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Microbial strain improvement by a htp genomic engineering platform

A microbial and engineering technology, applied in bioinformatics, ICT adaptation, recombinant DNA technology, etc., can solve the problems of low efficiency of microbial strain improvement programs, stagnant mutation accumulation performance improvement rate, etc.

Active Publication Date: 2020-06-02
ZYMERGEN INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0011] 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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  • Microbial strain improvement by a htp genomic engineering platform
  • Microbial strain improvement by a htp genomic engineering platform
  • Microbial strain improvement by a htp genomic engineering platform

Examples

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example 1

[0617] Example 1: Demonstration of HTP transformation and SNP library creation of coryneform bacteria

[0618] 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.

[0619] A. Cloning of Transformation Vectors

[0620] 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.

[0621] The SNP cassette used in this example was...

example 2

[0642] Example 2: HTP Genome Engineering - Construction of SNP Libraries to Repair / Improve Industrial Microbial Strains

[0643] 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.

[0644] A. Identification of SNPs in Diversity Pools

[0645] 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...

example 3

[0659] Example 3: HTP genome engineering - constructing a SNP exchange library to improve the strain performance of coryneform bacteria in terms of lysine production

[0660] This example provides an illustrative embodiment of a portion of the SNP-swapped HTP designer strain improvement program of Example 2, with the goal of improving the production yield and productivity of coryneform bacteria producing lysine.

[0661] Section B of this Example further illustrates the mutation pooling step of the HTP strain improvement program of the present invention. The example thus provides the combined experimental results of the first, second and third rounds of the HTP strain improvement method of the present invention.

[0662] Mutations in the second and third rounds of pooling were derived from separate gene library exchanges. These results thus also illustrate the ability of the HTP strain program to perform multibranch parallel tracing, and the "memory" of beneficial mutations c...

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Abstract

The invention relates to a microbial strain improvement by a 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.

Description

[0001] This application is a divisional application of an invention patent application with an application date of December 7, 2016, an application number of 201680037112.1, and an invention title of "Improvement of microbial strains using the HTP genome engineering platform". [0002] Cross References to Related Applications [0003] 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 [0004] 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...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00G16B50/20
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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