WO-2026096095-A1 - COMPOSITIONS AND METHODS FOR IMPROVED BIOPRODUCTION

Abstract

Provided herein are compositions and methods for engineering a bacterium comprising a reduced capacity for cellulose formation, a reduced formation, a reduced capacity for foaming behavior, or an increased capacity for cell density for enhancing bioprocessing outcomes associated with the fermentative production of industrially relevant bioproducts.

Inventors

• BORCHERT, Andrew John
• DRUMM, LAUREN ANN RILEY

Assignees

• NITTO DENKO CORPORATION
• SAFION RENEWABLES INC.

Dates

Publication Date

20260507

Application Date

20250912

Priority Date

20241031

Claims (20)

1. CLAIMS
2. We claim:
3. 1. An engi n eered b acteri um, com prising:
4. (a) a reduced capacity for cellulose formation compared to a capacity for cellulose formation of a wild type acetic acid bacterium (AAB),
5. (b) a reduced capacity for foaming behavior compared to a foaming behavior of said wild type AAB,
6. (c) an increased capacity for cell density compared to a capacity for cell density of said wild type AAB, or
7. (d) a combination thereof.
8. 2. The engineered bacterium of claim 1, comprising a reduced capacity for cellulose formation compared to a capacity for cellulose formation of said wild type AAB
9. 3. The engineered bacterium of claim 2, comprising a modification of at least one gene selected from the group consisting of: a gene encoding a bacterial cellulose synthesis protein, a gene encoding phosphoglucomutase, a gene encoding a UTP -glucose- 1- phosphate uridylyl transferase, and a gene encoding a di guanylate cyclase.
10. 4. The engineered bacterium of claim 3, wherein said modification comprises knockout, disruption, truncation, knockdown, or inhibition of said at least one gene.
11. 5. The engineered bacterium of any one of claims 2-4, comprising a modification of at least one gene selected from the group consisting of: a gene encoding a soluble cellulase protein, a gene encoding endoglucanase CelY, a gene encoding endoglucanase CelZ, a gene encoding N-Acyl-homoserine lactone acylase GqqA, and a gene encoding N-Acyl- homoserine lactone lactonase QsdRl.
12. 6. The engineered bacterium of claim 5, wherein said modification comprises enhanced expression of said at least one gene, heterologous expression of said at least one gene, or enhanced activity of a gene product associated with said at least one gene.
13. 7 The engineered bacterium of any one of claims 1-6, comprising a reduced capacity for foaming behavior compared to a foaming behavior of said wild type AAB. 8 The engineered bacterium of claim 7, comprising a reduced capacity for expression of GinA compared to a capacity for expression of GinA of said wild type acetic acid bacterium.
14. 9. The engineered bacterium of any one of claims 7-8, comprising a modification of at least one gene selected from the group consisting of: a gene encoding a GT2 family Glycosyltransferase, a gene encoding a N-Acyl-homoserine lactone-dependent transcriptional regulator, a gene encoding an Acyl-homoserine- lactone synthase, and a gene encoding an zAcyl-homoserine-lactone response regulator.
15. 10. The engineered bacterium of claim 9, wherein said modification comprises knockout, disruption, truncation, knockdown, or inhibition of said at least one gene.
16. 11. The engineered bacterium of any one of claims 7-10, comprising a modification of a gene encoding N-Acyl-homoserine lactone acylase GqqA or a gene encoding N-Acyl- homoserine lactone lactonase QsdRl.
17. 12. The engineered bacterium of claim 11, wherein said modification comprises enhanced expression of said at least one gene, heterologous expression of said at least one gene, or enhanced activity of a gene product associated with said at least one gene.
18. 13. The engineered bacterium of any one of claims 1-12, comprising an increased capacity for cell density compared to a capacity for cell density of a wild type B.
19. 14. The engineered bacterium of claim 13, comprising a modification of at least one gene selected from the group consisting of: a gene encoding a N-Acyl-homoserine lactone-dependent transcriptional regulator, a gene encoding an Acyl-homoserine- lactone synthase, a gene encoding an Acyl-homoserine-lactone response regulator, and a gene encoding an Outer Membrane Protein A (OmpA)-like protein.
20. 15. The engineered bacterium of any one of claims 13-14, wherein said modification comprises knockout, disruption, truncation, knockdown, or inhibition of said at least one gene.

Description

COMPOSITIONS AND METHODS FOR IMPROVED BIOPRODUCTION BACKGROUND [0001] Fermentation of bacteria can be used to yield bioproducts produced by the bacteria. Acetic acid bacteria are widespread and versatile organisms that can be used to produce bioproducts. SUMMARY [0002] Engineered bacterium which overcome limitations associated with scaled bioproduction may improve bacterial production of industrially relevant bioproducts. Provided herein, in some embodiments, are compositions and methods for enhancing bioprocessing and culture handling outcomes associated with fermentation-based production of industrially relevant bioproducts. The compositions and methods provided herein comprise an engineered bacterium that may reduce cellulose production, reduce foam formation, and/or improve cell density (e.g., improve volumetric productivity) during fermentation. [0003] Provided herein, in some embodiments, is an engineered bacterium that comprises (a) a reduced capacity for cellulose formation compared to a capacity for cellulose formation of a wild type acetic acid bacterium (AAB), (b) a reduced capacity for foaming behavior compared to a foaming behavior of the wild type AAB, (c) an increased capacity for cell density compared to a capacity for cell density of the wild type AAB, or (d) a combination thereof. [0004] In some embodiments, the engineered bacterium comprises a reduced capacity for cellulose formation compared to a capacity for cellulose formation of the wild type AAB. In some embodiments, the engineered bacterium comprises a modification of at least one gene selected from the group consisting of: a gene encoding a bacterial cellulose synthesis protein, a gene encoding phosphoglucomutase, a gene encoding a UTP-glucose-1 -phosphate uridylyltransferase, and a gene encoding a diguanylate cyclase In some embodiments, the modification comprises knockout, disruption, truncation, knockdown, or inhibition of the at least one gene. [0005] In some embodiments, the engineered bacterium comprises a reduced capacity for cellulose formation compared to a capacity for cellulose formation of the wild type AAB. In some embodiments, the engineered bacterium comprises a modification of at least one gene selected from the group consisting of: a gene encoding a soluble cellulase protein, a gene encoding endoglucanase CelY, a gene encoding endoglucanase CelZ, a gene encoding N-Acyl-homoserine lactone acylase GqqA, and a gene encoding N-Acyl-homoserine lactone lactonase QsdRl. In some embodiments, the -I- modification comprises enhanced expression of the at least one gene, heterologous expression of the at least one gene, or enhanced activity of a gene product associated with the at least one gene. [0006] In some embodiments, the engineered bacterium comprises a reduced capacity for foaming behavior compared to a foaming behavior of the wild type AAB. In some embodiments, the engineered bacterium comprises a reduced capacity for expression of GinA compared to a capacity for expression of GinA of the wild type acetic acid bacterium. In some embodiments, the engineered bacterium comprises a modification of at least one gene selected from the group consisting of: a gene encoding a GT2 family Glycosyltransferase, a gene encoding a N-Acyl-homoserine lactone-dependent transcriptional regulator, a gene encoding an Acyl-homoserine- lactone synthase, and a gene encoding an Acyl-homoserine-lactone response regulator. In some embodiments, the modification comprises knockout, disruption, truncation, knockdown, or inhibition of the at least one gene. [0007] In some embodiments, the engineered bacterium comprises a reduced capacity for foaming behavior compared to a foaming behavior of the wild type AAB. In some embodiments, the engineered bacterium comprises a modification of a gene encoding N-Acyl-homoserine lactone acylase GqqA or a gene encoding N-Acyl-homoserine lactone lactonase QsdRI. In some embodiments, the modification comprises enhanced expression of the at least one gene, heterologous expression of the at least one gene, or enhanced activity of a gene product associated with the at least one gene. [0008] In some embodiments, the engineered bacterium comprises an increased capacity for cell density compared to a capacity for cell density of a wild type AAB. In some embodiments, the engineered bacterium comprises a modification of at least one gene selected from the group consisting of: a gene encoding a N-Acyl-homoserine lactone-dependent transcriptional regulator, a gene encoding an Acyl-homoserine- lactone synthase, a gene encoding an Acyl-homoserine-lactone response regulator, and a gene encoding an Outer Membrane Protein A (OmpA)-like protein. In some embodiments, the modification comprises knockout, disruption, truncation, knockdown, or inhibition of the at least one gene. [0009] In some embodiments, the engineered bacterium comprises an increased capacity for cell density compared to a capacity for cell density of a wild t