DHAD variants and methods of screening

• US 10,287,566 B2
• Filed: 01/16/2017
• Issued: 05/14/2019
• Est. Priority Date: 03/15/2013
• Status: Active Grant

• Current Assignee: Gevo Incorporated
• Original Assignee: Butamax(TM) Advanced Biofuels LLC (BP PLC)
• Inventors: Kelly, Kristen J., Ye, Rick W.
• Primary Examiner(s): Gebreyesus, Kagnew H
• Application Number:
  US15/406,876
• Publication Number:
  US 20170226497A1
• Time in Patent Office: 848 Days
• CPC Class Codes: B01D 11/04 of solutions which are liquid
• CPC Class Codes: C12N 15/52 Genes encoding for enzymes or proenzymes
• CPC Class Codes: C12N 9/88 Lyases (4.)
• CPC Class Codes: C12P 7/16 Butanols
• CPC Class Codes: C12P 7/40 containing a carboxyl group including Peroxycarboxylic acids
• CPC Class Codes: C12Y 101/01001 Alcohol dehydrogenase (1.1.1.1)
• CPC Class Codes: C12Y 101/01086 Ketol-acid reductoisomerase (1.1.1.86)
• CPC Class Codes: C12Y 202/01006 Acetolactate synthase (2.2.1.6)
• CPC Class Codes: C12Y 402/01009 Dihydroxy-acid dehydratase (4.2.1.9), i.e. acetohydroxyacid dehydratase
• CPC Class Codes: Y02E 50/10 Biofuels, e.g. bio-diesel
• CPC Class Codes: Y02P 20/52 using catalysts, e.g. selective catalysts

Abstract

Methods of screening for dihydroxy-acid dehydratase (DHAD) variants that display increased DHAD activity are disclosed, along with DHAD variants identified by these methods. Such enzymes can result in increased production of compounds from DHAD requiring biosynthetic pathways. Also disclosed are isolated nucleic acids encoding the DHAD variants, recombinant host cells comprising the isolated nucleic acid molecules, and methods of producing butanol.

Claims

1. A method for the production of isobutanol comprising

(a) providing a recombinant host cell that comprises

(i) an isolated polypeptide having dihydroxy-acid dehydratase (DHAD) activity, wherein the polypeptide is at least 95% identical to a Streptococcus mutans DHAD of SEQ ID NO:

168 and comprises amino acid substitutions at position 33 and position 563, and

(ii) an isobutanol biosynthetic pathway, wherein the isobutanol biosynthetic pathway comprises the following substrate to product conversions;

(1) pyruvate to acetolactate catalyzed by an acetolactate synthase,

(2) acetolactate to 2,3-dihydroxyisovalerate catalyzed by a ketol-acid reductoisomerase,

(3) 2,3-dihydroxyisovalerate to α

-ketoisovalerate catalyzed by DHAD,

(4) α

-ketoisovalerate to isobutyraldehyde catalyzed by an α

-keto acid decarboxylase, and

(5) isobutyraldehyde to isobutanol catalyzed by an alcohol dehydrogenase;

(b) culturing the recombinant host cell in a fermentation medium under suitable conditions to produce isobutanol; and

(c) recovering the isobutanol.

2. The method of claim 1, wherein the recombinant host cell is a bacterial cell or a yeast cell.

3. The method of claim 2, wherein the bacterial cell is a member of a genus of bacteria selected from Clostridium, Zymomonas, Escherichia, Salmonella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Pediococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, and Streptococcus.

4. The method of claim 2, wherein the yeast cell is a member of a genus of yeast selected from Saccharomyces, Schizosaccharomyces, Hansenula, Kluyveromyces, Candida, Pichia, and Yarrowia.

5. The method of claim 1, wherein the recovering is by distillation, liquid-liquid extraction, adsorption, gas stripping, decantation, membrane evaporation, pervaporation, or combinations thereof.

6. The method of claim 5, wherein the recovering is by liquid-liquid extraction and the extractant is derived from biomass.

7. The method of claim 1, further comprising removing solids from the fermentation medium.

8. The method of claim 7, wherein the removing is by centrifugation, filtration, decantation, or combinations thereof.

9. The method of claim 7, wherein the removing occurs before the recovering.

10. The method of claim 1, wherein the recombinant host cell comprises the polypeptide of SEQ ID NO:

534.

11. The method of claim 1, wherein the recombinant host cell further comprises a disruption in an endogenous gene that encodes a mitochrondrial DHAD.

12. The method of claim 1, wherein the recombinant host cell further comprises a disruption in one or more endogenous genes affecting iron-sulfur cluster biosynthesis selected from FRA2, GRX3, and GRX4.

13. The method of claim 1, wherein the recombinant host cell has been further genetically engineered to upregulate the activity of at least one gene selected from AFT1 and AFT2.

14. The method of claim 1, wherein the recombinant host cell has been further genetically modified to disrupt a gene encoding pyruvate decarboxylase (PDC).