Microorganisms and methods for the production of caprolactone

Patent metadata

Field	Value
Publication number	US-11708592-B2
Application number	US-202017120005-A
Country	US
Kind code	B2
Filing date	Dec 11, 2020
Priority date	Nov 2, 2011
Publication date	Jul 25, 2023
Grant date	Jul 25, 2023

Abstract

The invention provides non-naturally occurring microbial organisms containing caprolactone pathways having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce caprolactone. The invention additionally provides methods of using such microbial organisms to produce caprolactone by culturing a non-naturally occurring microbial organism containing caprolactone pathways as described herein under conditions and for a sufficient period of time to produce caprolactone.

First claim

What is claimed is:

1. A non-naturally occurring microbial organism, said microbial organism having a caprolactone pathway and a reductive TCA pathway, wherein said non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding a caprolactone pathway enzyme expressed in a sufficient amount to produce caprolactone, wherein said caprolactone pathway comprises a pathway selected from:
(1) 1D, 1A, 1B, and 1C;
(2) 1E, 1B, 1C and 1D;
(3) 1F, 1A, 1B, 1C and 1D;
(4) 1F, 1E, 1B, 1C and 1D;
(5) 1A, 1B and 1G;
(6) 1E, 1B and 1G;
(7) 1F, 1A, 1B and 1G;
(8) 1F, 1E, 1B and 1G;
(9) 1A, 1B, 1C, 1J and 11;
(10) 1E, 1B, 1C, 1J and 11;
(11) 1F, 1A, 1B, 1C, 1J and 11;
(12) 1F, 1E, 1B, 1C, 1J and 11;
(13) 1A, 1B, 1H and 11;
(14) 1E, 1B, 1H and 11;
(15) 1F, 1A, 1B, 1H and 11;
(16) 1F, 1E, 1B, 1H and 11;
(17) 2A, 2B, 2C, 2D, 2E and 2F;
(18) 2A, 2B, 2C, 2D and 2G;
(19) 2A, 2B, 2C, 2D, 2E, 2J and 21;
(20) 2A, 2B, 2C, 2D, 2H and 21;
(21) 4A, 4B, 4C, 4D and 3A; and
(22) 5A, 5B, 5C an 3A,
wherein 1A is an adipyl-COA reductase, wherein 1B is an adipate semialdehyde reductase, wherein 1C is a 6-hydroxyhexanoyl-CoA transferase or a 6-hydroxyhexanoyl-CoA synthetase, wherein 1D is a 6-hydroxyhexanoyl-CoA cyclase or spontaneous cyclization, wherein 1E is an adipate reductase, wherein 1F is an adipyl-CoA transferase, an adipyl-CoA synthetase or an adipyl-CoA hydrolase, wherein 1G is a 6-hydroxyhexanoate cyclase, wherein 1H is a 6-hydroxyhexanoate kinase, wherein 1I is a 6-hydroxyhexanoyl phosphate cyclase or spontaneous cyclization, wherein 1J is a phosphotrans-6-hydroxyhexanoylase, wherein 2A is a 4-hydroxybutyryl-CoA:acetyl-CoA acyltransferase, wherein 2B is a 3-oxo-6-hydroxyhexanoyl-COA reductase, wherein 2C is a 3,6-dihydroxyhexanoyl-CoA dehydratase, wherein 2D is a 6-hydroxyhex-2-enoyl-COA reductase, wherein 2E is a 6-hydroxyhexanoyl-CoA transferase, a 6-hydroxyhexanoyl-CoA synthetase or a 6-hydroxyhexanoyl-CoA hydrolase, wherein 2F is a 6-hydroxyhexanoate cyclase, wherein 2G is a 6-hydroxyhexanoyl-CoA cyclase or spontaneous cyclization, wherein 2H is a phosphotrans-6-hydroxyhexanoylase, wherein 2I is a 6-hydroxyhexanoyl phosphate cyclase or spontaneous cyclization, wherein 2J is a 6-hydroxyhexanoate kinase, wherein 3A is a cyclohexanone monooxygenase, wherein 4A is an adipate semialdehyde dehydratase, wherein 4B is a cyclohexane-1,2-dione reductase, wherein 4C is a 2-hydroxycyclohexanone reductase, wherein 4D is a cyclohexane-1,2-diol dehydratase, wherein 5A is a 2-ketocyclohexane-1-carboxoyl-CoA hydrolase (acting on C—C), wherein 5B is a 2-ketocyclohexane-1-carboxoyl-CoA transferase, a 2-ketocyclohexane-1-carboxoyl-CoA synthetase or a 2-ketocyclohexane-1-carboxoyl-CoA hydrolase, and wherein 5C is a 2-ketocyclohexane-1-carboxylate decarboxylase.

2. The non-naturally occurring microbial organism of claim 1 , wherein said microbial organism comprises two, three, four, five, six or seven exogenous nucleic acids each encoding a caprolactone pathway enzyme.

3. The non-naturally occurring microbial organism of claim 2 , wherein said microbial organism comprises exogenous nucleic acids encoding each of the enzymes of at least one of the pathways selected from (1)-(22).

4. The non-naturally occurring microbial organism of claim 1 , wherein said at least one exogenous nucleic acid is a heterologous nucleic acid.

5. The non-naturally occurring microbial organism of claim 1 , wherein said non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

6. The non-naturally occurring microbial organism of claim 1 , wherein:
(i) said reductive TCA pathway comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme, wherein said at least one exogenous nucleic acid is selected from an ATP-citrate lyase, citrate lyase, a citryl-CoA synthetase, a citryl-CoA, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase;
(ii) said reductive TCA pathway comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme, wherein said at least one exogenous nucleic acid is selected from a pyruvate:ferredoxin oxidoreductase, a phosphoenolpyruvate carboxylase, a phosphoenolpyruvate carboxykinase, a CO dehydrogenase, and an H 2 hydrogenase; or
(iii) said non-naturally occurring microbial organism further comprises at least one exogenous nucleic acid encodes an enzyme selected from a CO dehydrogenase, an H 2 hydrogenase, and combinations thereof.

7. The non-naturally occurring microbial organism of claim 6 , wherein said microbial organism comprising (i) further comprises an exogenous nucleic acid encoding an enzyme selected from a pyruvate:ferredoxin oxidoreductase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an NAD(P)H:ferredoxin oxidoreductase, ferredoxin, and combinations thereof.

8. The non-naturally occurring microbial organism of claim 6 , wherein said microbial organism comprising (ii) further comprises an exogenous nucleic acid encoding an enzyme selected from an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, and combinations thereof.

9. The non-naturally occurring microbial organism of claim 6 , wherein said microbial organism comprising (i) comprises three exogenous nucleic acids encoding an ATP-citrate lyase or a citrate lyase, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase;
wherein said microbial organism comprising (ii) comprises five exogenous nucleic acids encoding a pyruvate:ferredoxin oxidoreductase, a phosphoenolpyruvate carboxylase, a phosphoenolpyruvate carboxykinase, a CO dehydrogenase, and an H 2 hydrogenase; or
wherein said microbial organism comprising (iii) comprises two exogenous nucleic acids encoding a CO dehydrogenase and an H 2 hydrogenase.

10. A method for producing caprolactone, comprising culturing the non-naturally occurring microbial organism of claim 1 under conditions and for a sufficient period of time to produce caprolactone.

11. Culture medium comprising bioderived caprolactone produced by a non-naturally occurring microbial organism of claim 1 , wherein said bioderived caprolactone has a carbon-12, carbon-13 and carbon-14 isotope ratio that reflects an atmospheric carbon dioxide uptake source.

12. The culture medium of claim 11 , wherein said culture medium is separated from a non-naturally occurring microbial organism having a caprolactone pathway.

13. Bioderived caprolactone produced by a non-naturally occurring microbial organism of claim 1 , and having a carbon-12, carbon-13 and carbon-14 isotope ratio that reflects an atmospheric carbon dioxide uptake source.

14. The bioderived caprolactone of claim 13 , wherein said bioderived caprolactone has an Fm value of at least 80%, at least 85%, at least 90%, at least 95% or at least 98%.

15. A composition comprising said bioderived caprolactone of claim 13 and a compound other than said bioderived caprolactone.

16. The composition of claim 15 , wherein said compound other than said bioderived caprolactone is a trace amount of a cellular portion of a non-naturally occurring microbial organism having a caprolactone pathway.

17. A biobased polymer comprising said bioderived caprolactone of claim 13 .

18. A biobased resin comprising said bioderived caprolactone of claim 13 .

19. A molde

Assignees

• Genomatica Inc

Inventors

• Burgard Anthony P
• Osterhout Robin E
• Pharkya Priti
• Burk Mark J

Classifications

• C12P17/08 Primary

  containing a hetero ring of at least seven ring members, e.g. zearalenone, macrolide aglycons · CPC title

• C07D313/04

  not condensed with other rings · CPC title

• C08G18/4277

  Caprolactone and/or substituted caprolactone · CPC title

• C08G63/08

  Lactones or lactides · CPC title

• C12N5/0018

  Culture media for cell or tissue culture (media for specific animal cell type C12N5/06) · CPC title