruption that allows repeated use of URA3 selection in the
construction of multiply disrupted yeast strains. Genetics. 1987
August; 116 (4):541-545).
[0272] The construct is amplified using standard techniques.
Transformation of C. tropicalis cells with this linear construct is
accomplished using standard electroporation techniques such as
those set forth in U.S. Pat. No. 5,648,247 or U.S. Pat. No.
5,204,252. Transformants are selected by plating and growing the
transformed cells on SC-URA media as described above in which only
transformants will survive. To remove the URA cassette, the
confirmed strain is then replated onto SC complete media containing
5-Fluoroorotic Acid (5-FOA) and confirmed for the loss of the URA
cassette.
Example 5
Assay of Cytochrome P450 with Activity on Six Carbon Chains in C.
Tropicalis
[0273] Cultures of C. tropicalis are cultured in YPD media to late
log phase and then exposed to hexane exposed to various
concentrations of hexane up to about 0.1 percent (v/v) induce the
expression of the cytochrome p450 gene having activity specific for
six carbon substrates. After about 2 hours exposure to the hexane
solution, cells were harvested and RNA isolated using techniques
described above. The specifically induced gene may be detected by
Northern blotting and/or quantitative RT-PCR.
[0274] Cells to be analyzed for cytochrome P450 activity are grown
under standard conditions and harvested for the production of
microsomes. Microsomes were prepared by lysing cells in
Tris-buffered sucrose (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.25M
sucrose). Differential centrifugation is performed first at
25,000.times.g then at 100,000.times.g to pellet cell debris then
microsomes, respectively. The microsome pellet is resuspended in
0.1 M phosphate buffer (pH 7.5), 1 mM EDTA to a final concentration
of approximately 10 mg protein/mL.
[0275] A reaction mixture containing approximately 0.3 mg
microsomes, 0.1 mM sodium hexanoate, 0.7 mM NADPH, 50 mM Tris-HCl
pH 7.5 in 1 mL is initiated by the addition of NADPH and incubated
at 37.degree. C. for 10 minutes. The reaction is terminated by
addition of 0.25 mL 5M HCl and 0.25 mL 2.5 ug/mL 10-hydroxydecanoic
acid is added as an internal standard (3.3 nmol). The mixture is
extracted with 4.5 mL diethyl ether under NaCl-saturated
conditions. The organic phase is transferred to a new tube and
evaporated to dryness. The residue is dissolved in acetonitrile
containing 10 mM 3-bromomethyl-7-methoxy-1,4-benzoxazin-2-one
(BrMB) and 0.1 mL of 15 mg/mL 18-crown-6 in acetonitril saturated
with K.sub.2CO.sub.3. The solution is incubated at 40.degree. C.
for 30 minutes before addition of 0.05 mL 2% acetic acid. The
fluorescently labeled omega-hydroxy fatty acids are resolved via
HPLC with detection at 430 nm and excitation at 355 nm.
Example 6
Examples of Polynucleotide Regulators
[0276] Provided in the tables hereafter are non-limiting examples
of regulator polynucleotides that can be utilized in embodiments
herein. Such polynucleotides may be utilized in native form or may
be modified for use herein. Examples of regulatory polynucleotides
include those that are regulated by oxygen levels in a system
(e.g., upregulated or downregulated by relatively high oxygen
levels or relatively low oxygen levels).
TABLE-US-00008 Regulated Yeast Promoters - Up-regulated by oxygen
Relative Relative Gene mRNA level mRNA level ORF name name
(Aerobic) (Anaerobic) Ratio YPL275W 4389 30 219.5 YPL276W 2368 30
118.4 YDR256C CTA1 2076 30 103.8 YHR096C HXT5 1846 30 72.4 YDL218W
1189 30 59.4 YCR010C 1489 30 48.8 YOR161C 599 30 29.9 YPL200W 589
30 29.5 YGR110W 1497 30 27 YNL237W YTP1 505 30 25.2 YBR116C 458 30
22.9 YOR348C PUT4 451 30 22.6 YBR117C TKL2 418 30 20.9 YLL052C 635
30 20 YNL195C 1578 30 19.4 YPR193C 697 30 15.7 YDL222C 301 30 15
YNL335W 294 30 14.6 YPL036W PMA2 487 30 12.8 YML122C 206 30 10.3
YGR067C 236 30 10.2 YPR192W 204 30 10.2 YNL014W 828 30 9.8 YFL061W
256 30 9.1 YNR056C 163 30 8.1 YOR186W 153 30 7.6 YDR222W 196 30 6.5
YOR338W 240 30 6.3 YPR200C 113 30 5.7 YMR018W 778 30 5.2 YOR364W
123 30 5.1 YNL234W 93 30 4.7 YNR064C 85 30 4.2 YGR213C RTA1 104 30
4 YCL064C CHA1 80 30 4 YOL154W 302 30 3.9 YPR150W 79 30 3.9 YPR196W
MAL63 30 30 3.6 YDR420W HKR1 221 30 3.5 YJL216C 115 30 3.5 YNL270C
ALP1 67 30 3.3 YHL016C DUR3 224 30 3.2 YOL131W 230 30 3 YOR077W
RTS2 210 30 3 YDR536W STL1 55 30 2.7 YNL150W 78 30 2.6 YHR212C 149
30 2.4 YJL108C 106 30 2.4 YGR069W 49 30 2.4 YDR106W 60 30 2.3
YNR034W SOL1 197 30 2.2 YEL073C 104 30 2.1 YOL141W 81 30 1.8
TABLE-US-00009 Regulated Yeast Promoters - Down-regulated by oxygen
Relative Relative Gene mRNA level mRNA level ORF name name
(Aerobic) (Anaerobic) Ratio YJR047C ANB1 30 4901 231.1 YMR319C FET4
30 1159 58 YPR194C 30 982 49.1 YIR019C STA1 30 981 22.8 YHL042W 30
608 12 YHR210C 30 552 27.6 YHR079B SAE3 30 401 2.7 YGL162W STO1 30
371 9.6 YHL044W 30 334 16.7 YOL015W 30 320 6.1 YCLX07W 30 292 4.2
YIL013C PDR11 30 266 10.6 YDR046C 30 263 13.2 YBR040W FIG1 30 257
12.8 YLR040C 30 234 2.9 YOR255W 30 231 11.6 YOL014W 30 229 11.4
YAR028W 30 212 7.5 YER089C 30 201 6.2 YFL012W 30 193 9.7 YDR539W 30
187 3.4 YHL043W 30 179 8.9 YJR162C 30 173 6 YMR165C SMP2 30 147 3.5
YER106W 30 145 7.3 YDR541C 30 140 7 YCRX07W 30 138 3.3 YHR048W 30
137 6.9 YCL021W 30 136 6.8 YOL160W 30 136 6.8 YCRX08W 30 132 6.6
YMR057C 30 109 5.5 YDR540C 30 83 4.2 YOR378W 30 78 3.9 YBR085W AAC3
45 1281 28.3 YER188W 47 746 15.8 YLL065W GIN11 50 175 3.5 YDL241W
58 645 11.1 YBR238C 59 274 4.6 YCR048W ARE1 60 527 8.7 YOL165C 60
306 5.1 YNR075W 60 251 4.2 YJL213W 60 250 4.2 YPL265W DIP5 61 772
12.7 YDL093W PMT5 62 353 5.7 YKR034W DAL80 63 345 5.4 YKR053C 66
1268 19.3 YJR147W 68 281 4.1
[0277] Known and putative DNA binding motifs
TABLE-US-00010 Regulator Known Consensus Motif SEQ ID NO: Abf1
TCRNNNNNNACG 50 Cbf1 RTCACRTG Gal4 CGGNNNNNNNNNNNCCG 51 Gcn4
TGACTCA Gcr1 CTTCC Hap2 CCAATNA Hap3 CCAATNA Hap4 CCAATNA Hsf1
GAANNTTCNNGAA 52 Ino2 ATGTGAAA Mata(A1) TGATGTANNT 53 Mcm1
CCNNNWWRGG 54 Mig1 WWWWSYGGGG 55 Pho4 CACGTG Rap1 RMACCCANNCAYY 56
Reb1 CGGGTRR Ste12 TGAAACA Swi4 CACGAAA Swi6 CACGAAA Yap1 TTACTAA
Putative DNA Binding Motifs Best Motif (scored by E- Best Motif
(scored by Regulator value) SEQ ID NO: Hypergeometric) SEQ ID NO:
Abf1 TYCGT--R-ARTGAYA 57 TYCGT--R-ARTGAYA 151 Ace2
RRRAARARAA-A-RARAA 58 GTGTGTGTGTGTGTG 152 Adr1 A-AG-GAGAGAG-GGCAG
59 YTSTYSTT-TTGYTWTT 153 Arg80 T--CCW-TTTKTTTC 60 GCATGACCATCCACG
154 Arg81 AAAAARARAAAARMA 61 GSGAYARMGGAMAAAAA 155 Aro80
YKYTYTTYTT----KY 62 TRCCGAGRYW-SSSGCGS 156 Ash1 CGTCCGGCGC 63
CGTCCGGCGC 157 Azf1 GAAAAAGMAAAAAAA 64 AARWTSGARG-A--CSAA 158 Bas1
TTTTYYTTYTTKY-TY-T 65 CS-CCAATGK--CS 159 Cad1 CATKYTTTTTTKYTY 66
GCT-ACTAAT 160 Cbf1 CACGTGACYA 67 CACGTGACYA 161 Cha4
CA---ACACASA-A 68 CAYAMRTGY-C 162 Cin5 none none Crz1
GG-A-A--AR-ARGGC- 69 TSGYGRGASA 163 Cup9 TTTKYTKTTY-YTTTKTY 70
K-C-C---SCGCTACKGC 164 Dal81 WTTKTTTTTYTTTTT-T 71 SR-GGCMCGGC-SSG
165 Dal82 TTKTTTTYTTC 72 TACYACA-CACAWGA 166 Dig1
AAA--RAA-GARRAA-AR 73 CCYTG-AYTTCW-CTTC 167 Dot6 GTGMAK-MGRA-G-G 74
GTGMAK-MGRA-G-G 168 Fhl1 -TTWACAYCCRTACAY-Y 75 -TTWACAYCCRTACAY-Y
169 Fkh1 TTT-CTTTKYTT-YTTTT 76 AAW-RTAAAYARG 170 Fkh2
AAARA-RAAA-AAAR-AA 77 GG-AAWA-GTAAACAA 171 Fzf1 CACACACACACACACAC
78 SASTKCWCTCKTCGT 172 Gal4 TTGCTTGAACGSATGCCA 79
TTGCTTGAACGSATGCCA 173 Gal4 (Gal) YCTTTTTTTTYTTYYKG 80
CGGM---CW-Y--CCCG 174 Gat1 none none Gat3 RRSCCGMCGMGRCGCGCS 81
RGARGTSACGCAKRTTCT 175 Gcn4 AAA-ARAR-RAAAARRAR 82 TGAGTCAY Gcr1
GGAAGCTGAAACGYMWRR 83 GGAAGCTGAAACGYMWRR 176 Gcr2
GGAGAGGCATGATGGGGG 84 AGGTGATGGAGTGCTCAG 177 Gln3 CT-CCTTTCT 85
GKCTRR-RGGAGA-GM 178 Grf10 GAAARRAAAAAAMRMARA 86 -GGGSG-T-SYGT-CGA
179 Gts1 G-GCCRS--TM 87 AG-AWGTTTTTGWCAAMA 180 Haa1 none none Hal9
TTTTTTYTTTTY-KTTTT 88 KCKSGCAGGCWTTKYTCT 181 Hap2
YTTCTTTTYT-Y-C-KT- 89 G-CCSART-GC 182 Hap3 T-SYKCTTTTCYTTY 90
SGCGMGGG--CC-GACCG 183 Hap4 STT-YTTTY-TTYTYYYY 91 YCT-ATTSG-C-GS
184 Hap5 YK-TTTWYYTC 92 T-TTSMTT-YTTTCCK-C 185 Hir1 AAAA-A-AARAR-AG
93 CCACKTKSGSCCT-S 186 Hir2 WAAAAAAGAAAA-AAAAR 94 CRSGCYWGKGC 187
Hms1 AAA-GG-ARAM 95 -AARAAGC-GGGCAC-C 188 Hsf1 TYTTCYAGAA--TTCY 96
TYTTCYAGAA--TTCY 189 Ime4 CACACACACACACACACA 97 CACACACACACACACACA
190 Ino2 TTTYCACATGC 98 SCKKCGCKSTSSTTYAA 191 Ino4 G--GCATGTGAAAA
99 G--GCATGTGAAAA 192 Ixr1 GAAAA-AAAAAAAARA-A 100 CTTTTTTTYYTSGCC
193 Leu3 GAAAAARAARAA-AA 101 GCCGGTMMCGSYC-- 194 Mac1
YTTKT--TTTTTYTYTTT 102 A--TTTTTYTTKYGC 195 Mal13 GCAG-GCAGG 103
AAAC-TTTATA-ATACA 196 Mal33 none none Mata1 GCCC-C CAAT-TCT-CK 197
Mbp1 TTTYTYKTTT-YYTTTTT 104 G-RR-A-ACGCGT-R 198 Mcm1
TTTCC-AAW-RGGAAA 105 TTTCC-AAW-RGGAAA 199 Met31 YTTYYTTYTTTTYTYTTC
106 Met4 MTTTTTYTYTYTTC 107 Mig1 TATACA-AGMKRTATATG 108 Mot3
TMTTT-TY-CTT-TTTWK 109 Msn1 KT--TTWTTATTCC-C 110 Msn2 ACCACC Msn4
R--AAAA-RA-AARAAAT 111 Mss11 TTTTTTTTCWCTTTKYC 112 Ndd1
TTTY-YTKTTTY-YTTYT 113 Nrg1 TTY--TTYTT-YTTTYYY 114 Pdr1
T-YGTGKRYGT-YG 115 Phd1 TTYYYTTTTTYTTTTYTT 116 Pho4 GAMAAAAAARAAAAR
117 Put3 CYCGGGAAGCSAMM-CCG 118 Rap1 GRTGYAYGGRTGY 119 Rcs1
KMAARAAAAARAAR 120 Reb1 RTTACCCGS Rfx1 AYGRAAAARARAAAARAA 121 Rgm1
GGAKSCC-TTTY-GMRTA 122 Rgt1 CCCTCC Rim101 GCGCCGC Rlm1
TTTTC-KTTTYTTTTTC 123 Rme1 ARAAGMAGAAARRAA 124 Rox1
YTTTTCTTTTY-TTTTT 125 Rph1 ARRARAAAGG- 126 Rtg1 YST-YK-TYTT-CTCCCM
127 Rtg3 GARA-AAAAR-RAARAAA 128 Sfl1 CY--GGSSA-C 129 Sfp1
CACACACACACACAYA 130 Sip4 CTTYTWTTKTTKTSA 131 Skn7
YTTYYYTYTTTYTYYTTT 132 Sko1 none Smp1 AMAAAAARAARWARA-AA 133 Sok2
ARAAAARRAAAAAG-RAA 134 Stb1 RAARAAAAARCMRSRAAA 135 Ste12
TTYTKTYTY-TYYKTTTY 136 Stp1 GAAAAMAA-AAAAA-AAA 137 Stp2
YAA-ARAARAAAAA-AAM 138 Sum1 TY-TTTTTTYTTTTT-TK 139 Swi4
RAARAARAAA-AA-R-AA 140 Swi5 CACACACACACACACACA 141 Swi6
RAARRRAAAAA-AAAMAA 142 Thi2 GCCAGACCTAC 143 Uga3 GG-GGCT Yap1
TTYTTYTTYTTTY-YTYT 144 Yap3 none Yap5 YKSGCGCGYCKCGKCGGS 145 Yap6
TTTTYYTTTTYYYYKTT 146
Yap7 none Yfl044c TTCTTKTYYTTTT 147 Yjl206c TTYTTTTYTYYTTTYTTT 148
Zap1 TTGCTTGAACGGATGCCA 149 Zms1 MG-MCAAAAATAAAAS 150
Transcriptional Repressors
TABLE-US-00011 [0278] Associated Gene(s) Description(s) WHI5
Repressor of G1 transcription that binds to SCB binding factor
(SBF) at SCB target promoters in early G1; phosphorylation of Whi5p
by the CDK, Cln3p/Cdc28p relieves repression and promoter binding
by Whi5; periodically expressed in G1 TUP1 General repressor of
transcription, forms complex with Cyc8p, involved in the
establishment of repressive chromatin structure through
interactions with histones H3 and H4, appears to enhance expression
of some genes ROX1 Heme-dependent repressor of hypoxic genes;
contains an HMG domain that is responsible for DNA bending activity
SFL1 Transcriptional repressor and activator; involved in
repression of flocculation-related genes, and activation of stress
responsive genes; negatively regulated by cAMP-dependent protein
kinase A subunit Tpk2p RIM101 Transcriptional repressor involved in
response to pH and in cell wall construction; required for alkaline
pH-stimulated haploid invasive growth and sporulation; activated by
proteolytic processing; similar to A. nidulans PacC RDR1
Transcriptional repressor involved in the control of multidrug
resistance; negatively regulates expression of the PDR5 gene;
member of the Gal4p family of zinc cluster proteins SUM1
Transcriptional repressor required for mitotic repression of middle
sporulation-specific genes; also acts as general replication
initiation factor; involved in telomere maintenance, chromatin
silencing; regulated by pachytene checkpoint XBP1 Transcriptional
repressor that binds to promoter sequences of the cyclin genes,
CYS3, and SMF2; expression is induced by stress or starvation
during mitosis, and late in meiosis; member of the Swi4p/Mbp1p
family; potential Cdc28p substrate NRG2 Transcriptional repressor
that mediates glucose repression and negatively regulates
filamentous growth; has similarity to Nrg1p NRG1 Transcriptional
repressor that recruits the Cyc8p-Tup1p complex to promoters;
mediates glucose repression and negatively regulates a variety of
processes including filamentous growth and alkaline pH response
CUP9 Homeodomain-containing transcriptional repressor of PTR2,
which encodes a major peptide transporter; imported peptides
activate ubiquitin-dependent proteolysis, resulting in degradation
of Cup9p and de-repression of PTR2 transcription YOX1
Homeodomain-containing transcriptional repressor, binds to Mcm1p
and to early cell cycle boxes (ECBs) in the promoters of cell
cycle- regulated genes expressed in M/G1 phase; expression is cell
cycle- regulated; potential Cdc28p substrate RFX1 Major
transcriptional repressor of DNA-damage-regulated genes, recruits
repressors Tup1p and Cyc8p to their promoters; involved in DNA
damage and replication checkpoint pathway; similar to a family of
mammalian DNA binding RFX1-4 proteins MIG3 Probable transcriptional
repressor involved in response to toxic agents such as hydroxyurea
that inhibit ribonucleotide reductase; phosphorylation by Snf1p or
the Mec1p pathway inactivates Mig3p, allowing induction of damage
response genes RGM1 Putative transcriptional repressor with
proline-rich zinc fingers; overproduction impairs cell growth YHP1
One of two homeobox transcriptional repressors (see also Yox1p),
that bind to Mcm1p and to early cell cycle box (ECB) elements of
cell cycle regulated genes, thereby restricting ECB-mediated
transcription to the M/G1 interval HOS4 Subunit of the Set3
complex, which is a meiotic-specific repressor of sporulation
specific genes that contains deacetylase activity; potential Cdc28p
substrate CAF20 Phosphoprotein of the mRNA cap-binding complex
involved in translational control, repressor of cap-dependent
translation initiation, competes with eIF4G for binding to eIF4E
SAP1 Putative ATPase of the AAA family, interacts with the Sin1p
transcriptional repressor in the two-hybrid system SET3 Defining
member of the SET3 histone deacetylase complex which is a
meiosis-specific repressor of sporulation genes; necessary for
efficient transcription by RNAPII; one of two yeast proteins that
contains both SET and PHD domains RPH1 JmjC domain-containing
histone demethylase which can specifically demethylate H3K36 tri-
and dimethyl modification states; transcriptional repressor of
PHR1; Rph1p phosphorylation during DNA damage is under control of
the MEC1-RAD53 pathway YMR181C Protein of unknown function; mRNA
transcribed as part of a bicistronic transcript with a predicted
transcriptional repressor RGM1/YMR182C; mRNA is destroyed by
nonsense-mediated decay (NMD); YMR181C is not an essential gene
YLR345W Similar to
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase enzymes
responsible for the metabolism of fructoso-2,6- bisphosphate; mRNA
expression is repressed by the Rfx1p-Tup1p- Ssn6p repressor
complex; YLR345W is not an essential gene MCM1 Transcription factor
involved in cell-type-specific transcription and pheromone
response; plays a central role in the formation of both repressor
and activator complexes PHR1 DNA photolyase involved in
photoreactivation, repairs pyrimidine dimers in the presence of
visible light; induced by DNA damage; regulated by transcriptional
repressor Rph1p HOS2 Histone deacetylase required for gene
activation via specific deacetylation of lysines in H3 and H4
histone tails; subunit of the Set3 complex, a meiotic-specific
repressor of sporulation specific genes that contains deacetylase
activity RGT1 Glucose-responsive transcription factor that
regulates expression of several glucose transporter (HXT) genes in
response to glucose; binds to promoters and acts both as a
transcriptional activator and repressor SRB7 Subunit of the RNA
polymerase II mediator complex; associates with core polymerase
subunits to form the RNA polymerase II holoenzyme; essential for
transcriptional regulation; target of the global repressor Tup1p
GAL11 Subunit of the RNA polymerase II mediator complex; associates
with core polymerase subunits to form the RNA polymerase II
holoenzyme; affects transcription by acting as target of activators
and repressors
Transcriptional Activators
TABLE-US-00012 [0279] Associated Gene(s) Description(s) SKT5
Activator of Chs3p (chitin synthase III), recruits Chs3p to the bud
neck via interaction with Bni4p; has similarity to Shc1p, which
activates Chs3p during sporulation MSA1 Activator of G1-specific
transcription factors, MBF and SBF, that regulates both the timing
of G1-specific gene transcription, and cell cycle initiation;
potential Cdc28p substrate AMA1 Activator of meiotic anaphase
promoting complex (APC/C); Cdc20p family member; required for
initiation of spore wall assembly; required for Clb1p degradation
during meiosis STB5 Activator of multidrug resistance genes, forms
a heterodimer with Pdr1p; contains a Zn(II)2Cys6 zinc finger domain
that interacts with a PDRE (pleotropic drug resistance element) in
vitro; binds Sin3p in a two-hybrid assay RRD2 Activator of the
phosphotyrosyl phosphatase activity of PP2A, peptidyl- prolyl
cis/trans-isomerase; regulates G1 phase progression, the
osmoresponse, microtubule dynamics; subunit of the Tap42p-Pph21p-
Rrd2p complex BLM10 Proteasome activator subunit; found in
association with core particles, with and without the 19S
regulatory particle; required for resistance to bleomycin, may be
involved in protecting against oxidative damage; similar to
mammalian PA200 SHC1 Sporulation-specific activator of Chs3p
(chitin synthase III), required for the synthesis of the chitosan
layer of ascospores; has similarity to Skt5p, which activates Chs3p
during vegetative growth; transcriptionally induced at alkaline pH
NDD1 Transcriptional activator essential for nuclear division;
localized to the nucleus; essential component of the mechanism that
activates the expression of a set of late-S-phase-specific genes
IMP2' Transcriptional activator involved in maintenance of ion
homeostasis and protection against DNA damage caused by bleomycin
and other oxidants, contains a C-terminal leucine-rich repeat LYS14
Transcriptional activator involved in regulation of genes of the
lysine biosynthesis pathway; requires 2-aminoadipate semialdehyde
as co- inducer MSN1 Transcriptional activator involved in
regulation of invertase and glucoamylase expression, invasive
growth and pseudohyphal differentiation, iron uptake, chromium
accumulation, and response to osmotic stress; localizes to the
nucleus HAA1 Transcriptional activator involved in the
transcription of TPO2, YRO2, and other genes putatively encoding
membrane stress proteins; involved in adaptation to weak acid
stress UGA3 Transcriptional activator necessary for
gamma-aminobutyrate (GABA)- dependent induction of GABA genes (such
as UGA1, UGA2, UGA4); zinc-finger transcription factor of the
Zn(2)-Cys(6) binuclear cluster domain type; localized to the
nucleus GCR1 Transcriptional activator of genes involved in
glycolysis; DNA-binding protein that interacts and functions with
the transcriptional activator Gcr2p GCR2 Transcriptional activator
of genes involved in glycolysis; interacts and functions with the
DNA-binding protein Gcr1p GAT1 Transcriptional activator of genes
involved in nitrogen catabolite repression; contains a GATA-1-type
zinc finger DNA-binding motif; activity and localization regulated
by nitrogen limitation and Ure2p GLN3 Transcriptional activator of
genes regulated by nitrogen catabolite repression (NCR),
localization and activity regulated by quality of nitrogen source
PUT3 Transcriptional activator of proline utilization genes,
constitutively binds PUT1 and PUT2 promoter sequences and undergoes
a conformational change to form the active state; has a
Zn(2)-Cys(6) binuclear cluster domain ARR1 Transcriptional
activator of the basic leucine zipper (bZIP) family, required for
transcription of genes involved in resistance to arsenic compounds
PDR3 Transcriptional activator of the pleiotropic drug resistance
network, regulates expression of ATP-binding cassette (ABC)
transporters through binding to cis-acting sites known as PDREs
(PDR responsive elements) MSN4 Transcriptional activator related to
Msn2p; activated in stress conditions, which results in
translocation from the cytoplasm to the nucleus; binds DNA at
stress response elements of responsive genes, inducing gene
expression MSN2 Transcriptional activator related to Msn4p;
activated in stress conditions, which results in translocation from
the cytoplasm to the nucleus; binds DNA at stress response elements
of responsive genes, inducing gene expression PHD1 Transcriptional
activator that enhances pseudohyphal growth; regulates expression
of FLO11, an adhesin required for pseudohyphal filament formation;
similar to StuA, an A. nidulans developmental regulator; potential
Cdc28p substrate FHL1 Transcriptional activator with similarity to
DNA-binding domain of Drosophila forkhead but unable to bind DNA in
vitro; required for rRNA processing; isolated as a suppressor of
splicing factor prp4 VHR1 Transcriptional activator, required for
the vitamin H-responsive element (VHRE) mediated induction of VHT1
(Vitamin H transporter) and BIO5 (biotin biosynthesis intermediate
transporter) in response to low biotin concentrations CDC20
Cell-cycle regulated activator of anaphase-promoting
complex/cyclosome (APC/C), which is required for metaphase/anaphase
transition; directs ubiquitination of mitotic cyclins, Pds1p, and
other anaphase inhibitors; potential Cdc28p substrate CDH1
Cell-cycle regulated activator of the anaphase-promoting
complex/cyclosome (APC/C), which directs ubiquitination of cyclins
resulting in mitotic exit; targets the APC/C to specific substrates
including Cdc20p, Ase1p, Cin8p and Fin1p AFT2 Iron-regulated
transcriptional activator; activates genes involved in
intracellular iron use and required for iron homeostasis and
resistance to oxidative stress; similar to Aft1p MET4
Leucine-zipper transcriptional activator, responsible for the
regulation of the sulfur amino acid pathway, requires different
combinations of the auxiliary factors Cbf1p, Met28p, Met31p and
Met32p CBS2 Mitochondrial translational activator of the COB mRNA;
interacts with translating ribosomes, acts on the COB mRNA
5'-untranslated leader CBS1 Mitochondrial translational activator
of the COB mRNA; membrane protein that interacts with translating
ribosomes, acts on the COB mRNA 5'-untranslated leader CBP6
Mitochondrial translational activator of the COB mRNA;
phosphorylated PET111 Mitochondrial translational activator
specific for the COX2 mRNA; located in the mitochondrial inner
membrane PET494 Mitochondrial translational activator specific for
the COX3 mRNA, acts together with Pet54p and Pet122p; located in
the mitochondrial inner membrane PET122 Mitochondrial translational
activator specific for the COX3 mRNA, acts together with Pet54p and
Pet494p; located in the mitochondrial inner membrane RRD1
Peptidyl-prolyl cis/trans-isomerase, activator of the
phosphotyrosyl phosphatase activity of PP2A; involved in G1 phase
progression, microtubule dynamics, bud morphogenesis and DNA
repair; subunit of the Tap42p-Sit4p-Rrd1p complex YPR196W Putative
maltose activator POG1 Putative transcriptional activator that
promotes recovery from pheromone induced arrest; inhibits both
alpha-factor induced G1 arrest and repression of CLN1 and CLN2 via
SCB/MCB promoter elements; potential Cdc28p substrate; SBF
regulated MSA2 Putative transcriptional activator, that interacts
with G1-specific transcription factor, MBF and G1-specific
promoters; ortholog of Msa2p, an MBF and SBF activator that
regulates G1-specific transcription and cell cycle initiation
PET309 Specific translational activator for the COX1 mRNA, also
influences stability of intron-containing COX1 primary transcripts;
localizes to the mitochondrial inner membrane; contains seven
pentatricopeptide repeats (PPRs) TEA1 Ty1 enhancer activator
required for full levels of Ty enhancer-mediated transcription; C6
zinc cluster DNA-binding protein PIP2 Autoregulatory
oleate-specific transcriptional activator of peroxisome
proliferation, contains Zn(2)-Cys(6) cluster domain, forms
heterodimer with Oaf1p, binds oleate response elements (OREs),
activates beta- oxidation genes CHA4 DNA binding transcriptional
activator, mediates serine/threonine activation of the catabolic
L-serine (L-threonine) deaminase (CHA1); Zinc-finger protein with
Zn[2]-Cys[6] fungal-type binuclear cluster domain SFL1
Transcriptional repressor and activator; involved in repression of
flocculation-related genes, and activation of stress responsive
genes; negatively regulated by cAMP-dependent protein kinase A
subunit Tpk2p RDS2 Zinc cluster transcriptional activator involved
in conferring resistance to ketoconazole CAT8 Zinc cluster
transcriptional activator necessary for derepression of a variety
of genes under non-fermentative growth conditions, active after
diauxic shift, binds carbon source responsive elements ARO80 Zinc
finger transcriptional activator of the Zn2Cys6 family; activates
transcription of aromatic amino acid catabolic genes in the
presence of aromatic amino acids SIP4 C6 zinc cluster
transcriptional activator that binds to the carbon source-
responsive element (CSRE) of gluconeogenic genes; involved in the
positive regulation of gluconeogenesis; regulated by Snf1p protein
kinase; localized to the nucleus SPT10 Putative histone acetylase,
sequence-specific activator of histone genes, binds specifically
and highly cooperatively to pairs of UAS elements in core histone
promoters, functions at or near the TATA box MET28 Basic leucine
zipper (bZIP) transcriptional activator in the Cbf1p- Met4p-Met28p
complex, participates in the regulation of sulfur metabolism GCN4
Basic leucine zipper (bZIP) transcriptional activator of amino acid
biosynthetic genes in response to amino acid starvation; expression
is tightly regulated at both the transcriptional and translational
levels CAD1 AP-1-like basic leucine zipper (bZIP) transcriptional
activator involved in stress responses, iron metabolism, and
pleiotropic drug resistance; controls a set of genes involved in
stabilizing proteins; binds consensus sequence TTACTAA INO2
Component of the heteromeric Ino2p/Ino4p basic helix-loop-helix
transcription activator that binds inositol/choline-responsive
elements (ICREs), required for derepression of phospholipid
biosynthetic genes in response to inositol depletion THI2 Zinc
finger protein of the Zn(II)2Cys6 type, probable transcriptional
activator of thiamine biosynthetic genes SWI4 DNA binding component
of the SBF complex (Swi4p-Swi6p), a transcriptional activator that
in concert with MBF (Mbp1-Swi6p) regulates late G1-specific
transcription of targets including cyclins and genes required for
DNA synthesis and repair HAP5 Subunit of the heme-activated,
glucose-repressed Hap2/3/4/5 CCAAT- binding complex, a
transcriptional activator and global regulator of respiratory gene
expression; required for assembly and DNA binding activity of the
complex HAP3 Subunit of the heme-activated, glucose-repressed
Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator
and global regulator of respiratory gene expression; contains
sequences contributing to both complex assembly and DNA binding
HAP2 Subunit of the heme-activated, glucose-repressed
Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator
and global regulator of respiratory gene expression; contains
sequences sufficient for both complex assembly and DNA binding HAP4
Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p
CCAAT-binding complex, a transcriptional activator and global
regulator of respiratory gene expression; provides the principal
activation function of the complex YML037C Putative protein of
unknown function with some characteristics of a transcriptional
activator; may be a target of Dbf2p-Mob1p kinase; GFP- fusion
protein co-localizes with clathrin-coated vesicles; YML037C is not
an essential gene TRA1 Subunit of SAGA and NuA4 histone
acetyltransferase complexes; interacts with acidic activators
(e.g., Gal4p) which leads to transcription activation; similar to
human TRRAP, which is a cofactor for c-Myc mediated oncogenic
transformation YLL054C Putative protein of unknown function with
similarity to Pip2p, an oleate- specific transcriptional activator
of peroxisome proliferation; YLL054C is not an essential gene RTG2
Sensor of mitochondrial dysfunction; regulates the subcellular
location of Rtg1p and Rtg3p, transcriptional activators of the
retrograde (RTG) and TOR pathways; Rtg2p is inhibited by the
phosphorylated form of Mks1p YBR012C Dubious open reading frame,
unlikely to encode a functional
protein; expression induced by iron-regulated transcriptional
activator Aft2p JEN1 Lactate transporter, required for uptake of
lactate and pyruvate; phosphorylated; expression is derepressed by
transcriptional activator Cat8p during respiratory growth, and
repressed in the presence of glucose, fructose, and mannose MRP1
Mitochondrial ribosomal protein of the small subunit; MRP1 exhibits
genetic interactions with PET122, encoding a COX3-specific
translational activator, and with PET123, encoding a small subunit
mitochondrial ribosomal protein MRP17 Mitochondrial ribosomal
protein of the small subunit; MRP17 exhibits genetic interactions
with PET122, encoding a COX3-specific translational activator TPI1
Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-
life is regulated by iron availability; transcription is controlled
by activators Reb1p, Gcr1p, and Rap1p through binding sites in the
5' non-coding region PKH3 Protein kinase with similarity to
mammalian phosphoinositide- dependent kinase 1 (PDK1) and yeast
Pkh1p and Pkh2p, two redundant upstream activators of Pkc1p;
identified as a multicopy suppressor of a pkh1 pkh2 double mutant
YGL079W Putative protein of unknown function; green fluorescent
protein (GFP)- fusion protein localizes to the endosome; identified
as a transcriptional activator in a high-throughput yeast
one-hybrid assay TFB1 Subunit of TFIIH and nucleotide excision
repair factor 3 complexes, required for nucleotide excision repair,
target for transcriptional activators PET123 Mitochondrial
ribosomal protein of the small subunit; PET123 exhibits genetic
interactions with PET122, which encodes a COX3 mRNA- specific
translational activator MHR1 Protein involved in homologous
recombination in mitochondria and in transcription regulation in
nucleus; binds to activation domains of acidic activators; required
for recombination-dependent mtDNA partitioning MCM1 Transcription
factor involved in cell-type-specific transcription and pheromone
response; plays a central role in the formation of both repressor
and activator complexes EGD1 Subunit beta1 of the nascent
polypeptide-associated complex (NAC) involved in protein targeting,
associated with cytoplasmic ribosomes; enhances DNA binding of the
Gal4p activator; homolog of human BTF3b STE5 Pheromone-response
scaffold protein; binds Ste11p, Ste7p, and Fus3p kinases, forming a
MAPK cascade complex that interacts with the plasma membrane and
Ste4p-Ste18p; allosteric activator of Fus3p that facilitates
Ste7p-mediated activation RGT1 Glucose-responsive transcription
factor that regulates expression of several glucose transporter
(HXT) genes in response to glucose; binds to promoters and acts
both as a transcriptional activator and repressor TYE7 Serine-rich
protein that contains a basic-helix-loop-helix (bHLH) DNA binding
motif; binds E-boxes of glycolytic genes and contributes to their
activation; may function as a transcriptional activator in
Ty1-mediated gene expression VMA13 Subunit H of the eight-subunit
V1 peripheral membrane domain of the vacuolar H+-ATPase (V-ATPase),
an electrogenic proton pump found throughout the endomembrane
system; serves as an activator or a structural stabilizer of the
V-ATPase GAL11 Subunit of the RNA polymerase II mediator complex;
associates with core polymerase subunits to form the RNA polymerase
II holoenzyme; affects transcription by acting as target of
activators and repressors VAC14 Protein involved in regulated
synthesis of Ptdlns(3,5)P(2), in control of trafficking of some
proteins to the vacuole lumen via the MVB, and in maintenance of
vacuole size and acidity; interacts with Fig4p; activator of
Fab1p
Example 7
Cloning of HEXA and HEXB genes
[0280] Aspergillus parasiticus (ATCC 24690) cultures were grown in
malt extract broth media (15 g/L malt extract broth, Difco) with
shaking at 25.degree. C. for 3 days. A. parasiticus pellets were
transferred to a 1.5 mL tube to provide a volume of pellets equal
to approximately 500 uL. The mycelia were frozen in a dry ice
ethanol bath, transferred to a mortar and pestle, and ground into a
fine powder. The powder was placed in a 1.5 mL tube with
approximately 500 uL 0.7 mm Zirconia beads, and total RNA was
prepared using a Ribopure Plant Kit (Ambion), according to
manufacturer's recommendations.
[0281] First strand synthesis of cDNA was performed with
gene-specific primers oAA0031 (for HEXA) and oAA0041 (for HEXB) in
a reaction containing 0.2 uL of gene-specific primer (10 uM), 300
ng total RNA, 1.0 uL dNTP (10 mM), and sterile water to bring the
volume to 13 uL. The total RNA/primer mixtures were heated at
65.degree. C. for 5 minutes then cooled on ice for 5 minutes before
the addition of 4 uL 5.times. First strand buffer, 1 uL 0.1M DTT, 1
uL H.sub.2O, and 1 uL Superscript III RT (Invitrogen). First strand
synthesis reactions were incubated at 55.degree. C. for 1 hour,
followed by inactivation of the enzyme at 70.degree. C. for 15
minutes and cooling of the reactions to 4.degree. C. The primers
utilized for isolation of HEXA and HEXB genes were configured to
independently amplify the HEXA and HEXB genes in fragments, having
fragment lengths in the range of between about 1.0 kilobases (kb)
to about 1.6 kb, with approximately 200 bp of overlapping sequence
between the fragments. The sequences are shown in the tables
below.
TABLE-US-00013 Oligonucleotides for cloning of HEXA DNA fragments
SEQ ID HEXA PCR product Oligos Sequence NO: sequence (bp) oAA0022
ATGGTCATCCAAGGGAAGAGATTGGCCGCCTCCTCTATTCAGC 200 1-1149 1149 oAA0023
GTAGGCGTCACAGGAAAGACTGCGTACCA 201 oAA0024
TATCACCAATGCTGGATGTAAAGAAGTCGCG 202 941-2270 1330 oAA0025
AATTGGGCTAGGAAACCGGGGATGC 203 oAA0026
CGGTCTAATGACGGCGCATGATATCATAGCCGAAACGGTCGAG 204 2067-3016 950
oAA0027 ACTTGGCTGGAGTCCATCCCTTCGGCA 205 oAA0028
CTGCCCGAGTTTGAAGTATCTCAACTTACCGCCGACGCCATG 206 2812-4181 1370
oAA0029 TGAGACGCGCTGCGCAGGGC 207 oAA0030 CGAGGTGATCGAGACGCAGATGC
208 3975-5016 1042 oAA0031 TTATGAAGCACCAGACATCAGCCCCAGC 209 oAA0046
gtactagtaaaaaaATGGTCATCCAAGGGAAGAGATTGGCCGCCT 210 1-5016 5041
CCTCTATTCAGC oAA0047 gtcccgggctaTTATGAAGCACCAGACATCAGCCCCAGC 211
oAA0051 tacccgggctattagtgatggtggtgatggtgTGAAGCACCAGAC 212 1-5016
5062 ATCAGCCCCAGC
TABLE-US-00014 Oligonucleotides for cloning of HEXB DNA fragments
SEQ ID HEXB PCR product Oligos Sequence NO: sequence (bp) oAA0032
ATGGGTTCCGTTAGTAGGGAACATGAGTCAATC 213 1-1166 1166 oAA0033
GTTCCTTGTGTGAGCTCCTGAATAAGACTGCATG 214 oAA0034
CCATCAAAATCCCCCTCTATCACACGGGCACTGGGAGCAAC 215 962-2042 1081 oAA0035
CCCACGCCTTGCGCATCTATAATCAGG 216 oAA0036
TGTCCGAATATTCTCCTCGTTGTAGGTAGTGGATT 217 1837-3527 1691 oAA0037
GCAGTAGTCGATAGGTACACATCCTTGGGGGTTCCATGACTGC 218 oAA0038
AGAGGATCAAGGCATTATACATGAGTCTGTGGAACTTGGGCTTTCC 219 3323-4461 1139
oAA0039 TTCCCCGTCCTCCATGGCCTTATGC 220 oAA0040
GGCCTTTGCGCGATACGCTGGTCTCTCGGGTCCCAT 221 4256-5667 1412 oAA0041
TCACGCCATTTGTTGAAGCAGGGAATG 222 oAA0048
gtactagtaaaaaaATGGGTTCCGTTAGTAGGGAACATGAGTCAA 223 1-5667 5694 TC
oAA0049 gtgtttaaacctaTCACGCCATTTGTTGAAGCAGGGAATG 224 oAA0111
ggtttaaacctatcagtgatggtggtgatggtgCGCCATTTGTTG 225 1-5667 5714
AAGCAGGGAATGAA
[0282] HEXA and HEXB gene fragments were PCR amplified using the
cDNA generated above by the addition of 5 uL 10.times.Pfu reaction
buffer, 1.0 uL dNTPs (10 mM), 1.0 uL Sense and Antisense Primer Mix
(10 uM), 1.0 uL Pfu Ultra Fusion HS (Agilent), 2.0 uL cDNA, 40 uL
sterile H.sub.2O. Thermocycling parameters used to amplify the HEXA
and HEXB genes were 94.degree. C. for 5 minutes, 40 cycles of
94.degree. C. 30 seconds, 62.degree. C. 40 seconds, 72.degree. C. 4
minutes, followed by 72.degree. C. 10 minutes and a 4.degree. C.
hold. PCR products of the correct size were gel purified and
ligated into pCR-Blunt II-TOPO (Invitrogen), transformed into
competent TOP10 E. coli cells (Invitrogen) and clones containing
PCR inserts were sequenced to confirm correct DNA sequence.
[0283] DNA fragments of HEXA and HEXB were PCR amplified using the
sequence-confirmed fragments in pCR-Bluntll as template in order to
produce overlapping DNA fragments covering the entire sequence of
both HEXA and HEXB. The overlapping DNA fragments for each gene
were combined in a 50 uL overlap extension PCR reaction containing
each DNA fragment at 0.2 nM, sense and antisense primers at 0.2 uM
each, 1.times.Pfu reaction buffer, 1.0 uL Pfu Ultra Fusion HS
polymerase, and 0.2 mM dNTPs. Unique restriction sites were
incorporated into the sense and antisense primers to allow for
cloning the HEXA and HEXB genes into p425GPD and p426GPD
respectively. For HEXA the restriction sites were SpeI/SmaI and for
HEXB the restriction sites were SpeI/PmeI. Ligation of the HEXA and
HEXB genes into p425GPD and p426GPD resulted in plasmids pAA020 and
pAA021 respectively. Variants of the HEXA and HEXB genes that
incorporated C-terminal 6.times.His tags (SEQ ID NO: 13) were
constructed by using an antisense primer encoding a 6.times.His
sequence (SEQ ID NO: 13). Ligation of the HEXA-6.times.His
(`6.times.His`disclosed as SEQ ID NO: 13) and HEXB-6.times.His
(`6.times.His` disclosed as SEQ ID NO: 13) genes into p425GPD and
p426GPD resulted in plasmids pAA031 and pAA032, respectively.
Vectors pAA020, pAA021, pAA031 and pAA032 were used to demonstrate
protein expression in S. cerevisiae, as shown in FIGS. 11 and
12.
Example 8
Cloning of STCJ and STCK Genes
[0284] Total RNA was prepared from Aspergillus nidulans (ATCC
38163), as described in Example 1. First strand synthesis of cDNA
was performed with gene-specific primers oAA0008 (for STCJ) and
oAA0021 (for STCK) in a reaction containing 0.2 uL of gene-specific
primer (10 uM), 300 ng total
[0285] RNA, 1.0 uL dNTP (10 mM), and sterile water to bring the
volume to 13 uL. The total RNA/primer mixtures were heated at
65.degree. C. for 5 minutes then cooled on ice for 5 minutes before
the addition of 4 uL 5.times. First strand buffer, 1 uL 0.1M DTT, 1
uL H.sub.2O, and 1 uL Superscript III RT (Invitrogen). First strand
synthesis reactions were incubated at 55.degree. C. for 1 hour,
followed by inactivation of the enzyme at 70.degree. C. for 15
minutes and cooling of the reactions to 4.degree. C. Primers design
strategies substantially similar to those described herein were
used to amplify the STCJ and STCK genes in fragments in the range
of between about 1.1 kb to about 1.6 kb, with approximately 200 bp
of overlapping sequence between the fragments. The primers used to
amplify the STCJ and STCK genes are shown in the tables below.
TABLE-US-00015 Oligonucleotides for cloning of STCJ DNA fragments
SEQ ID STCJ PCR Oligos Sequence NO: sequence product (bp) oAA0001
ATGACCCAAAAGACTATACAGCAGGTCCCAAGA 226 1-1290 1290 oAA0002
TATGGTGCATCGAATGTTGTTTGCCTGG 227 oAA0009
AAAATGCGTGAGCACTTTGTCCAGCGC 228 1021-2506 1486 oAA0004
CGACGTAATTGACGTTGTCAACATGCCG 229 oAA0005
CATCTCGGGTTCCCATCACTCCCTGAGTATGAC 230 2284-3424 1141 oAA0006
GACAAAGAAGCTGGACACCGCAGCCTTGGGATTCCACGAAC 231 oAA0007
GATCTGCCTTGTCGGTGGCTATGACGACCTTCAGCCTGAGGAGTCA 232 3234-4680 1447
oAA0008 TTAACGGATGATAGAGGCCAACGGCCAAAGACACCACTTGCGTACAC 233 oAA0126
cacacaactagtaaaaaaATGACCCAAAAGACTATACAGCAGGTCC 234 1-4680 4710
CAAGA oAA0127 tgtgtgcccgggTTAACGGATGATAGAGGCCAACGGCCAAAGACAC 235
CACTTGCGTACAC oAA0154
tacccgggctattagtgatggtggtgatggtgACGGATGATAGAGG 236 1-4680 4730
CCAAC
TABLE-US-00016 Oligonucleotides for cloning of STCK DNA fragments
SEQ ID STCK PCR Oligos Sequence NO: sequence product (bp) oAA0012
ATGACTCCATCACCGTTTCTCGATGCTGT 237 1-1110 1110 oAA0013
CACATGGGTAGCATCGTTCATTGCCCAACACAAAGCGGGCCAGTTA 238 ACTC oAA0014
GTCGAGCTAAGAGTGACTGATGCCATTGGC 239 901-2510 1610 oAA0015
CGTAATTCAGCTTCTGAACCTGAGCCCAGG 240 oAA0016 CTTTGCCCGGCCGTGGTTCGC
241 2301-3555 1255 oAA0017 CCCCCAAGCTCGACAACGGGC 242 oAA0018
TTCTCAAAATGCACCGGACTGATTACTTGGA 243 3350-4682 1333 oAA0019
CCCATTCCTCTCTCCTGCGTGCCCTGGCCGGTAAAGACGTAT 244 oAA0020
CCCTCCTTCGATGGACTTGTCCGGGCAAACGACCGGTTGCGAATGG 245 4477-5745 1268
AGAT oAA0021 CTACCTATTCTCTTCAACCCGCCGTAACAGC 246 oAA0128
cacacaactagtaaaaaaATGACTCCATCACCGTTTCTCGATGCTGT 247 1-5745 5775
oAA0129 tgtgtgcccgggCTACCTATTCTCTTCAACCCGCCGTAACAGC 248 oAA0170
tgtgtgcccgggctatcagtgatggtggtgatggtgCCTATTCTCT 249 1-5745 5796
TCAAC
[0286] STCJ and STCK fragments were amplified using the cDNA
prepared above in PCR reactions containing 5 uL 10.times.Pfu
reaction buffer, 1.0 uL dNTPs (10 mM), 1.0 uL Sense and Antisense
Primer Mix (10 uM), 1.0 uL Pfu Ultra Fusion HS (Agilent), 2.0 uL
cDNA, 40 uL sterile H.sub.2O. Thermocycling parameters used were
94.degree. C. for 5 minutes, 40 cycles of 94.degree. C. 30 seconds,
62.degree. C. 40 seconds, 72.degree. C. 4 minutes, followed by
72.degree. C. 10 minutes and a 4.degree. C. hold. PCR products of
the correct size were gel purified and ligated into pCR-Blunt
II-TOPO (Invitrogen), transformed into competent TOP10 E. coli
cells (Invitrogen). PCR inserts were sequenced to confirm the
correct DNA sequence. DNA fragments of STCJ and STCK were PCR
amplified using the sequence-confirmed fragments in pCR-Bluntll as
template in order to produce overlapping DNA fragments covering the
entire sequence of both STCJ and STCK. The overlapping DNA
fragments for each gene were combined in a 50 uL overlap extension
PCR reaction containing each DNA fragment at 0.2 nM, sense and
antisense primers at 0.2 uM each, 1.times.Pfu reaction buffer, 1.0
uL Pfu Ultra Fusion HS polymerase, and 0.2 mM dNTPs.
[0287] Sense and antisense primers were designed to incorporate
unique restriction sites for cloning the STCJ and STCK genes into
p425GPD and p426GPD respectively. For STCJ the restriction sites
were SpeI/XmaI and for STCK the restriction sites were SpeI/SmaI.
Ligation of the STCJ and STCK genes into p425GPD and p426GPD
resulted in plasmids pAA040 and pAA042 respectively. Variants of
the STCJ and STCK genes that incorporated C-terminal 6.times.His
tags (SEQ ID NO: 13) were constructed by using an antisense primer
encoding a 6.times.His sequence (SEQ ID NO: 13).
[0288] Ligation of the STCJ-6.times.His (`6.times.His` disclosed as
SEQ ID NO: 13) and STCK-6.times.His (`6.times.His` disclosed as SEQ
ID NO: 13) genes into p425GPD and p426GPD resulted in plasmids
pAA041 and pAA043. Vectors pAA040, pAA0421 pAA042 and pAA043 were
used to demonstrate protein expression in S. cerevisiae, as shown
in FIGS. 11 and 12.
Example 9
Design and Cloning of Hexa and Hexb Genes for C. Tropicalis
Alternate Genetic Code
[0289] The HEXA and HEXB genes contain multiple CTG codons, which
normally code for leucine. However, certain organisms, Candida
tropicalis for example, translate CTG as serine. DNA sequences for
HEXA and HEXB were prepared that replaced all CTG codons with TTG
codons, which is translated as leucine in C. tropicalis. The TTG
codon was chosen due to it being the most frequently used leucine
codon in C. tropicalis. The alternate genetic code (AGC) HEXA and
HEXB genes were synthesized as equal size fragments with 200 bp
overlaps and ligated into pUC57 vector (Integrated DNA
Technologies). DNA fragments of AGC-HEXA and AGC-HEXB were PCR
amplified using the fragments in pUC57 as template in order to
produce overlapping DNA fragments covering the entire sequence of
both AGC-HEXA and AGC-HEXB.
[0290] The overlapping DNA fragments for each gene were combined in
a 50 uL overlap extension PCR reaction containing each DNA fragment
at 0.2 nM, sense and antisense primers at 0.2 uM each, 1.times.Pfu
reaction buffer, 1.0 uL Pfu Ultra Fusion HS polymerase, and 0.2 mM
dNTPs. Sense and antisense primers incorporated unique Sapl
restriction sites for cloning the AGC-HEXA and AGC-HEXB genes into
pAA105 resulting in plasmids pAA127 and pAA129 respectively. Gene
variants of AGC-HEXA and AGC-HEXB that contained C-terminal
6.times.His tags (SEQ ID NO: 13) were ligated into pAA105 resulting
in plasmids pAA128 and pAA130 respectively. The alternate genetic
code primers used to alter leucine codons for C. tropicalis
expression of HEXA and HEXB are shown in the tables below.
TABLE-US-00017 Oligonucleotides for cloning of AGC-HEXA DNA
fragments AGC- PCR SEQ ID HEXA product Oligos Sequence NO: sequence
(bp) oAA0383 cacacagctcttctagaATGGTCATCCAAGGGAAGAG 250 1-1404 1421
oAA0055 AGTATCGACGTCGGCTGACTTGAGACCA 251 oAA0056
CCATCACATCCACAGTGGCGG 252 1205-2609 1405 oAA0057
AACCAGGCAAGTTCGACATAACCGGC 253 oAA0058 GTAGGCTATCCCCGTCTCCCCGATTATG
254 2410-3814 1405 oAA0059 TGATTGAGGTCAAGGATGATTTGTCCGAGA 255
oAA0060 TCTTCCTATCTATGCGGTCATTGCCAGCT 256 3615-5016 1419 oAA0384
cacacagctcttcctttTTATGAAGCACCAGACATCAAC 257 oAA0385
cacacagctcttcctttttagtgatggtggtgatggtgTGAAGCAC 258 1-5016 5071
CAGACATCAACCCCAACG
TABLE-US-00018 Oligonucleotides for cloning of AGC-HEXB DNA
fragments AGC- PCR SEQ ID HEXB product Oligos Sequence NO: sequence
(bp) oAA0386 cacacagctcttctagaATGGGTTCCGTTAGTAGGGA 259 1-1566 1583
oAA0064 CAAATCCTTGATGACAGAGATCTGCCAGGA 260 oAA0065
GCTGGGACTTTGTCGCTGCCGTTGCTCAAGCTGGAT 261 1367-2933 1567 oAA0066
ACTGCTCCTACTTTCTCGAACTTATAGAGCCCTTG 262 oAA0067
ATATCCGACGATGAGTCTGT 263 2734-4299 1566 oAA0068
ATGGACAATGGGACCCGAGA 264 oAA0069 GGACTTCTTGCACCGCTACG 265 4101-5667
1584 oAA0387 cacacagctcttcctttTCACGCCATTTGTTGAAGCAAAG 266 oAA0388
cacacagctcttccttttcagtgatggtggtgatggtgCGCCATTT 267 1-5667 5692
GTTGAAGCA
Example 10
Transformation of S. Cerevisiae Procedure
[0291] Competent cells of S. cerevisiae strain BY4742 were prepared
using the Frozen-EZ Yeast Transformation II Kit (Zymo Research)
following manufacturer's instructions. 50 uL aliquots of competent
cells were stored at -80.degree. C. until use. Competent cells were
transformed by the addition of 0.5-1.0 ug of intact plasmid DNA as
instructed by the Frozen-EZ Yeast Transformation II Kit (Zymo
Research). Selection for transformants was performed by plating on
selective media; SC-URA (for p426-based vectors) or SC-LEU (for
p425-based vectors).
Example 11
Transformation of C. Tropicalis Procedure
[0292] 5 mL YPD start cultures were inoculated with a single colony
of C. tropicalis and incubated overnight at 30.degree. C., with
shaking at about 200 rpm. The following day, fresh 25 mL YPD
cultures, containing 0.05% Antifoam B, were inoculated to an
initial OD.sub.600nm of 0.4 and the culture incubated at 30.degree.
C., with shaking at about 200 rpm until an OD.sub.600nm of 1.0-2.0
was reached. Cells were pelleted by centrifugation at
1,000.times.g, 4.degree. C. for 10 minutes. Cells were washed by
resuspending in 10 mL sterile water, pelleted, resuspended in 1 mL
sterile water and transferred to a 1.5 mL microcentrifuge tube. The
cells were then washed in 1 mL sterile TE/LiOAC solution, pH 7.5,
pelleted, resuspended in 0.25 mL TE/LiOAC solution and incubated
with shaking at 30.degree. C. for 30 minutes.
[0293] The cell solution was divided into 50 uL aliquots in 1.5 mL
tubes to which was added 5-8 ug of linearized DNA and 5 uL of
carrier DNA (boiled and cooled salmon sperm DNA, 10 mg/mL). 300 uL
of sterile PEG solution (40% PEG 3500, 1.times.TE, 1.times.LiOAC)
was added, mixed thoroughly and incubated at 30.degree. C. for 60
minutes with gentle mixing every 15 minutes. 40 uL of DMSO was
added, mixed thoroughly and the cell solution was incubated at
42.degree. C. for 15 minutes. Cells were then pelleted by
centrifugation at 1,000.times.g 30 seconds, resuspended in 500 uL
of YPD media and incubated at 30.degree. C. with shaking at about
200 rpm for 2 hours. Cells were then pelleted by centrifugation and
resuspended in 1 mL 1.times.TE, cells were pelleted again,
resuspended in 0.2 mL 1.times.TE and plated on selective media.
Plates were incubated at 30.degree. C. for growth of
transformants.
Example 12
HEXA and HEXB Expression in S. Cerevisiae
[0294] Plasmids pAA031 and pAA032 were transformed into competent
BY4742 S. cerevisiae cells independently and in combination.
Selection for transformants containing pAA031 was performed on
SC-LEU plates. Selection for transformants containing pAA032 was
performed on SC-URA plates. Selection for transformants containing
both pAA031 and pAA032 was performed on SC-URA-LEU plates. Single
colonies were used to inoculate 5 mL of SC drop out media and grown
overnight at 30.degree. C., with shaking as described herein. Cells
from 3 mL of overnight culture were harvested by centrifugation at
12,000 rpm for 2 minutes. Cell pellets were incubated at
-80.degree. C. until frozen.
[0295] Approximately 500 uL of cold 0.7 mm zirconia beads (Ambion)
were added on top of the frozen cell pellets. Yeast lysis buffer
(50 mM Tris pH 8.0, 0.1% Triton X100, 0.5 mM EDTA, 1.times.
ProCEASE protease inhibitors [G Biosciences]) was added to fill the
tube leaving as little air in the tube as possible, the tubes were
placed on ice during manipulations. Cells were broken using three,
2 minute cycles in a Bead Beater (BioSpec) with 1 minute rests on
ice between cycles. 200 uL of whole cell extract (WCE) was removed
to a new tube and the remainder of the whole cell extract was
centrifuged at 16,000.times.g, 4.degree. C. for 15 minutes to
pellet insoluble debris. The supernatant was removed to a new tube
as the soluble cell extract (SCE). The protein content in the
soluble cell extract was determined by Bradford assay (Pierce). A
volume of SCE containing 50 ug of protein (and the same volume WCE)
was precipitated by the addition of 4 volumes of cold 100% acetone.
After centrifugation at 16,000.times.g, and 4.degree. C. for 15
minutes, the supernatant was carefully removed and the pellet
washed with 200 uL of cold 80% acetone and centrifuged again. The
supernatant again was carefully removed and the cell pellets air
dried for 5 minutes.
[0296] Protein pellets were then resuspended in 1.times.LDS sample
buffer containing 50 mM DTT (Invitrogen) by incubating at
70.degree. C., with shaking at about 1200 rpm. After brief
centrifugation and cooling to room temperature, samples (20 ug)
were separated by SDS PAGE and transferred to nitrocellulose for
immunodetection with mouse anti-6.times.His antibodies
(`6.times.His` disclosed as SEQ ID NO: 13) (Abcam). Incubation in
1:5,000 primary antibody was performed overnight at room
temperature, incubation in 1:5,000 donkey anti-mouse HRP conjugate
secondary antibody was performed for 3 hours at room temperature,
and detection was performed with SuperSignal West Pico
chemiluminescent substrate (Pierce). Multiple clones displayed
soluble expression of both HEXA and HEXB subunits of hexanoate
synthase. As shown in FIG. 11, a substantial portion of the
expressed protein fractionated with the insoluble pellet. Strains
sAA061, sAA140, sAA141, sAA142 contained 6.times.His-tagged HEXA
and HEXB proteins (`6.times.His` disclosed as SEQ ID NO: 13).
Strain sAA048 contained only vectors p425GPD and p426GPD.
Example 13
STCJ and STCK Expression in S. Cerevisiae
[0297] Plasmids pAA041 and pAA043 were cotransformed into competent
BY4742 S. cerevisiae. Selection for transformants containing both
pAA041 and pAA043 was performed on SC-URA-LEU plates. Culture
growth, cell extract preparation, SDS PAGE, and immunodetection
were performed as described herein. One clone displayed soluble
expression of both STCJ and STCK subunits. As shown in FIG. 11, a
substantial portion of the expressed protein fractionated with the
insoluble pellet. Strain sAA144 contained 6.times.His-tagged STCJ
and STCK proteins (`6.times.His` disclosed as SEQ ID NO: 13).
Strain sAA048 contained only vectors p425GPD and p426GPD.
Example 14
HEXA and HEXB Expression in C. Tropicalis
[0298] Plasmids pAA128 and pAA130 were linearized using ClaI, and
cotransformed into competent sAA103 cells (ura3/ura3,
pox4::ura3/pox4::ura3, pox5::ura3/pox5::ura3). The ClaI recognition
sites in the HEXA and HEXB ORF's are blocked due to overlapping dam
methylation. Selection for transformants containing integrated
vector DNA was performed on SC-URA plates. Confirmation of vector
integration was performed by PCR using HEXA and HEXB specific
primers. Transformants that were PCR positive for both HEXA and
HEXB were selected for analysis of target protein expression.
Overnight culture growth was performed as described herein. Fresh 5
mL YPD cultures were inoculated from the overnight cultures to an
initial OD.sub.600nm of 0.4 and incubated until the OD.sub.600nm
reached .about.5-8, at which point the culture was harvested. Cell
extract preparation, SDS PAGE, and immunodetection were performed
as described herein. Strains sAA269 and sAA270 contained plasmids
pAA128 and pAA130 integrated into the genome for expression of
6.times.His-tagged HEXA and HEXB proteins (`6.times.His` disclosed
as SEQ ID NO: 13). Both strains displayed soluble expression of
6.times.His-tagged HEXA and HEXB subunits (`6.times.His` disclosed
as SEQ ID NO: 13) as shown in FIG. 12. 6.times.His tagged HEXA and
HEXB (`6.times.His` disclosed as SEQ ID NO: 13) expressed in
strains sAA269 and sAA270 are indicated with arrows. 6.times.His
tagged STCJ and STCK (`6.times.His` disclosed as SEQ ID NO: 13)
from strain sAA144 were included as a positive control. Strain
sAA103 is the parent strain for sAA269 and sAA270 and does not
contain integrated vectors for the expression of 6.times.His-tagged
HEXA and HEXB (`6.times.His` disclosed as SEQ ID NO: 13).
Example 15
Procedure for Recycling of the URA3 Marker
[0299] C. tropicalis has a limited number of selectable marker, as
compared to S. cerevisiae, therefore, the URA3 marker is "recycled"
to allow multiple rounds of selection using URA3. To reutilize the
URA3 marker for subsequent engineering of C. tropicalis, a single
colony having the Ura.sup.+ phenotype was inoculated into 3 mL YPD
and grown overnight at 30.degree. C. with shaking. The overnight
culture was then harvested by centrifugation and resuspended in 1
mL YNB+YE (6.7 g/L Yeast Nitrogen Broth, 3 g/L Yeast Extract). The
resuspended cells were then serially diluted in YNB+YE and 100 uL
aliquots plated on YPD plates (incubation overnight at 30.degree.
C.) to determine titer of the original suspension. Additionally,
triplicate 100 uL aliquots of the undiluted suspension were plated
on SC Dextrose (Bacto Agar 20 g/L, Uracil 0.3 g/L, Dextrose 20 g/L,
Yeast Nitrogen Broth 6.7 g/L, Amino Acid propout Mix 2.14 g/L) and
5-FOA. at 3 different concentrations (0.5, 0.75, 1 mg/mL).
[0300] Plates were incubated for at least 5 days at 30.degree. C.
Colonies arising on the SC Dextrose+5-FOA plates were resuspended
in 50 uL sterile, distilled water and 5 uL utilized to streak on to
YPD and SC-URA (SC Dextrose medium without Uracil) plates. Colonies
growing only on YPD and not on SC-URA plates were then inoculated
into 3 mL YPD and grown overnight at 30.degree. C. with shaking.
Overnight cultures were harvested by centrifugation and resuspended
in 1.5 mL YNB (6.7 g/L Yeast Nitrogen Broth). The resuspended cells
were serially diluted in YNB and 100 uL aliquots plated on YPD
plates and incubation overnight at 30.degree. C. to determine
initial titer. 1 mL of each undiluted cell suspension also was
plated on SC-URA and incubated for up to 7 days at 30.degree. C.
Colonies on the SC-URA plates are revertants and the isolate with
the lowest reversion frequency (<10.sup.-7) was used for
subsequent strain engineering.
Example 16
Omega Oxidation of Hexane and Hexanoic Acid to Adipic Acid
[0301] Starter cultures of strain sAA003 were grown in YPD.sub.2.0
(1% yeast extract, 2% peptone, 2% dextrose) overnight as described.
Starter cultures were used to inoculate 100 mL of fresh YPD.sub.2.0
to an initial OD.sub.600nm of 0.4 and incubated overnight at
30.degree. C., with shaking at about 200 rpm. The 100 mL culture
was pelleted by centrifugation at 4,000.times.g, 23.degree. C. for
10 minutes and resuspended in 100 mL fresh YPD.sub.0.1 media (1%
yeast extract, 1% peptone, 0.1% dextrose). The culture was divided
into 4.times.25 mL cultures to which were added either 1% hexane,
0.05% hexanoic acid, 1.0% hexanoic acid, or no other carbon source.
Strain sAA003 is completely blocked in .beta.-oxidation, therefore
fermentation tested the ability of the .beta.-oxidation pathway to
oxidize C6 substrates. Samples were taken at 24, 48, and 72 hours
and analyzed by LC-MS (Scripps Center for Mass Spectrometry) using
published methods for the detection of adipic acid (Cheng et al.,
2000). The data for the 72 hour time-point, shown in the table
below demonstrates that strain sAA003 was able to oxidize both
hexanoic acid and hexane to adipic acid. The results also indicate
that the 1% hexanoic acid level was toxic to the cells leading to
no production of adipic acid over background levels.
TABLE-US-00019 Oxidation of hexane and hexanoic acid to adipic acid
Time (h) MEDIA Adipic acid (mg/L) 0 YPD.sub.0.1 0.000 72
YPD.sub.0.1 0.005 72 YPD.sub.0.1 + 0.05% Hexanoic Acid 0.406 72
YPD.sub.0.1 + 1% Hexanoic Acid 0.003 72 YPD.sub.0.1 + 1% Hexane
0.091
Example 17
Identification of P450 Alleles Induced by Exposure to Hexane or
Hexanoic Acid
[0302] 350 mL cultures grown overnight in YNB-Salts+2.0% Glucose
(6.7 g/L Yeast Nitrogen Broth, 3.0 g/L Yeast Extract, 3.0 g/L
ammonium sulfate, 3.0 g/L monopotassium phosphate, 0.5 g/L sodium
chloride, and 20 g/L dextrose) were inoculated from a 3 mL
overnight culture of YPD (1% Yeast Extract, 2% Peptone, 2%
Dextrose), and used for RNA preparation. Cultures were harvested by
centrifugation. Each pellet was resuspended in 100 mL of YNB-Salts
medium with no glucose. A 1 mL aliquot was taken for RNA isolation
as a time=0 control. To each 100 mL suspension, a different inducer
was added, 1% glucose, 1% hexane or 0.05% hexanoic acid and
aliquoted as two 50 mL portions into 250 mL baffled flasks and
incubated for 2 or 4 hours at 30.degree. C. with shaking. At 2
hours and 4 hours, one flask for each inducer was harvested by
centrifugation and resuspended in its own spent media in order to
collapse culture foam. 1 mL samples were isolated by centrifugation
of 1 mL of each culture and RNA prepared using the RiboPure-Yeast
Kit, according to the manufacturer's directions, with an additional
extraction of the initial RNA preparations with 1 volume of
Chloroform:lsoamyl Alcohol (24:1) to the aqueous phase after lysis
and extraction with Phenol:Chloroform:lsoamyl Alcohol
(25:24:1).
[0303] Each RNA preparation was further purified by precipitation
with ethanol and treatment with DNase I, again according to
manufacturers' recommendations. All RNA preparations were shown to
be free of contaminating genomic DNA by electrophoresis and by
failure to prime a PCR product of the URA3 gene. First strand
synthesis reactions were completed for each RNA preparation using
Superscript III Reverse Transcriptase (Invitrogen), as described
herein. Reactions for each sample consisted of 1 uL oAA0542 (polyT
10 uM), 1 uL dNTP mix (10 mM each), 1 .mu.g RNA in 13 uL sterile,
distilled water. The RNA/primer mix was heated to 65.degree. C. for
5 minutes, and on ice for 1 minute. Primers were generated that
amplified a substantially unique area of each cytochrome P450 and
are shown in the table below.
[0304] PCR reactions were performed on the 2 hour induced cDNA
samples and compared to the Time=0 and genomic DNA controls. PCR
reactions for each cDNA and primer pair combination consisted of
0.5 uL template, sense and antisense primers at 0.4 uM each,
1.times.Taq DNA polymerase Buffer (New England Biolabs), 0.1 uL Taq
DNA polymerase, and 0.2 mM dNTPs and sterile, distilled water to 25
uL. Cycling parameters used were 95.degree. C. for 5 minutes, 30
cycles of 95.degree. C. 30 seconds, 50.degree. C. 40 seconds,
72.degree. C. 2 minutes, followed by 72.degree. C. 5 minutes and a
4.degree. C. hold. PCR reactions were electrophoresed on 1.2%
agarose gels to identify differential expression due to the inducer
used. Several P450s displayed increased induction in the presence
of hexane or hexanoic acid, however the results were not
quantitative. Two Cytochrome P450's, CYP52A15 and CYP52A16, showed
induction only in the presence of hexane and hexanoic acid and not
in the presence of glucose, as shown in FIG. 13. The primers used
for PCR analysis of induced expression are shown in the table
below.
TABLE-US-00020 Oligonucleotides for identification of P450 DNA
fragments PCR SEQ ID P450 product Oligos Sequence NO: P450 sequence
(bp) oAA0082 gattactgcagcagtattagtcttc 268 CYP52A12 60-249 190
oAA0083 gtcgaaaacttcatcggcaaag 269 oAA0084 cacgatattatcgccacatacttc
270 CYP52A13 10-256 247 oAA0085 cgggacgatcgagatcgtggatacg 271
oAA0086 caggatattatcgccacatacatc 272 CYP52A14 10-256 247 oAA0087
ctggacgattgagcgcttggatacg 273 oAA0088 cgtcttctccatcgtttgcccaagag
274 CYP52A15 5-199 195 oAA0089 ggtccctgacaaagttaccgagtg 275 oAA0090
cgtcttctccatcgtttgctcaggag 276 CYP52A16 5-199 195 oAA0091
gatccaacacgacgttaccgagcg 277 oAA0092 ggtatgtcgttgtgccagtgttg 278
CYP52A17 26-248 223 oAA0093 cccacgcttgggttcttggagtggtc 279 oAA0094
ggtatattgttgtgcctgtgttg 280 CYP52A18 26-248 223 oAA0095
ccgacgcttgggttcttggagctgtc 281 oAA0096 ggaaggatgaggtggtgcagtac 282
CYP52A19 1217-1458 242 oAA0097 gtcttgtgacaagtttggaaactc 283 oAA0098
gaaagaatgaggtggtgcaatac 284 CYP52A20 1217-1458 242 oAA0099
gtcctgtgacaagctagggaattc 285 oAA0104 ctatcgtgggatgtgatctgtgtcg 286
CYP52D2 19-231 213 oAA0105 ctcgaatctcttgacactgaactcg 287
Example 18
Cloning and Analysis of C. Tropicalis Fatty Alcohol Oxidase (FAO)
Alleles
[0305] Isolation of Fatty Alcohol Oxidase Genes from C.
Tropicalis
[0306] C. tropicalis (ATCC20336) fatty alcohol oxidase genes were
isolated by PCR amplification using primers generated to amplify
the sequence region covering promoter, fatty alcohol oxidase gene
(FAO) and terminator of the FAO1 sequence (GenBank accession number
of FAO1 AY538780). The primers used to amplify the fatty alcohol
oxidase nucleotide sequences from C. tropicalis strain ATCC20336,
are showing in the table below.
TABLE-US-00021 Oligonucleotides for cloning FAO alleles SEQ Oligo
Sequence ID NO: oAA0144 AACGACAAGATTAGATTGGTTGAGA 288 oAA0145
GTCGAGTTTGAAGTGTGTGTCTAAG 289 oAA0268
AGATCTCATATGGCTCCATTTTTGCCCGACCAGGT 290 CGACTACAAACACGTC oAA0269
ATCTGGATCCTCATTACTACAACTTGGCTTTGGTC 291 TTCAAGGAGTCTGCCAAACCTAAC
oAA0282 ACATCTGGATCCTCATTACTACAACTTGGCCTTGG 292 TCT oAA0421
CACACAGCTCTTCTAGAATGGCTCCATTTTTGCCC 293 GACCAGGTCGAC oAA0422
CACACAGCTCTTCCTTTCTACAACTTGGCTTTGGTC 294 TTCAAGGAGTCTGC oAA0429
GTCTACTGATTCCCCTTTGTC 295 oAA0281 TTCTCGTTGTACCCGTCGCA 296
[0307] PCR reactions contained 25 uL 2.times. master mix, 1.5 uL of
oAA0144 and oAA0145 (10 uM), 3.0 uL genomic DNA, and 19 uL sterile
H.sub.2O. Thermocycling parameters used were 98.degree. C. for 2
minutes, 35 cycles of 98.degree. C. 20 seconds, 52.degree. C. 20
seconds, 72.degree. C. 1 minute, followed by 72.degree. C. 5
minutes and a 4.degree. C. hold. PCR products of the correct size
were gel purified, ligated into pCR-Blunt II-TOPO (Invitrogen) and
transformed into competent TOP10 E. coli cells (Invitrogen). Clones
containing PCR inserts were sequenced to confirm correct DNA
sequence. Four FAO alleles were identified from sequence analysis
and designated as FAO-13, FAO-17, FAO-18 and FAO-20. The sequence
of the clone designated FAO-18 had a sequence that was
substantially identical to the sequence of FAO1 from Gen Bank. The
resulting plasmids of the four alleles were designated pAA083,
pAA084, pAA059 and pAA085, respectively. Sequence identity
comparisons of FAO genes isolated as described herein are shown in
the tables below.
TABLE-US-00022 DNA sequence identity FAO- FAO1 18 FAO-17 FAO-13
FAO-20 FAO2a FAO2b FAO1 100 100 98 96 95 83 82 FAO-18 100 98 96 95
83 82 FAO-17 100 98 98 83 82 FAO-13 100 99 83 83 FAO-20 100 83 83
FAO2a 100 96 FAO2b 100
TABLE-US-00023 Protein sequence identity FAO- FAO1 18 FAO-17 FAO-13
FAO-20 FAO2a FAO2b FAO1 100 100 99 98 98 81 80 FAO-18 100 99 98 98
81 80 FAO-17 100 99 99 82 81 FAO-13 100 99 82 81 FAO-20 100 82 81
FAO2a 100 97 FAO2b 100
TABLE-US-00024 Amino acid differences in FAO alleles 32 75 89 179
185 213 226 352 544 590 FAO1 E M G L Y T R H S P FAO-13 Q T A L Y A
K Q A A FAO-20 Q T A M D A K Q A A
[0308] Expression of FAO Alleles in E. Coli
[0309] To determine the levels of FAO enzyme activity with respect
to various carbon sources, the four isolated FAO alleles were
further cloned and over-expressed in E. coli. The FAOs were
amplified using the plasmids mentioned above as DNA template by PCR
with primers oAA0268 and oAA0269 for FAO-13 and FAO-20 and oAA0268
and oAA0282 for FAO-17 and FAO-18, using conditions as described
herein. PCR products of the correct size were gel purified and
ligated into pET11a vector between NdeI and BamHI sites and
transformed into BL21 (DE3) E. coli cells. The colonies containing
corresponding FAOs were confirmed by DNA sequencing. Unmodified
pET11a vector also was transformed into BL21 (DE3) cells, as a
control. The resulting strains and plasmids were designated sAA153
(pET11a), sAA154 (pAA079 containing FAO-13), sAA155 (pAA080
containing FAO-17), sAA156 (pAA081 containing FAO-18) and sAA157
(pAA082 containing FAO-20), respectively. The strains and plasmids
were used for FAO over-expression in E. coli. One colony of each
strain was transferred into 5 mL of LB medium containing 100
.mu.g/mL ampicillin and grown overnight at 37.degree. C., 200 rpm.
The overnight culture was used to inoculate a new culture to
OD.sub.600nm 0.2 in 25 ml LB containing 100 .mu.g/mlampicillin.
Cells were induced at OD.sub.600nm 0.8 with 0.3 mM IPTG for 3 hours
and harvested by centrifugation at 4.degree. C. 1,050.times.g for
10 minutes. The cell pellet was stored at -20.degree. C.
[0310] Expression of FAOs in C. Tropicalis
[0311] Two alleles, FAO-13 and FAO-20, were chosen for
amplification in C. tropicalis based on their substrate specificity
profile, as determined from enzyme assays of soluble cell extracts
of E. coli with over expressed FAOs. DNA fragments containing
FAO-13 and FAO-20 were amplified using plasmids pAA079 and pAA082
as DNA templates, respectively, by PCR with primers oAA0421 and
oAA0422. PCR products of the correct sizes were gel purified and
ligated into pCR-Blunt II-TOPO (Invitrogen), transformed into
competent TOP10 E. coli cells (Invitrogen) and clones containing
FAO inserts were sequenced to confirm correct DNA sequence.
Plasmids containing FAO-13 and FAO-20 were digested with Sapl and
ligated into vector pAA105, which includes the C. tropicalis PGK
promoter and terminator. The resulting plasmids were confirmed by
restriction digestion and DNA sequencing and designated as pAA115
(FAO-13) and pAA116 (FAO-20), respectively. Plasmids pAA115 and
pAA116 were linearized with SpeI, transformed into competent C.
tropicalis Ura.sup.- strains sAA002 (SU-2, ATCC20913) and sAA103.
The integration of FAO-13 and FAO-20 was confirmed by colony PCR
using primers oAA0429 and oAA0281. The resulting strains were
designated as sAA278 (pAA115 integrated in strain sAA002), sAA280
(pAA116 integrated in sAA002), sAA282 (pAA115 integrated in
sAA103), and sAA284 (pAA116 integrated in sAA103), and were used
for fatty alcohol oxidase over-expression in C. tropicalis.
[0312] One colony of each strain was inoculated into 5 ml YPD and
grown overnight as described herein. The overnight culture was used
to inoculate a new 25 mL YPD culture to about OD.sub.600nm 0.5. FAO
over-expression was regulated by the PGK promoter/terminator,
induced with glucose in the medium and expressed constitutively.
Strains sAA002 and sAA103 (e.g., untransformed starting strains)
were included as negative controls for FAO over-expression. Cells
were harvested at early log phase (OD.sub.600nm=in the range of
between about 3 to about 5) by centrifugation at 4.degree. C. for
10 minutes at 1,050.times.g. Cell pellets were stored at
-20.degree. C.
[0313] Cell Extract Preparation from E. Coli
[0314] Cell pellets from 25 mL of FAO expressing E. coli cultures
were resuspended in 10 mL phosphate-glycerol buffer containing 50
mM potassium phosphate buffer (pH7.6), 20% glycerol, 1 mM
Phenylmethylsulfonyl fluoride (PMSF), 2 uL Benzonase 25 U/uL, 20 uL
10 mg/mL lysozyme. The cells were then lysed by incubation at room
temperature for 50 minutes on a rotating shaker, and the cell
suspension centrifuged for 30 minutes at 4.degree. C. using
15,000.times.g for. The supernatant was aliquoted in 1.5 ml
microcentrifuge tubes and stored at -20.degree. C. for FAO enzyme
activity assays.
[0315] Cell Extract Preparation from C. Tropicalis
[0316] Frozen C. tropicalis cell pellets were resuspended in 1.2 ml
of phosphate-glycerol buffer containing 50 mM potassium phosphate
buffer (pH7.6), 20% glycerol, 1 mM Phenylmethylsulfonyl fluoride
(PMSF). Resuspended cells were transferred to 1.5 mL screw-cap
tubes containing about 500 uL of zirconia beads on ice. The cells
were lysed with a Bead Beater (Biospec) using 2 minute pulses and 1
minute rest intervals on ice. The process was repeated 3 times. The
whole cell extract was then transferred to a new 1.5 ml tube and
centrifuged at 16,000.times.g for 15 minutes at 4.degree. C. The
supernatant was transferred into a new tube and used for FAO enzyme
activity assays.
[0317] Protein Concentration Determination
[0318] Protein concentration of the cell extracts was determined
using the Bradford Reagent following manufacturers' recommendations
(Cat#23238, Thermo scientific).
[0319] FAO Enzyme Activity Assay
[0320] FAO enzyme activity assays were performed using a
modification of Eirich et al., 2004). The assay utilizes a
two-enzyme coupled reaction (e.g., FAO and horse radish peroxidase
(HRP)) and can be monitored by spectrophotometry. 1-Dodecanol was
used as a standard substrate for fatty alcohol oxidase enzymatic
activity assays. FAO oxidizes the dodecanol to dodecanal while
reducing molecular oxygen to hydrogen peroxide simultaneously. HRP
reduces (2,2'-azino-bis 3-ethylbenzthiazoline-6-sulfonic acid;
ABTS) in the two-enzyme coupled reaction, where the electron
obtained from oxidizing hydrogen peroxide to ABTS, which can be
measured by spectrometry at 405 nm. The assay was modified using
aminotriazole (AT) to prevent the destruction of H.sub.2O.sub.2 by
endogenous catalase, thus eliminating the need for microsomal
fractionation. The final reaction mixture (1.0 mL) for FAO enzyme
assay consisted of 5004 of 200 mM HEPES buffer, pH 7.6; 50 .mu.L of
a 10 mg/mL ABTS solution in deionized water; 104 of 5 mM solution
of dodecanol in acetone; 40 .mu.L of 1M AT and 5 .mu.L of a 2 mg/mL
horseradish peroxidase solution in 50 mM potassium phosphate
buffer, pH 7.6. Reaction activity was measured by measuring light
absorbance at 405 nm for 10 minutes at room temperature after
adding the extract. The amount of extract added to the reaction
mixture was varied so that the activity fell within the range of
0.2 to 1.0 .DELTA.A.sub.405nm/min. The actual amounts of extract
used were about 1.69 U/mg for E. coli expressed FAO-13, 0.018 U/mg
for E. coli expressed FAO-17, 0.35 U/mg for E. coli expressed
FAO-18 (e.g., FAO1), 0.47 U/mg E. coli expressed FAO-20, 0.036 U/mg
C. tropicalis (strain sAA278) expressed FAO-13, 0.016 U/mg C.
tropicalis (strain sAA282) expressed FAO-13, 0.032 U/mg C.
tropicalis (strain sAA280) expressed FAO-20 and 0.029 U/mg C.
tropicalis (strain sAA284) expressed FAO-20. FAO activity was
reported as activity units/mg of total protein (1 unit=1 .mu.mole
substrate oxidized/min). An extinction coefficient at 405 nm of
18.4 was used for ABTS and was equivalent to 0.5 mM oxidized
substrate. The results of the activity assays are shown in the
tables below.
TABLE-US-00025 FAO activity (units/mg total protein) on primary
alcohols 1- 1- 1- 1- 1- 1- 1- Butanol Pentanol Hexanol Octanol
Decanol Dodecanol Tetradecanol Hexadecanol FAO-13 0.01 0.09 1.17
82.67 70.94 100 79.35 58.88 FAO-17 0.72 0.26 1.06 66.23 22.00 100
47.86 60.98 FAO-18 0.07 0.11 0.26 60.56 54.56 100 114.47 50.65
FAO-20 0.07 0.11 0.91 55.96 74.57 100 89.52 42.59
TABLE-US-00026 FAO activity (units/mg total protein) on omega
hydroxy fatty acids 1- 12-OH- 16-OH- Dodecanol 6-OH-HA 10-OH-DA DDA
HDA FAO-13 100 4.18 4.14 6.87 8.57 FAO-17 100 1.18 0.00 0.59 0.94
FAO-18 100 0.00 0.00 4.87 2.94 FAO-20 100 0.03 0.04 2.25 7.46
Example 19
Construction of C. Tropicalis Shuttle Vector pAA061
[0321] Vector pAA061 was constructed from a pUC19 backbone to
harbor the selectable marker URA3 from C. tropicalis strain
ATCC20336 as well as modifications to allow insertion of C.
tropicalis promoters and terminators. A 1,507 bp DNA fragment
containing the promoter, ORF, and terminator of URA3 from C.
tropicalis ATCC20336 was amplified using primers oAA0124 and
oAA0125, shown in the table below. The URA3 PCR product was
digested with NdeI/MluI and ligated into the 2,505 bp fragment of
pUC19 digested with NdeI/BsmBI (an MluI compatible overhang was
produced by BsmBI). In order to replace the lac promoter with a
short 21 bp linker sequence, the resulting plasmid was digested
with SphI/SapI and filled in with a linker produced by annealing
oligos oAA0173 and oAA0174. The resulting plasmid was named pAA061,
and is shown in FIG. 30.
TABLE-US-00027 Oligonucleotides for construction of pAA061 SEQ PCR
ID product Oligos Sequence NO: (bp) oAA0124
cacacacatatgCGACGGGTACAACG 297 1507 AGAATT oAA0125
cacacaacgcgtAGACGAAGCCGTTC 298 TTCAAG oAA0173 ATGATCTGCCATGCCGAACTC
299 21 (linker) oAA0174 AGCGAGTTCGGCATGGCAGATCAT 300 CATG
Example 20
Cloning of C. Tropicalis PGK Promoter and Terminator
[0322] Vector pAA105 was constructed from base vector pAA061 to
include the phosphoglycerate kinase (PGK) promoter and terminator
regions from C. tropicalis ATCC20336 with an intervening multiple
cloning site (MCS) for insertion of open reading frames (ORF's).
The PGK promoter region was amplified by PCR using primers oAA0347
and oAA0348, shown in the table below. The 1,029 bp DNA fragment
containing the PGK promoter was digested with restriction enzymes
PstI/XmaI. The PGK terminator region was amplified by PCR using
primers oAA0351 and oAA0352, also shown in the table below. The 396
bp DNA fragment containing the PGK terminator was digested with
restriction enzymes XmaI/EcoRI. The 3,728 bp PstI/EcoRI DNA
fragment from pAA061 was used in a three piece ligation reaction
with the PGK promoter and terminator regions to produce pAA105. The
sequence between the PGK promoter and terminator contains
restriction sites for incorporating ORF's to be controlled by the
functionally linked constitutive PGK promoter.
TABLE-US-00028 Oligonucleotides for cloning C. tropicalis PGK
promoter and terminator SEQ PCR ID product Oligos Sequence NO: (bp)
oAA0347 CACACACTGCAGTTGTCCAATGTAATAATT 301 1028 TT oAA0348
CACACATCTAGACCCGGGCTCTTCTTCTG 302 AATAGGCAATTGATAAACTTACTTATC
oAA0351 GAGCCCGGGTCTAGATGTGTGCTCTTCCA 303 396 AAGTACGGTGTTGTTGACA
oAA0352 CACACACATATGAATTCTGTACTGGTAGAG 304 CTAAATT
Example 21
Cloning of the POX4 Locus
[0323] Primers oAA0138 and oAA0141 (shown in the table below) were
generated to amplify the entire sequence of NCBI accession number
M12160 for the YSAPOX4 locus from genomic DNA prepared from C.
tropicalis strain ATCC20336. The 2,845 bp PCR product was cloned
into the vector, pCR-Bluntll-TOPO (Invitrogen), sequenced and
designated pAA052, and is shown in FIG. 29.
TABLE-US-00029 Oligonucleotides for cloning of POX4 PCR SEQ product
Oligos Sequence ID NO: (bp) oAA0138 GAGCTCCAATTGTAATATTTCGGG 305
2845 oAA0141 GTCGACCTAAATTCGCAACTATCAA 306
Example 22
Cloning of the POX5 Locus
[0324] Primers oAA0179 and oAA0182 (shown in the table below) were
generated to amplify the entire sequence of NCBI accession number
M12161 for the YSAPOX5 locus from genomic DNA prepared from C.
tropicalis strain ATCC20336. The 2,624 bp PCR product was cloned
into the vector, pCR-Bluntll-TOPO (Invitrogen), sequenced and
designated pAA049, and is shown in FIG. 28.
TABLE-US-00030 Oligonucleotides for cloning of POX5 SEQ PCR ID
product Oligos Sequence NO: (bp) oAA0179
GAATTCACATGGCTAATTTGGCCTCGGTT 307 2624 CCACAACGCACTCAGCATTAAAAA
oAA0182 GAGCTCCCCTGCAAACAGGGAAACACTT 308 GTCATCTGATTT
Example 23
Construction of Strain sAA 105 and sAA 106
[0325] Functional POX4 alleles were restored in C. tropicalis
strain sAA003 (ATCC20962; ura3/ura3, pox4::ura3/pox4::ura3,
pox5::ura3/pox5::URA3) by transformation of sAA003 with POX4 linear
DNA to replace the ura3-disrupted loci with functional alleles. A
2,845 bp DNA fragment was amplified by PCR using primers oAA0138
and oAA0141 (described in Example 21) that contained the POX4 ORF
as well as 531 bp upstream and 184 bp downstream of the ORF, using
plasmid pAA052 as template. The purified PCR product was used to
transform competent sAA003 cells which were plated on YNB-agar
plates supplemented with hexadecane vapor as the carbon source
(e.g., by placing a filter paper soaked with hexadecane in the lid
of the inverted petri dish) and incubated at 30.degree. C. for 4-5
days. Colonies growing on hexadecane as the sole carbon source were
restreaked onto YPD-agar and incubated at 30.degree. C. Single
colonies were grown in YPD cultures and used for the preparation of
genomic DNA.
[0326] PCR analysis of the genomic DNA prepared from the
transformants was performed with oligos oAA0138 and oAA0141. An
URA3-disrupted POX4 would produce a PCR product of 5,045 bp, while
a functional POX4 would produce a PCR product of 2,845 bp. In
strain sAA105 only one PCR product was amplified with a size of
2,845 bp indicating that both POX4 alleles had been functionally
restored. In strain sAA106 PCR products of both 2,845 bp and 5,045
bp were amplified indicating that one POX4 allele had been
functionally restored while the other POX4 allele remained
disrupted by URA3. The resultant strain genotypes were: sAA105
(ura3/ura3, POX4/POX4, pox5::ura3/pox5::URA3) and sAA106
(ura3/ura3, POX4/pox4::ura3, pox5::ura3/pox5::URA3).
Example 24
Construction of Strain sAA 152
[0327] Functional POX5 alleles were restored in C. tropicalis
strain sAA103 (ura3/ura3, pox4::ura3/pox4::ura3,
pox5::ura3/pox5::ura3) by transformation of sAA103 with
PmII-linearized plasmid pAA086 (containing the POX5 promoter, gene,
terminator and a URA3 marker). Selection of transformants was
performed by plating on SC-URA agar plates. Verification of plasmid
integration was performed by PCR with primers oAA179 and oAA182
(described in Example 22). Integration of the plasmid was shown by
a PCR product of 2,584 bp indicating the presence of a functional
POX5 allele. Other POX5 alleles in sAA152 were disrupted with an
ura3 gene increasing the PCR product size for nonfunctional alleles
to 4,734 bp. Genotype for strain sAA152 is ura3/ura3,
pox4::ura3/pox4::ura3, pox5::ura3/pox5::ura3, ura3::POX5,URA3).
Example 25
Construction of Strain sAA232
[0328] Functional POX5 alleles were restored in C. tropicalis
strain sAA003 bp transformation of sAA003 with POX5 linear DNA to
replace the URA3-disrupted loci with a functional allele. A 2,584
bp DNA fragment was amplified by PCR using primers oAA0179 and
oAA0182 (described in Example 22) that contained the POX5 ORF as
well as 456 bp upstream and 179 bp downstream of the ORF using
plasmid pAA049 as template. The purified PCR product was used to
transform competent sAA003 cells which were plated on SC+URA+5FOA
plates and incubated at 30.degree. C. for 3-4 days. Colonies were
restreaked onto YPD-agar and incubated at 30.degree. C. Single
colonies were grown in YPD cultures and used for the preparation of
genomic DNA. PCR analysis of the genomic DNA prepared from the
transformants was performed with oligos oAA0179 and oAA0182. An
ura3-disrupted POX5 would produce a PCR product of 4,784 bp while a
functional POX5 would produce a PCR product of 2,584 bp. In strain
sAA232 PCR products of both 2,584 bp and 4,784 bp were amplified
indicating that one POX5 allele had been functionally restored
while the other POX5 allele remained disrupted by ura3. The
resultant genotype of strain sAA232 is ura3/ura3,
pox4::ura3/pox4::ura3, pox5::ura3/POX5. 5-FOA selection restored
the POX5 allele that had been disrupted with the functional URA3
leaving the sAA232 strain Ura.sup.-.
Example 26
Construction of Strain sAA235
[0329] Functional POX5 alleles were restored in C. tropicalis
strain sAA003 bp transformation of sAA003 with POX5 linear DNA to
replace the URA3-disrupted loci with a functional allele. A 2,584
bp DNA fragment was amplified by PCR using primers oAA0179 and
oAA0182 (described in Example 22) that contained the POX5 ORF as
well as 456 bp upstream and 179 bp downstream of the ORF using
plasmid pAA049 as template. The purified PCR product was used to
transform competent sAA003 cells which were plated on YNB-agar
plates supplemented with dodecane vapor as the carbon source (e.g.,
by placing a filter paper soaked with dodecane in the lid of the
inverted petri dish) and incubated at 30.degree. C. for 4-5 days.
Colonies growing on dodecane as the sole carbon source were
restreaked onto YPD-agar and incubated at 30.degree. C. Single
colonies were grown in YPD cultures and used for the preparation of
genomic DNA. PCR analysis of the genomic DNA prepared from the
transformants was performed with oligos oAA0179 and oAA0182. An
ura3-disrupted POX5 would produce a PCR product of 4,784 bp while a
functional POX5 would produce a PCR product of 2,584 bp. In strain
sAA235a PCR product of 2,584 bp was amplified indicating that both
POX5 alleles had been functionally restored. An unintended
consequence of the selection strategy (YNB-agar with dodecane) was
that the cells reverted back to an Ura phenotype. Without being
limited by any theory, it is believed the absence of uracil in the
solid media and the replacement of the only functional URA3 forced
the cells to mutate one of the other ura3 loci back to a functional
allele. Therefore the genotype of the strain sAA235 is believed to
be URA3/ura3, pox4::ura3/pox4::ura3, POX5/POX5. Verification of
which of the loci is the functional URA3 is underway.
Example 27
Construction of Strains with Amplified CPR and CYP52 Genes
[0330] Strains having an increased number of copies of cytochrome
P450 reductase (CPR) and/or for cytochrome P450 monooxygenase
(CYP52) genes were constructed to determine how over expression of
CPR and CYP52 affected diacid production.
[0331] Cloning and Integration of the CPR Gene.
[0332] A 3,019 bp DNA fragment encoding the CPR promoter, ORF, and
terminator from C. tropicalis ATCC750 was amplified by PCR using
primers oAA0171 and oAA0172 (see table below) incorporating unique
SapI and Sph I sites. The amplified DNA fragment was cut with the
indicated restriction enzymes and ligated into plasmid pAA061,
shown in FIG. 30, to produce plasmid pAA067, shown in FIG. 32.
Plasmid pAA067 was linearized with ClaI and transformed into C.
tropicalis Ura strain sAA103 (ura3/ura3, pox4::ura3/pox4::ura3,
pox5::ura3/pox5::ura3). Transformations were performed with plasmid
pAA067 alone and in combination with plasmids harboring the
CYP52A15 or CYP52A16 genes, described below.
[0333] Cloning and Integration of CYP52A15 Gene.
[0334] A 2,842 bp DNA fragment encoding the CYP52A15 promoter, ORF,
and terminator from C. tropicalis ATCC20336 was amplified by PCR
using primers oAA0175 and oAA0178 (see table below) and cloned into
pCR-Bluntll-TOPO for DNA sequence verification. The cloned CYP52A15
DNA fragment was isolated by restriction digest with XbaI/BamHI
(2,742 bp) and ligated into plasmid pAA061, shown in FIG. 30, to
produce plasmid pAA077, shown in FIG. 33. Plasmid pAA077 was
linearized with Pmll and transformed into C. tropicalis Ura strain
sAA103 (ura3/ura3, pox4::ura3/pox4::ura3, pox5::ura3/pox5::ura3).
pAA077 was cotransformed with plasmid pAA067 harboring the CPR
gene.
[0335] Cloning and Integration of CYP52A16 Gene.
[0336] A 2,728 bp DNA fragment encoding the CYP52A16 promoter, ORF,
and terminator from C. tropicalis ATCC20336 was amplified by PCR
using primers oAA0177 and oAA0178 (see table below) and cloned into
pCR-Bluntll-TOPO for DNA sequence verification. The cloned CYP52A16
DNA fragment was amplified with primers oAA0260 and oAA0261(see
table below) which incorporated unique SacI/XbaI restriction sites.
The amplified DNA fragment was digested with SacI and XbaI
restriction enzymes and ligated into plasmid pAA061 to produce
plasmid pAA078, shown in FIG. 34. Plasmid pAA078 was linearized
with ClaI and transformed into C. tropicalis Ura.sup.- strain
sAA103 (ura3/ura3, pox4::ura3/pox4::ura3, pox5::ura3/pox5::ura3).
pAA078 was cotransformed with plasmid pAA067 harboring the CPR
gene.
TABLE-US-00031 Oligonucleotides for cloning of CPR, CYP52A15 and
CYP52A16 SEQ PCR ID product Oligos Sequence NO: (bp) oAA0171
cacctcgctcttccAGCTGTCATGTCTATTC 309 3019 AATGCTTCGA oAA0172
cacacagcatgcTAATGTTTATATCGTTGAC 310 GGTGAAA oAA0175
cacaaagcggaagagcAAATTTTGTATTCTC 311 2842 AGTAGGATTTCATC oAA0178
cacacagcatgCAAACTTAAGGGTGTTGTA 312 GATATCCC oAA0177
cacacacccgggATCGACAGTCGATTACG 313 2772 TAATCCATATTATTT oAA0178
cacacagcatgCAAACTTAAGGGTGTTGTA 314 GATATCCC oAA0260
cacacagagctcACAGTCGATTACGTAATC 315 2772 CAT oAA0261
cacatctagaGCATGCAAACTTAAGGGTGT 316 TGTA
[0337] Preparation of Genomic DNA.
[0338] Genomic DNA was prepared from transformants for PCR
verification and for Southern blot analysis. Isolated colonies were
inoculated into 3 mL YPD and grown overnight at 30.degree. C. with
shaking. Cells were pelleted by centrifugation. To each pellet, 200
uL Breaking Buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM
Tris pH 8 and, 1 mM EDTA) was added, and the pellet resuspended and
transferred to a fresh tube containing 200 uL 0.5 mm
Zirconia/Silica Beads. 200 uL Phenol:Chloroform:lsoamyl Alcohol
(25:24:1) was added to each tube, followed by vortexing for 1
minute. Sterile distilled water was added (200 uL) to each tube and
the tubes were centrifuged at 13000 rpm for 10 minutes. The aqueous
layer was ethanol precipitated and washed with 70% ethanol. The
pellet was resuspended in 100-200 .mu.l 10 mM Tris, after drying.
Genomic DNA preparation for southern blot analysis was performed
using the same procedure on 25 mL cultures for each colony
tested.
[0339] Characterization of Strains with Amplified CPR and CYP52
Genes.
[0340] Verification of integrants was performed by PCR using
primers oAA0252 and oAA0256 (CPR), oAA0231 and oAA0281 (CYP52A15),
and oAA242 and oAA0257 (CYP52A16). The primers used for
verification are shown in the table below.
TABLE-US-00032 Oligonucleotides for PCR verification of CPR,
CYP52A15 and CYP52A16 PCR SEQ ID product Oligos Sequence NO: (bp)
oAA0252 TTAATGCCTTCTCAAGACAA 317 743 oAA0256 GGTTTTCCCAGTCACGACGT
318 oAA0231 CCTTGCTAATTTTCTTCTGTATAGC 319 584 oAA0281
TTCTCGTTGTACCCGTCGCA 320 oAA0242 CACACAACTTCAGAGTTGCC 321 974
oAA0257 TCGCCACCTCTGACTTGAGC 322
[0341] Southern blot analysis was used to determine the copy number
of the CPR, CYP52A15 and CYP52A15 genes. Biotinylated DNA probes
were prepared with gene specific oligonucleotides using the NEBIot
Phototope Kit from New England BioLabs (Catalog #N7550S) on PCR
products generated from each gene target as specified in the table
below. Southern Hybridizations were performed using standard
methods (e.g., Sambrook, J. and Russell, D. W. (2001) Molecular
Cloning: A Laboratory Manual, (3.sup.rd ed.), pp. 6.33-6.64. Cold
Spring Harbor Laboratory Press). Detection of hybridized probe was
performed using the Phototope-Star Detection Kit from New England
BioLabs (Catalog #N7020S). Copy number was determined by
densitometry of the resulting bands.
TABLE-US-00033 Oligonucleotides for Probe Template PCR of CPR,
CYP52A15 and CYP52A16 SEQ ID PCR product Oligos Sequence NO: Gene
Template (bp) oAA0250 AATTGAACATCAGAAGAGGA 323 CPR pAA067 1313
oAA0254 CCTGAAATTTCCAAATGGTGTCTAA 324 oAA0227 TTTTTTGTGCGCAAGTACAC
325 CYP52A15 pAA077 905 oAA0235 CAACTTGACGTGAGAAACCT 326 oAA0239
AGATGCTCGTTTTACACCCT 327 CYP52A16 pAA078 672 oAA0247
ACACAGCTTTGATGTTCTCT 328
Example 28
Strain Evaluation of Partially .beta.-Oxidation Blocked Strains
[0342] Fermentation of Methyl Laurate Feedstock.
[0343] 5 mL starter cultures, in SP92 media (6.7 g/L Difco yeast
nitrogen base, 3.0 g/L Difco yeast extract, 3.0 g/L ammonium
sulfate, 1.0 g/L potassium phosphate monobasic, 1.0 g/L potassium
phosphate dibasic, 75 g/L dextrose) were incubated overnight at
30.degree. C., with shaking and used to inoculate flasks containing
25 mL of SP92 media to an initial OD.sub.600nm of about 0.4.
Cultures were incubated approximately 18 hours at 30.degree. C.,
with shaking at about 200 rpm. Cells were pelleted by
centrifugation at 4.degree. C. for 10 minutes at 4,000.times.g,
then resuspended in SP92-D media (6.7 g/L Difco yeast nitrogen
base, 3.0 g/L Difco yeast extract, 3.0 g/L ammonium sulfate, 1.0
g/L potassium phosphate monobasic, 1.0 g/L potassium phosphate
dibasic) supplemented with 0.1% dextrose and 2% methyl laurate.
Incubation of the cultures continued at 30.degree. C., with shaking
and samples were taken for analysis of fatty acids and diacids by
gas chromatography (GC).
[0344] Sample for GC were prepared by adding 0.8 mL of 6.0M HCl to
1 mL of whole culture samples and the samples were stored at
4.degree. C. to await processing. Samples were processed by
incubating in a 60.degree. C. water bath for 5 minutes, after which
4.0 mL of MTBE was added to the 1.8 mL acidified whole culture
samples and vortexed for 20 seconds. The phases were allowed to
separate for 10 min at room temperature. 1 mL of the MTBE phase was
drawn and dried with sodium sulfate. Aliquots of the MTBE phase
were derivatized with BSTFA reagent (Regis Technologies Inc.) and
analyzed by GC equipped with a Flame Ionization Detector. The
results of the gas chromatography are shown in the table below.
TABLE-US-00034 Fatty acid and Diacid profile (g/L) in Methyl
Laurate fermentation Time C10 C8 C6 Strain (h) C12 Acid C12 Diacid
Diacid Diacid Diacid sAA105 0 0.00 0.00 0.00 0.00 0.00 24 0.05 0.00
0.00 0.07 0.42 48 0.00 0.00 0.00 0.00 0.00 sAA106 0 0.00 0.00 0.00
0.00 0.00 24 2.92 1.29 0.15 0.58 0.37 48 0.04 0.02 0.00 0.00 0.01
sAA152 0 0.02 0.00 0.00 0.00 0.00 24 0.58 0.55 0.07 0.43 0.03 48
0.00 0.03 0.00 0.05 0.58 sAA003 0 0.00 0.00 0.00 0.00 0.00 24 1.96
0.41 0.00 0.00 0.00 48 1.43 0.47 0.00 0.00 0.00
[0345] Fermentation of Methyl Myristate and Oleic Acid
Feedstocks.
[0346] Fermentations were performed essentially as described for
methyl laurate feedstock except that 2% methyl myristate or 2%
oleic acid was substituted for the 2% methyl laurate. The results
of the gas chromatography are shown in the tables below.
TABLE-US-00035 Fatty acid and Diacid profile (g/L) in Methyl
Myristate fermentation Time C14 C14 C12 C10 C8 Strain (h) Acid
Diacid Diacid Diacid Diacid C6 Diacid sAA105 0 0.02 0.00 0.00 0.00
0.00 0.00 24 0.02 0.00 0.00 0.00 0.00 0.29 48 0.01 0.00 0.00 0.00
0.00 0.03 sAA106 0 0.01 0.00 0.00 0.00 0.00 0.00 24 0.02 0.00 0.00
0.00 0.08 1.71 48 0.01 0.00 0.00 0.00 0.00 0.04 sAA232 0 0.01 0.00
0.00 0.00 0.00 0.00 24 0.01 0.00 0.00 0.00 0.59 0.26 48 0.01 0.00
0.00 0.00 0.35 0.47 sAA235 0 0.01 0.00 0.00 0.00 0.00 0.00 24 0.02
0.00 0.00 0.00 0.25 0.38 48 0.01 0.00 0.00 0.00 0.04 0.66 sAA003 0
0.02 0.01 0.01 0.00 0.00 0.00 24 0.55 0.25 0.00 0.00 0.00 0.00 48
0.49 0.38 0.00 0.00 0.00 0.00
TABLE-US-00036 Diacid profile (g/L) in Oleic acid fermentation Time
C14 C12 Strain (h) Diacid Diacid C10 Diacid C8 Diacid C6 Diacid
sAA105 0 0.00 0.00 0.00 0.00 0.00 24 0.00 0.00 0.00 0.00 0.03 48
0.00 0.00 0.00 0.00 0.01 sAA106 0 0.00 0.00 0.00 0.00 0.00 24 0.00
0.00 0.00 0.00 1.48 48 0.00 0.00 0.00 0.00 0.42 sAA232 0 0.00 0.00
0.00 0.00 0.00 24 0.00 0.00 0.00 0.00 0.09 48 0.00 0.00 0.00 0.00
0.10 sAA235 0 0.00 0.00 0.00 0.00 0.00 24 0.00 0.00 0.00 0.00 0.10
48 0.00 0.00 0.00 0.00 0.11
[0347] Fermentations also were performed using coconut oil as a
feed stock. Coconut oil contains a mixture of fatty acids of
different carbon chain lengths. The percent composition of fatty
acids, by weight, is about 6% capric acid (C10:0, where 0 refers to
the number of double or unsaturated bonds), about 47% lauric acid
(C12:0), about 18% myristic acid (C14:0), about 9% palmitic acid
(C16:0). About 3% stearic acid (C18:0), about 6% oleic acid (C18:1,
where 1 refers to the number of double bonds), and about 2%
linoleic acid (omega-6 fatty acid, C18:2). In some embodiments,
palm kernel oil can be substituted for coconut oil. Palm kernel oil
has a distribution of fatty acids similar to that of coconut oil.
Fermentations and GC were carried out essentially as described
herein with the exception of feedstock used. The result of
fermentations performed using coconut oil as a feedstock are
presented below.
TABLE-US-00037 Diacid profile (g/L) in Coconut Oil fermentation
Time C14 C12 Strain (h) Diacid Diacid C10 Diacid C8 Diacid C6
Diacid sAA105 0 0.00 0.00 0.00 0.00 0.00 24 0.00 0.00 0.00 0.00
0.00 48 0.00 0.00 0.00 0.00 0.00 sAA106 0 0.00 0.00 0.00 0.00 0.00
24 0.00 0.00 0.00 0.00 0.01 48 0.00 0.00 0.00 0.00 0.00 sAA152 0
0.00 0.00 0.00 0.00 0.00 24 0.00 0.00 0.00 0.00 0.43 48 0.00 0.00
0.00 0.00 0.45 sAA232 0 0.00 0.00 0.00 0.00 0.00 24 0.00 0.00 0.00
0.00 0.41 48 0.00 0.00 0.00 0.00 0.58 sAA235 0 0.00 0.00 0.00 0.00
0.00 24 0.00 0.00 0.00 0.00 0.43 48 0.00 0.00 0.00 0.00 0.76
Example 29
Strain Evaluation of Completely .beta.-Oxidation Blocked
Strains
[0348] Fermentations also were performed using methyl myristate as
a feed stock. Fermentations and GC were carried out essentially as
described herein with the exception of feedstock used. The result
of fermentations performed using coconut oil as a feedstock are
presented below.
TABLE-US-00038 C14 Diacid production in strains with amplified CPR,
CYP52A15, and/or CYP52A16 Strain C14 diacid, 72 h (g/L) CPR A15 A16
sAA003 0.98 2 1 1 sAA318 1.19 3 1 1 sAA239 2.75 3 1 3 sAA319 1.37 7
1 1 sAA238 1.93 7 2 1
Example 30
Nucleic Acid and Amino Acid Sequences of Novel Fatty Alcohol
Oxidase Genes
[0349] As noted above, novel fatty alcohol oxidase genes were
identified and cloned. The nucleotide and amino acid sequences of
the novel sequences are presented herein. Nucleotide and amino acid
sequence identity comparison are shown in Example 18.
[0350] Nucleotide Sequences
TABLE-US-00039 FAO-13 (SEQ ID NO: 1)
atggctccatttttgcccgaccaggtcgactacaaacacgtcgacacccttatgttattatgtgacgggatcat-
ccacga
aaccaccgtcgaccaaatcaaagacgttattgctcctgacttccctgctgacaagtacgaagagtacgtcagga-
cattca
ccaaaccctccgaaaccccagggttcagggaaaccgtctacaacacagtcaacgcaaacaccacggacgcaatc-
caccag
ttcattatcttgaccaatgttttggcatccagggtcttggctccagctttgaccaactcgttgacgcctatcaa-
ggacat
gagcttggaagaccgtgaaaaattgttggcctcgtggcgcgactccccaatcgctgccaaaaggaagttgttca-
ggttgg
tttctacgcttaccttggtcacgttcacgagattggccaatgagttgcatttgaaagccattcattatccagga-
agagaa
gaccgtgaaaaggcttatgaaacccaggagattgacccttttaagtaccagtttttggaaaaaccgaagtttta-
cggcgc
tgagttgtacttgccagatattgatgtgatcattattggatctggtgccggtgctggtgttgtggcccacactt-
tggcca
acgatggcttcaagagtttggttttggaaaagggcaaatactttagcaactccgagttgaactttgatgacaag-
gacggc
gttcaagaattataccaaagtggaggtactttgactacagtcaaccaacagttgtttgttcttgctggttccac-
ttttgg
tggcggtaccactgtcaattggtcagcctgtcttaagacgccattcaaggtgcgtaaggaatggtatgatgagt-
ttggtg
ttgactttgctgctgatgaagcatacgataaagcgcaggattatgtttggcagcaaatgggagcttctaccgaa-
ggcatc
acccactctttggctaacgagattattattgaaggtggtaagaaattaggttacaaggccaaggtattagacca-
aaacag
cggtggtcatcctcagcacagatgcggtttctgttatttgggctgtaagcacggtatcaagcagggttctgtta-
ataact
ggtttagagacgcagctgcccacggttcccagttcatgcaacaggttagagttttgcaaatacttaacaagaag-
gggatc
gcttacggtatcttgtgtgaggatgttgtaaccggcgccaagttcaccattactggccccaaaaagtttgttgt-
tgctgc
cggtgctttgaacactccatctgtgttggtcaactccggcttcaagaacaagaacatcggtaagaacttaactt-
tgcacc
cagtttctgtcgtgtttggtgattttggcaaagacgttcaagcagaccacttccacaactccatcatgactgcc-
ctttgt
tcagaagccgctgatttagacggcaagggccatggatgcagaattgaaaccatcttgaacgctccattcatcca-
ggcttc
attcttaccatggagaggtagtaacgaggctagacgagacttgttgcgttacaacaacatggtggcgatgttgc-
tcctta
gtcgtgacaccaccagtggttccgtttctgctcatccaaccaaacctgaagctttggttgtcgagtacgacgtg-
aacaag
tttgacagaaactcgatcttgcaggcattgttggtcactgctgacttgttgtatatccaaggtgccaagagaat-
ccttag
tccacaggcatgggtgccaatttttgaatccgacaagccaaaggataagagatcaatcaaggacgaggactatg-
tcgaat
ggagagccaaggttgccaagattcctttcgacacctacggctcaccttatggttcggcacatcaaatgtcttct-
tgccgt
atgtcaggtaagggtcctaaatacggtgctgttgacaccgatggtagattgtttgaatgttcgaatgtttatgt-
tgccga
tgcaagtcttttgccaactgcaagcggtgccaaccctatggtcaccaccatgactcttgccagacatgttgcgt-
taggtt tggcagactccttgaagaccaaagccaagttgtag FAO-17 (SEQ ID NO: 2)
atggctccatttttgcccgaccaggtcgactacaaacacgtcgacacccttatgttattatgtgacgggatcat-
ccacga
aaccaccgtggacgaaatcaaagacgtcattgcccctgacttccccgccgacaaatacgaggagtacgtcagga-
cattca
ccaaaccctccgaaaccccagggttcagggaaaccgtctacaacaccgtcaacgcaaacaccatggatgcaatc-
caccag
ttcattatcttgaccaatgttttgggatcaagggtcttggcaccagctttgaccaactcgttgactcctatcaa-
ggacat
gagcttggaagaccgtgaaaagttgttagcctcgtggcgtgactcccctattgctgctaaaaggaagttgttca-
ggttgg
tttctacgcttaccttggtcacgttcacgagattggccaatgagttgcatttgaaagccattcattatccagga-
agagaa
gaccgtgaaaaggcttatgaaacccaggagattgacccttttaagtaccagtttttggaaaaaccgaagtttta-
cggcgc
tgagttgtacttgccagatattgatgtgatcattattggatctggtgccggtgctggtgttgtggcccacactt-
tggcca
acgatggcttcaagagtttggttttggaaaagggcaaatactttagcaactccgagttgaactttgatgacaag-
gacggc
gttcaagaattataccaaagtggaggtactttgactacagtcaaccaacagttgtttgttcttgctggttccac-
ttttgg
tggcggtaccactgtcaattggtcagcctgtcttaagacgccattcaaggtgcgtaaggaatggtatgatgagt-
ttggtg
ttgactttgctgctgatgaagcatacgataaagcgcaggattatgtttggcagcaaatgggagcttctaccgaa-
ggcatc
acccactctttggctaacgagattattattgaaggtggtaagaaattaggttacaaggccaaggtattagacca-
aaacag
cggtggtcatcctcagcacagatgcggtttctgttatttgggttgtaagcacggtatcaagcagggctctgtta-
ataact
ggtttagagacgcagctgcccacggttctcagttcatgcaacaggttagagttttgcaaatccttaacaagaag-
ggcatc
gcttatggtatcttgtgtgaggatgttgtaaccggtgccaagttcaccattactggccccaaaaagtttgttgt-
tgccgc
cggcgccttaaacactccatctgtgttggtcaactccggattcaagaacaagaacatcggtaagaacttaactt-
tgcatc
cagtttctgtcgtgtttggtgattttggcaaagacgttcaagcagaccacttccacaactccatcatgactgcc-
ctttgt
tcagaagccgctgatttagacggcaagggccatggatgcagaattgaaaccatcttgaacgctccattcatcca-
ggcttc
attcttaccatggagaggtagtaacgaggctagacgagacttgttgcgttacaacaacatggtggcgatgttgc-
tcctta
gtcgtgacaccaccagtggttccgtttctgctcatccaaccaaacctgaagctttggttgtcgagtacgacgtg-
aacaag
tttgacagaaactcgatcttgcaggcattgttggtcactgctgacttgttgtatatccaaggtgccaagagaat-
ccttag
tccacaggcatgggtgccaatttttgaatccgacaagccaaaggataagagatcaatcaaggacgaggactatg-
tcgaat
ggagagccaaggttgccaagattcctttcgacacctacggctcaccttatggttcggcacatcaaatgtcttct-
tgccgt
atgtcaggtaagggtcctaaatacggtgctgttgacaccgatggtagattgtttgaatgttcgaatgtttatgt-
tgccga
tgcaagtcttttgccaactgcaagcggtgccaaccctatggtcaccaccatgactcttgcaagacatgttgcgt-
taggtt tggcagactccttgaagaccaaggccaagttgtag FAO-20 (SEQ ID NO: 3)
atggctccatttttgcccgaccaggtcgactacaaacacgtcgacacccttatgttattatgtgacgggatcat-
ccacga
aaccaccgtcgaccaaatcaaagacgttattgctcctgacttccctgctgacaagtacgaagagtacgtcagga-
cattca
ccaaaccctccgaaaccccagggttcagggaaaccgtctacaacacagtcaacgcaaacaccacggacgcaatc-
caccag
ttcattatcttgaccaatgttttggcatccagggtcttggctccagctttgaccaactcgttgacgcctatcaa-
ggacat
gagcttggaagaccgtgaaaaattgttggcctcgtggcgcgactccccaatcgctgccaaaaggaaattgttca-
ggttgg
tttccacgcttaccttggttactttcacgagattggccaatgagttgcatttgaaagccattcactatccagga-
agagaa
gaccgtgaaaaggcttatgaaacccaggagattgaccctttcaagtaccagtttatggaaaagccaaagtttga-
cggcgc
tgagttgtacttgccagatattgatgttatcattattggatctggtgccggtgctggtgttgtggcccacactt-
tggcca
acgatggcttcaagagtttggttttggaaaagggcaaatactttagcaactccgagttgaactttgatgacaag-
gacggc
gttcaagaattataccaaagtggaggtactttgactacagtcaaccaacagttgtttgttcttgctggttccac-
ttttgg
tggcggtaccactgtcaattggtcagcctgtcttaagacgccattcaaggtgcgtaaggaatggtatgatgagt-
ttggtg
ttgactttgctgctgatgaagcatacgataaagcgcaggattatgtttggcagcaaatgggagcttctaccgaa-
ggcatc
acccactctttggctaacgagattattattgaaggtggtaagaaattaggttacaaggccaaggtattagacca-
aaacag
cggtggtcatcctcagcacagatgcggtttctgttatttgggctgtaagcacggtatcaagcagggttctgtta-
ataact
ggtttagagacgcagctgcccacggttcccagttcatgcaacaggttagagttttgcaaatacttaacaagaag-
gggatc
gcttacggtatcttgtgtgaggatgttgtaaccggcgccaagttcaccattactggccccaaaaagtttgttgt-
tgctgc
cggtgctttgaacactccatctgtgttggtcaactccggcttcaagaacaagaacatcggtaagaacttaactt-
tgcacc
cagtttctgtcgtgtttggtgattttggcaaagacgttcaagcagaccacttccacaactccatcatgactgcc-
ctttgt
tcagaagccgctgatttagacggcaagggccatggatgcagaattgaaaccatcttgaacgctccattcatcca-
ggcttc
attcttaccatggagaggtagtaacgaggctagacgagacttgttgcgttacaacaacatggtggcgatgttgc-
tcctta
gtcgtgacaccaccagtggttccgtttctgctcatccaaccaaacctgaagctttggttgtcgagtacgacgtg-
aacaag
tttgacagaaactcgatcttgcaggcattgttggtcactgctgacttgttgtatatccaaggtgccaagagaat-
ccttag
tccacaggcatgggtgccaatttttgaatccgacaagccaaaggataagagatcaatcaaggacgaggactatg-
tcgaat
ggagagccaaggttgccaagattcctttcgacacctacggctcaccttatggttcggcacatcaaatgtcttct-
tgccgt
atgtcaggtaagggtcctaaatacggtgctgttgacaccgatggtagattgtttgaatgttcgaatgtttatgt-
tgccga
tgcaagtcttttgccaactgcaagcggtgccaaccctatggtcaccaccatgactcttgccagacatgttgcgt-
taggtt tggcagactccttgaagaccaaagccaagttgtag FAO2a (SEQ ID NO: 4)
atgaataccttcttgccagacgtgctcgaatacaaacacgtcgacacccttttgttattgtgtgacgggatcat-
ccacga
aaccacagtcgatcagatcaaggacgccattgctcccgacttccctgaggaccagtacgaggagtatctcaaga-
ccttca
ccaagccatctgagacccctgggttcagagaagccgtctacgacacgatcaacgccaccccaaccgatgccgtg-
cacatg
tgtattgtcttgaccaccgcattggactccagaatcttggcccccacgttgaccaactcgttgacgcctatcaa-
ggatat
gaccttgaaggagcgtgaacaattgttggcctcttggcgtgattccccgattgcggcaaagagaagattgttca-
gattga
tttcctcgcttaccttgacgacgtttacgagattggccagcgaattgcacttgaaagccatccactaccctggc-
agagac
ttgcgtgaaaaggcgtatgaaacccaggtggttgaccctttcaggtacctgtttatggagaaaccaaagtttga-
cggcgc
cgaattgtacttgccagatatcgacgtcatcatcattggatcaggcgccggtgctggtgtcatggcccacactc-
tcgcca
acgacgggttcaagaccttggttttggaaaagggaaagtatttcagcaactccgagttgaactttaatgacgct-
gatggc
gtgaaagagttgtaccaaggtaaaggtgctttggccaccaccaatcagcagatgtttattcttgccggttccac-
tttggg
cggtggtaccactgtcaactggtctgcttgccttaaaacaccatttaaagtgcgtaaggagtggtacgacgagt-
ttggtc
ttgaatttgctgccgatgaagcctacgacaaagcgcaggattatgtttggaaacaaatgggtgcttcaacagat-
ggaatc
actcactccttggccaacgaagttgtggttgaaggaggtaagaagttgggctacaagagcaaggaaattgagca-
gaacaa
cggtggccaccctgaccacccatgtggtttctgttacttgggctgtaagtacggtattaaacagggttctgtga-
ataact
ggtttagagacgcagctgcccacgggtccaagttcatgcaacaagtcagagttgtgcaaatcctcaacaagaat-
ggcgtc
gcttatggtatcttgtgtgaggatgtcgaaaccggagtcaggttcactattagtggccccaaaaagtttgttgt-
ttctgc
tggttctttgaacacgccaactgtgttgaccaactccggattcaagaacaagcacattggtaagaacttgacgt-
tgcacc
cagtttccaccgtgtttggtgactttggcagagacgtgcaagccgaccatttccacaaatctattatgacttcg-
ctttgt
tacgaggttgctgacttggacggcaagggccacggatgcagaatcgaaaccatcttgaacgctccattcatcca-
agcttc
tttgttgccatggagaggaagtgacgaggtcagaagagacttgttgcgttacaacaacatggtggccatgttgc-
ttatca
cgcgtgataccaccagtggttcagtttctgctgacccaaagaagcccgacgctttgattgtcgactatgagatt-
aacaag
tttgacaagaatgccatcttgcaagctttcttgatcacttccgacatgttgtacattgaaggtgccaagagaat-
cctcag
tccacagccatgggtgccaatctttgagtcgaacaagccaaaggagcaaagaacgatcaaggacaaggactatg-
ttgagt
ggagagccaaggctgctaagatacctttcgacacctacggttctgcatatgggtccgcacatcaaatgtccacc-
tgtcgt
atgtccggaaagggtcctaaatacggtgctgttgatactgatggtagattgtttgaatgttcgaatgtctatgt-
tgctga
tgctagtgttttgcctactgccagcggtgccaacccaatgatatccaccatgacctttgctagacagattgcgt-
taggtt tggctgactccttgaagaccaaacccaagttgtag FAO2b (SEQ ID NO: 5)
atgaataccttcttgccagacgtgctcgaatacaaacacgtcgatacccttttgttattatgtgacgggatcat-
ccacga
aaccacagtcgaccagatcagggacgccattgctcccgacttccctgaagaccagtacgaggagtatctcaaga-
ccttca
ccaagccatctgagacccctgggttcagagaagccgtctacgacacgatcaacagcaccccaaccgaggctgtg-
cacatg
tgtattgtattgaccaccgcattggactcgagaatcttggcccccacgttgaccaactcgttgacgcctatcaa-
ggatat
gaccttgaaagagcgtgaacaattgttggctgcctggcgtgattccccgatcgcggccaagagaagattgttca-
gattga
tttcctcacttaccttgacgacctttacgagattggccagcgacttgcacttgagagccatccactaccctggc-
agagac
ttgcgtgaaaaggcatatgaaacccaggtggttgaccctttcaggtacctgtttatggaaaaaccaaagtttga-
cggcac
cgagttgtacttgccagatatcgacgtcatcatcattggatccggtgccggtgctggtgtcatggcccacactt-
tagcca
acgacgggtacaagaccttggttttggaaaagggaaagtatttcagcaactccgagttgaactttaatgatgcc-
gatggt
atgaaagagttgtaccaaggtaaatgtgcgttgaccaccacgaaccagcagatgtttattcttgccggttccac-
tttggg
cggtggtaccactgttaactggtctgcttgtcttaaaacaccatttaaagtgcgtaaggagtggtacgacgagt-
ttggtc
ttgaatttgctgccgacgaagcctacgacaaagcacaagactatgtttggaaacaaatgggcgcttctaccgaa-
ggaatc
actcactctttggcgaacgcggttgtggttgaaggaggtaagaagttgggttacaagagcaaggaaatcgagca-
gaacaa
tggtggccatcctgaccacccctgtggtttctgttacttgggctgtaagtacggtattaagcagggttctgtga-
ataact
ggtttagagacgcagctgcccacgggtccaagttcatgcaacaagtcagagttgtgcaaatcctccacaataaa-
ggcgtc
gcttatggcatcttgtgtgaggatgtcgagaccggagtcaaattcactatcagtggccccaaaaagtttgttgt-
ttctgc
aggttctttgaacacgccaacggtgttgaccaactccggattcaagaacaaacacatcggtaagaacttgacgt-
tgcacc
cagtttcgaccgtgtttggtgactttggcagagacgtgcaagccgaccatttccacaaatctattatgacttcg-
ctctgt
tacgaagtcgctgacttggacggcaagggccacggatgcagaatcgagaccatcttgaacgctccattcatcca-
agcttc
tttgttgccatggagaggaagcgacgaggtcagaagagacttgttgcgttacaacaacatggtggccatgttgc-
ttatca
cccgtgacaccaccagtggttcagtttctgctgacccaaagaagcccgacgctttgattgtcgactatgacatc-
aacaag
tttgacaagaatgccatcttgcaagctttcttgatcacctccgacatgttgtacatcgaaggtgccaagagaat-
cctcag
tccacaggcatgggtgccaatctttgagtcgaacaagccaaaggagcaaagaacaatcaaggacaaggactatg-
tcgaat
ggagagccaaggctgccaagatacctttcgacacctacggttctgcctatgggtccgcacatcaaatgtccacc-
tgtcgt
atgtccggaaagggtcctaaatacggcgccgttgataccgatggtagattgtttgaatgttcgaatgtctatgt-
tgctga
tgctagtgttttgcctactgccagcggtgccaacccaatgatctccaccatgacgtttgctagacagattgcgt-
taggtt tggctgactctttgaagaccaaacccaagttgtag
[0351] In addition to the novel FAO genes isolated, a sequence
substantially identical to the sequence used for primer design,
described above, also was isolated. The nucleotide sequence of the
gene is presented below.
TABLE-US-00040 FAO-18 (SEQ ID NO: 6)
atggctccatttttgcccgaccaggtcgactacaaacacgtcgacacccttatgttattatgtgacgggatcat-
ccacga
aaccaccgtggacgaaatcaaagacgtcattgcccctgacttccccgccgacaaatacgaggagtacgtcagga-
cattca
ccaaaccctccgaaaccccagggttcagggaaaccgtctacaacaccgtcaacgcaaacaccatggatgcaatc-
caccag
ttcattatcttgaccaatgttttgggatcaagggtcttggcaccagctttgaccaactcgttgactcctatcaa-
ggacat
gagcttggaagaccgtgaaaagttgttagcctcgtggcgtgactcccctattgctgctaaaaggaagttgttca-
ggttgg
tttctacgcttaccttggtcacgttcacgagattggccaatgagttgcatttgaaagccattcattatccagga-
agagaa
gaccgtgaaaaggcttatgaaacccaggagattgacccttttaagtaccagtttttggaaaaaccgaagtttta-
cggcgc
tgagttgtacttgccagatattgatgtgatcattattggatctggggccggtgctggtgtcgtggcccacactt-
tgacca
acgacggcttcaagagtttggttttggaaaagggcagatactttagcaactccgagttgaactttgatgacaag-
gacggg
gttcaagaattataccaaagtggaggtactttgaccaccgtcaaccagcagttgtttgttcttgctggttccac-
ttttgg
tggtggtaccactgtcaattggtcggcctgtcttaaaacgccattcaaggtgcgtaaggaatggtatgatgagt-
ttggcg
ttgactttgctgccgatgaagcctacgacaaagcacaggattatgtttggcagcaaatgggagcttctaccgaa-
ggcatc
acccactctttggctaacgagattattattgaaggtggcaagaaattaggttacaaggccaaggtattagacca-
aaacag
cggtggtcatcctcatcacagatgcggtttctgttatttgggttgtaagcacggtatcaagcagggctctgtta-
ataact
ggtttagagacgcagctgcccacggttctcagttcatgcaacaggttagagttttgcaaatccttaacaagaag-
ggcatc
gcttatggtatcttgtgtgaggatgttgtaaccggtgccaagttcaccattactggccccaaaaagtttgttgt-
tgccgc
cggcgccttaaacactccatctgtgttggtcaactccggattcaagaacaagaacatcggtaagaacttaactt-
tgcatc
cagtttctgtcgtgtttggtgattttggcaaagacgttcaagcagatcacttccacaactccatcatgactgct-
ctttgt
tcagaagccgctgatttagacggcaagggtcatggatgcagaattgaaaccatcttgaacgctccattcatcca-
ggcttc
attcttaccatggagaggtagtaacgaggctagacgagacttgttgcgttacaacaacatggtggccatgttac-
ttctta
gtcgtgataccaccagtggttccgtttcgtcccatccaactaaacctgaagcattagttgtcgagtacgacgtg-
aacaag
tttgacagaaactccatcttgcaggcattgttggtcactgctgacttgttgtacattcaaggtgccaagagaat-
ccttag
tccccaaccatgggtgccaatttttgaatccgacaagccaaaggataagagatcaatcaaggacgaggactatg-
tcgaat
ggagagccaaggttgccaagattccttttgacacctacggctcgccttatggttcggcgcatcaaatgtcttct-
tgtcgt
atgtcaggtaagggtcctaaatacggtgctgttgataccgatggtagattgtttgaatgttcgaatgtttatgt-
tgctga
cgctagtcttttgccaactgctagcggtgctaatcctatggtcaccaccatgactcttgcaagacatgttgcgt-
taggtt tggcagactccttgaagaccaaggccaagttgtag
[0352] Clustal Nucleotide Sequence Alignments
[0353] CLUSTAL 2.0.12 Multiple Sequence Alignment
TABLE-US-00041 FAO-13
ATGGCTCCATTTTTGCCCGACCAGGTCGACTACAAACACGTCGACACCCTTATGTTATTA 60
FAO-20 ATGGCTCCATTTTTGCCCGACCAGGTCGACTACAAACACGTCGACACCCTTATGTTATTA
60 FAO-17
ATGGCTCCATTTTTGCCCGACCAGGTCGACTACAAACACGTCGACACCCTTATGTTATTA 60
FAO-18 ATGGCTCCATTTTTGCCCGACCAGGTCGACTACAAACACGTCGACACCCTTATGTTATTA
60 FAO2a
ATGAATACCTTCTTGCCAGACGTGCTCGAATACAAACACGTCGACACCCTTTTGTTATTG 60
FAO2b ATGAATACCTTCTTGCCAGACGTGCTCGAATACAAACACGTCGATACCCTTTTGTTATTA
60 *** * * ** ***** *** * **** ************** ****** ******* FAO-13
TGTGACGGGATCATCCACGAAACCACCGTCGACCAAATCAAAGACGTTATTGCTCCTGAC 120
FAO-20 TGTGACGGGATCATCCACGAAACCACCGTCGACCAAATCAAAGACGTTATTGCTCCTGAC
120 FAO-17
TGTGACGGGATCATCCACGAAACCACCGTGGACGAAATCAAAGACGTCATTGCCCCTGAC 120
FAO-18 TGTGACGGGATCATCCACGAAACCACCGTGGACGAAATCAAAGACGTCATTGCCCCTGAC
120 FAO2a
TGTGACGGGATCATCCACGAAACCACAGTCGATCAGATCAAGGACGCCATTGCTCCCGAC 120
FAO2b TGTGACGGGATCATCCACGAAACCACAGTCGACCAGATCAGGGACGCCATTGCTCCCGAC
120 ************************** ** ** * **** **** ***** ** ***
FAO-13 TTCCCTGCTGACAAGTACGAAGAGTACGTCAGGACATTCACCAAACCCTCCGAAACCCCA
180 FAO-20
TTCCCTGCTGACAAGTACGAAGAGTACGTCAGGACATTCACCAAACCCTCCGAAACCCCA 180
FAO-17 TTCCCCGCCGACAAATACGAGGAGTACGTCAGGACATTCACCAAACCCTCCGAAACCCCA
180 FAO-18
TTCCCCGCCGACAAATACGAGGAGTACGTCAGGACATTCACCAAACCCTCCGAAACCCCA 180
FAO2a TTCCCTGAGGACCAGTACGAGGAGTATCTCAAGACCTTCACCAAGCCATCTGAGACCCCT
180 FAO2b
TTCCCTGAAGACCAGTACGAGGAGTATCTCAAGACCTTCACCAAGCCATCTGAGACCCCT 180
***** * *** * ***** ***** *** *** ******** ** ** ** ***** FAO-13
GGGTTCAGGGAAACCGTCTACAACACAGTCAACGCAAACACCACGGACGCAATCCACCAG 240
FAO-20 GGGTTCAGGGAAACCGTCTACAACACAGTCAACGCAAACACCACGGACGCAATCCACCAG
240 FAO-17
GGGTTCAGGGAAACCGTCTACAACACCGTCAACGCAAACACCATGGATGCAATCCACCAG 240
FAO-18 GGGTTCAGGGAAACCGTCTACAACACCGTCAACGCAAACACCATGGATGCAATCCACCAG
240 FAO2a
GGGTTCAGAGAAGCCGTCTACGACACGATCAACGCCACCCCAACCGATGCCGTGCACATG 240
FAO2b GGGTTCAGAGAAGCCGTCTACGACACGATCAACAGCACCCCAACCGAGGCTGTGCACATG
240 ******** *** ******** **** ***** * * * * ** ** * *** * FAO-13
TTCATTATCTTGACCAATGTTTTGGCATCCAGGGTCTTGGCTCCAGCTTTGACCAACTCG 300
FAO-20 TTCATTATCTTGACCAATGTTTTGGCATCCAGGGTCTTGGCTCCAGCTTTGACCAACTCG
300 FAO-17
TTCATTATCTTGACCAATGTTTTGGGATCAAGGGTCTTGGCACCAGCTTTGACCAACTCG 300
FAO-18 TTCATTATCTTGACCAATGTTTTGGGATCAAGGGTCTTGGCACCAGCTTTGACCAACTCG
300 FAO2a
TGTATTGTCTTGACCACCGCATTGGACTCCAGAATCTTGGCCCCCACGTTGACCAACTCG 300
FAO2b TGTATTGTATTGACCACCGCATTGGACTCGAGAATCTTGGCCCCCACGTTGACCAACTCG
300 * *** * ******* * **** ** ** ******* ** * ************ FAO-13
TTGACGCCTATCAAGGACATGAGCTTGGAAGACCGTGAAAAATTGTTGGCCTCGTGGCGC 360
FAO-20 TTGACGCCTATCAAGGACATGAGCTTGGAAGACCGTGAAAAATTGTTGGCCTCGTGGCGC
360 FAO-17
TTGACTCCTATCAAGGACATGAGCTTGGAAGACCGTGAAAAGTTGTTAGCCTCGTGGCGT 360
FAO-18 TTGACTCCTATCAAGGACATGAGCTTGGAAGACCGTGAAAAGTTGTTAGCCTCGTGGCGT
360 FAO2a
TTGACGCCTATCAAGGATATGACCTTGAAGGAGCGTGAACAATTGTTGGCCTCTTGGCGT 360
FAO2b TTGACGCCTATCAAGGATATGACCTTGAAAGAGCGTGAACAATTGTTGGCTGCCTGGCGT
360 ***** *********** **** **** * ** ****** * ***** ** * *****
FAO-13 GACTCCCCAATCGCTGCCAAAAGGAAGTTGTTCAGGTTGGTTTCTACGCTTACCTTGGTC
420 FAO-20
GACTCCCCAATCGCTGCCAAAAGGAAATTGTTCAGGTTGGTTTCCACGCTTACCTTGGTT 420
FAO-17 GACTCCCCTATTGCTGCTAAAAGGAAGTTGTTCAGGTTGGTTTCTACGCTTACCTTGGTC
420 FAO-18
GACTCCCCTATTGCTGCTAAAAGGAAGTTGTTCAGGTTGGTTTCTACGCTTACCTTGGTC 420
FAO2a GATTCCCCGATTGCGGCAAAGAGAAGATTGTTCAGATTGATTTCCTCGCTTACCTTGACG
420 FAO2b
GATTCCCCGATCGCGGCCAAGAGAAGATTGTTCAGATTGATTTCCTCACTTACCTTGACG 420 **
***** ** ** ** ** ** * ******** *** **** * ********* FAO-13
ACGTTCACGAGATTGGCCAATGAGTTGCATTTGAAAGCCATTCATTATCCAGGAAGAGAA 480
FAO-20 ACTTTCACGAGATTGGCCAATGAGTTGCATTTGAAAGCCATTCACTATCCAGGAAGAGAA
480 FAO-17
ACGTTCACGAGATTGGCCAATGAGTTGCATTTGAAAGCCATTCATTATCCAGGAAGAGAA 480
FAO-18 ACGTTCACGAGATTGGCCAATGAGTTGCATTTGAAAGCCATTCATTATCCAGGAAGAGAA
480 FAO2a
ACGTTTACGAGATTGGCCAGCGAATTGCACTTGAAAGCCATCCACTACCCTGGCAGAGAC 480
FAO2b ACCTTTACGAGATTGGCCAGCGACTTGCACTTGAGAGCCATCCACTACCCTGGCAGAGAC
480 ** ** ************* ** ***** **** ****** ** ** ** ** *****
FAO-13 GACCGTGAAAAGGCTTATGAAACCCAGGAGATTGACCCTTTTAAGTACCAGTTTTTGGAA
540 FAO-20
GACCGTGAAAAGGCTTATGAAACCCAGGAGATTGACCCTTTCAAGTACCAGTTTATGGAA 540
FAO-17 GACCGTGAAAAGGCTTATGAAACCCAGGAGATTGACCCTTTTAAGTACCAGTTTTTGGAA
540 FAO-18
GACCGTGAAAAGGCTTATGAAACCCAGGAGATTGACCCTTTTAAGTACCAGTTTTTGGAA 540
FAO2a TTGCGTGAAAAGGCGTATGAAACCCAGGTGGTTGACCCTTTCAGGTACCTGTTTATGGAG
540 FAO2b
TTGCGTGAAAAGGCATATGAAACCCAGGTGGTTGACCCTTTCAGGTACCTGTTTATGGAA 540
*********** ************* * ********** * ***** **** **** FAO-13
AAACCGAAGTTTTACGGCGCTGAGTTGTACTTGCCAGATATTGATGTGATCATTATTGGA 600
FAO-20 AAGCCAAAGTTTGACGGCGCTGAGTTGTACTTGCCAGATATTGATGTTATCATTATTGGA
600 FAO-17
AAACCGAAGTTTTACGGCGCTGAGTTGTACTTGCCAGATATTGATGTGATCATTATTGGA 600
FAO-18 AAACCGAAGTTTTACGGCGCTGAGTTGTACTTGCCAGATATTGATGTGATCATTATTGGA
600 FAO2a
AAACCAAAGTTTGACGGCGCCGAATTGTACTTGCCAGATATCGACGTCATCATCATTGGA 600
FAO2b AAACCAAAGTTTGACGGCACCGAGTTGTACTTGCCAGATATCGACGTCATCATCATTGGA
600 ** ** ****** ***** * ** ***************** ** ** ***** ******
FAO-13 TCTGGTGCCGGTGCTGGTGTTGTGGCCCACACTTTGGCCAACGATGGCTTCAAGAGTTTG
660 FAO-20
TCTGGTGCCGGTGCTGGTGTTGTGGCCCACACTTTGGCCAACGATGGCTTCAAGAGTTTG 660
FAO-17 TCTGGTGCCGGTGCTGGTGTTGTGGCCCACACTTTGGCCAACGATGGCTTCAAGAGTTTG
660 FAO-18
TCTGGGGCCGGTGCTGGTGTCGTGGCCCACACTTTGACCAACGACGGCTTCAAGAGTTTG 660
FAO2a TCAGGCGCCGGTGCTGGTGTCATGGCCCACACTCTCGCCAACGACGGGTTCAAGACCTTG
660 FAO2b
TCCGGTGCCGGTGCTGGTGTCATGGCCCACACTTTAGCCAACGACGGGTACAAGACCTTG 660 **
** ************** *********** * ******* ** * ***** *** FAO-13
GTTTTGGAAAAGGGCAAATACTTTAGCAACTCCGAGTTGAACTTTGATGACAAGGACGGC 720
FAO-20 GTTTTGGAAAAGGGCAAATACTTTAGCAACTCCGAGTTGAACTTTGATGACAAGGACGGC
720 FAO-17
GTTTTGGAAAAGGGCAAATACTTTAGCAACTCCGAGTTGAACTTTGATGACAAGGACGGC 720
FAO-18 GTTTTGGAAAAGGGCAGATACTTTAGCAACTCCGAGTTGAACTTTGATGACAAGGACGGG
720 FAO2a
GTTTTGGAAAAGGGAAAGTATTTCAGCAACTCCGAGTTGAACTTTAATGACGCTGATGGC 720
FAO2b GTTTTGGAAAAGGGAAAGTATTTCAGCAACTCCGAGTTGAACTTTAATGATGCCGATGGT
720 ************** * ** ** ********************* **** ** ** FAO-13
GTTCAAGAATTATACCAAAGTGGAGGTACTTTGACTACAGTCAACCAACAGTTGTTTGTT 780
FAO-20 GTTCAAGAATTATACCAAAGTGGAGGTACTTTGACTACAGTCAACCAACAGTTGTTTGTT
780 FAO-17
GTTCAAGAATTATACCAAAGTGGAGGTACTTTGACTACAGTCAACCAACAGTTGTTTGTT 780
FAO-18 GTTCAAGAATTATACCAAAGTGGAGGTACTTTGACCACCGTCAACCAGCAGTTGTTTGTT
780 FAO2a
GTGAAAGAGTTGTACCAAGGTAAAGGTGCTTTGGCCACCACCAATCAGCAGATGTTTATT 780
FAO2b ATGAAAGAGTTGTACCAAGGTAAATGTGCGTTGACCACCACGAACCAGCAGATGTTTATT
780 * **** ** ****** ** * ** * *** * ** ** ** *** ***** ** FAO-13
CTTGCTGGTTCCACTTTTGGTGGCGGTACCACTGTCAATTGGTCAGCCTGTCTTAAGACG 840
FAO-20 CTTGCTGGTTCCACTTTTGGTGGCGGTACCACTGTCAATTGGTCAGCCTGTCTTAAGACG
840 FAO-17
CTTGCTGGTTCCACTTTTGGTGGCGGTACCACTGTCAATTGGTCAGCCTGTCTTAAGACG 840
FAO-18 CTTGCTGGTTCCACTTTTGGTGGTGGTACCACTGTCAATTGGTCGGCCTGTCTTAAAACG
840 FAO2a
CTTGCCGGTTCCACTTTGGGCGGTGGTACCACTGTCAACTGGTCTGCTTGCCTTAAAACA 840
FAO2b CTTGCCGGTTCCACTTTGGGCGGTGGTACCACTGTTAACTGGTCTGCTTGTCTTAAAACA
840 ***** *********** ** ** *********** ** ***** ** ** ***** **
FAO-13 CCATTCAAGGTGCGTAAGGAATGGTATGATGAGTTTGGTGTTGACTTTGCTGCTGATGAA
900 FAO-20
CCATTCAAGGTGCGTAAGGAATGGTATGATGAGTTTGGTGTTGACTTTGCTGCTGATGAA 900
FAO-17 CCATTCAAGGTGCGTAAGGAATGGTATGATGAGTTTGGTGTTGACTTTGCTGCTGATGAA
900 FAO-18
CCATTCAAGGTGCGTAAGGAATGGTATGATGAGTTTGGCGTTGACTTTGCTGCCGATGAA 900
FAO2a CCATTTAAAGTGCGTAAGGAGTGGTACGACGAGTTTGGTCTTGAATTTGCTGCCGATGAA
900 FAO2b
CCATTTAAAGTGCGTAAGGAGTGGTACGACGAGTTTGGTCTTGAATTTGCTGCCGACGAA 900
***** ** *********** ***** ** ******** **** ******** ** *** FAO-13
GCATACGATAAAGCGCAGGATTATGTTTGGCAGCAAATGGGAGCTTCTACCGAAGGCATC 960
FAO-20 GCATACGATAAAGCGCAGGATTATGTTTGGCAGCAAATGGGAGCTTCTACCGAAGGCATC
960 FAO-17
GCATACGATAAAGCGCAGGATTATGTTTGGCAGCAAATGGGAGCTTCTACCGAAGGCATC 960
FAO-18 GCCTACGACAAAGCACAGGATTATGTTTGGCAGCAAATGGGAGCTTCTACCGAAGGCATC
960 FAO2a
GCCTACGACAAAGCGCAGGATTATGTTTGGAAACAAATGGGTGCTTCAACAGATGGAATC 960
FAO2b GCCTACGACAAAGCACAAGACTATGTTTGGAAACAAATGGGCGCTTCTACCGAAGGAATC
960 ** ***** ***** ** ** ********* * ******** ***** ** ** ** ***
FAO-13 ACCCACTCTTTGGCTAACGAGATTATTATTGAAGGTGGTAAGAAATTAGGTTACAAGGCC
1020 FAO-20
ACCCACTCTTTGGCTAACGAGATTATTATTGAAGGTGGTAAGAAATTAGGTTACAAGGCC 1020
FAO-17 ACCCACTCTTTGGCTAACGAGATTATTATTGAAGGTGGTAAGAAATTAGGTTACAAGGCC
1020 FAO-18
ACCCACTCTTTGGCTAACGAGATTATTATTGAAGGTGGCAAGAAATTAGGTTACAAGGCC 1020
FAO2a ACTCACTCCTTGGCCAACGAAGTTGTGGTTGAAGGAGGTAAGAAGTTGGGCTACAAGAGC
1020 FAO2b
ACTCACTCTTTGGCGAACGCGGTTGTGGTTGAAGGAGGTAAGAAGTTGGGTTACAAGAGC 1020
** ***** ***** **** ** * ******* ** ***** ** ** ****** * FAO-13
AAGGTATTAGACCAAAACAGCGGTGGTCATCCTCAGCACAGATGCGGTTTCTGTTATTTG 1080
FAO-20 AAGGTATTAGACCAAAACAGCGGTGGTCATCCTCAGCACAGATGCGGTTTCTGTTATTTG
1080 FAO-17
AAGGTATTAGACCAAAACAGCGGTGGTCATCCTCAGCACAGATGCGGTTTCTGTTATTTG 1080
FAO-18 AAGGTATTAGACCAAAACAGCGGTGGTCATCCTCATCACAGATGCGGTTTCTGTTATTTG
1080 FAO2a
AAGGAAATTGAGCAGAACAACGGTGGCCACCCTGACCACCCATGTGGTTTCTGTTACTTG 1080
FAO2b AAGGAAATCGAGCAGAACAATGGTGGCCATCCTGACCACCCCTGTGGTTTCTGTTACTTG
1080 **** * * ** ** **** ***** ** *** * *** ** *********** ***
FAO-13 GGCTGTAAGCACGGTATCAAGCAGGGTTCTGTTAATAACTGGTTTAGAGACGCAGCTGCC
1140 FAO-20
GGCTGTAAGCACGGTATCAAGCAGGGTTCTGTTAATAACTGGTTTAGAGACGCAGCTGCC 1140
FAO-17 GGTTGTAAGCACGGTATCAAGCAGGGCTCTGTTAATAACTGGTTTAGAGACGCAGCTGCC
1140 FAO-18
GGTTGTAAGCACGGTATCAAGCAGGGCTCTGTTAATAACTGGTTTAGAGACGCAGCTGCC 1140
FAO2a GGCTGTAAGTACGGTATTAAACAGGGTTCTGTGAATAACTGGTTTAGAGACGCAGCTGCC
1140 FAO2b
GGCTGTAAGTACGGTATTAAGCAGGGTTCTGTGAATAACTGGTTTAGAGACGCAGCTGCC 1140
** ****** ******* ** ***** ***** *************************** FAO-13
CACGGTTCCCAGTTCATGCAACAGGTTAGAGTTTTGCAAATACTTAACAAGAAGGGGATC 1200
FAO-20 CACGGTTCCCAGTTCATGCAACAGGTTAGAGTTTTGCAAATACTTAACAAGAAGGGGATC
1200 FAO-17
CACGGTTCTCAGTTCATGCAACAGGTTAGAGTTTTGCAAATCCTTAACAAGAAGGGCATC 1200
FAO-18 CACGGTTCTCAGTTCATGCAACAGGTTAGAGTTTTGCAAATCCTTAACAAGAAGGGCATC
1200 FAO2a
CACGGGTCCAAGTTCATGCAACAAGTCAGAGTTGTGCAAATCCTCAACAAGAATGGCGTC 1200
FAO2b CACGGGTCCAAGTTCATGCAACAAGTCAGAGTTGTGCAAATCCTCCACAATAAAGGCGTC
1200 ***** ** ************* ** ****** ******* ** **** ** ** **
FAO-13 GCTTACGGTATCTTGTGTGAGGATGTTGTAACCGGCGCCAAGTTCACCATTACTGGCCCC
1260 FAO-20
GCTTACGGTATCTTGTGTGAGGATGTTGTAACCGGCGCCAAGTTCACCATTACTGGCCCC 1260
FAO-17 GCTTATGGTATCTTGTGTGAGGATGTTGTAACCGGTGCCAAGTTCACCATTACTGGCCCC
1260 FAO-18
GCTTATGGTATCTTGTGTGAGGATGTTGTAACCGGTGCCAAGTTCACCATTACTGGCCCC 1260
FAO2a GCTTATGGTATCTTGTGTGAGGATGTCGAAACCGGAGTCAGGTTCACTATTAGTGGCCCC
1260 FAO2b
GCTTATGGCATCTTGTGTGAGGATGTCGAGACCGGAGTCAAATTCACTATCAGTGGCCCC 1260
***** ** ***************** * ***** * ** ***** ** * ******* FAO-13
AAAAAGTTTGTTGTTGCTGCCGGTGCTTTGAACACTCCATCTGTGTTGGTCAACTCCGGC 1320
FAO-20 AAAAAGTTTGTTGTTGCTGCCGGTGCTTTGAACACTCCATCTGTGTTGGTCAACTCCGGC
1320 FAO-17
AAAAAGTTTGTTGTTGCCGCCGGCGCCTTAAACACTCCATCTGTGTTGGTCAACTCCGGA 1320
FAO-18 AAAAAGTTTGTTGTTGCCGCCGGCGCCTTAAACACTCCATCTGTGTTGGTCAACTCCGGA
1320 FAO2a
AAAAAGTTTGTTGTTTCTGCTGGTTCTTTGAACACGCCAACTGTGTTGACCAACTCCGGA 1320
FAO2b AAAAAGTTTGTTGTTTCTGCAGGTTCTTTGAACACGCCAACGGTGTTGACCAACTCCGGA
1320 *************** * ** ** * ** ***** *** * ****** *********
FAO-13 TTCAAGAACAAGAACATCGGTAAGAACTTAACTTTGCACCCAGTTTCTGTCGTGTTTGGT
1380 FAO-20
TTCAAGAACAAGAACATCGGTAAGAACTTAACTTTGCACCCAGTTTCTGTCGTGTTTGGT 1380
FAO-17 TTCAAGAACAAGAACATCGGTAAGAACTTAACTTTGCATCCAGTTTCTGTCGTGTTTGGT
1380 FAO-18
TTCAAGAACAAGAACATCGGTAAGAACTTAACTTTGCATCCAGTTTCTGTCGTGTTTGGT 1380
FAO2a TTCAAGAACAAGCACATTGGTAAGAACTTGACGTTGCACCCAGTTTCCACCGTGTTTGGT
1380 FAO2b
TTCAAGAACAAACACATCGGTAAGAACTTGACGTTGCACCCAGTTTCGACCGTGTTTGGT 1380
*********** **** *********** ** ***** ******** ********** FAO-13
GATTTTGGCAAAGACGTTCAAGCAGACCACTTCCACAACTCCATCATGACTGCCCTTTGT 1440
FAO-20 GATTTTGGCAAAGACGTTCAAGCAGACCACTTCCACAACTCCATCATGACTGCCCTTTGT
1440 FAO-17
GATTTTGGCAAAGACGTTCAAGCAGACCACTTCCACAACTCCATCATGACTGCCCTTTGT 1440
FAO-18 GATTTTGGCAAAGACGTTCAAGCAGATCACTTCCACAACTCCATCATGACTGCTCTTTGT
1440 FAO2a
GACTTTGGCAGAGACGTGCAAGCCGACCATTTCCACAAATCTATTATGACTTCGCTTTGT 1440
FAO2b GACTTTGGCAGAGACGTGCAAGCCGACCATTTCCACAAATCTATTATGACTTCGCTCTGT
1440 ** ******* ****** ***** ** ** ******** ** ** ****** * ** ***
FAO-13 TCAGAAGCCGCTGATTTAGACGGCAAGGGCCATGGATGCAGAATTGAAACCATCTTGAAC
1500 FAO-20
TCAGAAGCCGCTGATTTAGACGGCAAGGGCCATGGATGCAGAATTGAAACCATCTTGAAC 1500
FAO-17 TCAGAAGCCGCTGATTTAGACGGCAAGGGCCATGGATGCAGAATTGAAACCATCTTGAAC
1500 FAO-18
TCAGAAGCCGCTGATTTAGACGGCAAGGGTCATGGATGCAGAATTGAAACCATCTTGAAC 1500
FAO2a TACGAGGTTGCTGACTTGGACGGCAAGGGCCACGGATGCAGAATCGAAACCATCTTGAAC
1500 FAO2b
TACGAAGTCGCTGACTTGGACGGCAAGGGCCACGGATGCAGAATCGAGACCATCTTGAAC 1500 *
** * ***** ** *********** ** *********** ** ************ FAO-13
GCTCCATTCATCCAGGCTTCATTCTTACCATGGAGAGGTAGTAACGAGGCTAGACGAGAC 1560
FAO-20 GCTCCATTCATCCAGGCTTCATTCTTACCATGGAGAGGTAGTAACGAGGCTAGACGAGAC
1560 FAO-17
GCTCCATTCATCCAGGCTTCATTCTTACCATGGAGAGGTAGTAACGAGGCTAGACGAGAC 1560
FAO-18 GCTCCATTCATCCAGGCTTCATTCTTACCATGGAGAGGTAGTAACGAGGCTAGACGAGAC
1560 FAO2a
GCTCCATTCATCCAAGCTTCTTTGTTGCCATGGAGAGGAAGTGACGAGGTCAGAAGAGAC 1560
FAO2b GCTCCATTCATCCAAGCTTCTTTGTTGCCATGGAGAGGAAGCGACGAGGTCAGAAGAGAC
1560 ************** ***** ** ** *********** ** ****** *** *****
FAO-13 TTGTTGCGTTACAACAACATGGTGGCGATGTTGCTCCTTAGTCGTGACACCACCAGTGGT
1620 FAO-20
TTGTTGCGTTACAACAACATGGTGGCGATGTTGCTCCTTAGTCGTGACACCACCAGTGGT 1620
FAO-17 TTGTTGCGTTACAACAACATGGTGGCGATGTTGCTCCTTAGTCGTGACACCACCAGTGGT
1620 FAO-18
TTGTTGCGTTACAACAACATGGTGGCCATGTTACTTCTTAGTCGTGATACCACCAGTGGT 1620
FAO2a TTGTTGCGTTACAACAACATGGTGGCCATGTTGCTTATCACGCGTGATACCACCAGTGGT
1620 FAO2b
TTGTTGCGTTACAACAACATGGTGGCCATGTTGCTTATCACCCGTGACACCACCAGTGGT 1620
************************** ***** ** * * ***** ************ FAO-13
TCCGTTTCTGCTCATCCAACCAAACCTGAAGCTTTGGTTGTCGAGTACGACGTGAACAAG 1680
FAO-20 TCCGTTTCTGCTCATCCAACCAAACCTGAAGCTTTGGTTGTCGAGTACGACGTGAACAAG
1680 FAO-17
TCCGTTTCTGCTCATCCAACCAAACCTGAAGCTTTGGTTGTCGAGTACGACGTGAACAAG 1680
FAO-18 TCCGTTTCGTCCCATCCAACTAAACCTGAAGCATTAGTTGTCGAGTACGACGTGAACAAG
1680 FAO2a
TCAGTTTCTGCTGACCCAAAGAAGCCCGACGCTTTGATTGTCGACTATGAGATTAACAAG 1680
FAO2b TCAGTTTCTGCTGACCCAAAGAAGCCCGACGCTTTGATTGTCGACTATGACATCAACAAG
1680 ** ***** * * **** ** ** ** ** ** ******* ** ** * ****** FAO-13
TTTGACAGAAACTCGATCTTGCAGGCATTGTTGGTCACTGCTGACTTGTTGTATATCCAA 1740
FAO-20 TTTGACAGAAACTCGATCTTGCAGGCATTGTTGGTCACTGCTGACTTGTTGTATATCCAA
1740 FAO-17
TTTGACAGAAACTCGATCTTGCAGGCATTGTTGGTCACTGCTGACTTGTTGTATATCCAA 1740
FAO-18 TTTGACAGAAACTCCATCTTGCAGGCATTGTTGGTCACTGCTGACTTGTTGTACATTCAA
1740 FAO2a
TTTGACAAGAATGCCATCTTGCAAGCTTTCTTGATCACTTCCGACATGTTGTACATTGAA 1740
FAO2b TTTGACAAGAATGCCATCTTGCAAGCTTTCTTGATCACCTCCGACATGTTGTACATCGAA
1740 ******* ** * ******** ** ** *** **** * *** ******* ** **
FAO-13 GGTGCCAAGAGAATCCTTAGTCCACAGGCATGGGTGCCAATTTTTGAATCCGACAAGCCA
1800 FAO-20
GGTGCCAAGAGAATCCTTAGTCCACAGGCATGGGTGCCAATTTTTGAATCCGACAAGCCA 1800
FAO-17 GGTGCCAAGAGAATCCTTAGTCCACAGGCATGGGTGCCAATTTTTGAATCCGACAAGCCA
1800 FAO-18
GGTGCCAAGAGAATCCTTAGTCCCCAACCATGGGTGCCAATTTTTGAATCCGACAAGCCA 1800
FAO2a GGTGCCAAGAGAATCCTCAGTCCACAGCCATGGGTGCCAATCTTTGAGTCGAACAAGCCA
1800 FAO2b
GGTGCCAAGAGAATCCTCAGTCCACAGGCATGGGTGCCAATCTTTGAGTCGAACAAGCCA 1800
***************** ***** ** ************* ***** ** ******** FAO-13
AAGGATAAGAGATCAATCAAGGACGAGGACTATGTCGAATGGAGAGCCAAGGTTGCCAAG 1860
FAO-20 AAGGATAAGAGATCAATCAAGGACGAGGACTATGTCGAATGGAGAGCCAAGGTTGCCAAG
1860 FAO-17
AAGGATAAGAGATCAATCAAGGACGAGGACTATGTCGAATGGAGAGCCAAGGTTGCCAAG 1860
FAO-18 AAGGATAAGAGATCAATCAAGGACGAGGACTATGTCGAATGGAGAGCCAAGGTTGCCAAG
1860 FAO2a
AAGGAGCAAAGAACGATCAAGGACAAGGACTATGTTGAGTGGAGAGCCAAGGCTGCTAAG 1860
FAO2b AAGGAGCAAAGAACAATCAAGGACAAGGACTATGTCGAATGGAGAGCCAAGGCTGCCAAG
1860 ***** * *** * ********* ********** ** ************* *** ***
FAO-13 ATTCCTTTCGACACCTACGGCTCACCTTATGGTTCGGCACATCAAATGTCTTCTTGCCGT
1920 FAO-20
ATTCCTTTCGACACCTACGGCTCACCTTATGGTTCGGCACATCAAATGTCTTCTTGCCGT
1920
FAO-17 ATTCCTTTCGACACCTACGGCTCACCTTATGGTTCGGCACATCAAATGTCTTCTTGCCGT
1920 FAO-18
ATTCCTTTTGACACCTACGGCTCGCCTTATGGTTCGGCGCATCAAATGTCTTCTTGTCGT 1920
FAO2a ATACCTTTCGACACCTACGGTTCTGCATATGGGTCCGCACATCAAATGTCCACCTGTCGT
1920 FAO2b
ATACCTTTCGACACCTACGGTTCTGCCTATGGGTCCGCACATCAAATGTCCACCTGTCGT 1920
** ***** *********** ** * ***** ** ** *********** * ** *** FAO-13
ATGTCAGGTAAGGGTCCTAAATACGGTGCTGTTGACACCGATGGTAGATTGTTTGAATGT 1980
FAO-20 ATGTCAGGTAAGGGTCCTAAATACGGTGCTGTTGACACCGATGGTAGATTGTTTGAATGT
1980 FAO-17
ATGTCAGGTAAGGGTCCTAAATACGGTGCTGTTGACACCGATGGTAGATTGTTTGAATGT 1980
FAO-18 ATGTCAGGTAAGGGTCCTAAATACGGTGCTGTTGATACCGATGGTAGATTGTTTGAATGT
1980 FAO2a
ATGTCCGGAAAGGGTCCTAAATACGGTGCTGTTGATACTGATGGTAGATTGTTTGAATGT 1980
FAO2b ATGTCCGGAAAGGGTCCTAAATACGGCGCCGTTGATACCGATGGTAGATTGTTTGAATGT
1980 ***** ** ***************** ** ***** ** *********************
FAO-13 TCGAATGTTTATGTTGCCGATGCAAGTCTTTTGCCAACTGCAAGCGGTGCCAACCCTATG
2040 FAO-20
TCGAATGTTTATGTTGCCGATGCAAGTCTTTTGCCAACTGCAAGCGGTGCCAACCCTATG 2040
FAO-17 TCGAATGTTTATGTTGCCGATGCAAGTCTTTTGCCAACTGCAAGCGGTGCCAACCCTATG
2040 FAO-18
TCGAATGTTTATGTTGCTGACGCTAGTCTTTTGCCAACTGCTAGCGGTGCTAATCCTATG 2040
FAO2a TCGAATGTCTATGTTGCTGATGCTAGTGTTTTGCCTACTGCCAGCGGTGCCAACCCAATG
2040 FAO2b
TCGAATGTCTATGTTGCTGATGCTAGTGTTTTGCCTACTGCCAGCGGTGCCAACCCAATG 2040
******** ******** ** ** *** ******* ***** ******** ** ** *** FAO-13
GTCACCACCATGACTCTTGCCAGACATGTTGCGTTAGGTTTGGCAGACTCCTTGAAGACC 2100
FAO-20 GTCACCACCATGACTCTTGCCAGACATGTTGCGTTAGGTTTGGCAGACTCCTTGAAGACC
2100 FAO-17
GTCACCACCATGACTCTTGCAAGACATGTTGCGTTAGGTTTGGCAGACTCCTTGAAGACC 2100
FAO-18 GTCACCACCATGACTCTTGCAAGACATGTTGCGTTAGGTTTGGCAGACTCCTTGAAGACC
2100 FAO2a
ATATCCACCATGACCTTTGCTAGACAGATTGCGTTAGGTTTGGCTGACTCCTTGAAGACC 2100
FAO2b ATCTCCACCATGACGTTTGCTAGACAGATTGCGTTAGGTTTGGCTGACTCTTTGAAGACC
2100 * ********** **** ***** **************** ***** *********
FAO-13 AAAGCCAAGTTGTAG 2115 (SEQ ID NO: 1) FAO-20 AAAGCCAAGTTGTAG
2115 (SEQ ID NO: 3) FAO-17 AAGGCCAAGTTGTAG 2115 (SEQ ID NO: 2)
FAO-18 AAGGCCAAGTTGTAG 2115 (SEQ ID NO: 6) FAO2a AAACCCAAGTTGTAG
2115 (SEQ ID NO: 4) FAO2b AAACCCAAGTTGTAG 2115 (SEQ ID NO: 5) **
***********
[0354] Amino Acid Sequences
TABLE-US-00042 FAO-1 SEQ ID NO: 7
MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDEIKDVIAPDFPADKYEEYV
RTFTKPSETPGFRETVYNTVNANTMDAIHQFIILTNVLGSRVLAPALTNS
LTPIKDMSLEDREKLLASWRDSPIAAKRKLFRLVSTLTLVTFTRLANELH
LKAIHYPGREDREKAYETQEIDPFKYQFLEKPKFYGAELYLPDIDVIIIG
SGAGAGVVAHTLTNDGFKSLVLEKGRYFSNSELNFDDKDGVQELYQSGGT
LTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE
AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGH
PHHRCGFCYLGCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGI
AYGILCEDVVTGAKFTITGPKKFVVAAGALNTPSVLVNSGFKNKNIGKNL
TLHPVSVVFGDFGKDVQADHFHNSIMTALCSEAADLDGKGHGCRIETILN
APFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSGSVSSHPTKPE
ALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQPWVPIFESDKP
KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGA
VDTDGRLFECSNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKT KAKL FAO-13 SEQ
ID NO: 8 MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDQIKDVIAPDFPADKYEEYV
RTFTKPSETPGFRETVYNTVNANTTDAIHQFIILTNVLASRVLAPALTNS
LTPIKDMSLEDREKLLASWRDSPIAAKRKLFRLVSTLTLVTFTRLANELH
LKAIHYPGREDREKAYETQEIDPFKYQFLEKPKFYGAELYLPDIDVIIIG
SGAGAGVVAHTLANDGFKSLVLEKGKYFSNSELNFDDKDGVQELYQSGGT
LTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE
AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGH
PQHRCGFCYLGCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGI
AYGILCEDVVTGAKFTITGPKKFVVAAGALNTPSVLVNSGFKNKNIGKNL
TLHPVSVVFGDFGKDVQADHFHNSIMTALCSEAADLDGKGHGCRIETILN
APFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSGSVSAHPTKPE
ALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQAWVPIFESDKP
KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGA
VDTDGRLFECSNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKT KAKL FAO-20 SEQ
ID NO: 9 MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDQIKDVIAPDFPADKYEEYV
RTFTKPSETPGFRETVYNTVNANTTDAIHQFIILTNVLASRVLAPALTNS
LTPIKDMSLEDREKLLASWRDSPIAAKRKLFRLVSTLTLVTFTRLANELH
LKAIHYPGREDREKAYETQEIDPFKYQFMEKPKFDGAELYLPDIDVIIIG
SGAGAGVVAHTLANDGFKSLVLEKGKYFSNSELNFDDKDGVQELYQSGGT
LTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE
AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGH
PQHRCGFCYLGCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGI
AYGILCEDVVTGAKFTITGPKKFVVAAGALNTPSVLVNSGFKNKNIGKNL
TLHPVSVVFGDFGKDVQADHFHNSIMTALCSEAADLDGKGHGCRIETILN
APFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSGSVSAHPTKPE
ALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQAWVPIFESDKP
KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGA
VDTDGRLFECSNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKT KAKL FAO-17 SEQ
ID NO: 10 MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDEIKDVIAPDFPADKYEEYV
RTFTKPSETPGFRETVYNTVNANTMDAIHQFIILTNVLGSRVLAPALTNS
LTPIKDMSLEDREKLLASWRDSPIAAKRKLFRLVSTLTLVTFTRLANELH
LKAIHYPGREDREKAYETQEIDPFKYQFLEKPKFYGAELYLPDIDVIIIG
SGAGAGVVAHTLANDGFKSLVLEKGKYFSNSELNFDDKDGVQELYQSGGT
LTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE
AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGH
PQHRCGFCYLGCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGI
AYGILCEDVVTGAKFTITGPKKFVVAAGALNTPSVLVNSGFKNKNIGKNL
TLHPVSVVFGDFGKDVQADHFHNSIMTALCSEAADLDGKGHGCRIETILN
APFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSGSVSAHPTKPE
ALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQAWVPIFESDKP
KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGA
VDTDGRLFECSNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKT KAKl FAO-2a SEQ
ID NO: 11 MNTFLPDVLEYKHVDTLLLLCDGIIHETTVDQIKDAIAPDFPEDQYEEYL
KTFTKPSETPGFREAVYDTINATPTDAVHMCIVLTTALDSRILAPTLTNS
LTPIKDMTLKEREQLLASWRDSPIAAKRRLFRLISSLTLTTFTRLASELH
LKAIHYPGRDLREKAYETQVVDPFRYSFMEKPKFDGAELYLPDIDVIIIG
SGAGAGVMAHTLANDGFKTLVLEKGKYFSNSELNFNDADGVKELYQGKGA
LATTNQQMFILAGSTLGGGTTVNWSACLKTPFKVRKEWYDEFGLEFAADE
AYDKAQDYVWKQMGASTDGITHSLANEVVVEGGKKLGYKSKEIEQNNGGH
PDHPCGFCYLGCKYGIKQGSVNNWFRDAAAHGSKFMQQVRVVQILNKNGV
AYGILCEDVETGVRFTISGPKKFVVSAGSLNTPTVLTNSGFKNKHIGKNL
TLHPVSTVFGDFGRDVQADHFHKSIMTSLCYEVADLDGKGHGCRIETILN
APFIQASLLPWRGSDEVRRDLLRYNNMVAMLLITRDTTSGSVSADPKKPD
ALIVDYEINKFDKNAILQAFLITSDMLYIEGAKRILSPQPWVPIFESNKP
KEQRTIKDKDYVEWRAKAAKIPFDTYGSAYGSAHQMSTCRMSGKGPKYGA
VDTDGRLFECSNVYVADASVLPTASGANPMISTMTFARQIALGLADSLKT KPKL FAO-2b SEQ
ID NO: 12 MNTFLPDVLEYKHVDTLLLLCDGIIHETTVDQIRDAIAPDFPEDQYEEYL
KTFTKPSETPGFREAVYDTINSTPTEAVHMCIVLTTALDSRILAPTLTNS
LTPIKDMTLKEREQLLAAWRDSPIAAKRRLFRLISSLTLTTFTRLASDLH
LRAIHYPGRDLREKAYETQVVDPFRYSFMEKPKFDGTELYLPDIDVIIIG
SGAGAGVMAHTLANDGYKTLVLEKGKYFSNSELNFNDADGMKELYQGKCA
LTTTNQQMFILAGSTLGGGTTVNWSACLKTPFKVRKEWYDEFGLEFAADE
AYDKAQDYVWKQMGASTEGITHSLANAVVVEGGKKLGYKSKEIEQNNGGH
PDHPCGFCYLGCKYGIKQGSVNNWFRDAAAHGSKFMQQVRVVQILHNKGV
AYGILCEDVETGVKFTISGPKKFVVSAGSLNTPTVLTNSGFKNKHIGKNL
TLHPVSTVFGDFGRDVQADHFHKSIMTSLCYEVADLDGKGHGCRIETILN
APFIQASLLPWRGSDEVRRDLLRYNNMVAMLLITRDTTSGSVSADPKKPD
ALIVDYDINKFDKNAILQAFLITSDMLYIEGAKRILSPQAWVPIFESNKP
KEQRTIKDKDYVEWRAKAAKIPFDTYGSAYGSAHQMSTCRMSGKGPKYGA
VDTDGRLFECSNVYVADASVLPTASGANPMISTMTFARQIALGLADSLKT KPKL
[0355] Clustal Amino Acid Sequence Alignments
TABLE-US-00043 FAO-13
MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDQIKDVIAPDFPADKYEEYVRTFTKPSETP 60
FAO-20 MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDQIKDVIAPDFPADKYEEYVRTFTKPSETP
60 FAO-1
MAPFLPDQVDYKHVDTLMLLCDGIIHETTVDEIKDVIAPDFPADKYEEYVRTFTKPSETP 60
*******************************:**************************** FAO-13
GFRETVYNTVNANTTDAIHQFIILTNVLASRVLAPALTNSLTPIKDMSLEDREKLLASWR 120
FAO-20 GFRETVYNTVNANTTDAIHQFIILTNVLASRVLAPALTNSLTPIKDMSLEDREKLLASWR
120 FAO-1
GFRETVYNTVNANTMDAIHQFIILTNVLGSRVLAPALTNSLTPIKDMSLEDREKLLASWR 120
************** *************.******************************* FAO-13
DSPIAAKRKLFRLVSTLTLVTFTRLANELHLKAIHYPGREDREKAYETQEIDPFKYQFLE 180
FAO-20 DSPIAAKRKLFRLVSTLTLVTFTRLANELHLKAIHYPGREDREKAYETQEIDPFKYQFME
180 FAO-1
DSPIAAKRKLFRLVSTLTLVTFTRLANELHLKAIHYPGREDREKAYETQEIDPFKYQFLE 180
**********************************************************:* FAO-13
KPKFYGAELYLPDIDVIIIGSGAGAGVVAHTLANDGFKSLVLEKGKYFSNSELNFDDKDG 240
FAO-20 KPKFDGAELYLPDIDVIIIGSGAGAGVVAHTLANDGFKSLVLEKGKYFSNSELNFDDKDG
240 FAO-1
KPKFYGAELYLPDIDVIIIGSGAGAGVVAHTLTNDGFKSLVLEKGRYFSNSELNFDDKDG 240
**** ***************************:************:************** FAO-13
VQELYQSGGTLTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE 300
FAO-20 VQELYQSGGTLTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE
300 FAO-1
VQELYQSGGTLTTVNQQLFVLAGSTFGGGTTVNWSACLKTPFKVRKEWYDEFGVDFAADE 300
************************************************************ FAO-13
AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGHPQHRCGFCYL 360
FAO-20 AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGHPQHRCGFCYL
360 FAO-1
AYDKAQDYVWQQMGASTEGITHSLANEIIIEGGKKLGYKAKVLDQNSGGHPHHRCGFCYL 360
***************************************************:******** FAO-13
GCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGIAYGILCEDVVTGAKFTITGP 420
FAO-20 GCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGIAYGILCEDVVTGAKFTITGP
420 FAO-1
GCKHGIKQGSVNNWFRDAAAHGSQFMQQVRVLQILNKKGIAYGILCEDVVTGAKFTITGP 420
************************************************************ FAO-13
KKFVVAAGALNTPSVLVNSGFKNKNIGKNLTLHPVSVVFGDFGKDVQADHFHNSIMTALC 480
FAO-20 KKFVVAAGALNTPSVLVNSGFKNKNIGKNLTLHPVSVVFGDFGKDVQADHFHNSIMTALC
480 FAO-1
KKFVVAAGALNTPSVLVNSGFKNKNIGKNLTLHPVSVVFGDFGKDVQADHFHNSIMTALC 480
************************************************************ FAO-13
SEAADLDGKGHGCRIETILNAPFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSG 540
FAO-20 SEAADLDGKGHGCRIETILNAPFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSG
540 FAO-1
SEAADLDGKGHGCRIETILNAPFIQASFLPWRGSNEARRDLLRYNNMVAMLLLSRDTTSG 540
************************************************************ FAO-13
SVSAHPTKPEALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQAWVPIFESDKP 600
FAO-20 SVSAHPTKPEALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQAWVPIFESDKP
600 FAO-1
SVSSHPTKPEALVVEYDVNKFDRNSILQALLVTADLLYIQGAKRILSPQPWVPIFESDKP 600
***:*********************************************.********** FAO-13
KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGAVDTDGRLFEC 660
FAO-20 KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGAVDTDGRLFEC
660 FAO-1
KDKRSIKDEDYVEWRAKVAKIPFDTYGSPYGSAHQMSSCRMSGKGPKYGAVDTDGRLFEC 660
************************************************************ FAO-13
SNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKTKAKL 704 (SEQ ID NO: 8)
FAO-20 SNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKTKAKL 704 (SEQ ID NO:
9) FAO-1 SNVYVADASLLPTASGANPMVTTMTLARHVALGLADSLKTKAKL 704 (SEQ ID
NO: 7) ********************************************
Example 31
Examples of Embodiments
[0356] Provided Hereafter are Non-Limiting Examples of Certain
Embodiments.
[0357] A1. An engineered microorganism capable of producing adipic
acid, which microorganism comprises one or more altered activities
selected from the group consisting of 6-oxohexanoic acid
dehydrogenase activity, omega oxo fatty acid dehydrogenase
activity, 6-hydroxyhexanoic acid dehydrogenase activity, omega
hydroxyl fatty acid dehydrogenase activity, hexanoate synthase
activity, monooxygenase activity, monooxygenase reductase activity,
fatty alcohol oxidase activity, acyl-CoA ligase activity, acyl-CoA
oxidase activity, enoyl-CoA hydratase activity, 3-L-hydroxyacyl-CoA
dehydrogenase activity and acetyl-CoA C-acyltransferase
activity.
[0358] A1.1. The engineered microorganism of embodiment A1, which
comprises a genetic modification that adds or increases the
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase activity, 6-hydroxyhexanoic acid dehydrogenase
activity, omega hydroxyl fatty acid dehydrogenase activity,
hexanoate synthase activity, monooxygenase activity, monooxygenase
reductase activity, fatty alcohol oxidase activity, acyl-CoA ligase
activity, acyl-CoA oxidase activity, enoyl-CoA hydratase activity,
3-L-hydroxyacyl-CoA dehydrogenase activity and/or acetyl-CoA
C-acyltransferase activity.
[0359] A1.2. The engineered microorganism of embodiment Al, which
comprises a genetic modification that reduces the acyl-CoA oxidase
activity.
[0360] A1.3. The engineered microorganism of embodiment A1.1,
wherein the genetic modification comprises increased copies of a
polynucleotide that encodes a polypeptide having 6-oxohexanoic acid
dehydrogenase activity, omega oxo fatty acid dehydrogenase
activity, 6-hydroxyhexanoic acid dehydrogenase activity, omega
hydroxyl fatty acid dehydrogenase activity, hexanoate synthase
activity, monooxygenase activity, monooxygenase reductase activity,
fatty alcohol oxidase activity, acyl-CoA ligase activity, acyl-CoA
oxidase activity, enoyl-CoA hydratase activity, 3-L-hydroxyacyl-CoA
dehydrogenase activity or acetyl-CoA C-acyltransferase
activity.
[0361] A1.4. The engineered microorganism of embodiment A1.1,
wherein the genetic modification comprises insertion of a
heterologous promoter and/or 5' UTR, into genomic DNA of the
microorganism in functional connection with a polynucleotide that
encodes a polypeptide having 6-oxohexanoic acid dehydrogenase
activity, 6-hydroxyhexanoic acid dehydrogenase activity, hexanoate
synthase activity, monooxygenase activity, monooxygenase reductase
activity, fatty alcohol oxidase activity, acyl-CoA ligase activity,
acyl-CoA oxidase activity, enoyl-CoA hydratase activity,
3-L-hydroxyacyl-CoA dehydrogenase activity or acetyl-CoA
C-acyltransferase activity.
[0362] A2. The engineered microorganism of any one of embodiments
A1 to A1.4, which comprises an altered thioesterase activity.
[0363] A2.1. The engineered microorganism of embodiment A2, which
comprises a genetic alteration that adds or increases a
thioesterase activity.
[0364] A2.2. The engineered microorganism of embodiment A2.1, which
comprises a heterologous polynucleotide encoding a polypeptide
having thioesterase activity.
[0365] A3. The engineered microorganism of any one of embodiments
A1 to A2.2, which comprises a heterologous polynucleotide encoding
a polypeptide having 6-oxohexanoic acid dehydrogenase activity.
[0366] A3.1 The engineered microorganism of any one of embodiments
A1 to A3, which comprises a heterologous polynucleotide encoding a
polypeptide having omega oxo fatty acid dehydrogenase activity.
[0367] A4. The engineered microorganism of embodiment A3 and A3.1,
wherein the heterologous polynucleotide is from a bacterium.
[0368] A5. The engineered microorganism of embodiment A4, wherein
the bacterium is an Acinetobacter, Nocardia, Pseudomonas or
Xanthobacter bacterium.
[0369] A6. The engineered microorganism of embodiment A1 or A2,
which comprises a heterologous polynucleotide encoding a
polypeptide having 6-hydroxyhexanoic acid dehydrogenase
activity.
[0370] A6.1 The engineered microorganism of embodiment A1 or A2,
which comprises a heterologous polynucleotide encoding a
polypeptide having omega hydroxyl fatty acid dehydrogenase
activity
[0371] A7. The engineered microorganism of embodiment A6 or A6.1,
wherein the heterologous polynucleotide is from a bacterium.
[0372] A8. The engineered microorganism of embodiment A7, wherein
the bacterium is an Acinetobacter, Nocardia, Pseudomonas or
Xanthobacter bacterium.
[0373] A9. The engineered microorganism of embodiment A1 or A2,
which comprises a heterologous polynucleotide encoding a
polypeptide having hexanoate synthase subunit A activity.
[0374] A10. The engineered microorganism of embodiment A1 or A2,
which comprises a heterologous polynucleotide encoding a
polypeptide having hexanoate synthase subunit B activity.
[0375] A11. The engineered microorganism of embodiment A9 or A10,
wherein the heterologous polynucleotide independently is selected
from a bacterium.
[0376] A12. The engineered microorganism of embodiment A11, wherein
the bacterium is a Bacillus bacterium.
[0377] A13. The engineered microorganism of embodiment A12, wherein
the Bacillus bacterium is B. megaterium.
[0378] A14. The engineered microorganism of embodiment A1 or A2,
which comprises a heterologous polynucleotide encoding a
polypeptide having monooxygenase activity.
[0379] A15. The engineered microorganism of embodiment A14, wherein
the heterologous polynucleotide is from a fungus.
[0380] A16. The engineered microorganism of embodiment A15, wherein
the fungus is an Aspergillus fungus.
[0381] A17. The engineered microorganism of embodiment A16, wherein
the Aspergillus fungus is A. parasiticus.
[0382] A18. The engineered microorganism of embodiment A1 or A2,
which comprises a genetic modification that results in primary
hexanoate usage by monooxygenase activity.
[0383] A19. The engineered microorganism of embodiment A18, wherein
the genetic modification reduces a polyketide synthase
activity.
[0384] A20. The engineered microorganism of any one of embodiments
A1-A19, which is a eukaryote.
[0385] A21. The engineered microorganism of embodiment A20, which
is a yeast.
[0386] A22. The engineered microorganism of embodiment A21, wherein
the yeast is a Candida yeast.
[0387] A23. The engineered microorganism of embodiment A22, wherein
the Candida yeast is a C. tropicalis strain.
[0388] A24. The engineered microorganism of embodiment A20, which
is a fungus.
[0389] A25. The engineered microorganism of embodiment A24, wherein
the fungus is a Yarrowia fungus.
[0390] A26. The engineered microorganism of embodiment A25, wherein
the Yarrowia fungus is Y. lipolytica.
[0391] A27. The engineered microorganism of embodiment A24, wherein
the fungus is an Aspergillus fungus.
[0392] A28. The engineered microorganism of embodiment A27, wherein
the Aspergillus fungus is a A. parasiticus strain or a A. nidulans
strain.
[0393] A29. The engineered microorganism of any one of embodiments
A1-A28, which comprises a genetic modification that reduces
6-hydroxyhexanoic acid conversion.
[0394] A30. The engineered microorganism of embodiment A29, wherein
the genetic modification reduces 6-hydroxyhexanoic acid
dehydrogenase activity.
[0395] A31. The engineered microorganism of any one of embodiments
A1-A30, which comprises a genetic modification that reduces
beta-oxidation activity.
[0396] A32. The engineered microorganism of embodiment A31, wherein
the genetic modification renders beta-oxidation activity
undetectable.
[0397] A33. The engineered microorganism of embodiment A31, wherein
the genetic modification partially reduces beta-oxidation
activity.
[0398] A34. The engineered microorganism of any one of embodiments
A31 to A33, wherein the genetic modification comprises disrupting a
polynucleotide that encodes a polypeptide having an acyl-CoA
oxidase activity.
[0399] A35. The engineered microorganism of any one of embodiments
A31 to A33, wherein the genetic modification comprises disrupting a
promoter in functional connection with a polynucleotide that
encodes a polypeptide having the acyl-CoA oxidase activity.
[0400] A36. The engineered microorganism of embodiment A34 or A35,
wherein the polypeptide having the acyl-CoA oxidase activity is a
POX polypeptide.
[0401] A37. The engineered microorganism of embodiment A36, wherein
the POX polypeptide is a POX4 polypeptide, POX5 polypeptide or POX4
polypeptide and POX5 polypeptide.
[0402] A38. The engineered microorganism of any one of embodiments
A1 to A37, which is in contact with a feedstock.
[0403] A39. The engineered microorganism of embodiment A38, wherein
the feedstock comprises a saccharide.
[0404] A40. The engineered microorganism of embodiment A39, wherein
the saccharide is a monosaccharide, polysaccharide or a mixture or
a monosaccharide and polysaccharide.
[0405] A41. The engineered microorganism of embodiment A38, wherein
the feedstock comprises a paraffin.
[0406] A42. The engineered microorganism of embodiment A41, wherein
the paraffin is a saturated paraffin, unsaturated paraffin,
substituted paraffin, branched paraffin, linear paraffin or
combination thereof.
[0407] A43. The engineered microorganism of embodiment A41 or A42,
wherein the paraffin includes about 1 to about 60 carbon atoms.
[0408] A44. The engineered microorganism of embodiments A41 to A43,
wherein the paraffin is in a mixture of paraffins.
[0409] A45. The engineered microorganism of embodiment A44, wherein
the paraffins in the mixture of paraffins have a mean number of
carbon atoms of about 8 to about 18 carbon atoms.
[0410] A46. The engineered microorganism of embodiment A45, wherein
the mean number of carbon atoms is about 10 to about 16 carbon
atoms.
[0411] A46.1. The engineered microorganism of embodiment A46,
wherein the mean number of carbon atoms is about 12 atoms.
[0412] A47. The engineered microorganism of any one of embodiments
A41 to A46.1, wherein the paraffin is in a wax.
[0413] A48. The engineered microorganism of any one of embodiments
A41 to A46.1, wherein the paraffin is in an oil.
[0414] A49. The engineered microorganism of any one of embodiments
A41 to A48, wherein the paraffin is from a petroleum product.
[0415] A50. The engineered microorganism of embodiment A49, wherein
the petroleum product is a petroleum distillate.
[0416] A51. The engineered microorganism of any one of embodiments
A41 to A48, wherein the paraffin is from a plant or plant
product.
[0417] B1. An engineered microorganism that produces adipic acid,
which microorganism comprises an altered monooxygenase
activity.
[0418] B1.1. The engineered microorganism of embodiment B1, which
comprises a genetic modification that alters the monooxygenase
activity.
[0419] B1.2. The engineered microorganism of embodiment B1 or B1.1,
which comprises a genetic modification that alters a monooxygenase
activity selected from the group consisting of.
[0420] B2. The engineered microorganism of embodiment B1.1, which
comprises a heterologous polynucleotide encoding a polypeptide
having monooxygenase activity.
[0421] B3. The engineered microorganism of embodiment B2, wherein
the heterologous polynucleotide is from a fungus.
[0422] B4. The engineered microorganism of embodiment B3, wherein
the fungus is an Aspergillus fungus.
[0423] B5. The engineered microorganism of embodiment B4, wherein
the Aspergillus fungus is A. parasiticus.
[0424] B6. The engineered microorganism of any one of embodiments
B1-B5, which comprises a genetic modification that results in
substantial hexanoate usage by the monooxygenase activity.
[0425] B7. The engineered microorganism of embodiment B6, wherein
the genetic modification reduces a polyketide synthase
activity.
[0426] B8. The engineered microorganism of any one of embodiments
B1-B5, which comprises an altered hexanoate synthase activity.
[0427] B9. The engineered microorganism of embodiment B8, wherein
the altered hexanoate synthase activity is an altered hexanoate
synthase subunit A activity, altered hexanoate synthase subunit B
activity, or altered hexanoate synthase subunit A activity and
altered hexanoate synthase subunit B activity.
[0428] B9.1. The engineered microorganism of embodiment B9, which
comprises a genetic alteration that adds or increases hexanoate
synthase activity.
[0429] B10. The engineered microorganism of any one of embodiments
B8, B9 or B9.1, which comprises a heterologous polynucleotide
encoding a polypeptide having hexanoate synthase activity.
[0430] B11. The engineered microorganism of embodiment B10, wherein
the heterologous polynucleotide is from a fungus.
[0431] B12. The engineered microorganism of embodiment B11, wherein
the fungus is an Aspergillus fungus.
[0432] B13. The engineered microorganism of embodiment B11, wherein
the Aspergillus fungus is A. parasiticus.
[0433] B14. The engineered microorganism of any one of embodiments
B1-B13, which comprises an altered thioesterase activity.
[0434] B14.1. The engineered microorganism of embodiment B14, which
comprises a genetic modification that adds or increases the
thioesterase activity.
[0435] B14.2. The engineered microorganism of embodiment B14 or
B14.1, which comprises a heterologous polynucleotide encoding a
polypeptide having thioesterase activity.
[0436] B15. The engineered microorganism of any one of embodiments
B1-B14.2, which comprises an altered 6-oxohexanoic acid
dehydrogenase activity.
[0437] B15.1. The engineered microorganism of embodiment B15, which
comprises a genetic modification that adds or increases the
6-oxohexanoic acid dehydrogenase activity.
[0438] B15.2 The engineered microorganism of any one of embodiments
B1 to B15.1, which comprises an altered omega oxo fatty acid
dehydrogenase activity.
[0439] B15.3 The engineered microorganism of embodiment B15.2,
which comprises a genetic modification that adds or increases the
omega oxo fatty acid dehydrogenase activity
[0440] B16. The engineered microorganism of any one of embodiments
B15 to B15.3, which comprises a heterologous polynucleotide
encoding a polypeptide having 6-oxohexanoic acid dehydrogenase
activity.
[0441] B16.1 The engineered microorganism of any one of embodiments
B15 to B16, which comprises a heterologous polynucleotide encoding
a polypeptide having omega oxo fatty acid dehydrogenase
activity.
[0442] B17. The engineered microorganism of embodiment B16 or
B16.1, wherein the heterologous polynucleotide is from a
bacterium.
[0443] B18. The engineered microorganism of embodiment B17, wherein
the bacterium is a Acinetobacter, Nocardia, Pseudomonas or
Xanthobacter bacterium.
[0444] B19. The engineered microorganism of any one of embodiments
B1-B18, which comprises an altered 6-hydroxyhexanoic acid
dehydrogenase activity.
[0445] B19.1. The engineered microorganism of embodiment B19, which
comprises a genetic modification that adds or increases the
6-hydroxyhexanoic acid dehydrogenase activity.
[0446] B19.2 The engineered microorganism of any one of embodiments
B1-B19.1, which comprises an altered omega hydroxyl fatty acid
dehydrogenase activity.
[0447] B19.3 The engineered microorganism of embodiment B19.2,
which comprises a genetic modification that adds or increases the
omega hydroxyl fatty acid dehydrogenase activity.
[0448] B20. The engineered microorganism of any one of embodiments
B19 to B19.3, which comprises a heterologous polynucleotide
encoding a polypeptide having 6-hydroxyhexanoic acid dehydrogenase
activity.
[0449] B20.1 The engineered microorganism of any one of embodiments
B19 to B20, which comprises a heterologous polynucleotide encoding
a polypeptide having omega hydroxyl fatty acid dehydrogenase
activity.
[0450] B21. The engineered microorganism of embodiment B20 or
B20.1, wherein the heterologous polynucleotide is from a
bacterium.
[0451] B22. The engineered microorganism of embodiment B21, wherein
the bacterium is a Acinetobacter, Nocardia, Pseudomonas or
Xanthobacter bacterium.
[0452] B23. The engineered microorganism of any one of embodiments
B1-B22, which is a eukaryote.
[0453] B24. The engineered microorganism of embodiment B23, which
is a yeast.
[0454] B25. The engineered microorganism of embodiment B24, wherein
the yeast is a Candida yeast.
[0455] B26. The engineered microorganism of embodiment B25, wherein
the Candida yeast is C. tropicalis.
[0456] B27. The engineered microorganism of embodiment B23, which
is a fungus.
[0457] B28. The engineered microorganism of embodiment B27, wherein
the fungus is a Yarrowia fungus.
[0458] B29. The engineered microorganism of embodiment B28, wherein
the Yarrowia fungus is Y. lipolytica.
[0459] B30. The engineered microorganism of embodiment B27, wherein
the fungus is Aspergillus.
[0460] B31. The engineered microorganism of embodiment B30, wherein
the Aspergillus fungus is A. parasiticus or A. nidulans.
[0461] B32. The engineered microorganism of any one of embodiments
B1-B31, which comprises a genetic modification that reduces
6-hydroxyhexanoic acid conversion.
[0462] B33. The engineered microorganism of embodiment B32, wherein
the genetic modification reduces 6-hydroxyhexanoic acid
dehydrogenase activity.
[0463] B34. The engineered microorganism of any one of embodiments
B1-B33, which comprises a genetic modification that reduces
beta-oxidation activity.
[0464] B35. The engineered microorganism of embodiment B34, wherein
the genetic modification renders beta-oxidation activity
undetectable.
[0465] C1. A method for manufacturing adipic acid, which comprises
culturing an engineered microorganism of any one of embodiments
A1-B35 under culture conditions in which the cultured microorganism
produces adipic acid.
[0466] C1.1. The method of embodiment C1, wherein the host
microorganism from which the engineered microorganism is produced
does not produce a detectable amount of adipic acid.
[0467] C2. The method of embodiment C1 of C1.1, wherein the culture
conditions comprise fermentation conditions.
[0468] C3. The method of any one of embodiments C1-C2, wherein the
culture conditions comprise introduction of biomass.
[0469] C4. The method of C1 or C2, wherein the culture conditions
comprise introduction of glucose.
[0470] C5. The method of C1 or C2, wherein the culture conditions
comprise introduction of hexane.
[0471] C6. The method of any one of embodiments C1-C5, wherein the
adipic acid is produced with a yield of greater than about 0.3
grams per gram of glucose added.
[0472] C7. The method of any one of embodiments C.sub.1-C6, which
comprises purifying the adipic acid from the cultured
microorganisms.
[0473] C8. The method of embodiment C7, which comprises modifying
the adipic acid, thereby producing modified adipic acid.
[0474] C9. The method of any one of embodiments C1-C8, which
comprises placing the cultured microorganisms, the adipic acid or
the modified adipic acid in a container.
[0475] C10. The method of embodiment C9, which comprises shipping
the container.
[0476] D1. A method for manufacturing 6-hydroxyhexanoic acid, which
comprises culturing an engineered microorganism of any one of
embodiments A29, A30, B32 or B33 under culture conditions in which
the cultured microorganism produces 6-hydroxyhexanoic acid.
[0477] D1.1. The method of embodiment D1, wherein the host
microorganism from which the engineered microorganism is produced
does not produce a detectable amount of 6-hydroxyhexanoic acid.
[0478] D2. The method of embodiment D1 or D1.1, wherein the culture
conditions comprise fermentation conditions.
[0479] D3. The method of any one of embodiments D1-D2, wherein the
culture conditions comprise introduction of biomass.
[0480] D4. The method of D1 or D2, wherein the culture conditions
comprise introduction of glucose.
[0481] D5. The method of D1 or D2, wherein the culture conditions
comprise introduction of hexane.
[0482] D6. The method of any one of embodiments D1-D5, wherein the
6-hydroxyhexanoic acid is produced with a yield of greater than
about 0.3 grams per gram of glucose added.
[0483] D7. The method of any one of embodiments D1-D6, which
comprises purifying the 6-hydroxyhexanoic acid from the cultured
microorganisms.
[0484] D8. The method of embodiment D7, which comprises modifying
the 6-hydroxyhexanoic acid, thereby producing modified
6-hydroxyhexanoic acid.
[0485] D9. The method of any one of embodiments D1-D8, which
comprises placing the cultured microorganisms, the
6-hydroxyhexanoic acid or the modified 6-hydroxyhexanoic acid in a
container.
[0486] D10. The method of embodiment D9, which comprises shipping
the container.
[0487] E1. A method for preparing an engineered microorganism that
produces adipic acid, which comprises: [0488] (a) introducing a
genetic modification to a host organism that adds or increases
monooxygenase activity, thereby producing engineered microorganisms
having detectable and/or increased monooxygenase activity; and
[0489] (b) selecting for engineered microorganisms that produce
adipic acid.
[0490] E1.1. The method of embodiment E1, wherein the monooxygenase
activity is incorporation of a hydroxyl moiety into a six-carbon
molecule.
[0491] E1.2. The method of embodiment E1 or E1.1, wherein the
six-carbon molecule is hexanoate.
[0492] E2. A method for preparing an engineered microorganism that
produces adipic acid, which comprises: [0493] (a) culturing a host
organism with hexane as a nutrient source, thereby producing
engineered microorganisms having detectable monooxygenase activity;
and [0494] (b) selecting for engineered microorganisms that produce
adipic acid.
[0495] E2.1. The method of embodiment E2, wherein the monooxygenase
activity is incorporation of a hydroxyl moiety into a six-carbon
molecule.
[0496] E2.2. The method of embodiment E2 or E2.1, wherein the
six-carbon molecule is hexanoate.
[0497] E3. The method of any one of embodiments E1-E2.2, which
comprises selecting the engineered microorganisms that have a
detectable amount of the monooxygenase activity.
[0498] E4. The method of any one of embodiments E1-E3, which
comprises introducing a genetic modification that adds or increases
a hexanoate synthase activity, thereby producing engineered
microorganisms, and selecting for engineered microorganisms having
detectable and/or increased hexanoate synthase activity.
[0499] E5. The method of embodiment E4, wherein the genetic
modification encodes a polypeptide having a hexanoate synthase
subunit A activity, a hexanoate synthase subunit B activity, or a
hexanoate synthase subunit A activity and a hexanoate synthase
subunit B activity.
[0500] E6. The method of any one of embodiments E1-E5, which
comprises introducing a genetic modification that adds or increases
6-oxohexanoic acid dehydrogenase activity, thereby producing
engineered microorganisms, and selecting for engineered
microorganisms having detectable and/or increased 6-oxohexanoic
acid dehydrogenase activity relative to the host microorgansim.
[0501] E7. The method of any one of embodiments E1-E6, which
comprises introducing a genetic modification that adds or increases
a 6-hydroxyhexanoic acid dehydrogenase activity, thereby producing
engineered microorganisms, and selecting for engineered
microorganisms having a detectable and/or increased
6-hydroxyhexanoic acid dehydrogenase activity relative to the host
microorganism.
[0502] E7.1 The method of any one of embodiments E1-E7, which
comprises introducing a genetic modification that adds or increases
a 6-hydroxyhexanoic acid dehydrogenase activity, thereby producing
engineered microorganisms, and selecting for engineered
microorganisms having a detectable and/or increased omega hydroxyl
fatty acid dehydrogenase activity relative to the host
microorganism.
[0503] E8. The method of any one of embodiments E1-E7.1, which
comprises introducing a genetic modification that adds or increases
a thioesterase activity, thereby producing engineered
microorganisms, and selecting for engineered microorganisms having
a detectable and/or increased thioesterase activity relative to the
host microorganism.
[0504] E9. The method of any one of embodiments E1-E8, which
comprises introducing a genetic modification that reduces
6-hydroxyhexanoic acid conversion, thereby producing engineered
microorganisms, and selecting for engineered microorganisms having
reduced 6-hydroxyhexanoic acid conversion relative to the host
microorganism.
[0505] E10. The method of any one of embodiments E1-E9, which
comprises introducing a genetic modification that reduces
beta-oxidation activity, thereby producing engineered
microorganisms, and selecting for engineered microorganisms having
reduced beta-oxidation activity relative to the host
microorganism.
[0506] E11. The method of any one of embodiments E1-E11, which
comprises introducing a genetic modification that results in
substantial hexanoate usage by the monooxygenase activity, thereby
producing engineered microorganisms, and selecting for engineered
microorganisms in which substantial hexanoate usage is by the
monooxygenase activity relative to the host microorganism.
[0507] F1. A method for preparing a microorganism that produces
adipic acid, which comprises: (a) introducing one or more genetic
modifications to a host organism that add or increase one or more
activities selected from the group consisting of 6-oxohexanoic acid
dehydrogenase activity, omega oxo fatty acid dehydrogenase
activity, 6-hydroxyhexanoic acid dehydrogenase activity, omega
hydroxyl fatty acid dehydrogenase activity, hexanoate synthase
activity and monooxygenase activity, thereby producing engineered
microorganisms, and (b) selecting for engineered microorganisms
that produce adipic acid.
[0508] F2. The method of embodiment F1, which comprises selecting
for engineered microorganisms having one or more detectable and/or
increased activities selected from the group consisting of
6-oxohexanoic acid dehydrogenase activity, omega oxo fatty acid
dehydrogenase activity, 6-hydroxyhexanoic acid dehydrogenase
activity, omega hydroxyl fatty acid dehydrogenase activity,
hexanoate synthase activity and monooxygenase activity, relative to
the host microorganism.
[0509] F3. The method of embodiment F1 or F2, which comprises
introducing a genetic modification that reduces 6-hydroxyhexanoic
acid conversion, thereby producing engineered microorganisms, and
selecting for engineered microorganisms having reduced
6-hydroxyhexanoic acid conversion relative to the host
microorganism.
[0510] F4. The method of any one of embodiments F1-F3, which
comprises introducing a genetic modification that reduces
beta-oxidation activity, thereby producing engineered
microorganisms, and selecting for engineered microorganisms having
reduced beta-oxidation activity relative to the host
microorganism.
[0511] F5. The method of any one of embodiments F1-F4, which
comprises introducing a genetic modification that results in
substantial hexanoate usage by the monooxygenase activity, thereby
producing engineered microorganisms, and selecting for engineered
microorganisms in which substantial hexanoate usage is by the
monooxygenase activity relative to the host microorganism.
[0512] G1. A method for preparing a microorganism that produces
6-hydroxyhexanoic acid, which comprises: (a) introducing one or
more genetic modifications to a host organism that add or increase
one or more activities selected from the group consisting of
6-oxohexanoic acid dehydrogenase activity, hexanoate synthase
activity and monooxygenase activity, thereby producing engineered
microorganisms, (b) introducing a genetic modification to the host
organism that reduces 6-hydroxyhexanoic acid conversion, and (c)
selecting for engineered microorganisms that produce
6-hydroxyhexanoic acid.
[0513] G2. The method of embodiment G1, which comprises selecting
for engineered microorganisms having reduced 6-hydroxyhexanoic acid
conversion relative to the host microorganism.
[0514] G3. The method of embodiment G1 or G2, which comprises
selecting for engineered microorganisms having one or more
detectable and/or increased activities selected from the group
consisting of 6-oxohexanoic acid dehydrogenase activity, omega oxo
fatty acid dehydrogenase activity, 6-hydroxyhexanoic acid
dehydrogenase activity, omega hydroxyl fatty acid dehydrogenase
activity, hexanoate synthase activity and monooxygenase activity,
relative to the host microorganism.
[0515] G4. The method of any one of embodiments G1-G3, which
comprises introducing a genetic modification that reduces
beta-oxidation activity, thereby producing engineered
microorganisms, and selecting for engineered microorganisms having
reduced beta-oxidation activity relative to the host
microorganism.
[0516] G5. The method of any one of embodiments G1-G4, which
comprises introducing a genetic modification that results in
substantial hexanoate usage by the monooxygenase activity, thereby
producing engineered microorganisms, and selecting for engineered
microorganisms in which substantial hexanoate usage is by the
monooxygenase activity relative to the host microorganism.
[0517] H1. A method, comprising: [0518] contacting an engineered
microorganism with an feedstock comprising one or more
polysaccharides, wherein the engineered microorganism comprises:
[0519] a. a genetic alteration that blocks beta oxidation activity,
and [0520] b. a genetic alteration that adds or increases a
monooxygenase activity or a genetic alteration that adds or
increases hexanoate synthetase activity; and [0521] culturing the
engineered microorganism under conditions in which adipic acid is
produced.
[0522] H1.1. The method of embodiment H1, wherein the engineered
microorganism comprises a genetic alteration that adds or increases
hexanoate synthetase activity.
[0523] H1.2. The method of embodiment H1.1, wherein the engineered
microorganism comprises a heterologous polynucleotide encoding a
polypeptide having hexanoate synthase subunit A activity.
[0524] H1.3. The method of embodiment H1.1, wherein the engineered
microorganism comprises a heterologous polynucleotide encoding a
polypeptide having hexanoate synthase subunit B activity.
[0525] H1.4. The method of embodiment H1.2 or H1.3, wherein the
heterologous polynucleotide independently is selected from a
bacterium.
[0526] H1.5. The method of embodiment H1.4, wherein the bacterium
is a Bacillus bacterium.
[0527] H1.6. The method of embodiment H1.5, wherein the Bacillus
bacterium is B. megaterium.
[0528] H2. The method of any one of embodiment H1 or H1.6, wherein
the microorganism is a Candida yeast.
[0529] H3. The method of embodiment H2, wherein the microorganism
is a C. tropicalis strain.
[0530] H4. The method of any one of embodiments H1 to H3, wherein
the genetic alteration that increases monooxygenase activity
comprises a genetic alteration that increases cytochrome P450
reductase activity.
[0531] H5. The method of embodiment H4, wherein the genetic
alteration increases the number of copies of a polynucleotide that
encodes a polypeptide having the cytochrome P450 reductase
activity.
[0532] H6. The method of embodiment H4, wherein the genetic
alteration places a promoter in functional connection with a
polynucleotide that encodes a polypeptide having the cytochrome
P450 reductase activity.
[0533] H7. The method of any one of embodiments H1 to H6, wherein
the monooxygenase activity is a CYP52A15 activity, CYP52A16
activity, or a CYP52A15 activity and CYP52A16 activity.
[0534] H8. The method of any one of embodiments H1 to H7, wherein
the genetic alteration increases the number of copies of a
polynucleotide that encodes a polypeptide having the monooxygenase
activity.
[0535] H9. The method of any one of embodiments H1 to H7, wherein
the genetic alteration places a promoter in functional connection
with a polynucleotide that encodes a polypeptide having the
monooxygenase activity.
[0536] H10. The method of any one of embodiments H1 to H7, wherein
the genetic alteration that blocks beta oxidation activity disrupts
acyl-CoA oxidase activity.
[0537] H11. The method of embodiment H10, wherein the genetic
alteration disrupts POX4 and POX5 activity.
[0538] H12. The method of embodiment H10 or H11, wherein the
genetic alteration disrupts a polynucleotide that encodes a
polypeptide having the acyl-CoA oxidase activity.
[0539] H13. The method of embodiment H10 or H11, wherein the
genetic alteration disrupts a promoter in functional connection
with a polynucleotide that encodes a polypeptide having the
acyl-CoA oxidase activity.
[0540] H14. The method of any one of embodiments H1 to H13, wherein
the feedstock comprises a 6-carbon sugar.
[0541] H15. The method of any one of embodiments H1 to H13, wherein
the feedstock comprises a 5-carbon sugar.
[0542] H16. The method of any one of embodiments H1 to H15, wherein
the adipic acid is produced at a level of about 80% or more of
theoretical yield.
[0543] H17. The method of any one of embodiments H1 to H16,
comprising detecting the amount of adipic acid produced.
[0544] H18. The method of any one of embodiments H1 to H17,
comprising isolating the adipic acid produced.
[0545] H19. The method of any one of embodiments H1 to H18, wherein
the culture conditions comprise fermenting the engineered
microorganism.
[0546] I1. A method, comprising: [0547] contacting an engineered
microorganism with a feedstock comprising one or more paraffins,
wherein the engineered microorganism comprises a genetic alteration
that partially blocks beta oxidation activity; and [0548] culturing
the engineered microorganism under conditions in which adipic acid
is produced.
[0549] I1.1. The method of embodiment I1, wherein the microorganism
comprises a genetic alteration that increases a monooxygenase
activity.
[0550] I2. The method of embodiment I1 or I1.1, wherein the
microorganism is a Candida yeast.
[0551] I3. The method of embodiment I2, wherein the microorganism
is a C. tropicalis strain.
[0552] 14. The method of any one of embodiments I1 to I3, wherein
the genetic alteration that increases monooxygenase activity
comprises a genetic alteration that increases cytochrome P450
reductase activity.
[0553] I5. The method of embodiment I4, wherein the genetic
alteration increases the number of copies of a polynucleotide that
encodes a polypeptide having the cytochrome P450 reductase
activity.
[0554] I1. The method of embodiment I4, wherein the genetic
alteration places a promoter in functional connection with a
polynucleotide that encodes a polypeptide having the cytochrome
P450 reductase activity.
[0555] I1. The method of any one of embodiments I1 to 16, wherein
the monooxygenase activity is a CYP52A15 activity, CYP52A16
activity, or a CYP52A15 activity and CYP52A16 activity.
[0556] I8. The method of any one of embodiments I1 to 17, wherein
the genetic alteration increases the number of copies of a
polynucleotide that encodes a polypeptide having the monooxygenase
activity.
[0557] I9. The method of any one of embodiments I1 to 17, wherein
the genetic alteration places a promoter in functional connection
with a polynucleotide that encodes a polypeptide having the
monooxygenase activity.
[0558] I10. The method of any one of embodiments I1 to 17, wherein
the genetic alteration that blocks beta oxidation activity disrupts
acyl-CoA oxidase activity.
[0559] I11. The method of embodiment I10, wherein the genetic
alteration disrupts POX4 or POXS activity.
[0560] I12. The method of embodiment I10 or I11, wherein the
genetic alteration disrupts a polynucleotide that encodes a
polypeptide having the acyl-CoA oxidase activity.
[0561] I13. The method of embodiment I10 or I11, wherein the
genetic alteration disrupts a promoter in functional connection
with a polynucleotide that encodes a polypeptide having the
acyl-CoA oxidase activity.
[0562] I14. The method of any one of embodiments I1 to I13, wherein
the adipic acid is produced at a level of about 80% or more of
theoretical yield.
[0563] I15. The method of any one of embodiments I1 to I14,
comprising detecting the amount of adipic acid produced.
[0564] I116. The method of any one of embodiments I1 to I15,
comprising isolating the adipic acid produced.
[0565] I17. The method of any one of embodiments I1 to I16, wherein
the culture conditions comprise fermenting the engineered
microorganism.
[0566] I18. The method of any one of embodiments I1 to I17, wherein
the paraffin is a saturated paraffin, unsaturated paraffin,
substituted paraffin, branched paraffin, linear paraffin or
combination thereof.
[0567] I19. The method of any one of embodiments I1 to I18, wherein
the paraffin includes about 1 to about 60 carbon atoms.
[0568] I20. The method of any one of embodiments I1 to I19, wherein
the paraffin is in a mixture of paraffins.
[0569] I21. The method of embodiment I20, wherein the paraffins in
the mixture of paraffins have a mean number of carbon atoms of
about 8 to about I8 carbon atoms.
[0570] I22. The method of embodiment I21, wherein the mean number
of carbon atoms is about 10 to about 16 carbon atoms.
[0571] I23. The method of embodiment I22, wherein the mean number
of carbon atoms is about 12 atoms.
[0572] I24. The method of any one of embodiments I1 to I23, wherein
the paraffin is in a wax.
[0573] I25. The method of any one of embodiments I1 to I23, wherein
the paraffin is in an oil.
[0574] I26. The method of any one of embodiments I1 to I25, wherein
the paraffin is from a petroleum product.
[0575] I27. The method of embodiment I26, wherein the petroleum
product is a petroleum distillate.
[0576] I28. The method of any one of embodiments I1 to I127,
wherein the paraffin is from a plant or plant product.
[0577] J1. An isolated polynucleotide selected from the group
consisting of: [0578] a polynucleotide having a nucleotide sequence
96% or more identical to the nucleotide sequence of SEQ ID NO: 1;
[0579] a polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 8; and [0580] a polynucleotide having a
portion of a nucleotide sequence 96% or more identical to the
nucleotide sequence of SEQ ID NO: 1 and encodes a polypeptide
having fatty alcohol oxidase activity.
[0581] J2. An isolated polynucleotide selected from the group
consisting of: [0582] a polynucleotide having a nucleotide sequence
98% or more identical to the nucleotide sequence of SEQ ID NO: 2;
[0583] a polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 10; and [0584] a polynucleotide having a
portion of a nucleotide sequence 98% or more identical to the
nucleotide sequence of SEQ ID NO: 2 and encodes a polypeptide
having fatty alcohol oxidase activity.
[0585] J3. An isolated polynucleotide selected from the group
consisting of: [0586] a polynucleotide having a nucleotide sequence
95% or more identical to the nucleotide sequence of SEQ ID NO: 3;
[0587] a polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 9; and [0588] a polynucleotide having a
portion of a nucleotide sequence 95% or more identical to the
nucleotide sequence of SEQ ID NO: 3 and encodes a polypeptide
having fatty alcohol oxidase activity.
[0589] J3.1. An isolated polynucleotide selected from the group
consisting of: [0590] a polynucleotide having a nucleotide sequence
83% or more identical to the nucleotide sequence of SEQ ID NO: 4;
[0591] a polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 11; and [0592] a polynucleotide having a
portion of a nucleotide sequence 83% or more identical to the
nucleotide sequence of SEQ ID NO: 4 and encodes a polypeptide
having fatty alcohol oxidase activity.
[0593] J3.2. An isolated polynucleotide selected from the group
consisting of: [0594] a polynucleotide having a nucleotide sequence
82% or more identical to the nucleotide sequence of SEQ ID NO: 5;
[0595] a polynucleotide having a nucleotide sequence that encodes a
polypeptide of SEQ ID NO: 12; and [0596] a polynucleotide having a
portion of a nucleotide sequence 82% or more identical to the
nucleotide sequence of SEQ ID NO: 5 and encodes a polypeptide
having fatty alcohol oxidase activity.
[0597] J4. An expression vector comprising a polynucleotide of any
one of embodiments J1 to J3.2.
[0598] J5. An integration vector comprising a polynucleotide of any
one of embodiments J1 to J3.2.
[0599] J6. A microorganism comprising an expression vector of
embodiment J4 or an integration vector of embodiment J5.
[0600] J7. A culture comprising a microorganism of embodiment
J6.
[0601] J8. A fermentation device comprising a microorganism of
embodiment J7.
[0602] J9. A polypeptide encoded by a polynucleotide of any one of
embodiments J1 to J3 or produced by an expression vector of
embodiment J4 or microorganism of embodiment J6.
[0603] J10. An antibody that specifically binds to a polypeptide of
embodiment J9.
[0604] The entirety of each patent, patent application, publication
and document referenced herein hereby is incorporated by reference.
Citation of the above patents, patent applications, publications
and documents is not an admission that any of the foregoing is
pertinent prior art, nor does it constitute any admission as to the
contents or date of these publications or documents.
[0605] Modifications may be made to the foregoing without departing
from the basic aspects of the technology. Although the technology
has been described in substantial detail with reference to one or
more specific embodiments, those of ordinary skill in the art will
recognize that changes may be made to the embodiments specifically
disclosed in this application, yet these modifications and
improvements are within the scope and spirit of the technology.
[0606] The technology illustratively described herein suitably may
be practiced in the absence of any element(s) not specifically
disclosed herein. Thus, for example, in each instance herein any of
the terms "comprising," "consisting essentially of," and
"consisting of" may be replaced with either of the other two terms.
The terms and expressions which have been employed are used as
terms of description and not of limitation, and use of such terms
and expressions do not exclude any equivalents of the features
shown and described or portions thereof, and various modifications
are possible within the scope of the claimed technology. The term
"a" or "an" can refer to one of or a plurality of the elements it
modifies (e.g., "a reagent" can mean one or more reagents) unless
it is contextually clear either one of the elements or more than
one of the elements is described. The term "about" as used herein
refers to a value within 10% of the underlying parameter (i.e.,
plus or minus 10%), and use of the term "about" at the beginning of
a string of values modifies each of the values (i.e., "about 1, 2
and 3" refers to about 1, about 2 and about 3). For example, a
weight of "about 100 grams" can include weights between 90 grams
and 110 grams. Further, when a listing of values is described
herein (e.g., about 50%, 60%, 70%, 80%, 85% or 86%) the listing
includes all intermediate and fractional values thereof (e.g., 54%,
85.4%). Thus, it should be understood that although the present
technology has been specifically disclosed by representative
embodiments and optional features, modification and variation of
the concepts herein disclosed may be resorted to by those skilled
in the art, and such modifications and variations are considered
within the scope of this technology.
[0607] Certain embodiments of the technology are set forth in the
claim(s) that follow(s)
Sequence CWU 1
1
32812115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 1atggctccat ttttgcccga ccaggtcgac
tacaaacacg tcgacaccct tatgttatta 60tgtgacggga tcatccacga aaccaccgtc
gaccaaatca aagacgttat tgctcctgac 120ttccctgctg acaagtacga
agagtacgtc aggacattca ccaaaccctc cgaaacccca 180gggttcaggg
aaaccgtcta caacacagtc aacgcaaaca ccacggacgc aatccaccag
240ttcattatct tgaccaatgt tttggcatcc agggtcttgg ctccagcttt
gaccaactcg 300ttgacgccta tcaaggacat gagcttggaa gaccgtgaaa
aattgttggc ctcgtggcgc 360gactccccaa tcgctgccaa aaggaagttg
ttcaggttgg tttctacgct taccttggtc 420acgttcacga gattggccaa
tgagttgcat ttgaaagcca ttcattatcc aggaagagaa 480gaccgtgaaa
aggcttatga aacccaggag attgaccctt ttaagtacca gtttttggaa
540aaaccgaagt tttacggcgc tgagttgtac ttgccagata ttgatgtgat
cattattgga 600tctggtgccg gtgctggtgt tgtggcccac actttggcca
acgatggctt caagagtttg 660gttttggaaa agggcaaata ctttagcaac
tccgagttga actttgatga caaggacggc 720gttcaagaat tataccaaag
tggaggtact ttgactacag tcaaccaaca gttgtttgtt 780cttgctggtt
ccacttttgg tggcggtacc actgtcaatt ggtcagcctg tcttaagacg
840ccattcaagg tgcgtaagga atggtatgat gagtttggtg ttgactttgc
tgctgatgaa 900gcatacgata aagcgcagga ttatgtttgg cagcaaatgg
gagcttctac cgaaggcatc 960acccactctt tggctaacga gattattatt
gaaggtggta agaaattagg ttacaaggcc 1020aaggtattag accaaaacag
cggtggtcat cctcagcaca gatgcggttt ctgttatttg 1080ggctgtaagc
acggtatcaa gcagggttct gttaataact ggtttagaga cgcagctgcc
1140cacggttccc agttcatgca acaggttaga gttttgcaaa tacttaacaa
gaaggggatc 1200gcttacggta tcttgtgtga ggatgttgta accggcgcca
agttcaccat tactggcccc 1260aaaaagtttg ttgttgctgc cggtgctttg
aacactccat ctgtgttggt caactccggc 1320ttcaagaaca agaacatcgg
taagaactta actttgcacc cagtttctgt cgtgtttggt 1380gattttggca
aagacgttca agcagaccac ttccacaact ccatcatgac tgccctttgt
1440tcagaagccg ctgatttaga cggcaagggc catggatgca gaattgaaac
catcttgaac 1500gctccattca tccaggcttc attcttacca tggagaggta
gtaacgaggc tagacgagac 1560ttgttgcgtt acaacaacat ggtggcgatg
ttgctcctta gtcgtgacac caccagtggt 1620tccgtttctg ctcatccaac
caaacctgaa gctttggttg tcgagtacga cgtgaacaag 1680tttgacagaa
actcgatctt gcaggcattg ttggtcactg ctgacttgtt gtatatccaa
1740ggtgccaaga gaatccttag tccacaggca tgggtgccaa tttttgaatc
cgacaagcca 1800aaggataaga gatcaatcaa ggacgaggac tatgtcgaat
ggagagccaa ggttgccaag 1860attcctttcg acacctacgg ctcaccttat
ggttcggcac atcaaatgtc ttcttgccgt 1920atgtcaggta agggtcctaa
atacggtgct gttgacaccg atggtagatt gtttgaatgt 1980tcgaatgttt
atgttgccga tgcaagtctt ttgccaactg caagcggtgc caaccctatg
2040gtcaccacca tgactcttgc cagacatgtt gcgttaggtt tggcagactc
cttgaagacc 2100aaagccaagt tgtag 211522115DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
2atggctccat ttttgcccga ccaggtcgac tacaaacacg tcgacaccct tatgttatta
60tgtgacggga tcatccacga aaccaccgtg gacgaaatca aagacgtcat tgcccctgac
120ttccccgccg acaaatacga ggagtacgtc aggacattca ccaaaccctc
cgaaacccca 180gggttcaggg aaaccgtcta caacaccgtc aacgcaaaca
ccatggatgc aatccaccag 240ttcattatct tgaccaatgt tttgggatca
agggtcttgg caccagcttt gaccaactcg 300ttgactccta tcaaggacat
gagcttggaa gaccgtgaaa agttgttagc ctcgtggcgt 360gactccccta
ttgctgctaa aaggaagttg ttcaggttgg tttctacgct taccttggtc
420acgttcacga gattggccaa tgagttgcat ttgaaagcca ttcattatcc
aggaagagaa 480gaccgtgaaa aggcttatga aacccaggag attgaccctt
ttaagtacca gtttttggaa 540aaaccgaagt tttacggcgc tgagttgtac
ttgccagata ttgatgtgat cattattgga 600tctggtgccg gtgctggtgt
tgtggcccac actttggcca acgatggctt caagagtttg 660gttttggaaa
agggcaaata ctttagcaac tccgagttga actttgatga caaggacggc
720gttcaagaat tataccaaag tggaggtact ttgactacag tcaaccaaca
gttgtttgtt 780cttgctggtt ccacttttgg tggcggtacc actgtcaatt
ggtcagcctg tcttaagacg 840ccattcaagg tgcgtaagga atggtatgat
gagtttggtg ttgactttgc tgctgatgaa 900gcatacgata aagcgcagga
ttatgtttgg cagcaaatgg gagcttctac cgaaggcatc 960acccactctt
tggctaacga gattattatt gaaggtggta agaaattagg ttacaaggcc
1020aaggtattag accaaaacag cggtggtcat cctcagcaca gatgcggttt
ctgttatttg 1080ggttgtaagc acggtatcaa gcagggctct gttaataact
ggtttagaga cgcagctgcc 1140cacggttctc agttcatgca acaggttaga
gttttgcaaa tccttaacaa gaagggcatc 1200gcttatggta tcttgtgtga
ggatgttgta accggtgcca agttcaccat tactggcccc 1260aaaaagtttg
ttgttgccgc cggcgcctta aacactccat ctgtgttggt caactccgga
1320ttcaagaaca agaacatcgg taagaactta actttgcatc cagtttctgt
cgtgtttggt 1380gattttggca aagacgttca agcagaccac ttccacaact
ccatcatgac tgccctttgt 1440tcagaagccg ctgatttaga cggcaagggc
catggatgca gaattgaaac catcttgaac 1500gctccattca tccaggcttc
attcttacca tggagaggta gtaacgaggc tagacgagac 1560ttgttgcgtt
acaacaacat ggtggcgatg ttgctcctta gtcgtgacac caccagtggt
1620tccgtttctg ctcatccaac caaacctgaa gctttggttg tcgagtacga
cgtgaacaag 1680tttgacagaa actcgatctt gcaggcattg ttggtcactg
ctgacttgtt gtatatccaa 1740ggtgccaaga gaatccttag tccacaggca
tgggtgccaa tttttgaatc cgacaagcca 1800aaggataaga gatcaatcaa
ggacgaggac tatgtcgaat ggagagccaa ggttgccaag 1860attcctttcg
acacctacgg ctcaccttat ggttcggcac atcaaatgtc ttcttgccgt
1920atgtcaggta agggtcctaa atacggtgct gttgacaccg atggtagatt
gtttgaatgt 1980tcgaatgttt atgttgccga tgcaagtctt ttgccaactg
caagcggtgc caaccctatg 2040gtcaccacca tgactcttgc aagacatgtt
gcgttaggtt tggcagactc cttgaagacc 2100aaggccaagt tgtag
211532115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 3atggctccat ttttgcccga ccaggtcgac
tacaaacacg tcgacaccct tatgttatta 60tgtgacggga tcatccacga aaccaccgtc
gaccaaatca aagacgttat tgctcctgac 120ttccctgctg acaagtacga
agagtacgtc aggacattca ccaaaccctc cgaaacccca 180gggttcaggg
aaaccgtcta caacacagtc aacgcaaaca ccacggacgc aatccaccag
240ttcattatct tgaccaatgt tttggcatcc agggtcttgg ctccagcttt
gaccaactcg 300ttgacgccta tcaaggacat gagcttggaa gaccgtgaaa
aattgttggc ctcgtggcgc 360gactccccaa tcgctgccaa aaggaaattg
ttcaggttgg tttccacgct taccttggtt 420actttcacga gattggccaa
tgagttgcat ttgaaagcca ttcactatcc aggaagagaa 480gaccgtgaaa
aggcttatga aacccaggag attgaccctt tcaagtacca gtttatggaa
540aagccaaagt ttgacggcgc tgagttgtac ttgccagata ttgatgttat
cattattgga 600tctggtgccg gtgctggtgt tgtggcccac actttggcca
acgatggctt caagagtttg 660gttttggaaa agggcaaata ctttagcaac
tccgagttga actttgatga caaggacggc 720gttcaagaat tataccaaag
tggaggtact ttgactacag tcaaccaaca gttgtttgtt 780cttgctggtt
ccacttttgg tggcggtacc actgtcaatt ggtcagcctg tcttaagacg
840ccattcaagg tgcgtaagga atggtatgat gagtttggtg ttgactttgc
tgctgatgaa 900gcatacgata aagcgcagga ttatgtttgg cagcaaatgg
gagcttctac cgaaggcatc 960acccactctt tggctaacga gattattatt
gaaggtggta agaaattagg ttacaaggcc 1020aaggtattag accaaaacag
cggtggtcat cctcagcaca gatgcggttt ctgttatttg 1080ggctgtaagc
acggtatcaa gcagggttct gttaataact ggtttagaga cgcagctgcc
1140cacggttccc agttcatgca acaggttaga gttttgcaaa tacttaacaa
gaaggggatc 1200gcttacggta tcttgtgtga ggatgttgta accggcgcca
agttcaccat tactggcccc 1260aaaaagtttg ttgttgctgc cggtgctttg
aacactccat ctgtgttggt caactccggc 1320ttcaagaaca agaacatcgg
taagaactta actttgcacc cagtttctgt cgtgtttggt 1380gattttggca
aagacgttca agcagaccac ttccacaact ccatcatgac tgccctttgt
1440tcagaagccg ctgatttaga cggcaagggc catggatgca gaattgaaac
catcttgaac 1500gctccattca tccaggcttc attcttacca tggagaggta
gtaacgaggc tagacgagac 1560ttgttgcgtt acaacaacat ggtggcgatg
ttgctcctta gtcgtgacac caccagtggt 1620tccgtttctg ctcatccaac
caaacctgaa gctttggttg tcgagtacga cgtgaacaag 1680tttgacagaa
actcgatctt gcaggcattg ttggtcactg ctgacttgtt gtatatccaa
1740ggtgccaaga gaatccttag tccacaggca tgggtgccaa tttttgaatc
cgacaagcca 1800aaggataaga gatcaatcaa ggacgaggac tatgtcgaat
ggagagccaa ggttgccaag 1860attcctttcg acacctacgg ctcaccttat
ggttcggcac atcaaatgtc ttcttgccgt 1920atgtcaggta agggtcctaa
atacggtgct gttgacaccg atggtagatt gtttgaatgt 1980tcgaatgttt
atgttgccga tgcaagtctt ttgccaactg caagcggtgc caaccctatg
2040gtcaccacca tgactcttgc cagacatgtt gcgttaggtt tggcagactc
cttgaagacc 2100aaagccaagt tgtag 211542115DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
4atgaatacct tcttgccaga cgtgctcgaa tacaaacacg tcgacaccct tttgttattg
60tgtgacggga tcatccacga aaccacagtc gatcagatca aggacgccat tgctcccgac
120ttccctgagg accagtacga ggagtatctc aagaccttca ccaagccatc
tgagacccct 180gggttcagag aagccgtcta cgacacgatc aacgccaccc
caaccgatgc cgtgcacatg 240tgtattgtct tgaccaccgc attggactcc
agaatcttgg cccccacgtt gaccaactcg 300ttgacgccta tcaaggatat
gaccttgaag gagcgtgaac aattgttggc ctcttggcgt 360gattccccga
ttgcggcaaa gagaagattg ttcagattga tttcctcgct taccttgacg
420acgtttacga gattggccag cgaattgcac ttgaaagcca tccactaccc
tggcagagac 480ttgcgtgaaa aggcgtatga aacccaggtg gttgaccctt
tcaggtacct gtttatggag 540aaaccaaagt ttgacggcgc cgaattgtac
ttgccagata tcgacgtcat catcattgga 600tcaggcgccg gtgctggtgt
catggcccac actctcgcca acgacgggtt caagaccttg 660gttttggaaa
agggaaagta tttcagcaac tccgagttga actttaatga cgctgatggc
720gtgaaagagt tgtaccaagg taaaggtgct ttggccacca ccaatcagca
gatgtttatt 780cttgccggtt ccactttggg cggtggtacc actgtcaact
ggtctgcttg ccttaaaaca 840ccatttaaag tgcgtaagga gtggtacgac
gagtttggtc ttgaatttgc tgccgatgaa 900gcctacgaca aagcgcagga
ttatgtttgg aaacaaatgg gtgcttcaac agatggaatc 960actcactcct
tggccaacga agttgtggtt gaaggaggta agaagttggg ctacaagagc
1020aaggaaattg agcagaacaa cggtggccac cctgaccacc catgtggttt
ctgttacttg 1080ggctgtaagt acggtattaa acagggttct gtgaataact
ggtttagaga cgcagctgcc 1140cacgggtcca agttcatgca acaagtcaga
gttgtgcaaa tcctcaacaa gaatggcgtc 1200gcttatggta tcttgtgtga
ggatgtcgaa accggagtca ggttcactat tagtggcccc 1260aaaaagtttg
ttgtttctgc tggttctttg aacacgccaa ctgtgttgac caactccgga
1320ttcaagaaca agcacattgg taagaacttg acgttgcacc cagtttccac
cgtgtttggt 1380gactttggca gagacgtgca agccgaccat ttccacaaat
ctattatgac ttcgctttgt 1440tacgaggttg ctgacttgga cggcaagggc
cacggatgca gaatcgaaac catcttgaac 1500gctccattca tccaagcttc
tttgttgcca tggagaggaa gtgacgaggt cagaagagac 1560ttgttgcgtt
acaacaacat ggtggccatg ttgcttatca cgcgtgatac caccagtggt
1620tcagtttctg ctgacccaaa gaagcccgac gctttgattg tcgactatga
gattaacaag 1680tttgacaaga atgccatctt gcaagctttc ttgatcactt
ccgacatgtt gtacattgaa 1740ggtgccaaga gaatcctcag tccacagcca
tgggtgccaa tctttgagtc gaacaagcca 1800aaggagcaaa gaacgatcaa
ggacaaggac tatgttgagt ggagagccaa ggctgctaag 1860atacctttcg
acacctacgg ttctgcatat gggtccgcac atcaaatgtc cacctgtcgt
1920atgtccggaa agggtcctaa atacggtgct gttgatactg atggtagatt
gtttgaatgt 1980tcgaatgtct atgttgctga tgctagtgtt ttgcctactg
ccagcggtgc caacccaatg 2040atatccacca tgacctttgc tagacagatt
gcgttaggtt tggctgactc cttgaagacc 2100aaacccaagt tgtag
211552115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 5atgaatacct tcttgccaga cgtgctcgaa
tacaaacacg tcgataccct tttgttatta 60tgtgacggga tcatccacga aaccacagtc
gaccagatca gggacgccat tgctcccgac 120ttccctgaag accagtacga
ggagtatctc aagaccttca ccaagccatc tgagacccct 180gggttcagag
aagccgtcta cgacacgatc aacagcaccc caaccgaggc tgtgcacatg
240tgtattgtat tgaccaccgc attggactcg agaatcttgg cccccacgtt
gaccaactcg 300ttgacgccta tcaaggatat gaccttgaaa gagcgtgaac
aattgttggc tgcctggcgt 360gattccccga tcgcggccaa gagaagattg
ttcagattga tttcctcact taccttgacg 420acctttacga gattggccag
cgacttgcac ttgagagcca tccactaccc tggcagagac 480ttgcgtgaaa
aggcatatga aacccaggtg gttgaccctt tcaggtacct gtttatggaa
540aaaccaaagt ttgacggcac cgagttgtac ttgccagata tcgacgtcat
catcattgga 600tccggtgccg gtgctggtgt catggcccac actttagcca
acgacgggta caagaccttg 660gttttggaaa agggaaagta tttcagcaac
tccgagttga actttaatga tgccgatggt 720atgaaagagt tgtaccaagg
taaatgtgcg ttgaccacca cgaaccagca gatgtttatt 780cttgccggtt
ccactttggg cggtggtacc actgttaact ggtctgcttg tcttaaaaca
840ccatttaaag tgcgtaagga gtggtacgac gagtttggtc ttgaatttgc
tgccgacgaa 900gcctacgaca aagcacaaga ctatgtttgg aaacaaatgg
gcgcttctac cgaaggaatc 960actcactctt tggcgaacgc ggttgtggtt
gaaggaggta agaagttggg ttacaagagc 1020aaggaaatcg agcagaacaa
tggtggccat cctgaccacc cctgtggttt ctgttacttg 1080ggctgtaagt
acggtattaa gcagggttct gtgaataact ggtttagaga cgcagctgcc
1140cacgggtcca agttcatgca acaagtcaga gttgtgcaaa tcctccacaa
taaaggcgtc 1200gcttatggca tcttgtgtga ggatgtcgag accggagtca
aattcactat cagtggcccc 1260aaaaagtttg ttgtttctgc aggttctttg
aacacgccaa cggtgttgac caactccgga 1320ttcaagaaca aacacatcgg
taagaacttg acgttgcacc cagtttcgac cgtgtttggt 1380gactttggca
gagacgtgca agccgaccat ttccacaaat ctattatgac ttcgctctgt
1440tacgaagtcg ctgacttgga cggcaagggc cacggatgca gaatcgagac
catcttgaac 1500gctccattca tccaagcttc tttgttgcca tggagaggaa
gcgacgaggt cagaagagac 1560ttgttgcgtt acaacaacat ggtggccatg
ttgcttatca cccgtgacac caccagtggt 1620tcagtttctg ctgacccaaa
gaagcccgac gctttgattg tcgactatga catcaacaag 1680tttgacaaga
atgccatctt gcaagctttc ttgatcacct ccgacatgtt gtacatcgaa
1740ggtgccaaga gaatcctcag tccacaggca tgggtgccaa tctttgagtc
gaacaagcca 1800aaggagcaaa gaacaatcaa ggacaaggac tatgtcgaat
ggagagccaa ggctgccaag 1860atacctttcg acacctacgg ttctgcctat
gggtccgcac atcaaatgtc cacctgtcgt 1920atgtccggaa agggtcctaa
atacggcgcc gttgataccg atggtagatt gtttgaatgt 1980tcgaatgtct
atgttgctga tgctagtgtt ttgcctactg ccagcggtgc caacccaatg
2040atctccacca tgacgtttgc tagacagatt gcgttaggtt tggctgactc
tttgaagacc 2100aaacccaagt tgtag 211562115DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
6atggctccat ttttgcccga ccaggtcgac tacaaacacg tcgacaccct tatgttatta
60tgtgacggga tcatccacga aaccaccgtg gacgaaatca aagacgtcat tgcccctgac
120ttccccgccg acaaatacga ggagtacgtc aggacattca ccaaaccctc
cgaaacccca 180gggttcaggg aaaccgtcta caacaccgtc aacgcaaaca
ccatggatgc aatccaccag 240ttcattatct tgaccaatgt tttgggatca
agggtcttgg caccagcttt gaccaactcg 300ttgactccta tcaaggacat
gagcttggaa gaccgtgaaa agttgttagc ctcgtggcgt 360gactccccta
ttgctgctaa aaggaagttg ttcaggttgg tttctacgct taccttggtc
420acgttcacga gattggccaa tgagttgcat ttgaaagcca ttcattatcc
aggaagagaa 480gaccgtgaaa aggcttatga aacccaggag attgaccctt
ttaagtacca gtttttggaa 540aaaccgaagt tttacggcgc tgagttgtac
ttgccagata ttgatgtgat cattattgga 600tctggggccg gtgctggtgt
cgtggcccac actttgacca acgacggctt caagagtttg 660gttttggaaa
agggcagata ctttagcaac tccgagttga actttgatga caaggacggg
720gttcaagaat tataccaaag tggaggtact ttgaccaccg tcaaccagca
gttgtttgtt 780cttgctggtt ccacttttgg tggtggtacc actgtcaatt
ggtcggcctg tcttaaaacg 840ccattcaagg tgcgtaagga atggtatgat
gagtttggcg ttgactttgc tgccgatgaa 900gcctacgaca aagcacagga
ttatgtttgg cagcaaatgg gagcttctac cgaaggcatc 960acccactctt
tggctaacga gattattatt gaaggtggca agaaattagg ttacaaggcc
1020aaggtattag accaaaacag cggtggtcat cctcatcaca gatgcggttt
ctgttatttg 1080ggttgtaagc acggtatcaa gcagggctct gttaataact
ggtttagaga cgcagctgcc 1140cacggttctc agttcatgca acaggttaga
gttttgcaaa tccttaacaa gaagggcatc 1200gcttatggta tcttgtgtga
ggatgttgta accggtgcca agttcaccat tactggcccc 1260aaaaagtttg
ttgttgccgc cggcgcctta aacactccat ctgtgttggt caactccgga
1320ttcaagaaca agaacatcgg taagaactta actttgcatc cagtttctgt
cgtgtttggt 1380gattttggca aagacgttca agcagatcac ttccacaact
ccatcatgac tgctctttgt 1440tcagaagccg ctgatttaga cggcaagggt
catggatgca gaattgaaac catcttgaac 1500gctccattca tccaggcttc
attcttacca tggagaggta gtaacgaggc tagacgagac 1560ttgttgcgtt
acaacaacat ggtggccatg ttacttctta gtcgtgatac caccagtggt
1620tccgtttcgt cccatccaac taaacctgaa gcattagttg tcgagtacga
cgtgaacaag 1680tttgacagaa actccatctt gcaggcattg ttggtcactg
ctgacttgtt gtacattcaa 1740ggtgccaaga gaatccttag tccccaacca
tgggtgccaa tttttgaatc cgacaagcca 1800aaggataaga gatcaatcaa
ggacgaggac tatgtcgaat ggagagccaa ggttgccaag 1860attccttttg
acacctacgg ctcgccttat ggttcggcgc atcaaatgtc ttcttgtcgt
1920atgtcaggta agggtcctaa atacggtgct gttgataccg atggtagatt
gtttgaatgt 1980tcgaatgttt atgttgctga cgctagtctt ttgccaactg
ctagcggtgc taatcctatg 2040gtcaccacca tgactcttgc aagacatgtt
gcgttaggtt tggcagactc cttgaagacc 2100aaggccaagt tgtag
21157704PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 7Met Ala Pro Phe Leu Pro Asp Gln Val Asp Tyr
Lys His Val Asp Thr1 5 10 15Leu Met Leu Leu Cys Asp Gly Ile Ile His
Glu Thr Thr Val Asp Glu 20 25 30Ile Lys Asp Val Ile Ala Pro Asp Phe
Pro Ala Asp Lys Tyr Glu Glu 35 40 45Tyr Val Arg Thr Phe Thr Lys Pro
Ser Glu Thr Pro Gly Phe Arg Glu 50 55 60Thr Val Tyr Asn Thr Val Asn
Ala Asn Thr Met Asp Ala Ile His Gln65 70 75 80Phe Ile Ile Leu Thr
Asn Val Leu Gly Ser Arg Val Leu Ala Pro Ala 85 90 95Leu Thr Asn Ser
Leu Thr Pro Ile Lys Asp Met Ser Leu Glu Asp Arg 100 105 110Glu Lys
Leu Leu Ala Ser Trp Arg Asp Ser Pro Ile Ala Ala Lys Arg 115 120
125Lys Leu Phe Arg Leu Val Ser Thr Leu Thr Leu Val Thr Phe Thr Arg
130 135 140Leu Ala Asn Glu Leu His Leu Lys Ala Ile His Tyr Pro Gly
Arg Glu145 150 155 160Asp Arg Glu Lys Ala Tyr Glu Thr Gln Glu Ile
Asp Pro Phe Lys Tyr 165 170 175Gln Phe Leu Glu Lys Pro Lys Phe Tyr
Gly Ala Glu Leu Tyr Leu Pro 180 185 190Asp Ile Asp Val Ile Ile Ile
Gly Ser Gly Ala Gly Ala Gly Val Val 195 200 205Ala His Thr Leu Thr
Asn Asp Gly Phe Lys Ser Leu Val Leu Glu Lys 210 215 220Gly Arg Tyr
Phe Ser Asn Ser Glu Leu Asn Phe Asp Asp Lys Asp Gly225 230 235
240Val Gln Glu Leu Tyr Gln Ser Gly Gly Thr Leu Thr Thr Val Asn
Gln 245 250 255Gln Leu Phe Val Leu Ala Gly Ser Thr Phe Gly Gly Gly
Thr Thr Val 260 265 270Asn Trp Ser Ala Cys Leu Lys Thr Pro Phe Lys
Val Arg Lys Glu Trp 275 280 285Tyr Asp Glu Phe Gly Val Asp Phe Ala
Ala Asp Glu Ala Tyr Asp Lys 290 295 300Ala Gln Asp Tyr Val Trp Gln
Gln Met Gly Ala Ser Thr Glu Gly Ile305 310 315 320Thr His Ser Leu
Ala Asn Glu Ile Ile Ile Glu Gly Gly Lys Lys Leu 325 330 335Gly Tyr
Lys Ala Lys Val Leu Asp Gln Asn Ser Gly Gly His Pro His 340 345
350His Arg Cys Gly Phe Cys Tyr Leu Gly Cys Lys His Gly Ile Lys Gln
355 360 365Gly Ser Val Asn Asn Trp Phe Arg Asp Ala Ala Ala His Gly
Ser Gln 370 375 380Phe Met Gln Gln Val Arg Val Leu Gln Ile Leu Asn
Lys Lys Gly Ile385 390 395 400Ala Tyr Gly Ile Leu Cys Glu Asp Val
Val Thr Gly Ala Lys Phe Thr 405 410 415Ile Thr Gly Pro Lys Lys Phe
Val Val Ala Ala Gly Ala Leu Asn Thr 420 425 430Pro Ser Val Leu Val
Asn Ser Gly Phe Lys Asn Lys Asn Ile Gly Lys 435 440 445Asn Leu Thr
Leu His Pro Val Ser Val Val Phe Gly Asp Phe Gly Lys 450 455 460Asp
Val Gln Ala Asp His Phe His Asn Ser Ile Met Thr Ala Leu Cys465 470
475 480Ser Glu Ala Ala Asp Leu Asp Gly Lys Gly His Gly Cys Arg Ile
Glu 485 490 495Thr Ile Leu Asn Ala Pro Phe Ile Gln Ala Ser Phe Leu
Pro Trp Arg 500 505 510Gly Ser Asn Glu Ala Arg Arg Asp Leu Leu Arg
Tyr Asn Asn Met Val 515 520 525Ala Met Leu Leu Leu Ser Arg Asp Thr
Thr Ser Gly Ser Val Ser Ser 530 535 540His Pro Thr Lys Pro Glu Ala
Leu Val Val Glu Tyr Asp Val Asn Lys545 550 555 560Phe Asp Arg Asn
Ser Ile Leu Gln Ala Leu Leu Val Thr Ala Asp Leu 565 570 575Leu Tyr
Ile Gln Gly Ala Lys Arg Ile Leu Ser Pro Gln Pro Trp Val 580 585
590Pro Ile Phe Glu Ser Asp Lys Pro Lys Asp Lys Arg Ser Ile Lys Asp
595 600 605Glu Asp Tyr Val Glu Trp Arg Ala Lys Val Ala Lys Ile Pro
Phe Asp 610 615 620Thr Tyr Gly Ser Pro Tyr Gly Ser Ala His Gln Met
Ser Ser Cys Arg625 630 635 640Met Ser Gly Lys Gly Pro Lys Tyr Gly
Ala Val Asp Thr Asp Gly Arg 645 650 655Leu Phe Glu Cys Ser Asn Val
Tyr Val Ala Asp Ala Ser Leu Leu Pro 660 665 670Thr Ala Ser Gly Ala
Asn Pro Met Val Thr Thr Met Thr Leu Ala Arg 675 680 685His Val Ala
Leu Gly Leu Ala Asp Ser Leu Lys Thr Lys Ala Lys Leu 690 695
7008704PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 8Met Ala Pro Phe Leu Pro Asp Gln Val Asp Tyr
Lys His Val Asp Thr1 5 10 15Leu Met Leu Leu Cys Asp Gly Ile Ile His
Glu Thr Thr Val Asp Gln 20 25 30Ile Lys Asp Val Ile Ala Pro Asp Phe
Pro Ala Asp Lys Tyr Glu Glu 35 40 45Tyr Val Arg Thr Phe Thr Lys Pro
Ser Glu Thr Pro Gly Phe Arg Glu 50 55 60Thr Val Tyr Asn Thr Val Asn
Ala Asn Thr Thr Asp Ala Ile His Gln65 70 75 80Phe Ile Ile Leu Thr
Asn Val Leu Ala Ser Arg Val Leu Ala Pro Ala 85 90 95Leu Thr Asn Ser
Leu Thr Pro Ile Lys Asp Met Ser Leu Glu Asp Arg 100 105 110Glu Lys
Leu Leu Ala Ser Trp Arg Asp Ser Pro Ile Ala Ala Lys Arg 115 120
125Lys Leu Phe Arg Leu Val Ser Thr Leu Thr Leu Val Thr Phe Thr Arg
130 135 140Leu Ala Asn Glu Leu His Leu Lys Ala Ile His Tyr Pro Gly
Arg Glu145 150 155 160Asp Arg Glu Lys Ala Tyr Glu Thr Gln Glu Ile
Asp Pro Phe Lys Tyr 165 170 175Gln Phe Leu Glu Lys Pro Lys Phe Tyr
Gly Ala Glu Leu Tyr Leu Pro 180 185 190Asp Ile Asp Val Ile Ile Ile
Gly Ser Gly Ala Gly Ala Gly Val Val 195 200 205Ala His Thr Leu Ala
Asn Asp Gly Phe Lys Ser Leu Val Leu Glu Lys 210 215 220Gly Lys Tyr
Phe Ser Asn Ser Glu Leu Asn Phe Asp Asp Lys Asp Gly225 230 235
240Val Gln Glu Leu Tyr Gln Ser Gly Gly Thr Leu Thr Thr Val Asn Gln
245 250 255Gln Leu Phe Val Leu Ala Gly Ser Thr Phe Gly Gly Gly Thr
Thr Val 260 265 270Asn Trp Ser Ala Cys Leu Lys Thr Pro Phe Lys Val
Arg Lys Glu Trp 275 280 285Tyr Asp Glu Phe Gly Val Asp Phe Ala Ala
Asp Glu Ala Tyr Asp Lys 290 295 300Ala Gln Asp Tyr Val Trp Gln Gln
Met Gly Ala Ser Thr Glu Gly Ile305 310 315 320Thr His Ser Leu Ala
Asn Glu Ile Ile Ile Glu Gly Gly Lys Lys Leu 325 330 335Gly Tyr Lys
Ala Lys Val Leu Asp Gln Asn Ser Gly Gly His Pro Gln 340 345 350His
Arg Cys Gly Phe Cys Tyr Leu Gly Cys Lys His Gly Ile Lys Gln 355 360
365Gly Ser Val Asn Asn Trp Phe Arg Asp Ala Ala Ala His Gly Ser Gln
370 375 380Phe Met Gln Gln Val Arg Val Leu Gln Ile Leu Asn Lys Lys
Gly Ile385 390 395 400Ala Tyr Gly Ile Leu Cys Glu Asp Val Val Thr
Gly Ala Lys Phe Thr 405 410 415Ile Thr Gly Pro Lys Lys Phe Val Val
Ala Ala Gly Ala Leu Asn Thr 420 425 430Pro Ser Val Leu Val Asn Ser
Gly Phe Lys Asn Lys Asn Ile Gly Lys 435 440 445Asn Leu Thr Leu His
Pro Val Ser Val Val Phe Gly Asp Phe Gly Lys 450 455 460Asp Val Gln
Ala Asp His Phe His Asn Ser Ile Met Thr Ala Leu Cys465 470 475
480Ser Glu Ala Ala Asp Leu Asp Gly Lys Gly His Gly Cys Arg Ile Glu
485 490 495Thr Ile Leu Asn Ala Pro Phe Ile Gln Ala Ser Phe Leu Pro
Trp Arg 500 505 510Gly Ser Asn Glu Ala Arg Arg Asp Leu Leu Arg Tyr
Asn Asn Met Val 515 520 525Ala Met Leu Leu Leu Ser Arg Asp Thr Thr
Ser Gly Ser Val Ser Ala 530 535 540His Pro Thr Lys Pro Glu Ala Leu
Val Val Glu Tyr Asp Val Asn Lys545 550 555 560Phe Asp Arg Asn Ser
Ile Leu Gln Ala Leu Leu Val Thr Ala Asp Leu 565 570 575Leu Tyr Ile
Gln Gly Ala Lys Arg Ile Leu Ser Pro Gln Ala Trp Val 580 585 590Pro
Ile Phe Glu Ser Asp Lys Pro Lys Asp Lys Arg Ser Ile Lys Asp 595 600
605Glu Asp Tyr Val Glu Trp Arg Ala Lys Val Ala Lys Ile Pro Phe Asp
610 615 620Thr Tyr Gly Ser Pro Tyr Gly Ser Ala His Gln Met Ser Ser
Cys Arg625 630 635 640Met Ser Gly Lys Gly Pro Lys Tyr Gly Ala Val
Asp Thr Asp Gly Arg 645 650 655Leu Phe Glu Cys Ser Asn Val Tyr Val
Ala Asp Ala Ser Leu Leu Pro 660 665 670Thr Ala Ser Gly Ala Asn Pro
Met Val Thr Thr Met Thr Leu Ala Arg 675 680 685His Val Ala Leu Gly
Leu Ala Asp Ser Leu Lys Thr Lys Ala Lys Leu 690 695
7009704PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 9Met Ala Pro Phe Leu Pro Asp Gln Val Asp Tyr
Lys His Val Asp Thr1 5 10 15Leu Met Leu Leu Cys Asp Gly Ile Ile His
Glu Thr Thr Val Asp Gln 20 25 30Ile Lys Asp Val Ile Ala Pro Asp Phe
Pro Ala Asp Lys Tyr Glu Glu 35 40 45Tyr Val Arg Thr Phe Thr Lys Pro
Ser Glu Thr Pro Gly Phe Arg Glu 50 55 60Thr Val Tyr Asn Thr Val Asn
Ala Asn Thr Thr Asp Ala Ile His Gln65 70 75 80Phe Ile Ile Leu Thr
Asn Val Leu Ala Ser Arg Val Leu Ala Pro Ala 85 90 95Leu Thr Asn Ser
Leu Thr Pro Ile Lys Asp Met Ser Leu Glu Asp Arg 100 105 110Glu Lys
Leu Leu Ala Ser Trp Arg Asp Ser Pro Ile Ala Ala Lys Arg 115 120
125Lys Leu Phe Arg Leu Val Ser Thr Leu Thr Leu Val Thr Phe Thr Arg
130 135 140Leu Ala Asn Glu Leu His Leu Lys Ala Ile His Tyr Pro Gly
Arg Glu145 150 155 160Asp Arg Glu Lys Ala Tyr Glu Thr Gln Glu Ile
Asp Pro Phe Lys Tyr 165 170 175Gln Phe Met Glu Lys Pro Lys Phe Asp
Gly Ala Glu Leu Tyr Leu Pro 180 185 190Asp Ile Asp Val Ile Ile Ile
Gly Ser Gly Ala Gly Ala Gly Val Val 195 200 205Ala His Thr Leu Ala
Asn Asp Gly Phe Lys Ser Leu Val Leu Glu Lys 210 215 220Gly Lys Tyr
Phe Ser Asn Ser Glu Leu Asn Phe Asp Asp Lys Asp Gly225 230 235
240Val Gln Glu Leu Tyr Gln Ser Gly Gly Thr Leu Thr Thr Val Asn Gln
245 250 255Gln Leu Phe Val Leu Ala Gly Ser Thr Phe Gly Gly Gly Thr
Thr Val 260 265 270Asn Trp Ser Ala Cys Leu Lys Thr Pro Phe Lys Val
Arg Lys Glu Trp 275 280 285Tyr Asp Glu Phe Gly Val Asp Phe Ala Ala
Asp Glu Ala Tyr Asp Lys 290 295 300Ala Gln Asp Tyr Val Trp Gln Gln
Met Gly Ala Ser Thr Glu Gly Ile305 310 315 320Thr His Ser Leu Ala
Asn Glu Ile Ile Ile Glu Gly Gly Lys Lys Leu 325 330 335Gly Tyr Lys
Ala Lys Val Leu Asp Gln Asn Ser Gly Gly His Pro Gln 340 345 350His
Arg Cys Gly Phe Cys Tyr Leu Gly Cys Lys His Gly Ile Lys Gln 355 360
365Gly Ser Val Asn Asn Trp Phe Arg Asp Ala Ala Ala His Gly Ser Gln
370 375 380Phe Met Gln Gln Val Arg Val Leu Gln Ile Leu Asn Lys Lys
Gly Ile385 390 395 400Ala Tyr Gly Ile Leu Cys Glu Asp Val Val Thr
Gly Ala Lys Phe Thr 405 410 415Ile Thr Gly Pro Lys Lys Phe Val Val
Ala Ala Gly Ala Leu Asn Thr 420 425 430Pro Ser Val Leu Val Asn Ser
Gly Phe Lys Asn Lys Asn Ile Gly Lys 435 440 445Asn Leu Thr Leu His
Pro Val Ser Val Val Phe Gly Asp Phe Gly Lys 450 455 460Asp Val Gln
Ala Asp His Phe His Asn Ser Ile Met Thr Ala Leu Cys465 470 475
480Ser Glu Ala Ala Asp Leu Asp Gly Lys Gly His Gly Cys Arg Ile Glu
485 490 495Thr Ile Leu Asn Ala Pro Phe Ile Gln Ala Ser Phe Leu Pro
Trp Arg 500 505 510Gly Ser Asn Glu Ala Arg Arg Asp Leu Leu Arg Tyr
Asn Asn Met Val 515 520 525Ala Met Leu Leu Leu Ser Arg Asp Thr Thr
Ser Gly Ser Val Ser Ala 530 535 540His Pro Thr Lys Pro Glu Ala Leu
Val Val Glu Tyr Asp Val Asn Lys545 550 555 560Phe Asp Arg Asn Ser
Ile Leu Gln Ala Leu Leu Val Thr Ala Asp Leu 565 570 575Leu Tyr Ile
Gln Gly Ala Lys Arg Ile Leu Ser Pro Gln Ala Trp Val 580 585 590Pro
Ile Phe Glu Ser Asp Lys Pro Lys Asp Lys Arg Ser Ile Lys Asp 595 600
605Glu Asp Tyr Val Glu Trp Arg Ala Lys Val Ala Lys Ile Pro Phe Asp
610 615 620Thr Tyr Gly Ser Pro Tyr Gly Ser Ala His Gln Met Ser Ser
Cys Arg625 630 635 640Met Ser Gly Lys Gly Pro Lys Tyr Gly Ala Val
Asp Thr Asp Gly Arg 645 650 655Leu Phe Glu Cys Ser Asn Val Tyr Val
Ala Asp Ala Ser Leu Leu Pro 660 665 670Thr Ala Ser Gly Ala Asn Pro
Met Val Thr Thr Met Thr Leu Ala Arg 675 680 685His Val Ala Leu Gly
Leu Ala Asp Ser Leu Lys Thr Lys Ala Lys Leu 690 695
70010704PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 10Met Ala Pro Phe Leu Pro Asp Gln Val Asp Tyr
Lys His Val Asp Thr1 5 10 15Leu Met Leu Leu Cys Asp Gly Ile Ile His
Glu Thr Thr Val Asp Glu 20 25 30Ile Lys Asp Val Ile Ala Pro Asp Phe
Pro Ala Asp Lys Tyr Glu Glu 35 40 45Tyr Val Arg Thr Phe Thr Lys Pro
Ser Glu Thr Pro Gly Phe Arg Glu 50 55 60Thr Val Tyr Asn Thr Val Asn
Ala Asn Thr Met Asp Ala Ile His Gln65 70 75 80Phe Ile Ile Leu Thr
Asn Val Leu Gly Ser Arg Val Leu Ala Pro Ala 85 90 95Leu Thr Asn Ser
Leu Thr Pro Ile Lys Asp Met Ser Leu Glu Asp Arg 100 105 110Glu Lys
Leu Leu Ala Ser Trp Arg Asp Ser Pro Ile Ala Ala Lys Arg 115 120
125Lys Leu Phe Arg Leu Val Ser Thr Leu Thr Leu Val Thr Phe Thr Arg
130 135 140Leu Ala Asn Glu Leu His Leu Lys Ala Ile His Tyr Pro Gly
Arg Glu145 150 155 160Asp Arg Glu Lys Ala Tyr Glu Thr Gln Glu Ile
Asp Pro Phe Lys Tyr 165 170 175Gln Phe Leu Glu Lys Pro Lys Phe Tyr
Gly Ala Glu Leu Tyr Leu Pro 180 185 190Asp Ile Asp Val Ile Ile Ile
Gly Ser Gly Ala Gly Ala Gly Val Val 195 200 205Ala His Thr Leu Ala
Asn Asp Gly Phe Lys Ser Leu Val Leu Glu Lys 210 215 220Gly Lys Tyr
Phe Ser Asn Ser Glu Leu Asn Phe Asp Asp Lys Asp Gly225 230 235
240Val Gln Glu Leu Tyr Gln Ser Gly Gly Thr Leu Thr Thr Val Asn Gln
245 250 255Gln Leu Phe Val Leu Ala Gly Ser Thr Phe Gly Gly Gly Thr
Thr Val 260 265 270Asn Trp Ser Ala Cys Leu Lys Thr Pro Phe Lys Val
Arg Lys Glu Trp 275 280 285Tyr Asp Glu Phe Gly Val Asp Phe Ala Ala
Asp Glu Ala Tyr Asp Lys 290 295 300Ala Gln Asp Tyr Val Trp Gln Gln
Met Gly Ala Ser Thr Glu Gly Ile305 310 315 320Thr His Ser Leu Ala
Asn Glu Ile Ile Ile Glu Gly Gly Lys Lys Leu 325 330 335Gly Tyr Lys
Ala Lys Val Leu Asp Gln Asn Ser Gly Gly His Pro Gln 340 345 350His
Arg Cys Gly Phe Cys Tyr Leu Gly Cys Lys His Gly Ile Lys Gln 355 360
365Gly Ser Val Asn Asn Trp Phe Arg Asp Ala Ala Ala His Gly Ser Gln
370 375 380Phe Met Gln Gln Val Arg Val Leu Gln Ile Leu Asn Lys Lys
Gly Ile385 390 395 400Ala Tyr Gly Ile Leu Cys Glu Asp Val Val Thr
Gly Ala Lys Phe Thr 405 410 415Ile Thr Gly Pro Lys Lys Phe Val Val
Ala Ala Gly Ala Leu Asn Thr 420 425 430Pro Ser Val Leu Val Asn Ser
Gly Phe Lys Asn Lys Asn Ile Gly Lys 435 440 445Asn Leu Thr Leu His
Pro Val Ser Val Val Phe Gly Asp Phe Gly Lys 450 455 460Asp Val Gln
Ala Asp His Phe His Asn Ser Ile Met Thr Ala Leu Cys465 470 475
480Ser Glu Ala Ala Asp Leu Asp Gly Lys Gly His Gly Cys Arg Ile Glu
485 490 495Thr Ile Leu Asn Ala Pro Phe Ile Gln Ala Ser Phe Leu Pro
Trp Arg 500 505 510Gly Ser Asn Glu Ala Arg Arg Asp Leu Leu Arg Tyr
Asn Asn Met Val 515 520 525Ala Met Leu Leu Leu Ser Arg Asp Thr Thr
Ser Gly Ser Val Ser Ala 530 535 540His Pro Thr Lys Pro Glu Ala Leu
Val Val Glu Tyr Asp Val Asn Lys545 550 555 560Phe Asp Arg Asn Ser
Ile Leu Gln Ala Leu Leu Val Thr Ala Asp Leu 565 570
575Leu Tyr Ile Gln Gly Ala Lys Arg Ile Leu Ser Pro Gln Ala Trp Val
580 585 590Pro Ile Phe Glu Ser Asp Lys Pro Lys Asp Lys Arg Ser Ile
Lys Asp 595 600 605Glu Asp Tyr Val Glu Trp Arg Ala Lys Val Ala Lys
Ile Pro Phe Asp 610 615 620Thr Tyr Gly Ser Pro Tyr Gly Ser Ala His
Gln Met Ser Ser Cys Arg625 630 635 640Met Ser Gly Lys Gly Pro Lys
Tyr Gly Ala Val Asp Thr Asp Gly Arg 645 650 655Leu Phe Glu Cys Ser
Asn Val Tyr Val Ala Asp Ala Ser Leu Leu Pro 660 665 670Thr Ala Ser
Gly Ala Asn Pro Met Val Thr Thr Met Thr Leu Ala Arg 675 680 685His
Val Ala Leu Gly Leu Ala Asp Ser Leu Lys Thr Lys Ala Lys Leu 690 695
70011704PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 11Met Asn Thr Phe Leu Pro Asp Val Leu Glu Tyr
Lys His Val Asp Thr1 5 10 15Leu Leu Leu Leu Cys Asp Gly Ile Ile His
Glu Thr Thr Val Asp Gln 20 25 30Ile Lys Asp Ala Ile Ala Pro Asp Phe
Pro Glu Asp Gln Tyr Glu Glu 35 40 45Tyr Leu Lys Thr Phe Thr Lys Pro
Ser Glu Thr Pro Gly Phe Arg Glu 50 55 60Ala Val Tyr Asp Thr Ile Asn
Ala Thr Pro Thr Asp Ala Val His Met65 70 75 80Cys Ile Val Leu Thr
Thr Ala Leu Asp Ser Arg Ile Leu Ala Pro Thr 85 90 95Leu Thr Asn Ser
Leu Thr Pro Ile Lys Asp Met Thr Leu Lys Glu Arg 100 105 110Glu Gln
Leu Leu Ala Ser Trp Arg Asp Ser Pro Ile Ala Ala Lys Arg 115 120
125Arg Leu Phe Arg Leu Ile Ser Ser Leu Thr Leu Thr Thr Phe Thr Arg
130 135 140Leu Ala Ser Glu Leu His Leu Lys Ala Ile His Tyr Pro Gly
Arg Asp145 150 155 160Leu Arg Glu Lys Ala Tyr Glu Thr Gln Val Val
Asp Pro Phe Arg Tyr 165 170 175Ser Phe Met Glu Lys Pro Lys Phe Asp
Gly Ala Glu Leu Tyr Leu Pro 180 185 190Asp Ile Asp Val Ile Ile Ile
Gly Ser Gly Ala Gly Ala Gly Val Met 195 200 205Ala His Thr Leu Ala
Asn Asp Gly Phe Lys Thr Leu Val Leu Glu Lys 210 215 220Gly Lys Tyr
Phe Ser Asn Ser Glu Leu Asn Phe Asn Asp Ala Asp Gly225 230 235
240Val Lys Glu Leu Tyr Gln Gly Lys Gly Ala Leu Ala Thr Thr Asn Gln
245 250 255Gln Met Phe Ile Leu Ala Gly Ser Thr Leu Gly Gly Gly Thr
Thr Val 260 265 270Asn Trp Ser Ala Cys Leu Lys Thr Pro Phe Lys Val
Arg Lys Glu Trp 275 280 285Tyr Asp Glu Phe Gly Leu Glu Phe Ala Ala
Asp Glu Ala Tyr Asp Lys 290 295 300Ala Gln Asp Tyr Val Trp Lys Gln
Met Gly Ala Ser Thr Asp Gly Ile305 310 315 320Thr His Ser Leu Ala
Asn Glu Val Val Val Glu Gly Gly Lys Lys Leu 325 330 335Gly Tyr Lys
Ser Lys Glu Ile Glu Gln Asn Asn Gly Gly His Pro Asp 340 345 350His
Pro Cys Gly Phe Cys Tyr Leu Gly Cys Lys Tyr Gly Ile Lys Gln 355 360
365Gly Ser Val Asn Asn Trp Phe Arg Asp Ala Ala Ala His Gly Ser Lys
370 375 380Phe Met Gln Gln Val Arg Val Val Gln Ile Leu Asn Lys Asn
Gly Val385 390 395 400Ala Tyr Gly Ile Leu Cys Glu Asp Val Glu Thr
Gly Val Arg Phe Thr 405 410 415Ile Ser Gly Pro Lys Lys Phe Val Val
Ser Ala Gly Ser Leu Asn Thr 420 425 430Pro Thr Val Leu Thr Asn Ser
Gly Phe Lys Asn Lys His Ile Gly Lys 435 440 445Asn Leu Thr Leu His
Pro Val Ser Thr Val Phe Gly Asp Phe Gly Arg 450 455 460Asp Val Gln
Ala Asp His Phe His Lys Ser Ile Met Thr Ser Leu Cys465 470 475
480Tyr Glu Val Ala Asp Leu Asp Gly Lys Gly His Gly Cys Arg Ile Glu
485 490 495Thr Ile Leu Asn Ala Pro Phe Ile Gln Ala Ser Leu Leu Pro
Trp Arg 500 505 510Gly Ser Asp Glu Val Arg Arg Asp Leu Leu Arg Tyr
Asn Asn Met Val 515 520 525Ala Met Leu Leu Ile Thr Arg Asp Thr Thr
Ser Gly Ser Val Ser Ala 530 535 540Asp Pro Lys Lys Pro Asp Ala Leu
Ile Val Asp Tyr Glu Ile Asn Lys545 550 555 560Phe Asp Lys Asn Ala
Ile Leu Gln Ala Phe Leu Ile Thr Ser Asp Met 565 570 575Leu Tyr Ile
Glu Gly Ala Lys Arg Ile Leu Ser Pro Gln Pro Trp Val 580 585 590Pro
Ile Phe Glu Ser Asn Lys Pro Lys Glu Gln Arg Thr Ile Lys Asp 595 600
605Lys Asp Tyr Val Glu Trp Arg Ala Lys Ala Ala Lys Ile Pro Phe Asp
610 615 620Thr Tyr Gly Ser Ala Tyr Gly Ser Ala His Gln Met Ser Thr
Cys Arg625 630 635 640Met Ser Gly Lys Gly Pro Lys Tyr Gly Ala Val
Asp Thr Asp Gly Arg 645 650 655Leu Phe Glu Cys Ser Asn Val Tyr Val
Ala Asp Ala Ser Val Leu Pro 660 665 670Thr Ala Ser Gly Ala Asn Pro
Met Ile Ser Thr Met Thr Phe Ala Arg 675 680 685Gln Ile Ala Leu Gly
Leu Ala Asp Ser Leu Lys Thr Lys Pro Lys Leu 690 695
70012704PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 12Met Asn Thr Phe Leu Pro Asp Val Leu Glu Tyr
Lys His Val Asp Thr1 5 10 15Leu Leu Leu Leu Cys Asp Gly Ile Ile His
Glu Thr Thr Val Asp Gln 20 25 30 Ile Arg Asp Ala Ile Ala Pro Asp
Phe Pro Glu Asp Gln Tyr Glu Glu 35 40 45Tyr Leu Lys Thr Phe Thr Lys
Pro Ser Glu Thr Pro Gly Phe Arg Glu 50 55 60Ala Val Tyr Asp Thr Ile
Asn Ser Thr Pro Thr Glu Ala Val His Met65 70 75 80Cys Ile Val Leu
Thr Thr Ala Leu Asp Ser Arg Ile Leu Ala Pro Thr 85 90 95Leu Thr Asn
Ser Leu Thr Pro Ile Lys Asp Met Thr Leu Lys Glu Arg 100 105 110Glu
Gln Leu Leu Ala Ala Trp Arg Asp Ser Pro Ile Ala Ala Lys Arg 115 120
125Arg Leu Phe Arg Leu Ile Ser Ser Leu Thr Leu Thr Thr Phe Thr Arg
130 135 140Leu Ala Ser Asp Leu His Leu Arg Ala Ile His Tyr Pro Gly
Arg Asp145 150 155 160Leu Arg Glu Lys Ala Tyr Glu Thr Gln Val Val
Asp Pro Phe Arg Tyr 165 170 175Ser Phe Met Glu Lys Pro Lys Phe Asp
Gly Thr Glu Leu Tyr Leu Pro 180 185 190Asp Ile Asp Val Ile Ile Ile
Gly Ser Gly Ala Gly Ala Gly Val Met 195 200 205Ala His Thr Leu Ala
Asn Asp Gly Tyr Lys Thr Leu Val Leu Glu Lys 210 215 220Gly Lys Tyr
Phe Ser Asn Ser Glu Leu Asn Phe Asn Asp Ala Asp Gly225 230 235
240Met Lys Glu Leu Tyr Gln Gly Lys Cys Ala Leu Thr Thr Thr Asn Gln
245 250 255Gln Met Phe Ile Leu Ala Gly Ser Thr Leu Gly Gly Gly Thr
Thr Val 260 265 270Asn Trp Ser Ala Cys Leu Lys Thr Pro Phe Lys Val
Arg Lys Glu Trp 275 280 285Tyr Asp Glu Phe Gly Leu Glu Phe Ala Ala
Asp Glu Ala Tyr Asp Lys 290 295 300Ala Gln Asp Tyr Val Trp Lys Gln
Met Gly Ala Ser Thr Glu Gly Ile305 310 315 320Thr His Ser Leu Ala
Asn Ala Val Val Val Glu Gly Gly Lys Lys Leu 325 330 335Gly Tyr Lys
Ser Lys Glu Ile Glu Gln Asn Asn Gly Gly His Pro Asp 340 345 350His
Pro Cys Gly Phe Cys Tyr Leu Gly Cys Lys Tyr Gly Ile Lys Gln 355 360
365Gly Ser Val Asn Asn Trp Phe Arg Asp Ala Ala Ala His Gly Ser Lys
370 375 380Phe Met Gln Gln Val Arg Val Val Gln Ile Leu His Asn Lys
Gly Val385 390 395 400Ala Tyr Gly Ile Leu Cys Glu Asp Val Glu Thr
Gly Val Lys Phe Thr 405 410 415Ile Ser Gly Pro Lys Lys Phe Val Val
Ser Ala Gly Ser Leu Asn Thr 420 425 430Pro Thr Val Leu Thr Asn Ser
Gly Phe Lys Asn Lys His Ile Gly Lys 435 440 445Asn Leu Thr Leu His
Pro Val Ser Thr Val Phe Gly Asp Phe Gly Arg 450 455 460Asp Val Gln
Ala Asp His Phe His Lys Ser Ile Met Thr Ser Leu Cys465 470 475
480Tyr Glu Val Ala Asp Leu Asp Gly Lys Gly His Gly Cys Arg Ile Glu
485 490 495Thr Ile Leu Asn Ala Pro Phe Ile Gln Ala Ser Leu Leu Pro
Trp Arg 500 505 510Gly Ser Asp Glu Val Arg Arg Asp Leu Leu Arg Tyr
Asn Asn Met Val 515 520 525Ala Met Leu Leu Ile Thr Arg Asp Thr Thr
Ser Gly Ser Val Ser Ala 530 535 540Asp Pro Lys Lys Pro Asp Ala Leu
Ile Val Asp Tyr Asp Ile Asn Lys545 550 555 560Phe Asp Lys Asn Ala
Ile Leu Gln Ala Phe Leu Ile Thr Ser Asp Met 565 570 575Leu Tyr Ile
Glu Gly Ala Lys Arg Ile Leu Ser Pro Gln Ala Trp Val 580 585 590Pro
Ile Phe Glu Ser Asn Lys Pro Lys Glu Gln Arg Thr Ile Lys Asp 595 600
605Lys Asp Tyr Val Glu Trp Arg Ala Lys Ala Ala Lys Ile Pro Phe Asp
610 615 620Thr Tyr Gly Ser Ala Tyr Gly Ser Ala His Gln Met Ser Thr
Cys Arg625 630 635 640Met Ser Gly Lys Gly Pro Lys Tyr Gly Ala Val
Asp Thr Asp Gly Arg 645 650 655Leu Phe Glu Cys Ser Asn Val Tyr Val
Ala Asp Ala Ser Val Leu Pro 660 665 670Thr Ala Ser Gly Ala Asn Pro
Met Ile Ser Thr Met Thr Phe Ala Arg 675 680 685Gln Ile Ala Leu Gly
Leu Ala Asp Ser Leu Lys Thr Lys Pro Lys Leu 690 695
700136PRTArtificial SequenceDescription of Artificial Sequence
Synthetic 6xHis tag 13His His His His His His1 514419PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
14Met Val Ala Ala Ala Ala Thr Ser Ala Phe Phe Pro Val Pro Ala Pro1
5 10 15Gly Thr Ser Pro Lys Pro Gly Lys Ser Gly Asn Trp Pro Ser Ser
Leu 20 25 30Ser Pro Thr Phe Lys Pro Lys Ser Ile Pro Asn Ala Gly Phe
Gln Val 35 40 45Lys Ala Asn Ala Ser Ala His Pro Lys Ala Asn Gly Ser
Ala Val Asn 50 55 60Leu Lys Ser Gly Ser Leu Asn Thr Gln Glu Asp Thr
Ser Ser Ser Pro65 70 75 80Pro Pro Arg Ala Phe Leu Asn Gln Leu Pro
Asp Trp Ser Met Leu Leu 85 90 95Thr Ala Ile Thr Thr Val Phe Val Ala
Ala Glu Lys Gln Trp Thr Met 100 105 110Leu Asp Arg Lys Ser Lys Arg
Pro Asp Met Leu Val Asp Ser Val Gly 115 120 125Leu Lys Ser Ile Val
Arg Asp Gly Leu Val Ser Arg Gln Ser Phe Leu 130 135 140Ile Arg Ser
Tyr Glu Ile Gly Ala Asp Arg Thr Ala Ser Ile Glu Thr145 150 155
160Leu Met Asn His Leu Gln Glu Thr Ser Ile Asn His Cys Lys Ser Leu
165 170 175Gly Leu Leu Asn Asp Gly Phe Gly Arg Thr Pro Gly Met Cys
Lys Asn 180 185 190Asp Leu Ile Trp Val Leu Thr Lys Met Gln Ile Met
Val Asn Arg Tyr 195 200 205Pro Thr Trp Gly Asp Thr Val Glu Ile Asn
Thr Trp Phe Ser Gln Ser 210 215 220Gly Lys Ile Gly Met Ala Ser Asp
Trp Leu Ile Ser Asp Cys Asn Thr225 230 235 240Gly Glu Ile Leu Ile
Arg Ala Thr Ser Val Trp Ala Met Met Asn Gln 245 250 255Lys Thr Arg
Arg Phe Ser Arg Leu Pro Tyr Glu Val Arg Gln Glu Leu 260 265 270Thr
Pro His Phe Val Asp Ser Pro His Val Ile Glu Asp Asn Asp Gln 275 280
285Lys Leu His Lys Phe Asp Val Lys Thr Gly Asp Ser Ile Arg Lys Gly
290 295 300Leu Thr Pro Arg Trp Asn Asp Leu Asp Val Asn Gln His Val
Ser Asn305 310 315 320Val Lys Tyr Ile Gly Trp Ile Leu Glu Ser Met
Pro Ile Glu Val Leu 325 330 335Glu Thr Gln Glu Leu Cys Ser Leu Thr
Val Glu Tyr Arg Arg Glu Cys 340 345 350Gly Met Asp Ser Val Leu Glu
Ser Val Thr Ala Val Asp Pro Ser Glu 355 360 365Asn Gly Gly Arg Ser
Gln Tyr Lys His Leu Leu Arg Leu Glu Asp Gly 370 375 380Thr Asp Ile
Val Lys Ser Arg Thr Glu Trp Arg Pro Lys Asn Ala Gly385 390 395
400Thr Asn Gly Ala Ile Ser Thr Ser Thr Ala Lys Thr Ser Asn Gly Asn
405 410 415Ser Ala Ser 152109PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 15Met Ala Gln Ser Arg Gln
Leu Phe Leu Phe Gly Asp Gln Thr Ala Asp1 5 10 15Phe Val Pro Lys Leu
Arg Ser Leu Leu Ser Val Gln Asp Ser Pro Ile 20 25 30Leu Ala Ala Phe
Leu Asp Gln Ser His Tyr Val Val Arg Ala Gln Met 35 40 45Leu Gln Ser
Met Asn Thr Val Asp His Lys Leu Ala Arg Thr Ala Asp 50 55 60Leu Arg
Gln Met Val Gln Lys Tyr Val Asp Gly Lys Leu Thr Pro Ala65 70 75
80Phe Arg Thr Ala Leu Val Cys Leu Cys Gln Leu Gly Cys Phe Ile Arg
85 90 95Glu Tyr Glu Glu Ser Gly Asn Met Tyr Pro Gln Pro Ser Asp Ser
Tyr 100 105 110Val Leu Gly Phe Cys Met Gly Ser Leu Ala Ala Val Ala
Val Ser Cys 115 120 125Ser Arg Ser Leu Ser Glu Leu Leu Pro Ile Ala
Val Gln Thr Val Leu 130 135 140Ile Ala Phe Arg Leu Gly Leu Cys Ala
Leu Glu Met Arg Asp Arg Val145 150 155 160Asp Gly Cys Ser Asp Asp
Arg Gly Asp Pro Trp Ser Thr Ile Val Trp 165 170 175Gly Leu Asp Pro
Gln Gln Ala Arg Asp Gln Ile Glu Val Phe Cys Arg 180 185 190Thr Thr
Asn Val Pro Gln Thr Arg Arg Pro Trp Ile Ser Cys Ile Ser 195 200
205Lys Asn Ala Ile Thr Leu Ser Gly Ser Pro Ser Thr Leu Arg Ala Phe
210 215 220Cys Ala Met Pro Gln Met Ala Gln His Arg Thr Ala Pro Ile
Pro Ile225 230 235 240Cys Leu Pro Ala His Asn Gly Ala Leu Phe Thr
Gln Ala Asp Ile Thr 245 250 255Thr Ile Leu Asp Thr Thr Pro Thr Thr
Pro Trp Glu Gln Leu Pro Gly 260 265 270Gln Ile Pro Tyr Ile Ser His
Val Thr Gly Asn Val Val Gln Thr Ser 275 280 285Asn Tyr Arg Asp Leu
Ile Glu Val Ala Leu Ser Glu Thr Leu Leu Glu 290 295 300Gln Val Arg
Leu Asp Leu Val Glu Thr Gly Leu Pro Arg Leu Leu Gln305 310 315
320Ser Arg Gln Val Lys Ser Val Thr Ile Val Pro Phe Leu Thr Arg Met
325 330 335Asn Glu Thr Met Ser Asn Ile Leu Pro Asp Ser Phe Ile Ser
Thr Glu 340 345 350Thr Arg Thr Asp Thr Gly Arg Ala Ile Pro Ala Ser
Gly Arg Pro Gly 355 360 365Ala Gly Lys Cys Lys Leu Ala Ile Val Ser
Met Ser Gly Arg Phe Pro 370 375 380Glu Ser Pro Thr Thr Glu Ser Phe
Trp Asp Leu Leu Tyr Lys Gly Leu385 390 395 400Asp Val Cys Lys Glu
Val Pro Arg Arg Arg Trp Asp Ile Asn Thr His 405 410 415Val Asp Pro
Ser Gly Lys Ala Arg Asn Lys Gly Ala Thr Lys Trp Gly 420 425 430Cys
Trp Leu Asp Phe Ser Gly Asp Phe Asp Pro Arg Phe Phe Gly Ile 435 440
445Ser Pro Lys Glu Ala Pro Gln Met Asp Pro Ala Gln
Arg Met Ala Leu 450 455 460Met Ser Thr Tyr Glu Ala Met Glu Arg Ala
Gly Leu Val Pro Asp Thr465 470 475 480Thr Pro Ser Thr Gln Arg Asp
Arg Ile Gly Val Phe His Gly Val Thr 485 490 495Ser Asn Asp Trp Met
Glu Thr Asn Thr Ala Gln Asn Ile Asp Thr Tyr 500 505 510Phe Ile Thr
Gly Gly Asn Arg Gly Phe Ile Pro Gly Arg Ile Asn Phe 515 520 525Cys
Phe Glu Phe Ala Gly Pro Ser Tyr Thr Asn Asp Thr Ala Cys Ser 530 535
540Ser Ser Leu Ala Ala Ile His Leu Ala Cys Asn Ser Leu Trp Arg
Gly545 550 555 560Asp Cys Asp Thr Ala Val Ala Gly Gly Thr Asn Met
Ile Tyr Thr Pro 565 570 575Asp Gly His Thr Gly Leu Asp Lys Gly Phe
Phe Leu Ser Arg Thr Gly 580 585 590Asn Cys Lys Pro Tyr Asp Asp Lys
Ala Asp Gly Tyr Cys Arg Ala Glu 595 600 605Gly Val Gly Thr Val Phe
Ile Lys Arg Leu Glu Asp Ala Leu Ala Asp 610 615 620Asn Asp Pro Ile
Leu Gly Val Ile Leu Asp Ala Lys Thr Asn His Ser625 630 635 640Ala
Met Ser Glu Ser Met Thr Arg Pro His Val Gly Ala Gln Ile Asp 645 650
655Asn Met Thr Ala Ala Leu Asn Thr Thr Gly Leu His Pro Asn Asp Phe
660 665 670Ser Tyr Ile Glu Met His Gly Thr Gly Thr Gln Val Gly Asp
Ala Val 675 680 685Glu Met Glu Ser Val Leu Ser Val Phe Ala Pro Ser
Glu Thr Ala Arg 690 695 700Lys Ala Asp Gln Pro Leu Phe Val Gly Ser
Ala Lys Ala Asn Val Gly705 710 715 720His Gly Glu Gly Val Ser Gly
Val Thr Ser Leu Ile Lys Val Leu Met 725 730 735Met Met Gln His Asp
Thr Ile Pro Pro His Cys Gly Ile Lys Pro Gly 740 745 750Ser Lys Ile
Asn Arg Asn Phe Pro Asp Leu Gly Ala Arg Asn Val His 755 760 765Ile
Ala Phe Glu Pro Lys Pro Trp Pro Arg Thr His Thr Pro Arg Arg 770 775
780Val Leu Ile Asn Asn Phe Ser Ala Ala Gly Gly Asn Thr Ala Leu
Ile785 790 795 800Val Glu Asp Ala Pro Glu Arg His Trp Pro Thr Glu
Lys Asp Pro Arg 805 810 815Ser Ser His Ile Val Ala Leu Ser Ala His
Val Gly Ala Ser Met Lys 820 825 830Thr Asn Leu Glu Arg Leu His Gln
Tyr Leu Leu Lys Asn Pro His Thr 835 840 845Asp Leu Ala Gln Leu Ser
Tyr Thr Thr Thr Ala Arg Arg Trp His Tyr 850 855 860Leu His Arg Val
Ser Val Thr Gly Ala Ser Val Glu Glu Val Thr Arg865 870 875 880Lys
Leu Glu Met Ala Ile Gln Asn Gly Asp Gly Val Ser Arg Pro Lys 885 890
895Ser Lys Pro Lys Ile Leu Phe Ala Phe Thr Gly Gln Gly Ser Gln Tyr
900 905 910Ala Thr Met Gly Lys Gln Val Tyr Asp Ala Tyr Pro Ser Phe
Arg Glu 915 920 925Asp Leu Glu Lys Phe Asp Arg Leu Ala Gln Ser His
Gly Phe Pro Ser 930 935 940Phe Leu His Val Cys Thr Ser Pro Lys Gly
Asp Val Glu Glu Met Ala945 950 955 960Pro Val Val Val Gln Leu Ala
Ile Thr Cys Leu Gln Met Ala Leu Thr 965 970 975Asn Leu Met Thr Ser
Phe Gly Ile Arg Pro Asp Val Thr Val Gly His 980 985 990Ser Leu Gly
Glu Phe Ala Ala Leu Tyr Ala Ala Gly Val Leu Ser Ala 995 1000
1005Ser Asp Val Val Tyr Leu Val Gly Gln Arg Ala Glu Leu Leu Gln
1010 1015 1020Glu Arg Cys Gln Arg Gly Thr His Ala Met Leu Ala Val
Lys Ala 1025 1030 1035Thr Pro Glu Ala Leu Ser Gln Trp Ile Gln Asp
His Asp Cys Glu 1040 1045 1050Val Ala Cys Ile Asn Gly Pro Glu Asp
Thr Val Leu Ser Gly Thr 1055 1060 1065Thr Lys Asn Val Ala Glu Val
Gln Arg Ala Met Thr Asp Asn Gly 1070 1075 1080Ile Lys Cys Thr Leu
Leu Lys Leu Pro Phe Ala Phe His Ser Ala 1085 1090 1095Gln Val Gln
Pro Ile Leu Asp Asp Phe Glu Ala Leu Ala Gln Gly 1100 1105 1110Ala
Thr Phe Ala Lys Pro Gln Leu Leu Ile Leu Ser Pro Leu Leu 1115 1120
1125Arg Thr Glu Ile His Glu Gln Gly Val Val Thr Pro Ser Tyr Val
1130 1135 1140Ala Gln His Cys Arg His Thr Val Asp Met Ala Gln Ala
Leu Arg 1145 1150 1155Ser Ala Arg Glu Lys Gly Leu Ile Asp Asp Lys
Thr Leu Val Ile 1160 1165 1170Glu Leu Gly Pro Lys Pro Leu Ile Ser
Gly Met Val Lys Met Thr 1175 1180 1185Leu Gly Asp Lys Ile Ser Thr
Leu Pro Thr Leu Ala Pro Asn Lys 1190 1195 1200Ala Ile Trp Pro Ser
Leu Gln Lys Ile Leu Thr Ser Val Tyr Thr 1205 1210 1215Gly Gly Trp
Asp Ile Asn Trp Lys Lys Tyr His Ala Pro Phe Ala 1220 1225 1230Ser
Ser Gln Lys Val Val Asp Leu Pro Ser Tyr Gly Trp Asp Leu 1235 1240
1245Lys Asp Tyr Tyr Ile Pro Tyr Gln Gly Asp Trp Cys Leu His Arg
1250 1255 1260His Gln Gln Asp Cys Lys Cys Ala Ala Pro Gly His Glu
Ile Lys 1265 1270 1275Thr Ala Asp Tyr Gln Val Pro Pro Glu Ser Thr
Pro His Arg Pro 1280 1285 1290Ser Lys Leu Asp Pro Ser Lys Glu Ala
Phe Pro Glu Ile Lys Thr 1295 1300 1305Thr Thr Thr Leu His Arg Val
Val Glu Glu Thr Thr Lys Pro Leu 1310 1315 1320Gly Ala Thr Leu Val
Val Glu Thr Asp Ile Ser Arg Lys Asp Val 1325 1330 1335Asn Gly Leu
Ala Arg Gly His Leu Val Asp Gly Ile Pro Leu Cys 1340 1345 1350Thr
Pro Ser Phe Tyr Ala Asp Ile Ala Met Gln Val Gly Gln Tyr 1355 1360
1365Ser Met Gln Arg Leu Arg Ala Gly His Pro Gly Ala Gly Ala Ile
1370 1375 1380Asp Gly Leu Val Asp Val Ser Asp Met Val Val Asp Lys
Ala Leu 1385 1390 1395Val Pro His Gly Lys Gly Pro Gln Leu Leu Arg
Thr Thr Leu Thr 1400 1405 1410Met Glu Trp Pro Pro Lys Ala Ala Ala
Thr Thr Arg Ser Ala Lys 1415 1420 1425Val Lys Phe Ala Thr Tyr Phe
Ala Asp Gly Lys Leu Asp Thr Glu 1430 1435 1440His Ala Ser Cys Thr
Val Arg Phe Thr Ser Asp Ala Gln Leu Lys 1445 1450 1455Ser Leu Arg
Arg Ser Val Ser Glu Tyr Lys Thr His Ile Arg Gln 1460 1465 1470Leu
His Asp Gly His Ala Lys Gly Gln Phe Met Arg Tyr Asn Arg 1475 1480
1485Lys Thr Gly Tyr Lys Leu Met Ser Ser Met Ala Arg Phe Asn Pro
1490 1495 1500Asp Tyr Met Leu Leu Asp Tyr Leu Val Leu Asn Glu Ala
Glu Asn 1505 1510 1515Glu Ala Ala Ser Gly Val Asp Phe Ser Leu Gly
Ser Ser Glu Gly 1520 1525 1530Thr Phe Ala Ala His Pro Ala His Val
Asp Ala Ile Thr Gln Val 1535 1540 1545Ala Gly Phe Ala Met Asn Ala
Asn Asp Asn Val Asp Ile Glu Lys 1550 1555 1560Gln Val Tyr Val Asn
His Gly Trp Asp Ser Phe Gln Ile Tyr Gln 1565 1570 1575Pro Leu Asp
Asn Ser Lys Ser Tyr Gln Val Tyr Thr Lys Met Gly 1580 1585 1590Gln
Ala Lys Glu Asn Asp Leu Val His Gly Asp Val Val Val Leu 1595 1600
1605Asp Gly Glu Gln Ile Val Ala Phe Phe Arg Gly Leu Thr Leu Arg
1610 1615 1620Ser Val Pro Arg Gly Ala Leu Arg Val Val Leu Gln Thr
Thr Val 1625 1630 1635Lys Lys Ala Asp Arg Gln Leu Gly Phe Lys Thr
Met Pro Ser Pro 1640 1645 1650Pro Pro Pro Thr Thr Thr Met Pro Ile
Ser Pro Tyr Lys Pro Ala 1655 1660 1665Asn Thr Gln Val Ser Ser Gln
Ala Ile Pro Ala Glu Ala Thr His 1670 1675 1680Ser His Thr Pro Pro
Gln Pro Lys His Ser Pro Val Pro Glu Thr 1685 1690 1695Ala Gly Ser
Ala Pro Ala Ala Lys Gly Val Gly Val Ser Asn Glu 1700 1705 1710 Lys
Leu Asp Ala Val Met Arg Val Val Ser Glu Glu Ser Gly Ile 1715 1720
1725Ala Leu Glu Glu Leu Thr Asp Asp Ser Asn Phe Ala Asp Met Gly
1730 1735 1740Ile Asp Ser Leu Ser Ser Met Val Ile Gly Ser Arg Phe
Arg Glu 1745 1750 1755Asp Leu Gly Leu Asp Leu Gly Pro Glu Phe Ser
Leu Phe Ile Asp 1760 1765 1770Cys Thr Thr Val Arg Ala Leu Lys Asp
Phe Met Leu Gly Ser Gly 1775 1780 1785Asp Ala Gly Ser Gly Ser Asn
Val Glu Asp Pro Pro Pro Ser Ala 1790 1795 1800Thr Pro Gly Ile Asn
Pro Glu Thr Asp Trp Ser Ser Ser Ala Ser 1805 1810 1815Asp Ser Ile
Phe Ala Ser Glu Asp His Gly His Ser Ser Glu Ser 1820 1825 1830Gly
Ala Asp Thr Gly Ser Pro Pro Ala Leu Asp Leu Lys Pro Tyr 1835 1840
1845Cys Arg Pro Ser Thr Ser Val Val Leu Gln Gly Leu Pro Met Val
1850 1855 1860Ala Arg Lys Thr Leu Phe Met Leu Pro Asp Gly Gly Gly
Ser Ala 1865 1870 1875Phe Ser Tyr Ala Ser Leu Pro Arg Leu Lys Ser
Asp Thr Ala Val 1880 1885 1890Val Gly Leu Asn Cys Pro Tyr Ala Arg
Asp Pro Glu Asn Met Asn 1895 1900 1905Cys Thr His Gly Ala Met Ile
Glu Ser Phe Cys Asn Glu Ile Arg 1910 1915 1920Arg Arg Gln Pro Arg
Gly Pro Tyr His Leu Gly Gly Trp Ser Ser 1925 1930 1935Gly Gly Ala
Phe Ala Tyr Val Val Ala Glu Ala Leu Val Asn Gln 1940 1945 1950Gly
Glu Glu Val His Ser Leu Ile Ile Ile Asp Ala Pro Ile Pro 1955 1960
1965Gln Ala Met Glu Gln Leu Pro Arg Ala Phe Tyr Glu His Cys Asn
1970 1975 1980Ser Ile Gly Leu Phe Ala Thr Gln Pro Gly Ala Ser Pro
Asp Gly 1985 1990 1995Ser Thr Glu Pro Pro Ser Tyr Leu Ile Pro His
Phe Thr Ala Val 2000 2005 2010Val Asp Val Met Leu Asp Tyr Lys Leu
Ala Pro Leu His Ala Arg 2015 2020 2025Arg Met Pro Lys Val Gly Ile
Val Trp Ala Ala Asp Thr Val Met 2030 2035 2040Asp Glu Arg Asp Ala
Pro Lys Met Lys Gly Met His Phe Met Ile 2045 2050 2055Gln Lys Arg
Thr Glu Phe Gly Pro Asp Gly Trp Asp Thr Ile Met 2060 2065 2070Pro
Gly Ala Ser Phe Asp Ile Val Arg Ala Asp Gly Ala Asn His 2075 2080
2085Phe Thr Leu Met Gln Lys Glu His Val Ser Ile Ile Ser Asp Leu
2090 2095 2100Ile Asp Arg Val Met Ala 2105169PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 16Asp
Tyr Lys Asp Asp Asp Asp Lys Gly1 51714PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 17Gly
Lys Pro Ile Pro Asn Pro Leu Leu Gly Leu Asp Ser Thr1 5
101810PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 18Glu Gln Lys Leu Ile Ser Glu Glu Asp Leu1 5
101911PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 19Gln Pro Glu Leu Ala Pro Glu Asp Pro Glu Asp1 5
10209PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 20Tyr Pro Tyr Asp Val Pro Asp Tyr Ala1
52111PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 21Tyr Thr Asp Ile Glu Met Asn Arg Leu Gly Lys1 5
10227PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 22Cys Cys Xaa Xaa Xaa Cys Cys1 5236PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 23Cys
Cys Pro Gly Cys Cys1 5246PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 24Leu Val Pro Arg Gly Ser1
5255PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 25Asp Asp Asp Asp Lys1 5267PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 26Glu
Asn Leu Tyr Phe Gln Gly1 5278PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 27Leu Glu Val Leu Phe Gln Gly
Pro1 52843DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 28atggtcatcc aagggaagag attggccgcc tcctctattc agc
432929DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 29gtaggcgtca caggaaagac tgcgtacca
293031DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 30tatcaccaat gctggatgta aagaagtcgc g
313125DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 31aattgggcta ggaaaccggg gatgc 253243DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
32cggtctaatg acggcgcatg atatcatagc cgaaacggtc gag
433327DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 33acttggctgg agtccatccc ttcggca
273442DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 34ctgcccgagt ttgaagtatc tcaacttacc gccgacgcca tg
423520DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 35tgagacgcgc tgcgcagggc 203623DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
36cgaggtgatc gagacgcaga tgc 233728DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 37ttatgaagca ccagacatca
gccccagc 283833DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 38atgggttccg ttagtaggga acatgagtca atc
333934DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 39gttccttgtg tgagctcctg aataagactg catg
344041DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 40ccatcaaaat ccccctctat cacacgggca ctgggagcaa c
414127DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 41cccacgcctt gcgcatctat aatcagg
274235DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 42tgtccgaata ttctcctcgt tgtaggtagt ggatt
354343DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 43gcagtagtcg ataggtacac atccttgggg gttccatgac tgc
434446DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 44agaggatcaa ggcattatac atgagtctgt ggaacttggg
ctttcc 464525DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 45ttccccgtcc tccatggcct tatgc
254636DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 46ggcctttgcg cgatacgctg gtctctcggg tcccat
364727DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 47tcacgccatt tgttgaagca gggaatg
27485016DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 48atggtcatcc aagggaagag attggccgcc
tcctctattc agcttctcgc aagctcgtta 60gacgcgaaga agctttgtta tgagtatgac
gagaggcaag ccccaggtgt aacccaaatc 120accgaggagg cgcctacaga
gcaaccgcct ctctctaccc ctccctcgct accccaaacg 180cccaatattt
cgcctataag tgcttcaaag atcgtgatcg acgatgtggc gctatctcga
240gtgcaaattg ttcaggctct tgttgccaga aagttgaaga cggcaattgc
tcagcttcct 300acatcaaagt caatcaaaga gttgtcgggt ggtcggtctt
ctttgcagaa cgagctcgtg 360ggggatatac acaacgagtt cagctccatc
ccggatgcac cagagcagat cttgttgcgg 420gactttggcg acgccaaccc
aacagtgcaa ttggggaaaa cgtcctccgc ggcagttgcc 480aaactaatct
cgtccaagat gcctagtgac ttcaacgcca acgctattcg agcccaccta
540gcaaacaagt ggggtctagg acccttgcga caaacagcgg tgttgctcta
cgccattgcg 600tcagaacccc catcgcgttt agcttcatcg agcgcagcgg
aagagtactg ggacaacgtg 660tcatccatgt acgccgaatc
gtgtggcatc accctccgcc cgagacaaga cactatgaat 720gaagatgcta
tggcatcgtc ggcgattgat ccggctgtgg tagccgagtt ttccaagggg
780caccgtaggc tcggagttca acagttccaa gcgctagcag aatacttaca
aattgatttg 840tcggggtctc aagcctctca gtcggatgct ttggtggcgg
aacttcagca gaaagtcgat 900ctctggacgg ccgaaatgac ccccgagttt
ctcgccggga tatcaccaat gttggatgta 960aagaagtcgc gacgctatgg
ctcgtggtgg aacatggcac ggcaggatgt cttggccttc 1020tatcgccgtc
cttcctacag tgaattcgtg gacgacgcct tggccttcaa agtttttctc
1080aatcgtctct gtaaccgagc tgatgaggcc ctcctcaaca tggtacgcag
tctttcctgt 1140gacgcctact tcaagcaagg ttctttgccc ggatatcatg
ccgcctcgcg actccttgag 1200caggccatca catccacagt ggcggattgc
ccgaaggcac gcctcattct cccggcggtg 1260ggcccccaca ccaccattac
aaaggacggc acgattgaat acgcggaggc accgcgccag 1320ggagtgagtg
gtcccactgc gtacatccag tctctccgcc aaggcgcatc tttcattggt
1380ctcaagtcag ccgacgtcga tactcagagc aacttgaccg acgctttgct
tgacgccatg 1440tgcttagcac tccataatgg aatctcgttt gttggtaaaa
cctttttggt gacgggagcg 1500ggtcaggggt caataggagc gggagtggtg
cgtctattgt tagagggagg agcccgagta 1560ttggtgacga cgagcaggga
gccggcgacg acatccagat acttccagca gatgtacgat 1620aatcacggtg
cgaagttctc cgagttgcgg gtagttcctt gcaatctagc cagcgcccaa
1680gattgcgaag ggttgatccg gcacgtctac gatccccgtg ggctaaattg
ggatttggat 1740gccatccttc ccttcgctgc cgcgtccgac tacagcaccg
agatgcatga cattcgggga 1800cagagcgagt tgggccaccg gctaatgttg
gtcaatgtct tccgcgtgtt ggggcatatc 1860gtccactgta aacgagatgc
cggggttgac tgccatccga cgcaggtgtt gttgccattg 1920tcgccaaatc
acggcatctt cggtggcgat gggatgtatc cggagtcaaa gctagccctt
1980gagagcttgt tccatcgcat ccgatcagag tcttggtcag accagttatc
tatatgcggc 2040gttcgtatcg gttggacccg gtcgaccggt ctaatgacgg
cgcatgatat catagccgaa 2100acggtcgagg aacacggaat acgcacattt
tccgtggccg agatggcact caacatagcc 2160atgttgttaa cccccgactt
tgtggcccat tgtgaagatg gacctttgga tgccgatttc 2220accggcagct
tgggaacatt gggtagcatc cccggtttcc tagcccaatt gcaccagaaa
2280gtccagttgg cagccgaggt gatccgtgcc gtgcaggccg aggatgagca
tgagagattc 2340ttgtctccgg gaacaaaacc taccttgcaa gcacccgtgg
ccccaatgca cccccgcagt 2400agccttcgtg taggctatcc ccgtctcccc
gattatgagc aagagattcg cccgttgtcc 2460ccacggttgg aaaggttgca
agatccggcc aatgctgtgg tggtggtcgg gtactcggag 2520ttggggccat
ggggtagcgc gcgattacgg tgggaaatag agagccaggg ccagtggact
2580tcagccggtt atgtcgaact tgcctggttg atgaacctca tccgccacgt
caacgatgaa 2640tcctacgtcg gctgggtgga tactcagacc ggaaagccag
tgcgggatgg cgagatccag 2700gcattgtacg gggaccacat tgacaaccac
accggtatcc gtcctatcca gtccacctcg 2760tacaacccag agcgcatgga
ggtcttgcag gaggtcgctg tcgaggagga tttgcccgag 2820tttgaagtat
ctcaacttac cgccgacgcc atgcgtctcc gccatggagc taacgtttcc
2880atccgcccca gtggaaatcc cgacgcatgc cacgtgaagc ttaaacgagg
cgctgttatc 2940cttgttccca agacagttcc ctttgtttgg ggatcgtgtg
ccggtgagtt gccgaaggga 3000tggactccag ccaagtacgg catccctgag
aacctaattc atcaggtcga ccccgtcacg 3060ctctatacaa tttgctgcgt
ggcggaggca ttttacagtg ccggtataac tcaccctctt 3120gaggtctttc
gacacattca cctctcggaa ctaggcaact ttatcggatc ctccatgggt
3180gggccgacga agactcgtca gctctaccga gatgtctact tcgaccatga
gattccgtcg 3240gatgttttgc aagacactta tctcaacaca cctgctgcct
gggttaatat gctactcctt 3300ggctgcacgg ggccgatcaa aactcccgtc
ggcgcatgtg ccaccggggt cgagtcgatc 3360gattccggct acgagtcaat
catggcgggc aagacaaaga tgtgtcttgt gggtggctac 3420gacgatttgc
aggaggaggc atcgtatgga ttcgcacaac ttaaggccac ggtcaacgtt
3480gaagaggaga tcgcctgcgg tcgacagccc tcggagatgt cgcgccccat
ggctgagagt 3540cgtgctggct ttgtcgaggc gcatggctgc ggtgtacagt
tgttgtgtcg aggtgacatc 3600gccttgcaaa tgggtcttcc tatctatgcg
gtcattgcca gctcagccat ggccgccgac 3660aagatcggtt cctcggtgcc
agcaccgggc cagggcattc taagcttctc ccgtgagcgc 3720gctcgatcca
gtatgatatc cgtcacgtcg cgcccgagta gccgtagcag cacatcatct
3780gaagtctcgg acaaatcatc cttgacctca atcacctcaa tcagcaatcc
cgctcctcgt 3840gcacaacgcg cccgatccac cactgatatg gctccgttgc
gagcagcgct tgcgacttgg 3900gggttgacta tcgacgactt ggatgtggcc
tcattgcacg gcacctcgac gcgcggtaac 3960gatctcaatg agcccgaggt
gatcgagacg cagatgcgcc atttaggtcg cactcctggc 4020cgccccttgt
gggccatctg ccaaaagtca gtgacgggac accctaaagc cccagcggcc
4080gcatggatgc tcaatggatg cttgcaagta ttggactcgg ggttggtgcc
gggcaaccgc 4140aatcttgaca cgttggacga ggccttgcgc agcgcgtctc
atctctgctt ccctacgcgc 4200accgtgcagc tacgtgaggt caaggcattc
ttgttgacct catttggctt cggacagaag 4260gggggccaag tcgtcggcgt
tgcccccaag tacttctttg ctacgctccc ccgccccgag 4320gttgagggct
actatcgcaa ggtgagggtt cgaaccgagg cgggtgatcg cgcctacgcc
4380gcggcggtca tgtcgcaggc ggtggtgaag atccagacgc aaaacccgta
cgacgagccg 4440gatgcccccc gcatttttct cgatcccttg gcacgtatct
cccaggatcc gtcgacgggc 4500cagtatcggt ttcgttccga tgccactccc
gccctcgatg atgatgcttt gccacctccc 4560ggcgaaccca ccgagctagt
gaagggcatc tcctccgcct ggatcgagga gaaggtgcga 4620ccgcatatgt
ctcccggcgg cacggtgggc gtggacttgg ttcctctcgc ctccttcgac
4680gcatacaaga atgccatctt tgttgagcgc aattatacgg taagggagcg
cgattgggct 4740gaaaagagtg cggatgtgcg cgcggcctat gccagtcggt
ggtgtgcaaa agaggcggtg 4800ttcaaatgtc tccagacaca ttcacagggc
gcgggggcag ccatgaaaga gattgagatc 4860gagcatggag gtaacggcgc
accgaaagtc aagctccggg gtgctgcgca aacagcggcg 4920cggcaacgag
gattggaagg agtgcaattg agcatcagct atggcgacga tgcggtgata
4980gcggtggcgt tggggttgat gtctggtgct tcataa 5016495667DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
49atgggttccg ttagtaggga acatgagtca atccccatcc aggccgccca gagaggcgct
60gcccggatct gcgctgcttt tggaggtcaa gggtctaaca atttggacgt gttaaaaggt
120ctattggagt tatacaagcg gtatggccca gatttggatg agctactaga
cgtggcatcc 180aacacgcttt cgcagttggc atcttcccct gctgcaatag
acgtccacga accctggggt 240ttcgacctcc gacaatggtt gaccacaccg
gaggttgctc ctagcaaaga aattcttgcc 300ttgccaccac gaagctttcc
cttaaatacg ttacttagct tggcgctcta ttgtgcaact 360tgtcgagagc
ttgaacttga tcctgggcaa tttcgatccc tccttcatag ttccacgggg
420cattcccaag gcatattggc ggcggtggcc atcacccaag ccgagagctg
gccaaccttt 480tatgacgcct gcaggacggt gctccagatc tctttctgga
ttggactcga ggcttacctc 540ttcactccat cctccgccgc ctcggatgcc
atgatccaag attgcatcga acatggcgag 600ggccttcttt cctcaatgct
aagtgtctcc gggctctccc gctcccaagt tgagcgagta 660attgagcacg
tcaataaagg gctcggagaa tgcaaccgat gggttcactt ggccttggtt
720aactcccacg aaaagttcgt cttagcggga ccacctcaat ccttatgggc
cgtttgtctt 780catgtccgac ggatcagagc agacaatgac ctcgaccagt
cgcgtatctt gttccgcaac 840cgaaagccta tagtggatat attatttctt
cccatatccg caccatttca cacaccgtac 900ttggacggtg ttcaagatcg
cgttatcgag gctttgagct ctgcttcgtt ggctctccat 960tccatcaaaa
tccccctcta tcacacgggc actgggagca acctacaaga actacaacca
1020catcagctaa tcccgactct tatccgcgcc attaccgtgg accaattgga
ctggccgttg 1080gtttgccggg gcttgaacgc aacgcacgtg ttggactttg
gacctggaca aacatgcagt 1140cttattcagg agctcacaca aggaacaggt
gtatcagtga tccagttgac tactcaatcg 1200ggaccaaaac ccgttggagg
ccatttggcg gcagtgaact gggaggccga gtttggctta 1260cgacttcatg
ccaatgtcca cggtgcagct aaattgcaca accgtatgac aacattgctt
1320gggaagcctc ctgtgatggt agccggaatg acacctacta cggtgcgctg
ggactttgtc 1380gctgccgttg ctcaagctgg ataccacgtc gaattggctg
gtggtggcta ccacgcagag 1440cgccagttcg aggccgagat tcggcgcttg
gcaactgcca tcccagcaga tcatggcatc 1500acctgcaatc tcctctacgc
caagcctacg actttttcct ggcagatctc tgtcatcaag 1560gatttggtgc
gccagggagt tcccgtggaa ggaatcacca tcggcgccgg catcccttct
1620ccggaggtcg tccaagaatg tgtacagtcc atcggactca agcacatctc
attcaagcct 1680gggtctttcg aagccattca ccaagtcata cagatcgcgc
gtacccatcc taactttttg 1740atcgggttgc aatggaccgc aggacgaggg
ggaggacatc attcctggga agacttccat 1800ggacctattt tggcaaccta
cgctcaaatc cgatcatgtc cgaatattct cctcgttgta 1860ggtagtggat
tcggtggagg cccggacacg tttccctacc tcacgggcca atgggcccag
1920gcctttggct atccatgcat gcccttcgac ggagtgttgc tcggcagtcg
catgatggtg 1980gctcgggaag cccatacgtc agcccaggca aaacgcttga
ttatagatgc gcaaggcgtg 2040ggagatgcag attggcacaa gtctttcgat
gagcctaccg gcggcgtagt gacggtcaac 2100tcggaattcg gtcaacctat
ccacgttcta gctactcgcg gagtgatgtt gtggaaagaa 2160ctcgacaacc
gggtcttttc aatcaaagac acttctaagc gcttagaata tttgcgcaac
2220caccggcaag aaattgtgag ccgtcttaac gcagactttg cccgtccctg
gtttgccgtt 2280gacggacacg gacagaatgt ggagttggag gacatgacct
acctcgaggt tctccgccgt 2340ttgtgcgatc tcacgtatgt ttcccaccag
aagcgatggg tagatccatc atatcgaata 2400ttattgttgg acttcgttca
tttgcttcga gaacgattcc aatgcgctat tgacaacccc 2460ggcgaatatc
cactcgacat catcgtccgg gtggaagaga gcttgaagga taaagcatac
2520cgcacgcttt atccagaaga tgtctctctt ctaatgcatt tgttcagccg
acgtgacatc 2580aagcccgtac cattcatccc caggttggat gagcgttttg
agacctggtt taaaaaagac 2640tcattgtggc aatccgaaga tgtggaggcg
gtaattggac aggacgtcca gcgaatcttc 2700atcattcaag ggcctatggc
cgttcagtac tcaatatccg acgatgagtc tgttaaagac 2760attttacaca
atatttgtaa tcattacgtg gaggctctac aggctgattc aagagaaact
2820tctatcggcg atgtacactc gatcacgcaa aaacctctca gcgcgtttcc
tgggctcaaa 2880gtgacgacaa atagggtcca agggctctat aagttcgaga
aagtaggagc agtccccgaa 2940atggacgttc tttttgagca tattgtcgga
ttgtcgaagt catgggctcg gacatgtttg 3000atgagtaaat cggtctttag
ggacggttct cgtttgcata accccattcg cgccgcactc 3060cagctccagc
gcggcgacac catcgaggtg cttttaacag cagactcgga aattcgcaag
3120attcgactta tttcacccac gggggatggt ggatccactt ctaaggtcgt
attagagata 3180gtctctaacg acggacaaag agttttcgcc accttggccc
ctaacatccc actcagcccc 3240gagcccagcg tcgtcttttg cttcaaggtc
gaccagaagc cgaatgagtg gacccttgag 3300gaggatgcgt ctggccgggc
agagaggatc aaggcattat acatgagttt gtggaacttg 3360ggctttccga
acaaggcctc tgttttgggt cttaattcgc aattcacggg agaagaattg
3420atgatcacaa cggacaagat tcgtgatttc gaaagggtat tgcggcaaac
cagtcctctt 3480cagttgcagt catggaaccc ccaaggatgt gtacctatcg
actactgcgt ggtcatcgcc 3540tggtctgctc ttaccaagcc tttgatggtc
tcctctttga aatgcgacct cttggatttg 3600ctccacagcg ctataagctt
ccactatgct ccatctgtca aaccattgcg ggtgggcgat 3660attgtcaaaa
cctcatcccg tatcctagcg gtctcggtga gacctagggg aactatgttg
3720acggtgtcgg cggacattca gcgccaggga caacatgtag tcactgtcaa
atcagatttc 3780tttctcggag gccccgtttt ggcatgtgaa acccctttcg
aactcactga ggagcctgaa 3840atggttgtcc atgtcgactc tgaagtgcgc
cgtgctattt tacacagccg caagtggctc 3900atgcgagaag atcgcgcgct
agatttgcta gggaggcagc tcctcttcag attaaagagc 3960gaaaaattgt
tcaggccaga cggccagcta gcattgttac aggtaacagg ttccgtgttc
4020agctacagcc ccgatgggtc aacgacagca ttcggtcgcg tatacttcga
aagcgagtct 4080tgtacaggga acgtggtgat ggacttcttg caccgctacg
gtgcacctcg ggcgcagttg 4140ttggagttgc aacatcccgg gtggacgggc
acctctactg tggcagtaag aggtcctcga 4200cgcagccaat cctacgcacg
cgtctccctc gatcataatc ccatccatgt ttgtccggcc 4260tttgcgcgat
acgctggtct ctcgggtccc attgtccatg ggatggaaac ctctgccatg
4320atgcgcagaa ttgccgaatg ggccatcgga gatgcagacc ggtctcggtt
ccggagctgg 4380catatcacct tgcaagcacc cgtccacccc aacgaccctt
tgcgggtgga gttgcagcat 4440aaggccatgg aggacgggga aatggttttg
aaagtacaag catttaacga aaggacggaa 4500gaacgcgtag cggaggcaga
tgcccatgtt gagcaggaaa ctacggctta cgtcttctgt 4560ggccagggca
gtcaacgaca ggggatggga atggacttgt acgtcaactg tccggaggct
4620aaagcgttgt gggctcgcgc cgacaagcat ttgtgggaga aatatgggtt
ctccatcttg 4680cacattgtgc aaaacaaccc tccagccctc actgttcact
ttggcagcca gcgagggcgc 4740cgtattcgtg ccaactattt gcgcatgatg
ggacagccac cgatagatgg tagacatccg 4800cccatattga agggattgac
gcggaattcg acctcgtaca ccttctccta ttcccagggg 4860ttgttgatgt
ccacccagtt cgcccagccc gcattggcgt tgatggaaat ggctcagttc
4920gaatggctca aagcccaggg agtcgttcag aagggtgcgc ggttcgcggg
acattcgttg 4980ggagaatatg ccgcccttgg agcttgtgct tccttcctct
catttgaaga tctcatatct 5040ctcatctttt atcggggctt gaagatgcag
aatgcgttgc cgcgcgatgc caacggccac 5100accgactatg gaatgttggc
tgccgatcca tcgcggatag gaaaaggttt cgaggaagcg 5160agtttgaaat
gtcttgtcca tatcattcaa caggagaccg gctggttcgt ggaagtcgtc
5220aactacaaca tcaactcgca gcaatacgtc tgtgcaggcc atttccgagc
cctttggatg 5280ttgggtaaga tatgcgatga cctttcatgc caccctcaac
cggagactgt tgaaggccaa 5340gagctacggg ccatggtctg gaagcatgtc
ccgacggtgg agcaggtgcc ccgcgaggat 5400cgcatggaac gaggtcgagc
gaccattccg ttgccgggga tcgatatccc ataccattcg 5460accatgttac
gaggggagat tgagccttat cgtgaatatt tgtctgaacg tatcaaggtg
5520ggggatgtga agccgtgcga attggtggga cgctggatcc ctaatgttgt
tggccagcct 5580ttctccgtcg ataagtctta cgttcagttg gtgcacggca
tcacaggtag tcctcggctt 5640cattccttgc ttcaacaaat ggcgtga
56675012DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 50tcrnnnnnna cg
125117DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 51cggnnnnnnn nnnnccg
175213DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 52gaannttcnn gaa
135310DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 53tgatgtannt
105410DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 54ccnnnwwrgg
105510DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 55wwwwsygggg
105613DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 56rmacccannc ayy
135716DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 57tycgtnnrna rtgaya
165818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 58rrraararaa nanraraa
185918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 59anagngagag agnggcag
186015DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 60tnnccwnttt ktttc
156115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 61aaaaararaa aarma
156216DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 62ykytyttytt nnnnky
166310DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 63cgtccggcgc
106415DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 64gaaaaagmaa aaaaa
156518DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 65ttttyyttyt tkyntynt
186615DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 66catkyttttt tkyty
156710DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 67cacgtgacya
106814DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 68cannnacaca sana
146917DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 69ggnanannar narggcn
177018DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 70tttkytktty nytttkty
187117DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 71wttkttttty tttttnt
177211DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 72ttkttttytt c
117318DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 73aaannraang arraanar
187415DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 74gtgmaknmgr angng
157518DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 75nttwacaycc rtacayny
187618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 76tttnctttky ttnytttt
187718DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 77aaaranraaa naaarnaa
187817DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 78cacacacaca cacacac
177918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 79ttgcttgaac gsatgcca
188017DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 80yctttttttt yttyykg
178118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 81rrsccgmcgm grcgcgcs
188218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide
82aaanararnr aaaarrar 188318DNAArtificial SequenceDescription of
Artificial Sequence Synthetic binding motif oligonucleotide
83ggaagctgaa acgymwrr 188418DNAArtificial SequenceDescription of
Artificial Sequence Synthetic binding motif oligonucleotide
84ggagaggcat gatggggg 188510DNAArtificial SequenceDescription of
Artificial Sequence Synthetic binding motif oligonucleotide
85ctncctttct 108618DNAArtificial SequenceDescription of Artificial
Sequence Synthetic binding motif oligonucleotide 86gaaarraaaa
aamrmara 188711DNAArtificial SequenceDescription of Artificial
Sequence Synthetic binding motif oligonucleotide 87gngccrsnnt m
118818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 88ttttttyttt tynktttt
188918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 89yttcttttyt nyncnktn
189015DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 90tnsykctttt cytty
159118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 91sttnytttyn ttytyyyy
189211DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 92ykntttwyyt c
119315DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 93aaaananaar arnag
159418DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 94waaaaaagaa aanaaaar
189511DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 95aaanggnara m
119616DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 96tyttcyagaa nnttcy
169718DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 97cacacacaca cacacaca
189811DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 98tttycacatg c
119914DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 99gnngcatgtg aaaa
1410018DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 100gaaaanaaaa aaaarana
1810115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 101gaaaaaraar aanaa
1510218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 102yttktnnttt ttytyttt
1810310DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 103gcagngcagg
1010418DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 104tttytykttt nyyttttt
1810516DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 105tttccnaawn rggaaa
1610618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 106yttyyttytt ttytyttc
1810714DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 107mtttttytyt yttc
1410818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 108tatacanagm krtatatg
1810918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 109tmtttntync ttntttwk
1811016DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 110ktnnttwtta ttccnc
1611118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 111rnnaaaanra naaraaat
1811217DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 112ttttttttcw ctttkyc
1711318DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 113tttynytktt tynyttyt
1811418DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 114ttynnttytt nytttyyy
1811514DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 115tnygtgkryg tnyg
1411618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 116ttyyyttttt yttttytt
1811715DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 117gamaaaaaar aaaar
1511818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 118cycgggaagc sammnccg
1811913DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 119grtgyayggr tgy
1312014DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 120kmaaraaaaa raar
1412118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 121aygraaaara raaaaraa
1812218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 122ggaksccntt tyngmrta
1812317DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 123ttttcnkttt ytttttc
1712415DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 124araagmagaa arraa
1512517DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 125yttttctttt ynttttt
1712611DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 126arraraaagg n
1112718DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 127ystnykntyt tnctcccm
1812818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 128garanaaaar nraaraaa
1812911DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 129cynnggssan c
1113016DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 130cacacacaca cacaya
1613115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 131cttytwttkt tktsa
1513218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 132yttyyytytt tytyyttt
1813318DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 133amaaaaaraa rwaranaa
1813418DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 134araaaarraa aaagnraa
1813518DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 135raaraaaaar cmrsraaa
1813618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 136ttytktytyn tyykttty
1813718DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 137gaaaamaana aaaanaaa
1813818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 138yaanaraara aaaanaam
1813918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 139tyntttttty tttttntk
1814018DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 140raaraaraaa naanrnaa
1814118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 141cacacacaca cacacaca
1814218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 142raarrraaaa anaaamaa
1814311DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 143gccagaccta c
1114418DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 144ttyttyttyt ttynytyt
1814518DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 145yksgcgcgyc kcgkcggs
1814617DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 146ttttyytttt yyyyktt
1714713DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 147ttcttktyyt ttt
1314818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 148ttyttttyty ytttyttt
1814918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 149ttgcttgaac ggatgcca
1815016DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 150mgnmcaaaaa taaaas
1615116DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 151tycgtnnrna rtgaya
1615215DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 152gtgtgtgtgt gtgtg
1515317DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 153ytstysttnt tgytwtt
1715415DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 154gcatgaccat ccacg
1515517DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 155gsgayarmgg amaaaaa
1715618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 156trccgagryw nsssgcgs
1815710DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 157cgtccggcgc
1015818DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 158aarwtsgarg nanncsaa
1815914DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 159csnccaatgk nncs
1416010DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 160gctnactaat
1016110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 161cacgtgacya
1016211DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 162cayamrtgyn c
1116310DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 163tsgygrgasa
1016418DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 164kncncnnnsc gctackgc
1816515DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 165srnggcmcgg cnssg
1516615DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 166tacyacanca cawga
1516717DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 167ccytgnaytt cwncttc
1716815DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 168gtgmaknmgr angng
1516918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 169nttwacaycc rtacayny
1817013DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 170aawnrtaaay arg
1317116DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 171ggnaawangt aaacaa
1617215DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 172sastkcwctc ktcgt
1517318DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 173ttgcttgaac gsatgcca
1817417DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 174cggmnnncwn ynncccg
1717518DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 175rgargtsacg cakrttct
1817618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 176ggaagctgaa acgymwrr
1817718DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 177aggtgatgga gtgctcag
1817816DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif oligonucleotide 178gkctrrnrgg agangm
1617917DNAArtificial SequenceDescription of Artificial Sequence
Synthetic binding motif
oligonucleotide 179ngggsgntns ygtncga 1718018DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 180agnawgtttt tgwcaama 1818118DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 181kcksgcaggc wttkytct 1818211DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 182gnccsartng c 1118318DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 183sgcgmgggnn ccngaccg 1818414DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 184yctnattsgn cngs 1418518DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 185tnttsmttny tttccknc 1818615DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 186ccacktksgs cctns 1518711DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 187crsgcywgkg c 1118817DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 188naaraagcng ggcacnc 1718916DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 189tyttcyagaa nnttcy 1619018DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 190cacacacaca cacacaca 1819117DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 191sckkcgckst ssttyaa 1719214DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 192gnngcatgtg aaaa 1419315DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 193ctttttttyy tsgcc 1519415DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 194gccggtmmcg sycnn 1519515DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 195anntttttyt tkygc 1519617DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 196aaacntttat anataca 1719711DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 197caatntctnc k 1119815DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 198gnrrnanacg cgtnr 1519916DNAArtificial
SequenceDescription of Artificial Sequence Synthetic binding motif
oligonucleotide 199tttccnaawn rggaaa 1620043DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
200atggtcatcc aagggaagag attggccgcc tcctctattc agc
4320129DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 201gtaggcgtca caggaaagac tgcgtacca
2920231DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 202tatcaccaat gctggatgta aagaagtcgc g
3120325DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 203aattgggcta ggaaaccggg gatgc
2520443DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 204cggtctaatg acggcgcatg atatcatagc cgaaacggtc gag
4320527DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 205acttggctgg agtccatccc ttcggca
2720642DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 206ctgcccgagt ttgaagtatc tcaacttacc gccgacgcca tg
4220720DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 207tgagacgcgc tgcgcagggc 2020823DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
208cgaggtgatc gagacgcaga tgc 2320928DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
209ttatgaagca ccagacatca gccccagc 2821057DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
210gtactagtaa aaaaatggtc atccaaggga agagattggc cgcctcctct attcagc
5721139DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 211gtcccgggct attatgaagc accagacatc agccccagc
3921257DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 212tacccgggct attagtgatg gtggtgatgg tgtgaagcac
cagacatcag ccccagc 5721333DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 213atgggttccg ttagtaggga
acatgagtca atc 3321434DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 214gttccttgtg tgagctcctg
aataagactg catg 3421541DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 215ccatcaaaat ccccctctat
cacacgggca ctgggagcaa c 4121627DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 216cccacgcctt gcgcatctat
aatcagg 2721735DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 217tgtccgaata ttctcctcgt tgtaggtagt ggatt
3521843DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 218gcagtagtcg ataggtacac atccttgggg gttccatgac tgc
4321946DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 219agaggatcaa ggcattatac atgagtctgt ggaacttggg
ctttcc 4622025DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 220ttccccgtcc tccatggcct tatgc
2522136DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 221ggcctttgcg cgatacgctg gtctctcggg tcccat
3622227DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 222tcacgccatt tgttgaagca gggaatg
2722347DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 223gtactagtaa aaaaatgggt tccgttagta gggaacatga
gtcaatc 4722440DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 224gtgtttaaac ctatcacgcc atttgttgaa
gcagggaatg 4022559DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 225ggtttaaacc tatcagtgat ggtggtgatg
gtgcgccatt tgttgaagca gggaatgaa 5922633DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
226atgacccaaa agactataca gcaggtccca aga 3322728DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
227tatggtgcat cgaatgttgt ttgcctgg 2822827DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
228aaaatgcgtg agcactttgt ccagcgc 2722928DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
229cgacgtaatt gacgttgtca acatgccg 2823033DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
230catctcgggt tcccatcact ccctgagtat gac 3323141DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
231gacaaagaag ctggacaccg cagccttggg attccacgaa c
4123246DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 232gatctgcctt gtcggtggct atgacgacct tcagcctgag
gagtca 4623347DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 233ttaacggatg atagaggcca acggccaaag
acaccacttg cgtacac 4723451DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 234cacacaacta gtaaaaaaat
gacccaaaag actatacagc aggtcccaag a 5123559DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
235tgtgtgcccg ggttaacgga tgatagaggc caacggccaa agacaccact tgcgtacac
5923651DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 236tacccgggct attagtgatg gtggtgatgg tgacggatga
tagaggccaa c 5123729DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 237atgactccat caccgtttct cgatgctgt
2923850DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 238cacatgggta gcatcgttca ttgcccaaca caaagcgggc
cagttaactc 5023930DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 239gtcgagctaa gagtgactga tgccattggc
3024030DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 240cgtaattcag cttctgaacc tgagcccagg
3024121DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 241ctttgcccgg ccgtggttcg c 2124221DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
242cccccaagct cgacaacggg c 2124331DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 243ttctcaaaat gcaccggact
gattacttgg a 3124442DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 244cccattcctc tctcctgcgt gccctggccg
gtaaagacgt at 4224550DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 245ccctccttcg atggacttgt
ccgggcaaac gaccggttgc gaatggagat 5024631DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
246ctacctattc tcttcaaccc gccgtaacag c 3124747DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
247cacacaacta gtaaaaaaat gactccatca ccgtttctcg atgctgt
4724843DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 248tgtgtgcccg ggctacctat tctcttcaac ccgccgtaac agc
4324951DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 249tgtgtgcccg ggctatcagt gatggtggtg atggtgccta
ttctcttcaa c 5125037DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 250cacacagctc ttctagaatg gtcatccaag
ggaagag 3725128DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 251agtatcgacg tcggctgact tgagacca
2825221DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 252ccatcacatc cacagtggcg g 2125326DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
253aaccaggcaa gttcgacata accggc 2625428DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
254gtaggctatc cccgtctccc cgattatg 2825530DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
255tgattgaggt caaggatgat ttgtccgaga 3025629DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
256tcttcctatc tatgcggtca ttgccagct 2925739DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
257cacacagctc ttccttttta tgaagcacca gacatcaac 3925864DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
258cacacagctc ttccttttta gtgatggtgg tgatggtgtg aagcaccaga
catcaacccc 60aacg 6425937DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 259cacacagctc ttctagaatg
ggttccgtta gtaggga 3726030DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 260caaatccttg atgacagaga
tctgccagga 3026136DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 261gctgggactt tgtcgctgcc gttgctcaag
ctggat 3626235DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 262actgctccta ctttctcgaa cttatagagc ccttg
3526320DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 263atatccgacg atgagtctgt 2026420DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
264atggacaatg ggacccgaga 2026520DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 265ggacttcttg caccgctacg
2026640DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 266cacacagctc ttccttttca cgccatttgt tgaagcaaag
4026755DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 267cacacagctc ttccttttca gtgatggtgg tgatggtgcg
ccatttgttg aagca 5526825DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 268gattactgca gcagtattag tcttc
2526922DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 269gtcgaaaact tcatcggcaa ag 2227024DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
270cacgatatta tcgccacata cttc 2427125DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
271cgggacgatc gagatcgtgg atacg 2527224DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
272caggatatta tcgccacata catc 2427325DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
273ctggacgatt gagcgcttgg atacg 2527426DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
274cgtcttctcc atcgtttgcc caagag 2627524DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
275ggtccctgac aaagttaccg agtg 2427626DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
276cgtcttctcc atcgtttgct caggag 2627724DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
277gatccaacac gacgttaccg agcg 2427823DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
278ggtatgtcgt tgtgccagtg ttg 2327926DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
279cccacgcttg ggttcttgga gtggtc 2628023DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
280ggtatattgt tgtgcctgtg ttg 2328126DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
281ccgacgcttg ggttcttgga gctgtc 2628223DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
282ggaaggatga ggtggtgcag tac 2328324DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
283gtcttgtgac aagtttggaa actc 2428423DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
284gaaagaatga ggtggtgcaa tac 2328524DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
285gtcctgtgac aagctaggga attc 2428625DNAArtificial
SequenceDescription of
Artificial Sequence Synthetic primer 286ctatcgtggg atgtgatctg tgtcg
2528725DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 287ctcgaatctc ttgacactga actcg
2528825DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 288aacgacaaga ttagattggt tgaga
2528925DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 289gtcgagtttg aagtgtgtgt ctaag
2529051DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 290agatctcata tggctccatt tttgcccgac caggtcgact
acaaacacgt c 5129159DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 291atctggatcc tcattactac aacttggctt
tggtcttcaa ggagtctgcc aaacctaac 5929238DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
292acatctggat cctcattact acaacttggc cttggtct 3829347DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
293cacacagctc ttctagaatg gctccatttt tgcccgacca ggtcgac
4729450DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 294cacacagctc ttcctttcta caacttggct ttggtcttca
aggagtctgc 5029521DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 295gtctactgat tcccctttgt c
2129620DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 296ttctcgttgt acccgtcgca 2029732DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
297cacacacata tgcgacgggt acaacgagaa tt 3229832DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
298cacacaacgc gtagacgaag ccgttcttca ag 3229921DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
299atgatctgcc atgccgaact c 2130028DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 300agcgagttcg gcatggcaga
tcatcatg 2830132DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 301cacacactgc agttgtccaa tgtaataatt tt
3230256DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 302cacacatcta gacccgggct cttcttctga ataggcaatt
gataaactta cttatc 5630348DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 303gagcccgggt ctagatgtgt
gctcttccaa agtacggtgt tgttgaca 4830437DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
304cacacacata tgaattctgt actggtagag ctaaatt 3730524DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
305gagctccaat tgtaatattt cggg 2430625DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
306gtcgacctaa attcgcaact atcaa 2530753DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
307gaattcacat ggctaatttg gcctcggttc cacaacgcac tcagcattaa aaa
5330840DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 308gagctcccct gcaaacaggg aaacacttgt catctgattt
4030941DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 309cacctcgctc ttccagctgt catgtctatt caatgcttcg a
4131038DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 310cacacagcat gctaatgttt atatcgttga cggtgaaa
3831145DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 311cacaaagcgg aagagcaaat tttgtattct cagtaggatt
tcatc 4531238DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 312cacacagcat gcaaacttaa gggtgttgta
gatatccc 3831344DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 313cacacacccg ggatcgacag tcgattacgt
aatccatatt attt 4431438DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 314cacacagcat gcaaacttaa
gggtgttgta gatatccc 3831533DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 315cacacagagc tcacagtcga
ttacgtaatc cat 3331634DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 316cacatctaga gcatgcaaac
ttaagggtgt tgta 3431720DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 317ttaatgcctt ctcaagacaa
2031820DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 318ggttttccca gtcacgacgt 2031925DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
319ccttgctaat tttcttctgt atagc 2532020DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
320ttctcgttgt acccgtcgca 2032120DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 321cacacaactt cagagttgcc
2032220DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 322tcgccacctc tgacttgagc 2032320DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 323aattgaacat cagaagagga 2032425DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 324cctgaaattt ccaaatggtg tctaa 2532520DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 325ttttttgtgc gcaagtacac 2032620DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 326caacttgacg tgagaaacct 2032720DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 327agatgctcgt tttacaccct 2032820DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 328acacagcttt gatgttctct 20
* * * * *
References