公开(公告)号：US20110195466A1

公开(公告)日：2011-08-11

申请号：US13088256

申请日：2011-04-15

Applicant: Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

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

IPC: C12P11/00 ,  C12N1/00 ,  C12P7/46

CPC classification number: C12N15/52 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/001 ,  C12N9/1029 ,  C12N9/1096 ,  C12N9/80 ,  C12N9/88 ,  C12P7/44 ,  C12P7/46 ,  C12P7/62 ,  C12P13/001 ,  C12P13/005 ,  C12P13/02 ,  C12P17/10 ,  C12Y101/01035 ,  C12Y102/0101 ,  C12Y103/01031 ,  C12Y206/01 ,  C12Y402/01

Abstract: The invention provides a non-naturally occurring microbial organism having an adipate, 6-aminocaproic acid or caprolactam pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in the respective adipate, 6-aminocaproic acid or caprolactam pathway. The invention additionally provides a method for producing adipate, 6-aminocaproic acid or caprolactam. The method can include culturing an adipate, 6-aminocaproic acid or caprolactam producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an adipate, 6-aminocaproic acid or caprolactam pathway enzyme in a sufficient amount to produce the respective product, under conditions and for a sufficient period of time to produce adipate, 6-aminocaproic acid or caprolactam.

Abstract translation: 本发明提供了具有己二酸，6-氨基己酸或己内酰胺途径的非天然存在的微生物。 微生物生物体含有至少一种编码相应己二酸，6-氨基己酸或己内酰胺途径中的酶的外源核酸。 本发明另外提供了生产己二酸，6-氨基己酸或己内酰胺的方法。 该方法可以包括培养己二酸，6-氨基己酸或己内酰胺生产微生物，其中微生物生物体表达至少一种编码己二酸，6-氨基己酸或己内酰胺途径酶的外源核酸，其量足以产生相应的产物 在条件下和足够的时间内生产己二酸，6-氨基己酸或己内酰胺。

公开(公告)号：US20110159572A1

公开(公告)日：2011-06-30

申请号：US12947790

申请日：2010-11-16

Applicant: Mark J. Burk ,  Anthony P. Burgard ,  Robin E. Osterhout ,  Jun Sun

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

IPC: C12N1/00

CPC classification number: C12P7/18 ,  B01D3/002 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/001 ,  C12N9/1029 ,  C12N9/1096 ,  C12N9/12 ,  C12N9/13 ,  C12N9/16 ,  C12N9/88 ,  C12N9/90 ,  C12N9/93 ,  C12N15/52 ,  C12N15/70 ,  C12N15/81 ,  C12Y101/01157 ,  C12Y402/01055

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. The invention additionally provides methods of using such microbial organisms to produce BDO.

Abstract translation: 本发明提供包含1,4-丁二醇（BDO）途径的非天然存在的微生物生物，该途径包含至少一种编码足够数量产生BDO的BDO途径酶的外源核酸。 本发明还提供了使用这种微生物生产BDO的方法。

公开(公告)号：US20110003344A1

公开(公告)日：2011-01-06

申请号：US12875068

申请日：2010-09-02

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: C12P19/32 ,  C12N1/00

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：US20090191593A1

公开(公告)日：2009-07-30

申请号：US12358217

申请日：2009-01-22

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: C12P19/60 ,  C12N1/00

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。

公开(公告)号：US20060147899A1

公开(公告)日：2006-07-06

申请号：US11188136

申请日：2005-07-21

Applicant: Imandokht Famili ,  Christophe Schilling

Inventor： Imandokht Famili ,  Christophe Schilling

IPC: C12Q1/00 ,  G06F19/00

CPC classification number: G06F19/12 ,  G01N33/5008 ,  G01N2500/10 ,  G06F19/18 ,  G06F19/28 ,  G06F19/704

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.