U.S. patent application number 15/211237 was filed with the patent office on 2016-12-08 for methods for biosynthesizing 1,3 butadiene.
This patent application is currently assigned to INVISTA NORTH AMERICA S.A.R.L.. The applicant listed for this patent is INVISTA NORTH AMERICA S.A.R.L.. Invention is credited to Adriana Leonora Botes, Changlin Chen, Alex Van Eck Conradie, Paul S. Pearlman.
Application Number | 20160355843 15/211237 |
Document ID | / |
Family ID | 48797535 |
Filed Date | 2016-12-08 |
United States Patent
Application |
20160355843 |
Kind Code |
A1 |
Pearlman; Paul S. ; et
al. |
December 8, 2016 |
METHODS FOR BIOSYNTHESIZING 1,3 BUTADIENE
Abstract
This document describes biochemical pathways for producing
butadiene by forming two vinyl groups in a butadiene synthesis
substrate. These pathways described herein rely on enzymes such as
mevalonate diphosphate decarboxylase, isoprene synthase, and
dehydratases for the final enzymatic step.
Inventors: |
Pearlman; Paul S.;
(Thornton, PA) ; Chen; Changlin; (Ingleby Barwick,
GB) ; Botes; Adriana Leonora; (East Cleveland,
GB) ; Conradie; Alex Van Eck; (Eaglescliffe,
GB) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
INVISTA NORTH AMERICA S.A.R.L. |
Wilmington |
DE |
US |
|
|
Assignee: |
INVISTA NORTH AMERICA
S.A.R.L.
Wilmington
DE
|
Family ID: |
48797535 |
Appl. No.: |
15/211237 |
Filed: |
July 15, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13691623 |
Nov 30, 2012 |
9422578 |
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15211237 |
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13524973 |
Jun 15, 2012 |
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13691623 |
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61566085 |
Dec 2, 2011 |
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61498408 |
Jun 17, 2011 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Y 402/03027 20130101;
C07C 11/167 20130101; C12N 15/52 20130101; C08F 136/06 20130101;
C12N 9/88 20130101; C12N 9/001 20130101; C12Y 103/08 20130101; Y02E
50/343 20130101; Y02E 50/30 20130101; C08J 5/00 20130101; C12Y
402/01 20130101; C12Y 401/01033 20130101; C12P 5/026 20130101; C08J
2347/00 20130101; Y02P 20/52 20151101; C12P 5/02 20130101 |
International
Class: |
C12P 5/02 20060101
C12P005/02; C08J 5/00 20060101 C08J005/00; C07C 11/167 20060101
C07C011/167; C08F 136/06 20060101 C08F136/06; C12N 15/52 20060101
C12N015/52; C12N 9/88 20060101 C12N009/88 |
Claims
1. A method for the biosynthesis of butadiene, said method
comprising forming two terminal vinyl groups in a butadiene
synthesis substrate.
2. The method of claim 1, wherein a first vinyl group is
enzymatically formed in said butadiene synthesis substrate to
produce a compound selected from the group consisting of
2-oxopent-4-enoate, propenyl-CoA, (R) 3-hydroxypent-4-enoate,
2,4-pentadienoyl-[acp], 2,4-pentadienoyl-CoA, crotonyl-CoA, and
3-buten-2-ol.
3. The method of claim 2, wherein 2-oxopent-4-enoate is produced by
forming a first vinyl group in (i) 4-oxalocrotonate using an
4-oxalocrotonate decarboxylase classified in EC 4.1.1.77, (ii)
2-hydroxymuconate semialdehyde using a
2-hydroxymuconate-semialdehyde hydrolase classified in EC 3.7.1.9,
(iii) 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate using a
2-hydroxy-6-oxonona-2,4-dienedioate hydrolase classified in EC
3.7.1.14, or (iv) by converting 2-hydroxymuconate semialdehyde to
2-hydroxymuconate using a 2 aminomuconate semialdehyde
dehydrogenase classified under EC 1.2.1.32, converting
2-hydroxymuconate to 4-oxalocrotonate using a 2-hydroxymuconate
tautomerase classified under EC 5.3.2.6, and converting
4-oxalocrotonate to 2-oxopent-4-enoate using a 4-oxalocrotonate
decarboxylase classified under EC 4.1.1.77.
4. (canceled)
5. The method according to claim 3, wherein (i) 2-hydroxymuconate
semialdehyde is produced by converting catechol to
2-hydroxymuconate semilaldehyde using a catechol 2,3-dioxygenase
classified under EC 1.13.11.2, (ii) 2-hydroxymuconate semialdehyde
is produced by converting
5-carboxy-2-hydroxymuconate-6-semiladehyde using a
5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase or (iii)
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate is produced by converting
2,3-dihydroxy phenylpropionate using a 3-carboxyethylcatechol
2,3-dioxygenase classified under EC 1.13.11.16.
6. The method according to claim 5, wherein said catechol is
produced by converting anthranilate using an anthranilate
1,2-dioxygenase classified under EC 1.14.12.1 or by converting
protocatechuate using a protocatechuate decarboxylase classified
under EC 4.1163; said 5-carboxy-2-hydroxymuconate-6-semialdehyde
decarboxylase is encoded by praH or produced by converting
protocatechuate using a protocatechuate 2,3-dioxygenase, wherein
said protocatechuate 2,3-dioxygenase is optionally encoded by praA;
or said 2,3-dihydroxyphenylpropionate is produced by converting
cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol using a
3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl) propanoate
dehydrogenase classified under EC 1.3.1.87.
7. The method of claim 6, wherein anthranilate is produced by
converting chorismate using an anthranilate synthase classified
under EC 4.1.3.27 or protocatechuate is produced by converting
3-dehydroshikimate using a 3-dehydroshikimate dehydratase
classified under EC 4.2.1.118.
8-13. (canceled)
14. The method of claim 6, wherein 2,3-dihydroxyphenylpropionate is
produced by converting
cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol using a
3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl) propanoate
dehydrogenase classified under EC 1.3.1.87; wherein
cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol is produced by
converting 3-phenyl-propionate using a 3-phenylpropanoate
dioxygenase classified under EC 1.14.12.19; wherein
3-phenyl-propionate is produced by converting E-cinnamate using a
2-enoate reductase classified under EC 1.3.1.31; and/or wherein
E-cinnamate is produced by converting L-phenylalanine using a
phenylalanine ammonia-lyase classified under EC 4.3.1.24.
15-17. (canceled)
18. The method according to claim 1, where said butadiene synthesis
substrate is propanoyl-CoA.
19. The method according to claim 18, where propenoyl-CoA is the
compound that is produced by forming a first vinyl group in (i)
propanoyl-CoA using a butyryl-CoA dehydrogenase classified under EC
1.3.8.1 or a medium-chain acyl-CoA dehydrogenase classified under
EC 1.3.8.7, where propanoyl-CoA is optionally produced by
converting (2S)-methylmalonyl-CoA using a methylmalonyl-CoA
carboxytransferase classified under EC 2.1.3.1 or a
methylmalonyl-CoA decarboxylase classified under EC 4.1.1.41; (ii)
lactoyl-CoA using a lactoyl-CoA dehydratase classified under EC
4.2.1.54, where lactoyl-CoA is optionally produced by converting
L-lactate using a proprionate CoA-transferase classified under EC
2.8.3.1, wherein L-lactate is optionally produced by converting
pyruvate using an L-lactate dehydrogenase classified under EC
1.1.1.27; or (iii) 3-hydroxypropionyl-CoA using a
3-hydroxypropionyl-CoA dehydratase classified under EC 4.2.1.116,
wherein 3-hydroxypropionyl-CoA is optionally produced by converting
3-hydroxypropionate using a 3-hydroxyisobutyryl-CoA hydrolase
classified under EC 3.1.2.4 or by converting malonate semialdehyde
using a 3-hydroxypropionate dehydrogenase classified under EC
1.1.1.59, wherein malonate semiladehyde is optionally produced by
converting malonyl-CoA using a malonyl-CoA reductase classified
under EC 1.2.1.75; by converting 2-oxo-butyrate using a
2-ketobutyrate formate-lyase classified under EC 2.3.1.-, wherein
said 2-ketobutyrate formate-lyase is optionally encoded by tdcE or
wherein 2-oxo-butyrate is optionally produced by converting
L-threonine using a threonine ammonia lyase classified under EC
4.3.1.19; by converting propanol using a propionaldehyde
dehydrogenase wherein said propionaldehyde dehydrogenase is
optionally encoded by pduP or wherein propanol is optionally
produced by converting 1,2-propanediol using a propanediol
dehydratase classified under EC 4.2.1.28; from levulinic acid by
converting levulinyl-CoA using a transferase classified under EC
2.3.1.-, wherein levulinyl-CoA is optionally produced by converting
levulinyl acid using an acyl-CoA synthetase or ligase classified
under EC 6.2.1.-; or by converting propenoyl-CoA using a
butyryl-CoA dehydrogenase classified under EC 1.3.8.1 or a
medium-chain acyl-CoA dehydrogenase classified under EC
1.3.8.7.
20. (canceled)
21. The method of claim 19, wherein (2S)-methylmalonyl-CoA is
produced by converting (2R)-methylmalonyl-CoA using a
methylmalonyl-CoA epimerase classified under EC 5.1.99.1; and/or
wherein (2R)-methylmalonyl-CoA is produced by converting
succinyl-CoA using a methylmalonyl-CoA mutase classified under EC
5.4.99.2.
22-36. (canceled)
37. The method of claim 2, where (R) 3-hydroxypent-4-enoate
propenoyl-CoA is produced by forming a first vinyl in (R)
3-hydroxypentanoate using a desaturase/monooxygenas, wherein said
desaturase is optionally a gene product of MdpJ e, or cytochrome
P450, wherein said cytochrome P450 is optionally a gene product of
the CYP4 family, wherein (R) 3-hydroxy-pentanoate is optionally
produced by converting (R) 3-hydroxypentanoyl-CoA using a
thioesterase classified under EC 3.1.2.-, wherein said thioesterase
is optionally a gene product of tesB, wherein (R)
3-hydroxypentanoyl-CoA is optionally produced by converting
3-oxopentanoyl-CoA using an acetoacetyl-CoA reductase classified
under EC 1.1.1.36, wherein said acetoacetyl-CoA reductase is
optionally a gene product of phaB and/or wherein 3-oxopentanoyl-CoA
is optionally produced by converting propanoyl-CoA using an
acetyl-CoA C-acyltransferase classified under EC 2.3.1.16.
38-40. (canceled)
41. The method of claim 2, wherein 2,4-pentadienoyl-[acp] is
produced by forming a first vinyl group in pent-2-enoyl-acp using
an acyl-[acp] dehydrogenase, wherein pent-2-enoyl-[acp] is
optionally produced by converting (R) 3-hydroxypentanoyl-[acp]
using a 3-Hydroxyacyl-[acp] dehydratase classified under EC
4.2.1.59 or by converting pent-2-enoyl-CoA using an acyl
transferase, wherein (R) 3-hydroxypentanoyl-[acp] is optionally
produced by converting 3-oxopentanoyl-[acp] using a 3-oxoacyl-[acp]
reductase classified under EC 1.1.1.100, and/or wherein
3-oxopentanoyl-[acp] is optionally produced by converting
propanoyl-CoA using a beta-ketoacyl-[acp] synthase I classified
under EC 2.3.1.41, wherein said beta-ketoacyl-[acp] synthase I is
optionally a gene product of tcsB, and an acyl-transferase such as
tcsA; or wherein pent-2-enoyl-CoA is optionally produced by
converting (R) 3-hydroxypentanoyl-CoA using an enoyl-CoA hydratase
classified under EC 4.2.1.119, wherein said enoyl-CoA hydratase is
optionally a gene product of phaJ, wherein (R)
3-hydroxypentanoyl-CoA is optionally produced by converting
3-oxopentanoyl-CoA using an acetoacetyl-CoA reductase classified
under EC 1.1.1.36, wherein said acetoacetyl-CoA reductase is
optionally a gene product of phaB, and/or wherein
3-oxopentanoyl-CoA is optionally produced by converting
propanoyl-CoA using an acetyl-CoA C-acyltransferase classified
under EC 2.3.1.16.
42. The method of claim 2, wherein 2,4-pentadienoyl-CoA is produced
by forming a first vinyl group in (i) 5-hydroxypentanoyl-CoA using
a 5-hydroxyvaleryl-CoA dehydratase classified under EC 4.2.1.-,
wherein said 5-hydroxyvaleryl-CoA dehydratase optionally originates
from Clostridium viride and/or wherein 5-hydroxypentanoyl-CoA is
optionally produced by converting either 5-hydroxypentanoate using
5-hydroxypentanoate CoA-transferase classified under EC 2.8.3.14 or
pentanoyl-CoA using a cytochrome P450, wherein said cytochrome P450
is optionally a gene product of CYP153A6, wherein
5-hydroxypentanoate is optionally produced by converting
5-oxopentanoate using a 5-hydroxyvalerate dehydrogenase or by
converting 5-aminovalerate using a 5-aminovalerate transaminase
classified under EC 2.6.1.48, wherein 5-hydroxyvalerate
dehydrogenase is optionally a gene product of cpnD or a
dehydrogenase from Clostridium viride, wherein 5-aminovalerate is
optionally produced by converting D-proline using a D-proline
reductase classified under EC 1.21.4.1, wherein D-proline is
optionally produced by converting L-proline using a proline
racemase classified under EC 5.1.1.4, wherein L-proline is
optionally produced by converting (S)-1-Pyrroline-5-carboxylate
using a pyrroline-5-carboxylate reductase classified under EC
1.5.1.2, wherein (S)-1-Pyrroline-5-carboxylate is optionally
produced by spontaneous conversion of L-glutamate 5-semialdehyde,
wherein L-glutamate 5-semialdehyde is optionally produced by
converting L-glutamyl-5-phosphate using a glutamate-5-semialdehyde
dehydrogenase classified under EC 1.2.1.41, and/or wherein
L-glutamyl-5-phosphate is optionally produced by converting
L-glutamate using glutamate 5-kinase classified under EC 2.7.2.11,
or wherein pentanoyl-CoA is optionally produced by converting
pent-2-enoyl-CoA using a trans-2-enoyl-CoA reductase classified
under EC 1.3.1.38; or (ii) pent-3-enoyl-CoA using a 2,4-dienoyl
coenzyme A reductase classified under EC 1.3.1.34, wherein
pent-3-enoyl-CoA is optionally produced by converting
pent-2-enoyl-CoA using an isomerase classified under EC
5.3.3.8.
43. (canceled)
44. The method of claim 2, where crotonyl-CoA is produced by
forming a first vinyl group in (i) glutaconyl-CoA using a
glutaconyl-CoA decarboxylase classified under EC 4.1.1.70, wherein
glutaconyl-CoA is optionally produced by converting
2-hydroxyglutaryl-CoA using a dehydratase classified under EC
4.2.1.-, wherein 2-hydroxyglutaryl-CoA is optionally produced by
converting 2-hydroxyglutarate using a glutaconate CoA-transferase
classified under EC 2.8.3.12 and/or wherein 2-hydroxyglutarate is
optionally produced by converting 2-oxoglutarate using a
2-hydroxyglutarate dehydrogenase classified under EC 1.1.99.2; (ii)
4-hydroxybutryl-CoA using a 4-hydroxybutanoyl-CoA dehydratase
classified under EC 4.2.1.120 and a vinylacetyl-CoA isomerase
classified under EC 5.3.3.3, wherein 4-hydroxybutyryl-CoA is
optionally produced by converting 4-hydroxybutyrate using a
CoA-transferase, wherein said CoA-transferase is optionally a gene
product of Ck-cat2, wherein 4-hydroxybutyrate is optionally
produced by converting succinate semialdehyde using a
4-hydroxybutyrate dehydrogenase classified under EC 1.1.1.61,
and/or wherein succinate semialdehyde is optionally produced by
converting succinyl-CoA using a succinate-semialdehyde
dehydrogenase classified under EC 1.2.1.76; or (iii) (R)
3-hydroxybutanoyl-CoA using an enoyl-CoA hydratase classified under
EC 4.2.1.119, wherein enoyl-CoA hydratase is optionally a gene
product of phaJ, wherein 3-hydroxybutanoyl-CoA is optionally
produced by converting acetoacetyl-CoA using 3-hydroxybutyryl-CoA
dehydrogenase classified under EC 1.1.1.36, wherein acetoacetyl-CoA
is optionally produced by converting acetyl-CoA using acetyl-CoA
C-acetyltransferase classified under EC 2.3.1.9, and/or wherein
acetyl-CoA C-acyltransferase is optionally a gene product of
BktB.
45. (canceled)
46. The method of claim 1, where the second vinyl group is
enzymatically formed in (R) 3-hydroxypent-4-enoate by a mevalonate
diphosphate decarboxylase (MDD), wherein said mevalonate
diphosphate decarboxylase is optionally classified under EC
4.1.1.33 and its amino acid sequence comprises a minimum number of
four serine residues within five residues either side of the
catalytic arginine residue of the catalytic cleft, wherein said
mevalonate diphosphate decarboxylase optionally originates from the
genus Streptococcus or Staphylococcus, wherein (R)
3-hydroxypent-4-enoate is optionally produced by converting
3-hydroxypent-4-enoyl-CoA using a thioesterase classified under EC
3.1.2.- or by converting (R) 3-hydroxypent-4-enoyl-CoA using a
thioesterase classified under EC 3.1.2.- and/or wherein said
thioesterase is the gene product of tesB, wherein
3-hydroxypent-4-enoyl-CoA is optionally produced by converting
2,4-pentadienoyl-CoA using an enoyl-CoA dehydratase 2 classified
under EC 4.2.1, wherein 2,4-pentadienoyl-CoA is optionally produced
by converting 2-hydroxypent-4-enoyl-CoA using a
2-Hydroxyisocaproyl-CoA dehydratase, wherein said
2-Hydroxyisocaproyl-CoA dehydratase is optionally a gene product of
the initiator HadI and HadBC, wherein 2-hydroxypent-4-enoyl-CoA is
produced by converting 2-hydroxypent-4-enoate using a
CoA-transferase, wherein said CoA-transferase is optionally a gene
product of GctAB, wherein 2-hydroxypent-4-enoate is optionally
produced by converting 2-oxopent-4-enoate using a
(R)-2-hydroxyisocaproate dehydrogenase, and/or wherein said
(R)-2-hydroxyisocaproate dehydrogenase is optionally a gene product
of LdhA from Clostridium difficile, or wherein (R)
3-hydroxypent-4-enoyl-CoA is optionally produced by converting
3-oxopent-4-enoyl-CoA using an acetoacetyl-CoA reductase classified
under EC 1.1.1.36, wherein said acetoacetyl-CoA reductase is
optionally a gene product of phaB wherein 3-oxopent-4-enoyl-CoA is
optionally produced by converting propenyl-CoA using a
.beta.-ketothiolase classified under EC 2.3.1.16, by converting
(R)-3-hydroxypen-4-enoyl-[acp] using a (R)-3-hydroxyacyl-ACP:CoA
transacylase, wherein said (R)-3-hydroxyacyl-ACP:CoA transacylase
is optionally a gene product of phaG, and/or wherein
(R)-3-hydroxypen-4-enoyl-[acp] is optionally produced by converting
2,4 pentadienoyl-[acp] using a 3-hydroxyacyl-[acyl-carrier-protein]
dehydratase classified under EC 4.2.1.59, or by converting
2,4-pentadienoyl-CoA using an enoyl-CoA dehydratase 2 classified
under EC 4.2.1.119; or by enzymatic formation in either
2-buten-1-ol diphosphate or 3-buten-2-ol diphosphate by an isoprene
synthase (ISPS), wherein 2-buten-1-ol diphosphate is optionally
produced by converting 2-buten-1-ol phosphate using a
phosphomevalonate kinase classified under EC 2.7.4.2 or using a
diphosphokinase classified under EC 2.7.6.- or by converting
2-buten-1-ol using a mevalonate kinase classified under EC
2.7.1.36, wherein 2-buten-1-ol is optionally produced by converting
2-buten-1-al using an allyl-alcohol dehydrogenase classified under
EC 1.1.1.54, wherein 2-buten-1-al is optionally produced by
converting crotonic acid using a long-chain-aldehyde dehydrogenase
classified under EC 1.2.1.48, and/or wherein crotonic acid is
optionally produced by converting crotonyl-CoA using a
succinate-CoA ligase classified under EC 6.2.1.5; or 3-buten-2-ol
diphosphate is optionally produced by converting 3-buten-2-ol using
a diphosphokinase classified under EC 2.7.6.-, where said
diphosphokinase is optionally a thiamine diphosphokinase classified
under EC 2.7.6.2, or 3-buten-2-ol phosphate using a
phosphomevalonate kinase classified under EC 2.7.4.2, wherein
3-buten-2-ol phosphate is optionally produced by converting
3-buten-2-ol using mevalonate kinase classified under EC
2.7.1.36.
47-108. (canceled)
109. The method of claim 1, wherein said method is performed using
isolated enzymes, cell lysates comprising enzymes or in a
recombinant host.
110-112. (canceled)
113. The method according to claim 109, where said recombinant host
cells are retained in ceramic hollow fibre membranes to maintain a
high cell density during fermentation.
114. The method of claim 109, wherein the principal carbon source
fed to the fermentation derives from biological or non-biological
feedstocks.
115. The method of claim 114, where the biological feedstock is or
derives from monosaccharides, disaccharides, lignocellulose,
hemicellulose, cellulose, lignin such as levulinic acid and
furfural, lignin, triglycerides such as glycerol and fatty acids,
agricultural waste or municipal waste or the non-biological
feedstock is or derives from either natural gas, syngas, carbon
monoxide CO.sub.2/H.sub.2, methanol, ethanol, or waste stream from
a chemical or petrochemical industry.
116-119. (canceled)
120. The method of claim 109, wherein the recombinant host is a
prokaryote either from the genus Escherichia such as Escherichia
coli; from the genus Clostridia such as Clostridium ljungdahlii,
Clostridium autoethanogenum or Clostridium kluyveri; from the genus
Corynebacteria such as Corynebacterium glutamicum; from the genus
Cupriavidus such as Cupriavidus necator or Cupriavidus
metallidurans; from the genus Pseudomonas such as Pseudomonas
fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the
genus Delftia such as Delftia acidovorans; from the genus Bacillus
such as Bacillus subtillis; from the genus Lactobacillus such as
Lactobacillus delbrueckii; or from the genus Lactococcus such as
Lactococcus lactis or a eukaryote either from the genus Aspergillus
such as Aspergillus niger; from the genus Saccharomyces such as
Saccharomyces cerevisiae; from the genus Pichia such as Pichia
pastoris; from the genus Yarrowia such as Yarrowia lipolytica; from
the genus Issatchenkia such as Issatchenkia orientalis; from the
genus Debaryomyces such as Debaryomyces hansenii; from the genus
Arxula such as Arxula adenoinivorans; or from the genus
Kluyveromyces such as Kluyveromyces lactis.
121. (canceled)
122. The method of claim 109, wherein in the recombinant host:
enzymes catalyzing the hydrolysis of propionyl-CoA and acetyl-CoA
are attenuated; enzymes consuming propanoyl-CoA via the
methyl-citrate cycle are attenuated; enzymes consuming
propanoyl-CoA to pyruvate are attenuated; enzymes consuming
propanoyl-CoA to malonyl-CoA are attenuated; a feedback-resistant
threonine deaminase is genetically engineered; .beta.-ketothiolases
catalysing the condensation of acetyl-CoA to acetoacetyl-CoA such
as the gene products of AtoB or phaA are attenuated; polymer
synthase enzymes in a host strain that naturally accumulates
polyhydroxyalkanoates are attenuated; a gene encoding a
phosphotransacetylase, such as pta, is attenuated; a gene encoding
an acetate kinase degrading propanoate, such as ack, is attenuated;
a gene encoding the degradation of pyruvate to lactate is
attenuated; a gene encoding the degradation of phosphoenolpyruvate
to succinate such as frdBC is attenuated; a gene encoding the
degradation of acetyl-CoA to ethanol such as adhE is attenuated;
enzymes catalysing anaplerotic reactions supplementing the citric
acid cycle intermediates are amplified; a puridine nucleotide
transhydrogenase gene such as UdhA is overexpressed; a
glyceraldehyde-3P-dehydrogenase gene such as GapN is overexpressed;
a malic enzyme gene such as maeA or maeB is overexpressed; a
glucose-6-phosphate dehydrogenase gene such as zwf is
overexpressed; a fructose 1,6 diphosphatase gene such as fbp is
overexpressed; efflux of butadiene across the cell membrane to the
extracellular media is enhanced or amplified by genetically
engineering structural modifications to the cell membrane; efflux
of butadiene across the cell membrane to the extracellular media is
enhanced or amplified by genetically engineering an increase to any
associated transporter activity for butadiene; or oxygenases
degrading butadiene to toxic intermediates such as
1,2-epoxy-3-butene and 1,2:3,4-diepoxybutane are attenuated in the
host organism.
123-149. (canceled)
150. A recombinant host for the biosynthesis of butadiene, said
recombinant host being capable of forming two terminal vinyl groups
in a butadiene synthesis substrate in accordance with the method of
claim 1.
151. The recombinant host of claim 150, wherein a first vinyl group
is enzymatically formed in said butadiene synthesis substrate to
produce a compound selected from the group consisting of
2-oxopent-4-enoate, propenyl-CoA, (R) 3-hydroxypent-4-enoate,
2,4-pentadienoyl-[acp], 2,4-pentadienoyl-CoA, crotonyl-CoA, and
3-buten-2-ol.
152. The recombinant host of claim 150, wherein the second vinyl
group is enzymatically formed in either (R) 3-hydroxypent-4-enoate
by a mevalonate diphosphate decarboxylase (MDD), 2-buten-1-ol
diphosphate or 3-buten-2-ol diphosphate by an isoprene synthase
(ISPS) or 3-buten-2-ol or 2-buten-1-ol by a dehydratase in enzyme
class EC 4.2.1.
153. A bio-derived, bio-based or fermentation-derived product,
wherein said product comprises: i. a composition comprising at
least one bio-derived, bio-based or fermentation-derived compound
according to claim 1 or any combination thereof, ii. a bio-derived,
bio-based or fermentation-derived polymer comprising the
bio-derived, bio-based or fermentation-derived composition or
compound of i., or any combination thereof, iii. a bio-derived,
bio-based or fermentation-derived resin comprising the bio-derived,
bio-based or fermentation-derived compound or bio-derived,
bio-based or fermentation-derived composition of i. or any
combination thereof or the bio-derived, bio-based or
fermentation-derived polymer of ii. or any combination thereof, iv.
a molded substance obtained by molding the bio-derived, bio-based
or fermentation-derived polymer of ii. or the bio-derived,
bio-based or fermentation-derived resin of iii., or any combination
thereof, v. a bio-derived, bio-based or fermentation-derived
formulation comprising the bio-derived, bio-based or
fermentation-derived composition of i., bio-derived, bio-based or
fermentation-derived compound of i., bio-derived, bio-based or
fermentation-derived polymer of ii., bio-derived, bio-based or
fermentation-derived resin of iii., or bio-derived, bio-based or
fermentation-derived molded substance of iv, or any combination
thereof, or vi. a bio-derived, bio-based or fermentation-derived
semi-solid or a non-semi-solid stream, comprising the bio-derived,
bio-based or fermentation-derived composition of i., bio-derived,
bio-based or fermentation-derived compound of i., bio-derived,
bio-based or fermentation-derived polymer of ii., bio-derived,
bio-based or fermentation-derived resin of iii., bio-derived,
bio-based or fermentation-derived formulation of v., or
bio-derived, bio-based or fermentation-derived molded substance of
iv., or any combination thereof.
154. A non-naturally occurring biochemical network comprising at
least one substrate of FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5, FIG.
6, FIG. 7, FIG. 8, FIG. 9, FIG. 10 or FIG. 11, at least one
exogenous nucleic acid encoding a polypeptide having the activity
of at least one enzyme of FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5,
FIG. 6, FIG. 7, FIG. 8, FIG. 9, FIG. 10 or FIG. 11 and at least one
product of FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5, FIG. 6, FIG. 7,
FIG. 8, FIG. 9, FIG. 10 or FIG. 11.
155. A non-naturally occurring composition, comprising at least one
substrate of FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5, FIG. 6, FIG.
7, FIG. 8, FIG. 9, FIG. 10 or FIG. 11, wherein said substrate is
optionally bio-based, bio-derived or fermentation derived; at least
one exogenous nucleic acid encoding a polypeptide having the
activity of at least one enzyme of FIG. 1, FIG. 2, FIG. 3, FIG. 4,
FIG. 5, FIG. 6, FIG. 7, FIG. 8, FIG. 9, FIG. 10 or FIG. 11; and at
least one bio-based, bio-derived or fermentation derived product of
FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5, FIG. 6, FIG. 7, FIG. 8,
FIG. 9, FIG. 10 or FIG. 11.
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This patent application is a divisional of U.S. application
Ser. No. 13/691,623 filed Nov. 30, 2012, which claims the benefit
of priority from U.S. Provisional Application No. 61/566,085, filed
Dec. 2, 2011 and which is a continuation-in-part of U.S.
application Ser. No. 13/524,973, filed Jun. 15, 2012, which claims
the benefit of priority from U.S. Provisional Application No.
61/498,408, filed Jun. 17, 2011, all of which are incorporated
herein by reference in their entireties.
TECHNICAL FIELD
[0002] This invention relates to methods for biosynthesizing
1,3-butadiene, and more particularly to synthesizing 1,3-butadiene
using one or more isolated enzymes such as dehydrogenases,
monooxygenases, desaturases, dehydratases, and decarboxylases, or
using recombinant host cells expressing one or more of such
enzymes.
BACKGROUND
[0003] 1,3-Butadiene (hereinafter butadiene) is an important
monomer for the production of synthetic rubbers including
styrene-butadiene-rubber (SBR), polybutadiene (PB),
styrene-butadiene latex (SBL), acrylonitrile-butadiene-styrene
resins (ABS), nitrile rubber, and adiponitrile, which is used in
the manufacture of Nylon-66 (White, Chemico-Biological
Interactions, 2007, 166, 10-14).
[0004] Butadiene is typically produced as a co-product from the
steam cracking process, distilled to a crude butadiene stream, and
purified via extractive distillation (White, Chemico-Biological
Interactions, 2007, 166, 10-14).
[0005] On-purpose butadiene has been prepared among other methods
by dehydrogenation of n-butane and n-butene (Houdry process); and
oxidative dehydrogenation of n-butene (Oxo-D or O-X-D process)
(White, Chemico-Biological Interactions, 2007, 166, 10-14).
[0006] Industrially, 95% of global butadiene production is
undertaken via the steam cracking process using petrochemical-based
feedstocks such as naphtha. Production of on-purpose butadiene is
not significant, given the high cost of production and low process
yield (White, Chemico-Biological Interactions, 2007, 166,
10-14).
[0007] Given a reliance on petrochemical feedstocks and, for
on-purpose butadiene, energy intensive catalytic steps;
biotechnology offers an alternative approach via biocatalysis.
Biocatalysis is the use of biological catalysts, such as enzymes,
to perform biochemical transformations of organic compounds.
[0008] Accordingly, against this background, it is clear that there
is a need for sustainable methods for producing intermediates, in
particular butadiene, wherein the methods are biocatalyst based
(Jang et al., Biotechnology & Bioengineering, 2012, 109(10),
2437-2459).
[0009] Both bioderived feedstocks and petrochemical feedstocks are
viable starting materials for the biocatalysis processes.
[0010] The generation of two vinyl groups into medium carbon chain
length enzyme substrates is a key consideration in synthesizing
butadiene via biocatalysis processes.
[0011] There are no known enzyme pathways leading to the synthesis
of butadiene in prokaryotes or eukaryotes. Three potential pathways
have been suggested for producing 1,3-butadiene from biomass-sugar:
(1) from acetyl-CoA via crotonyl-CoA; (2) from
erythrose-4-phosphate; and (3) via a condensation reaction with
malonyl-CoA and acetyl-CoA. However, no information using these
strategies has been reported (Jang et al., Biotechnology &
Bioengineering, 2012, 109(10), 2437-2459).
[0012] The closest analogous compound synthesized by prokaryotes or
eukaryotes is 2-methyl-1,3-butadiene (isoprene), given the short
five carbon chain length and two vinyl groups. Isoprene may be
synthesised via two routes leading to the precursor
dimethylvinyl-PP, viz. the mevalonate and the non-mevalonate
pathway (Kuzuyama, Biosci. Biotechnol. Biochem., 2002, 66(8),
1619-1627).
[0013] The mevalonate pathway incorporates a decarboxylase enzyme,
mevalonate diphosphate decarboxylase (hereafter MDD), that
generates the first vinyl-group in the precursors leading to
isoprene (Kuzuyama, Biosci. Biotechnol. Biochem., 2002, 66(8),
1619-1627).
[0014] Mevalonate diphosphate decarboxylase (EC 4.1.1.33) may thus
be earmarked as a candidate enzyme in the synthesis of butadiene
from non-native substrates.
[0015] In elucidating the role of the 3-methyl group associated
with the native substrate, mevalonate diphosphate, it has been
demonstrated that the turn-over number, k.sub.cat, for
3-hydroxy-5-diphosphatepentanoic acid as shown in FIG. 12(a) is
dramatically lower at 0.23.+-.0.05 [s.sup.-1] as opposed to the
nominal 8.33.+-.1 [s.sup.-1] for the native substrate (Dhe-Paganon
et al., Biochemistry, 1994, 33, 13355-13362). In addition, the
reaction with substrate only progressed as far as phosphorylation
of the 3-hydroxyl group, i.e., no decarboxylated product was
detectable, implying that the decarboxylation rate is decreased at
least 300 fold compared to the native substrate. In conclusion, the
3-methyl group was deemed indispensible in stabilizing the
carbo-cation transition state (Dhe-Paganon et al., Biochemistry,
1994, 33, 13355-13362).
[0016] It has been demonstrated that the MDD enzyme from
Saccharomyces cerevisiae accepts 3-hydroxy-3-methyl-butyrate (FIG.
12(b)), which includes the 3-methyl group stabilizing the
carbocation transition state, as a substrate converting the
substrate to isobutene. However, the specific activity is
dramatically lower at 4.810.sup.-6 [.mu.mol/(minmg)] as opposed to
the native substrate activity of 6.4 [.mu.mol/(minmg)] (Gogerty
& Bobik, Applied & Environmental Microbiology, 2010,
76(24), 8004-8010).
[0017] The key substrate binding interactions of serine and
arginine residues on the periphery of the catalytic cleft with the
pyrophosphate group of the native substrate mevalonate diphosphate
have been elucidated. Correct substrate orientation within the
catalytic cleft is thus important to enzyme activity, which
plausibly accounts for the low activity of MDD when accepting
3-hydroxy-3-methyl-butyrate (FIG. 14(b)) as substrate (Barta et
al., Biochemistry, 2012, 51, 5611-5621).
[0018] The importance of the 3-methyl group and the pyrophosphate
group associated with the native substrate in underpinning the
activity of MDD teaches against using MDD in the synthesis of
butadiene from non-native precursors that do not contain these key
groups.
[0019] The enzyme, isoprene synthase (hereinafter ISPS), generates
the second vinyl group in the final precursor, dimethylvinyl-PP, of
isoprene synthesis.
[0020] Isoprene synthase (EC 4.2.3.27) may thus be earmarked as a
candidate enzyme in the synthesis of butadiene from non-native
substrates.
[0021] Similar to MDD, the 3-methyl group associated with the
native substrate dimethylvinyl-PP plays an important role in
stabilizing the carbo-cation that has been postulated as a
transient intermediate (Silver & Fall, J. Biol. Chem., 1995,
270(22), 13010-13016; Kuzma et al., Current Microbiology, 1995, 30,
97-103).
[0022] The importance of the 3-methyl group in underpinning the
activity of ISPS teaches against using ISPS for the synthesis of
butadiene from non-native precursors that do not contain the
3-methyl group.
[0023] In addition to MDD and ISPS, microorganisms can generate
vinyl groups in metabolites typically via dehydratase, ammonia
lyase, desaturase, or decarboxylase activity. However, these enzyme
activities rarely catalyse the formation of terminal vinyl groups.
Dehydratases and ammonia lyases typically accept fatty acid
analogues that have activated hydrogen atoms or aromatic compounds,
where the aromatic ring serves as an electron withdrawing group.
Desaturases predominate in fatty acid synthesis, generating
unsaturated bonds at fixed non-terminal positions along long chain
fatty acids. In turn, decarboxylases acting on the terminal
carboxyl group typically leave the associated alpha functional
group at the terminal position after catalysis. Therefore, the
associated enzymatic activity of these enzymes teaches against
their use for the generation of terminal vinyl groups in short or
medium chain carbon metabolites leading to the synthesis of
butadiene.
SUMMARY
[0024] This document is based at least in part on the discovery
that it is possible to construct biochemical pathways for producing
medium chain carbon metabolites, in which two vinyl groups can be
formed, leading to the synthesis of butadiene. These pathways
described herein rely on enzymes such as MDD, ISPS and dehydratases
for the final enzymatic step.
[0025] Prior to the inventors' surprising discovery, it was not
known that enzymes capable of forming two terminal vinyl groups in
a medium chain carbon metabolite existed or could be produced for
the synthesis of butadiene.
[0026] Thus, in one aspect, this document provides enzymes that can
convert butadiene synthesis substrates into butadiene. As used
herein, the term "butadiene synthesis substrate" refers to a
substrate for which an enzyme can catalyze a reaction that results
directly in 1,3-butadiene or in a product that, after one or more
enzyme-catalyzed reactions, is converted to 1,3-butadiene.
[0027] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in 4-oxalocrotonate,
2-hydroxymuconate semialdehyde, or
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate to produce
2-oxopent-4-enoate. See, FIG. 2.
[0028] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in propanoyl-CoA,
lactoyl-CoA, or 3-hydroxypropionyl-CoA to produce propenoyl-CoA.
See, FIG. 3.
[0029] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in (R)
3-hydroxy-pentanoate to produce 3-hydroxypent-4-enoate. See, FIG.
4.
[0030] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in pent-2-enoyl
[acp] to produce 2, 4-pentadienoyl-[acp]. See FIG. 5.
[0031] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in
5-hydroxypentanoyl-CoA (via 5-hydroxy-pent-2-enoyl-CoA as
intermediate) or pent-3-enoyl-CoA to produce 2,4-pentadienoyl-CoA.
See, FIG. 6.
[0032] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in
4-hydroxybutyryl-CoA, (R) 3-hydroxybutanoyl-CoA or glutaconyl-CoA
to produce crotonyl-CoA. See, FIG. 7.
[0033] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in 2-butanol to
produce 3-buten-2-ol. See, FIG. 8.
[0034] In some embodiments, the second vinyl group leading to the
synthesis of butadiene is formed by inevalonate diphosphate
decarboxylase (MDD), an enzyme classified under EC 4.1.1.33 (FIG.
9). For example, 2-hydroxypent-4-enoate is converted consecutively
by two or more enzymes; producing butadiene in the last enzymatic
conversion by decarboxylation directly (FIG. 1, reaction X).
[0035] In some embodiments, the second vinyl group leading to the
synthesis of butadiene is formed by isoprene synthase (ISPS), an
enzyme classified under EC 4.2.3.27 (FIG. 10). For example,
activated butenols (diphosphoesters) may be generated by one or
more enzymes from butenols (FIG. 1, reaction II); producing
butadiene in the last enzymatic conversion by dephosphorylation
directly (FIG. 1, reaction III).
[0036] In some embodiments, the second vinyl group leading to the
synthesis of butadiene is formed by a dehydratase enzyme classified
in EC 4.2.1.-, such as linalool dehydratase (EC 4.2.1.127),
kievitone hydratase (EC 4.2.1.95), oleate hydratase (EC 4.2.1.53)
and carotenoid 1,2-hydratase (EC 4.2.1.131) (FIG. 11). Such
dehydratases accept hydroxylated substrates such as butenols. For
example, butenols may be generated in one or more enzymatic steps
from butanediols, butanols, butenes, butenals or C5 alkenols (FIG.
1, reactions IV, V, VI, VII, IX) by dehydratase, hydratase,
desaturase, dehydrogenase or decarboxylase activity; producing
butadiene in the last enzymatic conversion by dehydration directly
(FIG. 1, reaction D. Butenols include, for example, 1-buten-1-ol,
2-buten-1-ol and 3-buten-2-ol (see FIG. 1).
[0037] For example, this document provides enzymes that convert
butenols into butadiene. This conversion can be performed by a
single enzyme, or may be performed by two or more enzymes, acting
sequentially (that is to say, for example, a first enzyme acts on a
four carbon molecule to produce a first butenol, and that first
butenol then is acted upon by a second enzyme to produce butadiene)
(see, e.g., FIG. 1, reaction I).
[0038] This document also provides methods of producing butadiene
from a unsaturated hydroxylated four carbon molecule, comprising at
least one biocatalytic step. For example, the butenol can be
activated to the corresponding butenol diphosphoester before
conversion to butadiene (see, e.g., FIG. 1, reactions II &
III). In some embodiments, the butenol is selected from the group
consisting of 1 buten 2 ol, 1 buten 3 ol, 1 buten 4 ol, 2 buten 1
ol, 2 buten 2 ol, 2 buten 3 ol or 2 buten 4 ol. For butenol such as
1-buten-1-ol, 1-buten-2-ol, 2-buten-2-ol, and 2-buten-3-ol the
butenol can be generated in situ as the enolate of the
corresponding ketone or aldehyde such as 1-butanal or
2-butanone.
[0039] In some embodiments, a butenol is produced from four carbon
molecules selected from the group consisting of a butanediol
(1,4-butanediol, 1,3-butanediol,2,3-butanediol) (FIG. 1, reaction
IV) or a butanol (1-butanol, or 2-butanol) (FIG. 1, reaction V) or
a butene (1-butene or 2-butene) (FIG. 1, Reaction VI) or a butenal
such as 1-butenal or 2-butenal, or a 2-keto-but-1-ene (FIG. 1,
reaction VII) by the action of an enzyme.
[0040] The reactions performed by the enzymes can be net
dehydration (i.e., the removal of H.sub.2O from the molecule by an
enzyme having dehydratase activity, reaction IV), dehydrogenation
(i.e., the removal of hydrogen from the molecule, which in the
reactions catalysed by the enzymes results in a desaturation of the
carbon backbone of the molecule) by an enzyme or enzyme complex
having desaturase activity, reaction V), hydroxylation (i.e., the
replacement of a hydrogen with a hydroxyl group) by an enzyme with
hydroxylase activity, such as an alkene monooxygenase or Cytochrome
P450 or .omega.-hydroxylase (reaction VI), or reduction by an
oxidoreductase/ketone reductase to convert butenals or C4
unsaturated ketones to butenols. For the dehydration step, the
enzyme may be the same enzyme class as the enzyme class used for
the dehydration of the butenol to butadiene or may be of another
enzyme class. Migration of the double bond in the butenols may be
catalysed by isomerases.
[0041] This document also provides an enzyme from the enzyme class
4.2.1.-. which converts butanediols to butenol (FIG. 1, reaction
VIII).
[0042] In some embodiments, a butenol such as 1-buten-4-ol is
produced from a five carbon molecule such as 2-hydroxypent-4-enoate
by the action of a decarboxylase (such as a decarboxylase from EC
4.1.1.-) (FIG. 1, reaction IX). 2-hydroxypent-4-enoate may also be
converted directly into butadiene by a decarboxylase or GHMP kinase
without formation of the intermediate butenol (FIG. 1, Reaction
X).
[0043] In some embodiments, the butenol is selected from the group
consisting of 1 buten 2 ol, 1 buten 3 ol, 1 buten 4 ol, 2 buten 1
ol, 2 buten 2 ol, 2 buten 3 ol or 2 buten 4 ol. For butenol such as
1-buten-2-ol, 2-buten-2-ol, and 2-buten-3-ol the butenol can be
generated in situ as the enolate of the corresponding ketone or
aldehyde such as 1-butanal or 2-butanone.
[0044] In one aspect, this document features a method for the
biosynthesis of butadiene. The method includes forming two terminal
vinyl groups in a butadiene synthesis substrate. A first vinyl
group can be enzymatically formed in the butadiene synthesis
substrate to produce a compound selected from the group consisting
of 2-oxopent-4-enoate, propenyl-CoA, (R) 3-hydroxypent-4-enoate,
2,4-pentadienoyl-[acp], 2,4-pentadienoyl-CoA, crotonyl-CoA, and
3-buten-2-ol.
[0045] In one aspect, 2-oxopent-4-enoate can be produced by forming
a first vinyl group in (i) 4-oxalocrotonate using an
4-oxalocrotonate decarboxylase classified in EC 4.1.1.77, (ii)
2-hydroxymuconate semialdehyde using a
2-hydroxymuconate-semialdehyde hydrolase classified in EC 3.7.1.9,
or (iii) 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate using a
2-hydroxy-6-oxonona-2,4-dienedioate hydrolase classified in EC
3.7.1.14. 2-oxopent-4-enoate can be produced by converting
2-hydroxymuconate semialdehyde to 2-hydroxymuconate using a 2
aminomuconate semialdehyde dehydrogenase classified under EC
1.2.1.32, converting 2-hydroxymuconate to 4-oxalocrotonate using a
2-hydroxymuconate tautomerase classified under EC 5.3.2.6, and
converting 4-oxalocrotonate to 2-oxopent-4-enoate using a
4-oxalocrotonate decarboxylase classified under EC 4.1.1.77.
2-hydroxymuconate semialdehyde can be produced by converting
catechol to 2-hydroxymuconate semilaldehyde using a catechol
2,3-dioxygenase classified under EC 1.13.11.2. Catechol is produced
by converting anthranilate using an anthranilate 1,2-dioxygenase
classified under EC 1.14.12.1 or by converting protocatechuate
using a protocatechuate decarboxylase classified under EC 4.1.1.63.
Anthranilate can be produced by converting chorismate using an
anthranilate synthase classified under EC 4.1.3.27. Protocatechuate
can be produced by converting 3-dehydroshikimate using a
3-dehydroshikimate dehydratase classified under EC 4.2.1.118.
[0046] In one aspect, 2-hydroxymuconate semialdehyde can be
produced by converting 5-carboxy-2-hydroxymuconate-6-semiladehyde
using a 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase
such as a 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase
is encoded by praH. The 5-carboxy-2-hydroxymuconate-6-semiladehyde
can be produced by converting protocatechuate using a
protocatechuate 2,3-dioxygenase such as protocatechuate
2,3-dioxygenase is encoded by praA.
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate can be produced by
converting 2,3-dihydroxy phenylpropionate using a
3-carboxyethylcatechol 2,3-dioxygenase classified under EC
1.13.11.16. 2,3-dihydroxyphenylpropionate can be produced by
converting cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol using
a 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl) propanoate
dehydrogenase classified under EC 1.3.1.87.
Cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol can be produced
by converting 3-phenyl-propionate using a 3-phenylpropanoate
dioxygenase classified under EC 1.14.12.19. The 3-phenyl-propionate
can be produced by converting E-cinnamate using a 2-enoate
reductase classified under EC 1.3.1.31. E-cinnamate can be produced
by converting L-phenylalanine using a phenylalanine ammonia-lyase
classified under EC 4.3.1.24.
[0047] In one aspect, the butadiene synthesis substrate can be
propanoyl-CoA. Propenoyl-CoA can be produced by forming a first
vinyl group in (i) propanoyl-CoA using a butyryl-CoA dehydrogenase
classified under EC 1.3.8.1 or a medium-chain acyl-CoA
dehydrogenase classified under EC 1.3.8.7, (ii) lactoyl-CoA using a
lactoyl-CoA dehydratase classified under EC 4.2.1.54, or (iii)
3-hydroxypropionyl-CoA using a 3-hydroxypropionyl-CoA dehydratase
classified under EC 4.2.1.116. The propanoyl-CoA can be produced by
converting (2S)-methylmalonyl-CoA using a methylmalonyl-CoA
carboxytransferase classified under EC 2.1.3.1 or a
methylmalonyl-CoA decarboxylase classified under EC 4.1.1.41. The
(2S)-methylmalonyl-CoA can be produced by converting
(2R)-methylmalonyl-CoA using a methylmalonyl-CoA epimerase
classified under EC 5.1.99.1. The (2R)-methylmalonyl-CoA can be
produced by converting succinyl-CoA using a methylmalonyl-CoA
mutase classified under EC 5.4.99.2.
[0048] The propanoyl-CoA can be produced by converting
2-oxo-butyrate using a 2-ketobutyrate formate-lyase classified
under EC 2.3.1.- such as the 2-ketobutyrate formate-lyase encoded
by tdcE. The 2-oxo-butyrate can be produced by converting
L-threonine using a threonine ammonia lyase classified under EC
4.3.1.19.
[0049] The propanoyl-CoA can be produced by converting propanol
using a propionaldehyde dehydrogenase such as a propionaldehyde
dehydrogenase is encoded by pduP Propanol can be produced by
converting 1,2-propanediol using a propanediol dehydratase
classified under EC 4.2.1.28.
[0050] The propanoyl-CoA can be produced from levulinic acid by
converting levulinyl-CoA using a transferase classified under EC
2.3.1.-. The levulinyl-CoA can be produced by converting levulinyl
acid using an acyl-CoA synthetase or ligase classified under EC
6.2.1.-.
[0051] The lactoyl-CoA can be produced by converting L-lactate
using a proprionate CoA-transferase classified under EC 2.8.3.1.
L-lactate can be produced by converting pyruvate using an L-lactate
dehydrogenase classified under EC 1.1.1.27.
[0052] The 3-hydroxypropionyl-CoA can be produced by converting
3-hydroxypropionate using a 3-hydroxyisobutyryl-CoA hydrolase
classified under EC 3.1.2.4 or by converting malonate semialdehyde
using a 3-hydroxypropionate dehydrogenase classified under EC
1.1.1.59. The malonate semiladehyde is produced by converting
malonyl-CoA using a malonyl-CoA reductase classified under EC
1.2.1.75.
[0053] The propanoyl-CoA can be produced by converting
propenoyl-CoA using a butyryl-CoA dehydrogenase classified under EC
1.3.8.1 or a medium-chain acyl-CoA dehydrogenase classified under
EC 1.3.8.7.
[0054] The (R) 3-hydroxypent-4-enoate propenoyl-CoA can be produced
by forming a first vinyl in (R) 3-hydroxypentanoate using a
desaturase/monooxygenase or cytochrome P450. The (R)
3-hydroxy-pentanoate can be produced by converting (R)
3-hydroxypentanoyl-CoA using a thioesterase classified under EC
3.1.2.-. The (R) 3-hydroxypentanoyl-CoA can be produced by
converting 3-oxopentanoyl-CoA using an acetoacetyl-CoA reductase
classified under EC 1.1.1.36. The 3-oxopentanoyl-CoA can be
produced by converting propanoyl-CoA using an acetyl-CoA
C-acyltransferase classified under EC 2.3.1.16.
[0055] The 2,4-pentadienoyl-[acp] can be produced by forming a
first vinyl group in pent-2-enoyl-acp using an acyl-[acp]
dehydrogenase. The 2,4-pentadienoyl-CoA can be produced by forming
a first vinyl group in (i) 5-hydroxypentanoyl-CoA using a
5-hydroxyvaleryl-CoA dehydratase classified under EC 4.2.1.- or
(ii) pent-3-enoyl-CoA using a 2,4-dienoyl coenzyme A reductase
classified under EC 1.3.1.34. The 5-hydroxyvaleryl-CoA dehydratase
can originate from Clostridium viride.
[0056] The crotonyl-CoA can be produced by forming a first vinyl
group in (i) glutaconyl-CoA using a glutaconyl-CoA decarboxylase
classified under EC 4.1.1.70, (ii) 4-hydroxybutryl-CoA using a
4-hydroxybutanoyl-CoA dehydratase classified under EC 4.2.1.120 and
a vinylacetyl-CoA isomerase classified under EC 5.3.3.3, or (iii)
(R) 3-hydroxybutanoyl-CoA using an enoyl-CoA hydratase classified
under EC 4.2.1.119.
[0057] The 3-buten-2-ol can be produced by forming a first vinyl
group in 2-butanol using a desaturase or a monooxygenase.
[0058] The second vinyl group is enzymatically formed in (R)
3-hydroxypent-4-enoate by a mevalonate diphosphate decarboxylase
(MDD). The MDD can be classified under EC 4.1.1.33. The MDD can
include a minimum of four serine residues within five residues
either side of the catalytic arginine residue of the catalytic
cleft. The MDD can be from the genus Streptococcus or
Staphylococcus.
[0059] The second vinyl group can be enzymatically formed in either
2-buten-1-ol diphosphate or 3-buten-2-ol diphosphate by an isoprene
synthase (ISPS). The second vinyl group can be enzymatically formed
in either 3-buten-2-ol or 2-buten-1-ol by a dehydratase in enzyme
class EC 4.2.1.- such as a linalool dehydratase (EC 4.2.1.127), a
kievitone hydrase (EC 4.2.1.95), an oleate hydratase (EC 4.2.1.53)
or a carotenoid 1,2-hydratase (EC 4.2.1.131).
[0060] The pent-2-enoyl-[acp] can be produced by converting (R)
3-hydroxypentanoyl-[acp] using a 3-Hydroxyacyl-[acp] dehydratase
classified under EC 4.2.1.59. The (R) 3-hydroxypentanoyl-[acp] can
be produced by converting 3-oxopentanoyl-[acp] using a
3-oxoacyl-[acp] reductase classified under EC 1.1.1.100.
[0061] 3-oxopentanoyl-[acp] can be produced by converting
propanoyl-CoA using a beta-ketoacyl-[acp] synthase I classified
under EC 2.3.1.41 and an acyl-transferase such as tcsA.
[0062] The pent-2-enoyl-[acp] can be produced by converting
pent-2-enoyl-CoA using an acyl transferase. The pent-2-enoyl-CoA
can be produced by converting (R) 3-hydroxypentanoyl-CoA using an
enoyl-CoA hydratase classified under EC 4.2.1.119. The (R)
3-hydroxypentanoyl-CoA can be produced by converting
3-oxopentanoyl-CoA using an acetoacetyl-CoA reductase classified
under EC 1.1.1.36.
[0063] The 3-oxopentanoyl-CoA can be produced by converting
propanoyl-CoA using an acetyl-CoA C-acyltransferase classified
under EC 2.3.1.16.
[0064] The pent-3-enoyl-CoA can be produced by converting
pent-2-enoyl-CoA using an isomerase classified under EC
5.3.3.8.
[0065] The 5-hydroxypentanoyl-CoA can be produced by converting
either (i) 5-hydroxypentanoate using 5-hydroxypentanoate
CoA-transferase classified under EC 2.8.3.14 or (ii) pentanoyl-CoA
using a cytochrome P450 such as the gene product of CYP153A6. The
5-hydroxypentanoate can be produced by converting 5-oxopentanoate
using a 5-hydroxyvalerate dehydrogenase such as the gene product of
cpnD or the dehydrogenase from Clostridium viride. The
5-oxopentanoate can be produced by converting 5-aminovalerate using
a 5-aminovalerate transaminase classified under EC 2.6.1.48. The
5-aminovalerate can be produced by converting D-proline using a
D-proline reductase classified under EC 1.21.4.1. D-proline can be
produced by converting L-proline using a proline racemase
classified under EC 5.1.1.4. L-proline can be produced by
converting (S)-1-Pyrroline-5-carboxylate using a
pyrroline-5-carboxylate reductase classified under EC 1.5.1.2.
(S)-1-Pyrroline-5-carboxylate can be produced by spontaneous
conversion of L-glutamate 5-semialdehyde. L-glutamate
5-semialdehyde can be produced by converting L-glutamyl-5-phosphate
using a glutamate-5-semialdehyde dehydrogenase classified under EC
1.2.1.41. The L-glutamyl-5-phosphate can be produced by converting
L-glutamate using glutamate 5-kinase classified under EC
2.7.2.11.
[0066] The pentanoyl-CoA can be produced by converting
pent-2-enoyl-CoA using a trans-2-enoyl-CoA reductase classified
under EC 1.3.1.38.
[0067] Glutaconyl-CoA can be produced by converting
2-hydroxyglutaryl-CoA using a dehydratase classified under EC
4.2.1.- The 2-hydroxyglutaryl-CoA can be produced by converting
2-hydroxyglutarate using a glutaconate CoA-transferase classified
under EC 2.8.3.12. The 2-hydroxyglutarate can be produced by
converting 2-oxoglutarate using a 2-hydroxyglutarate dehydrogenase
classified under EC 1.1.99.2. The 3-hydroxybutanoyl-CoA can be
produced by converting acetoacetyl-CoA using 3-hydroxybutyryl-CoA
dehydrogenase classified under EC 1.1.1.36. The acetoacetyl-CoA can
be produced by converting acetyl-CoA using acetyl-CoA
C-acetyltransferase classified under EC 2.3.1.9.
[0068] The 4-hydroxybutyryl-CoA can be produced by converting
4-hydroxybutyrate using a CoA-transferase such as the gene product
of Ck-cat2. The 4-hydroxybutyrate can be produced by converting
succinate semialdehyde using a 4-hydroxybutyrate dehydrogenase
classified under EC 1.1.1.61. The succinate semialdehyde can be
produced by converting succinyl-CoA using a succinate-semialdehyde
dehydrogenase classified under EC 1.2.1.76.
[0069] The 2-butanol can be produced by converting butanone using a
(R)-specific secondary alcohol dehydrogenase classified under EC
1.1.1.B4. The butanone can be produced by converting 2,3 butanediol
using a propanediol dehydratase classified under EC 4.2.1.28. The
2,3 butanediol can be produced by converting (R)-acetoin using a
(R,R)-butanediol dehydrogenase classified under EC 1.1.1.4.
(R)-acetoin can be produced by converting 2-acetolactate using an
acetolactate decarboxylase classified under EC 4.1.1.5. The
2-acetolactate can be produced by converting pyruvate using an
acetolactate synthase classified under EC 2.2.1.6. The (R)
3-hydroxypent-4-enoate can be produced by converting
3-hydroxypent-4-enoyl-CoA using a thioesterase classified under EC
3.1.2, The 3-hydroxypent-4-enoyl-CoA can be produced by converting
2,4-pentadienoyl-CoA using an enoyl-CoA dehydratase 2 classified
under EC 4.2.1. The 2,4-pentadienoyl-CoA can be produced by
converting 2-hydroxypent-4-enoyl-CoA using a
2-Hydroxyisocaproyl-CoA dehydratase such as the gene products of
the initiator HadI and HadBC. The 2-hydroxypent-4-enoyl-CoA can be
produced by converting 2-hydroxypent-4-enoate using a
CoA-transferase such the gene product of GctAB. The
2-hydroxypent-4-enoate can be produced by converting
2-oxopent-4-enoate using a (R)-2-hydroxyisocaproate dehydrogenase
such as the gene product of LdhA from Clostridium difficile.
[0070] The (R)-hydroxypent-4-enoate can be produced by converting
(R) 3-hydroxypent-4-enoyl-CoA using a thioesterase classified under
EC 3.1.2.-. The (R) 3-hydroxypent-4-enoyl-CoA can be produced by
converting 3-oxopent-4-enoyl-CoA using an acetoacetyl-CoA reductase
classified under EC 1.1.1.36. The 3-oxopent-4-enoyl-CoA can be
produced by converting propenoyl-CoA using a .beta.-ketothiolase
classified under EC 2.3.1.16. The (R)-hydroxypent-4-enoate can be
produced by converting (R) 3-hydroxypent-4-enoyl-CoA using a
thioesterase classified under EC 3.1.2.-. The (R)
3-hydroxypent-4-enoyl-CoA can be produced by converting
(R)-3-hydroxypen-4-enoyl-[acp] using a (R)-3-hydroxyacyl-ACP:CoA
transacylase such as the gene product of phaG.
(R)-3-hydroxypen-4-enoyl-[acp] can be produced by converting 2,4
pentadienoyl-[acp] using a 3-hydroxyacyl-[acyl-carrier-protein]
dehydratase classified under EC 4.2.1.59. (R)
3-hydroxypent-4-enoyl-CoA can be produced by converting
2,4-pentadienoyl-CoA using an enoyl-CoA dehydratase 2 classified
under EC 4.2.1.119.
[0071] 2-buten-1-ol diphosphate can be produced by converting
2-buten-1-ol phosphate using a phosphomevalonate kinase classified
under EC 2.7.4.2 or using a diphosphokinase classified under EC
2.7.6.-. The 2-buten-1-ol phosphate can be produced by converting
2-buten-1-ol using a mevalonate kinase classified under EC
2.7.1.36. The 2-buten-1-ol can be produced by converting
2-buten-1-al using an allyl-alcohol dehydrogenase classified under
EC 1.1.1.54. The 2-buten-1-al can be produced by converting
crotonic acid using a long-chain-aldehyde dehydrogenase classified
under EC 1.2.1.48. Crotonic acid can be produced by converting
crotonyl-CoA using a succinate-CoA ligase classified under EC
6.2.1.5.
[0072] The 2-buten-1-ol diphosphate can be produced by converting
2-buten-1-ol using a diphosphokinase classified under EC 2.7.6.-
such as a thiamine diphosphokinase classified under EC 2.7.6.2.
[0073] The 3-buten-2-ol diphosphate can be produced by converting
3-buten-2-ol using a diphosphokinase classified under EC 2.7.6.- or
3-buten-2-ol phosphate using a phosphomevalonate kinase classified
under EC 2.7.4.2. The 3-buten-2-ol phosphate can be produced by
converting 3-buten-2-ol using mevalonate kinase classified under EC
2.7.1.36.
[0074] In any of the methods described herein, the method can be
performed using isolated enzymes, using cell lysates comprising the
enzymes, or using a recombinant host. The recombinant host can be
anaerobically, micro-aerobically or aerobically cultivated.
Recombinant host cells can be retained in ceramic hollow fiber
membranes to maintain a high cell density during fermentation. The
principal carbon source fed to the fermentation can derive from
biological or non-biological feedstocks. For example, the
biological feedstock is or derives from monosaccharides,
disaccharides, lignocellulose, hemicellulose, cellulose, lignin
such as levulinic acid and furfural, lignin, triglycerides such as
glycerol and fatty acids, agricultural waste or municipal waste.
The non-biological feedstock is or derives from either natural gas,
syngas, CO.sub.2/H.sub.2, methanol, ethanol, non-volatile residue
(NVR) or caustic wash waste stream from cyclohexane oxidation
processes.
[0075] The host microorganism can be a prokaryote from the genus
Escherichia such as Escherichia coli; from the genus Clostridia
such as Clostridium ljungdahlii, Clostridium autoethanogenum or
Clostridium kluyveri; from the genus Corynebacteria such as
Corynebacterium glutamicum; from the genus Cupriavidus such as
Cupriavidus necator or Cupriavidus metallidurans; from the genus
Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or
Pseudomonas oleavorans; from the genus Delftia such as Delftia
acidovorans; from the genus Bacillus such as Bacillus subtillis;
from the genus Lactobacillus such as Lactobacillus delbrueckii; or
from the genus Lactococcus such as Lactococcus lactis. The host
microorganism can be a eukaryote from the genus Aspergillus such as
Aspergillus niger; from the genus Saccharomyces such as
Saccharomyces cerevisiae; from the genus Pichia such as Pichia
pastoris; from the genus Yarrowia such as Yarrowia lipolytica; from
the genus Issatchenkia such as Issatchenkia orientalis; from the
genus Debaryomyces such as Debaryomyces hansenii; from the genus
Arxula such as Arxula adenoinivorans; or from the genus
Kluyveromyces such as Kluyveromyces lactis.
[0076] In the recombinant hosts described herein, the enzymes
catalyzing the hydrolysis of propionyl-CoA and acetyl-CoA can be
attenuated; the enzymes consuming propanoyl-CoA via the
methyl-citrate cycle can be attenuated; the enzymes consuming
propanoyl-CoA to pyruvate can be attenuated; the enzymes consuming
propanoyl-CoA to malonyl-CoA can be attenuated; a
feedback-resistant threonine deaminase can be genetically
engineered into the host organism; the .beta.-ketothiolases
catalyzing the condensation of acetyl-CoA to acetoacetyl-CoA such
as the gene products of AtoB or phaA can be attenuated; the polymer
synthase enzymes in a host strain that naturally accumulates
polyhydroxyalkanoates can be attenuated; a gene encoding a
phosphotransacetylase, such as pta, can be attenuated; a gene
encoding an acetate kinase degrading propanoate, such as ack, is
attenuated; a gene encoding the degradation of pyruvate to lactate
can be attenuated; a gene encoding the degradation of
phosphoenolpyruvate to succinate such as frdBC is attenuated; a
gene encoding the degradation of acetyl-CoA to ethanol such as adhE
can be attenuated; the enzymes catalyzing anaplerotic reactions
supplementing the citric acid cycle intermediates can be amplified;
a puridine nucleotide transhydrogenase gene such as UdhA can be
overexpressed; a glyceraldehyde-3P-dehydrogenase gene such as GapN
can be overexpressed in the host organisms; a malic enzyme gene
such as maeA or maeB is overexpressed in the host organism; a
glucose-6-phosphate dehydrogenase gene such as zwf is overexpressed
in the host organism; a fructose 1,6 diphosphatase gene such as fbp
is overexpressed in the host organism; the efflux of butadiene
across the cell membrane to the extracellular media can be enhanced
or amplified by genetically engineering structural modifications to
the cell membrane; or the efflux of butadiene across the cell
membrane to the extracellular media is enhanced or amplified by
genetically engineering an increase to any associated transporter
activity for butadiene; oxygenases degrading butadiene to toxic
intermediates such as 1,2-epoxy-3-butene and 1,2:3,4-diepoxybutane
are attenuated in the host organism.
[0077] In any of the methods described herein, the thioesterase can
be the gene product of tesB; the acetoacetyl-CoA reductase can be
the gene product of phaB; the acetyl-CoA C-acyltransferase can be
the gene product of BktB; the enoyl-CoA hydratase can be the gene
product of phaJ; the desaturase can be the gene product of MdpJ;
the cytochrome P450 can be a gene product of the CYP4 family; the
beta-ketoacyl-[acp] synthase I can be the gene product of tcsB; the
acyl-transferase can be the gene product of tcsA.
[0078] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention pertains.
Although methods and materials similar or equivalent to those
described herein can be used to practice the invention, suitable
methods and materials are described below. All publications, patent
applications, patents, and other references mentioned herein are
incorporated by reference in their entirety. In case of conflict,
the present specification, including definitions, will control. In
addition, the materials, methods, and examples are illustrative
only and not intended to be limiting.
[0079] The details of one or more embodiments of the invention are
set forth in the accompanying drawings and the description below.
Other features, objects, and advantages of the invention will be
apparent from the description and drawings, and from the claims.
The word "comprising" in the claims may be replaced by "consisting
essentially of" or with "consisting of," according to standard
practice in patent law.
DESCRIPTION OF DRAWINGS
[0080] FIG. 1 is a schematic overview of the principal enzyme
activities leading to 1,3 butadiene from C4 aldehydes and ketones,
C4 hydroxy-aldehydes and diketones, butenes, butenals or
unsaturated ketones, butenols, butanediols, C5 alkenols, and
activated butenols.
[0081] FIG. 2 is a schematic of biochemical pathways leading to
butadiene using 2-oxopent-4-enoate as a central precursor.
[0082] FIG. 3 is a schematic of biochemical pathways leading to
butadiene using propenoyl-CoA as a central precursor.
[0083] FIG. 4 is a schematic of biochemical pathways leading to
butadiene using 3-hydroxy-4-pentenoate as a central precursor.
[0084] FIG. 5 is a schematic of biochemical pathways leading to
butadiene using 2,4-pentadienoyl-[acp] as a central precursor.
[0085] FIG. 6 is a schematic of biochemical pathways leading to
butadiene using 2,4-pentadienoyl-CoA as a central precursor.
[0086] FIG. 7 is a schematic of biochemical pathways leading to
butadiene using crotonyl-CoA as a central precursor.
[0087] FIG. 8 is a schematic of biochemical pathways leading to
butadiene using 3-buten-2-ol as a central precursor.
[0088] FIG. 9 is a schematic of biochemical pathways to synthesize
butadiene using mevalonate diphosphate decarboxylase.
[0089] FIG. 10 is a schematic of biochemical pathways to synthesize
butadiene using isoprene synthase.
[0090] FIG. 11 is a schematic of biochemical pathways to synthesize
butadiene using dehydratases.
[0091] FIG. 12 is the structure of alternate substrates accepted by
MDD, (a) is 3-hydroxy-5-diphosphatepentanoic acid and (b) is
3-hydroxy-3-methyl-butyrate.
[0092] FIG. 13 is the amino acid sequences for MDD enzymes from
Saccharomyces cerevisiae (Uniprot Accession No. P32377, SEQ ID
NO:1), Staphylococcus epidermidis (Uniprot Accession No. Q7CCL9,
SEQ ID NO:2), and Streptococcus pneumonia (Uniprot Accession No.
B8ZLF3, SEQ ID NO:3), highlighting the conserved residues within
the catalytic cleft of the enzyme in bold.
DETAILED DESCRIPTION
[0093] In particular, this document provides enzymes, non-natural
pathways, cultivation strategies, feedstocks, host microorganisms
and attenuations to the host's biochemical network, which generates
two terminal vinyl groups in four and five carbon chain metabolites
leading to the synthesis of 1,3 butadiene (referred to as
"butadiene" herein) from central precursors or central metabolites.
As used herein, the term "central precursor" is used to denote a
key metabolite in a pathway leading to the synthesis of butadiene.
The term "central metabolite" is used herein to denote a metabolite
that is produced in all microorganisms to support growth.
[0094] As such, host microorganisms described herein can include
endogenous pathways that can be manipulated such that butadiene can
be produced. In an endogenous pathway, the host microorganism
naturally expresses all of the enzymes catalyzing the reactions
within the pathway. A host microorganism containing an engineered
pathway does not naturally express all of the enzymes catalyzing
the reactions within the pathway but has been engineered such that
all of the enzymes within the pathway are expressed in the host.
Within an engineered pathway, the enzymes can be from a single
source, i.e., from one species, or can be from multiple sources,
i.e., different species. Nucleic acids encoding the enzymes
described herein have been identified from various organisms and
are readily available in publicly available databases such as
GenBank or EMBL. Engineered hosts can naturally express none or
some (e.g., one or more, two or more, three or more, four or more,
five or more, or six or more) of the enzymes of the pathways
described herein. Endogenous genes of the engineered hosts also can
be disrupted to prevent the formation of undesirable metabolites or
prevent the loss of intermediates in the pathway through other
enzymes acting on such intermediates. Engineered hosts can be
referred to as recombinant hosts or recombinant host cells. Thus,
as described herein recombinant hosts can include nucleic acids
encoding one or more of a decarboxylase, a dehydrogenase, a
desaturase, a monooxygenase, an acyl [acyl carrier protein (acp)]
dehydrogenase, a dehydratase, or a hydratase as described in more
detail below.
[0095] In addition, the production of butadiene can be performed in
vitro using the isolated enzymes described herein, using a lysate
(e.g., a cell lysate) from a host microorganism as a source of the
enzymes, or using a plurality of lysates from different host
microorganisms as the source of the enzymes.
[0096] FIG. 1 provides an overview of the principal enzyme
activities that can be used to produce butadiene from various four
or five carbon molecules, including C4 aldehydes and ketones, C4
hydroxy-aldehydes and diketones, butenes, butenals or unsaturated
ketones, butenols, butanediols, C5 alkenols, and activated
butenols.
Enzymes Generating the First Terminal Vinyl Group in the
Biosynthesis of Butadiene
[0097] As depicted in FIGS. 2-8, the first vinyl group can be
formed in 4-oxalocrotonate, 2-hydroxymuconate semialdehyde,
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate, propanoyl-CoA,
lactoyl-CoA, 3-hydroxypropionyl-CoA, (R) 3-hydroxy-pentanoate,
pent-2-enoyl-[acp], 5-hydroxypentanoyl-CoA (via
5-hydroxy-pent-2-enoyl-CoA), pent-3-enoyl-CoA 4-hydroxybutyryl-CoA,
glutaconyl-CoA, (R) 3-hydroxybutanoyl-CoA or 2-butanol to produce
such compounds as 2-oxopent-4-enoate, propenoyl-CoA, (R)
3-hydroxypent-4-enoate, (R) 3-hydroxypent-4-enoyl-[acp],
2,4-pentadienoyl-CoA, crotonyl-CoA, and 3-buten-2-ol.
[0098] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in 4-oxalocrotonate,
2-hydroxymuconate semialdehyde, or
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate by 4-oxalocrotonate
decarboxylase (EC 4.1.1.77), 2-hydroxymuconate-semialdehyde
hydrolase (EC 3.7.1.9) or 2-hydroxy-6-oxonona-2,4-dienedioate
hydrolase (EC 3.7.1.14) to produce 2-oxopent-4-enoate. See, e.g.,
FIG. 2.
[0099] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in propanoyl-CoA,
lactoyl-CoA, 3-hydroxypropionyl-CoA by butyryl-CoA dehydrogenase
(EC 1.3.8.1), medium-chain acyl-CoA dehydrogenase (EC 1.3.8.7),
lactoyl-CoA dehydratase (EC 4.2.1.54) or 3-hydroxypropionyl-CoA
dehydratase (EC 4.2.1.116) to produce propenoyl-CoA. See, e.g.,
FIG. 3.
[0100] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in (R)
3-hydroxy-pentanoate by a desaturase or monooxygenase such as the
gene product of MdpJ or cytochrome P450 such as the gene product of
the CYP4 family to produce (R) 3-hydroxypent-4-enoate. See, e.g.,
FIG. 4.
[0101] The gene product of the monooxygenase, MdpJ, desaturates the
terminal of the ethyl group adjacent to a secondary alcohol
(Schafer et al., Applied and Environmental Microbiology, 2012,
78(24)).
[0102] The gene product of the cytochrome P450 CYP4 family has
displayed specificity for terminal desaturation rather than
w-hydroxylation of the C5 carboxylic acid, valproic acid (Rettie et
al., Biochemistry, 1995, 34, 7889-7895).
[0103] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in
pent-2-enoyl-[acp] by an acyl-[acp] dehydrogenase such as the gene
product of TcsD to produce 2,4 pentadienoyl-[acp]. See, e.g., FIG.
5.
[0104] The gene product of the acyl-[acp] dehydrogenase TcsD
desaturates the terminal methylene of pent-2-enoyl-[acp] to
2,4-pentadienoyl-[acp] (Mo et al., J. Am. Chem. Soc., 2011, 133(4),
976-985).
[0105] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in
5-hydroxypentanoyl-CoA (via 5-hydroxy-pent-2-enoyl-CoA by a
5-hydroxyvaleryl-CoA dehydratase (EC 4.2.1.-) or 2,4-dienoyl
coenzyme A reductase (EC 1.3.1.34) to produce 2,4-pentadienoyl-CoA.
See, e.g., FIG. 6.
[0106] The dehydration of 5-hydroxyvalerate by 5-hydroxyvaleryl-CoA
dehydratase to 2,4 pentadienoyl-CoA has been characterized from
Clostridium viride (Eikmanns and Buckel, Eur. J. Biochem., 1991,
197, 661-668).
[0107] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is enzymatically formed in
3-hydroxybutanoyl-CoA, 4-hydroxybutyryl-CoA or glutaconyl-CoA by an
enoyl-CoA hydratase an by an enoyl-CoA hydratase (EC 4.2.1.119)
such as the gene product of phaJ, a 4-hydroxybutanoyl-CoA
dehydratase (EC 4.2.1.120) or a glutaconyl-CoA decarboxylase (EC
4.1.1.70) to produce crotonyl-CoA. See, e.g., FIG. 7.
[0108] The reversible dehydratase, 4-hydroxybutanoyl-CoA
dehydratase, has been characterised has been characterized in
several Clostridium species, such as Clostridium kluyveri,
providing for a route to crotonyl-CoA via the central metabolite,
succinate (Scherf et al., Arch. Microbiol, 1994, 161(3), 239-245;
Sherf and Buckel, Eur. J. Biochem., 1993, 215, 421-429).
[0109] The biotin-dependent decarboxylase, glutaconyl-CoA
decarboxylase, maintains the position of the substrate's vinyl
group after decarboxylation, providing a route to crotonyl-CoA via
the central metabolite, 2-oxoglutarate (Kerstin et al., The EMBO
Journal, 2003, 22(14), 3493-3502).
[0110] In some embodiments, the first vinyl group leading to the
synthesis of butadiene is formed in 2-butanol by a desaturase or a
monooxygenase such as the gene product of MdpJ or cytochrome P450
such as the gene product of the CYP4 family to produce
3-buten-2-ol. See, e.g., FIG. 8.
Enzymes Generating the Second Terminal Vinyl Group in the
Biosynthesis of Butadiene
[0111] As depicted in FIGS. 9-11, the second vinyl group can be
enzymatically formed using a mevalonate diphosphate decarboxylase
(MDD), an isoprene synthase (ISPS), or a dehydratase.
[0112] In some embodiments, the second vinyl group leading to the
synthesis of butadiene is formed by a mevalonate diphosphate
decarboxylase (MDD), an enzyme classified under EC 4.1.1.33. See,
e.g., FIG. 9.
[0113] In some embodiments, the second vinyl group leading to the
synthesis of butadiene is enzymatically formed by an isoprene
synthase (ISPS), an enzyme classified under 4.2.3.27. See, e.g.,
FIG. 10.
[0114] In some embodiments, the second vinyl group leading to the
synthesis of butadiene is enzymatically formed by a dehydratase in
enzyme class EC 4.2.1.-, particularly linalool dehydratase (EC
4.2.1.127), kievitone hydratase (EC 4.2.1.95), oleate hydratase (EC
4.2.1.53) or carotenoid 1,2-hydratase (EC 4.2.1.131). See, e.g.,
FIG. 11.
[0115] Linalool may be regarded as 3-buten-2-ol substituted with an
isohexenyl R-group at the alpha position. The dehydration of
linalool to myrcene is favored thermodynamically and likely
proceeds via deprotonation, where the R-group has no mechanistic
role (Bordkorb et al., J. Biol. Chem., 2010, 285(40),
30436-30442).
[0116] Oleate hydratase converts long chain unsaturated fatty acid,
oleic acid, to (R)-10-hydroxystearate. However, in screening 165
homologues to the oleate hydratase sequence of E. meningoseptica,
several accepted isobutanol as substrate forming isobutene (Bianca
et al., Appl. Microbiol Biotechnol., 2012, 93, 1377-1387).
Biochemical Pathways
Pathways Using 2-Oxopent-4-Enoate as Central Precursor to
Butadiene
[0117] Pathways leading to the production of 2-oxopent-4-enoate
from aromatic compounds such as protocatechuate (Kasai et al., J.
Bacteriol., 2009, 191(21), 6758-6768), catechol (He and Spain, J.
Bacteriol., 1998, 180(9), 2502-2506), anthranilate (Muraki et al.,
Applied and Environmental Microbiology, 2003, 69(3), 1564-1572) and
3-phenylpropionic acid (Ferrandez et al., J. Bacteriol., 1997,
179(8), 2573-2581) are well characterized. Carbon flux from the
central metabolites may be directed to these degradation pathways
via 3-dehydroshikimate by 3-dehydroshikimate dehydratase (EC
4.2.1.118), via chorismate by anthranilate synthase (EC 4.1.3.27),
and via L-phenylalanine by phenylalanine ammonia lyase (EC
4.3.1.24) and 2-enoate reductase (EC 1.3.1.31).
[0118] In some embodiments, 2-oxopent-4-enoate is synthesized from
the central metabolite, chorismate, by conversion to anthranilate
by anthranilate synthase (EC 4.1.3.27); followed by conversion to
catechol by anthranilate 1,2-dioxygenase (EC 1.14.12.1); followed
by conversion to 2-hydroxymuconate semialdehyde by catechol
2,3-dioxygenase (EC 1.13.11.2); followed by conversion to
2-oxopent-4-enoate by 2-hydroxymuconate-semialdehyde hydrolase (EC
3.7.1.9). In addition, 2-hydroxymuconate semialdehyde can be
converted to 2-hydroxymuconate by aminomuconate semialdehyde
dehydrogenase (EC 1.2.1.32), 2-hydroxymuconate can be converted to
4-oxalocrotonate by 2-hydroxymuconate tautomerase (EC 5.3.2.6), and
4-oxalocrotonate can be converted to 2-oxopent-4-enoate
4-oxalocrotonate decarboxylase (EC 4.1.1.77). See, e.g., FIG.
2.
[0119] In some embodiments, 2-oxopent-4-enoate is synthesized from
the central metabolite, 3-dehydroshikimate, by conversion to
protocatechuate by 3-dehydroshikimate dehydratase (EC 4.2.1.118);
followed by conversion to catechol by protocatechuate decarboxylase
(EC 4.1.1.63); followed by conversion to 2-hydroxymuconate
semialdehyde by catechol 2,3-dioxygenase (EC 1.13.11.2); followed
by conversion to 2-oxopent-4-enoate by
2-hydroxymuconate-semialdehyde hydrolase (EC 3.7.1.9) or by
aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32),
2-hydroxymuconate tautomerase (EC 5.3.2.6) and 4-oxalocrotonate
decarboxylase (EC 4.1.1.77). See, e.g., FIG. 2.
[0120] In some embodiments, 2-oxopent-4-enoate is synthesized from
the central metabolite, 3-dehydroshikimate, by conversion to
protocatechuate by 3-dehydroshikimate dehydratase (EC 4.2.1.118);
followed by conversion to
5-carboxy-2-hydroxymuconate-6-semialdehyde by protocatechuate 2,
3-dioxygenase such as the gene product of praA; followed by
conversion to 2-hydroxymuconate semialdehyde by
5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase such as
the gene product of praH; followed by conversion to
2-oxopent-4-enoate by 2-hydroxymuconate-semialdehyde hydrolase (EC
3.7.1.9) or by aminomuconate semialdehyde dehydrogenase (EC
1.2.1.32), 2-hydroxymuconate tautomerase (EC 5.3.2.6) and
4-oxalocrotonate decarboxylase (EC 4.1.1.77). See, e.g., FIG.
2.
[0121] In some embodiment, 2-oxopent-4-enoate is synthesized from
the central metabolite, L-phenylalanine, by conversion to
E-cinnamate by phenylalanine ammonia-lyase (EC 4.3.1.24); followed
by conversion to 3-phenyl-propionate by 2-enoate reductase (EC
1.3.1.31); followed by conversion to
cis-3-(carboxy-ethyl)-3,5-cyclo-hexadiene-1,2-diol by
3-phenylpropanoate dioxygenase (EC 1.14.12.19); followed by
conversion to 2,3-dihydroxyphenylpropionate by 3-(cis-5,
6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase (EC
1.3.1.87); followed by conversion to
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate by 3-carboxyethylcatechol
2, 3-dioxygenase (EC 1.13.11.16); followed by conversion to
2-oxopent-4-enoate by 2-hydroxy-6-oxonona-2, 4-dienedioate
hydrolase (EC 3.7.1.14). See, e.g., FIG. 2.
[0122] In some embodiments, butadiene is synthesized from
2-oxopent-4-enoate by conversion to 2-hydroxypent-4-enoate by
(R)-2-hydroxyisocaproate dehydrogenase such as the gene product of
LdhA; followed by conversion to 2-hydroxypent-4-enoyl-CoA by CoA
transferase such as the gene product of GctAB; followed by
conversion to 2,4-pentadienoyl-CoA by 2-Hydroxyisocaproyl-CoA
dehydratase such as the gene products of the initiator HadI and
HadBC; followed by conversion to (R)-3-hydroxypent-4-enoyl-CoA by
enoyl-CoA dehydratase 2 (EC 4.1.1.119); followed by conversion to
(R)-3-hydroxypent-4-enoate by a thioesterase (EC 3.1.2.-) such as
the gene product of tesB; followed by conversion to butadiene by
mevalonate diphosphate decarboxylase (EC 4.1.1.33). See, e.g., FIG.
9.
[0123] (R)-2-hydroxyisocaproate dehydrogenase (gene product of
LdhA) accepts 2-oxopentanoate and 2-oxohexanoate as substrates
(Kim, On the enzymatic mechanism of 2-hydroxyisocaproyl-CoA
dehydratase from Clostridium difficile, 2004, Ph.D. dissertation,
Philipps-Universitat, Marburg, 2004). 2-oxopentanoate is a near
substrate analogue of 2-oxopent-4-enoate.
[0124] Glutaconate CoA-transferase (GctAB) is a promiscuous enzyme
accepting carbon chains ranging from 3 to 6 carbons in length, that
are branched and unbranched, alpha-substituted and unsubstituted
monocarboxylic and dicarboxylic acids (see, e.g., Buckel et al.,
Eur. J. Biochem., 1981, 118, 315-321). 2-hydroxypent-4-enoic acid
has comparable structure and functional groups where CoA activation
is required for the activity of 2-Hydroxyisocaproyl-CoA
dehydratase.
[0125] 2-Hydroxyisocaproyl-CoA dehydratase (HadI & HadBC)
accepts the substrate analogue 2-hydroxypent-4-enoyl-CoA as
substrate, synthesizing 2,4-pentadienoyl-CoA (Kim et al., Nature
Letters, 2008, 452, 239-243).
[0126] The hydrolysis of short and medium carbon chain acyl-CoA
substrates has been demonstrated using the gene product of tesB
(Liu et al., Appl. Microbiol. Biotechnol., 2007, 76, 811-818). The
thioesterase II gene product of tesB hydrolyses
(R)-3-hydroxypentanoyl-CoA efficiently (Martin and Prather, Journal
of Biotechnology, 2009, 139, 61-67).
Pathways to Propanoyl-CoA as Precursor Leading to Central
Precursors to Butadiene
[0127] In some embodiments, propanoyl-Coenzyme A (CoA) is a
precursor leading to central precursors in the synthesis of
butadiene (see, e.g., FIG. 3).
[0128] In some embodiments, propanoyl-CoA is synthesized from the
central metabolite, succinyl-CoA, by conversion of succinyl-CoA to
(2R)-methylmalonyl-CoA by methylmalonyl-CoA mutase (EC 5.4.99.2);
followed by conversion to (2S)-methylmalonyl-CoA by
methylmalonyl-CoA epimerase (EC 5.1.99.1); followed by conversion
to propanoyl-CoA by methylmalonyl-CoA carboxytransferase (EC
2.1.3.1) or methylmalonyl-CoA decarboxylase (EC 4.1.1.41). See
e.g., FIG. 3.
[0129] In some embodiments, propanoyl-CoA is synthesized from the
central metabolite, L-threonine, by conversion of L-threonine to
2-oxobutyrate by threonine ammonia lyase (EC 4.3.1.19); followed by
conversion to propanoyl-CoA by 2-ketobutyrate formate-lyase such as
the gene product of tdcE (EC 2.3.1.-) (see, Tseng et al., Microbial
Cell Factories, 2010, 9:96). See, e.g., FIG. 3.
[0130] The intracellular accumulation of propanoyl-CoA from
L-threonine as a precursor to other products has been demonstrated
(Tseng et al., Microbial Cell Factories, 2010, 9:96).
[0131] In some embodiments, propanoyl-CoA is synthesized from
1,2-propanediol by conversion to propanal by propanediol
dehydratase (EC 4.2.1.28); followed by conversion to propanoyl-CoA
by CoA-dependent propionaldehyde dehydrogenase such as the gene
product of pduP (see Luo et al., Bioresource Technology, 2012, 103,
1-6) See, e.g., FIG. 3.
[0132] The intracellular accumulation of propanoyl-CoA from 1,2
propanediol has been reported (Luo et al., Bioresource Technology,
2012, 103, 1-6).
[0133] In some embodiments, propanoyl-CoA is synthesized from the
carbon source, levulinic acid, by conversion of levulinic acid to
levulinyl-CoA by acyl-CoA synthetase or ligase (EC 6.2.1.-);
followed by conversion to propanoyl-CoA by a transferase in EC
2.3.1.- (Jaremko and Yu, Journal of Biotechnology, 2011, 155, 2011,
293-298). See, e.g., FIG. 3.
[0134] In some embodiments, propanoyl-CoA is synthesized from the
central metabolite, pyruvate, by conversion of pyruvate to
L-lactate by L-lactate dehydrogenase (EC 1.1.1.27); followed by
conversion to lactoyl-CoA by proprionate CoA-transferase (EC
2.8.3.1); followed by conversion to propenoyl-CoA by lactoyl-CoA
dehydratase (EC 4.2.1.54); followed by conversion to propanoyl-CoA
by butyryl-CoA dehydrogenase (EC 1.3.8.1) or medium-chain acyl-CoA
dehydrogenase (EC 1.3.8.7). See, e.g., FIG. 3.
[0135] In some embodiments, propanoyl-CoA is synthesized from the
central metabolite, malonyl-CoA, by conversion of malonyl-CoA to
malonate semialdehyde by malonyl-CoA reductase (EC 1.2.1.75);
followed by conversion to 3-hydroxypropionate by
3-hydroxypropionate dehydrogenase (EC 1.1.1.59); followed by
conversion to 3-hydroxypropionyl-CoA by 3-hydroxyisobutyryl-CoA
hydrolase (EC 3.1.2.4); followed by conversion to propenoyl-CoA by
3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116); followed by
conversion to propanoyl-CoA by butyryl-CoA dehydrogenase (EC
1.3.8.1) or medium-chain acyl-CoA dehydrogenase (EC 1.3.8.7). See,
e.g., FIG. 3.
Pathways Using Propenoyl-CoA as Central Precursor to Butadiene
[0136] In some embodiments, propenoyl-CoA is synthesized from
propanoyl-CoA by butyryl-CoA dehydrogenase (EC 1.3.8.1) or
medium-chain acyl-CoA dehydrogenase (EC 1.3.8.7). See, e.g., FIG.
3.
[0137] In some embodiments, propenoyl-CoA is synthesized from the
central metabolite, pyruvate, by conversion of pyruvate to
L-lactate by L-lactate dehydrogenase (EC 1.1.1.27); followed by
conversion to lactoyl-CoA by proprionate CoA-transferase (EC
2.8.3.1); followed by conversion to propenoyl-CoA by lactoyl-CoA
dehydratase (EC 4.2.1.54). See, e.g., FIG. 3.
[0138] In some embodiments, propenoyl-CoA is synthesized from the
central metabolite, malonyl-CoA, by conversion to malonate
semialdehyde by malonyl-CoA reductase (EC 1.2.1.75); followed by
conversion to 3-hydroxypropionate by 3-hydroxypropionate
dehydrogenase (EC 1.1.1.59); followed by conversion to
3-hydroxypropionyl-CoA by 3-hydroxyisobutyryl-CoA hydrolase (EC
3.1.2.4); followed by conversion to propenoyl-CoA by
3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116). See, e.g., FIG.
3.
[0139] In some embodiments, butadiene is synthesized from
propenoyl-CoA by conversion to 3-oxopent-4-enoyl-CoA by
fl-ketothiolase such as EC 2.3.1.16; followed by conversion to
(R)-3-hydroxypent-4-enoyl-CoA by acetoacetyl-CoA reductase (EC
1.1.1.36) such as the gene product of phaB; followed by conversion
to (R)-3-hydroxypent-4-enoate by a thioesterase (EC. 3.1.2.-) such
as the gene product of tesB; followed by conversion to butadiene by
mevalonate diphosphate decarboxylase (EC 4.1.1.33). See, e.g., FIG.
9.
Pathway Using (R) 3-Hydroxypent-4-Enoate as Central Precursor to
Butadiene
[0140] In some embodiments, (R) 3-hydroxypent-4-enoate is
synthesized from propanoyl-CoA by conversion to 3-oxopentanoyl-CoA
by acetyl-CoA C-acyltransferase (EC 2.3.1.16); followed by
conversion to (R) 3-hydroxypentanoyl-CoA by acetoacetyl-CoA
reductase (EC 1.1.1.36) such as the gene product of phaB; followed
by conversion to (R) 3-hydroxypent-4-enoyl-CoA by a thioesterase
such as the gene product of tesB (EC 3.1.2.-); followed by
conversion to (R) 3-hydroxypent-4-enoate by a desaturase such as
the gene product of MdpJ or cytochrome P450 such as the gene
product of the CYP4 family. See, e.g., FIG. 4.
[0141] Terminal desaturation of carboxylic acids by cytochrome P450
enzymes in the CYP4 family has been elucidated. CYP4B1 desaturates
the twelve carbon chain length fatty acid lauric acid by removing
the .omega.-1 hydrogen at the terminal (Guan et al.,
Chemico-Biology Interactions, 1998, 110, 103-121).
[0142] In some embodiments, butadiene is synthesized from (R)
3-hydroxypent-4-enoate by mevalonate diphosphate decarboxylase (EC
4.1.1.33). See, e.g., FIG. 9.
Pathway Using 2,4-pentadienoyl-[acp] as Central Precursor to
Butadiene
[0143] In some embodiments, (R) 3-hydroxypent-4-enoyl-[acp] is
synthesized from propanoyl-CoA by conversion of propanoyl-CoA to
3-oxopentanoyl-CoA by acetyl-CoA C-acyltransferase (EC 2.3.1.16);
followed by conversion to (R) 3-hydroxypentanoyl-CoA by
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.36) such as the gene
product of phaB; followed by conversion to pent-2-enoyl-CoA by
enoyl-CoA hydratase (EC 4.2.1.119) such as the gene product of
phaJ; followed by conversion to pent-2-enoyl-[acp] in reaction with
the gene product of an acyl transferase such as tcsA; followed by
conversion to (R) 2,4-pentadienoyl-[acp] by an acyl-[acp]
dehydrogenase such as the gene product of TcsD. See, e.g., FIG.
5.
[0144] In some embodiments, (R) 3-hydroxypent-4-enoyl-[acp] is
synthesized from propanoyl-CoA by conversion of propanoyl-CoA to
3-oxopentanoyl-[acp] by a Beta-ketoacyl-[acp] synthase I (EC
2.3.1.41) such as tcsB and an acyl-transferase such as tcsA;
followed by conversion to (R) 3-hydroxypentanoyl-CoA by
3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100); followed
by conversion to pent-2-enoyl-[acp] by 3-Hydroxyacyl-[acp]
dehydratase (EC 4.2.1.59); followed by conversion to
2,4-pentadienoyl-[acp] by acyl-[acp] dehydrogenase such as the gene
product of TcsD. See, e.g., FIG. 5.
[0145] In some embodiments, butadiene is synthesized from
(R)-3-hydroxypent-4-enoyl-[acp] by conversion to
(R)-3-hydroxypent-4-enoyl-CoA by (R)-3-hydroxyacyl-[acp]:CoA
transacylase such as the gene product of phaG; followed by
conversion to (R)-3-hydroxypent-4-enoate by a thioesterase such as
the gene product of tesB; followed by conversion to butadiene by
mevalonate diphosphate decarboxylase (EC 4.1.1.33). See, e.g., FIG.
9.
[0146] The gene product of phaJ (EC 4.2.1.119) is a key enzyme for
providing short and medium chain R-specific 3-hydroxyacyl-CoA
monomers from fatty acid synthesis to polyhydroxyalkanoate synthase
enzymes (Chung and Rhee, Biosci. Biotechnol. Biochem., 2012, 76(3),
613-616; Tsuge et al., International Journal of Biological
Macromolecules, 2003, 31, 195-205).
[0147] Utilizing 4-pentenoic acid as a carbon source to
polyhydroxyalkanoate-producing bacteria produces
(R)-3-hydroxypent-4-enoate via beta-oxidation. Accordingly,
4-pentenoic acid is converted to 2,4-pentadienoyl-CoA which is made
available to polymer synthase enzymes after hydration to
(R)-3-hydroxypent-4-enoate by R-specific enoyl-CoA dehydrase
activity (Ulmer et al., Macromolecules, 1994, 27, 1675-1679).
Pathway Using 2,4 pentadienoyl-CoA as Central Precursor to
Butadiene
[0148] In some embodiments, 2,4-pentadienoyl-CoA is synthesized
from propanoyl-CoA by conversion of propanoyl-CoA to
3-oxo-pentanoyl-CoA by an acetyl-CoA C-acyltransferase (EC
2.3.1.16) such as the gene product of bktB; followed by conversion
to (R) 3-hydroxypentanoyl-CoA by a 3-hydroxyacyl-CoA dehydrogenase
(EC 1.1.1.36) such as the gene product of phaB; followed by
conversion to pent-2-enoyl-CoA by an enoyl-CoA hydratase (EC
4.2.1.119) such as the gene product of phaJ; followed by conversion
to pent-3-enoyl-CoA by an isomerase (EC 5.3.3.8); followed by
conversion to 2,4,-pentadienoyl-CoA by a 2,4-dienoyl coenzyme A
reductase (EC 1.3.1.34). See, e.g., FIG. 6.
[0149] In some embodiments, 2,4-pentadienoyl-CoA is synthesized
from propanoyl-CoA by conversion of propanoyl-CoA to
3-oxo-pentanoyl-CoA by an acetyl-CoA C-acyltransferase (EC
2.3.1.16) such as the gene product of bktB; followed by conversion
to (R) 3-hydroxypentanoyl-CoA by a 3-hydroxyacyl-CoA dehydrogenase
(EC 1.1.1.36) such as the gene product of phaB; followed by
conversion to pent-2-enoyl-CoA by an enoyl-CoA hydratase (EC
4.2.1.119) such as the gene product of phaJ; followed by conversion
to pent-3-enoyl-CoA by an isomerase (EC 5.3.3.8); followed by
conversion to 2,4,-pentadienoyl-CoA by a 2,4-dienoyl coenzyme A
reductase (EC 1.3.1.34). See, e.g., FIG. 6.
[0150] In some embodiments, 2,4-pentadienoyl-CoA is synthesized
from propanoyl-CoA by conversion of propanoyl-CoA to
3-oxo-pentanoyl-CoA by an acetyl-CoA C-acyltransferase (EC
2.3.1.16) such as the gene product of bktB; followed by conversion
to (R) 3-hydroxypentanoyl-CoA by a 3-hydroxyacyl-CoA dehydrogenase
(EC 1.1.1.36) such as the gene product of phaB; followed by
conversion to 2E-pentenoyl-CoA by an enoyl-CoA hydratase (EC
4.2.1.119) such as the gene product of phaJ; followed by conversion
to pentanoyl-CoA by a trans-2-enoyl-CoA reductase such as EC
1.3.1.38; followed by conversion to 5-hydroxypentanoyl-CoA by a
cytochrome P450 monooxygenase such as the gene product of CYP153A6;
followed by conversion to 2,4,-pentadienoyl-CoA by a
5-hydroxyvaleryl-CoA dehydratase (EC 4.2.1.-) (e.g., from
Clostridium viride). See, e.g., FIG. 6.
[0151] In some embodiments, 2,4-pentadienoyl-CoA is synthesized
from the central metabolite, L-glutamic acid, by conversion of
L-glutamic acid to L-glutamyl-5-phosphate by a glutamate 5-kinase
(EC 2.7.2.11); followed by conversion to L-glutamate-5-semialdehyde
by a glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41); followed
by spontaneous conversion to (S)-1-pyrroline-5-carboxylate;
followed by conversion to L-proline by a pyrroline-5-carboxylate
reductase (EC 1.5.1.2); followed by conversion to D-proline by a
proline racemase (EC 5.1.1.4); followed by conversion to
5-aminovalerate by a D-proline reductase (EC 1.21.4.1); followed by
conversion to 5-oxopentanoate by a 5-aminovalerate transaminase (EC
2.6.1.48); followed by conversion to 5-hydroxypentanoate by a
5-hydroxyvalerate dehydrogenase such as the gene product of cpnD or
a dehydrogenase from Clostridium viride; followed by conversion to
5-hydroxypentanoyl-CoA by a 5-hydroxypentanoate CoA-transferase (EC
2.8.3.14); followed by conversion to 2,4-pentadienoyl-CoA by a
5-hydroxyvaleryl-CoA dehydratase (EC 4.2.1.-) (e.g., from
Clostridium viride). See, e.g., FIG. 6.
[0152] In some embodiments, butadiene is synthesized from
2,4-pentadienoyl-CoA by conversion of 2,4-pentadienoyl-CoA to
(R)-3-hydroxypent-4-enoyl-CoA by an enoyl-CoA dehydratase 2 (EC
4.2.1.119) such as the gene product of phaJ; followed by conversion
to (R)-3-hydroxypent-4-enoate by a thioesterase such as the gene
product of tesB; followed by conversion to butadiene by a
mevalonate diphosphate decarboxylase (EC 4.1.1.33). See, e.g., FIG.
9.
[0153] The gene product of phaJ (EC 4.2.1.119) is a key enzyme for
providing short and medium chain R-specific 3-hydroxyacyl-CoA
monomers from fatty acid synthesis to polyhydroxyalkanoate synthase
enzymes (Chung and Rhee, Biosci. Biotechnol. Biochem., 2012, 76(3),
613-616; Tsuge et al., International Journal of Biological
Macromolecules, 2003, 31, 195-205).
[0154] Utilizing 4-pentenoic acid as a carbon source to
polyhydroxyalkanoate-producing bacteria produces
(R)-3-hydroxypent-4-enoate via beta-oxidation. Accordingly,
4-pentenoic acid is converted to 2,4-pentadienoyl-CoA, which is
made available to polymer synthase enzymes after hydration to
(R)-3-hydroxypent-4-enoate by R-specific enoyl-CoA dehydrase
activity (see, e.g., Ulmer et al., Macromolecules, 1994, 27,
1675-1679).
Pathway Using Crotonyl-CoA as Central Precursor to Butadiene
[0155] In some embodiments, crotonyl-CoA is synthesized from the
central metabolite, acetyl-CoA, by conversion of acetyl-CoA to
acetoacetyl-CoA by an acetyl-CoA C-acetyltransferase (EC 2.3.1.9)
such as the gene product of atoB or phaA; followed by conversion to
(R) 3-hydroxybutanoyl-CoA by a 3-hydroxybutyryl-CoA dehydrogenase
(EC 1.1.1.36) such as the gene product of phaB; followed by
conversion to crotonyl-CoA by an enoyl-CoA hydratase (EC 4.2.1.119)
such as the gene product of phaJ. See, e.g., FIG. 7.
[0156] In some embodiments, crotonyl-CoA is synthesized from the
central metabolite, succinyl-CoA, by conversion of succinyl-CoA to
succinate semialdehyde by a succinate-semialdehyde dehydrogenase
(EC 1.2.1.76); followed by conversion to 4-hydroxybutyrate by a
4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); followed by
conversion to 4-hydroxybutyryl-CoA by a CoA-transferase such as the
gene product of Ck-cat2; followed by conversion to crotonyl-CoA by
a 4-hydroxybutanoyl-CoA dehydratase (EC 4.2.1.120) and a
vinylacetyl-CoA isomerase (EC 5.3.3.3). See, e.g., FIG. 7.
[0157] In some embodiments, crotonyl-CoA is synthesized from the
central metabolite, 2-oxo-glutarate, by conversion of
2-oxo-glutarate to 2-hydroxyglutarate by a 2-hydroxyglutarate
dehydrogenase (EC 1.1.99.2); followed by conversion to
2-hydroxyglutaryl-CoA by a glutaconate CoA-transferase (EC
2.8.3.12); followed by conversion to glutaconyl-CoA by a dehydrase
(EC 4.2.1.-); followed by conversion to crotonyl-CoA by a
glutaconyl-CoA decarboxylase (EC 4.1.1.70). See, e.g., FIG. 7.
[0158] In some embodiments, butadiene is synthesized from
crotonyl-CoA by conversion to crotonic acid by a succinate-CoA
ligase (EC 6.2.1.5); followed by conversion to 2-buten-al by a
long-chain-aldehyde dehydrogenase (EC 1.2.1.48); followed by
conversion to 2-buten-1-ol by an allyl-alcohol dehydrogenase (EC
1.1.1.54); followed by conversion to 2-buten-1-ol phosphate by a
mevalonate kinase (EC 2.7.1.36); followed by conversion to
2-buten-1-ol diphosphate by a phosphomevalonate kinase (EC
2.7.4.2); followed by conversion to butadiene by an isoprene
synthase (EC 4.2.3.27). See, e.g., FIG. 10.
[0159] In some embodiments, butadiene is synthesized from
crotonyl-CoA by conversion to crotonic acid by a succinate-CoA
ligase (EC 6.2.1.5); followed by conversion to 2-buten-al by a
long-chain-aldehyde dehydrogenase (EC 1.2.1.48); followed by
conversion to 2-buten-1-ol by an allyl-alcohol dehydrogenase (EC
1.1.1.54); followed by conversion to 2-buten-1-ol diphosphate by a
diphosphotransferases such as a thiamine diphosphokinase (EC
2.7.6.2); followed by conversion to butadiene by an isoprene
synthase (EC 4.2.3.27). See, e.g., FIG. 10.
[0160] In some embodiments, butadiene is synthesized from
crotonyl-CoA by conversion of crotonyl-CoA to crotonic acid by a
succinate-CoA ligase (EC 6.2.1.5); followed by conversion to
2-buten-al by a long-chain-aldehyde dehydrogenase (EC 1.2.1.48);
followed by conversion to 2-buten-1-ol by an allyl-alcohol
dehydrogenase (EC 1.1.1.54); followed by conversion to butadiene by
a dehydratase in enzyme class EC 4.2.1.-, such as linalool
dehydratase (EC 4.2.1.127), kievitone hydratase (EC 4.2.1.95),
oleate hydratase (EC 4.2.1.53) or carotenoid 1,2-hydratase (EC
4.2.1.131). See, e.g., FIG. 11.
Pathway Using 3-buten-2-ol as Central Precursor to Butadiene
[0161] In some embodiments, 3-buten-2-ol is synthesized from the
central metabolite, pyruvate, by conversion of pyruvate to
2-acetolactate by an acetolactate synthase (EC 2.2.1.6); followed
by conversion to (R)-acetoin by an acetolactate decarboxylase (EC
4.1.1.5); followed by conversion to 2,3 butanediol by a
(R,R)-butanediol dehydrogenase (EC 1.1.1.4); followed by conversion
to butanone by a propanediol dehydratase (EC 4.2.1.28); followed by
conversion to 2-butanol by a (R)-specific secondary alcohol
dehydrogenase (EC 1.1.1.B4); followed by conversion to 3-buten-2-ol
by a desaturase or a monooxygenase such as the gene product of MdpJ
or cytochrome P450 in, for example, the CYP4 family. See, e.g.,
FIG. 8.
[0162] In some embodiments, butadiene is synthesized from
3-buten-2-ol by conversion to 3-buten-2-ol phosphate by a
mevalonate kinase (EC 2.7.1.36); followed by conversion to
3-buten-2-ol diphosphate by a phosphomevalonate kinase (EC
2.7.4.2); followed by conversion to butadiene by an isoprene
synthase (EC 4.2.3.27). See, e.g., FIG. 10.
[0163] In some embodiments, butadiene is synthesized from
3-buten-2-ol by conversion to 3-buten-2-ol diphosphate by a
diphosphotransferases such as a thiamine diphosphokinase (EC
2.7.6.2); followed by conversion to butadiene by an isoprene
synthase (EC 4.2.3.27). See, e.g., FIG. 10.
[0164] In some embodiments, butadiene is synthesized from
3-buten-2-ol by a dehydratase in enzyme class EC 4.2.1.-, such as a
linalool dehydratase (EC 4.2.1.127), a kievitone hydratase (EC
4.2.1.95), an oleate hydratase (EC 4.2.1.53) or a carotenoid
1,2-hydratase (EC 4.2.1.131). See, e.g., FIG. 11.
Cultivation Strategy
[0165] In some embodiments, butadiene is biosynthesized in a
recombinant host using a fermentation strategy that can include
anaerobic, micro-aerobic or aerobic cultivation of the recombinant
host.
[0166] Pathways in the synthesis of butadiene that incorporate
enzymes requiring molecular oxygen and enzymes characterized in
vitro as being oxygen sensitive require a micro-aerobic cultivation
strategy maintaining a low dissolved oxygen concentration, whilst
maintaining sufficient oxygen transfer to prevent substrate
oxidation controlled conditions (Chayabatra & Lu-Kwang, Appl.
Environ. Microbiol., 2000, 66(2), 493 0 498).
[0167] In some embodiments, a cell retention strategy using, for
example, ceramic hollow fiber membranes is employed to achieve and
maintain a high cell density during either fed-batch or continuous
fermentation in the synthesis of butadiene.
[0168] In some embodiments, the principal carbon source fed to the
fermentation in the synthesis of butadiene derives from biological
or non-biological feedstocks.
[0169] In some embodiments, the biological feedstock is, includes,
or derives from, monosaccharides, disaccharides, lignocellulose,
hemicellulose, cellulose, lignin such as levulinic acid and
furfural, lignin, triglycerides such as glycerol and fatty acids,
agricultural waste or municipal waste.
[0170] The efficient catabolism of crude glycerol stemming from the
production of biodiesel has been demonstrated in several
microorganisms such as Escherichia coli, Cupriavidus necator,
Pseudomonas oleavorans, Pseudomonas putida and Yarrowia lipolytica
(Lee et al., Appl. Biochem. Biotechnol., 2012, 166, 1801-1813; Yang
et al., Biotechnology for Biofuels, 2012, 5:13; Meijnen et al.,
Appl. Microbiol. Biotechnol., 2011, 90, 885-893).
[0171] The efficient catabolism of lignocellulosic-derived
levulinic acid has been demonstrated in several organisms such as
Cupriavidus necator and Pseudomonas putida in the synthesis of
3-hydroxyvalerate via the precursor propanoyl-CoA (Jaremko and Yu,
Journal of Biotechnology, 2011, 155, 2011, 293-298; Martin and
Prather, Journal of Biotechnology, 2009, 139, 61-67).
[0172] The efficient catabolism of lignin-derived aromatic
compounds such benzoate analogues has been demonstrated in several
microorganisms such as Pseudomonas putida, Cupriavidus necator
(Bugg et al., Current Opinion in Biotechnology, 2011, 22, 394-400;
Perez-Pantoja et al., FEMS Microbiol. Rev., 2008, 32, 736-794).
[0173] The efficient utilization of agricultural waste, such as
olive mill waste water has been demonstrated in several
microorganisms, including Yarrowia lipolytica (Papanikolaou et al.,
Bioresour. Technol., 2008, 99(7), 2419-2428).
[0174] The efficient utilization of fermentable sugars such as
monosaccharides and disaccharides derived from cellulosic,
hemicellulosic, cane and beet molasses, cassava, corn and other
agricultural sources has been demonstrated for several
microorganism such as Escherichia coli, Corynebacterium glutamicum
and Lactobacillus delbrueckii and Lactococcus lactis (see, e.g.,
Hermann et al, Journal of Biotechnology, 2003, 104, 155-172; Wee et
al., Food Technol. Biotechnol., 2006, 44(2), 163-172; Ohashi et
al., Journal of Bioscience and Bioengineering, 1999, 87(5),
647-654).
[0175] The efficient utilization of furfural, derived from a
variety of agricultural lignocellulosic sources, has been
demonstrated for Cupriavidus necator (Li et al., Biodegradation,
2011, 22, 1215-1225).
[0176] In some embodiments, the non-biological feedstock is or
derives from natural gas, syngas, CO.sub.2/H.sub.2, methanol,
ethanol, non-volatile residue (NVR) or a caustic wash waste stream
from cyclohexane oxidation processes.
[0177] The efficient catabolism of methanol has been demonstrated
for the methylotropic yeast Pichia pastoris.
[0178] The efficient catabolism of ethanol has been demonstrated
for Clostridium kluyveri (Seedorf et al., Proc. Natl. Acad. Sci.
USA, 2008, 105(6) 2128-2133).
[0179] The efficient catabolism of CO.sub.2 and H.sub.2, which may
be derived from natural gas and other chemical and petrochemical
sources, has been demonstrated for Cupriavidus necator (Prybylski
et al., Energy, Sustainability and Society, 2012, 2:11).
[0180] The efficient catabolism of syngas has been demonstrated for
numerous microorganisms, such as Clostridium ljungdahlii and
Clostridium autoethanogenum (Kopke et al., Applied and
Environmental Microbiology, 2011, 77(15), 5467-5475).
[0181] The efficient catabolism of the non-volatile residue waste
stream from cyclohexane processes has been demonstrated for
numerous microorganisms, such as Delftia acidovorans and
Cupriavidus necator (Ramsay et al., Applied and Environmental
Microbiology, 1986, 52(1), 152-156).
[0182] In some embodiments, the host microorganism is a prokaryote.
For example, the prokaryote can be from the genus Escherichia such
as Escherichia coli; from the genus Clostridia such as Clostridium
ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri;
from the genus Corynebacteria such as Corynebacterium glutamicum;
from the genus Cupriavidus such as Cupriavidus necator or
Cupriavidus metallidurans; from the genus Pseudomonas such as
Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas
oleavorans; from the genus Delftia such as Delftia acidovorans;
from the genus Bacillus such as Bacillus subtillis; from the genus
Lactobacillus such as Lactobacillus delbrueckii; or from the genus
Lactococcus such as Lactococcus lactis. Such prokaryotes also can
be a source of genes to construct recombinant host cells described
herein that are capable of producing butadiene.
[0183] In some embodiments, the host microorganism is a eukaryote.
For example, the eukaryote can be from the genus Aspergillus such
as Aspergillus niger; from the genus Saccharomyces such as
Saccharomyces cerevisiae; from the genus Pichia such as Pichia
pastoris; or from the genus Yarrowia such as Yarrowia lipolytica;
from the genus Issatchenkia such as Issatchenkia orientalis; from
the genus Debaryomyces such as Debaryomyces hansenii; from the
genus Arxula such as Arxula adenoinivorans; or from the genus
Kluyveromyces such as Kluyveromyces lactis. Such eukaryotes also
can be a source of genes to construct recombinant host cells
described herein that are capable of producing butadiene.
Metabolic Engineering
[0184] The present document provides methods involving less than
all the steps described for all the above pathways. Such methods
can involve, for example, one, two, three, four, five, six, seven,
eight, nine, ten, or more of such steps. Where less than all the
steps are included in such a method, the first step can be any one
of the steps listed.
[0185] Furthermore, recombinant hosts described herein can include
any combination of the above enzymes such that one or more of the
steps, e.g., one, two, three, four, five, six, seven, eight, nine,
ten, or more of such steps, can be performed within a recombinant
host.
[0186] In addition, this document recognizes that where enzymes
have been described as accepting CoA-activated substrates,
analogous enzyme activities associated with [acp]-bound substrates
exist that are not necessarily in the same enzyme class.
[0187] Also, this document recognizes that where enzymes have been
described accepting (R)-enantiomers of substrate, analogous enzyme
activities associated with (S)-enantiomer substrates exist that are
not necessarily in the same enzyme class.
[0188] This document also recognizes that where an enzyme is shown
to accept a particular co-factor, such as NADPH, or co-substrate,
such as acetyl-CoA, many enzymes are promiscuous in terms of
accepting a number of different co-factors or co-substrates in
catalyzing a particular enzyme activity. Also, this document
recognizes that where enzymes have high specificity for e.g., a
particular co-factor such as NADH, an enzyme with similar or
identical activity that has high specificity for the co-factor
NADPH may be in a different enzyme class.
[0189] In some embodiments, the enzymes in the pathways outlined in
section 4.3 are the result of enzyme engineering via non-direct or
rational enzyme design approaches with aims of improving activity,
improving specificity, reducing feedback inhibition, reducing
repression, improving enzyme solubility, changing
stereo-specificity, or changing co-factor specificity.
[0190] In some embodiments, the enzymes in the pathways outlined in
section 4.3 are gene dosed, i.e., overexpressed, into the resulting
genetically modified organism via episomal or chromosomal
integration approaches.
[0191] In some embodiments, genome-scale system biology techniques
such as Flux Balance Analysis are utilized to devise genome scale
attenuation or knockout strategies for directing carbon flux to
butadiene.
[0192] Attenuation strategies include, but are not limited to; the
use of transposons, homologous recombination (double cross-over
approach), mutagenesis, enzyme inhibitors and RNAi
interference.
[0193] In some embodiments, fluxomic, metabolomic and
transcriptomal data are utilized to inform or support genome-scale
system biology techniques, thereby devising genome scale
attenuation or knockout strategies in directing carbon flux to
butadiene.
[0194] In some embodiments requiring intracellular availability of
propanoyl-CoA or propenoyl-CoA for butadiene synthesis, enzymes
catalyzing the hydrolysis of propionyl-CoA and acetyl-CoA can be
attenuated in the host organism.
[0195] In some embodiments requiring the intracellular availability
of propanoyl-CoA or propenoyl-CoA for butadiene synthesis, enzymes
consuming propanoyl-CoA via the methyl-citrate cycle are attenuated
in the host organism (Upton and Mckinney, Microbiology, 2007, 153,
3973-3982).
[0196] In some embodiments requiring the intracellular availability
of propanoyl-CoA or propenoyl-CoA for butadiene synthesis, enzymes
consuming propanoyl-CoA to pyruvate are attenuated in the host
organism.
[0197] In some embodiments requiring the intracellular availability
of propanoyl-CoA or propenoyl-CoA for butadiene synthesis, enzymes
consuming propanoyl-CoA to malonyl-CoA are attenuated in the host
organism.
[0198] In some embodiments requiring the intracellular availability
of propanoyl-CoA or propenoyl-CoA via L-threonine as central
metabolite for butadiene synthesis, a feedback-resistant threonine
deaminase is genetically engineered into the host organism (Tseng
et al., Microbial Cell Factories, 2010, 9:96).
[0199] In some embodiments requiring condensation of acetyl-CoA and
propanoyl-CoA/propenoyl-CoA for butadiene synthesis, the
fl-ketothiolases catalyzing the condensation of acetyl-CoA to
acetoacetyl-CoA such as the gene products of AtoB or phaA can be
attenuated.
[0200] In some embodiments using hosts that naturally accumulate
polyhydroxyalkanoates, the polymer synthase enzymes can be
attenuated in the host strain.
[0201] In some embodiments requiring the intracellular availability
of acetyl-CoA for butadiene synthesis, a host that is deficient
(e.g., attenuated level of activity) in one or more enzymes in the
acetate synthesis pathway can be used. For example, a host that is
deficient in a phosphotransacetylase (encoded by the pta gene) can
be used (Shen et al., Appl. Environ. Microbio., 2011, 77(9),
2905-2915).
[0202] In some embodiments requiring the intracellular availability
of acetyl-CoA for butadiene synthesis, a gene in an acetate
synthesis pathway encoding an acetate kinase, such as ack, is
attenuated.
[0203] In some embodiments requiring the intracellular availability
of acetyl-CoA for butadiene synthesis, a gene encoding the
degradation of pyruvate to lactate such as ldhA is attenuated (Shen
et al., Appl. Environ. Microbio., 2011, 77(9), 2905-2915).
[0204] In some embodiments requiring the intracellular availability
of acetyl-CoA for butadiene synthesis, a gene encoding the
degradation of phosphoenolpyruvate to succinate such as frdBC is
attenuated (see, e.g., Shen et al., 2011, supra).
[0205] In some embodiments requiring the intracellular availability
of acetyl-CoA for butadiene synthesis, a gene encoding the
degradation of acetyl-CoA to ethanol such as adhE is attenuated
(Shen et al., 2011, supra).
[0206] In some embodiments requiring the intracellular availability
of L-glutamate for butadiene synthesis, the enzymes catalyzing
anaplerotic reactions supplementing the citric acid cycle
intermediates are amplified.
[0207] In some embodiments using MDD to enzymatically form the
second vinyl group into butadiene, the thioesterase II gene product
of tesB hydrolyses (R)-3-hydroxypent-4-enoyl-CoA to
(R)-3-hydroxypent-4-enoate.
[0208] In some embodiments, where pathways require excess NADPH
co-factor in the synthesis of butadiene, a puridine nucleotide
transhydrogenase gene such as UdhA is overexpressed in the host
organisms (Brigham et al., Advanced Biofuels and Bioproducts, 2012,
Chapter 39, 1065-1090).
[0209] In some embodiments, where pathways require excess NADPH
co-factor in the synthesis of butadiene, a
glyceraldehyde-3P-dehydrogenase gene such as GapN is overexpressed
in the host organisms (Brigham et al., 2012, supra).
[0210] In some embodiments, where pathways require excess NADPH
co-factor in the synthesis of butadiene, a malic enzyme gene such
as maeA or maeB is overexpressed in the host organisms (Brigham et
al., 2012, supra).
[0211] In some embodiments, where pathways require excess NADPH
co-factor in the synthesis of butadiene, a glucose-6-phosphate
dehydrogenase gene such as zwf is overexpressed in the host
organisms (Lim et al., Journal of Bioscience and Bioengineering,
2002, 93(6), 543-549).
[0212] In some embodiments, where pathways require excess NADPH
co-factor in the synthesis of butadiene, a fructose 1,6
diphosphatase gene such as fbp is overexpressed in the host
organisms (Becker et al., Journal of Biotechnology, 2007, 132,
99-109).
[0213] In some embodiments, the efflux of butadiene across the cell
membrane to the extracellular media is enhanced or amplified by
genetically engineering structural modifications to the cell
membrane or increasing any associated transporter activity for
butadiene.
[0214] In some embodiments, oxygenases degrading butadiene to toxic
intermediates such as 1,2-epoxy-3-butene and 1,2:3,4-diepoxybutane
are attenuated in the host organism (see, e.g., Sweeney et al.,
Carcinogenesis, 1997, 18(4), 611-625).
[0215] The invention will be further described in the following
examples, which do not limit the scope of the invention described
in the claims.
EXAMPLES
Example 1
Enzyme Activity of Mevalonate Diphosphate Decarboxylase Accepting
3-Hydroxypent-4-Enoic Acid as Substrate
[0216] The his-tagged MDD genes from Saccharomyces cerevisiae,
Staphylococcus epidermidis and Streptococcus pneumonia were cloned
and expressed in E. coli in a shake flask culture containing Luria
Broth media.
[0217] The pellet from each of the induced shake flask cultures was
harvested by centrifugation, and then the pellet was resuspended
and lysed. The cell debris was separated from the supernatant via
centrifugation and filtered using a 0.2 .mu.m filter. The MDD
enzymes were purified from the supernatant using Ni-affinity
chromatography, concentrated and buffer exchanged via
ultrafiltration into 50 mM Tris buffer (pH=7.5), 100 mM NaCl, and
5% (v/v) glycerol using a 10 kDa polyethersulfone membrane.
[0218] Native enzyme activity was confirmed in a buffer composed of
50 mM Tris-HCl (pH=7.5), 100 mM NaCl, 5% (v/v) glycerol, 10 mM
MgCl.sub.2, 15 mM ATP and 5 mM of the native substrate mevalonate
diphosphate (from Sigma Aldrich) at 30.degree. C. The enzyme
activity assay reaction was initiated by adding 10 .mu.L of each
purified MDD enzyme to the assay buffer containing the substrate.
All three MDD enzymes accepted mevalonate diphosphate as substrate
as confirmed via LC-MS.
[0219] Non-native enzyme activity assays were undertaken in a
buffer composed of 50 mM Tris HCl (pH=7.5), 100 mM NaCl, 5% (v/v)
glycerol, 10 mM MgCl.sub.2, 15 mM ATP and 4 mM of the non-native
racemic substrate, 3-hydroxypent-4-enoic acid (purity >95%, from
Epison Chimie) at 30.degree. C. Non-native activity assay were
undertaken in 2 mL septum-sealed vials, thereby allowing butadiene
accumulation in the headspace. The reaction was initiated by adding
10 .mu.L of each purified MDD enzyme variant to the assay buffer
containing the substrate.
[0220] The three MDD enzymes from Saccharomyces cerevisiae,
Staphylococcus epidermidis and Streptococcus pneumonia had similar
chromatograms and spectra for non-native enzyme activity assays
using 3-hydroxypent-4-enoic acid as substrate.
[0221] The retention time for the butadiene standard and the assay
samples were within 2%. The ratio of the MS ion peak areas from the
butadiene standard and the MS ion peak areas of the samples agree
to within 20%. Also, the ion peak areas were above the limit of
quantitation for the GC/MS.
[0222] The MDD enzymes from Saccharomyces cerevisiae,
Staphylococcus epidermidis and Streptococcus pneumonia accepted
3-hydroxypent-4-enoic acid as substrate, synthesizing
butadiene.
Example 2
Amino Acid Residues Increasing the Activity of Mevalonate
Diphosphate Decarboxylase in Accepting 3-Hydroxypent-4-Enoic Acid
as Substrate
[0223] FIG. 13 provides the amino acid sequences for the MDD
enzymes from Saccharomyces cerevisiae, Staphylococcus epidermidis
and Streptococcus pneumonia, with the conserved residues within the
catalytic cleft of the enzyme in bold.
[0224] Using the total protein concentration and the purity from
densitometry, the enzyme concentration for the purified MDD from S.
cerevisiae was 385 .mu.g/mL and for the purified MDD from S.
pneumonia, it was 88 .mu.g/mL.
[0225] Given the incomplete conversion of 3-hydroxypent-4-enoic
acid as non-native substrate, the specific conversion of MDD from
S. cerevisiae was 809 [(peak area for m/z 54 ion)/(.mu.g MDD)] and
MDD from S. pneumonia's was 3200 [(peak area for m/z 54 ion)/(.mu.g
MDD)]. The specific conversion of MDD from S. pneumonia is thus
approximately four times greater than the specific conversion of
MDD from S. cerevisiae. The specific conversion of MDD from S.
epidermidis lies between the specific conversions of MDD from S.
pneumonia and S. cerevisiae (not calculated).
[0226] The amino acid residues in the region of the catalytic
arginine residue at R158 in S. cerevisiae, R144 in S. epidermidis
and R144 in S. pneumonia reveal a trend of increasing serine
density within 5 amino acid residues. R158 in S. cerevisiae has 3
serine residues within 5 amino acid residues (residues 153, 155,
and 159), R144 in S. epidermidis has 4 serine residues within 5
amino acid residues (residues 139, 141, 143, and 145) and R144 in
S. pneumonia has 5 serine residues within 5 amino acid residues
(residues 139, 141, 142, 143, and 145). See, e.g, FIG. 13.
[0227] MDD's activity in accepting 3-hydroxypent-4-enoic acid as
non-native substrate increases as the serine density increases
within the region of the catalytic arginine residue of the
catalytic cleft.
Example 3
Enzyme Activity of Isoprene Synthase Accepting
Trans-2-Butenylpyrophosphate as Substrate
[0228] The his-tagged isoprene synthase (ISPS) gene from Populus
alba was cloned and expressed in E. coli in a shake flask culture
containing Luria Broth media.
[0229] The pellet from each of the induced shake flask cultures was
harvested by centrifugation, and then the pellet was resuspended
and lysed. The cell debris was separated from the supernatant via
centrifugation and filtered through a 0.2 .mu.m filter. The ISPS
enzyme variants were purified from the supernatant using
Ni-affinity chromatography, concentrated and buffer exchanged into
50 mM Tris buffer (pH=7.5), 100 mM NaCl and 5% (v/v) glycerol using
a 10 kDa polyethersulfone membrane.
[0230] Native enzyme activity was confirmed in a buffer composed of
50 mM Tris.HCl (pH=7.5), 100 mM NaCl, 5% (v/v) glycerol, 20 mM
MgCl.sub.2 and 5 mM of the native substrate, dimethylallyl
diphosphate from Sigma-Aldrich, at 30.degree. C. The native
activity assay was undertaken in 2 mL septum-sealed vials, thereby
allowing isoprene accumulation in the headspace. The enzyme
activity assay reaction was initiated by adding 10 .mu.L of each
purified ISPS enzyme to the assay buffer containing the substrate.
ISPS from P. alba accepted dimethylallyl diphosphate as substrate
as confirmed via GC-MS.
[0231] Non-native enzyme activity assays were undertaken in a
buffer composed of 50 mM Tris.HCl (pH=7.5), 100 mM NaCl, 5% (v/v)
glycerol, 20 mM MgCl.sub.2 and 5 mM of the non-native substrate,
trans-2-butenylpyrophosphate (purity >90%) from DALTON Pharma
Services, at 30.degree. C. Non-native activity assay were
undertaken in 2 mL septum-sealed vials, thereby allowing butadiene
accumulation in the headspace. The enzyme activity assay reaction
was initiated by adding 10 .mu.L of the purified ISPS enzyme to the
assay buffer containing the substrate.
[0232] The retention time for the butadiene standard and the assay
samples are within 2%. The ratio of the MS ion peak areas from the
butadiene standard and the MS ion peak areas of the samples agree
to within 20%. Also, the ion peak areas were above the limit of
quantitation for the GC/MS.
[0233] The ISPS enzymes from Populus alba accepted
trans-2-butenylpyrophosphate as substrate, synthesising
butadiene.
OTHER EMBODIMENTS
[0234] It is to be understood that while the invention has been
described in conjunction with the detailed description thereof, the
foregoing description is intended to illustrate and not limit the
scope of the invention, which is defined by the scope of the
appended claims. Other aspects, advantages, and modifications are
within the scope of the following claims.
Sequence CWU 1
1
31396PRTSaccharomyces cerevisiae 1Met Thr Val Tyr Thr Ala Ser Val
Thr Ala Pro Val Asn Ile Ala Thr1 5 10 15 Leu Lys Tyr Trp Gly Lys
Arg Asp Thr Lys Leu Asn Leu Pro Thr Asn 20 25 30 Ser Ser Ile Ser
Val Thr Leu Ser Gln Asp Asp Leu Arg Thr Leu Thr 35 40 45 Ser Ala
Ala Thr Ala Pro Glu Phe Glu Arg Asp Thr Leu Trp Leu Asn 50 55 60
Gly Glu Pro His Ser Ile Asp Asn Glu Arg Thr Gln Asn Cys Leu Arg65
70 75 80 Asp Leu Arg Gln Leu Arg Lys Glu Met Glu Ser Lys Asp Ala
Ser Leu 85 90 95 Pro Thr Leu Ser Gln Trp Lys Leu His Ile Val Ser
Glu Asn Asn Phe 100 105 110 Pro Thr Ala Ala Gly Leu Ala Ser Ser Ala
Ala Gly Phe Ala Ala Leu 115 120 125 Val Ser Ala Ile Ala Lys Leu Tyr
Gln Leu Pro Gln Ser Thr Ser Glu 130 135 140 Ile Ser Arg Ile Ala Arg
Lys Gly Ser Gly Ser Ala Cys Arg Ser Leu145 150 155 160 Phe Gly Gly
Tyr Val Ala Trp Glu Met Gly Lys Ala Glu Asp Gly His 165 170 175 Asp
Ser Met Ala Val Gln Ile Ala Asp Ser Ser Asp Trp Pro Gln Met 180 185
190 Lys Ala Cys Val Leu Val Val Ser Asp Ile Lys Lys Asp Val Ser Ser
195 200 205 Thr Gln Gly Met Gln Leu Thr Val Ala Thr Ser Glu Leu Phe
Lys Glu 210 215 220 Arg Ile Glu His Val Val Pro Lys Arg Phe Glu Val
Met Arg Lys Ala225 230 235 240 Ile Val Glu Lys Asp Phe Ala Thr Phe
Ala Lys Glu Thr Met Met Asp 245 250 255 Ser Asn Ser Phe His Ala Thr
Cys Leu Asp Ser Phe Pro Pro Ile Phe 260 265 270 Tyr Met Asn Asp Thr
Ser Lys Arg Ile Ile Ser Trp Cys His Thr Ile 275 280 285 Asn Gln Phe
Tyr Gly Glu Thr Ile Val Ala Tyr Thr Phe Asp Ala Gly 290 295 300 Pro
Asn Ala Val Leu Tyr Tyr Leu Ala Glu Asn Glu Ser Lys Leu Phe305 310
315 320 Ala Phe Ile Tyr Lys Leu Phe Gly Ser Val Pro Gly Trp Asp Lys
Lys 325 330 335 Phe Thr Thr Glu Gln Leu Glu Ala Phe Asn His Gln Phe
Glu Ser Ser 340 345 350 Asn Phe Thr Ala Arg Glu Leu Asp Leu Glu Leu
Gln Lys Asp Val Ala 355 360 365 Arg Val Ile Leu Thr Gln Val Gly Ser
Gly Pro Gln Glu Thr Asn Glu 370 375 380 Ser Leu Ile Asp Ala Lys Thr
Gly Leu Pro Lys Glu385 390 395 2327PRTStaphylococcus epidermidis
2Met Val Lys Ser Gly Lys Ala Arg Ala His Thr Asn Ile Ala Leu Ile1 5
10 15 Lys Tyr Trp Gly Lys Ala Asp Glu Thr Tyr Ile Ile Pro Met Asn
Asn 20 25 30 Ser Leu Ser Val Thr Leu Asp Arg Phe Tyr Thr Glu Thr
Lys Val Thr 35 40 45 Phe Asp Pro Asp Phe Thr Glu Asp Cys Leu Ile
Leu Asn Gly Asn Glu 50 55 60 Val Asn Ala Lys Glu Lys Glu Lys Ile
Gln Asn Tyr Met Asn Ile Val65 70 75 80 Arg Asp Leu Ala Gly Asn Arg
Leu His Ala Arg Ile Glu Ser Glu Asn 85 90 95 Tyr Val Pro Thr Ala
Ala Gly Leu Ala Ser Ser Ala Ser Ala Tyr Ala 100 105 110 Ala Leu Ala
Ala Ala Cys Asn Glu Ala Leu Ser Leu Asn Leu Ser Asp 115 120 125 Thr
Asp Leu Ser Arg Leu Ala Arg Arg Gly Ser Gly Ser Ala Ser Arg 130 135
140 Ser Ile Phe Gly Gly Phe Ala Glu Trp Glu Lys Gly His Asp Asp
Leu145 150 155 160 Thr Ser Tyr Ala His Gly Ile Asn Ser Asn Gly Trp
Glu Lys Asp Leu 165 170 175 Ser Met Ile Phe Val Val Ile Asn Asn Gln
Ser Lys Lys Val Ser Ser 180 185 190 Arg Ser Gly Met Ser Leu Thr Arg
Asp Thr Ser Arg Phe Tyr Gln Tyr 195 200 205 Trp Leu Asp His Val Asp
Glu Asp Leu Asn Glu Ala Lys Glu Ala Val 210 215 220 Lys Asn Gln Asp
Phe Gln Arg Leu Gly Glu Val Ile Glu Ala Asn Gly225 230 235 240 Leu
Arg Met His Ala Thr Asn Leu Gly Ala Gln Pro Pro Phe Thr Tyr 245 250
255 Leu Val Gln Glu Ser Tyr Asp Ala Met Ala Ile Val Glu Gln Cys Arg
260 265 270 Lys Ala Asn Leu Pro Cys Tyr Phe Thr Met Asp Ala Gly Pro
Asn Val 275 280 285 Lys Val Leu Val Glu Lys Lys Asn Lys Gln Ala Val
Met Glu Gln Phe 290 295 300 Leu Lys Val Phe Asp Glu Ser Lys Ile Ile
Ala Ser Asp Ile Ile Ser305 310 315 320 Ser Gly Val Glu Ile Ile Lys
325 3317PRTStreptococcus pneumonia 3Met Asp Arg Glu Pro Val Thr Val
Arg Ser Tyr Ala Asn Ile Ala Ile1 5 10 15 Ile Lys Tyr Trp Gly Lys
Lys Lys Glu Lys Glu Met Val Pro Ala Thr 20 25 30 Ser Ser Ile Ser
Leu Thr Leu Glu Asn Met Tyr Thr Glu Thr Thr Leu 35 40 45 Ser Pro
Leu Pro Ala Asn Val Thr Ala Asp Glu Phe Tyr Ile Asn Gly 50 55 60
Gln Leu Gln Asn Glu Val Glu His Ala Lys Met Ser Lys Ile Ile Asp65
70 75 80 Arg Tyr Arg Pro Ala Gly Glu Gly Phe Val Arg Ile Asp Thr
Gln Asn 85 90 95 Asn Met Pro Thr Ala Ala Gly Leu Ser Ser Ser Ser
Ser Gly Leu Ser 100 105 110 Ala Leu Val Lys Ala Cys Asn Ala Tyr Phe
Lys Leu Gly Leu Asp Arg 115 120 125 Ser Gln Leu Ala Gln Glu Ala Lys
Phe Ala Ser Gly Ser Ser Ser Arg 130 135 140 Ser Phe Tyr Gly Pro Leu
Gly Ala Trp Asp Lys Asp Ser Gly Glu Ile145 150 155 160 Tyr Pro Val
Glu Thr Asp Leu Lys Leu Ala Met Ile Met Leu Val Leu 165 170 175 Glu
Asp Lys Lys Lys Pro Ile Ser Ser Arg Asp Gly Met Lys Leu Cys 180 185
190 Val Glu Thr Ser Thr Thr Phe Asp Asp Trp Val Arg Gln Ser Glu Lys
195 200 205 Asp Tyr Gln Asp Met Leu Ile Tyr Leu Lys Glu Asn Asp Phe
Ala Lys 210 215 220 Ile Gly Glu Leu Thr Glu Lys Asn Ala Leu Ala Met
His Ala Thr Thr225 230 235 240 Lys Thr Ala Ser Pro Ala Phe Ser Tyr
Leu Thr Asp Ala Ser Tyr Glu 245 250 255 Ala Met Asp Phe Val Arg Gln
Leu Arg Glu Lys Gly Glu Ala Cys Tyr 260 265 270 Phe Thr Met Asp Ala
Gly Pro Asn Val Lys Val Phe Cys Gln Glu Lys 275 280 285 Asp Leu Glu
His Leu Ser Glu Ile Phe Gly His Arg Tyr Arg Leu Ile 290 295 300 Val
Ser Lys Thr Lys Asp Leu Ser Gln Asp Asp Cys Cys305 310 315
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