IP Library › Granted Patent US 12,643,837
Granted Patent B2
US 12,643,837 · App. 17/922,712 · Granted Jun 2, 2026

Modified bacterial strains for improved fixation of nitrogen

Inventors: Karsten Temme (Berkeley, CA); Neal Shah (Berkeley, CA); Bilge Ozaydin Eskiyenenturk (Berkeley, CA); Sarah Bloch (Berkeley, CA); Alvin Tamsir (Berkeley, CA)
Assignee: Pivot Bio, Inc.
C05F11/08C12N1/205C12N15/52C12N15/74C12N2800/101C12R2001/22
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Quick Facts
Patent No.
US 12,643,837
App. No.
17/922,712
Granted
Jun 2, 2026
Kind
B2
Abstract

Methods and systems are provided for generating and utilizing a genetically engineered bacterium comprising a modification in a gene regulating nitrogen fixation or assimilation, wherein the modification in the gene regulating nitrogen fixation or assimilation results in one or more of: constitutive expression of a nifA gene in nitrogen limiting and non-nitrogen limiting conditions, activity of nifA in non-nitrogen limiting conditions, decreased uridylyl-transferase activity of GlnD, decreased adenylyl-removing activity of GlnE, and increased ammonium excretion.

Claims (18)

1 . A method of increasing the amount of atmospheric derived nitrogen in a plant, the method comprising contacting the plant, a part of the plant, or soil into which the plant is planted with a plurality of genetically engineered Klebsiella variicola bacteria comprising one or more genetic modifications in a gene regulating nitrogen fixation or assimilation and a plurality of genetically engineered Kosakonia sacchari bacteria comprising one or more genetic modifications in a gene regulating nitrogen fixation or assimilation, wherein:

the one or more genetic modifications in the plurality of genetically engineered Klebsiella variicola bacteria comprise a deletion of all or a portion of the coding sequence of the nifL gene and a deletion of a portion of the coding sequence of the glnD gene, and

the one or more genetic modifications in the plurality of genetically engineered Kosakonia sacchari bacteria comprise a deletion of all or a portion of the coding sequence of the nif gene, a deletion of all of the coding sequence of the glnD gene, and a deletion of a portion of the coding sequence of the glnE gene.

2 . The method of claim 1 , wherein all or a portion of the nifL coding sequence is replaced by a promoter.

3 . The method of claim 2 , wherein the promoter is a non-intergeneric promoter.

4 . The method of claim 1 , wherein the plurality of genetically engineered Klebsiella variicola bacteria are represented by bacteria deposited as ATCC Accession No. PTA-126740.

5 . The method of claim 1 , wherein the plurality of genetically engineered Kosakonia sacchari bacteria are represented by bacteria deposited as ATCC Accession No. PTA-126743.

6 . The method of claim 1 , wherein at least one of the plurality of genetically engineered Klebsiella variicola bacteria and the plurality of genetically engineered Kosakonia sacchari bacteria are non-intergeneric.

7 . A composition comprising a genetically engineered Klebsiella variicola bacterium and a genetically engineered Kosakonia sacchari bacterium, wherein the genetically engineered Klebsiella variicola bacterium and the genetically engineered Kosakonia sacchari bacterium each comprise one or more genetic modifications in a gene regulating nitrogen fixation or assimilation, wherein:

the one or more genetic modifications in the genetically engineered Klebsiella variicola bacterium comprise a deletion of all or a portion of the coding sequence of the nifL gene and a deletion of a portion of the coding sequence of the glnD gene, and

the one or more genetic modifications in the genetically engineered Kosakonia sacchari bacterium comprise a deletion of all or a portion of the coding sequence of the nifL gene, a deletion of all of the coding sequence of the glnD gene, and a deletion of a portion of the coding sequence of the glnE gene.

8 . The composition of claim 7 , wherein at least one of the one or more genetic modifications results in expression of nifA in nitrogen replete conditions in the genetically engineered Klebsiella variicola bacterium, in the genetically engineered Kosakonia sacchari bacterium, or both of the genetically engineered bacteria.

9 . The composition of claim 7 , wherein all or a portion of the nifL coding sequence is replaced by a promoter.

10 . The composition of claim 9 , wherein the promoter is a non-intergeneric promoter.

11 . The composition of claim 7 , wherein at least one of the genetically engineered Klebsiella variicola bacterium and the genetically engineered Kosakonia sacchari bacterium are non-intergeneric.

12 . The composition of claim 7 , wherein the genetically engineered Klebsiella variicola bacterium is represented by a bacterium deposited as ATCC Accession No. PTA-126740.

13 . The composition of claim 7 , wherein the genetically engineered Kosakonia sacchari bacterium is represented by a bacterium deposited as ATCC Accession No. PTA-126743.

14 . A microbial composition comprising a Kosakonia sacchari bacterium represented by a bacterium deposited as ATCC Accession No. PTA-126743, and a Klebsiella variicola bacterium represented by a bacterium deposited as ATCC Accession No. PTA-126740.

Assignments (2)
SECURITY INTEREST Recorded Dec 22, 2025
From: PIVOT BIO, INC.
To: HSBC BANK USA, N.A.
Reel/Frame 073285/0020 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 2, 2023
From: TEMME, KARSTEN; SHAH, NEAL; ESKIYENENTURK, BILGE OZAYDIN; BLOCH, SARAH; TAMSIR, ALVIN
To: PIVOT BIO, INC.
Reel/Frame 063843/0951 →
Priority Claims (2)
WO PCT/US2020/031201 · May 1, 2020 · international
WO PCT/US2021/113120 · Jan 12, 2021 · international
Continuity (2)
Provisional Application 63019247 · May 1, 2020
Related Publication 20230257317A1 · Aug 17, 2023
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