公开(公告)号：US11186854B2

公开(公告)日：2021-11-30

申请号：US16736405

申请日：2020-01-07

Applicant: Genomatica, Inc.

Inventor： Andreas W. Schirmer ,  Mathew A. Rude ,  Shane A. Brubaker

IPC: C12N9/88 ,  C12P7/64 ,  C12N9/02 ,  C10L1/02 ,  C12P7/04 ,  C12P7/24 ,  C12P5/02

Abstract: Compositions and methods for producing aldehydes, alkanes, and alkenes are described herein. The aldehydes, alkanes, and alkenes can be used in biofuels.

公开(公告)号：US11186853B2

公开(公告)日：2021-11-30

申请号：US16682332

申请日：2019-11-13

Applicant: Genomatica, Inc.

Inventor： Robin E. Osterhout ,  Anthony P. Burgard

IPC: C12P7/64 ,  C12N15/52 ,  C07C31/20 ,  C12N9/04 ,  C12N9/02 ,  C12N9/10 ,  C12N9/12 ,  C12N9/16 ,  C12N9/88 ,  C12N9/00 ,  C12P7/04 ,  C12P7/24

Abstract: The invention provides non-naturally occurring microbial organisms containing a fatty alcohol, fatty aldehyde or fatty acid pathway, wherein the microbial organisms selectively produce a fatty alcohol, fatty aldehyde or fatty acid of a specified length. Also provided are non-naturally occurring microbial organisms having a fatty alcohol, fatty aldehyde or fatty acid pathway, wherein the microbial organisms further include an acetyl-CoA pathway. In some aspects, the microbial organisms of the invention have select gene disruptions or enzyme attenuations that increase production of fatty alcohols, fatty aldehydes or fatty acids. The invention additionally provides methods of using the above microbial organisms to produce a fatty alcohol, a fatty aldehyde or a fatty acid.

公开(公告)号：US20210363556A1

公开(公告)日：2021-11-25

申请号：US17120005

申请日：2020-12-11

Applicant: Genomatica, Inc.

Inventor： Anthony P. Burgard ,  Robin E. Osterhout ,  Priti Pharkya ,  Mark J. Burk

IPC: C12P17/08 ,  C12N15/70 ,  C08G63/08 ,  C07D313/04 ,  C12N15/63 ,  C12P17/02 ,  C08G18/42 ,  C12N5/00 ,  C12N15/52

Abstract: The invention provides non-naturally occurring microbial organisms containing caprolactone pathways having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce caprolactone. The invention additionally provides methods of using such microbial organisms to produce caprolactone by culturing a non-naturally occurring microbial organism containing caprolactone pathways as described herein under conditions and for a sufficient period of time to produce caprolactone.

公开(公告)号：US20210309979A1

公开(公告)日：2021-10-07

申请号：US17116817

申请日：2020-12-09

Applicant: Genomatica, Inc.

Inventor： Andrew M. SHUMAKER ,  Bernardo M. DA COSTA ,  Kevin HOLDEN ,  Louis G. HOM ,  Tarah S. BARON ,  Noah HELMAN

IPC: C12N9/18 ,  C12N9/10 ,  C12P7/64

Abstract: The disclosure relates to enzyme variants with improved ester synthase properties for the production of fatty acid esters. Further contemplated are recombinant host cells that express such variants, cell cultures comprising the recombinant host cells and fatty acid ester compositions produced by such recombinant host cells.

公开(公告)号：US20210277426A1

公开(公告)日：2021-09-09

申请号：US16953050

申请日：2020-11-19

Applicant: Genomatica, Inc.

Inventor： Stephanie J. Culler ,  Nicholas Eakley ,  Kevin Gregory Hoff ,  Robin E. Osterhout ,  Priti Pharkya ,  Erik C. Ralph ,  Stephen J. Van Dien

IPC: C12P5/02 ,  C12N9/04 ,  C12N9/02 ,  C12P7/16 ,  C12P7/04

Abstract: Disclosed are methods and engineered microorganisms that enhance or improve the production of crotyl alcohol. The engineered microorganisms include genetic modifications in alcohol dehydrogenase, alkene reductase or both enzymatic activities. By such genetic modifications, a crotyl alcohol production pathway is provided or improved.

公开(公告)号：US20210241846A1

公开(公告)日：2021-08-05

申请号：US17018629

申请日：2020-09-11

Applicant: Genomatica, Inc.

Inventor： Imandokht Famili ,  Christophe H. Schilling

IPC: G16B5/00 ,  G16B50/00 ,  G16C20/30 ,  G01N33/50

Abstract: The invention provides a computer readable medium or media, having: (a) a first data structure relating a plurality of reactants to a plurality of reactions from a first cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (b) a second data structure relating a plurality of reactants to a plurality of reactions from a second cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (c) a third data structure relating a plurality of intra-system reactants to a plurality of intra-system reactions between said first and second cells, each of said intra-system reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (d) a constraint set for said plurality of reactions for said first, second and third data structures, and (e) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said first and second data structures, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells. The first, second and third data structures also can include a plurality of data structures. Additionally provided is a method for predicting a physiological function of a multicellular organism. The method includes: (a) providing a first data structure relating a plurality of reactants to a plurality of reactions from a first cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (b) providing a second data structure relating a plurality of reactants to a plurality of reactions from a second cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (c) providing a third data structure relating a plurality of intra-system reactants to a plurality of intra-system reactions between said first and second cells, each of said intra-system reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (d) providing a constraint set for said plurality of reactions for said first, second and third data structures; (e) providing an objective function, and (f) determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said first and second data structures, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells.

公开(公告)号：US20210230562A1

公开(公告)日：2021-07-29

申请号：US17001015

申请日：2020-08-24

Applicant: Genomatica, Inc.

Inventor： Andreas Schirmer ,  Baolong ZHU ,  Emanuela Popova

IPC: C12N9/04 ,  C12N15/62 ,  C12N9/02 ,  C12N15/81

Abstract: The disclosure relates to omega-hydroxylase-related fusion polypeptides that result in improved omega-hydroxylated fatty acid derivative production when expressed in recombinant host cells. The disclosure further relates to microorganisms for expressing the omega-hydroxylase-related fusion polypeptides for the production of omega-hydroxylated fatty acid derivatives.

公开(公告)号：US20210207178A1

公开(公告)日：2021-07-08

申请号：US16994240

申请日：2020-08-14

Applicant: Genomatica, Inc.

Inventor： Robin E. Osterhout ,  Anthony P. Burgard

IPC: C12P7/64 ,  C12P7/04 ,  C12P7/24 ,  C12N15/52 ,  C07C31/20 ,  C12N9/04 ,  C12N9/02 ,  C12N9/10 ,  C12N9/12 ,  C12N9/16 ,  C12N9/88 ,  C12N9/00

Abstract: The invention provides non-naturally occurring microbial organisms containing a fatty alcohol, fatty aldehyde or fatty acid pathway, wherein the microbial organisms selectively produce a fatty alcohol, fatty aldehyde or fatty acid of a specified length. Also provided are non-naturally occurring microbial organisms having a fatty alcohol, fatty aldehyde or fatty acid pathway, wherein the microbial organisms further include an acetyl-CoA pathway. In some aspects, the microbial organisms of the invention have select gene disruptions or enzyme attenuations that increase production of fatty alcohols, fatty aldehydes or fatty acids. The invention additionally provides methods of using the above microbial organisms to produce a fatty alcohol, a fatty aldehyde or a fatty acid.

公开(公告)号：US20210207111A1

公开(公告)日：2021-07-08

申请号：US16500188

申请日：2018-04-03

Applicant: Genomatica, Inc.

Inventor： Angelica Zabala BAUTISTA ,  Min Sun PARK ,  Alma Itzel RAMOS-SOLIS ,  Bernardo Moura TORRES DA COSTA ,  Behnaz BEHROUZIAN ,  Donald E. TRIMBUR ,  Emanuela POPOVA ,  Qijun HU ,  Stephen Bralley DEL CARDAYRE

IPC: C12N9/16 ,  C12P7/64

Abstract: The disclosure relates to engineered plant acyl-ACP thioesterases having improved activity for the production of medium-chain fatty acid derivatives including e.g., eight carbon and ten carbon fatty acids and fatty acid derivatives. The disclosure further relates to recombinant host cells comprising the engineered plant acyl-ACP thioesterases having improved activity for the production of medium-chain fatty acid derivatives. The disclosure also relates to methods of decreasing toxicity and improving production of medium-chain fatty acids and derivatives.

公开(公告)号：US11021695B2

公开(公告)日：2021-06-01

申请号：US15958229

申请日：2018-04-20

Applicant: GENOMATICA, INC.

Inventor： Louis Hom ,  Na Trinh ,  Murtaza Alibhai ,  Zhihao Hu ,  Eli Groban ,  Vikranth Arlagadda ,  Elizabeth Clarke

IPC: C12N9/16 ,  C12N15/00 ,  C12N9/18 ,  C12N15/63 ,  C10L1/02 ,  C07H21/04 ,  C12P21/06

Abstract: The present invention relates to novel mutant thioesterase enzymes and naturally-occurring equivalents thereof, compositions made from such enzymes and uses of thioesterase enzymes. In particular, the present invention provides mutant thioesterase enzymes that have altered properties, for example, altered substrate specificity, altered activity, altered selectivity, and/or altered proportional yields in the product mixtures. The present invention also provides polynucleotides encoding such mutant thioesterase enzymes, and vectors and host cells comprising such polynucleotides. The invention further provides for novel uses of thioesterases in the production of various fatty acid derivatives, which are useful as, or as components of, industrial chemicals and fuels.