Microorganisms and methods for the biosynthesis of adipate, hexamethylenediamine and 6-aminocaproic acid

Patent metadata

Field	Value
Publication number	US-11834690-B2
Application number	US-202117527902-A
Country	US
Kind code	B2
Filing date	Nov 16, 2021
Priority date	May 7, 2009
Publication date	Dec 5, 2023
Grant date	Dec 5, 2023

Abstract

The invention provides a non-naturally occurring microbial organism having a 6-aminocaproic acid, caprolactam, hexametheylenediamine or levulinic acid pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in the respective 6-aminocaproic acid, caprolactam, hexametheylenediamine or levulinic acid pathway. The invention additionally provides a method for producing 6-aminocaproic acid, caprolactam, hexametheylenediamine or levulinic acid. The method can include culturing a 6-aminocaproic acid, caprolactam or hexametheylenediamine producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding a 6-aminocaproic acid, caprolactam, hexametheylenediamine or levulinic acid pathway enzyme in a sufficient amount to produce the respective product, under conditions and for a sufficient period of time to produce 6-aminocaproic acid, caprolactam, hexametheylenediamine or levulinic acid.

First claim

What is claimed is:

1. A non-naturally occurring microbial organism, comprising a microbial organism having a hexamethylenediamine (HMDA) pathway comprising at least two exogenous nucleic acids each encoding a HMDA pathway enzyme expressed in a sufficient amount to produce HMDA, said HMDA pathway enzymes comprising: (i) a carboxylic acid reductase and a phosphopantetheine transferase, which catalyze the conversion of 6-aminocaproate to 6-aminocaproic semialdehyde; and (ii) a 6-aminocaproic semialdehyde aminotransferase or a 6-aminocaproic semialdehyde oxidoreductase (aminating), which catalyzes the conversion of 6-aminocaproic semialdehyde to hexamethylenediamine.

2. The non-naturally occurring microbial organism of claim 1 , wherein said microbial organism is bacteria, yeast, or fungi.

3. The non-naturally occurring microbial organism of claim 1 , wherein said microbial organism is bacteria selected from a group comprising Escherichia coli, Klebsiella oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli, Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Clostridium acetobutylicum, Pseudomonas fluorescens , and Pseudomonas putida.

4. The non-naturally occurring microbial organism of claim 3 , wherein the microbial organism is Escherichia coli.

5. The non-naturally occurring microbial organism of claim 1 , wherein said microbial organism is yeast or fungi selected from a group comprising Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger, Pichia pastoris, Rhizopus arrhizus , and Rhizopus oryzae.

6. The non-naturally occurring microbial organism of claim 1 , wherein the HMDA pathway comprises a set of exogenous nucleic acids encoding HMDA pathway enzymes expressed in a sufficient amount to produce HMDA, said set of exogenous nucleic acids encoding:
(i) a carboxylic acid reductase and a phosphopantetheine transferase, which catalyze the conversion of 6-aminocaproate to 6-aminocaproic semialdehyde; and
(ii) a 6-aminocaproic semialdehyde aminotransferase, which catalyzes the conversion of 6-aminocaproic semialdehyde to hexamethylenediamine.

7. The non-naturally occurring microbial organism of claim 1 , wherein the HMDA pathway comprises a set of exogenous nucleic acids encoding HMDA pathway enzymes expressed in a sufficient amount to produce HMDA, said set of exogenous nucleic acids encoding:
(i) a carboxylic acid reductase and a phosphopantetheine transferase, which catalyze the conversion of 6-aminocaproate to 6-aminocaproic semialdehyde; and
(ii) a 6-aminocaproic semialdehyde oxidoreductase (aminating), which catalyzes the conversion of 6-aminocaproic semialdehyde to hexamethylenediamine.

8. The non-naturally occurring microbial organism of claim 1 , wherein said microbial organism further comprises a 6-ACA pathway, comprising at least one exogenous nucleic acid encoding a 6-ACA pathway enzyme expressed in a sufficient amount to produce 6-ACA, said 6-ACA pathway enzymes comprising:
(i) a CoA-dependent aldehyde dehydrogenase or a 6-ACA aldehyde dehydrogenase, which catalyzes the conversion of adipyl-CoA to adipate semialdehyde; and
(ii) a 6-aminocaproate dehydrogenase, which catalyzes the conversion of adipate semialdehyde to 6-ACA; or a CoA-dependent aldehyde dehydrogenase, or a transaminase, wherein said transaminase converts adipate semialdehyde to 6-ACA.

9. The non-naturally occurring microbial organism of claim 8 , wherein said microbial organism further comprises an adipyl-CoA pathway, comprising at least one exogenous nucleic acid encoding an adipyl-CoA pathway enzyme expressed in a sufficient amount to produce adipyl-CoA, said adipyl-CoA pathway enzymes comprise
(i) a succinyl-CoA:acetyl-CoA acyl transferase or a β-ketothiolase, which catalyzes the conversion of succinyl-CoA and acetyl-CoA to 3-oxoadipyl-CoA;
(ii) a 3-hydroxyacyl-CoA dehydrogenase, which catalyzes the conversion of 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA;
(iii) a 3-hydroxyadipyl-CoA dehydratase or a crotonase, which catalyzes the conversion of 3-hydroxyadipyl-CoA to 5-carboxy-2-pentenoyl-CoA; and
(iv) a 5-carboxy-2-pentenoyl-CoA reductase or a trans-enoyl-CoA reductase, which catalyzes the conversion of 5-carboxy-2-pentenoyl-CoA to adipyl-CoA.

10. The non-naturally occurring microbial organism of claim 9 , wherein the (3-ketothiolase is derived from Escherichia coli.

11. The non-naturally occurring microbial organism of claim 9 , wherein the 3-hydroxyacyl-CoA dehydrogenase is derived from Escherichia coli.

12. The non-naturally occurring microbial organism of claim 9 , wherein crotonase is derived from Escherichia coli.

13. The non-naturally occurring microbial organism of claim 7 , wherein the carboxylic acid reductase and the phosphopantetheine transferase are derived from Mycobacterium avium subsp. paratuberculosis.

14. A method for producing hexamethylenediamine (HMDA), comprising culturing a non-naturally occurring microbial organism of claim 1 in culture medium under conditions and for a sufficient period of time to produce HMDA, wherein the culturing step comprises: a) a culture or growth condition wherein the amount of oxygen is less than 10% of saturation for dissolved oxygen in liquid media; or b) a sealed chamber of liquid or solid medium maintained with an atmosphere of less than 1% oxygen.

15. The method of claim 14 , wherein the HMDA is separated from the culture medium by way of continuous liquid-liquid extraction, pervaporation, membrane filtration, membrane separation, reverse osmosis, electrodialysis, distillation, crystallization, centrifugation, extractive filtration, ion exchange chromatography, size exclusion chromatography, adsorption chromatography, or ultrafiltration.

16. The method of claim 15 , wherein the HMDA is separated from the culture medium by distillation.

Assignees

• Genomatica Inc

Inventors

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

Classifications

• C12P17/10 Primary

  Nitrogen as only ring hetero atom · CPC title

• C12N1/38

  Chemical stimulation of growth or activity by addition of chemical compounds which are not essential growth factors; Stimulation of growth by removal of a chemical compound (C12N1/34 takes precedence) · CPC title

• C12N15/52 Primary

  Genes encoding for enzymes or proenzymes · CPC title

• C12P7/40

  containing a carboxyl group {including Peroxycarboxylic acids} · CPC title

• C12P7/44

  Polycarboxylic acids · CPC title