US 12,435,346 B2
Methods and organisms with increased carbon flux efficiencies
Anthony P. Burgard, Elizabeth, PA (US); Robin E. Osterhout, San Diego, CA (US); Stephen J. Van Dien, Encinitas, CA (US); Priti Pharkya, San Diego, CA (US); Tae Hoon Yang, Encinitas, CA (US); and Jungik Choi, San Diego, CA (US)
Assigned to Genomatica, Inc., San Diego, CA (US)
Filed by Genomatica, Inc., San Diego, CA (US)
Filed on Aug. 22, 2023, as Appl. No. 18/453,987.
Application 18/453,987 is a continuation of application No. 16/785,510, filed on Feb. 7, 2020, abandoned.
Application 16/785,510 is a continuation of application No. 15/108,259, granted, now 10,597,684, issued on Mar. 24, 2020, previously published as PCT/US2014/072178, filed on Dec. 23, 2014.
Claims priority of provisional application 62/013,390, filed on Jun. 17, 2014.
Claims priority of provisional application 61/921,292, filed on Dec. 27, 2013.
Prior Publication US 2024/0124904 A1, Apr. 18, 2024
Int. Cl. C12P 7/18 (2006.01); C07K 14/245 (2006.01); C12N 1/20 (2006.01); C12N 9/00 (2006.01); C12N 9/02 (2006.01); C12N 9/12 (2006.01); C12N 9/16 (2006.01); C12N 9/52 (2006.01); C12N 9/88 (2006.01); C12N 15/52 (2006.01); C12P 7/42 (2006.01)
CPC C12P 7/18 (2013.01) [C07K 14/245 (2013.01); C12N 1/20 (2013.01); C12N 9/0036 (2013.01); C12N 9/0057 (2013.01); C12N 9/1205 (2013.01); C12N 9/16 (2013.01); C12N 9/52 (2013.01); C12N 9/88 (2013.01); C12N 9/93 (2013.01); C12N 15/52 (2013.01); C12P 7/42 (2013.01); C12Y 106/01002 (2013.01); C12Y 110/03 (2013.01); C12Y 207/0104 (2013.01); C12Y 301/00 (2013.01); C12Y 301/02 (2013.01); C12Y 301/02002 (2013.01); C12Y 304/21092 (2013.01); C12Y 401/01031 (2013.01); C12Y 401/01032 (2013.01)] 19 Claims
 
1. A non-naturally occurring microbial organism comprising a gene disruption of a gene encoding YciA CoA hydrolase, increased expression of a pyridine nucleotide transhydrogenase, and a metabolically engineered pathway for producing a bioderived compound from a TCA cycle intermediate;
wherein the microbial organism further comprises one or more modifications selected from the group consisting of:
(a) a genetic alteration that increases expression of NADH dehydrogenase Ndh-I, cytochrome bo oxidase, or both NADH dehyrogenase Ndh-I and cytochrome bo oxidase;
(b) attenuation of one or more NAD (P) H dehydrogenases or NAD (P) H: quinine oxidoreductases, one or more ubiquinol oxidases, one or more NAD (P) H dehydrogenases, or one or more ubiquinol oxidases;
(c) a gene disruption of one or more endogenous nucleic acids encoding a menaquinol biosynthetic enzyme, or one or more nucleic acids encoding a dimethylmenaquinol biosynthetic enzyme;
(d) attenuation of protein encoding ATP-dependent Clp protease ATP-binding subunit (ClpA), pyruvate kinase or glucose phosphotransferase system (PTS); and
(e) a genetic alteration that increases expression of a phosphoenoylpyruvate carboxykinase (PEPCK), a phosphoenoylpyruvate carboxylase (PPC), or both a PEPCK and a PPC in said microbial organism.