Electron consuming ethanol production pathway to displace glycerol formation in S. cerevisiae

Patent metadata

Field	Value
Publication number	US-10465208-B2
Application number	US-201715828729-A
Country	US
Kind code	B2
Filing date	Dec 1, 2017
Priority date	Nov 20, 2012
Publication date	Nov 5, 2019
Grant date	Nov 5, 2019

Abstract

The present invention provides for a mechanism to completely replace the electron accepting function of glycerol formation with an alternative pathway to ethanol formation, thereby reducing glycerol production and increasing ethanol production. In some embodiments, the invention provides for a recombinant microorganism comprising a down-regulation in one or more native enzymes in the glycerol-production pathway. In some embodiments, the invention provides for a recombinant microorganism comprising an up-regulation in one or more enzymes in the ethanol-production pathway.

First claim

What is claimed is:

1. A co-culture comprising at least two host cells wherein
one of the host cells is a recombinant microorganism and comprises:
(i) a heterologous nucleic acid encoding a phosphoketolase;
(ii) at least one heterologous nucleic acid encoding an enzyme in an acetyl-CoA production pathway;
(iii) a heterologous nucleic acid encoding a bifunctional acetaldehyde-alcohol dehydrogenase; and,
(iv) at least one genetic modification that leads to the down-regulation of an enzyme in a glycerol-production pathway.

2. The co-culture of claim 1 , wherein the first host cell is a yeast and the second host cell is a yeast or bacterium.

3. The recombinant microorganism of claim 1 , wherein said phosphoketolase is a single-specificity phosphoketolase with the Enzyme Commission Number 4.1.2.9.

4. The recombinant microorganism of claim 1 , wherein said phosphoketolase is dual-specificity phosphoketolase with the Enzyme Commission Number 4.1.2.22.

5. The recombinant microorganism of claim 1 , wherein said phosphoketolase is from a genus selected from the group consisting of Aspergillus, Neurospora, Lactobacillus, Bifidobacterium, Penicillium, Leuconostoc , and Oenococcus.

6. The recombinant microorganism of claim 1 , wherein said phosphoketolase corresponds to a polypeptide selected from a group consisting of SEQ ID NOs: 9, 11, 12, 13, 14, 15, 62, 64, 66, 68, 70, 72, 74, 78, 94, and 102.

7. The recombinant microorganism of any one of claims 1 , wherein said enzyme in the acetyl-CoA production pathway is a phosphotransacetylase with Enzyme Commission Number 2.3.1.8 or a an acetate kinase with Enzyme Commission Number 2.7.2.12.

8. The recombinant microorganism of claim 7 , wherein said phosphotransacetylase or said acetate kinase is from a genus selected from the group consisting of Bifidobacterium, Lactobacillus, Clostridium, Leuconostoc and Oenococcus.

9. The recombinant microorganism of claim 8 , wherein said phosphotransacetylase corresponds to a polypeptide selected from a group consisting of SEQ ID NOs: 10, 34, 80, 82, 84, 86, and 96.

10. The recombinant microorganism of claim 7 , wherein said acetate kinase corresponds to a polypeptide selected from a group consisting of SEQ ID NOs: 16, 76, 88, 92, and 100.

11. The recombinant microorganism of claim 1 , wherein said bifunctional acetaldehyde-alcohol dehydrogenase is selected from a group of enzymes having both of the following Enzyme Commission Numbers: EC 1.2.1.10 and 1.1.1.1.

12. The recombinant microorganism of claim 11 , wherein said bifunctional acetaldehyde-alcohol dehydrogenase is from B. adolescentis and corresponds to a polypeptide encoded by SEQ ID NO: 44.

13. The recombinant microorganism of claim 1 , wherein said bifunctional acetaldehyde-alcohol dehydrogenase is an NADPH dependent bifunctional acetaldehyde-alcohol dehydrogenase selected from a group of enzymes having the following Enzyme Commission Numbers: EC 1.2.1.10 and 1.1.1.2.

14. The recombinant microorganism of claim 13 , wherein said NADPH dependent bifunctional acetaldehyde-alcohol dehydrogenase is derived from a genus selected from the group consisting of Leuconostoc and Oenococcus.

15. The recombinant microorganism of claim 13 , wherein said NADPH dependent bifunctional acetaldehyde-alcohol dehydrogenase corresponds to polypeptide selected from a group consisting of SEQ ID NOs: 90 and 98.

16. The recombinant microorganism of claim 1 , wherein said enzyme in the glycerol-production pathway is a glycerol-3-phosphate dehydrogenase with Enzyme Commission Number 1.1.1.8 or a glycerol-3-phosphate phosphatase with Enzyme Commission Number 3.1.3.21.

17. The recombinant microorganism of claim 16 , wherein said glycerol-3-phosphate dehydrogenase is selected from the group consisting of glycerol-3-phosphate dehydrogenase 1, glycerol-3-phosphate dehydrogenase 2, and combinations thereof.

18. The recombinant microorganism of claim 17 , wherein said glycerol-3-phosphate dehydrogenase 1 is from S. cerevisiae and corresponds to a polypeptide encoded by SEQ ID NO: 28.

19. The recombinant microorganism of claim 17 , wherein said glycerol-3-phosphate dehydrogenase 2 is from S. cerevisiae and corresponds to a polypeptide encoded by SEQ ID NO: 30.

20. The recombinant microorganism of claim 1 , wherein said microorganism further comprises at least one additional up-regulated enzyme, wherein the up-regulated enzyme is a transaldolase with Enzyme Commission Number 2.2.1.2, a transketolase with Enzyme Commission Number 2.2.1.1, a ribose-5-P isomerase with Enzyme Commission Number 5.3.1.6, or a ribulose-5-P 3-epimerase with Enzyme Commission Number 5.1.3.1.

21. The recombinant microorganism of claim 20 , wherein said transaldolase is from S. cerevisiae and corresponds to a polypeptide encoded by SEQ ID NO: 36, said transketolase is from S. cerevisiae and corresponds to a polypeptide encoded by SEQ ID NO: 38, said ribose-5-P isomerase is from S. cerevisiae and corresponds to a polypeptide encoded by SEQ ID NO: 40, or said ribulose-5-P 3-epimerase is from S. cerevisiae and corresponds to a polypeptide encoded by SEQ ID NO: 42.

22. The recombinant microorganism of claim 1 , wherein at least one enzyme in a glycolysis pathway is up-regulated.

23. The recombinant microorganism of claim 22 , wherein said enzyme in the glycolysis pathway is a pyruvate decarboxylase with Enzyme Commission Number 4.1.1.1, or is an alcohol dehydrogenase selected from a group of enzymes having the following Enzyme Commission Numbers: 1.1.1.1 and 1.1.1.2.

24. The recombinant microorganism of claim 1 , additionally comprising at least one genetic modification that leads to the down-regulation of aldehyde dehydrogenase selected from a group of enzymes having the following Enzyme Commission Numbers: 1.2.1.3, 1.2.1.4 and 1.2.1.10 or formate dehydrogenase selected from a group of enzymes having the following Enzyme Commission Numbers: 1.2.1.43 and 1.2.1.2.

25. The recombinant microorganism of claim 1 , additionally comprising at least one genetic modification that leads to the up-regulation of aldehyde dehydrogenase selected from a group of enzymes having the following Enzyme Commission Numbers: 1.2.1.3, 1.2.1.4 and 1.2.1.10 or a pyruvate formate lyase with Enzyme Commission Number: 2.3.1.54.

26. The recombinant microorganism of claim 24 , wherein said aldehyde dehydrogenase is acetaldehyde dehydrogenase from S. cerevisiae and corresponds to a polypeptide sequence selected from the group consisting of: SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, and SEQ ID NO: 26.

27. The recombinant microorganism of claim 24 , wherein said formate dehydrogenase is from S. cerevisiae and corresponds to a sequence selected from the group consisting of: a polypeptide sequence corresponding to SEQ ID NO: 32 and a polynucleotide sequence corresponding to SEQ ID NO: 33.

28. The recombinant microorganism of claim 25 , wherein said pyruvate formate lyase corresponds to a polypeptide encoded by SEQ ID NO: 48.

29. The recombinant microorganism of claim 1 , additionally comprising at least one genetic modification that leads to the up-regulation of a pyruvate formate lyase activating enzyme with Enzyme Commission Number 1.97.1.4.

30. The recombinant microorganism of claim 29 , wherein said pyruvate formate lyase activating enzyme corr

Assignees

• Lallemand Hungary Liquidity Man Llc

Inventors

• Shaw Iv Arthur J
• Argyros Aaron
• Barrett Trisha

Classifications

• C12N9/16

  acting on ester bonds (3.1) · CPC title

• C12N9/90

  Isomerases (5.) · CPC title

• C12N15/52

  Genes encoding for enzymes or proenzymes · CPC title

• C12Y202/01002

  Transaldolase (2.2.1.2) · CPC title

• C12Y102/0101

  Acetaldehyde dehydrogenase (acetylating) (1.2.1.10) · CPC title