Codexis Patent Applications

PROTEIN VARIANT GENERATION BY REGION SHUFFLING

Granted: November 3, 2016
Application Number: 20160319273
Region shuffling methods for efficiently introducing diversity and exploring sequence space are described. Libraries produced directly from these methods contain high fractions of protein variants harboring multiple beneficial mutations. Typically, the methods produce these variants efficiently without the need for sequencing beneficial mutants identified at intermediate stages of the process.

METHOD OF DEMULSIFYING AND PURIFYING ORGANIC PRODUCTS FROM AN EMULSION

Granted: February 25, 2016
Application Number: 20160052846
This invention provides methods to demulsify organic products from emulsions, using demulsifying solvents which act as a combination of demulsifier and low volume extraction solvent. The methods can be applied to purify organic products such as fatty alcohols from emulsions including those generated from fermentation broths.

MODIFIED NATIVE BETA-KETOACYL-ACP SYNTHASES AND ENGINEERED MICROORGANISMS

Granted: January 14, 2016
Application Number: 20160010115
Genetically engineered cells and microorganisms are provided that produce fatty alcohols and fatty acids. In particular, engineered microbial cells comprise a modified native gene having ?-ketoacyl-acp synthase activity.

PRODUCTION OF FATTY ALCOHOLS FROM ENGINEERED MICROORGANISMS

Granted: June 25, 2015
Application Number: 20150176040
Recombinant microorganisms are provided which have been engineered to produce fatty alcohols. Also provided are recombinant microorganisms which comprise a heterologous polynucleotide encoding a fatty alcohol reductase enzyme and an introduced polynucleotide encoding a ?-ketoacyl acyl carrier protein synthase.

ENDOGLUCANASE 1B

Granted: December 4, 2014
Application Number: 20140356914
The present invention provides endoglucanase 1b (EG1b) suitable for use in saccharification reactions.

BIOCATALYSTS AND METHODS FOR THE SYNTHESIS OF SUBSTITUTED LACTAMS

Granted: November 20, 2014
Application Number: 20140342412
The present disclosure relates to transaminase polypeptides capable of aminating a dicarbonyl substrate, and polynucleotides, vectors, host cells, and methods of making and using the transaminase polypeptides.

DIRECT BIOCATALYTIC PRODUCTION OF ACRYLIC ACID AND OTHER CARBOXYLIC ACID COMPOUNDS

Granted: November 20, 2014
Application Number: 20140342414
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…

BETA-GLUCOSIDASE VARIANTS

Granted: September 11, 2014
Application Number: 20140256018
The invention relates to recombinantly produced ?-glucosidase variants with enhanced thermoactivity compared to naturally occurring proteins. The invention also provides methods for producing a variant ?-glucosidase polypeptide with improved thermoactivity by identifying performance sensitive positions in a target ?-glucosidase polypeptide and substituting the residue at that position with a thermoactivity enhancing residue.

METHOD OF GENERATING AN OPTIMIZED, DIVERSE POPULATION OF VARIANTS

Granted: September 11, 2014
Application Number: 20140256557
The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides.

METHODS, SYSTEMS, AND SOFTWARE FOR IDENTIFYING FUNCTIONAL BIO-MOLECULES

Granted: September 4, 2014
Application Number: 20140249035
The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of 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. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention…

PENTOSE FERMENTATION BY A RECOMBINANT MICROORGANISM

Granted: August 28, 2014
Application Number: 20140242674
The present invention provides recombinant nucleic acid constructs comprising a xylose isomerase polynucleotide, a recombinant fungal host cell comprising a recombinant xylose isomerase polynucleotide, and related methods.

BIOCATALYTIC PROCESS FOR PREPARING ESLICARBAZEPINE AND ANALOGS THEREOF

Granted: July 17, 2014
Application Number: 20140199735
The present disclosure relates to biocatalysts and its uses for the efficient preparation of eslicarbazepine, eslicarbazepine acetate, and analogs thereof.

USE OF GLYCOSIDE HYDROLASE 61 FAMILY PROTEINS IN PROCESSING OF CELLULOSE

Granted: July 3, 2014
Application Number: 20140186896
The invention provides recombinant GH61 proteins obtained from Myceliophtora thermophila, and nucleic acids that encode such proteins. The invention also provides protein fractions isolated from M. thermophila supernatant that have GH61 protein activity. These preparations can be used to increase yield of products from reactions in which a cellulose-containing substrate undergoes saccharification by one or more cellulase enzymes, such as endoglucanase, ?-glucosidase, or…

PENTOSE FERMENTATION BY A RECOMBINANT MICROORGANISM

Granted: May 8, 2014
Application Number: 20140127780
The present invention provides methods and compositions suitable for use in the conversion of xylose to xylitol and xylulose, including nucleic acid constructs, recombinant fungal host cells, and related materials.

RECOMBINANT THERMOASCUS AURANTIACUS BETA-GLUCOSIDASE VARIANTS FOR PRODUCTION OF FERMENTABLE SUGARS FROM CELLULOSIC BIOMASS

Granted: April 24, 2014
Application Number: 20140113352
The present invention provides compositions and methods for the expression of recombinant ?-glucosidase variants, as well as their use in the production of fermentable sugars from cellulosic biomass.

Production of Fatty Alcohols with Fatty Alcohol Forming Acyl-CoA Reductases (FAR)

Granted: April 10, 2014
Application Number: 20140099686
The disclosure relates to methods of producing fatty alcohols from recombinant host cells comprising genes encoding heterologous fatty acyl-CoA reductase (FAR) enzymes. The disclosure further relates to FAR enzymes and functional fragments thereof derived from marine bacterium and particularly marine gamma proteobacterium such as Marinobacter and Oceanobacter; polynucleotides encoding the FAR enzymes and vectors and host cells comprising the same.

Recombinant Beta-Glucosidase Variants for Production of Soluble Sugars from Cellulosic Biomass

Granted: March 6, 2014
Application Number: 20140065678
The invention relates to recombinant expression of a variant form of a fungal C1 strain ?-glucosidase. The invention also relates to the generation of fermentable sugars from biomass and the production of biofuels by fermentation of the sugars using genetically modified organisms expressing the ?-glucosidase variant. The invention provides methods for producing a fermentable sugar, such as glucose, from cellobiose by contacting cellobiose with a recombinant ?-glucosidase variant protein,…

FUNGAL BETA-XYLOSIDASE VARIANTS

Granted: February 20, 2014
Application Number: 20140051119
The present invention provides fungal xylanase and/or beta-xylosidase enzymes suitable for use in saccharification reactions. The present application further provides genetically modified fungal organisms that produce xylanase and/or beta-xylosidases, 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…

PENTOSE FERMENTATION BY A RECOMBINANT MICROORGANISM

Granted: January 16, 2014
Application Number: 20140017765
The present invention provides recombinant nucleic acid constructs comprising a xylose isomerase polynucleotide, a recombinant fungal host cell comprising a recombinant xylose isomerase polynucleotide, and related methods.

BETA-GLUCOSIDASE VARIANT ENZYMES AND RELATED POLYNUCLEOTIDES

Granted: January 2, 2014
Application Number: 20140004586
The invention provides variants of the Azospirillum irakense CelA ?-glucosidase that have improve ?-glucosidase activity, particularly improved thermoactivity, compared to the wild type enzyme. The invention further provides related polynucleotides, vectors, host cell, and methods for making and using the variants.