U.S. patent application number 17/507587 was filed with the patent office on 2022-09-15 for organisms for the production of 1,3-butanediol.
The applicant listed for this patent is Genomatica, Inc.. Invention is credited to Anthony P. Burgard, Mark J. Burk, Robin E. Osterhout, Priti Pharkya.
Application Number | 20220290192 17/507587 |
Document ID | / |
Family ID | 1000006362474 |
Filed Date | 2022-09-15 |
United States Patent
Application |
20220290192 |
Kind Code |
A1 |
Burgard; Anthony P. ; et
al. |
September 15, 2022 |
ORGANISMS FOR THE PRODUCTION OF 1,3-BUTANEDIOL
Abstract
A non-naturally occurring microbial organism includes a
microbial organism having a 1,3-butanediol (1,3-BDO) pathway having
at least one exogenous nucleic acid encoding a 1,3-BDO pathway
enzyme expressed in a sufficient amount to produce 1,3-BDO. The
pathway includes an enzyme selected from a 2-amino-4-ketopentanoate
(AKP) thiolase, an AKP dehydrogenase, a 2-amino-4-hydroxypentanoate
aminotransferase, a 2-amino-4-hydroxypentanoate oxidoreductase
(deaminating), a 2-oxo-4-hydroxypentanoate decarboxylase, a
3-hydroxybutyraldehyde reductase, an AKP aminotransferase, an AKP
oxidoreductase (deaminating), a 2,4-dioxopentanoate decarboxylase,
a 3-oxobutyraldehyde reductase (ketone reducing), a
3-oxobutyraldehyde reductase (aldehyde reducing), a
4-hydroxy-2-butanone reductase, an AKP decarboxylase, a
4-aminobutan-2-one aminotransferase, a 4-aminobutan-2-one
oxidoreductase (deaminating), a 4-aminobutan-2-one ammonia-lyase, a
butenone hydratase, an AKP ammonia-lyase, an acetylacrylate
decarboxylase, an acetoacetyl-CoA reductase (CoA-dependent,
aldehyde forming), an acetoacetyl-CoA reductase (CoA-dependent,
alcohol forming), an acetoacetyl-CoA reductase (ketone reducing), a
3-hydroxybutyryl-CoA reductase (aldehyde forming), a
3-hydroxybutyryl-CoA reductase (alcohol forming), a
4-hydroxybutyryl-CoA dehydratase, and a crotonase. A method for
producing 1,3-BDO, includes culturing such microbial organisms
under conditions and for a sufficient period of time to produce
1,3-BDO.
Inventors: |
Burgard; Anthony P.;
(Elizabeth, PA) ; Burk; Mark J.; (San Diego,
CA) ; Osterhout; Robin E.; (San Diego, CA) ;
Pharkya; Priti; (San Diego, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Genomatica, Inc. |
San Diego |
CA |
US |
|
|
Family ID: |
1000006362474 |
Appl. No.: |
17/507587 |
Filed: |
October 21, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15616841 |
Jun 7, 2017 |
11180780 |
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17507587 |
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14673600 |
Mar 30, 2015 |
9708632 |
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15616841 |
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12772114 |
Apr 30, 2010 |
9017983 |
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14673600 |
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61174473 |
Apr 30, 2009 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Y 401/01 20130101;
C12Y 101/01 20130101; C12Y 403/01 20130101; C12Y 203/01 20130101;
C12Y 101/01157 20130101; C12N 9/0006 20130101; C12Y 102/01
20130101; C12N 9/1096 20130101; C12N 9/88 20130101; C12Y 206/01
20130101; C12N 15/52 20130101; C12Y 402/01 20130101; C12N 9/1029
20130101; C12N 9/0008 20130101; C12P 7/18 20130101; C07C 29/80
20130101 |
International
Class: |
C12P 7/18 20060101
C12P007/18; C12N 15/52 20060101 C12N015/52; C12N 9/04 20060101
C12N009/04; C07C 29/80 20060101 C07C029/80; C12N 9/02 20060101
C12N009/02; C12N 9/10 20060101 C12N009/10; C12N 9/88 20060101
C12N009/88 |
Claims
1-56. (canceled)
57. A non-naturally occurring microbial organism having a
1,3-butanediol (1,3-BDO) pathway, wherein said microbial organism
comprises at least one exogenous nucleic acid encoding a
3-hydroxybutyryl-CoA reductase (aldehyde forming) expressed in a
sufficient amount to produce 1,3-BDO.
58. The non-naturally occurring microbial organism of claim 57,
wherein said 3-hydroxybutyryl-CoA reductase (aldehyde forming) is
encoded by one or more genes selected from the group consisting of
acr1, sucD, bphG, bld, adhE, Msed_0709, mcr, asd-2, Saci_2370, Ald,
and eutE.
59. The non-naturally occurring microbial organism of claim 57,
wherein said microbial organism comprises two exogenous nucleic
acids, each encoding a 1,3-BDO pathway enzyme.
60. The non-naturally occurring microbial organism of claim 57,
wherein said microbial organism comprises three exogenous nucleic
acids, each encoding a 1,3-BDO pathway enzyme.
61. The non-naturally occurring microbial organism of claim 57,
wherein said microbial organism comprises four exogenous nucleic
acids, each encoding a 1,3-BDO pathway enzyme.
62. The non-naturally occurring microbial organism of claim 57,
wherein said at least one exogenous nucleic acid is a heterologous
nucleic acid.
63. The non-naturally occurring microbial organism of claim 57,
wherein said non-naturally occurring microbial organism is in a
substantially anaerobic culture medium.
64. The non-naturally occurring microbial organism of claim 57,
wherein said 1,3-BDO pathway comprises a set of 1,3-BDO pathway
enzymes, said set of 1,3-BDO pathway enzymes comprises (1) an
acetoacetyl-CoA reductase (ketone reducing); (2) a
3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a
3-hydroxybutyraldehyde reductase.
65. The non-naturally occurring microbial organism of claim 57,
wherein said 1,3-BDO pathway comprises a set of 1,3-BDO pathway
enzymes, said set of 1,3-BDO pathway enzymes comprises (1) a
4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a
3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a
3-hydroxybutyraldehyde reductase.
66. The non-naturally occurring microbial organism of claim 64,
wherein said acetoacetyl-CoA reductase (ketone reducing) is encoded
by one or more genes selected from the group consisting of thrA,
akthr2, hom6, hom1, hom2, fadB, fadJ, Hbd2, Hbd1, hbd, HSD17B10,
phbB, phaB, Msed_1423, Msed_0399, Msed_0389, Msed_1993, adh, adhA,
adh-A, mdh, ldhA, ldh, and bdh.
67. The non-naturally occurring microbial organism of claim 65,
wherein said 4-hydroxybutyryl-CoA dehydratase is encoded by one or
more genes selected from the group consisting of fumA, fumB, fumC,
fumH, fum1, MmcB, MmcC, hmd, BACCAP_02294, ANACOL_02527,
NtherDRAFT_2368, dmdA, dmdB, crt, crt1, ech paaA, paaB, phaA, phaB,
maoC, paaF, paaG, abfD, Msed_1220, fadA, fadB, fadI, fadJ, and
fadR.
68. The non-naturally occurring microbial organism of claim 65,
wherein said crotonase is encoded by one or more genes selected
from the group consisting of fumA, fumB, fumC, fumH, fum1, MmcB,
MmcC, hmd, BACCAP_02294, ANACOL_02527, NtherDRAFT_2368, dmdA, dmdB,
crt, crt1, ech paaA, paaB, phaA, phaB, maoC, paaF, paaG, abfD,
Msed_1220, fadA, fadB, fadI, fadJ, and fadR.
69. The non-naturally occurring microbial organism of claim 57,
wherein said microbial organism is a bacteria.
70. The non-naturally occurring microbial organism of claim 69,
wherein said bacteria is E. coli.
71. A culture medium comprising the non-naturally occurring
microbial organism of claim 57.
72. The culture medium of claim 71 further comprising 1,3-BDO.
73. A method for producing 1,3-BDO, comprising culturing the
non-naturally occurring microbial of claim 57 under conditions and
for a sufficient period of time to produce 1,3-BDO.
74. The method of claim 73 further comprising separating 1,3-BDO
from other components in the culture.
75. The method of claim 74, wherein the separating comprises
extraction, continuous liquid-liquid extraction, pervaporation,
membrane filtration, membrane separation, reverse osmosis,
electrodialysis, distillation, crystallization, centrifugation,
extractive filtration, ion exchange chromatography, size exclusion
chromatography, absorption chromatography, or ultrafiltration.
76. The method of claim 75, wherein the separating comprises
distillation.
77. The method of claim 74, further comprising converting the
1,3-BDO to another compound.
Description
STATEMENT OF RELATED APPLICATIONS
[0001] This application is a continuation of U.S. Non-provisional
application Ser. No. 15/616,841, filed Jun. 7, 2017, which is a
continuation of U.S. Non-provisional application Ser. No.
14/673,600, filed Mar. 30, 2015, now U.S. Pat. No. 9,708,632, which
is a continuation of U.S. Non-provisional application Ser. No.
12/772,114, filed Apr. 30, 2010, now U.S. Pat. No. 9,017,983, which
claims the benefit of priority of U.S. Provisional Application No.
61/174,473, filed Apr. 30, 2009, the entire contents of each of
which are incorporated herein by reference.
BACKGROUND OF THE INVENTION
[0002] The present invention relates generally to biosynthetic
processes and organisms capable of producing organic compounds.
More specifically, the invention relates to non-naturally occurring
organisms that can produce the commodity chemical
1,3-butanediol.
[0003] 1,3-butanediol (1,3-BDO) is a four carbon diol traditionally
produced from acetylene via its hydration. The resulting
acetaldehyde is then converted to 3-hydroxybutyraldehyde which is
subsequently reduced to form 1,3-BDO. In more recent years,
acetylene has been replaced by the less expensive ethylene as a
source of acetaldehyde. 1,3-BDO is commonly used as an organic
solvent for food flavoring agents. It is also used as a co-monomer
for polyurethane and polyester resins and is widely employed as a
hypoglycaemic agent. Optically active 1,3-BDO is a useful starting
material for the synthesis of biologically active compounds and
liquid crystals. A substantial commercial use of 1,3-butanediol is
subsequent dehydration to afford 1,3-butadiene (Ichikawa et al., J.
of Molecular Catalysis A--Chemical, 256:106-112 (2006); Ichikawa et
al., J. of Molecular Catalysis A--Chemical, 231:181-189 (2005)), a
25 billion lb/yr petrochemical used to manufacture synthetic
rubbers (e.g., tires), latex, and resins. The reliance on petroleum
based feedstocks for either acetylene or ethylene warrants the
development of a renewable feedstock based route to 1,3-butanediol
and to butadiene.
[0004] Thus, there exists a need to develop microorganisms and
methods of their use to produce 1,3-BDO. The present invention
satisfies this need and provides related advantages as well.
SUMMARY OF THE INVENTION
[0005] In some embodiments, the present invention is directed to a
non-naturally occurring microbial organism that includes a
microbial organism having a 1,3-butanediol (1,3-BDO) pathway having
at least one exogenous nucleic acid encoding a 1,3-BDO pathway
enzyme expressed in a sufficient amount to produce 1,3-BDO. The
1,3-BDO pathway includes an enzyme selected from the group
consisting of a 2-amino-4-ketopentanoate (AKP) thiolase, an AKP
dehydrogenase, a 2-amino-4-hydroxypentanoate aminotransferase, a
2-amino-4-hydroxypentanoate oxidoreductase (deaminating), a
2-oxo-4-hydroxypentanoate decarboxylase, a 3-hydroxybutyraldehyde
reductase, an AKP aminotransferase, an AKP oxidoreductase
(deaminating), a 2,4-dioxopentanoate decarboxylase, a
3-oxobutyraldehyde reductase (ketone reducing), a
3-oxobutyraldehyde reductase (aldehyde reducing), a
4-hydroxy-2-butanone reductase, an AKP decarboxylase, a
4-aminobutan-2-one aminotransferase, a 4-aminobutan-2-one
oxidoreductase (deaminating), a 4-aminobutan-2-one ammonia-lyase, a
butenone hydratase, an AKP ammonia-lyase, an acetylacrylate
decarboxylase, an acetoacetyl-CoA reductase (CoA-dependent,
aldehyde forming), an acetoacetyl-CoA reductase (CoA-dependent,
alcohol forming), an acetoacetyl-CoA reductase (ketone reducing), a
3-hydroxybutyryl-CoA reductase (aldehyde forming), a
3-hydroxybutyryl-CoA reductase (alcohol forming), a
4-hydroxybutyryl-CoA dehydratase, and a crotonase.
[0006] In some embodiments, the present invention is directed to a
method for producing 1,3-BDO that includes culturing such a
non-naturally occurring microbial organism, under conditions and
for a sufficient period of time to produce 1,3-BDO.
BRIEF DESCRIPTION OF THE DRAWINGS
[0007] FIG. 1 shows pathways to 1,3-BDO from alanine. Enzymes are:
A) AKP thiolase, B) AKP aminotransferase or AKP oxidoreductase
(deaminating), C) 2,4-dioxopentanoate decarboxylase, D)
3-oxobutyraldehyde reductase (aldehyde reducing), E) AKP
decarboxylase, F) 4-aminobutan-2-one ammonia-lyase, G) Butenone
hydratase, H) 4-hydroxy,2-butanone reductase, I) AKP ammonia-lyase,
J) acetylacrylate decarboxylase, K) 4-aminobutan-2-one
aminotransferase or 4-aminobutan-2-one oxidoreductase
(deaminating), L) AKP dehydrogenase, M) 2-amino-4-hydroxypentanoate
aminotransferase or 2-amino-4-hydroxypentanoate oxidoreductase
(deaminating), N) 2-oxo-4-hydroxypentanoate decarboxylase, O)
3-oxobutyraldehyde reductase (ketone reducing), and P)
3-hydroxybutyraldehyde reductase.
[0008] FIG. 2 shows pathways from acetoacetyl-CoA to
1,3-butanediol. Enzymes are: A) acetoacetyl-CoA reductase
(CoA-dependent, aldehyde forming), B) 3-oxobutyraldehyde reductase
(ketone reducing), C) 3-hydroxybutyraldehyde reductase, D)
acetoacetyl-CoA reductase (CoA-dependent, alcohol forming), E)
3-oxobutyraldehyde reductase (aldehyde reducing), F)
4-hydroxy,2-butanone reductase, G) acetoacetyl-CoA reductase
(ketone reducing), H) 3-hydroxybutyryl-CoA reductase (aldehyde
forming), and I) 3-hydroxybutyryl-CoA reductase (alcohol
forming).
[0009] FIG. 3 shows pathways from 4-hydroxybutyryl-CoA to
1,3-butanediol. Enzymes are: A) 4-hydroxybutyryl-CoA dehydratase,
B) crotonase, C) 3-hydroxybutyryl-CoA reductase (aldehyde forming),
D) 3-hydroxybutyraldehyde reductase, and E) 3-hydroxybutyryl-CoA
reductase (alcohol forming).
[0010] FIG. 4 shows aldehyde dehydrogenases showing significant
activity on 3-hydroxybutyl-CoA.
[0011] FIG. 5 shows the specific activity of bld from Clostridium
saccharoperbutylacetonicum on 3-Hydroxybutyryl-CoA before and after
dialysis.
[0012] FIG. 6 shows 1,3-BDO concentrations when
3-hydroxybutyraldehyde was added as a substrate and in the control
samples with no substrate. The GI numbers for the alcohol
dehydrogenases are shown.
[0013] FIG. 7 shows 1,3-BDO concentrations when
3-hydroxybutyryl-CoA was added as a substrate and in the control
samples with no substrate. The GI numbers for the alcohol
dehydrogenases are shown. The GI number for the aldehyde
dehydrogenase tested in conjunction is 163762382.
DETAILED DESCRIPTION OF THE INVENTION
[0014] This invention is directed, in part, to non-naturally
occurring microorganisms that express genes encoding enzymes that
catalyze 1,3-butanediol (1,3-BDO) production. Pathways for the
production of 1,3-butanediol disclosed herein are based on three
precursors: (i) D-alanine, (ii) acetoacetyl-CoA, and (iii)
4-hydroxybutyryl-CoA. Successfully engineering these pathways
entails identifying an appropriate set of enzymes with sufficient
activity and specificity, cloning their corresponding genes into a
production host, optimizing fermentation conditions, and assaying
for product formation following fermentation.
[0015] The conversion of alanine to 1,3-BDO can be accomplished by
a number of pathways in about five enzymatic steps as shown in FIG.
1. In the first step of all pathways (Step A), alanine and
acetyl-CoA are combined by 2-amino-4-ketopentanoate thiolase, a
highly selective enzyme. The product of this reaction,
2-amino-4-oxopentanoate (AKP) can then be transaminated, reduced,
decarboxylated or deaminated as shown in FIG. 1. Further synthetic
steps for the production of 1,3-BDO are discussed in detail below.
The theoretical yield of 1,3-BDO from each of these pathways is
calculated to be about 1.09 mole/mole of glucose consumed.
[0016] FIG. 2 outlines multiple routes for producing 1,3-BDO from
acetoacetyl-CoA. Each of these pathways from acetoacetyl-CoA to
1,3-BDO utilizes three reducing equivalents and provides a
theoretical yield of 1 mole of 1,3-BDO per mole of glucose
consumed. Other carbon substrates such as syngas can also be used
for the production of acetoacetyl-CoA. Gasification of glucose to
form syngas will result in the maximum theoretical yield of 1.09
moles of 1,3-BDO per mole of glucose consumed, assuming that 6
moles of CO and 6 moles of H.sub.2 are obtained from glucose
6CO+6H.sub.2.fwdarw.1.091C.sub.4H.sub.10O.sub.2+1.636CO.sub.2+0.545H.sub-
.2
[0017] 4-Hydroxybutyryl-CoA is an important starting metabolite
from which a number of industrially useful compounds can be made,
including 1,3-BDO as shown in FIG. 3. Although 4-hydroxybutyryl-CoA
is not a highly common central metabolite, methods for engineering
strains that synthesize 4-hydroxybutyryl-CoA have been described
previously by Applicants in U.S. Patent Application No.
2009/0075351. The 4-hydroxybutyryl-CoA to 1,3-butanediol pathway
has a theoretical yield of 1.09 mol/mol product yield assuming
glucose as the carbohydrate feedstock.
[0018] This invention is also directed, in part, to methods for
producing 1,3-BDO through culturing of these non-naturally
occurring microbial organisms. Dehydration of 1,3-BDO produced by
the organisms and methods described herein, provides an opportunity
to produce renewable butadiene in small end-use facilities
obviating the need to transport this flammable and reactive
chemical.
[0019] As used herein, the term "non-naturally occurring" when used
in reference to a microbial organism or microorganism of the
invention is intended to mean that the microbial organism has at
least one genetic alteration not normally found in a naturally
occurring strain of the referenced species, including wild-type
strains of the referenced species. Genetic alterations include, for
example, modifications introducing expressible nucleic acids
encoding metabolic polypeptides, other nucleic acid additions,
nucleic acid deletions and/or other functional disruption of the
microbial genetic material. Such modifications include, for
example, coding regions and functional fragments thereof, for
heterologous, homologous or both heterologous and homologous
polypeptides for the referenced species. Additional modifications
include, for example, non-coding regulatory regions in which the
modifications alter expression of a gene or operon. Exemplary
metabolic polypeptides include enzymes or proteins within a
1,3-butanediol biosynthetic pathway.
[0020] A metabolic modification refers to a biochemical reaction
that is altered from its naturally occurring state. Therefore,
non-naturally occurring microorganisms can have genetic
modifications to nucleic acids encoding metabolic polypeptides or,
functional fragments thereof. Exemplary metabolic modifications are
disclosed herein.
[0021] As used herein, the term "isolated" when used in reference
to a microbial organism is intended to mean an organism that is
substantially free of at least one component as the referenced
microbial organism is found in nature. The term includes a
microbial organism that is removed from some or all components as
it is found in its natural environment. The term also includes a
microbial organism that is removed from some or all components as
the microbial organism is found in non-naturally occurring
environments. Therefore, an isolated microbial organism is partly
or completely separated from other substances as it is found in
nature or as it is grown, stored or subsisted in non-naturally
occurring environments. Specific examples of isolated microbial
organisms include partially pure microbes, substantially pure
microbes and microbes cultured in a medium that is non-naturally
occurring.
[0022] As used herein, the terms "microbial," "microbial organism"
or "microorganism" is intended to mean any organism that exists as
a microscopic cell that is included within the domains of archaea,
bacteria or eukarya. Therefore, the term is intended to encompass
prokaryotic or eukaryotic cells or organisms having a microscopic
size and includes bacteria, archaea and eubacteria of all species
as well as eukaryotic microorganisms such as yeast and fungi. The
term also includes cell cultures of any species that can be
cultured for the production of a biochemical.
[0023] As used herein, the term "CoA" or "coenzyme A" is intended
to mean an organic cofactor or prosthetic group (nonprotein portion
of an enzyme) whose presence is required for the activity of many
enzymes (the apoenzyme) to form an active enzyme system. Coenzyme A
functions in certain condensing enzymes, acts in acetyl or other
acyl group transfer and in fatty acid synthesis and oxidation,
pyruvate oxidation and in other acetylation.
[0024] As used herein, the term "substantially anaerobic" when used
in reference to a culture or growth condition is intended to mean
that the amount of oxygen is less than about 10% of saturation for
dissolved oxygen in liquid media. The term also is intended to
include sealed chambers of liquid or solid medium maintained with
an atmosphere of less than about 1% oxygen.
[0025] "Exogenous" as it is used herein is intended to mean that
the referenced molecule or the referenced activity is introduced
into the host microbial organism. The molecule can be introduced,
for example, by introduction of an encoding nucleic acid into the
host genetic material such as by integration into a host chromosome
or as non-chromosomal genetic material such as a plasmid.
Therefore, the term as it is used in reference to expression of an
encoding nucleic acid refers to introduction of the encoding
nucleic acid in an expressible form into the microbial organism.
When used in reference to a biosynthetic activity, the term refers
to an activity that is introduced into the host reference organism.
The source can be, for example, a homologous or heterologous
encoding nucleic acid that expresses the referenced activity
following introduction into the host microbial organism. Therefore,
the term "endogenous" refers to a referenced molecule or activity
that is present in the host. Similarly, the term when used in
reference to expression of an encoding nucleic acid refers to
expression of an encoding nucleic acid contained within the
microbial organism. The term "heterologous" refers to a molecule or
activity derived from a source other than the referenced species
whereas "homologous" refers to a molecule or activity derived from
the host microbial organism. Accordingly, exogenous expression of
an encoding nucleic acid of the invention can utilize either or
both a heterologous or homologous encoding nucleic acid.
[0026] The non-naturally occurring microbial organisms of the
invention can contain stable genetic alterations, which refers to
microorganisms that can be cultured for greater than five
generations without loss of the alteration. Generally, stable
genetic alterations include modifications that persist greater than
10 generations, particularly stable modifications will persist more
than about 25 generations, and more particularly, stable genetic
modifications will be greater than 50 generations, including
indefinitely.
[0027] Those skilled in the art will understand that the genetic
alterations, including metabolic modifications exemplified herein,
are described with reference to a suitable host organism such as E.
coli and their corresponding metabolic reactions or a suitable
source organism for desired genetic material such as genes for a
desired metabolic pathway. However, given the complete genome
sequencing of a wide variety of organisms and the high level of
skill in the area of genomics, those skilled in the art will
readily be able to apply the teachings and guidance provided herein
to essentially all other organisms. For example, the E. coli
metabolic alterations exemplified herein can readily be applied to
other species by incorporating the same or analogous encoding
nucleic acid from species other than the referenced species. Such
genetic alterations include, for example, genetic alterations of
species homologs, in general, and in particular, orthologs,
paralogs or nonorthologous gene displacements.
[0028] An ortholog is a gene or genes that are related by vertical
descent and are responsible for substantially the same or identical
functions in different organisms. For example, mouse epoxide
hydrolase and human epoxide hydrolase can be considered orthologs
for the biological function of hydrolysis of epoxides. Genes are
related by vertical descent when, for example, they share sequence
similarity of sufficient amount to indicate they are homologous, or
related by evolution from a common ancestor. Genes can also be
considered orthologs if they share three-dimensional structure but
not necessarily sequence similarity, of a sufficient amount to
indicate that they have evolved from a common ancestor to the
extent that the primary sequence similarity is not identifiable.
Genes that are orthologous can encode proteins with sequence
similarity of about 25% to 100% amino acid sequence identity. Genes
encoding proteins sharing an amino acid similarity less that 25%
can also be considered to have arisen by vertical descent if their
three-dimensional structure also shows similarities. Members of the
serine protease family of enzymes, including tissue plasminogen
activator and elastase, are considered to have arisen by vertical
descent from a common ancestor.
[0029] Orthologs include genes or their encoded gene products that
through, for example, evolution, have diverged in structure or
overall activity. For example, where one species encodes a gene
product exhibiting two functions and where such functions have been
separated into distinct genes in a second species, the three genes
and their corresponding products are considered to be orthologs.
For the production of a biochemical product, those skilled in the
art will understand that the orthologous gene harboring the
metabolic activity to be introduced or disrupted is to be chosen
for construction of the non-naturally occurring microorganism. An
example of orthologs exhibiting separable activities is where
distinct activities have been separated into distinct gene products
between two or more species or within a single species. A specific
example is the separation of elastase proteolysis and plasminogen
proteolysis, two types of serine protease activity, into distinct
molecules as plasminogen activator and elastase. A second example
is the separation of mycoplasma 5'-3' exonuclease and Drosophila
DNA polymerase III activity. The DNA polymerase from the first
species can be considered an ortholog to either or both of the
exonuclease or the polymerase from the second species and vice
versa.
[0030] In contrast, paralogs are homologs related by, for example,
duplication followed by evolutionary divergence and have similar or
common, but not identical functions. Paralogs can originate or
derive from, for example, the same species or from a different
species. For example, microsomal epoxide hydrolase (epoxide
hydrolase I) and soluble epoxide hydrolase (epoxide hydrolase II)
can be considered paralogs because they represent two distinct
enzymes, co-evolved from a common ancestor, that catalyze distinct
reactions and have distinct functions in the same species. Paralogs
are proteins from the same species with significant sequence
similarity to each other suggesting that they are homologous, or
related through co-evolution from a common ancestor. Groups of
paralogous protein families include HipA homologs, luciferase
genes, peptidases, and others.
[0031] A nonorthologous gene displacement is a nonorthologous gene
from one species that can substitute for a referenced gene function
in a different species. Substitution includes, for example, being
able to perform substantially the same or a similar function in the
species of origin compared to the referenced function in the
different species. Although generally, a nonorthologous gene
displacement will be identifiable as structurally related to a
known gene encoding the referenced function, less structurally
related but functionally similar genes and their corresponding gene
products nevertheless will still fall within the meaning of the
term as it is used herein. Functional similarity requires, for
example, at least some structural similarity in the active site or
binding region of a nonorthologous gene product compared to a gene
encoding the function sought to be substituted. Therefore, a
nonorthologous gene includes, for example, a paralog or an
unrelated gene.
[0032] Therefore, in identifying and constructing the non-naturally
occurring microbial organisms of the invention having 1,3-BDO
biosynthetic capability, those skilled in the art will understand
with applying the teaching and guidance provided herein to a
particular species that the identification of metabolic
modifications can include identification and inclusion or
inactivation of orthologs. To the extent that paralogs and/or
nonorthologous gene displacements are present in the referenced
microorganism that encode an enzyme catalyzing a similar or
substantially similar metabolic reaction, those skilled in the art
also can utilize these evolutionally related genes.
[0033] Orthologs, paralogs and nonorthologous gene displacements
can be determined by methods well known to those skilled in the
art. For example, inspection of nucleic acid or amino acid
sequences for two polypeptides will reveal sequence identity and
similarities between the compared sequences. Based on such
similarities, one skilled in the art can determine if the
similarity is sufficiently high to indicate the proteins are
related through evolution from a common ancestor. Algorithms well
known to those skilled in the art, such as Align, BLAST, Clustal W
and others compare and determine a raw sequence similarity or
identity, and also determine the presence or significance of gaps
in the sequence which can be assigned a weight or score. Such
algorithms also are known in the art and are similarly applicable
for determining nucleotide sequence similarity or identity.
Parameters for sufficient similarity to determine relatedness are
computed based on well known methods for calculating statistical
similarity, or the chance of finding a similar match in a random
polypeptide, and the significance of the match determined. A
computer comparison of two or more sequences can, if desired, also
be optimized visually by those skilled in the art. Related gene
products or proteins can be expected to have a high similarity, for
example, 25% to 100% sequence identity. Proteins that are unrelated
can have an identity which is essentially the same as would be
expected to occur by chance, if a database of sufficient size is
scanned (about 5%). Sequences between 5% and 24% may or may not
represent sufficient homology to conclude that the compared
sequences are related. Additional statistical analysis to determine
the significance of such matches given the size of the data set can
be carried out to determine the relevance of these sequences.
[0034] Exemplary parameters for determining relatedness of two or
more sequences using the BLAST algorithm, for example, can be as
set forth below. Briefly, amino acid sequence alignments can be
performed using BLASTP version 2.0.8 (Jan. 5, 1999) and the
following parameters: Matrix: 0 BLOSUM62; gap open: 11; gap
extension: 1; x_dropoff: 50; expect: 10.0; wordsize: 3; filter: on.
Nucleic acid sequence alignments can be performed using BLASTN
version 2.0.6 (Sep. 16, 1998) and the following parameters: Match:
1; mismatch: -2; gap open: 5; gap extension: 2; x_dropoff: 50;
expect: 10.0; wordsize: 11; filter: off. Those skilled in the art
will know what modifications can be made to the above parameters to
either increase or decrease the stringency of the comparison, for
example, and determine the relatedness of two or more
sequences.
[0035] In some embodiments, the present invention provides a
non-naturally occurring microbial organism that includes a
microbial organism having a 1,3-butanediol (1,3-BDO) pathway with
at least one exogenous nucleic acid encoding a 1,3-BDO pathway
enzyme expressed in a sufficient amount to produce 1,3-BDO. The
1,3-BDO pathway includes an enzyme selected from the group
consisting of a 2-amino-4-ketopentanoate (AKP) thiolase, an AKP
dehydrogenase, a 2-amino-4-hydroxypentanoate aminotransferase, a
2-amino-4-hydroxypentanoate oxidoreductase (deaminating), a
2-oxo-4-hydroxypentanoate decarboxylase, a 3-hydroxybutyraldehyde
reductase, an AKP aminotransferase, an AKP oxidoreductase
(deaminating), a 2,4-dioxopentanoate decarboxylase, a
3-oxobutyraldehyde reductase (ketone reducing), a
3-oxobutyraldehyde reductase (aldehyde reducing), a
4-hydroxy-2-butanone reductase, an AKP decarboxylase, a
4-aminobutan-2-one aminotransferase, a 4-aminobutan-2-one
oxidoreductase (deaminating), a 4-aminobutan-2-one ammonia-lyase, a
butenone hydratase, an AKP ammonia-lyase, an acetylacrylate
decarboxylase, an acetoacetyl-CoA reductase (CoA-dependent,
aldehyde forming), an acetoacetyl-CoA reductase (CoA-dependent,
alcohol forming), an acetoacetyl-CoA reductase (ketone reducing), a
3-hydroxybutyryl-CoA reductase (aldehyde forming), a
3-hydroxybutyryl-CoA reductase (alcohol forming), a
4-hydroxybutyryl-CoA dehydratase, and a crotonase.
[0036] Any combination and any number of the aforementioned enzymes
can be introduced into a host microbial organism to complete a
1,3-BDO pathway, as exemplified in FIGS. 1-3. For example, the
non-naturally occurring microbial organism can include one, two,
three, four, five, up to all of the nucleic acids in a 1,3-BDO
pathway, each nucleic acid encoding a 1,3-BDO pathway enzyme. Such
nucleic acids can include heterologous nucleic acids, additional
copies of existing genes, and gene regulatory elements, as
explained further below. The pathways of the non-naturally
occurring microbial organisms of the invention are also suitably
engineered to be cultured in a substantially anaerobic culture
medium.
[0037] In some embodiments, the non-naturally occurring microbial
organisms having a 1,3-BDO pathway include a set of 1,3-BDO pathway
enzymes. A set of 1,3-BDO pathway enzymes represents a group of
enzymes that can convert alanine, acetoacetyl-CoA, or
4-hydroxybutyryl-CoA to 1,3-BDO, as show in FIGS. 1-3. Exemplary
sets of 1,3-BDO pathway enzymes to convert alanine to 1,3-BDO,
according to FIG. 1 include (a) (1) a 2-amino-4-ketopentanoate
(AKP) thiolase; (2) an AKP dehydrogenase; (3) a
2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase
(deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and
(5) a 3-hydroxybutyraldehyde reductase; (b) (1) a
2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
aminotransferase or oxidoreductase (deaminating); (3) a
2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde
reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde
reductase; (c) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2)
an AKP aminotransferase or oxidoreductase (deaminating); (3) a
2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde
reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone
reductase; (d) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2)
an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or
oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase
(ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase; (e)
(1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or
oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase
(aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase; (f)
(1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a
butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase; and
(g) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butenone
hydratase; and (5) a 4-hydroxy-2-butanone reductase;
[0038] Exemplary sets of 1,3-BDO pathway enzymes to convert
acetoacetyl-CoA to 1,3-BDO, according to FIG. 2 include (h) (1) an
acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a
3-oxobutyraldehyde reductase (ketone reducing); and (3) a
3-hydroxybutyraldehyde reductase; (i) (1) an acetoacetyl-CoA
reductase (CoA dependent, alcohol forming) and (2) a
4-hydroxy-2-butanone reductase; (j) (1) an acetoacetyl-CoA
reductase (CoA-dependent, aldehyde forming); (2) a
3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a
4-hydroxy-2-butanone reductase; (k) (1) an acetoacetyl-CoA
reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA
reductase (alcohol forming); and (1) (1) an acetoacetyl-CoA
reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase
(aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase;
[0039] Exemplary sets of 1,3-BDO pathway enzymes to convert
4-hydroxybutyryl-CoA to 1,3-BDO, according to FIG. 3 include (m)
(1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a
3-hydroxybutyryl-CoA reductase (alcohol forming); and (n) (1) a
4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a
3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a
3-hydroxybutyraldehyde reductase.
[0040] The conversion of alanine to 1,3-BDO can be accomplished by
a number of pathways involving about five enzymatic steps as shown
in FIG. 1. In the first step of all pathways (Step A), alanine and
acetyl-CoA are combined by 2-amino-4-ketopentanoate thiolase, a
highly selective enzyme. The product of this reaction,
2-amino-4-oxopentanoate (AKP) can then be transaminated, reduced,
decarboxylated or deaminated as shown in FIG. 1.
[0041] In one route, AKP converted to 2,4-dioxopentanoate, a 2-keto
acid similar in structure to alpha-ketoglutarate, by an
aminotransferase or deaminating oxidoreductase (Step B).
2,4-Dioxopentanoate is then converted to 3-oxobutyraldehyde by a
2-ketoacid decarboxylase (Step C). Reduction of the ketone and
aldehyde groups to their corresponding alcohols yields
1,3-butanediol. These reductions can occur in either order to form
the intermediates 3-hydroxybutyraldehyde (Steps O and P) or
4-hydroxy,2-butanone (Steps D and H).
[0042] In another route, the 4-oxo group of AKP is first reduced to
a secondary alcohol by AKP dehydrogenase (Step L). The product,
2-amino-4-hydroxypentanoate, is then converted to
2-oxo-4-hydroxypentanoate (Step M). The resulting 2-ketoacid is
decarboxylated to 3-hydroxybutyraldehyde (Step N). In the final
step of this route, the aldehyde of 3-hydroxybutyraldehyde is
reduced to a primary alcohol by 3-hydroxybutyraldehyde reductase,
forming 1,3-butanediol (Step P).
[0043] Yet another route involves decarboxylation of AKP by an
amino acid decarboxylase (Step E). The decarboxylation product,
4-aminobutan-2-one, can either be transaminated or oxidatively
deaminated to 3-oxobutyraldehyde (Step K) or deaminated to butenone
(Step F). When 3-oxobutyraldehyde is formed, two alcohol-forming
reduction steps are used to form 1,3-butanediol, as described
previously (Steps O and P, or Steps D and H). The deamination
product, butenone, is then hydrolyzed to 4-hydroxy,2-butanone (Step
G), which is reduced to 1,3-butanediol by 4-hydroxy-2-butanone
reductase (Step H).
[0044] Yet another route involves the deamination of AKP to
acetylacrylate (Step I). Acetylacrylate is decarboxylated to
butenone (Step J), which is then converted to 1,3-butandiol by
butenone hydratase (Step G) and 4-hydroxy,2-butanone reductase
(Step H).
[0045] Based on the routes described above for the production
1,3-BDO from alanine, in some embodiments, the non-naturally
occurring microbial organism has a set of 1,3-BDO pathway enzymes
that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an
AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate
aminotransferase or oxidoreductase (deaminating); (4) a
2-oxo-4-hydroxypentanoate decarboxylase; and (5) a
3-hydroxybutyraldehyde reductase. Any number of nucleic acids
encoding these enzymes can be introduced into a host microbial
organism including one, two, three, four, up to all five of the
nucleic acids that encode these enzymes. Where one, two, three, or
four exogenous nucleic acids are introduced, such nucleic acids can
be any permutation of the five nucleic acids.
[0046] In other embodiments non-naturally occurring microbial
organism has a set of 1,3-BDO pathway enzymes that includes (1) a
2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
aminotransferase or oxidoreductase (deaminating); (3) a
2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde
reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde
reductase. Any number of nucleic acids encoding these enzymes can
be introduced into a host microbial organism including one, two,
three, four, up to all five of the nucleic acids that encode these
enzymes. Where one, two, three, or four exogenous nucleic acids are
introduced, such nucleic acids can be any permutation of the five
nucleic acids.
[0047] In still other embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
aminotransferase or oxidoreductase (deaminating); (3) a
2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde
reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone
reductase. Any number of nucleic acids encoding these enzymes can
be introduced into a host microbial organism including one, two,
three, four, up to all five of the nucleic acids that encode these
enzymes. Where one, two, three, or four exogenous nucleic acids are
introduced, such nucleic acids can be any permutation of the five
nucleic acids.
[0048] In yet further embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or
oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase
(ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase. Any
number of nucleic acids encoding these enzymes can be introduced
into a host microbial organism including one, two, three, four, up
to all five of the nucleic acids that encode these enzymes. Where
one, two, three, or four exogenous nucleic acids are introduced,
such nucleic acids can be any permutation of the five nucleic
acids.
[0049] In yet still further embodiments, the non-naturally
occurring microbial organism has a set of 1,3-BDO pathway enzymes
that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an
AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or
oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase
(aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase. Any
number of nucleic acids encoding these enzymes can be introduced
into a host microbial organism including one, two, three, four, up
to all five of the nucleic acids that encode these enzymes. Where
one, two, three, or four exogenous nucleic acids are introduced,
such nucleic acids can be any permutation of the five nucleic
acids.
[0050] In still further embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a
butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase. Any
number of nucleic acids encoding these enzymes can be introduced
into a host microbial organism including one, two, three, four, up
to all five of the nucleic acids that encode these enzymes. Where
one, two, three, or four exogenous nucleic acids are introduced,
such nucleic acids can be any permutation of the five nucleic
acids.
[0051] In yet still further embodiments, the non-naturally
occurring microbial organism has a set of 1,3-BDO pathway enzymes
that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an
AKP ammonia-lyase; (3) a an acetylacrylate decarboxylase; (4) a
butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase. Any
number of nucleic acids encoding these enzymes can be introduced
into a host microbial organism including one, two, three, four, up
to all five of the nucleic acids that encode these enzymes. Where
one, two, three, or four exogenous nucleic acids are introduced,
such nucleic acids can be any permutation of the five nucleic
acids.
[0052] FIG. 2 outlines multiple routes for producing 1,3-butanediol
from acetoacetyl-CoA. One route through steps A, B and C utilizes
(i) CoA-dependent, aldehyde forming acetoacetyl-CoA reductase to
convert acetoacetyl-CoA into 3-oxobutyraldehyde (FIG. 2, Step A),
(ii) 3-oxobutyraldehyde reductase to reduce 3-oxobutyraldehyde to
3-hydroxybutyraldehyde (FIG. 2, Step B), and (iii) finally,
3-hydroxybutyraldehyde reductase to form 1,3-butanediol (FIG. 2,
Step C).
[0053] Alternatively, acetoacetyl-CoA can be reduced via the
aldehyde forming acetoacetyl-CoA reductase to form
4-hydroxy,2-butanone (FIG. 2, Step D). 4-hydroxy,2-butanone can
also be formed by the reduction of 3-oxobutyraldehyde by the
aldehyde reducing 3-oxobutyraldehyde reductase (FIG. 2, Step E).
Eventually, 4-hydroxy,2-butanone can be reduced to form 1,3-BDO by
4-hydroxy-2-butanone reductase (FIG. 2, Step F).
[0054] Yet another set of 1,3-BDO forming routes rely on the
reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA by the ketone
reducing acetoacetyl-CoA reductase (FIG. 2, Step G). This enzyme
reduces the ketone function in acetoacetyl-CoA to a hydroxyl group.
3-hydroxybutyryl-CoA can be reduced by the bifunctional
alcohol-forming 3-hydroxybutyryl-CoA reductase to form
1,3-butanediol (FIG. 2, Step I). Alternatively, it can first be
reduced to 3-hydroxybutyraldehyde via the aldehyde forming
3-hydroxybutyryl-CoA reductase (Step H) and 3-hydroxybutyraldehyde
can then be reduced as shown in Step C.
[0055] Based on the routes described above for the production
1,3-BDO from acetoacetyl-CoA, in some embodiments, the
non-naturally occurring microbial organism has a set of 1,3-BDO
pathway enzymes that includes (1) an acetoacetyl-CoA reductase
(CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde
reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde
reductase. Any number of nucleic acids encoding these enzymes can
be introduced into a host microbial organism including one, two up
to all three of the nucleic acids that encode these enzymes. Where
one or two exogenous nucleic acids are introduced, such nucleic
acids can be any permutation of the three nucleic acids.
[0056] In other embodiments, the non-naturally occurring microbial
organism has a set of 1,3-BDO pathway enzymes that includes (1) an
acetoacetyl-CoA reductase (CoA dependent, alcohol forming) and (2)
a 4-hydroxy-2-butanone reductase. Any number of nucleic acids
encoding these enzymes can be introduced into a host microbial
organism including one or both of the nucleic acids that encode
these enzymes. Where one exogenous nucleic acid is introduced, such
a nucleic acid can be either of the two nucleic acids.
[0057] In further embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde
forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing);
and (3) a 4-hydroxy-2-butanone reductase. Any number of nucleic
acids encoding these enzymes can be introduced into a host
microbial organism including one, two up to all three of the
nucleic acids that encode these enzymes. Where one or two exogenous
nucleic acids are introduced, such nucleic acids can be any
permutation of the three nucleic acids.
[0058] In yet further embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) an acetoacetyl-CoA reductase (ketone reducing) and (2)
a 3-hydroxybutyryl-CoA reductase (alcohol forming). Any number of
nucleic acids encoding these enzymes can be introduced into a host
microbial organism including one or both of the nucleic acids that
encode these enzymes. Where one exogenous nucleic acid is
introduced, such a nucleic acid can be either of the two nucleic
acids.
[0059] In still further embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a
3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a
3-hydroxybutyraldehyde reductase. Any number of nucleic acids
encoding these enzymes can be introduced into a host microbial
organism including one, two up to all three of the nucleic acids
that encode these enzymes. Where one or two exogenous nucleic acids
are introduced, such nucleic acids can be any permutation of the
three nucleic acids.
[0060] 4-hydroxybutyryl-CoA is an important starting metabolite
from which a number of industrially useful compounds can be made.
Although 4-hydroxybutyryl-CoA is not a highly common central
metabolite, methods for engineering strains that synthesize
4-hydroxybutyryl-CoA have been described in Burk et al. (US
20090075351). An exemplary method involves synthesizing
4-hydroxybutyryl-CoA from succinyl-CoA by employing genes encoding
succinic semialdehyde dehydrogenase (CoA-dependent),
4-hydroxybutyrate dehydrogenase, 4-hydroxybutyrate kinase, and
phosphotransbutyrylase activities.
[0061] The first step in the pathway involves the dehydration of
4-hydroxybutyryl-CoA (Step A, FIG. 3) followed by the hydration of
crotonoyl-CoA to form 3-hydroxybutyryl-CoA (Step B).
3-hydroxybutyryl-CoA then undergoes two reduction steps to form
1,3-butanediol carried out by either two enzymes (Steps C and D) or
a single dual-function enzyme (Step E).
[0062] Thus, in some embodiments, the non-naturally occurring
microbial organism has a set of 1,3-BDO pathway enzymes that
includes (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase;
and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming). Any
number of nucleic acids encoding these enzymes can be introduced
into a host microbial organism including one, two up to all three
of the nucleic acids that encode these enzymes. Where one or two
exogenous nucleic acids are introduced, such nucleic acids can be
any permutation of the three nucleic acids.
[0063] In other embodiments, the non-naturally occurring microbial
organism has a set of 1,3-BDO pathway enzymes that includes (1) a
4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a
3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a
3-hydroxybutyraldehyde reductase. Any number of nucleic acids
encoding these enzymes can be introduced into a host microbial
organism including one, two, three up to all four of the nucleic
acids that encode these enzymes. Where one, two, or three exogenous
nucleic acids are introduced, such nucleic acids can be any
permutation of the four nucleic acids.
[0064] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to 2-amino-4-hydroxypentanoate,
2-amino-4-hydroxypentanoate to 2-oxo-4-hydroxypentanoate,
2-oxo-4-hydroxypentanoate to 3-hydroxybutyraldehyde, and
3-hydroxybutyraldehyde to 1,3-BDO.
[0065] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to 2,4-dioxopentanoate, 2,4-dioxopentanoate
to 3-oxobutyraldehyde, 3-oxobutyraldehyde to
3-hydroxybutyraldehyde, and 3-hydroxybutyraldehyde to 1,3-BDO.
[0066] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to 2,4-dioxopentanoate, 2,4-dioxopentanoate
to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 4-hydroxy-2-butanone,
and 4-hydroxy-2-butanone to 1,3-BDO.
[0067] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to 4-aminobutan-2-one, 4-aminobutan-2-one
to 3-oxobutyraldehyde, 3-oxobutyraldehyde to
3-hydroxybutyraldehyde, and 3-hydroxybutyraldehyde to 1,3-BDO.
[0068] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to 4-aminobutan-2-one, 4-aminobutan-2-one
to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 4-hydroxy-2-butanone,
and 4-hydroxy-2-butanone to 1,3-BDO.
[0069] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to 4-aminobutan-2-one, 4-aminobutan-2-one
to butenone, butenone to 4-hydroxy-2-butanone, and
4-hydroxy-2-butanone to 1,3-BDO.
[0070] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of alanine to 2-amino-4-oxopentanoate,
2-amino-4-oxopentanoate to acetylacrylate, acetylacrylate to
butenone, butenone to 4-hydroxy-2-butanone, and
4-hydroxy-2-butanone to 1,3-BDO.
[0071] Thus, the invention provides a non-naturally occurring
microbial organism containing at least one exogenous nucleic acid
encoding an enzyme or protein, where the enzyme or protein converts
the substrates and products of a 1,3-BDO pathway converting alanine
to 1,3-BDO, as exemplified by the pathways shown in FIG. 1.
[0072] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of acetoacetyl-CoA to 4-hydroxy-2-butanone, and
4-hydroxy-2-butanone to 1,3-BDO.
[0073] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of acetoacetyl-CoA to 3-oxobutyraldehyde,
3-oxobutyraldehyde to 4-hydroxy-2-butanone, and
4-hydroxy-2-butanone to 1,3-BDO.
[0074] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of acetoacetyl-CoA to 3-oxobutyraldehyde,
3-oxobutyraldehyde to 3-hydroxybutyraldehyde, and
3-hydroxybutyraldehyde to 1,3-BDO.
[0075] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of acetoacetyl-CoA to 3-hydroxybutyryl-CoA,
3-hydroxybutyryl-CoA to 3-hydroxybutyraldehyde, and
3-hydroxybutyraldehyde to 1,3-BDO.
[0076] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of acetoacetyl-CoA to 3-hydroxybutyryl-CoA, and
3-hydroxybutyryl-CoA to 1,3-BDO.
[0077] Thus, the invention provides a non-naturally occurring
microbial organism containing at least one exogenous nucleic acid
encoding an enzyme or protein, where the enzyme or protein converts
the substrates and products of a 1,3-BDO pathway converting
acetoacetyl-CoA to 1,3-BDO, as exemplified by the pathways shown in
FIG. 2.
[0078] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of 4-hydroxybutyryl-CoA to crotonoyl-CoA,
crotonoyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to
3-hydroxybutyraldehyde, and 3-hydroxybutyraldehyde to 1,3-BDO.
[0079] In an additional embodiment, the invention provides a
non-naturally occurring microbial organism having a 1,3-BDO
pathway, wherein the non-naturally occurring microbial organism
comprises at least one exogenous nucleic acid encoding an enzyme or
protein that converts a substrate to a product selected from the
group consisting of 4-hydroxybutyryl-CoA to crotonoyl-CoA,
crotonoyl-CoA to 3-hydroxybutyryl-CoA, and 3-hydroxybutyryl-CoA to
1,3-BDO.
[0080] Thus, the invention provides a non-naturally occurring
microbial organism containing at least one exogenous nucleic acid
encoding an enzyme or protein, where the enzyme or protein converts
the substrates and products of a 1,3-BDO pathway, the pathway
converting 4-hydroxybutyryl-CoA to 1,3-BDO, as exemplified by the
pathways shown in FIG. 3.
[0081] Successfully engineering any of these pathways entails
identifying an appropriate set of enzymes with sufficient activity
and specificity, cloning their corresponding genes into a
production host, optimizing fermentation conditions, and assaying
for product formation following fermentation. To engineer a
production host for the production of any of the aforementioned
products, one or more exogenous DNA sequence(s) can be expressed in
microorganisms. In addition, the microorganisms can have endogenous
gene(s) functionally deleted. These modifications will enable the
production of 1,3-BDO using renewable feedstocks.
[0082] Below, we describe a number of biochemically characterized
genes capable of encoding enzymes that catalyze each of the steps
shown in FIGS. 1, 2 and 3. Although we describe this method for E.
coli, one skilled in the art can apply these teachings to
essentially any other organism. Specifically, genes are listed that
are native to E. coli in addition to genes in other organisms that
can be applied to catalyze the appropriate transformations when
properly cloned and expressed.
[0083] The invention is described herein with general reference to
the metabolic reaction, reactant or product thereof, or with
specific reference to one or more nucleic acids or genes encoding
an enzyme associated with or catalyzing, or a protein associated
with, the referenced metabolic reaction, reactant or product.
Unless otherwise expressly stated herein, those skilled in the art
will understand that reference to a reaction also constitutes
reference to the reactants and products of the reaction. Similarly,
unless otherwise expressly stated herein, reference to a reactant
or product also references the reaction, and reference to any of
these metabolic constituents also references the gene or genes
encoding the enzymes that catalyze or proteins involved in the
referenced reaction, reactant or product. Likewise, given the well
known fields of metabolic biochemistry, enzymology and genomics,
reference herein to a gene or encoding nucleic acid also
constitutes a reference to the corresponding encoded enzyme and the
reaction it catalyzes or a protein associated with the reaction as
well as the reactants and products of the reaction.
[0084] All transformations depicted in FIGS. 1-3 fall into the 8
general categories of transformations shown in Table 1. Below is
described a number of biochemically characterized genes in each
category. Specifically listed are genes that can be applied to
catalyze the appropriate transformations in FIGS. 1-3 when properly
cloned and expressed. Exemplary genes for each of the steps in
FIGS. 1-3 are provided further below in Tables 35-37.
[0085] Table 1 shows the enzyme types useful to convert common
central metabolic intermediates into 1,3-butanediol. The first
three digits of each label correspond to the first three Enzyme
Commission number digits which denote the general type of
transformation independent of substrate specificity.
TABLE-US-00001 TABLE 1 LABEL FUNCTION 1.1.1.a Oxidoreductase
(ketone to hydroxyl or aldehyde to alcohol) 1.1.1.c Oxidoreductase
(2 step, acyl-CoA to alcohol) 1.2.1.b Oxidoreductase (acyl-CoA to
aldehyde) 1.4.1.a Oxidoreductase (deaminating) 2.3.1.b
Acyltransferase 2.6.1.a Aminotransferase 4.1.1.a Carboxy-lyase
4.2.1.a Hydro-lyase 4.3.1.a Ammonia-lyase
[0086] Numerous transformation in FIGS. 1, 2 and 3 fall into the
category of oxidoreductases that reduce an aldehyde to alcohol. For
example, Steps D and P in FIG. 1 catalyzed by 3-oxobutyraldehyde
reductase (aldehyde reducing) and 3-hydroxybutyraldehyde reductase
respectively fall into this category. Similarly, Steps C and E in
FIG. 2 catalyzed by 3-hydroxybutyraldehyde reductase and
3-oxobutyraldehyde reductase (aldehyde reducing) respectively are
also oxidoreductases that convert the aldehyde functionality to
alcohol. Pathways in FIG. 3 involve oxidoreductases such as
3-hydroxybutyraldehyde reductase in Step D.
[0087] Exemplary genes encoding enzymes that catalyze the
conversion of an aldehyde to alcohol (i.e., alcohol dehydrogenase
or equivalently aldehyde reductase) include alrA encoding a
medium-chain alcohol dehydrogenase for C2-C14 (Tani et al., Appl.
Environ. Microbiol., 66:5231-5235 (2000)), ADH2 from Saccharomyces
cerevisiae (Atsumi et al., Nature, 451:86-89 (2008)), yqhD from E.
coli which has preference for molecules longer than C3
(Sulzenbacher et al., J. of Molecular Biology, 342:489-502 (2004)),
and bdh I and bdh II from C. acetobutylicum which converts
butyraldehyde into butanol (Walter et al., J. of Bacteriology,
174:7149-7158 (1992)). The gene product of yqhD catalyzes the
reduction of acetaldehyde, malondialdehyde, propionaldehyde,
butyraldehyde, and acrolein using NADPH as the cofactor (Perez et
al., J. Biol. Chem., 283:7346-7353 (2008)). The adhA gene product
from Zymomonas mobilis has been demonstrated to have activity on a
number of aldehydes including formaldehyde, acetaldehyde,
propionaldehyde, butyraldehyde, and acrolein (Kinoshita et al.,
Appl. Microbiol. Biotechnol, 22:249-254 (1985)). Additional
aldehyde reductase candidates are encoded by bdh in C.
saccharoperbutylacetonicum and Cbei_1722, Cbei_2181 and Cbei_2421
in C. beijerinckii.
[0088] Data related to the sequences for each of these exemplary
gene products can be found using the following GenBank accession
numbers shown in Table 2.
TABLE-US-00002 TABLE 2 Protein GENBANK ID GI NUMBER ORGANISM alrA
BAB12273.1 9967138 Acinetobacter sp. strain M-1 ADH2 NP_014032.1
6323961 Saccharomyces cerevisiae yqhD NP_417484.1 16130909
Escherichia coli bdh I NP_349892.1 15896543 Clostridium
acetobutylicum bdh II NP_349891.1 15896542 Clostridium
acetobutylicum adhA YP_162971.1 56552132 Zymomonas mobilis bdh
BAF45463.1 124221917 Clostridium saccharoperbutylacetonicum
Cbei_1722 YP_001308850 150016596 Clostridium beijerinckii Cbei_2181
YP_001309304 150017050 Clostridium beijerinckii Cbei_2421
YP_001309535 150017281 Clostridium beijerinckii
[0089] Enzymes exhibiting 3-hydroxybutyraldehyde reductase activity
(EC 1.1.1.61) also fall into this category. Such enzymes have been
characterized in Ralstonia eutropha (Bravo et al., J. Forensic
Sci., 49:379-387 (2004)), Clostridium kluyveri (Wolff et al.,
Protein Expr. Purif., 6:206-212 (1995)) and Arabidopsis thaliana
(Breitkreuz et al., J. Biol. Chem., 278:41552-41556 (2003)). Yet
another gene is the alcohol dehydrogenase adhI from Geobacillus
thermoglucosidasius (Jeon et al., J. Biotechnol., 135:127-133
(2008)). Data related to the sequences for each of these exemplary
gene products can be found using the following GenBank accession
numbers shown in Table 3.
TABLE-US-00003 TABLE 3 PROTEIN GENBANK ID GI NUMBER ORGANISM 4hbd
YP_726053.1 113867564 Ralstonia eutropha H16 4hbd L21902.1
146348486 Clostridium kluyveri DSM 555 4hbd Q94B07 75249805
Arabidopsis thaliana adhI AAR91477.1 40795502 Geobacillus
thermoglucosidasius M10EXG
[0090] Another exemplary enzyme is 3-hydroxyisobutyrate
dehydrogenase which catalyzes the reversible oxidation of
3-hydroxyisobutyrate to methylmalonate semialdehyde. This enzyme
participates in valine, leucine and isoleucine degradation and has
been identified in bacteria, eukaryotes, and mammals. The enzyme
encoded by P84067 from Thermus thermophilus HB8 has been
structurally characterized (Lokanath et al., J. Mol. Biol.,
352:905-917 (2005)). The reversibility of the human
3-hydroxyisobutyrate dehydrogenase was demonstrated using
isotopically-labeled substrate (Manning et al., Biochem J.,
231:481-484 (1985)). Additional genes encoding this enzyme include
3hidh in Homo sapiens (Hawes et al., Methods Enzymol, 324:218-228
(2000)) and Oryctolagus cuniculus (Hawes et al., supra; Chowdhury
et al., Biosci. Biotechnol Biochem., 60:2043-2047 (1996)), mmsB in
Pseudomonas aeruginosa and Pseudomonas putida (Liao et al., US
patent 20050221466), and dhat in Pseudomonas putida (Aberhart et
al., J. Chem. Soc., 6:1404-1406 (1979); Chowdhury et al., supra;
Chowdhury et al., Biosci. Biotechnol Biochem., 67:438-441 (2003)).
Data related to the sequences for each of these exemplary gene
products can be found using the following GenBank accession numbers
shown in Table 4.
TABLE-US-00004 TABLE 4 PROTEIN GENBANK ID GI NUMBER ORGANISM P84067
P84067 75345323 Thermus thermophilus 3hidh P31937.2 12643395 Homo
sapiens 3hidh P32185.1 416872 Oryctolagus cuniculus mmsB P28811.1
127211 Pseudomonas aeruginosa mmsB NP_746775.1 26991350 Pseudomonas
putida dhat Q59477.1 2842618 Pseudomonas putida
[0091] Oxidoreductases that convert a ketone functionality to the
corresponding hydroxyl group are also synthetic steps in the
disclosed pathways. Notably, Reactions L, O and H in FIG. 1
catalyzed by AKP dehydrogenase, 3-oxobutyraldehyde reductase
(ketone reducing), 4-hydroxy-2-butanone reductase respectively are
transformations of this category. The two latter transformations
are also encountered in Steps B and F respectively in FIG. 2. On
similar lines, the acetoacetyl-CoA reductase in Step G of FIG. 2
reduces acetoacetyl-CoA to 3-hydroxybutyryl-CoA.
[0092] The reduction of 4-oxo group of 2-amino-4-oxopentanoate
(AKP) by a dehydrogenase yields 2-amino-4-hydroxypentanoate (FIG.
1, step L). This reaction is very similar to the NAD(P)H-dependent
reduction of aspartate semialdehyde to homoserine catalyzed by
homoserine dehydrogenase (EC 1.1.13). In many organisms, including
E. coli, homoserine dehydrogenase is a bifunctional enzyme that
also catalyzes the ATP-dependent conversion of aspartate to
aspartyl-4-phosphate (Starnes et al., Biochemistry, 11:677-687
(1973)). The functional domains are catalytically independent and
connected by a linker region (Sibilli et al., J. Biol. Chem.,
256:10228-10230 (1981)) and both domains are subject to allosteric
inhibition by threonine. The homoserine dehydrogenase domain of the
E. coli enzyme, encoded by thrA, was separated from the aspartate
kinase domain, characterized, and found to exhibit high catalytic
activity and reduced inhibition by threonine (James et al.,
Biochemistry, 41:3720-3725 (2002)). This can be applied to other
bifunctional threonine kinases including, for example, hom1 of
Lactobacillus plantarum (Cahyanto et al., Microbiology, 152:205-112
(2006)) and Arabidopsis thaliana. The monofunctional homoserine
dehydrogenases encoded by hom6 in S. cerevisiae (Jacques et al.,
Biochem. Biophys. Acta, 1544:28-41 (2001)) and hom2 in
Lactobacillus plantarum (Cahyanto et al., supra) have been
functionally expressed and characterized in E. coli. Data related
to the sequences for each of these exemplary gene products can be
found using the following GenBank accession numbers shown in Table
5.
TABLE-US-00005 TABLE 5 PROTEIN GENBANK ID GI NUMBER ORGANISM thrA
AAC73113.1 1786183 Escherichia coli K12 akthr2 O81852 75100442
Arabidopsis thaliana hom6 CAA89671 1015880 Saccharomyces cerevisiae
hom1 CAD64819 28271914 Lactobacillus plantarum hom2 CAD63186
28270285 Lactobacillus plantarum
[0093] Acetoacetyl-CoA reductase (Step G, FIG. 2) catalyzing the
reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA participates
in the acetyl-CoA fermentation pathway to butyrate in several
species of Clostridia and has been studied in detail (Jones et al.,
Microbiol. Rev., 50:484-524 (1986)). The enzyme from Clostridium
acetobutylicum, encoded by hbd, has been cloned and functionally
expressed in E. coli (Youngleson et al., J Bacteriol.,
171:6800-6807 (1989)). Additionally, subunits of two fatty acid
oxidation complexes in E. coli, encoded by fadB and fad. J,
function as 3-hydroxyacyl-CoA dehydrogenases (Binstock et al.,
Methods Enzymol., 71C:403-411 (1981)). Yet other genes demonstrated
to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA are phbB from
Zoogloea ramigera (Ploux et al., Eur. J. Biochem., 174:177-182
(1988)) and phaB from Rhodobacter sphaeroides (Alber et al., Mol.
Microbiol., 61:297-309 (2006)). The former gene is NADPH-dependent,
its nucleotide sequence has been determined (Peoples et al., Mol.
Microbiol. 3:349-357 (1989)) and the gene has been expressed in E.
coli. Substrate specificity studies on the gene led to the
conclusion that it could accept 3-oxopropionyl-CoA as a substrate
besides acetoacetyl-CoA (Ploux et al., supra). Additional genes
include Hbd1 (C-terminal domain) and Hbd2 (N-terminal domain) in
Clostridium kluyveri (Hillmer and Gottschalk, Biochim. Biophys.
Acta 3334:12-23 (1974)) and HSD17B10 in Bos taurus (Wakil et al.,
J. Biol. Chem., 207:631-638 (1954)). Data related to the sequences
for each of these exemplary gene products can be found using the
following GenBank accession numbers shown in Table 6.
TABLE-US-00006 TABLE 6 Protein GENBANK ID GI NUMBER ORGANISM fadB
P21177.2 119811 Escherichia coli fadJ P77399.1 3334437 Escherichia
coli Hbd2 EDK34807.1 146348271 Clostridium kluyveri Hbd1 EDK32512.1
146345976 Clostridium kluyveri hbd P52041.2 Clostridium
acetobutylicum HSD17B10 O02691.3 3183024 Bos Taurus phbB P23238.1
130017 Zoogloea ramigera phaB YP_353825.1 77464321 Rhodobacter
sphaeroides
[0094] A number of similar enzymes have been found in other species
of Clostridia and in Metallosphaera sedula (Berg et al., Archaea.
Science, 318:1782-1786 (2007)) as shown in Table 7.
TABLE-US-00007 TABLE 7 Protein GenBank ID GI number Organism Hbd
NP_349314.1 NP_349314.1 Clostridium acetobutylicum Hbd AAM14586.1
AAM14586.1 Clostridium beijerinckii Msed_1423 YP_001191505
YP_001191505 Metallosphaera sedula Msed_0399 YP_001190500
YP_001190500 Metallosphaera sedula Msed_0389 YP_001190490
YP_001190490 Metallosphaera sedula Msed_1993 YP_001192057
YP_001192057 Metallosphaera sedula
[0095] An exemplary alcohol dehydrogenase that converts a ketone to
a hydroxyl group is the secondary alcohol dehydrogenase that was
shown to convert acetone to isopropanol in C. beijerinckii (Ismaiel
et al., J. Bacteriol., 175:5097-5105 (1993)) and T. brockii (Lamed
et al., Biochem. 1, 195:183-190 (1981); Peretz et al.,
Biochemistry, 28:6549-6555 (1989)). The gene product of adhA from
Pyrococcus furiosus, which exhibits maximum activity on 2-pentanol
and pyruvaldehyde, was shown to have very broad specificity which
includes isopropanol and acetone (Van der et al., Eur. J. Biochem.,
268:3062-3068 (2001)). Yet another secondary alcohol dehydrogenase
with activity on isopropanol and acetone is encoded by the gene
product of adh-A from Rhodococcus ruber (Edegger et al., Chem.
Commun. (Camb), 2402-2404 (2006); Kosjek et al., Biotechnol.
Bioeng., 86:55-62 (2004)). These genes along with others are listed
below in Table 8.
TABLE-US-00008 TABLE 8 Protein GenBank ID GI number Organism adh
AAA23199.2 60592974 Clostridium beijerinckii NRRL B593 adh P14941.1
113443 Thermoanaerobacter brockii HTD4 adhA AAC25556 3288810
Pyrococcus furiosus adh-A CAD36475 21615553 Rhodococcus ruber
[0096] Alternatively, there exist several exemplary alcohol
dehydrogenases that convert a ketone to a hydroxyl functional
group. Two such enzymes from E. coli are encoded by malate
dehydrogenase (mdh) and lactate dehydrogenase (ldhA). In addition,
lactate dehydrogenase from Ralstonia eutropha has been shown to
demonstrate high activities on substrates of various chain lengths
such as lactate, 2-oxobutyrate, 2-oxopentanoate and 2-oxoglutarate
(Steinbuchel et al., Eur. J. Biochem., 130:329-334 (1983)).
Conversion of the oxo functionality to the hydroxyl group can also
be catalyzed by 2-ketol, 3-butanediol reductase, an enzyme reported
to be found in rat and in human placenta (Suda et al., Arch.
Biochem. Biophys., 176:610-620 (1976); Suda et al., Biochem.
Biophys. Res. Commun., 77:586-591 (1977)). All of these enzymes can
provide a 3-oxobutyraldehyde reductase, and a 4-hydroxy-2-butanone
reductase. An additional enzyme for these steps is the
mitochondrial 3-hydroxybutyrate dehydrogenase (bdh) from the human
heart which has been cloned and characterized (Marks et al., J.
Biol. Chem. 267:15459-15463 (1992)). This enzyme is a dehydrogenase
that operates on a 3-hydroxyacid. Data related to the sequences for
each of these exemplary gene products can be found using the
following GenBank accession numbers shown in Table 9.
TABLE-US-00009 TABLE 9 Protein GenBank ID GI number Organism mdh
AAC76268.1 1789632 Escherichia coli ldhA NP_415898.1 16129341
Escherichia coli ldh YP_725182.1 113866693 Ralstonia eutropha bdh
AAA58352.1 177198 Homo sapiens
[0097] A number of organisms can catalyze the reduction of
4-hydroxy-2-butanone to 1,3-butanediol, including those belonging
to the genus Bacillus, Brevibacterium, Candida, and Klebsiella
among others, as described by Matsuyama et al. (1995).
[0098] Several transformations in FIGS. 2 and 3 rely on the
two-step reduction of acyl-CoA to the corresponding alcohol. For
example, Steps D and I in FIG. 2, involving the acetoacetyl-CoA
reductase (CoA-dependent, alcohol forming) and 3-hydroxybutyryl-CoA
reductase (alcohol forming), and Step E in FIG. 3 involving
3-hydroxybutyryl-CoA reductase (alcohol forming), shows such a
transformation.
[0099] Exemplary two-step oxidoreductases that convert an acyl-CoA
to alcohol include those that transform substrates such as
acetyl-CoA to ethanol (e.g., adhE from E. coli (Kessler et al.,
FEBS. Lett., 281:59-63 (1991)) and butyryl-CoA to butanol (e.g.
adhE2 from C. acetobutylicum (Fontaine et al., J. Bacteriol.,
184:821-830 (2002)). In addition to reducing acetyl-CoA to ethanol,
the enzyme encoded by adhE in Leuconostoc mesenteroides has been
shown to oxidize the branched chain compound isobutyraldehyde to
isobutyryl-CoA (Kazahaya et al., J. Gen. Appl. Microbiol., 18:43-55
(1972); Koo et al., Biotechnol. Lett., 27:505-510 (2005)). Data
related to the sequences for each of these exemplary gene products
can be found using the following GenBank accession numbers shown in
Table 10.
TABLE-US-00010 TABLE 10 Protein GenBank ID GI Number Organism adhE
NP_415757.1 16129202 Escherichia coli adhE2 AAK09379.1 12958626
Clostridium acetobutylicum adhE AAV66076.1 55818563 Leuconostoc
mesenteroides
[0100] Another exemplary enzyme can convert malonyl-CoA to 3-HP. An
NADPH-dependent enzyme with this activity has characterized in
Chloroflexus aurantiacus where it participates in the
3-hydroxypropionate cycle (Hugler et al., J. Bacteriol.,
184:2404-2410 (2002); Strauss et al., Eur. J. Biochem., 215:633-643
(1993)). This enzyme, with a mass of 300 kDa, is highly
substrate-specific and shows little sequence similarity to other
known oxidoreductases (Hugler et al., supra). No enzymes in other
organisms have been shown to catalyze this specific reaction;
however there is bioinformatic evidence that other organisms can
have similar pathways (Klatt et al., Environ. Microbiol.,
9:2067-2078 (2007)). Enzymes in other organisms including
Roseiflexus castenholzii, Erythrobacter sp. NAP1 and marine gamma
proteobacterium HTCC2080 can be inferred by sequence similarity.
Data related to the sequences for each of these exemplary gene
products can be found using the following GenBank accession numbers
shown in Table 11.
TABLE-US-00011 TABLE 11 Protein GenBank ID GI Number Organism mcr
AAS20429.1 42561982 Chloroflexus aurantiacus Rcas_2929
YP_001433009.1 156742880 Roseiflexus castenholzii NAP1_02720
ZP_01039179.1 85708113 Erythrobacter sp. NAP1 MGP2080_00535
ZP_01626393.1 119504313 marine gamma proteobacterium HTCC2080
[0101] Longer chain acyl-CoA molecules can be reduced by enzymes
such as the jojoba (Simmondsia chinensis) FAR which encodes an
alcohol-forming fatty acyl-CoA reductase. Its overexpression in E.
coli resulted in FAR activity and the accumulation of fatty alcohol
(Metz et al., Plant Physiology, 122:635-644 (2000)) (FAR,
AAD38039.1, 5020215, Simmondsia chinensis).
[0102] The pathways disclosed herein involve numerous
oxidoreductase-type transformations that convert an acyl-CoA to an
aldehyde. Specifically, Steps A and H in FIG. 2 catalyzed by
acetoacetyl-CoA reductase (aldehyde forming) and
3-hydroxybutyryl-CoA reductase (aldehyde forming), and Step C from
FIG. 3 showing the transformation catalyzed by 3-hydroxybutyryl-CoA
reductase.
[0103] Several acyl-CoA dehydrogenases are capable of reducing an
acyl-CoA to its corresponding aldehyde. Exemplary genes that encode
such enzymes include the Acinetobacter calcoaceticus acr1 encoding
a fatty acyl-CoA reductase (Reiser et al., J. of Bacteriology,
179:2969-2975 (1997)), the Acinetobacter sp. M-1 fatty acyl-CoA
reductase (Ishige et al., Appl. Environ. Microbiol., 68:1192-1195
(2002)), and a CoA- and NADP-dependent succinate semialdehyde
dehydrogenase encoded by the sucD gene in Clostridium kluyveri
(Sohling et al., J. Bacteriol., 178:871-880 (1996)). SucD of P.
gingivalis is another succinate semialdehyde dehydrogenase
(Takahashi et al., J. Bacteriol., 182:4704-4710 (2000)). The enzyme
acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by
bphG, is yet another enzyme demonstrated to oxidize and acylate
acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and
formaldehyde (Powlowski et al., J. Bacteriol., 175:377-385 (1993)).
In addition to reducing acetyl-CoA to ethanol, the enzyme encoded
by adhE in Leuconostoc mesenteroides has been shown to oxidize the
branched chain compound isobutyraldehyde to isobutyryl-CoA
(Kazahaya et al., supra; Koo et al., supra). Butyraldehyde
dehydrogenase catalyzes a similar reaction, conversion of
butyryl-CoA to butyraldehyde, in solventogenic organisms such as
Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci.
Biotechnol. Biochem., 71:58-61 (2007)). Additional aldehyde
dehydrogenase enzyme candidates are found in Desulfatibacillum
alkenivorans, Citrobacter koseri, Salmonella enterica,
Lactobacillus brevis and Bacillus selenitireducens. Data related to
the sequences for each of these exemplary gene products can be
found using the following GenBank accession numbers shown in Table
12.
TABLE-US-00012 TABLE 12 Protein GenBank ID GI Number Organism acr1
YP_047869.1 50086359 Acinetobacter calcoaceticus acr1 AAC45217
1684886 Acinetobacter baylyi acr1 BAB85476.1 18857901 Acinetobacter
sp. Strain M-1 sucD P38947.1 172046062 Clostridium kluyveri sucD
NP_904963.1 34540484 Porphyromonas gingivalis bphG BAA03892.1
425213 Pseudomonas sp adhE AAV66076.1 55818563 Leuconostoc
mesenteroides bld AAP42563.1 31075383 Clostridium
saccharoperbutylacetonicum ald ACL06658.1 218764192
Desulfatibacillum alkenivorans AK-01 ald YP_001452373 157145054
Citrobacter koseri ATCC BAA-895 pduP NP_460996.1 16765381
Salmonella enterica Typhimurium pduP ABJ64680.1 116099531
Lactobacillus brevis ATCC 367 BselDRAFT_1651 ZP_02169447 163762382
Bacillus selenitireducens MLS10
[0104] An additional enzyme type that converts an acyl-CoA to its
corresponding aldehyde is malonyl-CoA reductase which transforms
malonyl-CoA to malonic semialdehyde. Malonyl-CoA reductase is a key
enzyme in autotrophic carbon fixation via the 3-hydroxypropionate
cycle in thermoacidophilic archaeal bacteria (Berg et al., supra;
Thauer, R. K., Science, 318:1732-1733 (2007)). The enzyme utilizes
NADPH as a cofactor and has been characterized in Metallosphaera
and Sulfolobus spp (Alber et al., J. Bacteriol., 188:8551-8559
(2006); Hugler et al., supra). The enzyme is encoded by Msed_0709
in Metallosphaera sedula (Alber et al., supra; Berg et al., supra).
A gene encoding a malonyl-CoA reductase from Sulfolobus tokodaii
was cloned and heterologously expressed in E. coli (Alber et al.,
supra). This enzyme has also been shown to catalyze the conversion
of methylmalonyl-CoA to its corresponding aldehyde (2007). Although
the aldehyde dehydrogenase functionality of these enzymes is
similar to the bifunctional dehydrogenase from Chloroflexus
aurantiacus, there is little sequence similarity. Both malonyl-CoA
reductase enzymes have high sequence similarity to
aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the
reduction and concurrent dephosphorylation of aspartyl-4-phosphate
to aspartate semialdehyde. Additional genes can be found by
sequence homology to proteins in other organisms including
Sulfolobus solfataricus and Sulfolobus acidocaldarius and have been
listed below. Yet another enzyme for CoA-acylating aldehyde
dehydrogenase is the ald gene from Clostridium beijerinckii (Toth
et al., Appl. Environ. Microbiol., 65:4973-4980 (1999)). This
enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to
their corresponding aldehydes. This gene is very similar to eutE
that encodes acetaldehyde dehydrogenase of Salmonella typhimurium
and E. coli (Toth et al., supra). Data related to the sequences for
each of these exemplary gene products can be found using the
following GenBank accession numbers shown in Table 13.
TABLE-US-00013 TABLE 13 Protein GenBank ID GI Number Organism
MSED_0709 YP_001190808.1 146303492 Metallosphaera sedula mcr
NP_378167.1 15922498 Sulfolobus tokodaii asd-2 NP_343563.1 15898958
Sulfolobus solfataricus Saci_2370 YP_256941.1 70608071 Sulfolobus
acidocaldarius Ald AAT66436 9473535 Clostridium beijerinckii eutE
AAA80209 687645 Salmonella typhimurium eutE P77445 2498347
Escherichia coli
[0105] The oxidative deamination of amino groups to their
corresponding oxo groups is catalyzed by deaminating
oxidoreductases in the EC class 1.4.1. Such enzymes utilize
NAD.sup.+, NADP.sup.+ or FAD.sup.+ as acceptor. Enzymes in this
class can convert 2-amino-4-oxopentanoate to 2,4-dioxopentanoate
(FIG. 1, Step B), 2-amino-4-hydroxypentanoate to
2-oxo-4-hydroxypentanoate (FIG. 1, Step M) and 4-aminobutan-2-one
to 3-oxobutyraldehyde (FIG. 1, Step K). Exemplary oxidoreductases
operating on similar substrates include glutamate dehydrogenase
(deaminating), encoded by gdhA, leucine dehydrogenase
(deaminating), encoded by ldh, and aspartate dehydrogenase
(deaminating), encoded by nadX. The gdhA gene product from
Escherichia coli (McPherson et al., Nucleic. Acids Res.
11:5257-5266 (1983); Korber et al., J. Mol. Biol. 234:1270-1273
(1993)), gdh from Thermotoga maritima (Kort et al., Extremophiles
1:52-60 (1997); Lebbink et al., J. Mol. Biol. 280:287-296 (1998);
Lebbink et al., J. Mol. Biol. 289:357-369 (1999)), and gdhA1 from
Halobacterium salinarum (Ingoldsby et al., Gene. 349:237-244
(2005)) catalyze the reversible interconversion of glutamate to
2-oxoglutarate and ammonia, while favoring NADP(H), NAD(H), or
both, respectively. Additional glutamate dehydrogenase gene
candidates are found in Bacillus subtilis (Khan et al., Biosci.
Biotechnol Biochem. 69:1861-1870 (2005)), Nicotiana tabacum
(Purnell et al., Planta 222:167-180 (2005)), Oryza sativa (Abiko et
al., Plant Cell Physiol 46:1724-1734 (2005)), Haloferax
mediterranei (Diaz et al., Extremophiles. 10:105-115 (2006)),
Halobacterium salinarum (Hayden et al., FEMS Microbiol Lett.
211:37-41 (2002)) and yeast (Roca et al., Appl Environ. Microbiol
69:4732-4736 (2003)). The Nicotiana tabacum enzyme is composed of
alpha and beta subunits encoded by gdh1 and gdh2 (Purnell et al.,
Planta 222:167-180 (2005)). The ldh gene of Bacillus cereus encodes
the LeuDH protein that accepts a wide of range of substrates
including leucine, isoleucine, valine, and 2-aminobutanoate (Stoyan
et al., 1 Biotechnol 54:77-80 (1997); Ansorge et al., Biotechnol
Bioeng. 68:557-562 (2000)). The nadX gene from Thermotoga maritime
encoding for the aspartate dehydrogenase is involved in the
biosynthesis of NAD (Yang et al., J. Biol. Chem. 278:8804-8808
(2003)). Data related to the sequences for each of these exemplary
gene products can be found using the GenBank accession numbers
shown below in Table 14.
TABLE-US-00014 TABLE 14 Protein GenBank ID GI Number Organism gdhA
P00370 118547 Escherichia coli gdh P96110.4 6226595 Thermotoga
maritima gdhA1 NP_279651.1 15789827 Halobacterium salinarum rocG
NP_391659.1 16080831 Bacillus subtilis gdh1 AAR11534.1 38146335
Nicotiana tabacum gdh2 AAR11535.1 38146337 Nicotiana tabacum GDH
Q852M0 75243660 Oryza sativa GDH Q977U6 74499858 Haloferax
mediterranei GDH P29051 118549 Halobactreium salinarum GDH2
NP_010066.1 6319986 Saccharomyces cerevisiae ldh P0A393 61222614
Bacillus cereus nadX NP_229443.1 15644391 Thermotoga maritima
[0106] An enzyme with 4-aminobutan-2-one oxidoreductase
(deaminating) activity is required to convert 4-aminobutan-2-one to
its corresponding aldehyde (FIG. 1, Step K). Exemplary candidates
include 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) and lysine
6-dehydrogenase (EC 1.4.1.18). 3,5-Diaminohexanoate dehydrogenase
interconverts 3-amino acids and 3-oxoacids and has been
characterized in organisms that ferment lysine. The gene encoding
3,5-diaminohexanoate dehydrogenase, kdd, was recently identified in
Fusobacterium nucleatum (Kreimeyer et al., J Biol. Chem.
282:7191-7197 (2007)). The enzyme has been purified and
characterized in other organisms (Baker et al., J Biol. Chem.
247:7724-7734 (1972); Baker et al., Biochemistry 13:292-299 (1974))
but the genes associated with these enzymes are not known.
Candidates in other sequenced organisms can be inferred by sequence
homology. Lysine 6-dehydrogenase, encoded by the lysDH genes,
catalyzes the conversion of primary amines to their corresponding
aldehydes. This enzyme naturally catalyzes the reversible oxidative
deamination of the 6-amino group of L-lysine to form
2-aminoadipate-6-semialdehyde (Misono et al., J Bacteriol.
150:398-401 (1982)). Exemplary enzymes are found in Geobacillus
stearothermophilus (Heydari et al., Appl Environ. Microbiol
70:937-942 (2004)), Agrobacterium tumefaciens (Hashimoto et al., J
Biochem. 106:76-80 (1989); Misono and Nagasaki, J Bacteriol.
150:398-401 (1982)), and Achromobacter denitrificans
(Ruldeekulthamrong et al., BMB. Rep. 41:790-795 (2008)). Data
related to the sequences for each of these exemplary gene products
can be found using the following GenBank accession numbers shown in
Table 15.
TABLE-US-00015 TABLE 15 Protein GenBank ID GI Number Organism kdd
AAL93966.1 19713113 Fusobacterium nucleatum lysDH BAB39707 13429872
Geobacillus stearothermophilus lysDH NP_353966 15888285
Agrobacterium tumefaciens lysDH AAZ94428 74026644 Achromobacter
denitrificans
[0107] 2-Amino-4-oxopentanoate (AKP) thiolase or AKP thiolase
(AKPT) (Step 1, FIG. 1) is a pyridoxal phosphate-dependent enzyme
participating in ornithine degradation in Clostridium sticklandii
(Jeng et al., A. Biochemistry, 13:2898-2903 (1974); Kenklies et
al., Microbiology, 145:819-826 (1999)). A gene cluster encoding the
alpha and beta subunits of AKPT (or-2 (ortA) and or-3 (ortB)) was
recently identified and the biochemical properties of the enzyme
were characterized (Fonknechten et al., J. Bacteriol., In Press
(2009)). The enzyme is capable of operating in both directions and
reacts with the D-isomer of alanine. Enzyme engineering can be
performed to optimize function with L-alanine as a substrate. AKPT
from Clostridium sticklandii has been characterized but its protein
sequence has not yet been published. Enzymes with high sequence
homology are found in Clostridium difficile, Alkaliphilus
metalliredigenes QYF, Thermoanaerobacter sp. X514, and
Thermoanaerobacter tengcongensis MB4 (Fonknechten et al, supra).
Data related to the sequences for each of these exemplary gene
products can be found using the following GenBank accession numbers
shown in Table 16.
TABLE-US-00016 TABLE 16 Protein GenBank ID GI Number Organism ortA
(A) YP_001086914.1 126698017 Clostridium difficile 630 ortB
(.beta.) YP_001086915.1 126698018 Clostridium difficile 630
Amet_2368 (.alpha.) YP_001320181.1 150390132 Alkaliphilus
metalliredigenes QYF Amet_2369 (.beta.) YP_001320182.1 150390133
Alkaliphilus metalliredigenes QYF Teth514_1478 (.alpha.)
YP_001663101.1 167040116 Thermoanaerobacter sp. X514 Teth514_1479
(.beta.) YP_001663102.1 167040117 Thermoanaerobacter sp. X514
TTE1235 (.alpha.) NP_622858.1 20807687 Thermoanaerobacter
tengcongensis MB4 thrC (.beta.) NP_622859.1 20807688
Thermoanaerobacter tengcongensis MB4
[0108] The conversion of 2-amino-4-oxopentanoate (AKP) to
2,4-dioxopentanoate (Step B, FIG. 1) is accomplished by
2-amino-4-oxopentanoate aminotransferase or oxidoreductase
(deaminating). Selection of an appropriate enzyme for this
transformation is dependent on the stereochemistry of the
substrate. For example, if the substrate is in the D-configuration,
a D-amino acid aminotransferase (EC 2.6.1.21) can be utilized,
whereas the L-stereoisomer can utilize an L-aminotransferase such
as aspartate aminotransferase (EC 2.6.1.1).
[0109] Aspartate aminotransferase transfers an amino group from
aspartate to alpha-ketoglutarate, forming glutamate and
oxaloacetate. Aspartate is similar in structure to
2-amino-4-oxopentanoate. This conversion is catalyzed by, for
example, the gene products of aspC from Escherichia coli (Yagi et
al., FEBS Lett., 100:81-84 (1979); Yagi et al., Methods Enzymol.,
133:83-89 (1985)), AAT2 from Saccharomyces cerevisiae (Yagi et al.,
J. Biochem., 92:35-43 (1982)) and ASPS from Arabidopsis thaliana
(Kwok et al., J. Exp. Bot., 55:595-604 (2004); De la et al., Plant
1, 46:414-425 (2006); Wilkie et al., Protein Expr. Purif.,
12:381-389 (1998)). The enzyme from Rattus norvegicus has been
shown to transaminate alternate substrates such as
2-aminohexanedioic acid and 2,4-diaminobutyric acid (Recasens et
al., Biochemistry, 19:4583-4589 (1980)). Aminotransferases that
work on other amino-acid-like substrates can also catalyze this
transformation. Valine aminotransferase catalyzes the conversion of
valine and pyruvate to 2-ketoisovalerate and alanine. The E. coli
gene, avtA, encodes one such enzyme (Whalen et al., J. Bacteriol.,
150:739-746 (1982)). This gene product also catalyzes the amination
of .alpha.-ketobutyrate to generate .alpha.-aminobutyrate, although
the amine donor in this reaction has not been identified (Whalen et
al., J. Bacteriol., 158:571-574 (1984)). An additional candidate is
alpha-aminoadipate transaminase (EC 2.6.1.39), an enzyme that
participates in lysine biosynthesis and degradation in some
organisms. The enzyme from Thermus thermophilus, encoded by lysN,
is active with several alternate substrates including oxaloacetate,
2-oxoisocaproate, 2-oxoisovalerate, and 2-oxo-3-methylvalerate
(Miyazaki et al., Microbiol. 150:2327-2334 (2004)). A similar
enzyme from Homo sapiens has been characterized (Okuno et al., Enz.
Prot. 47:136-148 (1993)). Data related to the sequences for each of
these exemplary gene products can be found using the following
GenBank accession numbers shown in Table 17.
TABLE-US-00017 TABLE 17 Protein GenBank ID GI Number Organism aspC
NP_415448.1 16128895 Escherichia coli AAT2 P23542.3 1703040
Saccharomyces cerevisiae ASP5 P46248.2 20532373 Arabidopsis
thaliana got2 P00507 112987 Rattus norvegicus avtA YP_026231.1
49176374 Escherichia coli lysN BAC76939.1 31096548 Thermus
thermophilus AadAT-II Q8N5Z0.2 46395904 Homo sapiens
[0110] When the substrate is present as the D-stereoisomer,
transamination can be catalyzed by D-aminotransferase (EC
2.6.1.21), also known as D-amino acid aminotransferase and
D-alanine aminotransferase (DAAT). This class of enzymes is noted
for its broad substrate specificity, which is species-specific. The
D-aminotransferase from Bacillus species YM-1, encoded by dat, has
been cloned, sequenced (Tanizawa et al., J. Biol. Chem.,
264:2450-2454 (1989)) and the crystal structure has been solved
(Peisach et al., Biochemistry, 37:4958-4967 (1998)). This enzyme
has also been the subject of protein engineering studies to alter
the substrate specificity (Gutierrez et al., Eur. J. Biochem,
267:7218-7223 (2000); Gutierrez et al., Protein Eng., 11:53-58
(1998)). Additional genes are found in Bacillus licheniformis ATCC
10716 (Taylor et al., Biochim. Biophys. Acta., 1350:38-40 (1997)),
Staphylococcus haemolyticus (Pucci et al., J. Bacteriol.,
177:336-342 (1995)) and Bacillus subtilis (Martinez-Carrion et al.,
J. Biol. Chem., 240:3538-3546 (1965)). Data related to the
sequences for each of these exemplary gene products can be found
using the following GenBank accession numbers shown in Table
18.
TABLE-US-00018 TABLE 18 Protein GenBank ID GI Number Organism dat
P19938 118222 Bacillus sp. YM-1 dat P54692 1706292 Bacillus
licheniformis ATCC 10716 dat P54694 1706294 Staphylococcus
haemolyticus dat O07597.1 3121979 Bacillus subtilis
[0111] In reaction K of FIG. 1, 4-aminobutan-2-one is transaminated
to form 3-oxobutanal. This transformation can likely be catalyzed
by an aminotransferase that interconverts terminal amines and
aldehydes. Exemplary candidate enzymes are
beta-alanine/alpha-ketoglutarate aminotransferase, GABA
aminotransferase, 3-amino-2-methylpropionate transaminase,
lysine-6-aminotransferase, 2,4-diaminobutanoate transaminase,
putrescine aminotransferase and diamine aminotransferase.
[0112] Cargill has developed and patented a
beta-alanine/alpha-ketoglutarate aminotransferase for producing
3-HP from beta-alanine via malonyl-semialdehyde (Chandra et al.,
ARch. Microbiol., 176:443-451 (2001)). The gene product of SkPYD4
in Saccharomyces kluyveri was also shown to preferentially use
beta-alanine as the amino group donor (Aberhart et al., J. Chem.
Soc. 6:1404-1406 (1979)). SkUGA1 encodes a homologue of
Saccharomyces cerevisiae GABA aminotransferase, UGA1 (Ichikawa et
al., J. Mol. Catalysis A-Chem., 256:106-112 (2006)), whereas SkPYD4
encodes an enzyme involved in both .beta.-alanine and GABA
transamination (Aberthart et al., Supra).
3-amino-2-methylpropionate transaminase catalyzes the
transformation from methylmalonate semialdehyde to
3-amino-2-methylpropionate. The enzyme has been characterized in
Rattus norvegicus and Sus scrofa and is encoded by Abat (Chopra et
al., Protein Expr. Purif., 25:533-540 (2002), Kuznetsova et al.,
FEMS Microbiol. Rev., 29:263-279 (2005)). Enzyme candidates in
other organisms with high sequence homology to
3-amino-2-methylpropionate transaminase include Gta-1 in C. elegans
and gabT in Bacillus subtilis. Additionally, one of the native GABA
aminotransferases in E. coli, encoded by gene gabT, has been shown
to have broad substrate specificity (Fontaine et al., J.
Bacteriol., 184:821-830 (2002), Kanamasa et al., Appl. Microbiol
Biotechnol., 80:223-229 (2008)). The gene puuE encodes the other
4-aminobutyrate transaminase in E. coli (Drummond et al., J. Biol.
Chem., 235:318-325 (1960)).
[0113] Lysine-6-aminotransferase converts lysine to
alpha-aminoadipate semialdehyde. Candidate enzymes have been
characterized in Candida utilis (Hammer et al., J Basic Microbiol
32:21-27 (1992)), Flavobacterium lutescens (Fujii et al., J
Biochem. 128:391-397 (2000)) and Streptomyces clavuligenus (Romero
et al., J Ind. Microbiol Biotechnol 18:241-246 (1997)). A
recombinant lysine-6-aminotransferase from S. clavuligenus was
functionally expressed in E. coli (Tobin et al., J Bacteriol.
173:6223-6229 (1991)). The F. lutescens enzyme is specific to
alpha-ketoglutarate as the amino acceptor (Soda et al.,
Biochemistry 7:4110-4119 (1968)). An enzyme with diaminobutanoate
transaminase activity is encoded by the dat gene product in
Acinetobacter baumanii (Ikai et al., J Bacteriol. 179:5118-5125
(1997)). In addition to its natural substrate, 2,4-diaminobutyrate,
DAT transaminates the terminal amines of lysine, 4-aminobutyrate
and ornithine. Candidate putrescine aminotransferase enzymes are
encoded by ygjG in E. coli and spuC of Pseudomonas aeruginosa (Lu
et al., J Bacteriol. 184:3765-3773 (2002)). The ygiG gene product
reacts with the alternate substrates cadaverine, spermidine and
1,7-diaminoheptanoate (Samsonova et al., BMC. Microbiol 3:2 (2003);
Kim, J Biol. Chem. 239:783-786 (1964)).
[0114] Data related to the sequences for each of these exemplary
gene products can be found using the following GenBank accession
numbers shown in Table 19.
TABLE-US-00019 TABLE 19 Protein GenBank ID GI Number Organism
SkyPYD4 ABF58893.1 98626772 Saccharomyces kluyveri SkUGA1
ABF58894.1 98626792 Saccharomyces kluyveri UGA1 NP_011533.1 6321456
Saccharomyces cerevisiae Abat P50554.3 122065191 Rattus norvegicus
Abat P80147.2 120968 Sus scrofa Gta-1 Q21217.1 6016091
Caenorhabditis elegans gabT P94427.1 6016090 Bacillus subtilis gabT
P22256.1 16130576 Escherichia coli K12 puuE NP_415818.1 16129263
Escherichia coli K12 lat BAB13756.1 10336502 Flavobacterium
lutescens lat AAA26777.1 153343 Streptomyces clavuligenus dat
P56744.1 6685373 Acinetobacter baumanii ygjG NP_417544 145698310
Escherichia coli spuC AAG03688 9946143 Pseudomonas aeruginosa
[0115] In FIG. 1, Step C, 2,4-dioxopentanoate is decarboxylated to
form 3-oxobutyraldehyde by 2,4-dioxopentanoate decarboxylase.
2,4-dioxopentanoate is similar to the native substrates of pyruvate
decarboxylase (EC 4.1.1.1) and benzoylformate decarboxylase (EC
4.1.1.7). Pyruvate decarboxylase (PDC), also termed keto-acid
decarboxylase, is a key enzyme in alcoholic fermentation,
catalyzing the decarboxylation of pyruvate to acetaldehyde. The
enzyme from Saccharomyces cerevisiae has a broad substrate range
for aliphatic 2-keto acids including 2-ketobutyrate,
2-ketovalerate, 3-hydroxypyruvate and 2-phenylpyruvate (Li et al.,
Biochemistry, 38:10004-10012 (1999)). This enzyme has been
extensively studied, engineered for altered activity, and
functionally expressed in E. coli (Killenberg-Jabs et al., Eur. J.
Biochem., 268:1698-1704 (2001); Li et al., supra; Schure et al.,
Appl. Environ. Microbiol., 64:1303-1307 (1998)). The PDC from
Zymomonas mobilis, encoded by pdc, also has a broad substrate range
and has been a subject of directed engineering studies to alter the
affinity for different substrates (Siegert et al., Protein Eng.
Des. Sel., 18:345-357 (2005)). The crystal structure of this enzyme
is available (Killenberg-Jabs, supra). Other well-characterized PDC
enzymes include the enzymes from Acetobacter pasteurians (Chandra
et al., Arch. Microbiol. 176:443-451 (2001)) and Kluyveromyces
lactis (Krieger et al., Eur. J. Biochem., 269:3256-3263 (2002)).
Data related to the sequences for each of these exemplary gene
products can be found using the following GenBank accession numbers
shown in Table 20.
TABLE-US-00020 TABLE 20 Protein GenBank ID GI Number Organism pdc
P06672.1 118391 Zymomonas mobilis pdc1 P06169 30923172
Saccharomyces cerevisiae pdc Q8L388 20385191 Acetobacter
pasteurians pdc1 Q12629 52788279 Kluyveromyces lactis
[0116] Like PDC, benzoylformate decarboxylase (EC 4.1.1.7) has a
broad substrate range and has been the target of enzyme engineering
studies. The enzyme from Pseudomonas putida has been extensively
studied and crystal structures of this enzyme are available
(Polovnikova et al., Biochemistry 42:1820-1830 (2003); Hasson et
al., Biochemistry, 37:9918-9930 (1998)). Site-directed mutagenesis
of two residues in the active site of the Pseudomonas putida enzyme
altered the affinity (Km) of naturally and non-naturally occurring
substrates (Siegert et al., supra). The properties of this enzyme
have been further modified by directed engineering (Lingen et al.,
Chembiochem, 4:721-726 (2003); Lingen et al., Protein Eng.,
15:585-593 (2002)). The enzyme from Pseudomonas aeruginosa, encoded
by mdlC, has also been characterized experimentally (Barrowman et
al., FEMS Microbiology Letters, 34:57-60 (1986)). Additional genes
from Pseudomonas stutzeri, Pseudomonas fluorescens and other
organisms can be inferred by sequence homology or identified using
a growth selection system developed in Pseudomonas putida (Henning
et al., Appl. Environ. Microbiol., 72:7510-7517 (2006)). Data
related to the sequences for each of these exemplary gene products
can be found using the following GenBank accession numbers shown in
Table 21.
TABLE-US-00021 TABLE 21 Protein GenBank ID GI Number Organism mdlC
P20906.2 3915757 Pseudomonas putida mdlC Q9HUR2.1 81539678
Pseudomonas aeruginosa dpgB ABN80423.1 126202187 Pseudomonas
stutzeri ilvB-1 YP_260581.1 70730840 Pseudomonas fluorescens
[0117] A third enzyme capable of decarboxylating 2-oxoacids is
alpha-ketoglutarate decarboxylase (KGD). The substrate range of
this class of enzymes has not been studied to date. The KDC from
Mycobacterium tuberculosis (Tian et al., Proc. Natl. Acad. Sci.
USA, 102:10670-10675 (2005)) has been cloned and has been
functionally expressed in E. coli at Genomatica. KDC enzyme
activity has been detected in several species of Rhizobia including
Bradyrhizobium japonicum and Mesorhizobium loti (Green et al., J.
Bacteriol., 182:2838-2844 (2000)). Although the KDC-encoding
gene(s) have not been isolated in these organisms, the genome
sequences are available and several genes in each genome are
annotated as putative KDCs. A KDC from Euglena gracilis has also
been characterized but the gene associated with this activity has
not been identified to date (Shigeoka et al., Arch. Biochem.
Biophys., 288:22-28 (1991)). The first twenty amino acids starting
from the N-terminus were sequenced MTYKAPVKDVKFLLDKVFKV (Shigeoka
et al., supra). The gene can be identified by testing genes
containing this N-terminal sequence for KDC activity. Data related
to the sequences for each of these exemplary gene products can be
found using the following GenBank accession numbers shown in Table
22.
TABLE-US-00022 TABLE 22 Protein GenBank ID GI Number Organism kgd
O50463.4 160395583 Mycobacterium tuberculosis kgd NP_767092.1
27375563 Bradyrhizobium japonicum USDA110 kgd NP_105204.1 13473636
Mesorhizobium loti
[0118] A fourth enzyme for catalyzing this step is the branched
chain alpha-ketoacid decarboxylase (BCKA). This class of enzymes
has been shown to act on a variety of compounds varying in chain
length from 3 to 6 carbons (Oku et al., J. Biol. Chem.,
263:18386-18396 (1988); Smit et al., Appl. Environ. Microbiol.,
71:303-311 (2005)). The enzyme in Lactococcus lactis has been
characterized on a variety of branched and linear substrates
including 2-oxobutanoate, 2-oxohexanoate, 2-oxopentanoate,
3-methyl-2-oxobutanoate, 4-methyl-2-oxobutanoate and isocaproate
(Smit et al., supra). The enzyme has been structurally
characterized (Berthold et al., D. Biol. Crystallogr., 63:1217-1224
(2007)). Sequence alignments between the Lactococcus lactis enzyme
and the pyruvate decarboxylase of Zymomonas mobilis indicate that
the catalytic and substrate recognition residues are nearly
identical (Siegert et al., supra), so this enzyme is readily
amenable to directed engineering. Additional BCKA genes can be
identified by homology to the Lactococcus lactis protein sequence
(kdcA, AAS49166.1, 44921617, Lactococcus lactis). Many of the
high-scoring BLASTp hits to this enzyme are annotated as
indolepyruvate decarboxylases (EC 4.1.1.74). Indolepyruvate
decarboxylase (IPDA) is an enzyme that catalyzes the
decarboxylation of indolepyruvate to indoleacetaldehyde in plants
and plant bacteria.
[0119] 2-amino-4-ketopentanoate is decarboxylated to form
4-aminobutan-2-one by AKP decarboxylase in Step E of FIG. 1. This
transformation can be catalyzed by an amino acid decarboxylase.
Selection of an appropriate decarboxylase depends on the
stereochemical configuration of 4-amino-4-oxopentanoate. When this
compound is in a D-configuration, a D-amino acid decarboxylase can
be utilized. One such D-amino acid decarboxylase is diaminopimelate
decarboxylase (DDC, EC 4.1.1.20). This enzyme decarboxylates the
D-stereocenter of meso-diaminopimelate, catalyzing the final step
of lysine biosynthesis. DDC has been studied in many organisms
including E. coli (Momany et al., D. Biol. Crystallogr., 58:549-552
(2002)), Mycobacterium tuberculosis (Kefala et al., Acta.
Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 61:782-784
(2005); Gokulan et al., J. Biol. Chem., 278:18588-18596 (2003);
Andersen et al., Gene, 124:105-109 (1993)), Methylophilus
methylotrophus (Tsujimoto et al., J. Biotechnol, 124:327-337
(2006)), and Helicobacter pylori (Hu et al., J. Biol. Chem.,
283:21284-21293 (2008)). Alternately, the ornithine decarboxylase
(EC 4.1.1.17) from Homo sapiens has a weak activity on the D-isomer
of ornithine (Qu et al., Biochem. 1, 375:465-470 (2003); Fitzgerald
et al., DNA, 8:623-634 (1989)) and can be used for the
decarboxylation in step E. Data related to the sequences for each
of these exemplary gene products can be found using the following
GenBank accession numbers shown in Table 23.
TABLE-US-00023 TABLE 23 Protein GenBank ID GI Number Organism lysA
NP_417315.1 16130742 Escherichia coli lysA AAA25361.1 149964
Mycobacterium tuberculosis lysA BAC92756.1 37196770 Methylophilus
methylotrophus lysA ABW70801.1 158523325 Helicobacter pylori odc1
AA59969.1 386989 Homo sapiens
[0120] When 2-amino-4-ketopentanoate exhibits L-stereochemistry, an
amino acid decarboxylase such as aspartate decarboxylase (EC
4.1.1.11), ornithine decarboxylase (EC 4.1.1.17) or lysine
decarboxylase (EC 4.1.1.18) can be utilized. An exemplary enzyme is
aspartate decarboxylase (EC 4.1.1.11). 2-Amino-4-ketopentanoate
bears structural similarity to aspartate, the native substrate of
this enzyme. Aspartate decarboxylase participates in pantothenate
biosynthesis and is encoded by panD in Escherichia coli (Dusch et
al., Appl. Environ. Microbiol., 65:1530-1539 (1999); Ramjee et al.,
Biochem. 1, 323:661-669 (1997); Merkel et al., FEMS Microbiol.
Lett., 143:247-252 (1996); Schmitzberger et al., EMBO I,
22:6193-6204 (2003)). The enzymes from Mycobacterium tuberculosis
(Chopra et al., Protein Expr. Purif., 25:533-540 (2002)) and
Corynebacterium glutanicum (Dusch et al., supra) have been
expressed and characterized in E. coli. Lysine decarboxylase
enzymes are encoded in the E. coli genome by genes cadA and ldcC. A
lysine decarboxylase analogous to CadA was recently identified in
Vibrio parahaemolyticus (Tanaka et al., J Appl. Microbiol.
104:1283-1293 (2008)). The lysine decarboxylase from Selenomonas
ruminantium, encoded by ldc, bears sequence similarity to
eukaryotic ornithine decarboxylases, and accepts both L-lysine and
L-ornithine as substrates (Takatsuka et al., Biosci. Biotechnol
Biochem. 63:1843-1846 (1999)). Ornithine decarboxylase enzyme
candidates are found in Nicotiana glutinosa (Lee et al., Biochem.
J. 360:657-665 (2001)), Lactobacillus sp. 30a (Guirard et al., J
Biol. Chem. 255:5960-5964 (1980)) and Vibrio vulnificus (Lee et
al., J Biol. Chem. 282:27115-27125 (2007)). The residues involved
in substrate specificity Vibrio vulnificus have been elucidated
(Lee et al., supra).
[0121] Data related to the sequences for each of these exemplary
gene products can be found using the following GenBank accession
numbers shown in Table 24.
TABLE-US-00024 TABLE 24 Protein GenBank ID GI Number Organism panD
P0A790 67470411 Escherichia coli panD Q9X4N0 18203593
Corynebacterium glutanicum panD P65660.1 54041701 Mycobacterium
tuberculosis cadA AAA23536. 145458 Escherichia coli ldcC AAC73297.1
1786384 Escherichia coli ldc O50657.1 13124043 Selenomonas
ruminantium cadA AB124819.1 44886078 Vibrio parahaemolyticus
AF323910.1: AAG45222.1 12007488 Nicotiana glutinosa 1 . . . 1299
odc1 P43099.2 1169251 Lactobacillus sp. 30a VV2_1235 NP_763142.1
27367615 Vibrio vulnificus
[0122] In reaction J (FIG. 1), acetylacrylate is decarboxylated to
2-oxobutene by acetoacrylate decarboxylase. An enzyme catalyzing
this transformation has not been identified to date, but similar
reactions are catalyzed by the enzymes aconitate decarboxylase,
4-oxalocrotonate decarboxylase and cinnamate decarboxylase.
[0123] Aconitate decarboxylase catalyzes the final step in
itaconate biosynthesis in a strain of Candida and also in the
filamentous fungus Aspergillus terreus (Bonnarme et al.,
Bacteriol., 177:3573-3578 (1995); Willke et al., Appl. Microbiol.
Biotechnol., 56:289-295 (2001)). A cis-aconitate decarboxylase
(CAD) (EC 4.1.16), encoded by ATEG 09971, has been identified and
extensively studied in Aspergillus terreus and other related fungi.
Recently, the gene has been cloned and functionally characterized
(Kanamasa et al., Appl. Microbiol. Biotechnol., 80:223-229 (2008))
and (WO/2009/014437).
[0124] 4-oxalocronate decarboxylase has been isolated from numerous
organisms and characterized. Genes encoding this enzyme include
dmpH and dmpE in Pseudomonas sp. (strain 600) (Shingler et al., J.
Bacteriol., 174:711-724 (1992)), xylII and xylIII from Pseudomonas
putida (Kato et al., Arch. Microbiol., 168:457-463 (1997); Stanley
et al., Biochemistry, 39:3514 (2000); Lian et al., J. Am. Chem.
Soc., 116:10403-10411 (1994)) and Reut_B5691 and Reut_B5692 from
Ralstonia eutropha JMP 134 (Hughes et al., J. Bacteriol., 158:79-83
(1984)). The genes encoding the enzyme from Pseudomonas sp. (strain
600) have been cloned and expressed in E. coli (Shingler et al.,
supra). Data related to the sequences for each of these exemplary
gene products can be found using the following GenBank accession
numbers shown in Table 25.
TABLE-US-00025 TABLE 25 Protein GenBank ID GI Number Organism dmpH
CAA43228.1 45685 Pseudomonas sp. CF600 dmpE CAA43225.1 45682
Pseudomonas sp. CF600 xylII YP_709328.1 111116444 Pseudomonas
putida xylIII YP_709353.1 111116469 Pseudomonas putida Reut_B5691
YP_299880.1 73539513 Ralstonia eutropha JMP134 Reut_B5692
YP_299881.1 73539514 Ralstonia eutropha JMP134 ATEG_09971
EAU29420.1 114187720 Aspergillus terreus
[0125] An additional class of decarboxylases has been characterized
that catalyze the conversion of cinnamate (phenylacrylate) and
substituted cinnamate derivatives to the corresponding styrene
derivatives. These enzymes are common in a variety of organisms and
specific genes encoding these enzymes that have been cloned and
expressed in E. coli are: pad 1 from Saccharomyces cerevisae
(Clausen et al., Gene, 142:107-112 (1994)), pdc from Lactobacillus
plantarum (Barthelmebs et al., Appl. Environ. Microbiol.,
67:1063-1069 (2001); Rodriguez et al., J. Agric. Food Chem.,
56:3068-3072 (2008); Qi et al., Biochem. 1, 375:465-470 (2007)),
pofK (pad) from Klebsiella oxytoca (Uchiyama et al., Biosci.
Biotechnol. Biochem., 72:116-123 (2008); Hashidoko et al., Biosci.
Biotech. Biochem., 58:217-218 (1994)), Pedicoccus pentosaceus
(Barthelmebs et al., supra) and padC from Bacillus subtilis and
Bacillus pumilus (Cavin et al., Appl. Environ. Microbiol.,
64:1466-1471 (1998)). A ferulic acid decarboxylase from Pseudomonas
fluorescens also has been purified and characterized (Huang et al.,
J. Bacteriol., 176:5912-5918 (1994)). Importantly, this class of
enzymes has been shown to be stable and does not require either
exogenous or internally bound co-factors, thus making these enzymes
ideally suitable for biotransformations (Sariaslani, F. S., Annu.
Rev. Microbiol., 61:51-69 (2007)). Data related to the sequences
for each of these exemplary gene products can be found using the
following GenBank accession numbers shown in Table 26.
TABLE-US-00026 TABLE 26 Protein GenBank ID GI Number Organism pad1
AAB64980.1 1165293 Saccharomyces cerevisae pdc AAC45282.1 1762616
Lactobacillus plantarum pad BAF65031.1 149941608 Klebsiella oxytoca
padC NP_391320.1 16080493 Bacillus subtilis pad YP_804027.1
116492292 Pedicoccus pentosaceus pad CAC18719.1 11691810 Bacillus
pumilus
[0126] An additional enzyme for decarboxylation is acetoacetate
decarboxylase (EC 4.1.1.4), an enzyme that decarboxylates
acetoacetate to acetone and has therefore been studied for its role
in bacterial solventogenesis. Exemplary bacterial enzymes have been
characterized from Clostridium acetobutylicum (Benner et al., J.
Am. Chem. So. 103:993-994 (1981); HIghbarger et al., Biochemistry
35:41-46 (1996); Petersen et al., Appl. Environ. Microbiol.
56:3491-3498 (1990); Rozzel et al. I Am. Chem. Soc. 106:4937-4941
(1984)) Clostridium saccharoperbutylacetonicum (Kosaka, et al.,
Biosci. Biotechnol Biochem. 71:58-68 (2007)) and Clostridium
beijerinckii (Ravagnani et al. Mol. Microbiol. 37:1172-1185
(2000)). Acetoacetate decarboxylase activity has also been
demonstrated in Pseudomonas putida and Bacillus polymyxa but genes
are not associated with this activity to date (Matiasek et al.,
Curr. Microbiol. 42: 276-281 (2001)). Bacterial genes in other
organisms such as Clostridium botulinum and Bacillus
amyloliquefaciens can be identified by sequence homology. In humans
and other mammals, acetoacetate decarboxylase catalyzes the final
step of the ketone-body pathway (Kalapos, Biochim. Biophys. Acta
1621:122-139 (2003)), but genes associated with this activity have
not been identified to date. Data related to the sequences for each
of these exemplary gene products can be found using the following
GenBank accession numbers shown in Table 27.
TABLE-US-00027 TABLE 27 Protein GenBank ID GI Number Organism adc
NP_149328.1 15004868 Clostridium acetobutylicum adc AAP42566.1
31075386 Clostridium saccharoperbutylacetonicum cbei_3835
YP_001310906.1 150018652 Clostridium beijerinckii CLL_A2135
YP_001886324.1 187933144 Clostridium botulinum RBAM_030030
YP_001422565.1 154687404 Bacillus amyloliquefaciens
[0127] All the aforementioned gene candidates can also be used to
catalyze the decarboxylation of 2-oxo-4-hydroxypentanoate to
3-hydroxybutyraldehyde in Step N of FIG. 1.
[0128] Butenone hydratase (Step G, FIG. 1), 4-hydroxybutyryl-CoA
dehydratase (Step A, FIG. 3) and crotonase (Step A, FIG. 3) are
hydrolyase-type transformations. Specifically, the hydration of
butenone to 4-hydroxy-2-butanone (Step G, FIG. 1) can be
accomplished by an enzyme in the hydratase family of enzymes.
Enzymes that can carry out this transformation include fumarate
hydratase (EC 4.2.1.2), 2-(hydroxymethyl)glutarate dehydratase (EC
4.2.1.-), dimethylmaleate hydratase (EC 4.2.1.85) and citramalate
hydrolyase (EC 4.2.1.34).
[0129] Fumarate hydratase enzymes naturally catalyze the reversible
hydration of fumarate to malate. Although the ability of fumarate
hydratase to react with butanone as a substrate has not been
described in the literature, a wealth of structural information is
available for this enzyme and other researchers have successfully
engineered the enzyme to alter activity, inhibition and
localization (Weaver, T., B. Biol. Crystallogr., 61:1395-1401
(2005)). E. coli has three fumarases: FumA, FumB, and FumC that are
regulated by growth conditions. FumB is oxygen sensitive and only
active under anaerobic conditions. FumA is active under
microanaerobic conditions, and FumC is the only active enzyme in
aerobic growth (Tseng et al., J. Bacteriol., 183:461-467 (2001);
Woods et al., Biochem. Biophys. Acta., 954:14-26 (1988); Guest et
al., J. Gen. Microbiol., 131:2971-2984 (1985)). Additional enzymes
are found in Campylobacter jejuni (Smith et al., Int. J. Biochem.
Cell Biol., 31:961-975 (1999)), Thermus thermophilus (Mizobata et
al., Arch. Biochem. Biophys., 355:49-55 (1998)) and Rattus
norvegicus (Kobayashi et al., J. Biochem., 89:1923-1931 (1981)).
Similar enzymes with high sequence homology include fum1 from
Arabidopsis thaliana and fumC from Corynebacterium glutamicum. The
MmcBC fumarase from Pelotomaculum thermopropionicum is another
class of fumarase with two subunits (Shimoyama et al., FEMS
Microbiol. Lett., 270:207-213 (2007)). Data related to the
sequences for each of these exemplary gene products can be found
using the following GenBank accession numbers shown in Table
28.
TABLE-US-00028 TABLE 28 Protein GenBank ID GI Number Organism fumA
NP_416129.1 16129570 Escherichia coli fumB NP_418546.1 16131948
Escherichia coli fumC NP_416128.1 16129569 Escherichia coli fumC
O69294 9789756 Campylobacter jejuni fumC P84127 75427690 Thermus
thermophilus fumH P14408 120605 Rattus norvegicus fum1 P93033
39931311 Arabidopsis thaliana fumC Q8NRN8 39931596 Corynebacterium
glutamicum MmcB YP_001211906 147677691 Pelotomaculum
thermopropionicum MmcC YP_001211907 147677692 Pelotomaculum
thermopropionicum
[0130] Two additional hydratase enzymes are
2-(hydroxymethyl)glutarate dehydratase and dimethylmaleate
hydratase, enzymes studied for their role in nicotinate catabolism
in Eubacterium barkeri (formerly Clostridium barkeri) (Alhapel et
al., Proc. Natl. Acad. Sci. USA, 103:12341-12346 (2006)).
2-(Hydroxymethyl)glutarate dehydratase is a [4Fe-4S]-containing
enzyme that dehydrates 2-(hydroxymethyl)glutarate to
2-methylene-glutarate. This enzyme is encoded by hmd in Eubacterium
barkeri (Alhapel et al., supra). Similar enzymes with high sequence
homology are found in Bacteroides capillosus, Anaerotruncus
colihominis, and Natranaerobius thermophilius. These enzymes are
homologous to the alpha and beta subunits of [4Fe-4S]-containing
bacterial serine dehydratases (e.g., E. coli enzymes encoded by
tdcG, sdhB, and sdaA). Dimethylmaleate hydratase (EC 4.2.1.85) is a
reversible Fe'-dependent and oxygen-sensitive enzyme in the
aconitase family that hydrates dimethylmaleate to form
(2R,3S)-2,3-dimethylmalate. This enzyme is encoded by dmdAB in
Eubacterium barkeri (Alhapel, et al., supra; Kollmann-Koch et al.,
Physiol. Chem., 365:847-857 (1984)). Data related to the sequences
for each of these exemplary gene products can be found using the
following GenBank accession numbers shown in Table 29.
TABLE-US-00029 TABLE 29 Protein GenBank ID GI Number Organism hmd
ABC88407.1 86278275 Eubacterium barkeri BACCAP_02294 ZP_02036683.1
154498305 Bacteroides capillosus ATCC 29799 ANACOL_02527
ZP_02443222.1 167771169 Anaerotruncus colihominis DSM 17241
NtherDRAFT_2368 ZP_02852366.1 169192667 Natranaerobius thermophilus
JW/NM-WN-LF dmdA ABC88408 86278276 Eubacterium barkeri dmdB
ABC88409.1 86278277 Eubacterium barkeri
[0131] An additional enzyme is 2-methylmalate dehydratase, also
called citramalate hydrolyase, a reversible hydrolyase that
catalyzes the alpha, beta elimination of water from citramalate to
form mesaconate. This enzyme has been purified and characterized in
Clostridium tetanomorphum (Wang et al., J. Biol. Chem.,
244:2516-2526 (1969)). The activity of this enzyme has also been
detected in several bacteria in the genera Citrobacter and
Morganella in the context of the glutamate degradation VI pathway
(Kato et al., supra). Genes encoding this enzyme have not been
identified in any organism to date.
[0132] Hydration of crotonyl-CoA to form 3-hydroxybutyryl-CoA (Step
B, FIG. 3) is catalyzed by a crotonase (EC 4.2.1.55). These enzymes
are required for n-butanol formation in some organisms,
particularly Clostridial species, and also comprise one step of the
3-hydroxypropionate/4-hydroxybutyrate cycle in thermoacidophilic
Archaea of the genera Sulfolobus, Acidianus, and Metallosphaera.
Exemplary genes encoding crotonase enzymes can be found in C.
acetobutylicum (Boynton et al., J. Bacteriol., 178:3015-3024
(1996)), C. kluyveri (Hillmer et al., FEBS Lett., 21:351-354
(1972)), and Metallosphaera sedula (Berg et al., supra). Enoyl-CoA
hydratases, which are involved in fatty acid beta-oxidation and/or
the metabolism of various amino acids, can also catalyze the
hydration of crotonyl-CoA to form 3-hydroxybutyryl-CoA (Roberts et
al., Arch. Microbiol., 117:99-108 (1978); Agnihotri et al., Bioorg.
Med. Chem., 11:9-20 (2003); Conrad et al., J. Bacteriol.,
118:103-111 (1974)). An exemplary enoyl-CoA hydratase is the gene
product of ech from Pseudomonas putida (Roberts et al., supra). The
enoyl-CoA hydratases, phaA and phaB, of P. putida have been
indicated to carry out the hydroxylation of double bonds during
phenylacetate catabolism (Olivera et al., Proc. Natl. Acad. Sci
USA, 95:6419-6424 (1998)). The paaA and paaB from P. fluorescens
catalyze analogous transformations (Olivera et al., supra). Lastly,
a number of Escherichia coli genes have been shown to demonstrate
enoyl-CoA hydratase functionality including maoC (Park et al., J.
Bacteriol., 185:5391-5397 (2003)), paaF (Ismail et al., Eur. J.
Biochem., 270:3047-3054 (2003); Park et al., Appl. Biochem.
Biotechnol., 113-116:335-346 (2004); Park et al., Biotechnol
Bioeng., 86:681-686 (2004)) and paaG (Ismail et al., supra; Park et
al., supra; Park et al., supra). Data related to the sequences for
each of these exemplary gene products can be found using the
following GenBank accession numbers shown in Table 30.
TABLE-US-00030 TABLE 30 Protein GenBank ID GI Number Organism crt
NP_349318.1 15895969 Clostridium acetobutylicum crt1 YP_001393856
153953091 Clostridium kluyveri DSM 555 ech NP_745498.1 26990073
Pseudomonas putida phaA ABF82233.1 26990002 Pseudomonas putida phaB
ABF82234.1 26990001 Pseudomonas putida paaA NP_745427.1 106636093
Pseudomonas fluorescens paaB NP_745426.1 106636094 Pseudomonas
fluorescens maoC NP_415905.1 16129348 Escherichia coli paaF
NP_415911.1 16129354 Escherichia coli paaG NP_415912.1 16129355
Escherichia coli
[0133] Alternatively, the E. coli gene products of fadA and fadB
encode a multienzyme complex involved in fatty acid oxidation that
exhibits enoyl-CoA hydratase activity (Haller et al., Biochemistry
39:4622-4629 (2000); Martinez-Carrion et a., J. Biol. Chem.
240:3538-3546 (1965); Matthies et al., Appl. Environ. Micriobiol.
58:1435-1439 (1992)). Knocking out a negative regulator encoded by
fadR can be utilized to activate the fadB gene product (Jeng et
al., A. Biochemistry 13:2898-2903 (1974)). The fadI and fadJ genes
encode similar functions and are naturally expressed under
anaerobic conditions (Atsumi et al., Nature 451:86-89 (2008)). Data
related to the sequences for each of these exemplary gene products
can be found using the following GenBank accession numbers shown in
Table 31.
TABLE-US-00031 TABLE 31 Protein GenBank ID GI Number Organism fadA
YP_026272.1 49176430 Escherichia coli fadB NP_418288.1 16131692
Escherichia coli fadI NP_416844.1 16130275 Escherichia coli fadJ
NP_416843.1 16130274 Escherichia coli fadR NP_415705.1 16129150
Escherichia coli
[0134] The reversible condensation of 4-hydroxybutyryl-CoA to
crotonyl-CoA (Step A, FIG. 3) is catalyzed by the bifunctional
enzyme 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA
A-isomerase. This enzyme first dehydrates 4-hydroxybutyryl-CoA to
vinylacetyl-CoA, which subsequently rearranges to form
crotonoyl-CoA. The enzymes from Clostridium kluyveri and C.
aminobutyrium have been purified, characterized, and sequenced at
the N-terminal domain (Scherf et al., Eur. J. Biochem., 215:421-429
(1993); Scherf et al., Arch. Microbiol., 161:239-245 (1994)). The
abfD genes from C. aminobutyrium and C. kluyveri match exactly with
these N-terminal amino acid sequences, and have been indicated to
encode the 4-hydroxybutyryl-CoA dehydratases/vinylacetyl-CoA
A-isomerase activities. Similar genes are identified through
homology from genome projects, including abfD from Porphyromonas
gingivalis and Msed_1220 from Metallosphaera sedula. Data related
to the sequences for each of these exemplary gene products can be
found using the following GenBank accession numbers shown in Table
32.
TABLE-US-00032 TABLE 32 Protein GenBank ID GI Number Organism abfD
YP_001396399.1 153955634 Clostridium kluyveri abfD P55792 84028213
Clostridium aminobutyricum abfD YP_001928843 188994591
Porphyromonas gingivalis Msed_1220 YP_001191305.1 146303989
Metallosphaera sedula
[0135] Deamination of 2-amino-4-ketopentanoate (FIG. 1, Reaction I)
and of 4-aminobutan-2-one (Step F, FIG. 1) can be accomplished by
AKP ammonia-lyase and 4-aminobutan-2-one ammonia-lyase
respectively. These deaminations are very similar to the
deamination of aspartate to fumarate by aspartase. The enzyme has
been extensively studied and several crystal structures are
available. The E. coli enzyme has been shown to react with
alternate substrates such as aspartatephenylmethylester,
asparagine, benzyl-aspartate and malate (Ma et al., Ann. N.Y. Acad.
Sci., 672:60-65 (1992). In a separate study, directed evolution has
been implemented on this enzyme to alter substrate specificity
(Asano et al., Biomol. Eng., 22:95-101 (2005)). Enzymes with
aspartase functionality have also been characterized in Haemophilus
influenzae (Sjostrom et al., Biochem. Biophys. Acta., 1324:182-190
(1997)), Pseudomonas fluorescens (Takagi et al., J. Biochem.,
96:545-552 (1984)), Bacillus subtilis (Sjostrom et al., supra) and
Serratia marcescens (Takagi et al., J. Bacteriol., 161:1-6 (1985)).
Data related to the sequences for each of these exemplary gene
products can be found using the following GenBank accession numbers
shown in Table 33.
TABLE-US-00033 TABLE 33 Protein GenBank ID GI Number Organism aspA
NP_418562 90111690 Escherichia coli aspA P44324.1 1168534
Haemophilus influenzae aspA P07346.1 114273 Pseudomonas fluorescens
ansB P26899.1 251757243 Bacillus subtilus aspA P33109.1 416661
Serratia marcescens
[0136] A similar ammonia lyase reaction is catalyzed by
methylaspartase (EC 4.3.1.2), an enzyme participating in the
glutamate fermentation route via mesaconate (Kato et al., supra).
This enzyme, also known as beta-methylaspartase and
3-methylaspartate ammonia-lyase, naturally catalyzes the
deamination of threo-3-methylaspartate to mesaconate. The
3-methylaspartase from Clostridium tetanomorphum has been cloned,
functionally expressed in E. coli, and crystallized (Asuncion et
al., 57:731-733 (2001); Asuncion et al., J Biol Chem. 277:8306-8311
(2002); Botting et al., 27:2953-2955 (1988); Goda et al.,
31:10747-10756 (1992)). In Citrobacter amalonaticus, this enzyme is
encoded by BAA28709 (Kato et al., Arch. Microbiol 168:457-463
(1997)). 3-Methylaspartase has also been crystallized from E. coli
YG1002 (Asano et al., FEMS Microbiol Lett. 118:255-258 (1994))
although the protein sequence is not listed in public databases
such as GenBank. Data related to the sequences for each of these
exemplary gene products can be found using the following GenBank
accession numbers shown in Table 34.
TABLE-US-00034 TABLE 34 Protein GenBank ID GI Number Organism mal
AAB24070.1 259429 Clostridium tetanomorphum BAA28709 BAA28709.1
3184397 Citrobacter amalonaticus
[0137] In some embodiments, the 2-amino-4-ketopentanoate (AKP)
thiolase encoded by one or more genes selected from the group
consisting of ortA (.alpha.), ortB (.beta.), Amet_2368 (.alpha.),
Amet_2369 (.beta.), Teth514_1478 (.alpha.), Teth514_1479 (.beta.),
TTE1235 (.alpha.), and thrC (.beta.).
[0138] In some embodiments, the AKP dehydrogenase is encoded by one
or more genes selected from the group consisting of thrA, akthr2,
hom6, hom1, hom2, fadB, fadJ, Hbd2, Hbd1, hbd, HSD17B10, phbB,
phaB, Msed_1423, Msed_0399, Msed_0389, Msed_1993, adh, adhA, adh-A,
mdh, ldhA, ldh, and bdh.
[0139] In some embodiments, the 2-amino-4-hydroxypentanoate
aminotransferase is encoded by one or more genes selected from the
group consisting of aspC, AAT2, ASPS, got2, avtA, lysN, AadAT-II,
dat, lat, ygjG, spuC, SkyPYD4, SkUGA1, UGA1, Abat, Abat, Gta-1,
gabT, and puuE.
[0140] In some embodiments, the 2-amino-4-hydroxypentanoate
oxidoreductase (deaminating) is encoded by one or more genes
selected from the group consisting of gdhA, gdh, gdhA1, rocG, gdh1,
gdh2, GDH, GDH2, ldh and nadX.
[0141] In some embodiments, the 2-oxo-4-hydroxypentanoate
decarboxylase is encoded by one or more genes selected from the
group consisting of pdc, pdc1, md/C, dpgB, ilvB-1, kgd, kdcA, lysA,
panD, cadA, ldc, ldcC, AF323910.1:1 . . . 1299, odc1, VV2_1235,
dmpH, dmpE, xylII, xylIII, Reut_B5691, Reut_B5692, CAD, pad1, pofK
(pad), padC, pad, adc, cbei_3835, CLL_A2135, RBAM_030030,
[0142] In some embodiments, the 3-hydroxybutyraldehyde reductase is
encoded by one or more genes selected from the group consisting of
alrA, ADH2, yqhD, bdh I, bdh II, adhA, 4hbd, adhI, P84067, mmsb,
dhat, and 3hidh.
[0143] In some embodiments, the AKP aminotransferase is encoded by
one or more genes selected from the group consisting of aspC, AAT2,
ASPS, got2, avtA, lysN, AadAT-II, dat, lat, ygjG, spuC, SkyPYD4,
SkUGA1, UGA1, Abat, Gta-1, gabT, and puuE.
[0144] In some embodiments, the AKP oxidoreductase (deaminating) is
encoded by one or more genes selected from the group consisting of
gdhA, gdh, gdhA1, rocG, gdh1, gdh2, GDH, GDH2, ldh and nadX. In
some embodiments, the 2,4-dioxopentanoate decarboxylase is encoded
by one or more genes selected from the group consisting of pdc,
pdc1, md/C, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc, ldcC,
AF323910.1:1 . . . 1299, odc1, VV2_1235, dmpH, dmpE, xylII, xylIII,
Reut_B5691, Reut_B5692, CAD, pad1, padC, and pad, adc, cbei_3835,
CLL_A2135, RBAM_030030.
[0145] In some embodiments, the 3-oxobutyraldehyde reductase
(ketone reducing) is encoded by one or more genes selected from the
group consisting of thrA, akthr2, hom6, hom1, hom2, fadB, fad.,
Hbd2, Hbd1, hbd, HSD17B10, phbB, phaB, Msed_1423, Msed_0399,
Msed_0389, Msed_1993, adh, adhA, adh-A, mdh, ldhA, ldh, and
bdh.
[0146] In some embodiments, the 3-oxobutyraldehyde reductase
(aldehyde reducing) is encoded by one or more genes selected from
the group consisting of alrA, ADH2, yqhD, bdh I, bdh II, adhA,
4hbd, adhI, P84067, mmsb, dhat, and 3hidh.
[0147] In some embodiments, the 4-hydroxy-2-butanone reductase is
encoded by one or more genes selected from the group consisting of
thrA, akthr2, hom6, hom1, hom2, fadB, Hbd2, Hbd1, hbd, HSD17B10,
phbB, phaB, Msed_1423, Msed_0399, Msed_0389, Msed_1993, adh, adhA,
adh-A, mdh, ldhA, ldh, and bdh.
[0148] In some embodiments, the AKP decarboxylase is encoded by one
or more genes selected from the group consisting of pdc, pdc1,
mdlC, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc, ldcC,
AF323910.1:1 . . . 1299, odc1, VV2_1235, dmpH, dmpE, xylII, xylIII,
Reut_B5691, Reut_B5692, CAD, pad1, pofK(pad), padC, pad.
[0149] In some embodiments, the 4-aminobutan-2-one aminotransferase
is encoded by one or more genes selected from the group consisting
of aspC, AAT2, ASPS, got2, avtA, lysN, AadAT-II, dat, lat, ygjG,
spuC, SkyPYD4, SkUGA1, UGA1, Abat, Gta-1, gabT, and puuE.
[0150] In some embodiments, the 4-aminobutan-2-one oxidoreductase
(deaminating) is encoded by one or more genes selected from the
group consisting of gdhA, gdh, gdhA1, rocG, gdh1, gdh2, GDH, GDH2,
ldh, nadX, kdd and lysDH.
[0151] In some embodiments, the 4-aminobutan-2-one ammonia-lyase is
encoded by one or more genes selected from the group consisting of
aspA, ansB, mal and BAA28709.
[0152] In some embodiments, the butenone hydratase is encoded by
one or more genes selected from the group consisting of fumA, fumB,
fumC, fumH, fum1, MmcB, MmcC, hmd, BACCAP_02294, ANACOL_02527,
NtherDRAFT_2368, dmdA, dmdB, crt, crt1, ech paaA, paaB, phaA, phaB,
maoC, paaF, paaG, abfD, Msed_1220, fadA, fadB, fadI, fadJ, and
fadR.
[0153] In some embodiments, the AKP ammonia-lyase is encoded by one
or more genes selected from the group consisting of aspA, ansB, mal
and BAA28709.
[0154] In some embodiments, the acetylacrylate decarboxylase is
encoded by one or more genes selected from the group consisting of
pdc, pdc1, mdlC, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc,
ldcC, AF323910.1:1 . . . 1299, odc1, VV2_1235, dmpH, dmpE, xylII,
xylIII, Reut_B5691, Reut_B5692, CAD, pad1, pofK (pad), padC, pad,
adc, cbei_3835, CLL_A2135, RBAM_030030,)
[0155] In some embodiments, the acetoacetyl-CoA reductase
(CoA-dependent, aldehyde forming) is encoded by one or more genes
selected from the group consisting of acr1, sucD, bphG, bld, adhE,
Msed_0709, mcr, asd-2, Saci_2370, Ald, and eutE.
[0156] In some embodiments, the acetoacetyl-CoA reductase
(CoA-dependent, alcohol forming) is encoded by one or more genes
selected from the group consisting of adhE, adhE2, mcr, Rcas_2929,
NAP_1_02720, MGP2080_00535, and FAR.
[0157] In some embodiments, the acetoacetyl-CoA reductase (ketone
reducing) is encoded by one or more genes selected from the group
consisting of thrA, akthr2, horn 6, hom1, hom2, fadB, fadJ, Hbd2,
Hbd1, hbd, HSD17B10, phbB, phaB, Msed_1423, Msed_0399, Msed_0389,
Msed_1993, adh, adhA, adh-A, mdh, ldhA, ldh, and bdh.
[0158] In some embodiments, the 3-hydroxybutyryl-CoA reductase
(aldehyde forming) is encoded by one or more genes selected from
the group consisting of acr1, sucD, bphG, bld, adhE, Msed_0709,
mcr, asd-2, Saci_2370, Ald, and eutE.
[0159] In some embodiments, the 3-hydroxybutyryl-CoA reductase
(alcohol forming) is encoded by one or more genes selected from the
group consisting of adhE, adhE2, mcr, Rcas_2929, NAP_1_02720,
MGP2080_00535, and FAR.
[0160] In some embodiments, the 4-hydroxybutyryl-CoA dehydratase is
encoded by one or more genes selected from the group consisting of
fumA, fumB, fumC, fumH, fum1, MmcB, MmcC, hmd, BACCAP_02294,
ANACOL_02527, NtherDRAFT_2368, dmdA, dmdB, crt, crt1, ech, paaA,
paaB, phaA, phaB, maoC, paaF, paaG, abfD, Msed_1220, fadA, fadB,
fadI, fadJ, and fadR.
[0161] In some embodiments, the crotonase is encoded by one or more
genes selected from the group consisting of fumA, fumB, fumC, fumH,
fum1, MmcB, MmcC, hmd, BACCAP_02294, ANACOL_02527, NtherDRAFT_2368,
dmdA, dmdB, crt, crt1, ech paaA, paaB, phaA, phaB, maoC, paaF,
paaG, abfD, Msed_1220, fadA, fadB, fadI, fadJ, and fadR.
[0162] The non-naturally occurring microbial organisms of the
invention can be produced by introducing expressible nucleic acids
encoding one or more of the enzymes or proteins participating in
one or more 1,3-butanediol biosynthetic pathways. Depending on the
host microbial organism chosen for biosynthesis, nucleic acids for
some or all of a particular 1,3-butanediol biosynthetic pathway can
be expressed. For example, if a chosen host is deficient in one or
more enzymes or proteins for a desired biosynthetic pathway, then
expressible nucleic acids for the deficient enzyme(s) or protein(s)
are introduced into the host for subsequent exogenous expression.
Alternatively, if the chosen host exhibits endogenous expression of
some pathway genes, but is deficient in others, then an encoding
nucleic acid is needed for the deficient enzyme(s) or protein(s) to
achieve 1,3-butanediol biosynthesis. Thus, a non-naturally
occurring microbial organism of the invention can be produced by
introducing exogenous enzyme or protein activities to obtain a
desired biosynthetic pathway or a desired biosynthetic pathway can
be obtained by introducing one or more exogenous enzyme or protein
activities that, together with one or more endogenous enzymes or
proteins, produces a desired product such as 1,3-butanediol.
[0163] Depending on the 1,3-butanediol biosynthetic pathway
constituents of a selected host microbial organism, the
non-naturally occurring microbial organisms of the invention will
include at least one exogenously expressed 1,3-butanediol
pathway-encoding nucleic acid and up to all encoding nucleic acids
for one or more 1,3-butanediol biosynthetic pathways. For example,
1,3-butanediol biosynthesis can be established in a host deficient
in a pathway enzyme or protein through exogenous expression of the
corresponding encoding nucleic acid. In a host deficient in all
enzymes or proteins of an 1,3-butanediol pathway, exogenous
expression of all enzyme or proteins in the pathway can be
included, although it is understood that all enzymes or proteins of
a pathway can be expressed even if the host contains at least one
of the pathway enzymes or proteins. For example, exogenous
expression of all enzymes or proteins in a pathway for production
of 1,3-butanediol can be included.
[0164] Given the teachings and guidance provided herein, those
skilled in the art will understand that the number of encoding
nucleic acids to introduce in an expressible form will, at least,
parallel the 1,3-butanediol pathway deficiencies of the selected
host microbial organism. Therefore, a non-naturally occurring
microbial organism of the invention can have one, two, three, four,
five, up to all nucleic acids encoding the enzymes or proteins
constituting an 1,3-butanediol biosynthetic pathway disclosed
herein. In some embodiments, the non-naturally occurring microbial
organisms also can include other genetic modifications that
facilitate or optimize 1,3-butanediol biosynthesis or that confer
other useful functions onto the host microbial organism. One such
other functionality can include, for example, augmentation of the
synthesis of one or more of the 1,3-butanediol pathway precursors
such as acetyl-CoA.
[0165] Generally, a host microbial organism is selected such that
it produces the precursor of an 1,3-butanediol pathway, either as a
naturally produced molecule or as an engineered product that either
provides de novo production of a desired precursor or increased
production of a precursor naturally produced by the host microbial
organism. For example, acetyl-CoA is produced naturally in a host
organism such as E. coli. A host organism can be engineered to
increase production of a precursor, as disclosed herein. In
addition, a microbial organism that has been engineered to produce
a desired precursor can be used as a host organism and further
engineered to express enzymes or proteins of an 1,3-butanediol
pathway.
[0166] In some embodiments, a non-naturally occurring microbial
organism of the invention is generated from a host that contains
the enzymatic capability to synthesize 1,3-butanediol. In this
specific embodiment it can be useful to increase the synthesis or
accumulation of an 1,3-butanediol pathway product to, for example,
drive 1,3-butanediol pathway reactions toward 1,3-butanediol
production. Increased synthesis or accumulation can be accomplished
by, for example, overexpression of nucleic acids encoding one or
more of the above-described 1,3-butanediol pathway enzymes or
proteins. Over expression the enzyme or enzymes and/or protein or
proteins of the 1,3-butanediol pathway can occur, for example,
through exogenous expression of the endogenous gene or genes, or
through exogenous expression of the heterologous gene or genes.
Therefore, naturally occurring organisms can be readily generated
to be non-naturally occurring microbial organisms of the invention,
for example, producing 1,3-butanediol, through overexpression of
one, two, three, four, five, that is, up to all nucleic acids
encoding 1,3-butanediol biosynthetic pathway enzymes or proteins.
In addition, a non-naturally occurring organism can be generated by
mutagenesis of an endogenous gene that results in an increase in
activity of an enzyme in the 1,3-butanediol biosynthetic
pathway.
[0167] In particularly useful embodiments, exogenous expression of
the encoding nucleic acids is employed. Exogenous expression
confers the ability to custom tailor the expression and/or
regulatory elements to the host and application to achieve a
desired expression level that is controlled by the user. However,
endogenous expression also can be utilized in other embodiments
such as by removing a negative regulatory effector or induction of
the gene's promoter when linked to an inducible promoter or other
regulatory element. Thus, an endogenous gene having a naturally
occurring inducible promoter can be up-regulated by providing the
appropriate inducing agent, or the regulatory region of an
endogenous gene can be engineered to incorporate an inducible
regulatory element, thereby allowing the regulation of increased
expression of an endogenous gene at a desired time. Similarly, an
inducible promoter can be included as a regulatory element for an
exogenous gene introduced into a non-naturally occurring microbial
organism.
[0168] It is understood that, in methods of the invention, any of
the one or more exogenous nucleic acids can be introduced into a
microbial organism to produce a non-naturally occurring microbial
organism of the invention. The nucleic acids can be introduced so
as to confer, for example, 1,3-butanediol biosynthetic pathway onto
the microbial organism. Alternatively, encoding nucleic acids can
be introduced to produce an intermediate microbial organism having
the biosynthetic capability to catalyze some of the required
reactions to confer 1,3-butanediol biosynthetic capability. For
example, a non-naturally occurring microbial organism having
1,3-butanediol biosynthetic pathway can comprise at least two
exogenous nucleic acids encoding desired enzymes or proteins. Thus,
it is understood that any combination of two or more enzymes or
proteins of a biosynthetic pathway can be included in a
non-naturally occurring microbial organism of the invention.
Similarly, it is understood that any combination of three or more
enzymes or proteins of a biosynthetic pathway can be included in a
non-naturally occurring microbial organism of the invention and so
forth, as desired, so long as the combination of enzymes and/or
proteins of the desired biosynthetic pathway results in production
of the corresponding desired product. Similarly, any combination of
four, or more enzymes or proteins of a biosynthetic pathway as
disclosed herein can be included in a non-naturally occurring
microbial organism of the invention, as desired, so long as the
combination of enzymes and/or proteins of the desired biosynthetic
pathway results in production of the corresponding desired
product.
[0169] In addition to the biosynthesis of 1,3-butanediol as
described herein, the non-naturally occurring microbial organisms
and methods of the invention also can be utilized in various
combinations with each other and with other microbial organisms and
methods well known in the art to achieve product biosynthesis by
other routes. For example, one alternative to produce
1,3-butanediol other than use of the 1,3-butanediol producers is
through addition of another microbial organism capable of
converting 1,3-butanediol pathway intermediate to 1,3-butanediol.
One such procedure includes, for example, the fermentation of a
microbial organism that produces 1,3-butanediol pathway
intermediate. The 1,3-butanediol pathway intermediate can then be
used as a substrate for a second microbial organism that converts
the 1,3-butanediol pathway intermediate to 1,3-butanediol. The
1,3-butanediol pathway intermediate can be added directly to
another culture of the second organism or the original culture of
the 1,3-butanediol pathway intermediate producers can be depleted
of these microbial organisms by, for example, cell separation, and
then subsequent addition of the second organism to the fermentation
broth can be utilized to produce the final product without
intermediate purification steps.
[0170] In other embodiments, the non-naturally occurring microbial
organisms and methods of the invention can be assembled in a wide
variety of subpathways to achieve biosynthesis of, for example,
1,3-butanediol. In these embodiments, biosynthetic pathways for a
desired product of the invention can be segregated into different
microbial organisms, and the different microbial organisms can be
co-cultured to produce the final product. In such a biosynthetic
scheme, the product of one microbial organism is the substrate for
a second microbial organism until the final product is synthesized.
For example, the biosynthesis of 1,3-butanediol can be accomplished
by constructing a microbial organism that contains biosynthetic
pathways for conversion of one pathway intermediate to another
pathway intermediate or the product. Alternatively, 1,3-butanediol
also can be biosynthetically produced from microbial organisms
through co-culture or co-fermentation using two organisms in the
same vessel, where the first microbial organism produces
1,3-butanediol intermediate and the second microbial organism
converts the intermediate to 1,3-butanediol.
[0171] Given the teachings and guidance provided herein, those
skilled in the art will understand that a wide variety of
combinations and permutations exist for the non-naturally occurring
microbial organisms and methods of the invention together with
other microbial organisms, with the co-culture of other
non-naturally occurring microbial organisms having subpathways and
with combinations of other chemical and/or biochemical procedures
well known in the art to produce 1,3-butanediol.
[0172] Sources of encoding nucleic acids for 1,3-butanediol pathway
enzyme or protein can include, for example, any species where the
encoded gene product is capable of catalyzing the referenced
reaction. Such species include both prokaryotic and eukaryotic
organisms including, but not limited to, bacteria, including
archaea and eubacteria, and eukaryotes, including yeast, plant,
insect, animal, and mammal, including human. Exemplary species for
such sources include, for example, Escherichia coli, as well as
other exemplary species disclosed herein or available as source
organisms for corresponding genes. However, with the complete
genome sequence available for now more than 550 species (with more
than half of these available on public databases such as the NCBI),
including 395 microorganism genomes and a variety of yeast, fungi,
plant, and mammalian genomes, the identification of genes encoding
the requisite 1,3-butanediol biosynthetic activity for one or more
genes in related or distant species, including for example,
homologues, orthologs, paralogs and nonorthologous gene
displacements of known genes, and the interchange of genetic
alterations between organisms is routine and well known in the art.
Accordingly, the metabolic alterations enabling biosynthesis of
1,3-butanediol described herein with reference to a particular
organism such as E. coli can be readily applied to other
microorganisms, including prokaryotic and eukaryotic organisms
alike. Given the teachings and guidance provided herein, those
skilled in the art will know that a metabolic alteration
exemplified in one organism can be applied equally to other
organisms.
[0173] In some instances, such as when an alternative
1,3-butanediol biosynthetic pathway exists in an unrelated species,
1,3-butanediol biosynthesis can be conferred onto the host species
by, for example, exogenous expression of a paralog or paralogs from
the unrelated species that catalyzes a similar, yet non-identical
metabolic reaction to replace the referenced reaction. Because
certain differences among metabolic networks exist between
different organisms, those skilled in the art will understand that
the actual gene usage between different organisms can differ.
However, given the teachings and guidance provided herein, those
skilled in the art also will understand that the teachings and
methods of the invention can be applied to all microbial organisms
using the cognate metabolic alterations to those exemplified herein
to construct a microbial organism in a species of interest that
will synthesize 1,3-butanediol.
[0174] Host microbial organisms can be selected from, and the
non-naturally occurring microbial organisms generated in, for
example, bacteria, yeast, fungus or any of a variety of other
microorganisms applicable to fermentation processes. Exemplary
bacteria include species selected from Escherichia coli, Klebsiella
oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus
succinogenes, Mannheimia succiniciproducens, Rhizobium etli,
Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter
oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus
plantarum, Streptomyces coelicolor, Clostridium acetobutylicum,
Pseudomonas fluorescens, and Pseudomonas putida. Exemplary yeasts
or fungi include species selected from Saccharomyces cerevisiae,
Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces
marxianus, Aspergillus terreus, Aspergillus niger and Pichia
pastoris. E. coli is a particularly useful host organism since it
is a well characterized microbial organism suitable for genetic
engineering. Other particularly useful host organisms include yeast
such as Saccharomyces cerevisiae.
[0175] Methods for constructing and testing the expression levels
of a non-naturally occurring 1,3-butanediol-producing host can be
performed, for example, by recombinant and detection methods well
known in the art. Such methods can be found described in, for
example, Sambrook et al., Molecular Cloning: A Laboratory Manual,
Third Ed., Cold Spring Harbor Laboratory, New York (2001); and
Ausubel et al., Current Protocols in Molecular Biology, John Wiley
and Sons, Baltimore, Md. (1999).
[0176] Exogenous nucleic acid sequences involved in a pathway for
production of 1,3-butanediol can be introduced stably or
transiently into a host cell using techniques well known in the art
including, but not limited to, conjugation, electroporation,
chemical transformation, transduction, transfection, and ultrasound
transformation. For exogenous expression in E. coli or other
prokaryotic cells, some nucleic acid sequences in the genes or
cDNAs of eukaryotic nucleic acids can encode targeting signals such
as an N-terminal mitochondrial or other targeting signal, which can
be removed before transformation into prokaryotic host cells, if
desired. For example, removal of a mitochondrial leader sequence
led to increased expression in E. coli (Hoffmeister et al., J.
Biol. Chem. 280:4329-4338 (2005)). For exogenous expression in
yeast or other eukaryotic cells, genes can be expressed in the
cytosol without the addition of leader sequence, or can be targeted
to mitochondrion or other organelles, or targeted for secretion, by
the addition of a suitable targeting sequence such as a
mitochondrial targeting or secretion signal suitable for the host
cells. Thus, it is understood that appropriate modifications to a
nucleic acid sequence to remove or include a targeting sequence can
be incorporated into an exogenous nucleic acid sequence to impart
desirable properties. Furthermore, genes can be subjected to codon
optimization with techniques well known in the art to achieve
optimized expression of the proteins.
[0177] An expression vector or vectors can be constructed to
include one or more 1,3-butanediol biosynthetic pathway encoding
nucleic acids as exemplified herein operably linked to expression
control sequences functional in the host organism. Expression
vectors applicable for use in the microbial host organisms of the
invention include, for example, plasmids, phage vectors, viral
vectors, episomes and artificial chromosomes, including vectors and
selection sequences or markers operable for stable integration into
a host chromosome. Additionally, the expression vectors can include
one or more selectable marker genes and appropriate expression
control sequences. Selectable marker genes also can be included
that, for example, provide resistance to antibiotics or toxins,
complement auxotrophic deficiencies, or supply critical nutrients
not in the culture media. Expression control sequences can include
constitutive and inducible promoters, transcription enhancers,
transcription terminators, and the like which are well known in the
art. When two or more exogenous encoding nucleic acids are to be
co-expressed, both nucleic acids can be inserted, for example, into
a single expression vector or in separate expression vectors. For
single vector expression, the encoding nucleic acids can be
operationally linked to one common expression control sequence or
linked to different expression control sequences, such as one
inducible promoter and one constitutive promoter. The
transformation of exogenous nucleic acid sequences involved in a
metabolic or synthetic pathway can be confirmed using methods well
known in the art. Such methods include, for example, nucleic acid
analysis such as Northern blots or polymerase chain reaction (PCR)
amplification of mRNA, or immunoblotting for expression of gene
products, or other suitable analytical methods to test the
expression of an introduced nucleic acid sequence or its
corresponding gene product. It is understood by those skilled in
the art that the exogenous nucleic acid is expressed in a
sufficient amount to produce the desired product, and it is further
understood that expression levels can be optimized to obtain
sufficient expression using methods well known in the art and as
disclosed herein.
[0178] The invention provides a method for producing 1,3-BDO that
includes culturing the non-naturally occurring microbial organism
disclosed herein, under conditions and for a sufficient period of
time to produce 1,3-BDO, including organisms that incorporate one,
two, three, four, five, up to all exogenous nucleic acids encoding
enzymes that complete a 1,3-BDO pathway. The 1,3-BDO pathways
include a set of 1,3-BDO pathway enzymes, where the set of 1,3-BDO
pathway enzymes are identified as above, namely: (a) (1) a
2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase;
(3) a 2-amino-4-hydroxypentanoate aminotransferase or
oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate
decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase; (b) (1)
a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
aminotransferase or oxidoreductase (deaminating); (3) a
2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde
reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde
reductase; (c) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2)
an AKP aminotransferase or oxidoreductase (deaminating); (3) a
2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde
reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone
reductase; (d) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2)
an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or
oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase
(ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase; (e)
(1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or
oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase
(aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase; (f)
(1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a
butanone hydratase; and (5) a 4-hydroxy-2-butanone reductase; (g)
(1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP
ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butanone
hydratase; and (5) a 4-hydroxy-2-butanone reductase; (h) (1) an
acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a
3-oxobutyraldehyde reductase (ketone reducing); and (3) a
3-hydroxybutyraldehyde reductase; (i) (1) an acetoacetyl-CoA
reductase (CoA dependent, alcohol forming) and (2) a
4-hydroxy-2-butanone reductase; (j) (1) an acetoacetyl-CoA
reductase (CoA-dependent, aldehyde forming); (2) a
3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a
4-hydroxy-2-butanone reductase; (k) (1) an acetoacetyl-CoA
reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA
reductase (alcohol forming); (1) (1) an acetoacetyl-CoA reductase
(ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde
forming); and (3) a 3-hydroxybutyraldehyde reductase; (m) (1) a
4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a
3-hydroxybutyryl-CoA reductase (alcohol forming); and (n) (1) a
4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a
3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a
3-hydroxybutyraldehyde reductase.
[0179] Suitable purification and/or assays to test for the
production of 1,3-butanediol can be performed using well known
methods. Suitable replicates such as triplicate cultures can be
grown for each engineered strain to be tested. For example, product
and byproduct formation in the engineered production host can be
monitored. The final product and intermediates, and other organic
compounds, can be analyzed by methods such as HPLC (High
Performance Liquid Chromatography), GC-MS (Gas Chromatography-Mass
Spectroscopy) and LC-MS (Liquid Chromatography-Mass Spectroscopy)
or other suitable analytical methods using routine procedures well
known in the art. The release of product in the fermentation broth
can also be tested with the culture supernatant. Byproducts and
residual glucose can be quantified by HPLC using, for example, a
refractive index detector for glucose and alcohols, and a UV
detector for organic acids (Lin et al., Biotechnol. Bioeng.
90:775-779 (2005)), or other suitable assay and detection methods
well known in the art. The individual enzyme or protein activities
from the exogenous DNA sequences can also be assayed using methods
well known in the art (see, for example, WO/2008/115840 and Hanai
et al., Appl. Environ. Microbiol. 73:7814-7818 (2007)).
[0180] The 1,3-butanediol can be separated from other components in
the culture using a variety of methods well known in the art. Such
separation methods include, for example, extraction procedures as
well as methods that include continuous liquid-liquid extraction,
pervaporation, membrane filtration, membrane separation, reverse
osmosis, electrodialysis, distillation, crystallization,
centrifugation, extractive filtration, ion exchange chromatography,
size exclusion chromatography, adsorption chromatography, and
ultrafiltration. All of the above methods are well known in the
art.
[0181] Any of the non-naturally occurring microbial organisms
described herein can be cultured to produce and/or secrete the
biosynthetic products of the invention. For example, the
1,3-butanediol producers can be cultured for the biosynthetic
production of 1,3-butanediol.
[0182] For the production of 1,3-butanediol, the recombinant
strains are cultured in a medium with carbon source and other
essential nutrients. It is highly desirable to maintain anaerobic
conditions in the fermenter to reduce the cost of the overall
process. Such conditions can be obtained, for example, by first
sparging the medium with nitrogen and then sealing the flasks with
a septum and crimp-cap. For strains where growth is not observed
anaerobically, microaerobic conditions can be applied by
perforating the septum with a small hole for limited aeration.
Exemplary anaerobic conditions have been described previously and
are well-known in the art. Exemplary aerobic and anaerobic
conditions are described, for example, in United States Publication
No. US-2009-0047719, filed Aug. 10, 2007. Fermentations can be
performed in a batch, fed-batch or continuous manner, as disclosed
herein.
[0183] If desired, the pH of the medium can be maintained at a
desired pH, in particular neutral pH, such as a pH of around 7 by
addition of a base, such as NaOH or other bases, or acid, as needed
to maintain the culture medium at a desirable pH. The growth rate
can be determined by measuring optical density using a
spectrophotometer (600 nm), and the glucose uptake rate by
monitoring carbon source depletion over time.
[0184] In addition to renewable feedstocks such as those
exemplified above, the 1,3-butanediol microbial organisms of the
invention also can be modified for growth on syngas as its source
of carbon. In this specific embodiment, one or more proteins or
enzymes are expressed in the 1,3-butanediol producing organisms to
provide a metabolic pathway for utilization of syngas or other
gaseous carbon source.
[0185] Organisms of the present invention can utilize, for example,
any carbohydrate source which can supply a source of carbon to the
non-naturally occurring microorganism. Such sources include, for
example, sugars such as glucose, xylose, arabinose, galactose,
mannose, fructose and starch. Other sources of carbohydrate
include, for example, renewable feedstocks and biomass. Exemplary
types of biomasses that can be used as feedstocks in the methods of
the invention include cellulosic biomass, hemicellulosic biomass
and lignin feedstocks or portions of feedstocks. Such biomass
feedstocks contain, for example, carbohydrate substrates useful as
carbon sources such as glucose, xylose, arabinose, galactose,
mannose, fructose and starch. Given the teachings and guidance
provided herein, those skilled in the art will understand that
renewable feedstocks and biomass other than those exemplified above
also can be used for culturing the microbial organisms of the
invention for the production of 1,3-butanediol.
[0186] Accordingly, given the teachings and guidance provided
herein, those skilled in the art will understand that a
non-naturally occurring microbial organism can be produced that
secretes the biosynthesized compounds of the invention when grown
on a carbon source such as, syngas, CO and/or CO2. Such compounds
include, for example, 1,3-butanediol and any of the intermediate
metabolites in the 1,3-butanediol pathway. All that is required is
to engineer in one or more of the required enzyme or protein
activities to achieve biosynthesis of the desired compound or
intermediate including, for example, inclusion of some or all of
the 1,3-butanediol biosynthetic pathways. Accordingly, the
invention provides a non-naturally occurring microbial organism
that produces and/or secretes 1,3-butanediol when grown on a
carbohydrate or other carbon source and produces and/or secretes
any of the intermediate metabolites shown in the 1,3-butanediol
pathway when grown on a carbohydrate or other carbon source. The
1,3-butanediol producing microbial organisms of the invention can
initiate synthesis from an intermediate, for example,
acetyl-CoA.
[0187] The non-naturally occurring microbial organisms of the
invention are constructed using methods well known in the art as
exemplified herein to exogenously express at least one nucleic acid
encoding an 1,3-butanediol pathway enzyme or protein in sufficient
amounts to produce 1,3-butanediol. It is understood that the
microbial organisms of the invention are cultured under conditions
sufficient to produce 1,3-butanediol. Following the teachings and
guidance provided herein, the non-naturally occurring microbial
organisms of the invention can achieve biosynthesis of
1,3-butanediol resulting in intracellular concentrations between
about 0.1-2000 mM or more. Generally, the intracellular
concentration of 1,3-butanediol is between about 3-1800 mM,
particularly between about 5-1700 mM and more particularly between
about 8-1600 mM, including about 100 mM, 200 mM, 500 mM, 800 mM, or
more. Intracellular concentrations between and above each of these
exemplary ranges also can be achieved from the non-naturally
occurring microbial organisms of the invention.
[0188] In some embodiments, culture conditions include anaerobic or
substantially anaerobic growth or maintenance conditions. Exemplary
anaerobic conditions have been described previously and are well
known in the art. Exemplary anaerobic conditions for fermentation
processes are described herein and are described, for example, in
U.S. patent application No. US 2009/0047719, filed Aug. 10, 2007.
Any of these conditions can be employed with the non-naturally
occurring microbial organisms as well as other anaerobic conditions
well known in the art. Under such anaerobic conditions, the
1,3-butanediol producers can synthesize 1,3-butanediol at
intracellular concentrations of 5-10 mM or more as well as all
other concentrations exemplified herein. It is understood that,
even though the above description refers to intracellular
concentrations, 1,3-butanediol producing microbial organisms can
produce 1,3-butanediol intracellularly and/or secrete the product
into the culture medium.
[0189] The culture conditions can include, for example, liquid
culture procedures as well as fermentation and other large scale
culture procedures. As described herein, particularly useful yields
of the biosynthetic products of the invention can be obtained under
anaerobic or substantially anaerobic culture conditions.
[0190] As described herein, one exemplary growth condition for
achieving biosynthesis of 1,3-butanediol includes anaerobic culture
or fermentation conditions. In certain embodiments, the
non-naturally occurring microbial organisms of the invention can be
sustained, cultured or fermented under anaerobic or substantially
anaerobic conditions. Briefly, anaerobic conditions refer to an
environment devoid of oxygen. Substantially anaerobic conditions
include, for example, a culture, batch fermentation or continuous
fermentation such that the dissolved oxygen concentration in the
medium remains between 0 and 10% of saturation. Substantially
anaerobic conditions also includes growing or resting cells in
liquid medium or on solid agar inside a sealed chamber maintained
with an atmosphere of less than 1% oxygen. The percent of oxygen
can be maintained by, for example, sparging the culture with an
N.sub.2/CO.sub.2 mixture or other suitable non-oxygen gas or
gases.
[0191] The culture conditions described herein can be scaled up and
grown continuously for manufacturing of 1,3-butanediol. Exemplary
growth procedures include, for example, fed-batch fermentation and
batch separation; fed-batch fermentation and continuous separation,
or continuous fermentation and continuous separation. All of these
processes are well known in the art. Fermentation procedures are
particularly useful for the biosynthetic production of commercial
quantities of 1,3-butanediol. Generally, and as with non-continuous
culture procedures, the continuous and/or near-continuous
production of 1,3-butanediol will include culturing a non-naturally
occurring 1,3-butanediol producing organism of the invention in
sufficient nutrients and medium to sustain and/or nearly sustain
growth in an exponential phase. Continuous culture under such
conditions can be include, for example, 1 day, 2, 3, 4, 5, 6 or 7
days or more. Additionally, continuous culture can include 1 week,
2, 3, 4 or 5 or more weeks and up to several months. Alternatively,
organisms of the invention can be cultured for hours, if suitable
for a particular application. It is to be understood that the
continuous and/or near-continuous culture conditions also can
include all time intervals in between these exemplary periods. It
is further understood that the time of culturing the microbial
organism of the invention is for a sufficient period of time to
produce a sufficient amount of product for a desired purpose.
[0192] Fermentation procedures are well known in the art. Briefly,
fermentation for the biosynthetic production of 1,3-butanediol can
be utilized in, for example, fed-batch fermentation and batch
separation; fed-batch fermentation and continuous separation, or
continuous fermentation and continuous separation. Examples of
batch and continuous fermentation procedures are well known in the
art.
[0193] In addition to the above fermentation procedures using the
1,3-butanediol producers of the invention for continuous production
of substantial quantities of 1,3-butanediol, the 1,3-butanediol
producers also can be, for example, simultaneously subjected to
chemical synthesis procedures to convert the product to other
compounds or the product can be separated from the fermentation
culture and sequentially subjected to chemical conversion to
convert the product to other compounds, if desired.
[0194] In some embodiments, syngas can be used as a carbon
feedstock. Important process considerations for a syngas
fermentation are high biomass concentration and good gas-liquid
mass transfer (Bredwell et al., Biotechnol Prog., 15:834-844
(1999). The solubility of CO in water is somewhat less than that of
oxygen. Continuously gas-sparged fermentations can be performed in
controlled fermenters with constant off-gas analysis by mass
spectrometry and periodic liquid sampling and analysis by GC and
HPLC. The liquid phase can function in batch mode. Fermentation
products such as alcohols, organic acids, and residual glucose
along with residual methanol are quantified by HPLC (Shimadzu,
Columbia Md.), for example, using an Aminex.RTM. series of HPLC
columns (for example, HPX-87 series) (BioRad, Hercules Calif.),
using a refractive index detector for glucose and alcohols, and a
UV detector for organic acids. The growth rate is determined by
measuring optical density using a spectrophotometer (600 nm). All
piping in these systems is glass or metal to maintain anaerobic
conditions. The gas sparging is performed with glass frits to
decrease bubble size and improve mass transfer. Various sparging
rates are tested, ranging from about 0.1 to 1 vvm (vapor volumes
per minute). To obtain accurate measurements of gas uptake rates,
periodic challenges are performed in which the gas flow is
temporarily stopped, and the gas phase composition is monitored as
a function of time.
[0195] In order to achieve the overall target productivity, methods
of cell retention or recycle are employed. One method to increase
the microbial concentration is to recycle cells via a tangential
flow membrane from a sidestream. Repeated batch culture can also be
used, as previously described for production of acetate by Moorella
(Sakai et al., J Biosci. Bioeng, 99:252-258 (2005)). Various other
methods can also be used (Bredwell et al., Biotechnol Prog.,
15:834-844 (1999); Datar et al., Biotechnol Bioeng, 86:587-594
(2004)). Additional optimization can be tested such as overpressure
at 1.5 atm to improve mass transfer (Najafpour et al., Enzyme and
Microbial Technology, 38[1-2], 223-228 (2006)).
[0196] Once satisfactory performance is achieved using pure
H.sub.2/CO as the feed, synthetic gas mixtures are generated
containing inhibitors likely to be present in commercial syngas.
For example, a typical impurity profile is 4.5% CH4, 0.1%
C.sub.2H.sub.2, 0.35% C.sub.2H.sub.6, 1.4% C.sub.2H.sub.4, and 150
ppm nitric oxide (Datar et al., Biotechnol Bioeng, 86:587-594
(2004)). Tars, represented by compounds such as benzene, toluene,
ethylbenzene, p-xylene, o-xylene, and naphthalene, are added at ppm
levels to test for any effect on production. For example, it has
been shown that 40 ppm NO is inhibitory to C. carboxidivorans
(Ahmed et al., Biotechnol Bioeng, 97:1080-1086 (2007)). Cultures
are tested in shake-flask cultures before moving to a fermentor.
Also, different levels of these potential inhibitory compounds are
tested to quantify the effect they have on cell growth. This
knowledge is used to develop specifications for syngas purity,
which is utilized for scale up studies and production. If any
particular component is found to be difficult to decrease or remove
from syngas used for scale up, an adaptive evolution procedure is
utilized to adapt cells to tolerate one or more impurities.
[0197] Advances in the field of protein engineering make it
feasible to alter any of the enzymes disclosed herein to act
efficiently on substrates not known to be natural to them. Below
are several examples of broad-specificity enzymes from diverse
classes of interest and methods that have been used for evolving
such enzymes to act on non-natural substrates.
[0198] One class of enzymes in the pathways disclosed herein is the
oxidoreductases that interconvert ketones or aldehydes to alcohols
(1.1.1). Enzymes in this class that can operate on a wide range of
substrates. An alcohol dehydrogenase (1.1.1.1) purified from the
soil bacterium Brevibacterium sp KU 1309 (Hirano et al., J. Biosci.
Bioeng. 100:318-322 (2005)) was shown to operate on a plethora of
aliphatic as well as aromatic alcohols with high activities. Table
33 shows the activity of the enzyme and its K.sub.m on different
alcohols. The enzyme is reversible and has very high activity on
several aldehydes also as shown in Table 34.
TABLE-US-00035 TABLE 33 RELATIVE K.sub.M SUBSTRATE ACTIVITY (%)
(MM) 2-Phenylethanol 100 0.025 (S)-2-Phenylpropanol 156 0.157
(R)-2-Phenylpropanol 63 0.020 Benzyl alcohol 199 0.012
3-Phenylpropanol 135 0.033 Ethanol 76 1-Butanol 111 1-Octanol 101
1-Dodecanol 68 1-Phenylethanol 46 2-Propanol 54
[0199] In this Table, the activity of 2-phenylethanol,
corresponding to 19.2 U/mg, was taken as 100%.
TABLE-US-00036 TABLE 34 RELATIVE .kappa..sub.M SUBSTRATE ACTIVITY
(%) (MM) Phenylacetaldehyde 100 0.261 2-Phenylpropionaldehyde 188
0.864 1-Octylaldehyde 87 Acetophenone 0
[0200] Lactate dehydrogenase (1.1.1.27) from Ralstonia eutropha is
another enzyme that has been demonstrated to have high activities
on several 2-oxoacids such as 2-oxobutyrate, 2-oxopentanoate and
2-oxoglutarate (a C5 compound analogous to 2-oxoadipate)
(Steinbuchel et al., supra). Column 2 in Table 35 demonstrates the
activities of ldhA from R. eutropha (formerly A. eutrophus) on
different substrates (Steinbuchel et al., supra).
TABLE-US-00037 TABLE 35 Activity of L(+)- lactate dehydro- L(+)-
D(-)- genase from lactate dehydro- lactate dehydro- A. eustrophus
genase from genase from Substrate % rabbit muscle L. leischmanii
Glyoxylate 8.7 23.9 5.0 Pyruvate 100.0 100.0 100.0 2-Oxobutyrate
107.0 18.6 1.1 2-Oxovalerate 125.0 0.7 0.0 3-Methyl-2- 28.5 0.0 0.0
oxobutyrate 3-Methyl-2- 5.3 0.0 0.0 oxovalerate 4-Methyl-2- 39.0
1.4 1.1 oxopentanoate Oxaloacetate 0.0 33.1 23.1 2-Oxoglutarate
79.6 0.0 0.0 3- 33.6 74.3 40.0 Fluoropyruvate
[0201] Oxidoreductases that can convert 2-oxoacids to their
acyl-CoA counterparts (1.2.1) have been shown to accept multiple
substrates as well. For example, branched-chain 2-keto-acid
dehydrogenase complex (BCKAD), also known as 2-oxoisovalerate
dehydrogenase (1.2.1.25), participates in branched-chain amino acid
degradation pathways, converting 2-keto acids derivatives of
valine, leucine and isoleucine to their acyl-CoA derivatives and
CO.sub.2. In some organisms including Rattus norvegicus (Paxton et
al., Biochem. J. 234:295-303 (1986)) and Saccharomyces cerevisiae
(Sinclair et al., Biochem. Mol. Biol. Int. 31:911-922 (1993)), this
complex has been shown to have a broad substrate range that
includes linear oxo-acids such as 2-oxobutanoate and
alpha-ketoglutarate, in addition to the branched-chain amino acid
precursors.
[0202] Members of yet another class of enzymes, namely
aminotransferases (2.6.1), have been reported to act on multiple
substrates. Aspartate aminotransferase (aspAT) from Pyrococcus
furiosus has been identified, expressed in E. coli and the
recombinant protein characterized to demonstrate that the enzyme
has the highest activities towards aspartate and
alpha-ketoglutarate but lower, yet significant activities towards
alanine, glutamate and the aromatic amino acids (Ward et al.,
Archaea. 1:133-141 (2002)). In another instance, an
aminotransferase identified from Leishmania mexicana and expressed
in E. coli Vernal et al., FEMS Microbiol. Lett. 229:217-222 (2003))
was reported to have a broad substrate specificity towards tyrosine
(activity considered 100% on tyrosine), phenylalanine (90%),
tryptophan (85%), aspartate (30%), leucine (25%) and methionine
(25%) respectively (Vernal et al., Mol. Biochem. Parasitol.
96:83-92 (1998)). Similar broad specificity has been reported for a
tyrosine aminotransferase from Trypanosoma cruzi, even though both
of these enzymes have a sequence homology of only 6%. Note that the
latter enzyme can accept leucine, methionine as well as tyrosine,
phenylalanine, tryptophan and alanine as efficient amino donors
(Nowicki et al., Biochim. Biophys. Acta 1546: 268-281 (2001)).
[0203] In contrast to these examples where the enzymes naturally
have broad substrate specificities, numerous enzymes have been
modified using directed evolution to broaden their specificity
towards their non-natural substrates. Alternatively, the substrate
preference of an enzyme has also been changed using directed
evolution. For example, it has been reported that the
enantioselectivity of a lipase from Pseudomonas aeruginosa was
improved significantly. This enzyme hydrolyzed p-nitrophenyl
2-methyldecanoate with only 2% enantiomeric excess (ee) in favor of
the (S)-acid. However, after four successive rounds of error-prone
mutagenesis and screening, a variant was produced that catalyzed
the requisite reaction with 81% ee Reetz et al., Angew. Chem. Int.
Ed Engl. 36:2830-2832 (1997)).
[0204] Directed evolution methods have made possible the
modification of an enzyme to function on an array of unnatural
substrates. The substrate specificity of the lipase in P.
aeruginosa was broadened by randomization of amino acid residues
near the active site. This allowed for the acceptance of
alpha-substituted carboxylic acid esters by this enzyme Reetz et
al., Angew. Chem. Int. Ed Engl. 44:4192-4196 (2005)). In another
successful attempt, DNA shuffling was employed to create an
Escherichia coli aminotransferase that accepted (3-branched
substrates, which were poorly accepted by the wild-type enzyme
(Yano et al., Proc. Natl. Acad. Sci. U.S.A 95:5511-5515 (1998)).
Specifically, at the end of four rounds of shuffling, the activity
of aspartate aminotransferase for valine and 2-oxovaline increased
by up to five orders of magnitude, while decreasing the activity
towards the natural substrate, aspartate, by up to 30-fold.
Recently, an algorithm was used to design a retro-aldolase that
could be used to catalyze the carbon-carbon bond cleavage in a
non-natural and non-biological substrate,
4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone. These algorithms
used different combinations of four different catalytic motifs to
design new enzymes and 20 of the selected designs for experimental
characterization had four-fold improved rates over the uncatalyzed
reaction (Jiang et al., Science 319:1387-1391 (2008)). Thus, not
only are these engineering approaches capable of expanding the
array of substrates on which an enzyme can act, but allow the
design and construction of very efficient enzymes. For example, a
method of DNA shuffling (random chimeragenesis on transient
templates or RACHITT) was reported to lead to an engineered
monooxygenase that had an improved rate of desulfurization on
complex substrates as well as 20-fold faster conversion of a
non-natural substrate (Coco et al. Nat. Biotechnol. 19:354-359
(2001)). Similarly, the specific activity of a sluggish mutant
triosephosphate isomerase enzyme was improved up to 19-fold from
1.3 fold (Hermes et al., Proc. Natl. Acad. Sci. U.S.A 87:696-700
(1990)). This enhancement in specific activity was accomplished by
using random mutagenesis over the whole length of the protein and
the improvement could be traced back to mutations in six amino acid
residues.
[0205] The effectiveness of protein engineering approaches to alter
the substrate specificity of an enzyme for a desired substrate has
also been demonstrated. Isopropylmalate dehydrogenase from Thermus
thermophilus was modified by changing residues close to the active
site so that it could now act on malate and D-lactate as substrates
(Fujita et al., Biosci. Biotechnol Biochem. 65:2695-2700 (2001)).
In this study as well as in others, it was pointed out that one or
a few residues could be modified to alter the substrate
specificity. A case in point is the dihydroflavonol 4-reductase for
which a single amino acid was changed in the presumed
substrate-binding region that could preferentially reduce
dihydrokaempferol Johnson et al., Plant 25:325-333 (2001)). The
substrate specificity of a very specific isocitrate dehydrogenase
from Escherichia coli was changed form isocitrate to
isopropylmalate by changing one residue in the active site (Doyle
et al., Biochemistry 40:4234-4241 (2001)). In a similar vein, the
cofactor specificity of a NAD.sup.+-dependent
1,5-hydroxyprostaglandin dehydrogenase was altered to NADP.sup.+ by
changing a few residues near the N-terminal end Cho et al., Arch.
Biochem. Biophys. 419:139-146 (2003)). Sequence analysis and
molecular modeling analysis were used to identify the key residues
for modification, which were further studied by site-directed
mutagenesis.
[0206] A fucosidase was evolved from a galactosidase in E. coli by
DNA shuffling and screening (Zhang et al., Proc Natl Acad Sci U S.
A 94:4504-4509 (1997)). Similarly, aspartate aminotransferase from
E. coli was converted into a tyrosine aminotransferase using
homology modeling and site-directed mutagenesis (Onuffer et al.,
Protein Sci. 4:1750-1757 (1995)). Site-directed mutagenesis of two
residues in the active site of benzoylformate decarboxylase from P.
putida reportedly altered the affinity (K.sub.m) towards natural
and non-natural substrates Siegert et al., Protein Eng Des Sel
18:345-357 (2005)). Cytochrome c peroxidase (CCP) from
Saccharomyces cerevisiae was subjected to directed molecular
evolution to generate mutants with increased activity against the
classical peroxidase substrate guaiacol, thus changing the
substrate specificity of CCP from the protein cytochrome c to a
small organic molecule. After three rounds of DNA shuffling and
screening, mutants were isolated which possessed a 300-fold
increased activity against guaiacol and up to 1000-fold increased
specificity for this substrate relative to that for the natural
substrate (Iffland et al., Biochemistry 39:10790-10798 (2000)).
[0207] In some cases, enzymes with different substrate preferences
than both the parent enzymes have been obtained. For example,
biphenyl-dioxygenase-mediated degradation of polychlorinated
biphenyls was improved by shuffling genes from two bacteria,
Pseudomonas pseudoalcaligens and Burkholderia cepacia (Kumamaru et
al., Nat. Biotechnol 16, 663-666 (1998)). The resulting chimeric
biphenyl oxygenases showed different substrate preferences than
both the parental enzymes and enhanced the degradation activity
towards related biphenyl compounds and single aromatic ring
hydrocarbons such as toluene and benzene which were originally poor
substrates for the enzyme.
[0208] It is not only possible to change the enzyme specificity but
also to enhance the activities on those substrates on which the
enzymes naturally have low activities. One study demonstrated that
amino acid racemase from P. putida that had broad substrate
specificity (on lysine, arginine, alanine, serine, methionine,
cysteine, leucine and histidine among others) but low activity
towards tryptophan could be improved significantly by random
mutagenesis Kino et al., Appl. Microbiol. Biotechnol. 73:1299-1305
(2007)). Similarly, the active site of the bovine BCKAD was
engineered to favor alternate substrate acetyl-CoA (Meng et al.
Biochemistry 33:12879-12885 (1994)). An interesting aspect of these
approaches is that even when random methods have been applied to
generate these mutated enzymes with efficacious activities, the
exact mutations or structural changes that confer the improvement
in activity can be identified. For example, in the aforementioned
study, the mutations that facilitated improved activity on
tryptophan could be traced back to two different positions.
[0209] Directed evolution has also been used to express proteins
that are difficult to express. For example, by subjecting the
horseradish peroxidase to random mutagenesis and gene
recombination, mutants could be extracted that had more than
14-fold activity than the wild type (Lin et al., Biotechnol. Prog.
15:467-471 (1999)).
[0210] A final example of directed evolution shows the extensive
modifications to which an enzyme can be subjected to achieve a
range of desired functions. The enzyme, lactate dehydrogenase from
Bacillus stearothermophilus was subjected to site-directed
mutagenesis, and three amino acid substitutions were made at sites
that were indicated to determine the specificity towards different
hydroxyacids (Clarke et al., Biochem. Biophys. Res. Commun.
148:15-23 (1987)). After these mutations, the specificity for
oxaloacetate over pyruvate was increased to 500 in contrast to the
wild type enzyme that had a catalytic specificity for pyruvate over
oxaloacetate of 1000. This enzyme was further engineered using
site-directed mutagenesis to have activity towards branched-chain
substituted pyruvates (Wilks et al., Biochemistry 29:8587-8591
(1990)). Specifically, the enzyme had a 55-fold improvement in
K.sub.cat for alpha-ketoisocaproate. Three structural modifications
were made in the same enzyme to change its substrate specificity
from lactate to malate. The enzyme was highly active and specific
towards malate (Wilks et al., Science 242:1541-1544 (1988)). The
same enzyme from B. stearothermophilus was subsequently engineered
to have high catalytic activity towards alpha-keto acids with
positively charged side chains, such as those containing ammonium
groups (Hogan et al., Biochemistry 34:4225-4230 (1995)). Mutants
with acidic amino acids introduced at position 102 of the enzyme
favored binding of such side chain ammonium groups. The results
obtained proved that the mutants showed up to 25-fold improvements
in k.sub.cat/K.sub.m values for omega-amino-alpha-keto acid
substrates. This enzyme was also structurally modified to function
as a phenyllactate dehydrogenase instead of a lactate dehydrogenase
(Wilks et al., Biochemistry 31:7802-7806 (1992)). Restriction sites
were introduced into the gene for the enzyme which allowed a region
of the gene to be excised. This region coded for a mobile surface
loop of polypeptide (residues 98-110) which normally seals the
active site vacuole from bulk solvent and is a major determinant of
substrate specificity. The variable length and sequence loops were
inserted into the cut gene and used to synthesize hydroxyacid
dehydrogenases with altered substrate specificities. With one
longer loop construction, activity with pyruvate was reduced
one-million-fold but activity with phenylpyruvate was largely
unaltered. A switch in specificity (k.sub.cat/K.sub.m) of
390,000-fold was achieved. The 1700:1 selectivity of this enzyme
for phenylpyruvate over pyruvate is that required in a
phenyllactate dehydrogenase.
[0211] As indicated above, directed evolution is a powerful
approach that involves the introduction of mutations targeted to a
specific gene in order to improve and/or alter the properties of an
enzyme. Improved and/or altered enzymes can be identified through
the development and implementation of sensitive high-throughput
screening assays that allow the automated screening of many enzyme
variants (e.g., >10.sup.4). Iterative rounds of mutagenesis and
screening typically are performed to afford an enzyme with
optimized properties. Computational algorithms that can help to
identify areas of the gene for mutagenesis also have been developed
and can significantly reduce the number of enzyme variants that
need to be generated and screened.
[0212] Numerous directed evolution technologies have been developed
(for reviews, see Hibbert, E. G., F. Baganz, H. C. Hailes, J. M.
Ward, G. J. Lye, J. M. Woodley, and P. A. Dalby, 2005, Directed
evolution of biocatalytic processes. Biomol. Eng 22:11-19; Huisman,
G. W. and J. J. Lalonde, 2007, Enzyme evolution for chemical
process applications, p. 717-742. In R. N. Patel (ed.),
Biocatalysis in the pharmaceutical and biotechnology industries.
CRC Press; Otten, L. G. and W. J. Quax. 2005. Directed evolution:
selecting today's biocatalysts. Biomol. Eng 22:1-9; and Sen, S., D.
Venkata, V, and B. Mandal, 2007, Developments in directed evolution
for improving enzyme functions. Appl Biochem. Biotechnol
143:212-223.) to be effective at creating diverse variant libraries
and these methods have been successfully applied to the improvement
of a wide range of properties across many enzyme classes.
[0213] Enzyme characteristics that have been improved and/or
altered by directed evolution technologies include, for example,
selectivity/specificity--for conversion of non-natural substrates;
temperature stability--for robust high temperature processing; pH
stability--for bioprocessing under lower or higher pH conditions;
substrate or product tolerance--so that high product titers can be
achieved; binding (K.sub.m)--broadens substrate binding to include
non-natural substrates; inhibition (K.sub.i)--to remove inhibition
by products, substrates, or key intermediates; activity
(k.sub.cat)--increases enzymatic reaction rates to achieve desired
flux; expression levels--increases protein yields and overall
pathway flux; oxygen stability--for operation of air sensitive
enzymes under aerobic conditions; and anaerobic activity--for
operation of an aerobic enzyme in the absence of oxygen.
[0214] The following exemplary methods have been developed for the
mutagenesis and diversification of genes to target desired
properties of specific enzymes. Any of these can be used to
alter/optimize activity of a decarboxylase enzyme.
[0215] EpPCR (Pritchard, L., D. Come, D. Kell, J. Rowland, and M.
Winson, 2005, A general model of error-prone PCR. J Theor. Biol
234:497-509.) introduces random point mutations by reducing the
fidelity of DNA polymerase in PCR reactions by the addition of Mn'
ions, by biasing dNTP concentrations, or by other conditional
variations. The five step cloning process to confine the
mutagenesis to the target gene of interest involves: 1) error-prone
PCR amplification of the gene of interest; 2) restriction enzyme
digestion; 3) gel purification of the desired DNA fragment; 4)
ligation into a vector; 5) transformation of the gene variants into
a suitable host and screening of the library for improved
performance. This method can generate multiple mutations in a
single gene simultaneously, which can be useful. A high number of
mutants can be generated by EpPCR, so a high-throughput screening
assay or a selection method (especially using robotics) is useful
to identify those with desirable characteristics.
[0216] Error-prone Rolling Circle Amplification (epRCA) (Fujii, R.,
M. Kitaoka, and K. Hayashi, 2004, One-step random mutagenesis by
error-prone rolling circle amplification. Nucleic Acids Res
32:e145; and Fujii, R., M. Kitaoka, and K. Hayashi, 2006,
Error-prone rolling circle amplification: the simplest random
mutagenesis protocol. Nat. Protoc. 1:2493-2497.) has many of the
same elements as epPCR except a whole circular plasmid is used as
the template and random 6-mers with exonuclease resistant
thiophosphate linkages on the last 2 nucleotides are used to
amplify the plasmid followed by transformation into cells in which
the plasmid is re-circularized at tandem repeats. Adjusting the
Mn.sup.2+ concentration can vary the mutation rate somewhat. This
technique uses a simple error-prone, single-step method to create a
full copy of the plasmid with 3-4 mutations/kbp. No restriction
enzyme digestion or specific primers are required. Additionally,
this method is typically available as a kit.
[0217] DNA or Family Shuffling (Stemmer, W. P. 1994, DNA shuffling
by random fragmentation and reassembly: in vitro recombination for
molecular evolution. Proc Natl Acad Sci US.A 91:10747-10751; and
Stemmer, W. P. 1994. Rapid evolution of a protein in vitro by DNA
shuffling. Nature 370:389-391.) typically involves digestion of 2
or more variant genes with nucleases such as Dnase I or EndoV to
generate a pool of random fragments that are reassembled by cycles
of annealing and extension in the presence of DNA polymerase to
create a library of chimeric genes. Fragments prime each other and
recombination occurs when one copy primes another copy (template
switch). This method can be used with >1 kbp DNA sequences. In
addition to mutational recombinants created by fragment reassembly,
this method introduces point mutations in the extension steps at a
rate similar to error-prone PCR. The method can be used to remove
deleterious random neutral mutations that might confer
antigenicity.
[0218] Staggered Extension (StEP) (Zhao, H., L. Giver, Z. Shao, J.
A. Affholter, and F. H. Arnold, 1998, Molecular evolution by
staggered extension process (StEP) in vitro recombination. Nat.
Biotechnol 16:258-261.) entails template priming followed by
repeated cycles of 2 step PCR with denaturation and very short
duration of annealing/extension (as short as 5 sec). Growing
fragments anneal to different templates and extend further, which
is repeated until full-length sequences are made. Template
switching means most resulting fragments have multiple parents.
Combinations of low-fidelity polymerases (Taq and Mutazyme) reduce
error-prone biases because of opposite mutational spectra.
[0219] In Random Priming Recombination (RPR) random sequence
primers are used to generate many short DNA fragments complementary
to different segments of the template. (Shao, Z., H. Zhao, L.
Giver, and F. H. Arnold, 1998, Random-priming in vitro
recombination: an effective tool for directed evolution. Nucleic
Acids Res 26:681-683.) Base misincorporation and mispriming via
epPCR give point mutations. Short DNA fragments prime one another
based on homology and are recombined and reassembled into
full-length by repeated thermocycling. Removal of templates prior
to this step assures low parental recombinants. This method, like
most others, can be performed over multiple iterations to evolve
distinct properties. This technology avoids sequence bias, is
independent of gene length, and requires very little parent DNA for
the application.
[0220] In Heteroduplex Recombination linearized plasmid DNA is used
to form heteroduplexes that are repaired by mismatch repair.
(Volkov, A. A., Z. Shao, and F. H. Arnold. 1999. Recombination and
chimeragenesis by in vitro heteroduplex formation and in vivo
repair. Nucleic Acids Res 27:e18; and Volkov, A. A., Z. Shao, and
F. H. Arnold. 2000. Random chimeragenesis by heteroduplex
recombination. Methods Enzymol. 328:456-463.) The mismatch repair
step is at least somewhat mutagenic. Heteroduplexes transform more
efficiently than linear homoduplexes. This method is suitable for
large genes and whole operons.
[0221] Random Chimeragenesis on Transient Templates (RACHITT)
(Coco, W. M., W. E. Levinson, M. J. Crist, H. J. Hektor, A.
Darzins, P. T. Pienkos, C. H. Squires, and D. J. Monticello, 2001,
DNA shuffling method for generating highly recombined genes and
evolved enzymes. Nat. Biotechnol 19:354-359.) employs Dnase I
fragmentation and size fractionation of ssDNA. Homologous fragments
are hybridized in the absence of polymerase to a complementary
ssDNA scaffold. Any overlapping unhybridized fragment ends are
trimmed down by an exonuclease. Gaps between fragments are filled
in, and then ligated to give a pool of full-length diverse strands
hybridized to the scaffold (that contains U to preclude
amplification). The scaffold then is destroyed and is replaced by a
new strand complementary to the diverse strand by PCR
amplification. The method involves one strand (scaffold) that is
from only one parent while the priming fragments derive from other
genes; the parent scaffold is selected against. Thus, no
reannealing with parental fragments occurs. Overlapping fragments
are trimmed with an exonuclease. Otherwise, this is conceptually
similar to DNA shuffling and StEP. Therefore, there should be no
siblings, few inactives, and no unshuffled parentals. This
technique has advantages in that few or no parental genes are
created and many more crossovers can result relative to standard
DNA shuffling.
[0222] Recombined Extension on Truncated templates (RETT) entails
template switching of unidirectionally growing strands from primers
in the presence of unidirectional ssDNA fragments used as a pool of
templates. (Lee, S. H., E. J. Ryu, M. J. Kang, E.-S. Wang, Z. C. Y.
Piao, K. J. J. Jung, and Y. Shin, 2003, A new approach to directed
gene evolution by recombined extension on truncated templates
(RETT). J. Molec. Catalysis 26:119-129.) No DNA endonucleases are
used. Unidirectional ssDNA is made by DNA polymerase with random
primers or serial deletion with exonuclease. Unidirectional ssDNA
are only templates and not primers. Random priming and exonucleases
don't introduce sequence bias as true of enzymatic cleavage of DNA
shuffling/RACHITT. RETT can be easier to optimize than StEP because
it uses normal PCR conditions instead of very short extensions.
Recombination occurs as a component of the PCR steps--no direct
shuffling. This method can also be more random than StEP due to the
absence of pauses.
[0223] In Degenerate Oligonucleotide Gene Shuffling (DOGS)
degenerate primers are used to control recombination between
molecules; (Bergquist, P. L. and M. D. Gibbs, 2007, Degenerate
oligonucleotide gene shuffling. Methods Mol. Biol 352:191-204;
Bergquist, P. L., R. A. Reeves, and M. D. Gibbs, 2005, Degenerate
oligonucleotide gene shuffling (DOGS) and random drift mutagenesis
(RNDM): two complementary techniques for enzyme evolution. Biomol.
Eng 22:63-72; Gibbs, M. D., K. M. Nevalainen, and P. L. Bergquist,
2001, Degenerate oligonucleotide gene shuffling (DOGS): a method
for enhancing the frequency of recombination with family shuffling.
Gene 271:13-20.) this can be used to control the tendency of other
methods such as DNA shuffling to regenerate parental genes. This
method can be combined with random mutagenesis (epPCR) of selected
gene segments. This can be a good method to block the reformation
of parental sequences. No endonucleases are needed. By adjusting
input concentrations of segments made, one can bias towards a
desired backbone. This method allows DNA shuffling from unrelated
parents without restriction enzyme digests and allows a choice of
random mutagenesis methods.
[0224] Incremental Truncation for the Creation of Hybrid Enzymes
(ITCHY) creates a combinatorial library with 1 base pair deletions
of a gene or gene fragment of interest. (Ostermeier et al., Proc
Natl Acad Sci US.A. 96:3562-3567 (1999); Ostermeier et al., 1999
Nat. Biotechnol. 17:1205-1209 (1999)) Truncations are introduced in
opposite direction on pieces of 2 different genes. These are
ligated together and the fusions are cloned. This technique does
not require homology between the 2 parental genes. When ITCHY is
combined with DNA shuffling, the system is called SCRATCHY (see
below). A major advantage of both is no need for homology between
parental genes; for example, functional fusions between an E. coli
and a human gene were created via ITCHY. When ITCHY libraries are
made, all possible crossovers are captured.
[0225] Thio-Incremental Truncation for the Creation of Hybrid
Enzymes (THIO-ITCHY) is almost the same as ITCHY except that
phosphothioate dNTPs are used to generate truncations. (Lutz, S.,
M. Ostermeier, and S. J. Benkovic, 2001, Rapid generation of
incremental truncation libraries for protein engineering using
alpha-phosphothioate nucleotides. Nucleic Acids Res 29:E16.)
Relative to ITCHY, THIO-ITCHY can be easier to optimize, provide
more reproducibility, and adjustability.
[0226] SCRATCHY-ITCHY combined with DNA shuffling is a combination
of DNA shuffling and ITCHY; therefore, allowing multiple
crossovers. (Lutz et al., Proc Natl Acad Sci US.A. 98:11248-11253
(2001).) SCRATCHY combines the best features of ITCHY and DNA
shuffling. Computational predictions can be used in optimization.
SCRATCHY is more effective than DNA shuffling when sequence
identity is below 80%.
[0227] In Random Drift Mutagenesis (RNDM) mutations made via epPCR
followed by screening/selection for those retaining usable
activity. (Bergquist et al., Biomol. Eng. 22:63-72 (2005).) Then,
these are used in DOGS to generate recombinants with fusions
between multiple active mutants or between active mutants and some
other desirable parent. Designed to promote isolation of neutral
mutations; its purpose is to screen for retained catalytic activity
whether or not this activity is higher or lower than in the
original gene. RNDM is usable in high throughput assays when
screening is capable of detecting activity above background. RNDM
has been used as a front end to DOGS in generating diversity. The
technique imposes a requirement for activity prior to shuffling or
other subsequent steps; neutral drift libraries are indicated to
result in higher/quicker improvements in activity from smaller
libraries. Though published using epPCR, this could be applied to
other large-scale mutagenesis methods.
[0228] Sequence Saturation Mutagenesis (SeSaM) is a random
mutagenesis method that: 1) generates pool of random length
fragments using random incorporation of a phosphothioate nucleotide
and cleavage; this pool is used as a template to 2) extend in the
presence of "universal" bases such as inosine; 3) replication of a
inosine-containing complement gives random base incorporation and,
consequently, mutagenesis. (Wong et al., Biotechnol J. 3:74-82
(2008); Wong Nucleic Acids Res 32:e26; Wong et al., Anal. Biochem.
341:187-189 (2005).) Using this technique it can be possible to
generate a large library of mutants within 2-3 days using simple
methods. This is very non-directed compared to mutational bias of
DNA polymerases. Differences in this approach makes this technique
complementary (or alternative) to epPCR.
[0229] In Synthetic Shuffling, overlapping oligonucleotides are
designed to encode "all genetic diversity in targets" and allow a
very high diversity for the shuffled progeny. (Ness, et al., Nat.
Biotechnol 20:1251-1255 (2002).) In this technique, one can design
the fragments to be shuffled. This aids in increasing the resulting
diversity of the progeny. One can design sequence/codon biases to
make more distantly related sequences recombine at rates
approaching more closely related sequences and it doesn't require
possessing the template genes physically.
[0230] Nucleotide Exchange and Excision Technology NexT exploits a
combination of dUTP incorporation followed by treatment with uracil
DNA glycosylase and then piperidine to perform endpoint DNA
fragmentation. (Muller et al., Nucleic Acids Res 33:e117 (2005))
The gene is reassembled using internal PCR primer extension with
proofreading polymerase. The sizes for shuffling are directly
controllable using varying dUPT::dTTP ratios. This is an end point
reaction using simple methods for uracil incorporation and
cleavage. One can use other nucleotide analogs such as
8-oxo-guanine with this method. Additionally, the technique works
well with very short fragments (86 bp) and has a low error rate.
Chemical cleavage of DNA means very few unshuffled clones.
[0231] In Sequence Homology-Independent Protein Recombination
(SHIPREC) a linker is used to facilitate fusion between 2
distantly/unrelated genes; nuclease treatment is used to generate a
range of chimeras between the two. Result is a single crossover
library of these fusions. (Sieber, V., C. A. Martinez, and F. H.
Arnold. 2001. Libraries of hybrid proteins from distantly related
sequences. Nat. Biotechnol 19:456-460.) This produces a limited
type of shuffling; mutagenesis is a separate process. This
technique can create a library of chimeras with varying fractions
of each of 2 unrelated parent genes. No homology is needed. SHIPREC
was tested with a heme-binding domain of a bacterial CP450 fused to
N-terminal regions of a mammalian CP450; this produced mammalian
activity in a more soluble enzyme.
[0232] In Gene Site Saturation Mutagenesis (GSSM) the starting
materials are a supercoiled dsDNA plasmid with insert and 2 primers
degenerate at the desired site for mutations. (Kretz, K. A., T. H.
Richardson, K. A. Gray, D. E. Robertson, X. Tan, and J. M. Short,
2004, Gene site saturation mutagenesis: a comprehensive mutagenesis
approach. Methods Enzymol. 388:3-11.) Primers carry the mutation of
interest and anneal to the same sequence on opposite strands of
DNA; mutation in the middle of the primer and .about.20 nucleotides
of correct sequence flanking on each side. The sequence in the
primer is NNN or NNK (coding) and MNN (noncoding) (N=all 4, K=G, T,
M=A, C). After extension, DpnI is used to digest dam-methylated DNA
to eliminate the wild-type template. This technique explores all
possible amino acid substitutions at a given locus (i.e., one
codon). The technique facilitates the generation of all possible
replacements at one site with no nonsense codons and equal or
near-equal representation of most possible alleles. It does not
require prior knowledge of structure, mechanism, or domains of the
target enzyme. If followed by shuffling or Gene Reassembly, this
technology creates a diverse library of recombinants containing all
possible combinations of single-site up-mutations. The utility of
this technology combination has been demonstrated for the
successful evolution of over 50 different enzymes, and also for
more than one property in a given enzyme.
[0233] Combinatorial Cassette Mutagenesis (CCM) involves the use of
short oligonucleotide cassettes to replace limited regions with a
large number of possible amino acid sequence alterations.
(Reidhaar-Olson, J. F., J. U. Bowie, R. M. Breyer, J. C. Hu, K. L.
Knight, W. A. Lim, M. C. Mossing, D. A. Parsell, K. R. Shoemaker,
and R. T. Sauer, 1991, Random mutagenesis of protein sequences
using oligonucleotide cassettes. Methods Enzymol. 208:564-586; and
Reidhaar-Olson, J. F. and R. T. Sauer, 1988, Combinatorial cassette
mutagenesis as a probe of the informational content of protein
sequences. Science 241:53-57.) Simultaneous substitutions at 2 or 3
sites are possible using this technique. Additionally, the method
tests a large multiplicity of possible sequence changes at a
limited range of sites. It has been used to explore the information
content of lambda repressor DNA-binding domain.
[0234] Combinatorial Multiple Cassette Mutagenesis (CMCM) is
essentially similar to CCM except it is employed as part of a
larger program: 1) Use of epPCR at high mutation rate to 2) ID hot
spots and hot regions and then 3) extension by CMCM to cover a
defined region of protein sequence space. (Reetz, M. T., S.
Wilensek, D. Zha, and K. E. Jaeger, 2001, Directed Evolution of an
Enantioselective Enzyme through Combinatorial Multiple-Cassette
Mutagenesis. Angew. Chem. Int. Ed Engl. 40:3589-3591.) As with CCM,
this method can test virtually all possible alterations over a
target region. If used along with methods to create random
mutations and shuffled genes, it provides an excellent means of
generating diverse, shuffled proteins. This approach was successful
in increasing, by 51-fold, the enantioselectivity of an enzyme.
[0235] In the Mutator Strains technique conditional is mutator
plasmids allow increases of 20- to 4000-X in random and natural
mutation frequency during selection and to block accumulation of
deleterious mutations when selection is not required. (Selifonova,
O., F. Valle, and V. Schellenberger, 2001, Rapid evolution of novel
traits in microorganisms. Appl Environ Microbiol 67:3645-3649.)
This technology is based on a plasmid-derived mutD5 gene, which
encodes a mutant subunit of DNA polymerase III. This subunit binds
to endogenous DNA polymerase III and compromises the proofreading
ability of polymerase III in any of the strain that harbors the
plasmid. A broad-spectrum of base substitutions and frameshift
mutations occur. In order for effective use, the mutator plasmid
should be removed once the desired phenotype is achieved; this is
accomplished through a temperature sensitive origin of replication,
which allows plasmid curing at 41.degree. C. It should be noted
that mutator strains have been explored for quite some time (e.g.,
see Winter and coworkers, 1996, J. Mol. Biol. 260, 359-3680. In
this technique very high spontaneous mutation rates are observed.
The conditional property minimizes non-desired background
mutations. This technology could be combined with adaptive
evolution to enhance mutagenesis rates and more rapidly achieve
desired phenotypes.
[0236] "Look-Through Mutagenesis (LTM) is a multidimensional
mutagenesis method that assesses and optimizes combinatorial
mutations of selected amino acids." (Rajpal, A., N. Beyaz, L.
Haber, G. Cappuccilli, H. Yee, R. R. Bhatt, T. Takeuchi, R. A.
Lerner, and R. Crea, 2005, A general method for greatly improving
the affinity of antibodies by using combinatorial libraries. Proc
Natl Acad Sci US.A 102:8466-8471.) Rather than saturating each site
with all possible amino acid changes, a set of 9 is chosen to cover
the range of amino acid R-group chemistry. Fewer changes per site
allows multiple sites to be subjected to this type of mutagenesis.
A >800-fold increase in binding affinity for an antibody from
low nanomolar to picomolar has been achieved through this method.
This is a rational approach to minimize the number of random
combinations and should increase the ability to find improved
traits by greatly decreasing the numbers of clones to be screened.
This has been applied to antibody engineering, specifically to
increase the binding affinity and/or reduce dissociation. The
technique can be combined with either screens or selections.
[0237] Gene Reassembly is a DNA shuffling method that can be
applied to multiple genes at one time or to creating a large
library of chimeras (multiple mutations) of a single gene. (on the
world-wide web at
www.verenium.com/Pages/Technology/EnzymeTech/TechEnzyTGR.html)
Typically this technology is used in combination with
ultra-high-throughput screening to query the represented sequence
space for desired improvements. This technique allows multiple gene
recombination independent of homology. The exact number and
position of cross-over events can be pre-determined using fragments
designed via bioinformatic analysis. This technology leads to a
very high level of diversity with virtually no parental gene
reformation and a low level of inactive genes. Combined with GSSM,
a large range of mutations can be tested for improved activity. The
method allows "blending" and "fine tuning" of DNA shuffling, e.g.
codon usage can be optimized.
[0238] In Silico Protein Design Automation PDA is an optimization
algorithm that anchors the structurally defined protein backbone
possessing a particular fold, and searches sequence space for amino
acid substitutions that can stabilize the fold and overall protein
energetics. (Hayes, R. J., J. Bentzien, M. L. Ary, M. Y. Hwang, J.
M. Jacinto, J. Vielmetter, A. Kundu, and B. I. Dahiyat, 2002,
Combining computational and experimental screening for rapid
optimization of protein properties. Proc Natl Acad Sci US.A
99:15926-15931.) This technology allows in silico structure-based
entropy predictions in order to search for structural tolerance
toward protein amino acid variations. Statistical mechanics is
applied to calculate coupling interactions at each
position-structural tolerance toward amino acid substitution is a
measure of coupling. Ultimately, this technology is designed to
yield desired modifications of protein properties while maintaining
the integrity of structural characteristics. The method
computationally assesses and allows filtering of a very large
number of possible sequence variants (10.sup.50). Choice of
sequence variants to test is related to predictions based on most
favorable thermodynamics and ostensibly only stability or
properties that are linked to stability can be effectively
addressed with this technology. The method has been successfully
used in some therapeutic proteins, especially in engineering
immunoglobulins. In silico predictions avoid testing
extraordinarily large numbers of potential variants. Predictions
based on existing three-dimensional structures are more likely to
succeed than predictions based on hypothetical structures. This
technology can readily predict and allow targeted screening of
multiple simultaneous mutations, something not possible with purely
experimental technologies due to exponential increases in
numbers.
[0239] Iterative Saturation Mutagenesis (ISM) involves 1) Use
knowledge of structure/function to choose a likely site for enzyme
improvement. 2) Saturation mutagenesis at chosen site using
Stratagene QuikChange (or other suitable means). 3) Screen/select
for desired properties. 4) With improved clone(s), start over at
another site and continue repeating. (Reetz, M. T. and J. D.
Carballeira, 2007, Iterative saturation mutagenesis (ISM) for rapid
directed evolution of functional enzymes. Nat. Protoc. 2:891-903;
and Reetz, M. T., J. D. Carballeira, and A. Vogel, 2006, Iterative
saturation mutagenesis on the basis of B factors as a strategy for
increasing protein thermostability. Angew. Chem. Int. Ed Engl.
45:7745-7751.) This is a proven methodology assures all possible
replacements at a given position are made for
screening/selection.
[0240] Any of the aforementioned methods for mutagenesis can be
used alone or in any combination. Additionally, any one or
combination of the directed evolution methods can be used in
conjunction with adaptive evolution techniques.
[0241] To generate better producers, metabolic modeling can be
utilized to optimize growth conditions. Modeling can also be used
to design gene knockouts that additionally optimize utilization of
the pathway (see, for example, U.S. patent publications US
2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US
2003/0059792, US 2002/0168654 and US 2004/0009466, and U.S. Pat.
No. 7,127,379). Modeling analysis allows reliable predictions of
the effects on cell growth of shifting the metabolism towards more
efficient production of 1,3-butanediol.
[0242] One computational method for identifying and designing
metabolic alterations favoring biosynthesis of a desired product is
the OptKnock computational framework (Burgard et al., Biotechnol.
Bioeng. 84:647-657 (2003)). OptKnock is a metabolic modeling and
simulation program that suggests gene deletion strategies that
result in genetically stable microorganisms which overproduce the
target product. Specifically, the framework examines the complete
metabolic and/or biochemical network of a microorganism in order to
suggest genetic manipulations that force the desired biochemical to
become an obligatory byproduct of cell growth. By coupling
biochemical production with cell growth through strategically
placed gene deletions or other functional gene disruption, the
growth selection pressures imposed on the engineered strains after
long periods of time in a bioreactor lead to improvements in
performance as a result of the compulsory growth-coupled
biochemical production. Lastly, when gene deletions are constructed
there is a negligible possibility of the designed strains reverting
to their wild-type states because the genes selected by OptKnock
are to be completely removed from the genome. Therefore, this
computational methodology can be used to either identify
alternative pathways that lead to biosynthesis of a desired product
or used in connection with the non-naturally occurring microbial
organisms for further optimization of biosynthesis of a desired
product.
[0243] Briefly, OptKnock is a term used herein to refer to a
computational method and system for modeling cellular metabolism.
The OptKnock program relates to a framework of models and methods
that incorporate particular constraints into flux balance analysis
(FBA) models. These constraints include, for example, qualitative
kinetic information, qualitative regulatory information, and/or DNA
microarray experimental data. OptKnock also computes solutions to
various metabolic problems by, for example, tightening the flux
boundaries derived through flux balance models and subsequently
probing the performance limits of metabolic networks in the
presence of gene additions or deletions. OptKnock computational
framework allows the construction of model formulations that enable
an effective query of the performance limits of metabolic networks
and provides methods for solving the resulting mixed-integer linear
programming problems. The metabolic modeling and simulation methods
referred to herein as OptKnock are described in, for example, U.S.
2002/0168654, WO 2002/055995, and U.S. 2009/0047719.
[0244] Another computational method for identifying and designing
metabolic alterations favoring biosynthetic production of a product
is a metabolic modeling and simulation system termed SimPheny.RTM..
This computational method and system is described in, for example,
U.S. 2003/0233218, filed Jun. 14, 2002, and in WO/2003/106998.
SimPheny.RTM. is a computational system that can be used to produce
a network model in silico and to simulate the flux of mass, energy
or charge through the chemical reactions of a biological system to
define a solution space that contains any and all possible
functionalities of the chemical reactions in the system, thereby
determining a range of allowed activities for the biological
system. This approach is referred to as constraints-based modeling
because the solution space is defined by constraints such as the
known stoichiometry of the included reactions as well as reaction
thermodynamic and capacity constraints associated with maximum
fluxes through reactions. The space defined by these constraints
can be interrogated to determine the phenotypic capabilities and
behavior of the biological system or of its biochemical
components.
[0245] These computational approaches are consistent with
biological realities because biological systems are flexible and
can reach the same result in many different ways. Biological
systems are designed through evolutionary mechanisms that have been
restricted by fundamental constraints that all living systems must
face. Therefore, constraints-based modeling strategy embraces these
general realities. Further, the ability to continuously impose
further restrictions on a network model via the tightening of
constraints results in a reduction in the size of the solution
space, thereby enhancing the precision with which physiological
performance or phenotype can be predicted.
[0246] Given the teachings and guidance provided herein, those
skilled in the art will be able to apply various computational
frameworks for metabolic modeling and simulation to design and
implement biosynthesis of a desired compound in host microbial
organisms. Such metabolic modeling and simulation methods include,
for example, the computational systems exemplified above as
SimPheny.RTM. and OptKnock. For illustration of the invention, some
methods are described herein with reference to the OptKnock
computation framework for modeling and simulation. Those skilled in
the art will know how to apply the identification, design and
implementation of the metabolic alterations using OptKnock to any
of such other metabolic modeling and simulation computational
frameworks and methods well known in the art.
[0247] The methods described above will provide one set of
metabolic reactions to disrupt. Elimination of each reaction within
the set or metabolic modification can result in a desired product
as an obligatory product during the growth phase of the organism.
Because the reactions are known, a solution to the bilevel OptKnock
problem also will provide the associated gene or genes encoding one
or more enzymes that catalyze each reaction within the set of
reactions. Identification of a set of reactions and their
corresponding genes encoding the enzymes participating in each
reaction is generally an automated process, accomplished through
correlation of the reactions with a reaction database having a
relationship between enzymes and encoding genes.
[0248] Once identified, the set of reactions that are to be
disrupted in order to achieve production of a desired product are
implemented in the target cell or organism by functional disruption
of at least one gene encoding each metabolic reaction within the
set. One particularly useful means to achieve functional disruption
of the reaction set is by deletion of each encoding gene. However,
in some instances, it can be beneficial to disrupt the reaction by
other genetic aberrations including, for example, mutation,
deletion of regulatory regions such as promoters or cis binding
sites for regulatory factors, or by truncation of the coding
sequence at any of a number of locations. These latter aberrations,
resulting in less than total deletion of the gene set can be
useful, for example, when rapid assessments of the coupling of a
product are desired or when genetic reversion is less likely to
occur.
[0249] To identify additional productive solutions to the above
described bilevel OptKnock problem which lead to further sets of
reactions to disrupt or metabolic modifications that can result in
the biosynthesis, including growth-coupled biosynthesis of a
desired product, an optimization method, termed integer cuts, can
be implemented. This method proceeds by iteratively solving the
OptKnock problem exemplified above with the incorporation of an
additional constraint referred to as an integer cut at each
iteration. Integer cut constraints effectively prevent the solution
procedure from choosing the exact same set of reactions identified
in any previous iteration that obligatorily couples product
biosynthesis to growth. For example, if a previously identified
growth-coupled metabolic modification specifies reactions 1, 2, and
3 for disruption, then the following constraint prevents the same
reactions from being simultaneously considered in subsequent
solutions. The integer cut method is well known in the art and can
be found described in, for example, Burgard et al., Biotechnol.
Prog. 17:791-797 (2001). As with all methods described herein with
reference to their use in combination with the OptKnock
computational framework for metabolic modeling and simulation, the
integer cut method of reducing redundancy in iterative
computational analysis also can be applied with other computational
frameworks well known in the art including, for example,
SimPheny.RTM..
[0250] The methods exemplified herein allow the construction of
cells and organisms that biosynthetically produce a desired
product, including the obligatory coupling of production of a
target biochemical product to growth of the cell or organism
engineered to harbor the identified genetic alterations. Therefore,
the computational methods described herein allow the identification
and implementation of metabolic modifications that are identified
by an in silico method selected from OptKnock or SimPheny.RTM.. The
set of metabolic modifications can include, for example, addition
of one or more biosynthetic pathway enzymes and/or functional
disruption of one or more metabolic reactions including, for
example, disruption by gene deletion.
[0251] As discussed above, the OptKnock methodology was developed
on the premise that mutant microbial networks can be evolved
towards their computationally predicted maximum-growth phenotypes
when subjected to long periods of growth selection. In other words,
the approach leverages an organism's ability to self-optimize under
selective pressures. The OptKnock framework allows for the
exhaustive enumeration of gene deletion combinations that force a
coupling between biochemical production and cell growth based on
network stoichiometry. The identification of optimal gene/reaction
knockouts requires the solution of a bilevel optimization problem
that chooses the set of active reactions such that an optimal
growth solution for the resulting network overproduces the
biochemical of interest (Burgard et al., Biotechnol. Bioeng.
84:647-657 (2003)).
[0252] An in silico stoichiometric model of E. coli metabolism can
be employed to identify essential genes for metabolic pathways as
exemplified previously and described in, for example, U.S. patent
publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US
2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466,
and in U.S. Pat. No. 7,127,379. As disclosed herein, the OptKnock
mathematical framework can be applied to pinpoint gene deletions
leading to the growth-coupled production of a desired product.
Further, the solution of the bilevel OptKnock problem provides only
one set of deletions. To enumerate all meaningful solutions, that
is, all sets of knockouts leading to growth-coupled production
formation, an optimization technique, termed integer cuts, can be
implemented. This entails iteratively solving the OptKnock problem
with the incorporation of an additional constraint referred to as
an integer cut at each iteration, as discussed above.
[0253] It is understood that modifications which do not
substantially affect the activity of the various embodiments of
this invention are also included within the definition of the
invention provided herein. Accordingly, the following examples are
intended to illustrate but not limit the present invention.
Example I
1,3-butanediol Synthesis Via Alanine
[0254] This example describes the generation of a microbial
organism capable of producing 1,3-butanediol using the alanine
pathway in FIG. 1 via Steps A, B, C, D and H.
[0255] Escherichia coli is used as a target organism to engineer a
1,3-butanediol-producing pathway as shown in FIG. 1. E. coli
provides a good host for generating a non-naturally occurring
microorganism capable of producing 1,3-butanediol. E. coli is
amenable to genetic manipulation and is known to be capable of
producing various products, like ethanol, acetic acid, formic acid,
lactic acid, and succinic acid, effectively under anaerobic or
microaerobic conditions.
[0256] To generate an E. coli strain engineered to produce
1,3-butanediol, nucleic acids encoding the enzymes utilized in the
alanine pathway as described previously, are expressed in E. coli
using well known molecular biology techniques (see, for example,
Sambrook, supra, 2001; Ausubel supra, 1999; Roberts et al., supra,
1989).
[0257] In particular, the ortA (YP_001086914.1), ortB
(YP_001086915.1), dat (P19938), and pdc (P06672) genes encoding the
AKP thiolase, AKP aminotransferase and 2,4-dioxopentanoate
decarboxylase activities, respectively, are cloned into the pZE13
vector (Expressys, Ruelzheim, Germany) under the PA1/lacO promoter.
In addition, the yqhD (NP_417484.1) and adh (AAA23199.2) genes
encoding 3-oxobutyraldehyde reductase (aldehyde reducing) and
4-hydroxy,2-butanone reductase, respectively are cloned into the
pZA33 vector (Expressys, Ruelzheim, Germany) under the PA1/lacO
promoter. The two sets of plasmids are transformed into E. coli
strain MG1655 to express the proteins and enzymes required for
1,3-butanediol synthesis via the alanine pathway. Note that E. coli
possesses the ability to form D-alanine.
[0258] The resulting genetically engineered organism is cultured in
glucose containing medium following procedures well known in the
art (see, for example, Sambrook et al., supra, 2001). The
expression of alanine pathway genes is corroborated using methods
well known in the art for determining polypeptide expression or
enzymatic activity, including for example, Northern blots, PCR
amplification of mRNA, immunoblotting. Enzymatic activities of the
expressed enzymes are confirmed using assays specific for the
individually activities. The ability of the engineered E. coli
strain to produce 1,3-butanediol is confirmed using HPLC, gas
chromatography-mass spectrometry (GCMS) or liquid
chromatography-mass spectrometry (LCMS).
[0259] Microbial strains engineered to have a functional
1,3-butanediol synthesis pathway are further augmented by
optimization for efficient utilization of the pathway. Briefly, the
engineered strain is assessed to determine whether any of the
exogenous genes are expressed at a rate limiting level. Expression
is increased for any enzymes expressed at low levels that can limit
the flux through the pathway by, for example, introduction of
additional gene copy numbers.
[0260] To generate better producers, metabolic modeling is utilized
to optimize growth conditions. Modeling is also used to design gene
knockouts that additionally optimize utilization of the pathway
(see, for example, U.S. patent publications US 2002/0012939, US
2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US
2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379).
Modeling analysis allows reliable predictions of the effects on
cell growth of shifting the metabolism towards more efficient
production of 1,3-butanediol. One modeling method is the bilevel
optimization approach, OptKnock (Burgard et al., Biotechnol.
Bioengineer. 84:647-657 (2003)), which is applied to select gene
knockouts that collectively result in better production of
1,3-butanediol. Adaptive evolution also can be used to generate
better producers of, for example, alanine or
2-amino-4-oxopentanoate intermediates or the 1,3-butanediol
product. Adaptive evolution is performed to improve both growth and
production characteristics (Fong and Palsson, Nat. Genet.
36:1056-1058 (2004); Alper et al., Science 314:1565-1568 (2006)).
Based on the results, subsequent rounds of modeling, genetic
engineering and adaptive evolution can be applied to the
1,3-butanediol producer to further increase production.
[0261] For large-scale production of 1,3-butanediol, the above
alanine pathway-containing organism is cultured in a fermenter
using a medium known in the art to support growth of the organism
under anaerobic conditions. Fermentations are performed in either a
batch, fed-batch or continuous manner. Anaerobic conditions are
maintained by first sparging the medium with nitrogen and then
sealing culture vessel (e.g., flasks can be sealed with a septum
and crimp-cap). Microaerobic conditions also can be utilized by
providing a small hole for limited aeration. The pH of the medium
is maintained at a pH of 7 by addition of an acid, such as H2SO4.
The growth rate is determined by measuring optical density using a
spectrophotometer (600 nm), and the glucose uptake rate by
monitoring carbon source depletion over time. Byproducts such as
undesirable alcohols, organic acids, and residual glucose can be
quantified by HPLC (Shimadzu) with an HPX-087 column (BioRad),
using a refractive index detector for glucose and alcohols, and a
UV detector for organic acids, Lin et al., Biotechnol. Bioeng.,
775-779 (2005).
Example II
1,3-BDO Synthesis Using Acetoacetyl-COA as the Intermediate
[0262] This Example describes the generation of a microbial
organism capable of producing 1,3-butanediol using acetoacetyl-CoA
as the precursor (Steps G, H and I in FIG. 2).
[0263] Escherichia coli is used as a target organism to engineer
the pathway through Steps G (conversion of acetoacetyl-CoA into
3-hydroxybutyryl-CoA), H (conversion of 3-hydroxybutyryl-CoA into
3-hydroxybutyraldehyde) and I (conversion of 3-hydroxybutyraldehyde
into 1,3-butanediol) in FIG. 2. E. coli provides a good host for
generating a non-naturally occurring microorganism capable of
producing 1,3-butanediol. E. coli is amenable to genetic
manipulation and is known to be capable of producing various
products, like ethanol, acetic acid, formic acid, lactic acid, and
succinic acid, effectively under anaerobic or microaerobic
conditions.
[0264] To generate an E. coli strain engineered to produce
1,3-butanediol, nucleic acids encoding the enzymes utilized in the
disclosed pathway (Steps G, H and I) as described previously, are
expressed in E. coli using well known molecular biology techniques
(see, for example, Sambrook, supra, 2001; Ausubel supra, 1999;
Roberts et al., supra, 1989). Note that E. coli has a native
thiolase encoded by atoB (Accession number: NP_416728.1) that
condenses two molecules of acetyl-CoA to form acetoacetyl-CoA.
[0265] Further, hbd (NP_349314.1) encoding acetoacetyl-CoA
reductase (ketone reducing), is cloned into the pZE13 vector
(Expressys, Ruelzheim, Germany) under the PA1/lacO promoter. The
plasmid is transformed into E. coli strain MG1655 to express the
enzyme required for the formation of 3-hydroxybutyryl-CoA via
acetoacetyl-CoA. An aldehyde dehydrogenase (selected from Table A
below) that converts 3-hydroxybutyryl-CoA into
3-hydroxybutyraldehyde, and an alcohol dehydrogenase (selected from
Table B below) that further reduces 3-hydroxybutyraldehyde into
1,3-BDO are also cloned into the pZE13 vector under the PA1/lacO
promoter.
[0266] The resulting genetically engineered organism is cultured in
glucose containing medium following procedures well known in the
art (see, for example, Sambrook et al., supra, 2001). The
expression of the pathway genes is corroborated using methods well
known in the art for determining polypeptide expression or
enzymatic activity, including, for example, Northern blots, PCR
amplification of mRNA, immunoblotting. Enzymatic activities of the
expressed enzymes are confirmed using assays specific for the
individually activities. The ability of the engineered E. coli
strain to produce 1,3-butanediol is confirmed using HPLC, gas
chromatography-mass spectrometry (GCMS) or liquid
chromatography-mass spectrometry (LCMS).
[0267] Microbial strains engineered to have a functional
1,3-butanediol synthesis pathway are further augmented by
optimization for efficient utilization of the pathway. Briefly, the
engineered strain is assessed to determine whether any of the
exogenous genes are expressed at a rate limiting level. Expression
is increased for any enzymes expressed at low levels that can limit
the flux through the pathway by, for example, introduction of
additional gene copy numbers.
[0268] To generate better producers, metabolic modeling is utilized
to optimize growth conditions. Modeling is also used to design gene
knockouts that additionally optimize utilization of the pathway
(see, for example, U.S. patent publications US 2002/0012939, US
2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US
2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379).
Modeling analysis allows reliable predictions of the effects on
cell growth of shifting the metabolism towards more efficient
production of 1,3-butanediol. One modeling method is the bilevel
optimization approach, OptKnock (Burgard et al., Biotechnol.
Bioengineer. 84:647-657 (2003)), which is applied to select gene
knockouts that collectively result in better production of
1,3-butanediol. Adaptive evolution also can be used to generate
better producers of, for example, the acetyl-CoA intermediate or
the 1,3-butanediol product. Adaptive evolution is performed to
improve both growth and production characteristics (Fong and
Palsson, Nat. Genet. 36:1056-1058 (2004); Alper et al., Science
314:1565-1568 (2006)). Based on the results, subsequent rounds of
modeling, genetic engineering and adaptive evolution can be applied
to the 1,3-butanediol producer to further increase production.
[0269] For large-scale production of 1,3-butanediol, the
recombinant organism is cultured in a fermenter using a medium
known in the art to support growth of the organism under anaerobic
conditions. Fermentations are performed in either a batch,
fed-batch or continuous manner. Anaerobic conditions are maintained
by first sparging the medium with nitrogen and then sealing culture
vessel (e.g., flasks can be sealed with a septum and crimp-cap).
Microaerobic conditions also can be utilized by providing a small
hole for limited aeration. The pH of the medium is maintained at a
pH of 7 by addition of an acid, such as H2SO4. The growth rate is
determined by measuring optical density using a spectrophotometer
(600 nm), and the glucose uptake rate by monitoring carbon source
depletion over time. Byproducts such as undesirable alcohols,
organic acids, and residual glucose can be quantified by HPLC
(Shimadzu) with an HPX-087 column (BioRad), using a refractive
index detector for glucose and alcohols, and a UV detector for
organic acids (Lin et al., Biotechnol. Bioeng., 90:775-779
(2005)).
[0270] Several aldehyde dehydrogenases were tested for activity on
3-hydroxybutyryl-CoA. Crude lysates of bacteria, each strain
carrying one out of six genes listed in Table A below encoding for
an aldehyde dehydrogenase was tested for activity on
3-hydroxybutyryl-CoA by measuring the release of CoA moiety. The
genes that were tested and were found to have significant activity
on 3-HBCoA encode the proteins with the following accession and GI
numbers:
TABLE-US-00038 TABLE A Protein GenBank ID GI Number Organism bld
AAP42563.1 31075383 Clostridium saccharoperbutylacetonicum ald
ACL06658.1 1. 218764192 Desulfatibacillum alkenivorans AK-01 ald
YP_001452373 2. 157145054 Citrobacter koseri ATCC BAA-895 pduP 3.
NP_460996.1 4. 16765381 Salmonella enterica Typhimurium pduP 5.
ABJ64680.1 6. 116099531 Lactobacillus brevis ATCC 367 7.
BselDRAFT_1651 8. ZP_02169447 9. 163762382 Bacillus
selenitireducens MLS10
[0271] To correct for background activity in the lysate, measured
activities were compared to a negative control without ALD gene
(vector only, "Vo"). FIG. 4 shows the specific activity of each of
the tested genes on 3-hydroxybutyryl-CoA. The gene ids are shown on
the x-axis.
[0272] Further, bld (GenBank ID: AAP42563.1, GI number: 31075383)
was also tested for activity on 3-HBCoA. The following FIG. 5 shows
the activity of the gene on 3-hydroxybutyryl-CoA before and after
dialysis.
[0273] Alcohol dehydrogenases that were tested for activity on
3-hydroxybutyraldehyde and demonstrated to have significant
activity are listed below.
TABLE-US-00039 TABLE B Protein GenBank ID GI Number Organism Bdh
YP_001309304 150017050 Clostridium beijerinckii (Cbei_2181) Bdh
YP_001309535.1 150016596 Clostridium beijerinckii (Cbei_1722) Bdh
YP_001309535.1 150017281 Clostridium beijerinckii (Cbei_2421)
[0274] The following protocol was used to demonstrate alcohol
dehydrogenase activity (i.e., conversion of 3-hydroxybutyraldehyde
to 1,3-BDO) and combined aldehyde and alcohol dehydrogenase
activities (i.e., conversion of 3-hydroxybutyryl-CoA into
1,3-BDO).
[0275] Chemically competent cells were transformed with plasmids
containing either an aldehyde dehydrogenase or an alcohol
dehydrogenase (listed in Tables A and B above). Colonies from the
plates were picked and grown in LB plus 100 ug/ml carbenecillin
overnight, then 0.6 mL was used to inoculate 60 mL culture of each
alcohol dehydrogenase, or 1.5 mL was used to inoculate a 500 mL
culture of each aldehyde dehydrogenase. Cells were grown at
37.degree. C. to an O.D. of .about.0.7 and induced with IPTG. The
cultures were incubated at 30.degree. C. during protein expression
for 4 hours. The cell cultures were divided into 30 ml aliquots,
centrifuged and the cell pellets were stored at -80.degree. C. A
sample of the cell culture was used to estimate final cell
density.
[0276] Combinations of alcohol dehydrogenases and aldehyde
dehydrogenases were screened in a 96-well plate format with
3-hydroxybutyryl-CoA as a substrate plus a control (no substrate).
Alternatively, for testing the alcohol dehydrogenases activity,
only the alcohol dehydrogenases were added with and without the
substrate, 3-hydroxybutyraldehyde. Preparation of cell lysates was
performed on ice in the coldroom (4.degree. C.). Final cell density
was used to calculate the quantity of Bug Buster cell lysis reagent
for each cell pellet. Lysozyme (10 uL) and benzonase (10 uL) were
added to 35 ml bugbuster and gently inverted to mix. First, 50
.mu.m of dithiothreitol (100 mM stock) was added to the pellet,
then 0.5 ml per O.D. of 1.0 (at 600 nm) of the Bug Buster plus
enzyme mixture was added to the cell pellet and gently mixed to
resuspend.
[0277] To each well, 50 ul of 1 M MOPS (pH=7.5), and 25 ul of
cofactor mixture (4 mM NADH and 4 mM NADPH), both 100 uL aldehyde
dehydrogenase cell lysate, 150 uL alcohol dehydrogenase cell lysate
or only 150 uL alcohol dehydrogenase cell lysate was added and
gently mixed. Then, the relevant substrate was added to the wells.
25 mg of 3-hydroxybutyryl CoA was resuspended in 250 uL water and 5
ul was added to each well testing for both alcohol and aldehyde
dehydrogenase activities for a final concentration of 1.8 mM. For
testing only the alcohol dehydrogenase activity, 50 uL of
3-hydroxybutyraldehyde (prepared by mixing 0.6 ml acetaldehyde in 5
ml water plus catalytic base (one pellet of NaOH) Guthrie, J. P.
(reference attached) was added to each well. The final
concentration of 3-hydroxybutyraldehyde in each well was
approximately 50 mM. The 96-deepwell plate was sealed with a
plastic PCR seal and incubated at 30.degree. C. shaking overnight
(18 hours total). Because protein and cell debris form precipitates
during the incubation period, the plates were centrifuged for 10
min at 4500.times.g, and the supernate was filtered through a
Whatman 96-well filter plate (0.45 .mu.m) prior to LC-MS analysis.
Samples were analyzed for 1,3-butanediol formation.
[0278] FIG. 6 shows 1,3-BDO concentrations when
3-hydroxybutyraldehyde was added as a substrate and in the control
samples with no substrate. The GI numbers for the alcohol
dehydrogenases are shown.
[0279] FIG. 7 shows 1,3-BDO concentrations when
3-hydroxybutyryl-CoA was added as a substrate and in the control
samples with no substrate. The GI numbers for the alcohol
dehydrogenases are shown. The GI number for the aldehyde
dehydrogenase tested in conjunction is 163762382.
Example III
1,3-BDO Synthesis Using 4-Hydroxybutyryl-COA as the
Intermediate
[0280] This Example describes the generation of a microbial
organism capable of producing 1,3-butanediol using
4-hydroxybutyryl-CoA as the precursor (Steps A, B and E in FIG.
3).
[0281] Escherichia coli is used as a target organism to engineer
the pathway through Steps A, B and E in FIG. 3. E. coli provides a
good host for generating a non-naturally occurring microorganism
capable of producing 1,3-butanediol. E. coli is amenable to genetic
manipulation and is known to be capable of producing various
products, like ethanol, acetic acid, formic acid, lactic acid, and
succinic acid, effectively under anaerobic or microaerobic
conditions.
[0282] To generate an E. coli strain engineered to produce
1,3-butanediol, nucleic acids encoding the enzymes utilized in the
disclosed pathway (Steps A, B and E) as described previously, are
expressed in E. coli using well known molecular biology techniques
(see, for example, Sambrook, supra, 2001; Ausubel supra, 1999;
Roberts et al., supra, 1989). A recombinant strain that has ben
engineered to produce significant quantities of
4-hydroxybutyryl-CoA has been described by the applicants
previously (Burk et al. (US 20090075351) and will be used for
inserting the proposed pathway to 1,3-butanediol.
[0283] Further, abfD (YP_3001396399.1), crt (NP_349318.1) and adhE2
(AAK09379.1) genes encoding 4-hydroxybutyryl-CoA dehydratase,
crotonase and 3-hydroxybutyryl-CoA reductase (alcohol forming)
activities respectively, are cloned into the pZE13 vector
(Expressys, Ruelzheim, Germany) under the PA1/lacO promoter. The
plasmid is transformed into the recombinant E. coli strain
producing 4-hydroxybutyryl-CoA to express the proteins and enzymes
required for 1,3-butanediol synthesis from this metabolite.
[0284] The resulting genetically engineered organism is cultured in
glucose containing medium following procedures well known in the
art (see, for example, Sambrook et al., supra, 2001). The
expression of the pathway genes is corroborated using methods well
known in the art for determining polypeptide expression or
enzymatic activity, including, for example, Northern blots, PCR
amplification of mRNA, immunoblotting. Enzymatic activities of the
expressed enzymes are confirmed using assays specific for the
individually activities. The ability of the engineered E. coli
strain to produce 1,3-butanediol is confirmed using HPLC, gas
chromatography-mass spectrometry (GCMS) or liquid
chromatography-mass spectrometry (LCMS).
[0285] Microbial strains engineered to have a functional
1,3-butanediol synthesis pathway are further augmented by
optimization for efficient utilization of the pathway. Briefly, the
engineered strain is assessed to determine whether any of the
exogenous genes are expressed at a rate limiting level. Expression
is increased for any enzymes expressed at low levels that can limit
the flux through the pathway by, for example, introduction of
additional gene copy numbers.
[0286] To generate better producers, metabolic modeling is utilized
to optimize growth conditions. Modeling is also used to design gene
knockouts that additionally optimize utilization of the pathway
(see, for example, U.S. patent publications US 2002/0012939, US
2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US
2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379).
Modeling analysis allows reliable predictions of the effects on
cell growth of shifting the metabolism towards more efficient
production of 1,3-butanediol. One modeling method is the bilevel
optimization approach, OptKnock (Burgard et al., Biotechnol.
Bioengineer. 84:647-657 (2003)), which is applied to select gene
knockouts that collectively result in better production of
1,3-butanediol. Adaptive evolution also can be used to generate
better producers of, for example, the acetyl-CoA intermediate or
the 1,3-butanediol product. Adaptive evolution is performed to
improve both growth and production characteristics (Fong and
Palsson, Nat. Genet. 36:1056-1058 (2004); Alper et al., Science
314:1565-1568 (2006)). Based on the results, subsequent rounds of
modeling, genetic engineering and adaptive evolution can be applied
to the 1,3-butanediol producer to further increase production.
[0287] For large-scale production of 1,3-butanediol, the
recombinant organism is cultured in a fermenter using a medium
known in the art to support growth of the organism under anaerobic
conditions. Fermentations are performed in either a batch,
fed-batch or continuous manner. Anaerobic conditions are maintained
by first sparging the medium with nitrogen and then sealing culture
vessel (e.g., flasks can be sealed with a septum and crimp-cap).
Microaerobic conditions also can be utilized by providing a small
hole for limited aeration. The pH of the medium is maintained at a
pH of 7 by addition of an acid, such as H.sub.2SO.sub.4. The growth
rate is determined by measuring optical density using a
spectrophotometer (600 nm), and the glucose uptake rate by
monitoring carbon source depletion over time. Byproducts such as
undesirable alcohols, organic acids, and residual glucose can be
quantified by HPLC (Shimadzu) with an HPX-087 column (BioRad),
using a refractive index detector for glucose and alcohols, and a
UV detector for organic acids (Lin et al., Biotechnol Bioeng.
90:775-779 (2005))
TABLE-US-00040 TABLE 36 (Ref: FIG. 1) EC Desired Desired Enzyme
Gene GenBank ID Known Step class substrate product name name (if
available) Organism Substrates A 2.3.1.b D-alanine 2-amino-4- AKP
Thiolase ortA YP_001086914.1 Clostridium D-alanine oxo- difficile
630 pentanoate ortB YP_001086915.1 Clostridium D-alanine difficile
630 Amet_2368 YP_001320181.1 Alkaliphilus D-alanine
metalliredigenes QYF Amet_2369 YP_001320182.1 Alkaliphilus
D-alanine metalliredigenes QYF Teth514_1478 YP_001663101.1
Thermoanaero- D-alanine bacter sp. X514 Teth514_1479 YP_001663102.1
Thermoanaero- D-alanine bacter sp. X514 B 2.6.1.a 2-amino-4-
2,4-oxo- 2-amino-4- aspC NP_415448.1 Escherichia coli L-aspartate
oxo- pentanoate oxopentanoate pentanoate aminotrans- ferase or
oxidoreductase (deaminating) avtA YP_026231.1 Escherichia coli
L-alanine, L-valine AAT2 P23542.3 Saccharomyces L-aspartate
cerevisae dat P19938 Bacillus sp. D-alanine, D-2- YM-1
aminobutanoate, D-aspartate dat O07597 Bacillus subtilis D-alanine,
D-2- aminobutanoate, D-aspartate ldh P0A393 Bacillus cereus
L-leucine, L-valine, 2-ami- nobutanoate, L- isoleucine nadX
NP_229443.1 Thermotoga L-aspartate maritima C 4.1.1.a 2,4-dioxo-
3-oxobutanal 2,4-dioxo- pdc P06672.1 Zymomonas 2-ketobutyrate
pentanoate pentanoate mobilus decarboxylase pdc1 P06169
Saccharomyces 2-ketobutyrate, 3- cerevisae hydroxypyruvate mdlC
P20906.2 Pseudomonas 2-ketobutyrate putdia kgd O50463.4
Mycobacterium alpha-ketoglutarate tuberculosis D 1.1.1.a 3-oxobu-
4-hydroxy, 2- 3-oxobu- alrA BAB12273.1 Acinetobacter sp. C2-C14
aldehydes tyraldehyde butanone tyraldehyde Strain M-1 reductase
(aldehyde reducing) ADH2 NP_014032.1 Saccharymyces propionaldehyde,
cerevisiae isobutyraldehyde, butyraldehyde, 2- methylbu-
tyraldehyde, 3- methylbu- tyraldehyde, 2-phenylac- etaldehyde yqhD
NP_417484.1 Escherichia coli acetaldehyde, malondialdehyde,
propanaldehyde, butanaldehyde, and acrolein bdh I NP_349892.1
Clostridium butyraldehyde acetobutylicum bdh II NP_349891.1
Clostridium butyraldehyde acetobutylicum 4hbd YP_726053.1 Ralstonia
succinate eutropha semialdehyde H16 ADHI AAR91477.1 Geobacillus
ethanol, 1-butanol, thermogluco- 1-pentanol, sidasius 1-heptanol,
M10EXG 1-hexanol, 1-octanol, 2-propanol mmsb P28811.1 Pseudomonas
3- aeruginosa hydroxybu- tyraldehydre, malonic semialdehyde,
methylmalonate semialdehyde P84067 P84067 Thermus methylmalonate
thermophilus semialdehyde E 4.1.1.a 2-amino-4- 4-ami- 2-amino-4-
lysA NP_417315.1 Escherichia coli meso- oxo- nobutan-2-
oxopentanoate diaminopimelate pentanoate one decarboxylase lysA
AAA25361.1 Mycobacterium meso- tuberculosis diaminopimelate lysA
BAC92756.1 Methylophilus meso- methylotrophus diaminopimelate odc1
AA59967.1 Homo sapiens D-ornithine panD P0A790 Escherichia coli
L-aspartate panD Q9X4N0 Corynebacterium L-aspartate glutanicum panD
P65660 Mycobacterium L-aspartate tuberculosis F 4.3.1.a 4-ami-
butenone 4-ami- aspA NP_418562 Escherichia coli L-aspartate
nobutan-2-one nobutan-2-one K12 subsp. ammonia lyase MG1655 aspA
P44324.1 Haemophilus L-aspartate influenzae aspA P07346.1
Pseudomonas L-aspartate fluorescens ansB P26899.1 Bacillus subtilus
L-aspartate aspA P33109.1 Serratia L-aspartate marcescens G 4.2.1.a
butenone 4-hydroxy,2- butenone fumA P0AC33 Escherichia coli
fumarate butanone hydratase K12 fumC P05042 Escherichia coli
fumarate K12 fumC O69294 Campylobacter fumarate jejuni fumC P84127
Thermus fumarate thermophilus fumH P14408 Rattus norvegicus
fumarate hmd ABC88407.1 Eubacterium 2-methylene- barkeri glutarate
dmdA ABC88408 Eubacterium dimethylmaleate barkeri dmdB ABC88409.1
Eubacterium dimethylmaleate barkeri H 1.1.1.a 4-hydroxy, 2-
1,3-butanediol 4-hydroxy, 2- bdh AAA58352.1 Homo sapiens
3-oxobutyrate butanone butanone reductase adh AAA23199.2
Clostridium acetone beijerinckii NRRL B593 adhA AAC25556 Pyrococuus
2-pentanaol, furiosus pyruvaldehyde ldh YP_725182.1 Ralstonia
lactate, 2- eutropha oxobutyrate, 2-oxopentaonotae, 2-oxoglutarate
adh P14941.1 Thermoanaero- acetone bacter brockii HTD4 I 4.3.1.a
2-amino-4- acetylacrylate 2-amino-4- aspA NP_418562 Escherichia
coli L-aspartate oxo- oxopentanoate K12 subsp. pentanoate ammonia
lyase MG1655 aspA P44324.1 Haemophilus L-aspartate influenzae aspA
P07346.1 Pseudomonas L-aspartate fluorescens ansB P26899.1 Bacillus
subtilus L-aspartate aspA P33109.1 Serratia L-aspartate marcescens
J 4.1.1.a acetylacrylate butenone acetylacrylate xylII YP_709328.1
Pseudomonas 4-oxalocrotonate decarboxylase putida xylIII
YP_709353.1 Pseudomonas 4-oxalocrotonate putida dmpH CAA43228.1
Pseudomonas sp. 4-oxalocrotonate CF600 dmpE CAA43225.1 Pseudomonas
sp. 4-oxalocrotonate CF600 pdc U63827 Lactobacillus cinnamate and
plantarum derivatives pad AB330293 Klebsiella cinnamate and oxytoca
derivatives K 2.6.1.a 4-ami- 3-oxobutanal 4-ami- SkyPYD4 ABF58893
Saccharomyces beta-alanine nobutan-2-one nobutan-2-one kluyveri
aminotrans- ferase or oxidoreductase (deaminating) gabT P22256
Escherichia coli 4-aminobutyrate Abat P50554 Rattus norvegicus
3-amino-2- methylpropionate UGA1 NP_011533 Saccharomyces
4-aminobutyrate cerevisae kdd AAL93966.1 Fusobacterium 3,5-
nucleatum diaminohexanoate lysDH BAB39707 Geobacillus L-lysine
stearothermophilus L 1.1.1.a 2-amino-4- 2-amino-4- 2-amino-4- thrA
AAC73113 Escherichia coli aspartate oxo- hydroxy- oxopentanoate
semialdehyde pentanoate pentanoate dehydrogenase hom6 CAA89671
Saccharomyces aspartate cerevisae semialdehyde hom2 CAD63186
Lactobacillus aspartate plantarum semialdehyde akthr2 O81852
Arabidopsis aspartate thaliana semialdehyde hom1 CAD64819
Lactobacillus aspartate plantarum semialdehyde M 2.6.1.a 2-amino-4-
2-oxo-4- 2-amino-4- aspC NP_415448.1 Escherichia coli L-aspartate
hydroxy- hydroxy- hydroxy- pentanoate pentanoate pentanoate
aminotrans- ferase or oxidoreductase (deaminating) avtA YP_026231.1
Escherichia coli L-alanine, L-valine AAT2 P23542.3 Saccharomyces
L-aspartate cerevisae dat Bacillus sp. P19938 D-alanine, YM-1
D-2-aminobutanoate, D-aspartate dat Bacillus O07597 D-alanine,
subtilis D-2-aminobutanoate, D-aspartate ldh P0A393 Bacillus cereus
L-leucine, L-valine, 2-ami- nobutanoate, L- isoleucine nadX
NP_229443.1 Thermotoga L-aspartate maritima N 4.1.1.a 2-oxo-4-
3-hydroxybutanal 2-oxo-4- pdc P06672.1 Zymomonas 2-ketobutyrate
hydroxy- hydroxy- mobilus pentanoate pentanoate pdc1 P06169
Saccharomyces 2-ketobutyrate, cerevisae 3-hydroxypyruvate mdlC
P20906.2 Pseudomonas 2-ketobutyrate putdia kgd O50463.4
Mycobacterium alpha-ketoglutarate tuberculosis O 1.1.1.a 3-oxobu-
3-hydroxybu- 3-oxobu- bdh AAA58352.1 Homo sapiens 3-oxobutyrate
tyraldehyde tyraldehyde tyraldehyde reductase (ketone reducing) adh
AAA23199.2 Clostridium acetone beijerinckii
NRRL B593 adhA AAC25556 Pyrococuus 2-pentanaol, furiosus
pyruvaldehyde ldh YP_725182.1 Ralstonia lactate, eutropha
2-oxobutyrate, 2-oxopentaonotae, 2-oxoglutarate adh P14941.1
Thermoanaero- acetone bacter brockii HTD4 P 1.1.1.a 3-hydroxybu-
1,3-butanediol 3-hydroxybu- alrA BAB12273.1 Acinetobacter sp.
C2-C14 aldehydes tyraldehyde tyraldehyde Strain M-1 reductase ADH2
NP_014032.1 Saccharymyces propionaldehyde, cerevisiae
isobutyraldehyde, butyraldehyde, 2-methylbutyr- aldehyde,
3-methylbutyr- aldehyde, 2-phenylac- etaldehyde yqhD NP_417484.1
Escherichia coli acetaldehyde, malondialdehyde, propanaldehyde,
butanaldehyde, and acrolein bdh I NP_349892.1 Clostridium
butyraldehyde acetobutylicum bdh II NP_349891.1 Clostridium
butyraldehyde acetobutylicum 4hbd YP_726053.1 Ralstonia succinate
eutropha semialdehyde H16 ADHI AAR91477.1 Geobacillus ethanol,
1-butanol, thermogluco- 1-pentanol, sidasius 1-heptanol, M10EXG
1-hexanol, 1-octanol, 2-propanol mmsb P28811.1 Pseudomonas
3-hydroxybu- aeruginosa tyraldehyde, malonic semialdehyde,
methylmalonate semialdehyde P84067 P84067 Thermus methylmalonate
thermophilus semialdehyde
TABLE-US-00041 TABLE 37 (Ref: FIG. 2) EC Desired Desired Enzyme
Gene GenBank ID Known Step class substrate product name name (if
available) Organism Substrates A 1.2.1.b acetoace-
3-oxobutyraldehyde acetoacetyl- Ald AAT66436 Clostridium
butyryl-CoA tyl-CoA CoA reductase beijerinckii (aldehdye forming)
sucD NP_904963.1 Porphyromonas succinyl-CoA gingivalis bphG
BAA03892.1 Pseudomonas sp acetaldehyde, propionaldehyde,
butyraldehyde, isobutyraldehyde and formaldehyde Msed_0709
YP_001190808.1 Metallosphaera malonyl-CoA sedula mcr NP_378167
Sulfolobus malonyl-CoA, tokodaii methylmalonyl- CoA B 1.1.1.a
3-oxobutyr- 3- 3-oxobutyr- bdh AAA58352.1 Homo sapiens
3-oxobutyrate aldehyde hydroxybu- aldehyde tyraldehyde reductase
(ketone- reducing) adh AAA23199.2 Clostridium acetone beijerinckii
NRRL B593 adhA AAC25556 Pyrococuus 2-pentanaol, furiosus
pyruvaldehyde ldh YP_725182.1 Ralstonia lactate, 2- eutropha
oxobutyrate, 2- oxopentaonotae, 2- oxoglutarate adh P14941.1
Thermoanaero- acetone bacter brockii HTD4 C 1.1.1.a 3-hydroxybu-
1,3-butanediol 3-hydroxy- alrA BAB12273.1 Acinetobacter sp. C2-C14
aldehydes tyraldehyde butyraldehyde Strain M-1 reductase ADH2
NP_014032.1 Saccharymyces propionaldehyde, cerevisiae
isobutyraldehyde, butyraldehyde, 2-methylbutyr- aldehyde,
3-methylbutyr- aldehyde, 2-phenylacet- aldehyde yqhD NP_417484.1
Escherichia coli acetaldehyde, malondialdehyde, propanaldehyde,
butanaldehyde, and acrolein bdh I NP_349892.1 Clostridium
butyraldehyde acetobutylicum bdh II NP_349891.1 Clostridium
butyraldehyde acetobutylicum 4hbd YP_726053.1 Ralstonia succinate
eutropha H16 semialdehyde ADHI AAR91477.1 Geobacillus ethanol,
1-butanol, thermogluco- 1-pentanol, sidasius 1-heptanol, M10EXG
1-hexanol, 1-octanol, 2-propanol mmsb P28811.1 Pseudomonas
3-hydroxybutyr- aeruginosa aldehyde, malonic semialdehyde,
methylmalonate semialdehyde P84067 P84067 Thermus methylmalonate
thermophilus semialdehyde D 1.1.1.c acetoace- 4-hydroxy,
acetoacetyl- adhE2 AAK09379.1 Clostridium butanoyl-CoA tyl-CoA
2-butanone CoA reductase acetobutylicum (alcohol - forming) mcr
AAS20429.1 Chloroflexus malonyl-CoA aurantiacus FAR AAD38039.1
Simmondsia long chain acyl- chinensis CoA E 1.1.1.a 3-oxobutyr-
4-hydroxy, 3-oxobutyraldehdye alrA BAB12273.1 Acinetobacter sp.
C2-C14 aldehydes aldehyde 2-butanone reductase Strain M-1 (aldehyde
reducing) ADH2 NP_014032.1 Saccharymyces propionaldehyde ,
cerevisiae isobutyraldehyde, butyraldehyde, 2- methylbu-
tyraldehyde, 3-methylbutyr- aldehyde, 2- phenylacetalde- hyde yqhD
NP_417484.1 Escherichia coli acetaldehyde, malondialdehyde,
propanaldehyde, butanaldehyde, and acrolein bdh I NP_349892.1
Clostridium butyraldehyde acetobutylicum bdh II NP_349891.1
Clostridium butyraldehyde acetobutylicum 4hbd YP_726053.1 Ralstonia
succinate eutropha H16 semialdehyde ADHI AAR91477.1 Geobacillus
ethanol, 1-butanol, thermogluco- 1-pentanol, 1- sidasius heptanol,
1- M10EXG hexanol, 1-octanol, 2-propanol mmsb P28811.1 Pseudomonas
3- aeruginosa hydroxybutyralde- hyde, malonic semialdehyde,
methylmalonate semialdehyde P84067 P84067 Thermus methylmalonate
thermophilus semialdehyde F 1.1.1.a 4-hydroxy, 1,3-butanediol
4-hydroxy, 2- bdh AAA58352.1 Homo sapiens 3-oxobutyrate 2-butanone
butanone reductase adh AAA23199.2 Clostridium acetone beijerinckii
NRRL B593 adhA AAC25556 Pyrococuus 2-pentanaol, furiosus
pyruvaldehyde ldh YP_725182.1 Ralstonia lactate, 2- eutropha
oxobutyrate, 2-oxopentaonotae, 2-oxoglutarate adh P14941.1
Thermoanaero- acetone bacter brockii HTD4 G 1.1.1.a acetoace-
3-hydroxybu- acetaocetyl hbd NP_349314.1 Clostridium
acetoacetyl-CoA tyl-CoA tyryl-CoA CoA reductase acetobutylicum
(ketone reducing) hbd AAM14586.1 Clostridium acetoacetyl-CoA
beijerinckii Hbd2 EDK34807.1 Clostridium acetoacetyl-CoA kluyveri
Hbd1 EDK32512.1 Clostridium acetoacetyl-CoA kluyveri Msed_1423
YP_001191505 Metallosphaera 3-hydroxybutyryl- sedula CoA
(suspected) Msed_0399 YP_001190500 Metallosphaera 3-hydroxybutyryl-
sedula CoA (suspected) Msed_0389 YP_001190490 Metallosphaera
3-hydroxybutyryl- sedula CoA (suspected) Msed_1993 YP_001192057
Metallosphaera 3-hydroxybutyryl- sedula CoA (suspected) fadB
P21177.2 Escherichia coli 3-oxoacyl-CoA fadJ P77399.1 Escherichia
coli 3-oxoacyl-CoA H 1.2.1.b 3-hydroxybu- 3-hydroxybu- 3-hydroxy-
Ald AAT66436 Clostridium butyryl-CoA tyryl- tyraldehyde butyryl-CoA
beijerinckii CoA redcutase (aldehyde forming) sucD NP_904963.1
Porphyromonas succinyl-CoA gingivalis bphG BAA03892.1 Pseudomonas
sp acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde
and formaldehyde Msed_0709 YP_001190808.1 Metallosphaera
malonyl-CoA sedula mcr NP_378167 Sulfolobus malonyl-CoA, tokodaii
methylmalonyl- CoA I 1.1.1.c 3-hydroxybu- 1,3-butanediol 3-hydroxy-
adhE2 AAK09379.1 Clostridium butanoyl-CoA tyryl- butyryl-CoA
acetobutylicum CoA reductase (alcohol forming) mcr AAS20429.1
Chloroflexus malonyl-CoA aurantiacus FAR AAD38039.1 Simmondsia long
chain acyl- chinensis CoA
TABLE-US-00042 TABLE 38 (Ref: FIG. 3) EC Desired Desired Enzyme
Gene GenBank ID Known Step class substrate product name name (if
available) Organism Substrates A 4.2.1.a 4-hydroxybutyryl-
crotonyl-CoA 4-hydroxy- abfD YP_001396399.1 Clostridium
4-hydroxybutyryl- CoA butyryl-CoA kluyveri DSM 555 CoA dehydratase
abfD P55792 Clostridium 4-hydroxybutyryl- aminobutyricum CoA abfD
YP_001928843 Porphyromonas 4-hydroxybutyryl- gingivalis ATCC CoA
33277 B 4.2.1.a crotonyl-CoA 3-hydroxybutyryl- crotonase crt
NP_349318.1 Clostridium 3-hydroxybutyryl- CoA acetobutylicum CoA
crt1 YP_001393856 Clostridium 3-hydroxybutyryl- kluyveri DSM 555
CoA crt YP_001929291.1 Porphyromonas example based on gingivalis
ATCC sequence similarity 33277 paaA NP_745427.1 Pseudomonas
enoyl-CoA, cis- putida dihydrodiol derivative of phenylacetyl-CoA
paaB NP_745426.1 Pseudomonas enoyl-CoA, cis- putida dihydrodiol
derivative of phenylacetyl-CoA phaA ABF82233.1 Pseudomonas
enoyl-CoA, cis- fluorescens dihydrodiol derivative of
phenylacetyl-CoA phaB ABF82234.1 Pseudomonas enoyl-CoA, cis-
fluorescens dihydrodiol derivative of phenylacetyl-CoA maoC
NP_415905.1 Escherichia coli enoyl-CoA, cis- dihydrodiol derivative
of phenylacetyl-CoA paaF NP_415911.1 Escherichia coli enoyl-CoA,
cis- dihydrodiol derivative of phenylacetyl-CoA paaG NP_415912.1
Escherichia coli enoyl-CoA, cis-dihydrodiol derivative of
phenylacetyl-CoA C 1.2.1.b 3-hydroxybutyryl- 3-hydroxy- 3-hydroxy-
Ald AAT66436 Clostridium butyryl-CoA CoA butyraldehyde butyryl-CoA
beijerinckii reductase (aldehyde forming) sucD NP_904963.1
Porphyromonas succinyl-CoA gingivalis bphG BAA03892.1 Pseudomonas
sp acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde
and formaldehyde Msed_0709 YP_001190808.1 Metallosphaera
malonyl-CoA sedula mcr NP_378167 Sulfolobus tokodaii malonyl-CoA,
methylmalonyl- CoA D 1.1.1.a 3-hydroxy- 1,3-butanediol 3-hydroxy-
alrA BAB12273.1 Acinetobacter sp. C2-C14 aldehydes butyraldehyde
butyraldehyde Strain M-1 reductase ADH2 NP_014032.1 Saccharymyces
propionaldehyde, cerevisiae isobutyraldehyde, butyraldehyde,
2-methylbutyr- aldehyde, 3-methylbutyr- aldehyde, 2-phenylacet-
aldehyde yqhD NP_417484.1 Escherichia coli acetaldehyde,
malondialdehyde, propanaldehyde, butanaldehyde, and acrolein bdh I
NP_349892.1 Clostridium butyraldehyde acetobutylicum bdh II
NP_349891.1 Clostridium butyraldehyde acetobutylicum 4hbd
YP_726053.1 Ralstonia eutropha succinate H16 semialdehyde ADHI
AAR91477.1 Geobacillus ethanol, 1-butanol, thermoglucosidasius
1-pentanol, M10EXG 1-heptanol, 1-hexanol, 1-octanol, 2-propanol
mmsb P28811.1 Pseudomonas 3-hydroxy- aeruginosa butyraldehyde,
malonic semialdehyde, methylmalonate semialdehyde P84067 P84067
Thermus methylmalonate thermophilus semialdehyde E 1.1.1.c
3-hydroxybutyryl- 1,3-butanediol 3-hydroxy- adhE2 AAK09379.1
Clostridium butanoyl-CoA CoA butyryl-CoA acetobutylicum reductase
(alcohol forming) mcr AAS20429.1 Chloroflexus malonyl-CoA
aurantiacus FAR AAD38039.1 Simmondsia long chain acyl- chinensis
CoA
[0288] Although the invention has been described with reference to
the disclosed embodiments, those skilled in the art will readily
appreciate that the specific examples and studies detailed above
are only illustrative of the invention. It should be understood
that various modifications can be made without departing from the
spirit of the invention. Accordingly, the invention is limited only
by the following claims.
Sequence CWU 1
1
1120PRTEuglena gracilis 1Met Thr Tyr Lys Ala Pro Val Lys Asp Val
Lys Phe Leu Leu Asp Lys1 5 10 15Val Phe Lys Val 20
* * * * *
References