Zymergen Inc.

Amyris, Inc.

Zach Serber

Kenneth S Bruno

Shawn Manchester

Shawn Szyjka

Erik Jedediah Dean

Michael Flashman

Aaron Kimball

Barbara Frewen

Katherine Gora

Erin Shellman

Thomas Treynor

Raymond Lowe

Sunil S Chandran

Jeffrey A Ubersax

Andrew Horwitz

Patrick J Westfall

Grayson Wawrzyn

Kyle Rothschild-Mancinelli

Fern R McSorley

Warren Lau

Christine Roche

Savita Ganesan

Youngnyun Kim

Darren M Platt

Kenneth Toshiki Takeoka

Stacy-Anne Morgan

Robert Haushalter

Christy Wisnewski

Prabha Ramakrishnan

Matthew Davis

Michael Flaschman

Erik Jedehiah Dean

Kasia Gora

Katherine G Gora

Michael Blaisse

The present disclosure provides isolated nepetalactone oxidoreductase polypeptides (NORs), nepetalactol synthases (NEPSs), and related polynucleotides, engineered host cells, and cultures, as well as methods for producing NORs and NEPSs, and for using them to produce nepetalactol, nepetalactone, and dihydronepetalactone. The present disclosure also provides methods for engineering cells (e.g., microbial cells) to produce nepetalactone from a fermentation substrate such as glucose, as well as engineered cells having this capability and related cultures and methods for producing nepetalactone.

Nepetalactol oxidoreductases, nepetalactol synthases, and microbes capable of producing nepetalactone

The present disclosure provides machine learning techniques for computationally predicting the phenotypic performance of combinations of genetic variations and for designing new improved host cells. The machine learning models and methods described herein are host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any host cell parameter of interest.

HTP genomic engineering platform

The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.

Automated system for HTP genomic engineering

Microbial strain improvement by a HTP genomic engineering platform

Provided herein are methods of integrating one or more exogenous nucleic acids into one or more selected target sites of a host cell genome. In certain embodiments, the methods comprise contacting the host cell genome with one or more integration polynucleotides comprising an exogenous nucleic acid to be integrated into a genomic target site, and a nuclease capable of causing a double-strand break near or within the genomic target site.

Methods for genomic modification

The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with promer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.

Compositions and methods for the assembly of polynucleotides

Growing community of inventors

Sausalito, CA, United States of America

Zach Serber