公开(公告)号：US20190284592A1

公开(公告)日：2019-09-19

申请号：US16433804

申请日：2019-06-06

Applicant: Genomatica, Inc.

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

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

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：US20190264242A1

公开(公告)日：2019-08-29

申请号：US16137264

申请日：2018-09-20

Applicant: Genomatica, Inc.

Inventor： Anthony P. BURGARD ,  Robin E. OSTERHOUT ,  Jun SUN ,  Priti PHARKYA

IPC: C12P7/42 ,  C12P7/18 ,  C12P7/16 ,  C12P7/52 ,  C12N9/02 ,  C12P7/04

Abstract: A non-naturally occurring microbial organism includes a microbial organism having a reductive TCA or Wood-Ljungdahl pathway in which at least one exogenous nucleic acid encoding these pathway enzymes is expressed in a sufficient amount to enhance carbon flux through acetyl-CoA. A method for enhancing carbon flux through acetyl-CoA includes culturing theses non-naturally occurring microbial organisms under conditions and for a sufficient period of time to produce a product having acetyl-CoA as a building block. Another non-naturally occurring microbial organism includes at least one exogenous nucleic acid encoding an enzyme expressed in a sufficient amount to enhance the availability of reducing equivalents in the presence of carbon monoxide or hydrogen, thereby increasing the yield of redox-limited products via carbohydrate-based carbon feedstock. A method for enhancing the availability of reducing equivalents in the presence of carbon monoxide or hydrogen includes culturing this organism for a sufficient period of time to produce a product.

公开(公告)号：US10273508B2

公开(公告)日：2019-04-30

申请号：US15148759

申请日：2016-05-06

Applicant: Genomatica, Inc.

Inventor： Stephen J. Van Dien ,  Anthony P. Burgard ,  Robert Haselbeck ,  Catherine J. Pujol-Baxley ,  Wei Niu ,  John D. Trawick ,  Harry Yim ,  Mark J. Burk ,  Robin E. Osterhout ,  Jun Sun

IPC: C12N9/00 ,  C12N9/02 ,  C12N9/04 ,  C12N9/10 ,  C12N9/16 ,  C12N9/88 ,  C12P7/18 ,  C12N15/52

Abstract: The invention provides non-naturally occurring microbial organisms comprising a 1,4-butanediol (BDO) pathway comprising at least one exogenous nucleic acid encoding a BDO pathway enzyme expressed in a sufficient amount to produce BDO and further optimized for expression of BDO. The invention additionally provides methods of using such microbial organisms to produce BDO.

公开(公告)号：US10227616B2

公开(公告)日：2019-03-12

申请号：US15303931

申请日：2015-04-14

Applicant: Novamont S.p.A. ,  Genomatica, Inc.

Inventor： Maria Dani ,  Giuseppe Ruggiero ,  Davide Perini ,  Alice Bianchi

IPC: C12P7/18

Abstract: Process for the synthesis of 1,4-butanediol comprising fermentation of a culture medium by a microorganism provided with at least one metabolic pathway for the synthesis of 1,4-butanediol and able to use saccharose, in which said culture medium comprises a glucose and saccharose mixture comprising, based on the combined weight of glucose and saccharose, 10-90% by weight of saccharose and 10-90% by weight of glucose.

公开(公告)号：US20190062758A1

公开(公告)日：2019-02-28

申请号：US15925301

申请日：2018-03-19

Applicant: Genomatica, Inc.

Inventor： Mark J. Burk ,  Stephen J. Van Dien ,  Anthony P. Burgard ,  Wei Niu

IPC: C12N15/52 ,  B01D3/00 ,  C12N15/70 ,  C12P17/04 ,  C12P7/52 ,  C12P7/42 ,  C12P7/18 ,  C12N9/00 ,  C12N9/88 ,  C12N9/02 ,  C12N9/04 ,  C12N15/81

Abstract: The invention provides a non-naturally occurring microbial biocatalyst including a microbial organism having a 4-hydroxybutanoic acid (4-HB) biosynthetic pathway having at least one exogenous nucleic acid encoding 4-hydroxybutanoate dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, or α-ketoglutarate decarboxylase, wherein the exogenous nucleic acid is expressed in sufficient amounts to produce monomeric 4-hydroxybutanoic acid (4-HB). Also provided is a non-naturally occurring microbial biocatalyst including a microbial organism having 4-hydroxybutanoic acid (4-HB) and 1,4-butanediol (BDO) biosynthetic pathways, the pathways include at least one exogenous nucleic acid encoding 4-hydroxybutanoate dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, 4-hydroxybutyrate:CoA transferase, 4-butyrate kinase, phosphotransbutyrylase, α-ketoglutarate decarboxylase, aldehyde dehydrogenase, alcohol dehydrogenase or an aldehyde/alcohol dehydrogenase, wherein the exogenous nucleic acid is expressed in sufficient amounts to produce 1,4-butanediol (BDO). Additionally provided is a method for the production of 4-HB. The method includes culturing a non-naturally occurring microbial organism having a 4-hydroxybutanoic acid (4-HB) biosynthetic pathway including at least one exogenous nucleic acid encoding 4-hydroxybutanoate dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase or α-ketoglutarate decarboxylase under substantially anaerobic conditions for a sufficient period of time to produce monomeric 4-hydroxybutanoic acid (4-HB). Further provided is a method for the production of BDO. The method includes culturing a non-naturally occurring microbial biocatalyst, comprising a microbial organism having 4-hydroxybutanoic acid (4-HB) and 1,4-butanediol (BDO) biosynthetic pathways, the pathways including at least one exogenous nucleic acid encoding 4-hydroxybutanoate dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, 4-hydroxybutyrate:CoA transferase, 4-hydroxybutyrate kinase, phosphotranshydroxybutyrylase, α-ketoglutarate decarboxylase, aldehyde dehydrogenase, alcohol dehydrogenase or an aldehyde/alcohol dehydrogenase for a sufficient period of time to produce 1,4-butanediol (BDO). The 4-HB and/or BDO products can be secreted into the culture medium.

公开(公告)号：US20190032095A1

公开(公告)日：2019-01-31

申请号：US16041271

申请日：2018-07-20

Applicant: Genomatica, Inc.

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

IPC: C12P7/44 ,  C12P7/24 ,  C12N9/10 ,  C12P9/00 ,  C12N9/02 ,  C07C51/43 ,  C12N9/12 ,  C08G63/183 ,  C12N9/88 ,  C12N9/04 ,  C12P7/62 ,  C07F9/09 ,  C12P7/40 ,  C07C63/26 ,  C07C63/04

Abstract: The invention provides non-naturally occurring microbial organisms having a (2-hydroxy-3-methyl-4-oxobutoxy)phosphonate (2H3M4OP) pathway, p-toluate pathway, and/or terephthalate pathway. The invention additionally provides methods of using such organisms to produce 2H3M4OP, p-toluate or terephthalate. Also provided herein are processes for isolating bio-based aromatic carboxylic acid, in particular, p-toluic acid or terephthalic acid, from a culture medium, wherein the processes involve contacting the culture medium with sufficient carbon dioxide (CO2) to lower the pH of the culture medium to produce a precipitate comprised of the aromatic carboxylic acid.

公开(公告)号：US20190010479A1

公开(公告)日：2019-01-10

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 ,  C12P7/16 ,  C07K16/40 ,  C12N15/82 ,  C08F36/06 ,  C12P5/02

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：US20180334690A1

公开(公告)日：2018-11-22

申请号：US15889788

申请日：2018-02-06

Applicant: Genomatica, Inc.

Inventor： Mark J. Burk ,  Christophe H. Schilling ,  Anthong P. Burgard ,  John D. Trawick

IPC: C12P7/18 ,  C12N9/10 ,  C12P19/32 ,  C12N9/02 ,  C12N9/00 ,  C12N15/70

CPC classification number: C12P7/18 ,  C12N9/0008 ,  C12N9/0036 ,  C12N9/1007 ,  C12N9/93 ,  C12N15/70 ,  C12P19/32 ,  Y02E50/343

Abstract: The invention provides a non-naturally occurring microbial organism having an acetyl-CoA pathway and the capability of utilizing syngas or syngas and methanol. In one embodiment, the invention provides a non-naturally occurring microorganism, comprising one or more exogenous proteins conferring to the microorganism a pathway to convert CO, CO2 and/or H2 to acetyl-coenzyme A (acetyl-CoA), methyl tetrahydrofolate (methyl-THF) or other desired products, wherein the microorganism lacks the ability to convert CO or CO2 and H2 to acetyl-CoA or methyl-THF in the absence of the one or more exogenous proteins. For example, the microbial organism can contain at least one exogenous nucleic acid encoding an enzyme or protein in an acetyl-CoA pathway. The microbial organism is capable of utilizing synthesis gases comprising CO, CO2 and/or H2, alone or in combination with methanol, to produce acetyl-CoA. The invention additionally provides a method for producing acetyl-CoA, for example, by culturing an acetyl-CoA producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an acetyl-CoA pathway enzyme or protein in a sufficient amount to produce acetyl-CoA, under conditions and for a sufficient period of time to produce acetyl-CoA.

公开(公告)号：US20180237847A1

公开(公告)日：2018-08-23

申请号：US15752884

申请日：2016-08-19

Applicant: GENOMATICA, INC.

Inventor： Stephanie CULLER ,  Ihsiung Brandon CHEN ,  Priti PHARKYA ,  Steve VAN DIEN ,  Nelson BARTON

IPC: C12Q1/6869 ,  C12N15/09 ,  C12N5/16 ,  A61K36/02 ,  A61K35/66 ,  A61K36/06 ,  C40B40/04

CPC classification number: C12Q1/6869 ,  A61K35/66 ,  A61K36/02 ,  A61K36/06 ,  A61K2236/15 ,  A61K2236/30 ,  C12N5/16 ,  C12N15/09 ,  C12N2330/50 ,  C12P19/34 ,  C12P21/02 ,  C40B40/04 ,  Y02A50/409 ,  Y02A50/469 ,  A61K35/12

Abstract: In alternative embodiments, provided herein are transcription/translation (TX-TL) systems and methods of using them for use as rapid prototyping platforms for the synthesis, modification and identification of natural products (NPs), and natural product analogs (NPAs) and secondary metabolites, from biosynthetic gene cluster pipelines. In alternative embodiments, exemplary TX-TL systems as provided herein are used for the combinatorial biosynthesis of natural products (NPs), natural product analogs (NPAs) and secondary metabolites. In alternative embodiments, exemplary TX-TL systems as provided herein are used for the rapid prototyping of complex biosynthetic pathways as a way to rapidly assess combinatorial and biosynthetic designs before moving to cellular hosts. In alternative embodiments, these exemplary TX-TL systems are multiplexed for high-throughput (HT) automation and for prototyping engineered platforms for the synthesis or modification of natural products (NPs), and natural product analogs (NPAs) and secondary metabolites analogs.

公开(公告)号：US10006055B2

公开(公告)日：2018-06-26

申请号：US14869872

申请日：2015-09-29

Applicant: Genomatica, Inc.

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

IPC: C12P7/04 ,  C12N15/52 ,  C12P5/02 ,  C12N15/70 ,  C12P7/16

CPC classification number: C12P7/04 ,  C12N15/52 ,  C12N15/70 ,  C12P5/026 ,  C12P7/16

Abstract: The invention provides non-naturally occurring microbial organisms having a butadiene or crotyl alcohol pathway. The invention additionally provides methods of using such organisms to produce butadiene or crotyl alcohol.