Optimization of crossover points for directed evolution
Granted: July 17, 2012
Patent Number:
8224580
Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and…
Production of fatty alcohols with fatty alcohol forming acyl-CoA reductases (FAR)
Granted: July 10, 2012
Patent Number:
8216815
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.
Endoglucanases
Granted: June 26, 2012
Patent Number:
8206960
The present invention relates to variant endoglucanases and particularly endoglucanases having improved properties over wild-type endoglucanase.
Recombinant halohydrin dehalogenase polypeptides
Granted: May 29, 2012
Patent Number:
8187856
The present disclosure provides engineered halohydrin dehalogenase (HHDH) polypeptides having improved enzyme properties as compared to the wild-type HHDH enzyme HheC and other reference engineered HHDH polypeptides. Also provided are polynucleotides encoding the engineered HHDH enzymes, host cells capable of expressing the engineered HHDH enzymes, and methods of using the engineered HHDH enzymes to synthesize a variety of chiral compounds including chiral epoxides and chiral alcohols.
Biocatalytic processes for the preparation of substantially stereomerically pure fused bicyclic proline compounds
Granted: May 15, 2012
Patent Number:
8178333
The present disclosure provides monoamine oxidase enzymes and methods of their use in biocatalytic processes for the preparation of substantially enantiomerically pure heterobicyclic compounds of the following structural formulas, wherein A, M, M?, and R5 are as described herein.
Methods of populating data structures for use in evolutionary simulations
Granted: May 1, 2012
Patent Number:
8170806
In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the…
Recombinant ?-glucosidase variants for production of soluble sugars from cellulosic biomass
Granted: March 27, 2012
Patent Number:
8143050
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,…
Optimization of crossover points for directed evolution
Granted: January 31, 2012
Patent Number:
8108150
Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and…
Halohydrin dehalogenases and related polynucleotides
Granted: January 24, 2012
Patent Number:
8101395
The present invention relates to novel halohydrin dehalogenase polypeptides and the polynucleotides that encode them. These polypeptides are useful in the production of 4-substituted-3-butyric acid derivatives and vicinal cyano, hydroxyl substituted carboxylic acid esters. The invention also provides related vectors, host cells and methods.
Ketoreductases for the production of (S,E)-methyl 2-(3-(3-(2-(7-chloroquinolin-2-yl)vinyl)phenyl)-3-hroxypropyl)benzoate
Granted: January 3, 2012
Patent Number:
8088610
The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize a variety of chiral compounds.
Endoglucanases
Granted: January 3, 2012
Patent Number:
8088608
The present invention relates to variant endoglucanases and particularly endoglucanases having improved properties over wild-type endoglucanase.
Evolution of whole cells and organisms by recursive sequence recombination
Granted: December 13, 2011
Patent Number:
8076138
The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.
Ketoreductases and uses thereof
Granted: December 6, 2011
Patent Number:
8071347
The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize a variety of chiral compounds.
Oligonucleotide mediated nucleic acid recombination
Granted: November 15, 2011
Patent Number:
8058001
Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.
Methods and compositions for cellular and metabolic engineering
Granted: November 1, 2011
Patent Number:
8048674
The present invention is generally directed to the evolution of new metabolic pathways and the enhancement of bioprocessing through a process herein termed recursive sequence recombination. Recursive sequence recombination entails performing iterative cycles of recombination and screening or selection to “evolve” individual genes, whole plasmids or viruses, multigene clusters, or even whole genomes. Such techniques do not require the extensive analysis and computation required by…
Oligonucleotide mediated nucleic acid recombination
Granted: October 4, 2011
Patent Number:
8029988
Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.
Alanine 2,3-aminomutases and related polynucleotides
Granted: October 4, 2011
Patent Number:
8030051
The present disclosure relates generally to polypeptides having improved alanine 2,3-aminomutase (AAM) activity, the polynucleotides encoding the AAM polypeptides, and expression vectors and host cells for expressing the AAM polypeptides.
Integrated systems and methods for diversity generation and screening
Granted: September 6, 2011
Patent Number:
8014961
Integrated systems and methods for diversity generation and screening are provided. The systems use common fluid and array handling components to provide nucleic acid diversification, transcription, translation, product screening and subsequent diversification reactions.
Methods for generating polynucleotides having desired characteristics by iterative selection and recombination
Granted: July 19, 2011
Patent Number:
7981614
A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins.
Ketoreductase polypeptides for the production of ()-3-hydroxythiolane
Granted: July 12, 2011
Patent Number:
7977078
The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize chiral compounds.
