Zymergen Inc.

Shawn Manchester

Katherine Gora

Kenneth S Bruno

Shawn Szyjka

Michael Flashman

Aaron Kimball

Erik Jedediah Dean

Barbara Frewen

Thomas Treynor

Erin Shellman

Zach Serber

Zachariah Serber

Patrick J Westfall

Kyle Rothschild-Mancinelli

Alexander Neckelmann

Youngnyun Kim

Benjamin Mason

Alexi Goranov

Jeffrey Mellin

Michael Blaisse

Kasia Gora

Erik Jedehiah Dean

Michael Flaschman

Matthew Davis

Prabha Ramakrishnan

Christy Wisnewski

Robert Haushalter

Stacy-Anne Morgan

The present disclosure provides novel bacterial strains with altered expression or start codon modification of one or more RNA degradation/processing genes. The RNA degradation genes of the present disclosure are controlled by heterologous promoters. The present disclosure further describes methods for generating microbial strains comprising heterologous promoter sequences operably linked to RNA degradation/processing genes.

Genetic perturbation of the RNA degradosome protein complex

The disclosure relates to host cells having altered NADPH availability, allowing for increased production of compounds produced using NADPH, and methods of use thereof. NADPH availability is altered by one or more of: expressing an altered GAPDH, expressing a variant glutamate dehydrogenase (gdh), aspartate semialdehyde dehydrogenase (asd), dihydropicolinate reductase (dapB), and meso-diaminopimelate dehydrogenase (ddh), expressing a novel nicotinamide nucleotide transhydrogenase, expressing a novel threonine aldolase, and expressing or modulating the expression of a pyruvate carboxylase in the host cells.

Genomic engineering of biosynthetic pathways leading to increased NADPH

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.

HTP genomic engineering platform

The present disclosure provides systems and methods for host cell improvement utilizing epistatic effects. The systems and methods described herein are host cell agnostic and therefore can be implemented across taxa. Furthermore, the disclosed systems and methods can be implemented to modulate or improve any host cell parameter of interest.

Systems and methods for host cell improvement utilizing epistatic effects

Provided are native promoters comprising polynucleotides isolated from, and mutant promoters derived therefrom, which may be used to regulate, i.e., either increase or decrease, gene expression. Also provided are promoter ladders comprising a plurality of the promoters having incrementally increasing promoter activity. Also provided are host cells and recombinant vectors comprising the promoters, and methods of expressing genes of interest and producing biomolecules using the host cells.

Promoters from

Automated system for HTP genomic engineering

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.

Microbial strain improvement by a HTP genomic engineering platform

The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial hemoglobin gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial hemoglobin gene whose expression is controlled by a nativepromoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial hemoglobin genes using a promoter ladder comprising a plurality of promoters derived from

Methods for generating a bacterial hemoglobin library and uses thereof

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Oakland, CA, United States of America

Shawn Manchester