Generation of acyl amino acids

• US 10,640,799 B2
• Filed: 05/14/2018
• Issued: 05/05/2020
• Est. Priority Date: 03/15/2013
• Status: Active Grant

• Current Assignee: Modular Genetics, Inc.
• Original Assignee: Modular Genetics, Inc.
• Inventors: Jarrell, Kevin A., Reznik, Gabriel O., Vishwanath, Prashanth, Pynn, Michelle
• Primary Examiner(s): Saidha, Tekchand
• Application Number:
  US15/978,634
• Publication Number:
  US 20180340198A1
• Time in Patent Office: 722 Days
• CPC Class Codes: A01N 37/36 containing at least one carboxylic group or a thio analogue, or a derivative thereof, and a singly bound oxygen or sulfur atom attached to the same carbon skeleton, this oxygen or sulfur atom not being a member of a carboxylic group or of a thio analogue, or of a derivative thereof, e.g. hydroxy-carboxylic acids
• CPC Class Codes: C07C 235/06 having the nitrogen atoms of the carboxamide groups bound to hydrogen atoms or to acyclic carbon atoms
• CPC Class Codes: C12N 9/80 acting on amide bonds in linear amides (3.5.1)
• CPC Class Codes: C12N 9/93 Ligases (6)
• CPC Class Codes: C12P 13/02 Amides, e.g. chloramphenicol or polyamides; Imides or polyimides; Urethanes, i.e. compounds comprising N-C=O structural element or polyurethanes peptides C12P21/00 or C07K
• CPC Class Codes: C12Y 603/02 Acid—amino-acid ligases (peptide synthases)(6.3.2)

Abstract

In certain embodiments, the present invention comprises compositions and methods useful in the generation of acyl amino acids. In certain embodiments, the present invention provides an engineered polypeptide comprising a peptide synthetase domain; in some such embodiments, the engineered polypeptide comprises only a single peptide synthetase domain. In some embodiments, the present invention provides an engineered peptide synthetase that is substantially free of a thioesterase domain, and/or a reductase domain. In certain embodiments, the present invention provides an acyl amino acid composition comprising a plurality of different forms of an acyl amino acid. In some such compositions, substantially all of the acyl amino acids within the composition contain the same amino acid moiety and differ with respect to acyl moiety. We also described populations where the fatty acid si for example 95% one length (C14, myristic).

Claims

1. A Bacillus subtilis cell engineered to (i) express at least one engineered peptide synthetase lacking a thioesterase domain and lacking a reductase domain, which peptide synthetase synthesizes an acyl amino acid, and (ii) lack endogenous α

-keto acid dehydrogenase activity.

2. A method comprising culturing the engineered cell of claim 1 under conditions and for a time sufficient for an acyl amino acid composition to be made.

3. The Bacillus subtilis cell of claim 1, wherein the engineered peptide synthetase comprises a peptide synthetase domain, which includes an adenylation (A) domain, a thiolation (T) domain, and a condensation (C) domain.

4. The Bacillus subtilis cell of claim 1, wherein the engineered peptide synthetase contains only a single peptide synthetase domain that includes an adenylation (A) domain, a thiolation (T) domain, and a condensation (C) domain.

5. The Bacillus subtilis cell of claim 1, wherein the engineered peptide synthetase is or comprises a peptide synthetase domain that links a fatty acid to an amino acid as found in a peptide synthetase that synthesizes a lipopeptide.

6. The method of preparing a product comprising claim 2, further comprising steps of:

enriching the acyl amino acid composition for a particular acyl amino acid; and

combining the enriched acyl amino acid composition with at least one other component to produce a product.

7. The Bacillus subtilis cell of claim 5, wherein the peptide synthetase domain is or comprises Module 1 of a surfactin (srf) synthetase.

8. The Bacillus subtilis cell of claim 7, wherein the srf synthetase is srfAA.

9. The Bacillus subtilis cell of claim 5, wherein the peptide synthetase domain is or comprises Module 1 of a mycosubtilisin synthetase.

10. The Bacillus subtilis cell of claim 9, wherein the mycosubtilisin synthetase is or comprises MycA.

11. The Bacillus subtilis cell of claim 5, wherein the peptide synthetase domain is or comprises Module 1 of a daptomycin synthetase.

12. The Bacillus subtilis cell of claim 11, wherein the daptomycin synthetase is or comprises dptA1.

13. The Bacillus subtilis cell of claim 1, wherein the cell is engineered to lack at least one or more functional subunits of the α

-keto acid dehydrogenase.

14. The Bacillus subtilis cell of claim 13, wherein the cell is engineered to delete bkdAA and bkdAB genes that encode E1 and E1β

subunits, respectively, of the α

-keto acid dehydrogenase.

15. The method of claim 2, wherein the culturing comprises culturing the engineered cell in the presence of isobutyric acid to produce an acyl amino acid composition that is enriched in acyl amino acid with a branched fatty acid tail length of C14, relative to an acyl amino acid composition produced by a Bacillus subtilis cell that synthesizes an acyl amino acid and retains endogenous α

-keto acid dehydrogenase activity.

16. The method of claim 10, wherein the culturing comprises culturing the engineered cell in the presence of 2-methylbutyric acid at a concentration that is sufficient to produce an acyl amino acid composition that is enriched in acyl amino acid with an odd-numbered anteiso branched fatty acid tail, relative to an acyl amino acid composition produced by a Bacillus subtilis cell that synthesizes an acyl amino acid and retains endogenous α

-keto acid dehydrogenase activity.

17. The method of claim 2, wherein the culturing comprises culturing the engineered cell in the presence of 2-methylbutyric acid at a concentration that is sufficient to produce an acyl amino acid composition that is enriched in acyl amino acid with an even-numbered unbranched fatty acid tail, relative to an acyl amino acid composition produced by a Bacillus subtilis cell that synthesizes an acyl amino acid and retains endogenous α

-keto acid dehydrogenase activity.

18. The method of claim 2, wherein the culturing comprises culturing the engineered cell in the presence of isovaleric acid at a concentration that is sufficient to produce an acyl amino acid composition that is enriched in acyl amino acid with an odd-numbered iso branched fatty acid tail, relative to an acyl amino acid composition produced by a Bacillus subtilis cell that synthesizes an acyl amino acid and retains endogenous α

-keto acid dehydrogenase activity.

19. The method of claim 2, wherein the culturing comprises culturing the engineered cell in the presence of isovaleric acid at a concentration that is sufficient to produce an acyl amino acid composition that is enriched in acyl amino acid with an even-numbered unbranched fatty acid tail, relative to an acyl amino acid composition produced by a Bacillus subtilis cell that synthesizes an acyl amino acid and retains endogenous α

-keto acid dehydrogenase activity.

20. The method of claim 2, further comprising a step of cleaving acyl amino acid within the acyl amino acid composition to generate a free fatty acid and an amino acid.

21. The method of claim 20, wherein the step of cleaving comprises contacting the acyl amino acid composition with an acylase.