公开(公告)号：US20230287435A1

公开(公告)日：2023-09-14

申请号：US17772990

申请日：2020-10-28

Applicant: Genomatica, Inc.

Inventor： Harish Nagarajan ,  Gionata Scalcinati ,  Tae Hoon Yang

IPC: C12N15/52 ,  C12P7/18

CPC classification number: C12N15/52 ,  C12P7/18 ,  C12Y202/01006 ,  C12Y104/99001 ,  C12Y501/01001 ,  C12Y102/01003 ,  C12Y602/01001 ,  C12Y203/03001

Abstract: The present disclosure provides microbial organisms having decreased production of unwanted by-products (e.g, pyruvate-, CO2—, TCA-derived by-products; acetate; ethanol; and/or, alanine) to enhance carbon flux through acetyl-CoA, which can increase production of acetyl-CoA derived compounds (e.g, 1,3-BDO, MMA, and (3R)-hydroxybutyl (3R)-hydroxybutyrate, or any other acetyl-CoA derived compounds), and products made from any of these compounds. Also provided are one or more exogenous nucleic acids encoding enzymes that can decrease production of unwanted by-products (e.g, aldehyde dehydrogenase, acetyl-CoA synthase, amino acid dehydrogenase, alanine racemase, and/or citrate synthase), and/or one or more gene attenuations occurring in genes (e.g., acetolactate synthase) that result in decreased production of unwanted by-products. Various combinations of the exogenous nucleic acids and gene deletions are also provided in the present disclosure. Methods of making and using the same, including methods for culturing cells, and for the production of the various products are also provided.

公开(公告)号：US20220348890A1

公开(公告)日：2022-11-03

申请号：US17605499

申请日：2020-04-24

Applicant: Genomatica, Inc.

Inventor： Amit M. Shah ,  Harish Nagarajan ,  Joseph Roy Warner ,  Russell Scott Komor

IPC: C12N9/10 ,  C12P13/00

Abstract: Disclosed are transaminase (TA) enzymes and nucleic acids encoding them. In some cases, the transaminase enzymes are non-natural, engineered transaminases. Also disclosed are biosynthetic methods and engineered microorganisms that enhance or improve the biosynthesis of 6-aminocaproate, hexamethylenediamine, caproic acid, caprolactone, or caprolactam. The engineered microorganisms include exogenous TA and in some cases engineered TA.

公开(公告)号：US10941454B2

公开(公告)日：2021-03-09

申请号：US15578488

申请日：2016-05-26

Applicant: GENOMATICA, INC. ,  BRASKEM S.A.

Inventor： Stephanie J. Culler ,  Robert J. Haselbeck ,  Harish Nagarajan ,  Iuri Estrada Gouvea ,  Daniel Johannes Koch ,  Mateus Schreiner Garcez Lopes ,  Lucas Pedersen Parizzi

IPC: C12N9/88 ,  C12N9/90 ,  C07K16/40 ,  C08F36/06 ,  C12N15/82 ,  C12P5/02 ,  C12P7/16

Abstract: In alternative embodiments, provided are non-natural or genetically engineered vinylisomerase-dehydratase enzymes, including alkenol dehydratases, linalool dehydratases and crotyl alcohol dehydratases. In alternative embodiments, provided are non-natural or genetically engineered polypeptides having an activity comprising, for example, a vinylisomerase-dehydratase, an alkenol dehydratase, a linalool dehydratase and/or a crotyl alcohol dehydratase activity, or a combination thereof. In alternative embodiments, also provided are non-natural or genetically engineered nucleic acids (polynucleotides) encoding polypeptides described herein, expression or cloning vehicles comprising or having contained therein nucleic acids as described herein, and non-natural or genetically engineered cells comprising or having contained therein nucleic acids as described herein. In alternative embodiments, also provided are methods for making various organic compounds, including methyl vinyl carbinol and butadiene.

公开(公告)号：US10563180B2

公开(公告)日：2020-02-18

申请号：US15027169

申请日：2014-10-03

Applicant: Genomatica Inc.

Inventor： Stefan Andrae ,  Michael Patrick Kuchinskas ,  Jingyi Li ,  Harish Nagarajan ,  Priti Pharkya

IPC: C12N9/04 ,  C12P7/24

Abstract: Described herein are non-natural NAD+-dependent alcohol dehydrogenases (ADHs) capable of at least two fold greater conversion of methanol or ethanol to formaldehyde or acetaldehyde, respectively, as compared to its unmodified counterpart. Nucleic acids encoding the non-natural alcohol dehydrogenases, as well as expression constructs including the nucleic acids, and engineered cells comprising the nucleic acids or expression constructs are described. Also described are engineered cells expressing a non-natural NAD+-dependent alcohol dehydrogenase, optionally include one or more additional metabolic pathway transgene(s), methanol metabolic pathway genes, target product pathway genes, cell culture compositions including the cells, methods for promoting production of the target product or intermediate thereof from the cells, compositions including the target product or intermediate, and products made from the target product or intermediate.

公开(公告)号：US12203102B2

公开(公告)日：2025-01-21

申请号：US17812636

申请日：2022-07-14

Applicant: Genomatica, Inc.

Inventor： Kevin Hoff ,  Cara Ann Tracewell ,  Kui Chan ,  Michael Kuchinskas ,  Harish Nagarajan

IPC: C12N9/04 ,  C12N9/10 ,  C12P7/18 ,  C12P7/24 ,  C12P7/52 ,  C12P19/32

Abstract: The present disclosure provides thiolases and polypeptide variants of 3-hydroxybutyryl-CoA dehydrogenase, nucleic acids encoding the same, vectors comprising the nucleic acids, and cells comprising the polypeptide variants and/or thiolase, the nucleic acids, and/or the vectors. The present disclosure also provides methods of making and using the same, including methods for culturing cells, and for the production of various products, including 3-hydroxybutyryl-CoA (3-HB-CoA), 3-hydroxybutyraldehyde (3-HBal), 3-hydroxybutyrate (3-HB), 1,3-butanediol (1,3-BDO), and esters and amides thereof, and products made from any of these.

公开(公告)号：US20230139515A1

公开(公告)日：2023-05-04

申请号：US17812636

申请日：2022-07-14

Applicant: Genomatica, Inc.

Inventor： Kevin Hoff ,  Cara Ann Tracewell ,  Kui Chan ,  Michael Kuchinskas ,  Harish Nagarajan

IPC: C12N9/04 ,  C12N9/10 ,  C12P7/18 ,  C12P7/24 ,  C12P7/52 ,  C12P19/32

Abstract: The present disclosure provides thiolases and polypeptide variants of 3-hydroxybutyryl-CoA dehydrogenase, nucleic acids encoding the same, vectors comprising the nucleic acids, and cells comprising the polypeptide variants and/or thiolase, the nucleic acids, and/or the vectors. The present disclosure also provides methods of making and using the same, including methods for culturing cells, and for the production of various products, including 3-hydroxybutyryl-CoA (3-HB-CoA), 3-hydroxybutyraldehyde (3-HBal), 3-hydroxybutyrate (3-HB), 1,3-butanediol (1,3-BDO), and esters and amides thereof, and products made from any of these.

公开(公告)号：US20220333142A1

公开(公告)日：2022-10-20

申请号：US17605120

申请日：2020-04-24

Applicant: Genomatica, Inc.

Inventor： Amit M. Shah ,  Harish Nagarajan ,  Michael Angus Noble

IPC: C12P7/40 ,  C12P13/00 ,  C12N1/20 ,  C12N15/70 ,  C12N15/52

Abstract: Disclosed are trans-enoyl CoA reductase (TER) enzymes and nucleic acids encoding them. In some cases, the TER enzymes are non-natural, engineered trans-enoyl CoA reductase. TER enzymes were shown to catalyse the conversion of 5-carboxy-2-pentenoyl-CoA into adipyl-CoA for improved adipate production and the conversion of crotonyl-CoA into 6-aminocaproate. The enzymes can be used in biosynthetic methods and engineered microorganisms that enhance or improve the biosynthesis of 6-aminocaproate, hexamethylenediamine, caproic acid, caprolactone, or caprolactam. The engineered microorganisms include exogenous TER and in some cases engineered TER.

公开(公告)号：US20220177895A1

公开(公告)日：2022-06-09

申请号：US17255352

申请日：2019-06-26

Applicant: Genomatica, Inc.

Inventor： Harish Nagarajan ,  Tae Hoon Yang ,  Ali Khodayari

IPC: C12N15/52 ,  C12N9/02 ,  C12N9/16 ,  C12N9/88 ,  C12N9/90 ,  C12P13/00 ,  C12P5/00 ,  C12P5/02 ,  C12P7/16 ,  C12P7/18 ,  C12P7/24 ,  C12P7/42 ,  C12P7/46 ,  C12P7/6409

Abstract: Described herein are engineered cells including ones having synthetic methylotrophy which include an NADH-dependent enzyme capable of converting G3P to 3PG (e.g., B. methanolicus gapN) and/or fructose-1,6-bisphosphatase, along with hexulose-6-phosphate synthase, 6-phospho-3-hexuloisomerase, a phosphoketolase, or a combination thereof. Engineered cells of the disclosure beneficially maintain adequate pool sizes of phosphorylated C3 and/or C4 compounds, and/or provide increased levels of NADPH. As such, the modifications allow for the generation of C6 compounds from C1 (e.g., a methanol feedstod) and C5 compounds, the regeneration of C5 compounds from C6 compounds by carbon rearrangement, and an improved balance between regeneration of C5 compounds and lower glycolysis. In turn, this allows the engineered microorganism to generate sufficient quantities of metabolic precursors (e.g., acetyl-CoA) which can be used in a bioproduct pathway, and the engineered cells can include further modifications to those pathway enzymes allowing for production of a desired bioproduct.

公开(公告)号：US11898172B2

公开(公告)日：2024-02-13

申请号：US16498336

申请日：2018-03-29

Applicant: Genomatica, Inc.

Inventor： Kevin Hoff ,  Cara Ann Tracewell ,  Kui Chan ,  Michael Kuchinskas ,  Harish Nagarajan

IPC: C12N9/04 ,  C12N9/10 ,  C12P7/18 ,  C12P7/24 ,  C12P7/52 ,  C12P19/32

CPC classification number: C12N9/0006 ,  C12N9/1029 ,  C12P7/18 ,  C12P7/24 ,  C12P7/52 ,  C12P19/32 ,  C12Y101/01157 ,  C12Y203/01009

Abstract: The present disclosure provides thiolases and polypeptide variants of 3-hydroxybutyryl-CoA dehydrogenase, nucleic acids encoding the same, vectors comprising the nucleic acids, and cells comprising the polypeptide variants and/or thiolase, the nucleic acids, and/or the vectors. The present disclosure also provides methods of making and using the same, including methods for culturing cells, and for the production of various products, including 3-hydroxybutyryl-CoA (3-HB-CoA), 3-hydroxybutyraldehyde (3-HBal), 3-hydroxybutyrate (3-HB), 1,3-butanediol (1,3-BDO), and esters and amides thereof, and products made from any of these.

公开(公告)号：US20230374473A1

公开(公告)日：2023-11-23

申请号：US18316993

申请日：2023-05-12

Applicant: Genomatica, Inc.

Inventor： Michael A. Noble ,  Kevin G. Hoff ,  Anna Lechner ,  Harish Nagarajan

IPC: C12N9/10 ,  C12P7/22 ,  C12P7/42

CPC classification number: C12N9/1085 ,  C12P7/22 ,  C12P7/42

Abstract: Described herein are prenyltransferases including non-natural variants thereof having at least one amino acid substitution as compared to its corresponding natural or unmodified prenyltransferases and that are capable of at least two-fold greater rate of formation of cannabinoids such as cannabigerolic acid, cannabigerovarinic acid, cannabigerorcinic acid, and cannabigerol, as compared to a wild type control. Prenyltransferase variants also demonstrated regioselectivity to desired cannabinoid isomers such as CDBA (3-GOLA), 3-GDVA, 3-GOSA, and CBG (2-GOL). The prenyltransferase variants can be used to form prenylated aromatic compounds, and can be expressed in an engineered microbe having a pathway to such compounds, which include 3-GOLA, 3-GDVA, 3-GOSA, and CBG. 3-GOLA can be used for the preparation of cannabigerol (CBG), which can be used in therapeutic compositions.