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    MICROORGANISMS AND METHODS FOR THE PRODUCTION OF BUTADIENE USING ACETYL-COA
    1.
    发明申请
    MICROORGANISMS AND METHODS FOR THE PRODUCTION OF BUTADIENE USING ACETYL-COA 审中-公开
    使用乙酰辅酶A生产二倍体的微生物和方法

    公开(公告)号：WO2016007365A1

    公开(公告)日：2016-01-14

    申请号：PCT/US2015/038945

    申请日：2015-07-02

    Applicant: GENOMATICA, INC.

    Inventor： PHARKYA, Priti ,  BURGARD, Anthony, P. ,  BURK, Mark, J.

    IPC: C12N15/70 ,  C12P5/02 ,  C12N15/63 ,  C12N15/03

    CPC classification number: C12P5/026 ,  C01B3/00 ,  C08F36/06 ,  C08F36/14 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/0067 ,  C12N9/10 ,  C12N9/12 ,  C12N15/52 ,  C12P3/00 ,  C12P7/40 ,  C12Y101/02007 ,  C12Y101/03013 ,  C12Y102/99003 ,  Y02E50/343

    Abstract: The invention provides non-naturally occurring microbial organisms containing butadiene or 2,4- pentadienoate pathways comprising at least one exogenous nucleic acid encoding a butadiene or 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate. The organism can further contain a hydrogen synthesis pathway. The invention additionally provides methods of using such microbial organisms to produce butadiene or 2,4-pentadienoate by culturing a non-naturally occurring microbial organism containing butadiene or 2,4-pentadienoate pathways as described herein under conditions and for a sufficient period of time to produce butadiene or 2,4-pentadienoate. Hydrogen can be produced together with the production of butadiene or 2,4- pentadienoate.

    Abstract translation: 本发明提供了含有丁二烯或2,4-戊二烯酸通路的非天然存在的微生物生物，其包含至少一种编码丁二烯或2,4-戊二烯酸酯途径酶的外源核酸，其表达量足以产生丁二烯或2,4-戊二烯酸 。 生物体还可以含有氢合成途径。 本发明另外提供了使用这种微生物生物体来生产丁二烯或2,4-戊二烯酸盐的方法，其通过在条件和足够的时间段内培养含有本文所述的丁二烯或2,4-戊二烯酸酯途径的非天然存在的微生物生物 生产丁二烯或2,4-戊二烯酸。 可以与丁二烯或2,4-戊二烯酸2,4-二酮的生产一起生产氢。

    MICROORGANISM FOR PRODUCING PRIMARY ALCOHOLS AND RELATED COMPOUNDS AND METHODS RELATED THERETO
    3.
    发明申请
    MICROORGANISM FOR PRODUCING PRIMARY ALCOHOLS AND RELATED COMPOUNDS AND METHODS RELATED THERETO 审中-公开
    生产主要酒精的微生物及相关化合物及其相关方法

    公开(公告)号：WO2012177726A1

    公开(公告)日：2012-12-27

    申请号：PCT/US2012/043293

    申请日：2012-06-20

    Applicant: GENOMATICA, INC. ,  BURGARD, Anthony, P. ,  OSTERHOUT, Robin, E. ,  SUN, Jun ,  PHARKYA, Priti

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

    IPC: C12P5/02 ,  C12N15/74 ,  C12N1/00

    CPC classification number: C12P7/04 ,  C12N15/52 ,  C12P7/24 ,  C12P7/6409 ,  C12P7/6436

    Abstract: The invention provides a non-naturally occurring microbial organism having a microbial organism having at least one exogenous gene insertion and/or one or more gene disruptions that confer production of primary alcohols and at least one exogenous nucleic acid that encodes an enzyme that increases the yields of the primary alcohol by (i) enhancing carbon fixation via the reductive TCA cycle, and/or (ii) accessing additional reducing equivalents from gaseous carbon sources and/or syngas components such as CO, C02, and/or H2. A method for producing long chain alcohols includes culturing these non-naturally occurring microbial organisms.

    Abstract translation: 本发明提供了具有至少一种外源基因插入和/或一种或多种基因破坏的非天然存在的微生物生物体，所述基因破坏产生伯醇和至少一种编码增加产量的酶的外源核酸 通过（i）通过还原TCA循环增强碳固定，和/或（ii）从气态碳源和/或合成气组分如CO，CO 2和/或H 2获得另外的还原当量。 制备长链醇的方法包括培养这些非天然存在的微生物。

    MICROORGANISMS FOR PRODUCING 1,3-BUTANEDIOL AND METHODS RELATED THERETO
    4.
    发明申请
    MICROORGANISMS FOR PRODUCING 1,3-BUTANEDIOL AND METHODS RELATED THERETO 审中-公开
    用于生产1,3-丁二醇的微生物及其相关方法

    公开(公告)号：WO2012177619A2

    公开(公告)日：2012-12-27

    申请号：PCT/US2012/043117

    申请日：2012-06-19

    Applicant: GENOMATICA, INC. ,  BURGARD, Anthony, P. ,  BURK, Mark, J. ,  OSTERHOUT, Robin, E. ,  SUN, Jun ,  PHARKYA, Priti

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

    IPC: C12N1/21 ,  C12P7/18

    CPC classification number: C12P7/18 ,  C12N15/52

    Abstract: Provided herein is a non-naturally occurring microbial organism having a 1,3-butanediol (1,3 -BDO) pathway and comprising at least one exogenous nucleic acid encoding a 1,3 -BDO pathway enzyme expressed in a sufficient amount to produce 1,3 -BDO. In some embodiments, the pathway includes reducing equivalents from CO or hydrogen. In certain embodiments, a 1,3-BDO pathway proceeds by way of central metabolites pyruvate, succinate or alpha-ketoglutarate. Also provided herein is a method for producing 1,3-BDO, includes culturing such microbial organisms under conditions and for a sufficient period of time to produce 1,3-BDO.

    Abstract translation: 本文提供了具有1,3-丁二醇（1,3-BOD）途径的非天然存在的微生物生物，并且包含至少一种编码1,3 -BDO途径酶的外源核酸，其以足够的量表达以产生1 ，3 -BDO。 在一些实施方案中，该途径包括从CO或氢中还原当量。 在某些实施方案中，1,3-BDO途径通过中枢代谢物丙酮酸，琥珀酸或α-酮戊二酸进行。 本文还提供了一种生产1,3-BDO的方法，包括在条件和足够的时间内培养这些微生物以产生1,3-BDO。

    MICROORGANISMS FOR PRODUCING METHACRYLIC ACID AND METHACRYLATE ESTERS AND METHODS RELATED THERETO
    5.
    发明申请
    MICROORGANISMS FOR PRODUCING METHACRYLIC ACID AND METHACRYLATE ESTERS AND METHODS RELATED THERETO 审中-公开
    生产甲基丙烯酸和甲基丙烯酸酯的微生物及其相关方法

    公开(公告)号：WO2012135789A2

    公开(公告)日：2012-10-04

    申请号：PCT/US2012/031733

    申请日：2012-03-30

    Applicant: GENOMATICA, INC. ,  BURK, Mark, J. ,  BURGARD, Anthony, P. ,  OSTERHOUT, Robin, E. ,  SUN, Jun ,  PHARKYA, Priti

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

    IPC: C12P7/40

    CPC classification number: C12P7/40 ,  C12P7/42 ,  C12P7/62 ,  C12P19/32

    Abstract: The invention provides a non-naturally occurring microbial organism having a methacrylic acid, methacrylate ester, 3-hydroxyisobutyrate and/or 2-hydroxyisobutyrate pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in a methacrylic acid pathway. The invention additionally provides a method for producing methacrylic acid, methacrylate ester, 3-hydroxyisobutyrate and/or 2- hydroxyisobutyrate. The method can include culturing methacrylic acid, methacrylate ester, 3-hydroxyisobutyrate and/or 2-hydroxyisobutyrate producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding a methacrylic acid pathway enzyme in a sufficient amount to produce methacrylic acid, methacrylate ester, 3-hydroxyisobutyrate and/or 2-hydroxyisobutyrate, under conditions and for a sufficient period of time to produce methacrylic acid, methacrylate ester, 3-hydroxyisobutyrate and/or 2-hydroxyisobutyrate.

    Abstract translation: 本发明提供具有甲基丙烯酸，甲基丙烯酸酯，3-羟基异丁酸酯和/或2-羟基异丁酸酯途径的非天然存在的微生物生物。 微生物生物体含有编码甲基丙烯酸途径中的酶的至少一种外源核酸。 本发明另外提供了生产甲基丙烯酸，甲基丙烯酸酯，3-羟基异丁酸酯和/或2-羟基异丁酸酯的方法。 该方法可以包括培养产生甲基丙烯酸，甲基丙烯酸酯，3-羟基异丁酸酯和/或2-羟基异丁酸酯的微生物，其中微生物生物体表达至少一种编码甲基丙烯酸途径酶的外源核酸，其量足以产生甲基丙烯酸， 甲基丙烯酸酯，3-羟基异丁酸酯和/或2-羟基异丁酸酯在条件下和足够的时间以产生甲基丙烯酸，甲基丙烯酸酯，3-羟基异丁酸酯和/或2-羟基异丁酸酯。

    ORGANISMS FOR THE PRODUCTION OF CYCLOHEXANONE
    7.
    发明申请
    ORGANISMS FOR THE PRODUCTION OF CYCLOHEXANONE 审中-公开
    生产环己酮的有机体

    公开(公告)号：WO2010132845A1

    公开(公告)日：2010-11-18

    申请号：PCT/US2010/035015

    申请日：2010-05-14

    Applicant: GENOMATICA, INC. ,  OSTERHOUT, Robin, E. ,  BURGARD, Anthony, P. ,  BURK, Mark, J. ,  PHARKYA, Priti

    Inventor： OSTERHOUT, Robin, E. ,  BURGARD, Anthony, P. ,  BURK, Mark, J. ,  PHARKYA, Priti

    IPC: A61K48/00 ,  C07C49/00

    CPC classification number: C12P7/26 ,  C12N9/16 ,  C12N9/88 ,  C12N9/93 ,  C12N15/52 ,  C12N15/70

    Abstract: A non-naturally occurring microbial organism has cyclohexanone pathways that include at least one exogenous nucleic acid encoding a cyclohexanone pathway enzyme. A pathway includes a 2-ketocyclohexane-1 -carboxyl-CoA hydrolase (acting on C-C bond), a 2-ketocyclohexane-l- carboxylate decarboxylase and an enzyme selected from a 2-ketocyclohexane-l-carboxyl-CoA hydrolase (acting on thioester), a 2-ketocyclohexane-l -carboxyl-CoA transferase, and a 2- ketocyclohexane-1-carboxyl-CoA synthetase. A pathway includes an enzyme selected from a 6- ketocyclohex-1-ene-l-carboxyl-CoA hydrolase (acting on C-C bond), a 6-ketocyclohex- 1 -ene- 1 - carboxyl-CoA synthetase, a 6-ketocyclohex-l-ene-l-carboxyl-CoA hydrolase (acting on thioester), a 6-ketocyclohex- 1 -ene- 1 -carboxyl-CoA transferase, a 6-ketocyclohex- 1 -ene- 1 - carboxyl-CoA reductase, a 6-ketocyclohex- 1 -ene- 1 -carboxylate decarboxylase, a 6- ketocyclohex-1 -ene- 1 -carboxylate reductase, a 2-ketocyclohexane-l-carboxyl-CoA synthetase, a 2-ketocyclohexane-l -carboxyl-CoA transferase, a 2-ketocyclohexane-l-carboxyl-CoA hydrolase (acting on thioester), a 2-ketocyclohexane-l -carboxylate decarboxylase, and a cyclohexanone dehydrogenase. A pathway includes an adipate semialdehyde dehydratase, a cyclohexane-1,2- diol dehydrogenase, and a cyclohexane-l,2-diol dehydratase. A pathway includes a 3- oxopimelate decarboxylase, a 4-acetylbutyrate dehydratase, a 3-hydroxycyclohexanone dehydrogenase, a 2-cyclohexenone hydratase, a cyclohexanone dehydrogenase and an enzyme selected from a 3-oxopimeloyl-CoA synthetase, a 3-oxopimeloyl-CoA hydrolase (acting on thioester), and a 3-oxopimeloyl-coA transferase. Each these pathways can include a PEP carboxykinase. A method for producing cyclohexanone includes culturing these non-naturally occurring microbial organisms.

    Abstract translation: 非天然存在的微生物有机体具有包含至少一种编码环己酮途径酶的外源核酸的环己酮途径。 途径包括2-酮环己烷-1-羧基-CoA水解酶（作用于CC键），2-酮环己烷-1-羧酸脱羧酶和选自2-酮环己烷-1-羧基-CoA水解酶（酶作用于硫酯） ），2-酮环己烷-1-羧基-CoA转移酶和2-酮环己烷-1-羧基-CoA合成酶。 途径包括选自6-酮环己-1-烯-1-羧基-CoA水解酶（作用于CC键）的酶，6-酮环己-1-烯-1-羧基-CoA合成酶，6-酮环己基 - 1-烯-1-羧基-CoA水解酶（作用于硫酯），6-酮环己-1-烯-1-羧基-CoA转移酶，6-酮环己-1-烯-1-羧基-CoA还原酶，6 2-环己-1-烯-1-羧酸脱羧酶，6-酮环己-1-烯-1-羧酸还原酶，2-酮环己烷-1-羧基-CoA合成酶，2-酮环己烷-1-羧基-CoA转移酶， 2-酮环己烷-1-羧基-CoA水解酶（作用于硫酯），2-酮环己烷-1-羧酸脱羧酶和环己酮脱氢酶。 途径包括己二酸半醛脱水酶，环己烷-1,2-二醇脱氢酶和环己烷-1,2-二醇脱水酶。 途径包括3-氧代庚酸酯脱羧酶，4-乙酰基丁酸脱水酶，3-羟基环己酮脱氢酶，2-环己烯酮水合酶，环己酮脱氢酶和选自3-氧代木糖酰辅酶A合成酶，3-氧代木糖酰-CoA水解酶 （作用于硫酯）和3-氧代木糖酰辅酶A转移酶。 每个这些途径可以包括PEP羧基激酶。 生产环己酮的方法包括培养这些非天然存在的微生物。

    METHANOL DEHYDROGENASE FUSION PROTEINS
    8.
    发明申请
    METHANOL DEHYDROGENASE FUSION PROTEINS 审中-公开
    甲醇脱氢酶融合蛋白

    公开(公告)号：WO2017075208A1

    公开(公告)日：2017-05-04

    申请号：PCT/US2016/059096

    申请日：2016-10-27

    Applicant: GENOMATICA, INC.

    Inventor： BARTON, Nelson R. ,  LI, Jingyi ,  WARNER, Joseph R. ,  PHARKYA, Priti

    IPC: C07K14/195 ,  C12N15/62 ,  C12N5/00

    CPC classification number: C12Y503/01027 ,  C07K2319/00 ,  C12N9/0006 ,  C12N9/88 ,  C12N9/90 ,  C12N15/52 ,  C12Y401/02043

    Abstract: Described herein are fusion proteins including methanol dehydrogenase (MeDH) and at least one other polypeptide such as 3-hexulose-6-phosphate dehydrogenase (HPS) or 6-phospho-3-hexuloisomerase (PHI), such as DHAS synthase or fructose-6-Phosphate aldolase or such as DHA synthase or DHA kinase. In a localized manner, the fusion protein can promote the conversion of methanol to formaldehyde and then to a ketose phosphate such as hexulose 6-phosphate or then to DHA and G3P. When expressed in cells, the fusion proteins can promote methanol uptake and rapid conversion to the ketose phosphate or to the DHA and D3P, which in turn can be used in a pathway for the production of a desired bioproduct. Beneficially, the rapid conversion to the ketose phosphate or to the DHA and G3P can avoid the undesirable accumulation of formaldehyde in the cell. Also described are engineered cells expressing the fusion protein, 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.

    Abstract translation: 本文描述了融合蛋白，其包括甲醇脱氢酶（MeDH）和至少一种其他多肽如3-己酮糖-6-磷酸脱氢酶（HPS）或6-磷酸-3-己酮糖异构酶（PHI）， 如DHAS合酶或果糖-6-磷酸醛缩酶或例如DHA合酶或DHA激酶。 以局部方式，融合蛋白可以促进甲醇转化为甲醛，然后转化为磷酸酮糖如己酮糖6-磷酸，然后转化为DHA和G3P。 当在细胞中表达时，融合蛋白可以促进甲醇吸收并快速转化为磷酸酮糖或DHA和D3P，其又可用于生产期望的生物产品的途径中。 有利的是，快速转化为磷酸酮糖或DHA和G3P可以避免细胞中不希望的甲醛累积。 还描述了表达融合蛋白的工程细胞，任选地包括一种或多种另外的代谢途径转基因，甲醇代谢途径基因，靶产物途径基因，包括细胞的细胞培养组合物，用于促进目标产物或中间产物生成的方法 包括目标产物或中间体的组合物，以及由目标产物或中间体制备的产物。

    ALCOHOL DEHYDROGENASE VARIANTS
    10.
    发明申请
    ALCOHOL DEHYDROGENASE VARIANTS 审中-公开
    酒精脱水变异

    公开(公告)号：WO2015051298A2

    公开(公告)日：2015-04-09

    申请号：PCT/US2014/059135

    申请日：2014-10-03

    Applicant: GENOMATICA, INC.

    Inventor： ANDRAE, Stefan ,  KUCHINSKAS, Michael Patrick ,  LI, Jingyi ,  NAGARAJAN, Harish ,  PHARKYA, Priti

    IPC: C12P7/16 ,  C12N1/21

    CPC classification number: C12N9/0006 ,  C12P7/18 ,  C12P7/24 ,  C12Y101/01001 ,  C12Y101/01244 ,  Y02P20/127

    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.

    Abstract translation: 本文描述了与其未修饰的对应物相比，能够分别甲醇或乙醇转化为甲醛或乙醛的至少两倍的非天然NAD +依赖性醇脱氢酶（ADH）。 描述了编码非天然醇脱氢酶的核酸，以及包含核酸的表达构建体和包含核酸或表达构建体的工程化细胞。 还描述了表达非天然NAD +依赖性醇脱氢酶的工程细胞，任选地包括一种或多种另外的代谢途径转基因，甲醇代谢途径基因，靶产物途径基因，包括细胞的细胞培养组合物，促进生产的方法 的靶产物或其中间体，包括靶产物或中间体的组合物，以及由目标产物或中间体制成的产品。

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