Abstract: The invention provides biocatalytic methods for the manufacture of pure single enantiomer compounds. This invention provides methods of screening for enzymes which are highly enantioselective or enzymes that can provide any desired stereoisomer of a compound. The invention provides the use of single enantiomer substrates in performing a growth screen of a clonal library to identify highly stereoselective enzymes. In one aspect, methods for screening and identification of enzymes, e.g., transaminases, nitrilases, aldolases, epoxide hydrolases are provided. Methods for the production and screening of gene libraries generated from nucleic acids isolated from more than one organism for enzyme, e.g., transaminase, activities are also provided.
Type:
Grant
Filed:
June 21, 2002
Date of Patent:
July 19, 2011
Assignee:
Verenium Corporation
Inventors:
David Weiner, Tim Hitchman, Lishan Zhao, Mark J. Burk, Grace Desantis, Sarah Richardson Hanson, Aileen Milan, Toby Richardson, Patti Kretz, William Greenberg
Abstract: In one aspect, the invention is directed to polypeptides having an amylase activity, polynucleotides encoding the polypeptides, and methods for making and using these polynucleotides and polypeptides. In one aspect, the polypeptides of the invention can be used as amylases, for example, alpha amylases, to catalyze the hydrolysis of starch into sugars. In one aspect, the invention provides delayed release compositions comprising an desired ingredient coated by a latex polymer coating.
Type:
Application
Filed:
June 24, 2010
Publication date:
July 14, 2011
Applicant:
VERENIUM CORPORATION
Inventors:
WALTER CALLEN, TOBY RICHARDSON, GERHARD FREY, KEVIN A. GRAY, JANNE S. KEROVUO, MALGORZATA SLUPSKA, NELSON R. BARTON, EILEEN O'DONOGHUE, CARL MILLER
Abstract: The invention provides novel polypeptides having phospholipase activity, including, e.g., phospholipase A, B, C and D activity, patatin activity, phosphatidic acid phosphatases (PAP)) and/or lipid acyl hydrolase (LAH) activity, nucleic acids encoding them and antibodies that bind to them. Industrial methods, e.g., oil degumming, and products comprising use of these phospholipases are also provided.
Type:
Grant
Filed:
March 8, 2005
Date of Patent:
July 12, 2011
Assignee:
Verenium Corporation
Inventors:
Svetlana Gramatikova, Geoff Hazlewood, David Lam, Nelson R. Barton, Blake G. Sturgis, Dan E. Robertson, Jincai Li, Joel A. Kreps, Roderick James Fielding, Robert C. Brown, Amit Vasavada, Xuqiu Tan, Adrian Badillo, Wilhelmus P. Van Hoek, Giselle Janssen, Charles Isaac, Mark J. Burk
Abstract: A method for producing progeny polynucleotides and polypeptides by Gene Site Saturation Mutagenesis (GSSM). The method provides a set of degenerate primers corresponding to codons of a template polynucleotide, and performs polymerase elongation to produce progeny polynucleotides, which contain sequences corresponding to the degenerate primers. The progeny polynucleotides can be expressed and screened for directed evolution.
Abstract: The invention relates to polypeptides having glucanase, e.g., endoglucanase, mannanase, xylanase activity or a combination of these activities, and polynucleotides encoding them. In one aspect, the glucanase activity is an endoglucanase activity (e.g., endo-1,4-beta-D-glucan 4-glucano hydrolase activity) and comprises hydrolysis of 1,4-beta-D-glycosidic linkages in cellulose, cellulose derivatives (e.g., carboxy methyl cellulose and hydroxy ethyl cellulose) lichenin, beta-1,4 bonds in mixed beta-1,3 glucans, such as cereal beta-D-glucans or xyloglucans and other plant material containing cellulosic parts. In addition, methods of designing new enzymes and methods of use thereof are also provided. In alternative aspects, the new glucanases e.g., endoglucanases, mannanases, xylanases have increased activity and stability at increased pH and temperature.
Type:
Grant
Filed:
July 2, 2004
Date of Patent:
June 14, 2011
Assignees:
Verenium Corporation, Syngenta Participations AG
Inventors:
Brian Steer, Walter Callen, Shaun Healey, Derrick Pulliam
Abstract: The invention provides novel polypeptides having phospholipase activity, including, e.g., phospholipase A, B, C and D activity, patatin activity, lipid acyl hydrolase (LAH) activity, nucleic acids encoding them and antibodies that bind to them. Industrial methods, e.g., oil degumming, and products comprising use of these phospholipases are also provided.
Type:
Grant
Filed:
January 22, 2007
Date of Patent:
May 17, 2011
Assignee:
Verenium Corporation
Inventors:
Svetlana Gramatikova, Geoff Hazlewood, David Lam, Nelson R. Barton, Blake G. Sturgis, Dan E. Robertson, Jincai Li, Joel A. Kreps, Roderick James Fielding, Robert C. Brown, Amit Vasavada, Xuqiu Tan, Adrian Badillo, Wilhelmus P. Van Hoek, Giselle Janssen, Charles Isaac, Mark J. Burk
Abstract: The invention provides novel processes for making ethyl-4-cyano-3-hydroxybutyrate, e.g., (R)-ethyl 4-cyano-3-hydroxybutyric acid, and 4-cyano-3-hydroxybutyric acid. The invention provides protocols for making and 4-cyano-3-hydroxybutyric acid and ethyl-4-cyano-3-hydroxybutyrate by whole cell processes, cell lysate processes, “one pot processes” and “multi-pot” processes using a variety of parameters.
Type:
Grant
Filed:
June 13, 2003
Date of Patent:
April 26, 2011
Assignee:
Verenium Corporation
Inventors:
Mark J. Burk, Grace Desantis, Brian Morgan, Zoulin Zhu
Abstract: The invention provides novel polypeptides having phospholipase activity, including, e.g., phospholipase A, B, C and D activity, patatin activity, phosphatidic acid phosphatases (PAP) and/or lipid acyl hydrolase (LAH) activity, nucleic acids encoding them and antibodies that bind to them. Industrial methods, e.g., oil degumming, and products comprising use of these phospholipases are also provided.
Abstract: In one aspect, the invention is directed to polypeptides having an amylase activity, polynucleotides encoding the polypeptides, and methods for making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used as amylases to catalyze the hydrolysis of starch into sugars.
Type:
Application
Filed:
April 7, 2010
Publication date:
March 31, 2011
Applicant:
VERENIUM CORPORATION
Inventors:
Kevin A. Gray, Nahla Aboushadi, James B. Garrett
Abstract: A treatment system and process is described herein to separate constituent parts from aqueous-based products or by-products, such as wastewater from a cellulosic ethanol process. The treatment system may include an ultrafiltration system, a first reverse osmosis system and a second reverse osmosis system. The treatment system may be configured to operate in modified batch mode.
Abstract: This invention relates generally to enzymes, polynucleotides encoding the enzymes, the use of such polynucleotides and polypeptides and more specifically to enzymes having isomerase activity, e.g., racemase activity, e.g., amino acid racemase activity, alanine racemase activity, and/or epimerase activity, and/or catalyze the re-, arrangement of atoms within a molecule, catalyze the conversion of one isomer into another, catalyze the conversion of an optically active substrate into a raceme, which is optically inactive, catalyze the interconversion of substrate enantiomers, catalyze the stereochemical inversion around the asymmetric carbon atom in a substrate having only one center of asymmetry, catalyze the stereochemical inversion of the configuration around an asymmetric carbon atom in a substrate having more than one asymmetric center, and/or catalyze the racemization of amino acids.
Type:
Application
Filed:
December 22, 2008
Publication date:
March 3, 2011
Applicant:
VERENIUM CORPORATION
Inventors:
David P. Weiner, Peter Luginbuhl, Analia Bueno, Joslin M. Cuenca, Mervyn L. De Souza, Sherry Kollmann
Abstract: This invention relates generally to enzymes, polynucleotides encoding the enzymes, the use of such polynucleotides and polypeptides and more specifically to enzymes having transferase activity, e.g., transaminase activity, e.g., d-amino-acid transferase activity, and/or oxidoreductase activity, e.g., dehydrogenase activity, e.g., damino-acid dehydrogenase activity, and/or catalyze the transfer of a chemical group, catalyze transamination, catalyze the reaction: D-alanine+2-oxoglutarate<=>pyruvate+D-glutamate, and/or catalyze an oxidation-reduction reaction, catalyze the removal of hydrogen atoms, and/or catalyze the reaction: D-amino acid+H2O+acceptor<=>a 2-oxo acid+NH3+reduced acceptor.
Type:
Application
Filed:
December 31, 2008
Publication date:
February 10, 2011
Applicant:
VERENIUM CORPORATION
Inventors:
David P. Weiner, Peter Luginbuhl, Analia Bueno, Joslin M. Cuenca, Erin Marasco
Abstract: This invention provides polypeptides having lyase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides having ammonia lyase activity, e.g., phenylalanine ammonia lyase, tyrosine ammonia lyase and/or histidine ammonia lyase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural and industrial contexts.
Type:
Application
Filed:
May 29, 2007
Publication date:
February 3, 2011
Applicant:
VERENIUM CORPORATION
Inventors:
David Weiner, Alexander Varvak, Toby Richardson, Mircea Podar, Ellen Burke, Shaun Healey
Abstract: The invention relates to enzymes having xylanase, mannanase and/or glucanase activity, e.g., catalyzing hydrolysis of internal ?-1,4-xylosidic linkages or endo-?-1,4-glucanase linkages; and/or degrading a linear polysaccharide beta-1,4-xylan into xylose. Thus, the invention provides methods and processes for breaking down hemicellulose, which is a major component of the cell wall of plants, including methods and processes for hydrolyzing hemicelluloses in any plant or wood or wood product, wood waste, paper pulp, paper product or paper waste or byproduct. In addition, methods of designing new xylanases, mannanases and/or glucanases and methods of use thereof are also provided. The xylanases, mannanases and/or glucanases have increased activity and stability at increased pH and temperature.
Abstract: The invention provides a purified, isolated, synthetic or recombinant phytase enzyme (e.g., SEQ ID NO:2) initially derived from Escherichia coli B. The enzyme has a molecular weight of about 47.1 kilodaltons and has phytase activity (SEQ ID NO:2). The enzyme can be produced from native or recombinant host cells and can be used to aid in the digestion of phytate where desired. In particular, the phytase of the present invention can be used in foodstuffs to improve the feeding value of phytate rich ingredients.
Abstract: The invention provides isolated and recombinant phytase enzymes. In one aspect, the phytases are produced by modification of the wild type appA of E. coli. The enzyme can be produced from recombinant host cells. The phytases of the invention can be used to aid in the digestion of phytate where desired. In particular, the phytases of the invention can be used in foodstuffs to improve the feeding value of phytate rich ingredients. The phytases of the invention can be thermotolerant and/or thermostable. Also provided are methods for obtaining a variant polynucleotide encoding a phytase and for obtaining a phytase with thermostability or thermotolerant at high or low temperatures.
Type:
Grant
Filed:
October 31, 2007
Date of Patent:
November 2, 2010
Assignee:
Verenium Corporation
Inventors:
Jay M. Short, Kevin A. Gray, Nelson R. Barton, James B. Garrett, Eileen O'Donoghue, Dan E. Robertson
Abstract: The invention relates to nitrilases and to nucleic acids encoding the nitrilases. In addition methods of designing new nitrilases and method of use thereof are also provided. The nitrilases have increased activity and stability at increased pH and temperature.
Type:
Application
Filed:
February 29, 2008
Publication date:
October 28, 2010
Applicant:
VERENIUM CORPORATION
Inventors:
Grace DeSantis, Jennifer Chaplin, Ellen Chi, Aileen Milan, Jay Short, David Weiner, Mark Madden, Darcy Madden, Dan Robertson
Abstract: The invention provides laccases, polynucleotides encoding these enzymes, the methods of making and using these polynucleotides and polypeptides.
Type:
Application
Filed:
April 21, 2010
Publication date:
October 21, 2010
Applicant:
VERENIUM CORPORATION
Inventors:
Tim Hitchman, Dan E. Robertson, Masao Hiraiwa, Yoko Phillips, Kevin A. Gray
Abstract: The invention relates to nitrilases and to nucleic acids encoding the nitrilases. In addition methods of designing new nitrilases and method of use thereof are also provided. The nitrilases have increased activity and stability at increased pH and temperature.
Type:
Grant
Filed:
September 9, 2009
Date of Patent:
October 12, 2010
Assignee:
Verenium Corporation
Inventors:
Grace DeSantis, Jay Short, Mark Burk, Kelvin Wong, Kelly Chatman, Bob Farwell
Abstract: A thermostable glycosidase enzymes derived from various Thermococcus, Staphylothermus and Pyrococcus organisms is disclosed. The enzymes are produced from native or recombinant host cells and can be utilized in the food processing industry, pharmaceutical industry and in the textile industry, detergent industry and in the baking industry.
Type:
Grant
Filed:
October 2, 2007
Date of Patent:
October 5, 2010
Assignee:
Verenium Corporation
Inventors:
Edward J. Bylina, Ronald Swanson, Eric Mathur, David E. Lam