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Improvement of microbial strains using the htp genome engineering platform

A microbial and genomic technology, applied in the field of high-throughput microbial genome engineering, can solve the problems of low efficiency of microbial strain improvement programs, stagnant mutation accumulation performance improvement rate, etc.

Active Publication Date: 2020-03-20
ZYMERGEN INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0010] Traditional microbial strain improvement programs are not only inefficient, but the process also increases the deleterious mutagenic load of industrial strains
Mutation accumulation in industrial strains subjected to these types of procedures can become evident and may lead to an eventual stagnation in the rate of performance improvement

Method used

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  • Improvement of microbial strains using the htp genome engineering platform
  • Improvement of microbial strains using the htp genome engineering platform
  • Improvement of microbial strains using the htp genome engineering platform

Examples

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example

[0613] The following examples are provided to illustrate various embodiments of the invention and are not intended to limit the invention in any way. Those skilled in the art will recognize that changes therein and other uses are encompassed within the spirit of the invention as defined by the scope of the claims.

[0614] A brief table of contents is provided below to assist the reader only. This list is not intended to limit the scope of the examples or disclosure of this application.

[0615] Table 5.1 - Table of Contents for Example Sections

[0616]

[0617]

example 1

[0618] Example 1: Demonstration of HTP transformation and SNP library creation of coryneform bacteria

[0619] This example illustrates an embodiment of the HTP genetic engineering method of the present invention. Host cells are transformed with multiple SNP sequences of different sizes, all targeting different regions of the genome. The results demonstrate that the method of the present invention is capable of producing any kind of rapid genetic change across the entire genome of the host cell.

[0620] A. Cloning of Transformation Vectors

[0621] A variety of SNPs were randomly selected from Corynebacterium glutamicum (ATCC21300) and cloned into a Corynebacterium cloning vector using yeast homologous recombination cloning technology to assemble the vector, wherein each SNP is flanked by a direct repeat region, as described above in "Assembly / Cloning of custom plastids" section and as described in image 3 described in.

[0622] The SNP cassette used in this example was...

example 2

[0643] Example 2: HTP Genome Engineering - Construction of SNP Libraries to Repair / Improve Industrial Microbial Strains

[0644] This example illustrates several aspects of the SNP exchange library in the HTP strain improvement program of the present invention. In particular, the examples illustrate several conceived approaches to rehabilitate currently existing industrial strains. This example describes up-swing and down-swing approaches to explore the phenotypic solution space arising from multiple genetic differences that may exist between "basic", "intermediate" and industrial strains.

[0645] A. Identification of SNPs in Diversity Pools

[0646] An exemplary strain improvement program using the methods of the invention is performed on an industrial microorganism strain (referred to herein as "C"). The diversity pool strains used in this procedure are indicated by A, B and C. Strain A represents the original production host strain prior to any mutagenesis. Strain C re...

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Abstract

The present invention provides a computer-driven HTP microbial genome engineering platform that integrates molecular biology, automation and advanced machine learning solutions. The integrated platform uses a set of HTP molecular tools to create HTP genetic design libraries, which are obtained using inter alia scientific insights and iterative pattern recognition. The HTP genome engineering platform described herein is microbial strain host agnostic and thus enables construction across taxa. Additionally, the disclosed platform can be constructed to modulate or improve any microbial host parameter of interest.

Description

[0001] Cross References to Related Applications [0002] This application claims U.S. Provisional Application No. 62 / 264,232, filed December 7, 2015, U.S. Non-Provisional Application No. 15 / 140,296, filed April 27, 2016, and U.S. Priority to Provisional Application No. 62 / 368,786, said US Provisional Application, including all descriptions, references, drawings and claims, each of which is incorporated herein by reference in its entirety for all purposes. technical field [0003] The present invention relates to high-throughput (HTP) microbial genome engineering. The disclosed HTP genome engineering platform is computer driven and integrates molecular biology, automation and advanced machine learning approaches. This integrated platform uses a set of HTP molecular tools to create HTP genetically designed libraries, derived inter alia using scientific insights and iterative pattern recognition. [0004] Statement about the sequence listing [0005] The Sequence Listing as...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/00C12N15/10G16B50/20
CPCG16B30/00G16B50/20C12N15/1058C12N15/1079G16B30/10
Inventor Z·塞尔贝尔E·J·迪安S·曼彻斯特K·戈拉M·弗拉斯曼E·谢尔曼A·金博尔S·希捷卡B·弗勒旺T·特赖诺尔K·S·布鲁诺
Owner ZYMERGEN INC
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