IP Library › Granted Patent US 12,371,673
Granted Patent B2
US 12,371,673 · App. 18/191,774 · Granted Jul 29, 2025

Aldehyde dehydrogenase variants and methods of using same

Inventors: Amit Shah (San Diego, CA); Joseph Warner (Oceanside, CA)
Assignee: Genomatica, Inc.
C12N9/0008C12N15/90C12P7/04C12P7/62C12P13/02C12Y102/01003
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Quick Facts
Patent No.
US 12,371,673
App. No.
18/191,774
Granted
Jul 29, 2025
Kind
B2
Abstract

The invention provides polypeptides and encoding nucleic acids of aldehyde dehydrogenase variants. The invention also provides cells expressing aldehyde dehydrogenase variants. The invention further provides methods for producing 3-hydroxybutyraldehyde (3-HBal) and/or 1,3-butanediol (1,3-BDO), or an ester or amide thereof, comprising culturing cells expressing an aldehyde dehydrogenase variant or using lysates of such cells. The invention additional provides methods for producing 4-hydroxybutyraldehyde (4-HBal) and/or 1,4-butanediol (1,4-BDO), or an ester or amide thereof, comprising culturing cells expressing an aldehyde dehydrogenase variant or using lysates of such cells.

Claims (48)

1. An isolated nucleic acid molecule selected from:

(a) a nucleic acid molecule encoding a polypeptide comprising an amino acid sequence that is a variant of SEQ ID NO: 1, wherein said amino acid sequence comprises the amino acid substitution 166M and F442N, wherein the amino acid sequence has at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 1 and wherein said polypeptide has aldehyde dehydrogenase activity; and

(b) a nucleic acid molecule that is complementary to (a).

2. The isolated nucleic acid molecule of claim 1 , wherein the amino acid sequence, in addition to the substitution 166M and F442N, comprises one or more amino acid substitutions selected from the group consisting of K65A, A73S, C174S, M204R, C220V, M2271, T230C, A243P, A243Q, C267A, C356T, R396H, E437P, S447P, C4641 and A467V, as compared to the amino acid sequence of SEQ ID NO: 1.

3. The isolated nucleic acid molecule of claim 1 , wherein the amino acid sequence comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 of the amino acid substitutions selected from the group consisting of K65A, A73S, C174S, M204R, C220V, M2271, T230C, A243P, A243Q, C267A, C356T, R396H, E437P, S447P, C4641 and A467V.

4. The isolated nucleic acid molecule of claim 1 , wherein the amino acid sequence comprises one of the following groups of amino acid substitutions:

A) K65A, C174S, M204R, C220V, A243Q, C267A, C356T, R396H, E437P, C4641 and A467V;

B) K65A, A73S, C174S, M204R, C220V, M2271, T230C, A243P, C267A, C356T, R396H, E437P, S447P, C4641 and A467V;

C) C174S, M204R, C220V, A243Q, C267A, C356T, R396H, E437P, C4641 and A467V;

D) C174S, M204R, C220V, A243P, C267A, C356T, R396H, E437P, C4641, and A467V and E) K65A, C174S, M204R, C220V, A243P, C267A, C356T, R396H, E437P, C4641 and A467V.

5. A vector containing the nucleic acid molecule of claim 1 .

6. An isolated polypeptide comprising an amino acid sequence that is a variant of SEQ ID NO: 1, wherein said amino acid sequence comprises the amino acid substitution 166M and F442N, wherein the amino acid sequence has at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 1 and wherein the isolated polypeptide has aldehyde dehydrogenase activity.

7. The isolated polypeptide of claim 6 , wherein the amino acid sequence, in addition to the substitution 166M and F442N, comprises one or more amino acid substitutions selected from the group consisting of K65A, A73S, C174S, M204R, C220V, M2271, T230C, A243P, A243Q, C267A, C356T, R396H, E437P, S447P, C4641 and A467V, as compared to the amino acid sequence of SEQ ID NO: 1.

8. The isolated polypeptide of claim 6 , wherein the amino acid sequence comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 of the amino acid substitutions selected from the group consisting of K65A, A73S, C174S, M204R, C220V, M2271, T230C, A243P, A243Q, C267A, C356T, R396H, E437P, S447P, C4641 and A467V.

9. The isolated polypeptide of claim 6 , wherein the amino acid sequence comprises one of the following groups of amino acid substitutions:

A) K65A, C174S, M204R, C220V, A243Q, C267A, C356T, R396H, E437P, C4641 and A467V;

B) K65A, A73S, C174S, M204R, C220V, M2271, T230C, A243P, C267A, C356T, R396H, E437P, S447P, C4641 and A467V;

C) C174S, M204R, C220V, A243Q, C267A, C356T, R396H, E437P, C4641 and A467V;

D) C174S, M204R, C220V, A243P, C267A, C356T, R396H, E437P, C4641 and A467V and

E) K65A, C174S, M204R, C220V, A243P, C267A, C356T, R396H, E437P, C4641 and A467V.

10. The isolated polypeptide of claim 6 , wherein the polypeptide:

(a) can convert 3-hydroxybutyryl-CoA to 3-hydroxybutyraldehyde;

(b) can convert 4-hydroxybutyryl-CoA to 4-hydroxybutyraldehyde;

(c) has higher activity relative to a polypeptide consisting of SEQ ID NO: 1;

(d) has higher activity for 3-hydroxy-(R)-butyryl-CoA over 3-hydroxy-(S)-butyryl-CoA;

(e) has higher specificity for 4-hydroxybutyryl-CoA over acetyl-CoA;

(f) produces decreased byproducts in a cell or cell extract relative to a cell or cell extract comprising a polypeptide consisting of SEQ ID NO: 1, wherein optionally the byproduct is ethanol or 4-hydroxy-2-butanone; and/or

(g) has a higher kcat relative to a polypeptide consisting of SEQ ID NO: 1.

11. A cell comprising the nucleic acid of claim 1 .

12. The cell of claim 11 , wherein the cell is a microbial organism.

13. The cell of claim 11 , wherein said cell:

(a) comprises a pathway that produces 3-hydroxybutyraldehyde (3-HBal) and/or 1,3-butanediol (1,3-BDO), or an ester or amide thereof;

(b) comprises a pathway that produces 4-hydroxybutyraldehyde (4-HBal) and/or 1,4-butanediol (1,4-BDO), or an ester or amide thereof;

(c) is capable of fermentation;

(d) comprising at least one substrate for said polypeptide, wherein the substrate is 3-hydroxybutyryl-CoA or 3-hydroxy-(R)-butyryl-CoA; 4-hydroxybutyryl-CoA; or

(e) has higher activity for 3-hydroxy-(R)-butyryl-CoA over 3-hydroxy-(S)-butyryl-CoA.

14. A composition comprising the polypeptide of claim 6 and at least one substrate for said polypeptide.

15. A culture medium comprising the cell of claim 11 .

16. A method of constructing a host strain comprising introducing the nucleic acid of claim 1 into a cell that is capable of fermentation.

17. A method for producing 3-hydroxybutyraldehyde (3-HBal) and/or 1,3-butanediol (1,3-BDO), or an ester or amide thereof, comprising culturing the cell of claim 11 to produce 3-HBal and/or 1,3-BDO, or an ester or amide thereof.

18. A method for producing 4-hydroxybutyraldehyde (4-HBal) and/or 1,4-butanediol (1,4-BDO), or an ester or amide thereof, comprising culturing the cell of claim 11 to produce 4-HBal and/or 1,4-BDO, or an ester or amide thereof.

19. A method for producing 3-hydroxybutyraldehyde (3-HBal) and/or 1,3-butanediol (1,3-BDO), or an ester or amide thereof, comprising providing a substrate to the polypeptide of claim 6 and converting the substrate to 3-HBal and/or 1,3-BDO, wherein the substrate is a racemic mixture of 1,3-hydroxybutyryl-CoA.

20. A method for producing 4-hydroxybutyraldehyde (4-HBal) and/or 1,4-butanediol (1,4-BDO), or an ester or amide thereof, comprising providing a substrate to the polypeptide of claim 6 and converting the substrate to 4-HBal and/or 1,4-BDO, wherein the substrate is 1,4-hydroxybutyryl-CoA.

21. A method for producing 3-HBal and/or 1,3-BDO, or 4-HBal and/or 1,4-BDO, comprising incubating a lysate of the cell of claim 11 to produce 3-HBal and/or 1,3-BDO, or 4-HBal and/or 1,4-BDO.

22. The isolated polypeptide of claim 6 , wherein the amino acid sequence has at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 1.

23. The isolated polypeptide of claim 6 , wherein the amino acid sequence has at least 98% sequence identity to the amino acid sequence of SEQ ID NO: 1.

24. The isolated polypeptide of claim 6 , wherein the amino acid sequence has at least 99% sequence identity to the amino acid sequence of SEQ ID NO: 1.

25. The isolated polypeptide of claim 6 , wherein the amino acid sequence is identical to the amino acid sequence referenced as SEQ ID NO: 1 with the exception of the amino acid substitution 166M and F442N.

Assignments (3)
SECURITY INTEREST Recorded Feb 10, 2026
From: GENOMATICA, INC.
To: AGAIN BIO APS
Reel/Frame 074708/0001 →
SECURITY INTEREST Recorded Dec 9, 2025
From: GENOMATICA, INC.
To: NOVO HOLDINGS A/S, AS COLLATERAL AGENT
Reel/Frame 073915/0027 →
SECURITY INTEREST Recorded Jun 2, 2025
From: GENOMATICA, INC.
To: OXFORD FINANCE LLC
Reel/Frame 071471/0770 →
Continuity (4)
Continuation 17280181
Provisional Application 62740830 · Oct 3, 2018
Provisional Application 62737053 · Sep 26, 2018
Related Publication 20230416698A1 · Dec 28, 2023
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