公开(公告)号：US20140017733A1

公开(公告)日：2014-01-16

申请号：US13914475

申请日：2013-06-10

申请人： Codexis, Inc.

发明人： Nicholas John Agard ,  David Elgart ,  Jie Yang ,  Goutami Banerjee ,  Jeanne Bonomo Benoit ,  Dipnath Baidyaroy

IPC分类号： C12P19/14

CPC分类号： C12P19/14 ,  C12N9/2402 ,  C12N9/248 ,  C12N9/2482 ,  C12P7/14 ,  C12P7/16 ,  C12P19/02 ,  C12Y302/01008 ,  C12Y302/01037 ,  Y02E50/16

摘要： The present invention provides fungal xylanase and/or xylosidase enzymes suitable for use in saccharification reactions. The present invention provides xylanase and xylosidase enzymes suitable for use in saccharification reactions. The present application further provides genetically modified fungal organisms that produce xylanase(s) and/or xylosidase(s), as well as enzyme mixtures exhibiting enhanced hydrolysis of cellulosic material to fermentable sugars, enzyme mixtures produced by the genetically modified fungal organisms, and methods for producing fermentable sugars from cellulose using such enzyme mixtures. In some embodiments, the xylanase and xylosidase enzyme(s) are M. thermophila enzymes.

摘要翻译： 本发明提供了适用于糖化反应的真菌木聚糖酶和/或木糖苷酶。 本发明提供适用于糖化反应的木聚糖酶和木糖酶。 本申请还提供了生产木聚糖酶和/或木糖苷酶的遗传修饰的真菌生物，以及表现出纤维素材料水解为可发酵糖的酶混合物，由遗传修饰的真菌生物体产生的酶混合物和方法 用于使用这种酶混合物从纤维素生产可发酵糖。 在一些实施方案中，木聚糖酶和木糖苷酶是嗜热嗜热乳杆菌酶。

公开(公告)号：US09684771B2

公开(公告)日：2017-06-20

申请号：US14167713

申请日：2014-01-29

申请人： Codexis, Inc.

发明人： Gregory Allan Cope ,  Nicholas John Agard

IPC分类号： G01N33/48 ,  G06F19/00 ,  G06F19/12 ,  G06F19/16 ,  G06F19/18 ,  G06G7/58 ,  C40B50/02

CPC分类号： C40B50/02 ,  C12N15/1058 ,  G06F19/12 ,  G06F19/16 ,  G06F19/18 ,  G06F19/701

摘要： The present invention provides methods for identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. More specifically, some embodiments of the present invention provide methods for building sequence-activity models comprising multiplicative terms and using the models to guide directed evolution. In some embodiments, the sequence-activity models include one or more interaction terms, each of which including an interaction coefficient representing the contribution to activity of two or more defined residues. In some embodiments, the models describe relation between protein or nucleic acid sequences and protein activities. In some embodiments, the present invention also provides methods for preparing sequence-activity models, including but not limited to stepwise addition or subtraction techniques, Bayesian regression, ensemble regression and other methods. The present invention further provides digital systems and software for performing the methods provided herein.

公开(公告)号：US20170204405A1

公开(公告)日：2017-07-20

申请号：US15479222

申请日：2017-04-04

申请人： Codexis, Inc.

发明人： Gregory Allan Cope ,  Nicholas John Agard

IPC分类号： C12N15/10 ,  G06F19/16 ,  G06F19/12

摘要： The present invention provides methods for identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. More specifically, some embodiments of the present invention provide methods for building sequence-activity models comprising multiplicative terms and using the models to guide directed evolution. In some embodiments, the sequence-activity models include one or more interaction terms, each of which including an interaction coefficient representing the contribution to activity of two or more defined residues. In some embodiments, the models describe relation between protein or nucleic acid sequences and protein activities. In some embodiments, the present invention also provides methods for preparing sequence-activity models, including but not limited to stepwise addition or subtraction techniques, Bayesian regression, ensemble regression and other methods. The present invention further provides digital systems and software for performing the methods provided herein.

公开(公告)号：US20160186222A1

公开(公告)日：2016-06-30

申请号：US15071414

申请日：2016-03-16

申请人： Codexis, Inc.

发明人： Nicholas John Agard ,  David Elgart ,  Jie Yang ,  Goutami Banerjee ,  Jeanne Bonomo Benoit ,  Dipnath Baidyaroy

IPC分类号： C12P19/14 ,  C12P7/14 ,  C12P7/16 ,  C12P19/02

CPC分类号： C12P19/14 ,  C12N9/2402 ,  C12N9/248 ,  C12N9/2482 ,  C12P7/14 ,  C12P7/16 ,  C12P19/02 ,  C12Y302/01008 ,  C12Y302/01037 ,  Y02E50/16

摘要： The present invention provides fungal xylanase and/or xylosidase enzymes suitable for use in saccharification reactions. The present invention provides xylanase and xylosidase enzymes suitable for use in saccharification reactions. The present application further provides genetically modified fungal organisms that produce xylanase(s) and/or xylosidase(s), as well as enzyme mixtures exhibiting enhanced hydrolysis of cellulosic material to fermentable sugars, enzyme mixtures produced by the genetically modified fungal organisms, and methods for producing fermentable sugars from cellulose using such enzyme mixtures. In some embodiments, the xylanase and xylosidase enzyme(s) are M. thermophila enzymes.

公开(公告)号：US08956844B2

公开(公告)日：2015-02-17

申请号：US13914475

申请日：2013-06-10

申请人： Codexis, Inc.

发明人： Nicholas John Agard ,  David Elgart ,  Jie Yang ,  Goutami Banerjee ,  Jeanne Bonomo Benoit ,  Dipnath Baidyaroy

IPC分类号： C12N1/00 ,  C12N9/24 ,  C07H21/04 ,  C12P19/14

CPC分类号： C12P19/14 ,  C12N9/2402 ,  C12N9/248 ,  C12N9/2482 ,  C12P7/14 ,  C12P7/16 ,  C12P19/02 ,  C12Y302/01008 ,  C12Y302/01037 ,  Y02E50/16

摘要： The present invention provides fungal xylanase and/or xylosidase enzymes suitable for use in saccharification reactions. The present invention provides xylanase and xylosidase enzymes suitable for use in saccharification reactions. The present application further provides genetically modified fungal organisms that produce xylanase(s) and/or xylosidase(s), as well as enzyme mixtures exhibiting enhanced hydrolysis of cellulosic material to fermentable sugars, enzyme mixtures produced by the genetically modified fungal organisms, and methods for producing fermentable sugars from cellulose using such enzyme mixtures. In some embodiments, the xylanase and xylosidase enzyme(s) are M. thermophila enzymes.

摘要翻译： 本发明提供了适用于糖化反应的真菌木聚糖酶和/或木糖苷酶。 本发明提供适用于糖化反应的木聚糖酶和木糖酶。 本申请还提供了生产木聚糖酶和/或木糖苷酶的遗传修饰的真菌生物，以及表现出纤维素材料水解为可发酵糖的酶混合物，由遗传修饰的真菌生物体产生的酶混合物和方法 用于使用这种酶混合物从纤维素生产可发酵糖。 在一些实施方案中，木聚糖酶和木糖苷酶是嗜热嗜热乳杆菌酶。

公开(公告)号：US20150125903A1

公开(公告)日：2015-05-07

申请号：US14597013

申请日：2015-01-14

申请人： Codexis, Inc.

发明人： Nicholas John Agard ,  David Elgart ,  Jie Yang ,  Goutami Banerjee ,  Jeanne Bonomo Benoit ,  Dipnath Baidyaroy

IPC分类号： C12P19/14 ,  C12P19/02 ,  C12N9/24

CPC分类号： C12P19/14 ,  C12N9/2402 ,  C12N9/248 ,  C12N9/2482 ,  C12P7/14 ,  C12P7/16 ,  C12P19/02 ,  C12Y302/01008 ,  C12Y302/01037 ,  Y02E50/16

摘要： The present invention provides fungal xylanase and/or xylosidase enzymes suitable for use in saccharification reactions. The present invention provides xylanase and xylosidase enzymes suitable for use in saccharification reactions. The present application further provides genetically modified fungal organisms that produce xylanase(s) and/or xylosidase(s), as well as enzyme mixtures exhibiting enhanced hydrolysis of cellulosic material to fermentable sugars, enzyme mixtures produced by the genetically modified fungal organisms, and methods for producing fermentable sugars from cellulose using such enzyme mixtures. In some embodiments, the xylanase and xylosidase enzyme(s) are M. thermophila enzymes.

摘要翻译： 本发明提供了适用于糖化反应的真菌木聚糖酶和/或木糖苷酶。 本发明提供适用于糖化反应的木聚糖酶和木糖酶。 本申请还提供了生产木聚糖酶和/或木糖苷酶的遗传修饰的真菌生物，以及表现出纤维素材料水解为可发酵糖的酶混合物，由遗传修饰的真菌生物体产生的酶混合物和方法 用于使用这种酶混合物从纤维素生产可发酵糖。 在一些实施方案中，木聚糖酶和木糖苷酶是嗜热嗜热乳杆菌酶。

公开(公告)号：US20140342414A1

公开(公告)日：2014-11-20

申请号：US14345495

申请日：2012-09-21

申请人： Codexis, Inc.

发明人： Fernando Valle ,  Nicholas John Agard ,  Christopher Noriega

IPC分类号： C12P7/40 ,  C12N9/16

CPC分类号： C12P7/40 ,  C12N9/16 ,  C12P7/42 ,  C12P2203/00 ,  C12Q1/6886 ,  C12Q2600/158 ,  C12Y301/02

摘要： The present disclosure relates to biocatalytic methods or processes for the synthesis of acrylic acid and its derivatives, or other carboxylic acid compounds of the formula R—CO2H, wherein R is a carbon chain of 5 carbons or fewer, such as methacrylic acid or 3-hydroxypropionic acid. More specifically, the disclosure relates to methods of using an acyl-CoA hydrolase (such as a thioesterase) as a biocatalyst for the hydrolysis (and removal of the CoA moiety) of a substrate acyl-CoA compound to produce the corresponding carboxylic acid compound, such as acrylic acid. In some embodiments, the disclosure provides non-naturally occurring microorganisms that have been transformed with a heterologous acyl-CoA hydrolase, such as a thioesterase, that is capable of hydrolyzing an acyl-CoA produced in a pathway of the microorganism and produce the corresponding carboxylic acid compound, thereby allowing methods for the direct fermentative production of the compound.

摘要翻译： 本公开涉及用于合成丙烯酸及其衍生物或式R-CO 2 H的其它羧酸化合物的生物催化方法或方法，其中R为5个或更少碳原子的碳链，例如甲基丙烯酸或3- 羟基丙酸。 更具体地，本公开涉及使用酰基-CoA水解酶（例如硫酯酶）作为生物催化剂用于底物酰基辅酶A化合物的水解（和除去CoA部分）以产生相应的羧酸化合物的方法， 如丙烯酸。 在一些实施方案中，本公开提供了已经用异源酰基辅酶A水解酶（例如硫酯酶）转化的非天然存在的微生物，其能够水解在微生物的途径中产生的酰基辅酶A并产生相应的羧酸 酸化合物，从而允许化合物的直接发酵生产的方法。

公开(公告)号：US20140221216A1

公开(公告)日：2014-08-07

申请号：US14167713

申请日：2014-01-29

申请人： Codexis, Inc.

发明人： Gregory Allan Cope ,  Nicholas John Agard

IPC分类号： G06F19/00

CPC分类号： C40B50/02 ,  C12N15/1058 ,  G06F19/12 ,  G06F19/16 ,  G06F19/18 ,  G06F19/701

摘要： The present invention provides methods for identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. More specifically, some embodiments of the present invention provide methods for building sequence-activity models comprising multiplicative terms and using the models to guide directed evolution. In some embodiments, the sequence-activity models include one or more interaction terms, each of which including an interaction coefficient representing the contribution to activity of two or more defined residues. In some embodiments, the models describe relation between protein or nucleic acid sequences and protein activities. In some embodiments, the present invention also provides methods for preparing sequence-activity models, including but not limited to stepwise addition or subtraction techniques, Bayesian regression, ensemble regression and other methods. The present invention further provides digital systems and software for performing the methods provided herein.

摘要翻译： 本发明提供了从复杂的生物分子文库或这些文库的集合中鉴定具有所需性质或最适合于获得这些性质的生物分子的方法。 更具体地，本发明的一些实施例提供了构建包括乘法术语的序列活动模型并使用该模型来指导定向进化的方法。 在一些实施方案中，序列活性模型包括一个或多个相互作用项，每个相互作用项包括表示两个或多个限定残基对活性的贡献的相互作用系数。 在一些实施方案中，模型描述蛋白质或核酸序列与蛋白质活性之间的关系。 在一些实施方案中，本发明还提供了制备序列活性模型的方法，包括但不限于逐步加法或减法技术，贝叶斯回归，整体回归和其他方法。 本发明还提供用于执行本文提供的方法的数字系统和软件。