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A high-throughput (HTP) genomic engineering platform for improving saccharopolyspora spinosa

A technology of Saccharopolyspora and polyspora, which is applied in the field of high-throughput microbial genome engineering, can solve the problems in the field of Saccharopolyspora genome engineering and prevent researchers from making full use of it

Pending Publication Date: 2020-03-24
ZYMERGEN INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

These challenges have hampered the field of genome engineering in Saccharopolyspora and prevented researchers from exploiting the full potential of this microbial system

Method used

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  • A high-throughput (HTP) genomic engineering platform for improving saccharopolyspora spinosa
  • A high-throughput (HTP) genomic engineering platform for improving saccharopolyspora spinosa
  • A high-throughput (HTP) genomic engineering platform for improving saccharopolyspora spinosa

Examples

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example

[0836] The following examples are provided to illustrate various embodiments of the present disclosure and are not intended to limit the present disclosure in any way. Those skilled in the art will recognize that changes therein and other uses are encompassed within the spirit of the disclosure as defined by the scope of the claims.

[0837] 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.

[0838] Table 6 - Contents of the example chapter.

[0839]

[0840]

example 1

[0841] Example 1: Illustration of HTP transformation and SNP library creation of Saccharopolyspora

[0842] This example illustrates an embodiment of the HTP genetic engineering method of the present disclosure. Host cells are transformed with multiple SNP sequences of different sizes, all targeting different regions of the genome. The results demonstrate that the methods of the present disclosure are capable of generating rapid genetic changes of any kind across the entire genome of a host cell.

[0843] A. Cloning of Transformation Vectors

[0844] Multiple SNPs will be randomly selected from a predetermined Saccharopolyspora strain (e.g., S. spinosa strain) and cloned into a Saccharopolyspora cloning vector using yeast homologous recombination cloning techniques to assemble the vector, in which each The SNP flanks the cis-repeat region as described above in the "Assembly / Clone Custom Plasmids" section and as described in image 3 described in.

[0845] The SNP cassette ...

example 2

[0858] Example 2: HTP Genome Engineering - Construction of SNP Libraries to Repair / Improve Industrial Microbial Strains

[0859] This example illustrates several aspects of the SNP exchange library in the HTP strain improvement program of the present disclosure. 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.

[0860] A. Identification of SNPs in Diversity Pools

[0861] An exemplary strain improvement program using the methods of the present disclosure will be performed on an industrial microbial 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. St...

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Abstract

The present disclosure provides a HTP microbial genomic engineering platform for Saccharopolyspora spp. 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 iterativepattern recognition.

Description

[0001] Cross References to Related Applications [0002] This application claims priority to US Provisional Patent Application Serial No. 62 / 515,934, filed June 6, 2017, which is hereby incorporated by reference in its entirety. [0003] Statement Regarding the Sequence Listing [0004] The Sequence Listing associated with this application is provided in text format instead of a paper copy and is hereby incorporated by reference into this specification. The name of the text file containing the sequence listing is ZYMR_013_01WO_SeqList_ST25.txt. The text file is approximately 185KB, was created on June 6, 2018, and was submitted electronically via EFS-Web. technical field [0005] The present disclosure 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 solutions. This integrated platform leverages a set of HTP molecular ...

Claims

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Application Information

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IPC IPC(8): C12N15/10
CPCC12N15/1058C12N15/1079C12N1/20C12N15/74C12N15/902C12N15/1086C12N15/1082
Inventor B·梅森A·戈拉诺夫P·凯利Y·基姆S·莫迪N·帕苏马尔蒂B·米基特斯P·埃涅尔特
Owner ZYMERGEN INC
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