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    Microorganisms and methods for carbon-efficient biosynthesis of MEK and 2-butanol
    133.
    发明授权
    Microorganisms and methods for carbon-efficient biosynthesis of MEK and 2-butanol 有权
    微生物和MEK和2-丁醇的碳有效生物合成方法

    公开(公告)号：US08420375B2

    公开(公告)日：2013-04-16

    申请号：US12813469

    申请日：2010-06-10

    Applicant: Robin E. Osterhout ,  Wei Niu ,  Anthony P. Burgard

    Inventor： Robin E. Osterhout ,  Wei Niu ,  Anthony P. Burgard

    IPC: C12N1/20 ,  C12N1/00 ,  C12N9/00 ,  C12P7/26 ,  C12P7/16 ,  C12P21/06 ,  C07H21/04

    CPC classification number: C12P7/26 ,  C12N15/52 ,  C12P7/16 ,  Y02E50/10

    Abstract: A non-naturally occurring microbial organism has at least one exogenous nucleic acid encoding a MEK pathway enzyme expressed in a sufficient amount to produce MEK. The MEK pathway includes an enzyme selected from an acetoacetyl-CoA dehydrogenase (bifunctional), an acetoacetyl-CoA aldehyde dehydrogenase, a 3-oxobutyraldehyde reductase, a 3-oxobutanol dehydratase, an MEK oxidoreductase, a 3-oxobutyraldehyde aminotransferase, a 4-aminobutan-2-one deaminase, a 2-amino-4-ketopentanoate (AKP) thiolase, an AKP aminotransferase, a 2,4-dioxopentanoate decarboxylase, an AKP deaminase, an acetylacrylate decarboxylase, an AKP decarboxylase, a glutamate dehydrogenase, a 3-oxobutyraldehyde oxidoreductase (aminating) and an AKP oxidoreductase (aminating). A 2-butanol pathway further includes an MEK reductase. A method for producing MEK or 2-butanol includes culturing these organisms under conditions and for a sufficient period of time to produce MEK or 2-butanol.

    Abstract translation: 非天然存在的微生物有至少一种编码MEK途径酶的外源核酸，其表达量足以产生MEK。 MEK途径包括选自乙酰乙酰辅酶A脱氢酶（双功能），乙酰乙酰辅酶A醛脱氢酶，3-氧代丁醛还原酶，3-氧代丁醇脱水酶，MEK氧化还原酶，3-氧代丁醛氨基转移酶，4-氨基丁酸 -2-酮脱氨酶，2-氨基-4-酮戊酸酯（AKP）硫解酶，AKP氨基转移酶，2,4-二氧代戊酸脱羧酶，AKP脱氨酶，乙酰丙酸酯脱羧酶，AKP脱羧酶，谷氨酸脱氢酶， 氧化丁醛氧化还原酶（胺化）和AKP氧化还原酶（胺化）。 2-丁醇途径还包括MEK还原酶。 包括生产MEK或2-丁醇的方法包括在条件和足够的时间内培养这些生物体以产生MEK或2-丁醇。

    Microorganisms for Producing 1,3-Butanediol and Methods Related Thereto
    135.
    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：US20120329113A1

    公开(公告)日：2012-12-27

    申请号：US13528593

    申请日：2012-06-20

    Applicant: ANTHONY P. BURGARD ,  MARK J. BURK ,  ROBIN E. OSTERHOUT ,  JUN SUN ,  PRITI PHARKYA

    Inventor： ANTHONY P. BURGARD ,  MARK J. BURK ,  ROBIN E. OSTERHOUT ,  JUN SUN ,  PRITI PHARKYA

    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-BDO）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。

    Methods and organisms for utilizing synthesis gas or other gaseous carbon sources and methanol
    137.
    发明授权
    Methods and organisms for utilizing synthesis gas or other gaseous carbon sources and methanol 有权
    利用合成气或其他气态碳源和甲醇的方法和生物

    公开(公告)号：US08323950B2

    公开(公告)日：2012-12-04

    申请号：US13106764

    申请日：2011-05-12

    Applicant: Mark J. Burk ,  Christophe H. Schilling ,  Anthony P. Burgard ,  John D. Trawick

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

    IPC: C12N1/20 ,  C12N1/00 ,  C12P19/60 ,  C12P19/32 ,  C12P11/00 ,  C12P7/26 ,  C12P5/02 ,  C07H21/04

    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.

    Abstract translation: 本发明提供具有乙酰-CoA途径的非天然存在的微生物生物体，以及利用合成气或合成气和甲醇的能力。 在一个实施方案中，本发明提供非天然存在的微生物，其包含一种或多种外源蛋白质，赋予微生物将CO，CO 2和/或H 2转化为乙酰辅酶A（乙酰辅酶A），甲基四氢叶酸（甲基 -THF）或其它所需产物，其中微生物缺乏在不存在一种或多种外源蛋白的情况下将CO或CO 2和H 2转化为乙酰辅酶A或甲基-THF的能力。 例如，微生物生物体可以含有至少一种编码乙酰辅酶A途径中的酶或蛋白质的外源核酸。 微生物生物能够单独或与甲醇组合使用包含CO，CO 2和/或H 2的合成气体，以产生乙酰辅酶A。 本发明另外提供了生产乙酰辅酶A的方法，例如通过培养产生乙酰辅酶A的微生物，其中微生物生物体表达至少一种编码乙酰辅酶A途径酶或蛋白质的外源核酸，其量足够 在条件下和足够的时间内产生乙酰辅酶A产生乙酰辅酶A。

    MICROORGANISMS AND METHODS FOR THE BIOSYNTHESIS OF FUMARATE, MALATE, AND ACRYLATE
    138.
    发明申请
    MICROORGANISMS AND METHODS FOR THE BIOSYNTHESIS OF FUMARATE, MALATE, AND ACRYLATE 审中-公开
    富马酸和丙烯酸的生物合成的微生物和方法

    公开(公告)号：US20120237990A1

    公开(公告)日：2012-09-20

    申请号：US13372332

    申请日：2012-02-13

    Applicant: Mark J. BURK ,  Anthony P. Burgard ,  Priti Pharkya

    Inventor： Mark J. BURK ,  Anthony P. Burgard ,  Priti Pharkya

    IPC: C12P7/40 ,  C12N1/15 ,  C12N1/19

    CPC classification number: C12P7/46 ,  C12N9/88 ,  C12P7/40

    Abstract: A non-naturally occurring eukaryotic or prokaryotic organism includes one or more gene disruptions occurring in genes encoding enzymes imparting increased fumarate, malate or acrylate production in the organism when the gene disruption reduces an activity of the enzyme. The one or more gene disruptions confers increased production of acrylate onto the organism. Organisms that produce acrylate have an acrylate pathway that at least one exogenous nucleic acid encoding an acrylate pathway enzyme expressed in a sufficient amount to produce acrylate, the acrylate pathway comprising a decarboxylase. Methods of producing fumarate, malate or acrylate include culturing these organisms.

    Abstract translation: 非天然存在的真核生物或原核生物包括当基因破坏降低酶的活性时，编码在赋予生物体中增加的富马酸盐，苹果酸或丙烯酸酯产生的酶的基因中发生的一种或多种基因破坏。 一个或多个基因破坏使丙烯酸酯的生产增加到生物体上。 生产丙烯酸酯的生物体具有丙烯酸酯途径，至少一种编码丙烯酸酯途径酶的外源核酸以足够的量表达以产生丙烯酸酯，丙烯酸酯途径包含脱羧酶。 产生富马酸盐，苹果酸盐或丙烯酸盐的方法包括培养这些生物体。

    SYSTEMS AND METHODS FOR CONSTRUCTING GENOMIC-BASED PHENOTYPIC MODELS
    140.
    发明申请
    SYSTEMS AND METHODS FOR CONSTRUCTING GENOMIC-BASED PHENOTYPIC MODELS 有权
    用于构建基于基因的相位模型的系统和方法

    公开(公告)号：US20110231166A1

    公开(公告)日：2011-09-22

    申请号：US12947814

    申请日：2010-11-16

    Applicant: Christophe H. Schilling

    Inventor： Christophe H. Schilling

    IPC: G06G7/58 ,  G06F17/10

    CPC classification number: G06F19/12

    Abstract: The invention provides a computer implemented process for constructing a scalable output network model of a bioparticle. The process includes computer implemented steps of: (a) accessing a database of network gene components including an annotated network set of open reading frames (ORFs) of a bioparticle genome; (b) forming a data structure associating the network gene components with network reaction components, the data structure establishing a data set specifying a network model of connectivity and flow of the network reaction components, and (c) transforming the data set into a mathematical description of reactant fluxes defining the network model of connectivity and flow, wherein the mathematical description defines a scalable output network model of a bioparticle.

    Abstract translation: 本发明提供了一种用于构建生物颗粒的可伸缩输出网络模型的计算机实现过程。 该过程包括计算机实现的步骤：（a）访问网络基因组件的数据库，包括生物颗粒基因组的开放阅读框（ORF）的注释网络集合; （b）形成将网络基因组件与网络反应组件相关联的数据结构，数据结构建立指定网络反应组件的连通性和流程的网络模型的数据集，以及（c）将数据集变换为数学描述 反应物通量定义了连通性和流量的网络模型，其中数学描述定义了生物颗粒的可伸缩输出网络模型。

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