Microorganisms and methods for producing alkenes

Patent metadata

Field	Value
Publication number	US-9988648-B2
Application number	US-201213619284-A
Country	US
Kind code	B2
Filing date	Sep 14, 2012
Priority date	Sep 16, 2011
Publication date	Jun 5, 2018
Grant date	Jun 5, 2018

Abstract

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

First claim

What is claimed is:

1. A non-naturally occurring microbial organism, said microbial organism having an alkene pathway and comprising at least one exogenous nucleic acid encoding an alkene pathway enzyme expressed in a sufficient amount to convert an alcohol to an alkene, wherein said alkene pathway comprises alkene pathway enzymes selected from:
(1) an alcohol kinase that transfers a phosphate group to a hydroxyl group, and a phosphate lyase that converts an alkyl-phosphate to an alkene, wherein the alcohol kinase is selected from enzymes having an E.C. number selected from the group consisting of 2.7.1.30 (glycerol kinase), 2.7.1.36 (mevalonate kinase), or 2.7.1.39 (homoserine kinase);
(2) a diphosphokinase that transfers a di-phosphate group to a hydroxyl group and a diphosphate lyase that converts an alkyl di-phosphate to an alkene, wherein the diphosphokinase is selected from enzymes having an E.C. number selected from the group consisting of, 2.7.6.1 (ribose-phosphate diphosphokinase) or 2.7.6.2 (thiamine diphosphokinase); or
(3) an alcohol kinase that transfers a phosphate group to a hydroxyl group, an alkyl phosphate kinase that transfers a phosphate group to a phosphate group of an alkyl-phosphate, and a diphosphate lyase that converts an alkyl di-phosphate to an alkene, wherein:
(i) the alcohol kinase is selected from enzymes having an E.C. number selected from the group consisting of 2.7.1.30 (glycerol kinase), 2.7.1.36 (mevalonate kinase), or 2.7.1.39 (homoserine kinase);
(ii) the alkyl phosphate kinase is selected from enzymes having an E.C. number selected from the group consisting of 2.7.4.2 (phosphomevalonate kinase), 2.7.4.18 (farnesyl-diphosphate kinase); and
(iii) the diphosphate lyase is selected from enzymes having an E.C. number selected from the group consisting of 4.2.3.5 (Chorismate synthase), 4.2.3.15 (Myrcene synthase), 4.2.3.36 (Terpentriene synthase), 4.2.3.46 ((E, E)-alpha-Farnesene synthase), or 4.2.3.47 (Beta-Farnesene synthase);

wherein said alcohol is a compound of Formula (I)

and wherein said alkene is a compound of Formula (II)

wherein,
(a) R 1 , R 2 , R 3 , and R 4 of Formula I and R 1 , R 2 , R 3 , and R 4 of Formula II are the same and are independently hydrogen or linear saturated C 1-6 alkyl, and
(b) wherein R 1 , R 2 , R 3 , and R 4 are selected such that the compound of Formula (II) is a linear saturated C 8 alkene.

2. The non-naturally occurring microbial organism of claim 1 , wherein said microbial organism comprises two exogenous nucleic acids each encoding an alkene pathway enzyme when the microbial organism comprises an alkene pathway selected from (1) or (2) and the microbial organism comprises two or three exogenous nucleic acids each encoding an alkene pathway enzyme when the microbial organism comprises an alkene pathway selected from (3).

3. The non-naturally occurring microbial organism of claim 2 , wherein said two exogenous nucleic acids encode an alcohol kinase and a phosphate lyase.

4. The non-naturally occurring microbial organism of claim 2 , wherein said two exogenous nucleic acids encode a diphosphokinase and a diphosphate lyase.

5. The non-naturally occurring microbial organism of claim 2 , wherein said three exogenous nucleic acids encode an alcohol kinase, an alkyl phosphate kinase and a diphosphate lyase.

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

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

8. A method for producing an alkene comprising culturing the non-naturally occurring microbial organism of claim 1 comprising said alkene pathway under conditions and for a sufficient period of time to produce a linear saturated C 8 alkene of Formula (II) of claim 1 .

9. The non-naturally occurring microbial organism of claim 3 , wherein the alcohol kinase is:
(1) a mevalonate kinase from Saccharomyces cerevisiae, Methanocaldococcus jannaschi, Homo sapiens, Arabidopsis thaliana col., Methanosarcina mazei or Streptococcus pneumonia;
(2) a glycerol kinase from Escherichia coli, Saccharomyces cerevisiae , or Thermotoga maritime; or
(3) a homoserine kinase from Escherichia coli, Saccharomyces cerevisiae or Streptomyces sp. ACT-1.

10. The non-naturally occurring microbial organism of claim 3 , wherein the alcohol kinase is:
(1) a mevalonate kinase corresponding to GenBank ID: CAA39359.1, CAA39359.1 (GI number: 3684), AAH16140.1 (GI number 16359371), NP_851084.1 (GI number 30690651), NP_633786.1 (GI number 21227864), or NP_357932.1 (GI number 15902382);
(2) a glycerol kinase corresponding to GenBank ID: AP_003883.1 (GI number 89110103), NP_228760.1 (GI number 15642775), NP_229230.1 (GI number 15642775), or NP_011831.1 (GI number 82795252); or
(3) a homoserine kinase corresponding to GenBank ID: BAB96580.2 (GI number 85674277), ZP_06280784.1 (GI number 282871792), or AAA35154.1 (GI number 172978).

11. The non-naturally occurring microbial organism of claim 3 , wherein the phosphate lyase is:
(1) a chorismate synthase from Escherichia coli, Streptococcus pneumoniae, Neurospora crassa , or Saccharomyces cerevisiae;
(2) a myrcene synthase from Solanum lycopersicum, Picea abies, Abies grandis , or Arabidopsis thaliana ; or
(3) a farnesyl diphosphate from Arabidopsis thaliana, Picea abies, Cucumis sativus, Matus×domestica , or Zea mays.

12. The non-naturally occurring microbial organism of claim 3 , wherein the phosphate lyase is:
(1) a chorismate synthase corresponding to GenBank ID: NP_416832.1 (GI number 16130264), ACH47980.1 (GI number 197205483), AAC49056.1 (GI number 976375), or CAA42745.1 (GI number 3387);
(2) a myrcene synthase corresponding to GenBank ID: ACN58229.1 (GI number 224579303), AAS47690.2 (GI number 77546864), 024474.1 (GI number 17367921), or EC07543.1 (GI number 330252449); or
(3) a farnesyl diphosphate corresponding to GenBank ID: A4FVP2.1 (GI number 205829248), POCJ43.1 (GI number 317411866), AAS47697.1 (GI number 44804601), AAU05951.1 (GI number 51537953), Q84LB2.2 (GI number 75241161), or Q84ZW8.1 (GI number 75149279).

13. The non-naturally occurring microbial organism of claim 5 , wherein the alcohol kinase is:
(1) a mevalonate kinase from Saccharomyces cerevisiae, Methanocaldococcus jannaschi, Homo sapiens, Arabidopsis thaliana col., Methanosarcina mazei or Streptococcus pneumonia;
(2) a glycerol kinase from Escherichia coli, Saccharomyces cerevisiae , or Thermotoga maritime; or
(3) a homoserine kinase from Escherichia coli, Saccharomyces cerevisiae or Streptomyces sp. ACT-1.

14. The non-naturally occurring microbial organism of claim 5 , wherein the alcohol kinase is:
(1) a mevalonate kinase corresponding to GenBank ID: CAA39359.1 (GI number 3684), Q58487.1 (2497517), AAH16140.1 (GI number 16359371), NP_851084.1 (GI number 30690651), NP_633786.1 (GI number 21227864), or NP_357932.1 (GI number 15902382);
(2) a glycerol kinase corresponding to GenBank ID: AP_003883.1 (GI number 89110103), NP_228760.1 (GI number 15642775), NP_229230.1 (GI number 15642775), or NP_011831.1 (GI number 82795252); or
(3) a homoserine kinase corresponding to GenBank ID: BAB96580.2 (GI number 85674277), ZP_06280784.1 (GI number 282871792), or AAA35154.1 (GI nu

Assignees

• Burk Mark J
• Osterhout Robin E
• Genomatica Inc

Inventors

• Burk Mark J
• Osterhout Robin E

Classifications

• C12P5/002

  cyclic (compounds containing at least three condensed carbocyclic rings C12P15/00) · CPC title

• C12P5/026 Primary

  Unsaturated compounds, i.e. alkenes, alkynes or allenes · CPC title

• C12N9/1235

  Diphosphotransferases (2.7.6) · CPC title

• C12N9/88

  Lyases (4.) · CPC title

• C12N9/1229

  Phosphotransferases with a phosphate group as acceptor (2.7.4) · CPC title