Microbial strain improvement by a HTP genomic engineering platform

Patent metadata

Field	Value
Publication number	US-10647980-B2
Application number	US-201916458376-A
Country	US
Kind code	B2
Filing date	Jul 1, 2019
Priority date	Dec 7, 2015
Publication date	May 12, 2020
Grant date	May 12, 2020

Abstract

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.

First claim

What is claimed is:

1. A computer-implemented high-throughput method for engineering a host cell to have improved phenotypic performance, comprising:
a) accessing a training data set containing one or more genetic alteration input variables and one or more measured phenotypic performance output variables,
i) wherein the one or more genetic alteration input variables represent one or more genetic alterations that have been introduced into a host cell through application of one or more libraries, and
ii) wherein the one or more measured phenotypic performance output variables represent one or more phenotypic performance measurements that are associated with the introduced genetic alterations;

b) developing a predictive machine learning model that is populated with the training data set;
c) generating, in silico, a pool of design candidate host cells incorporating the one or more genetic alterations;
d) utilizing the predictive machine learning model to predict the expected phenotypic performance of each member of the pool of design candidate host cells,
i) wherein at least one design candidate host cell comprises a consolidated combination of genetic alterations from among the genetic alterations of step (a), in a genomic sequence, said combination being uncharacterized for improving the phenotypic performance at the time that step (d) is carried out;
ii) wherein the expected phenotypic performance predicted by the machine learning model is based upon the introduced genetic alterations and their associated phenotypic performance measurements of step (a);
and

e) providing a subset of the design candidate host cells for use in creating engineered host cells;

wherein the one or more libraries are selected from the group consisting of: a promoter swap library, a SNP swap library, a start/stop codon library, an optimized sequence library, a terminator swap library, and combinations thereof.

2. The method of claim 1 , wherein the predictive machine learning model incorporates epistatic effects.

3. The method of claim 1 , wherein the predictive machine learning model incorporates at least one of the following: linear regression, kernel ridge regression, logistic regression, neural networks, support vector machines (SVMs), decision trees, hidden Markov models, Bayesian networks, a Gram-Schmidt process, reinforcement-based learning, cluster-based learning, hierarchical clustering, genetic algorithms, or combinations thereof.

4. The method of claim 1 , wherein the predictive machine learning model is supervised, semi-supervised, or unsupervised.

5. The method of claim 1 , wherein the one or more genetic alterations comprise at least one genetic alteration selected from the group consisting of: a single nucleotide polymorphism, nucleotide sequence insertion, nucleotide sequence deletion, and nucleotide sequence replacements.

6. The method of claim 1 , wherein the one or more genetic alterations comprise one or more heterologous promoters from a promoter ladder operably linked to an endogenous target gene.

7. The method of claim 1 , wherein the improved phenotypic performance is increased or more efficient production of a product of interest, said product of interest selected from the group consisting of: a small molecule, enzyme, protein, peptide, amino acid, organic acid, synthetic compound, fuel, alcohol, primary extracellular metabolite, secondary extracellular metabolite, intracellular component molecule, and combinations thereof.

8. The method of claim 7 , wherein the improved phenotypic performance is increased or more efficient production of lysine or citric acid.

9. The method of claim 1 , comprising step (f): manufacturing at least one member of the subset of design candidate host cells to create engineered host cells, and wherein (a)-(f) are repeated until an engineered host cell exhibits a desired level of improved phenotypic performance.

10. A computer-implemented method for engineering a host cell to have beneficial combinations of genetic alterations, comprising:
a) populating a predictive machine learning model with a training data set, containing: i) at least one genetic alteration input variable representing at least one genetic alteration that has been introduced into a host cell, and ii) at least one measured phenotypic performance output variable representing at least one phenotypic performance measurement associated with the introduced genetic alteration;
b) generating, in silico, a pool of design candidate host cells incorporating the at least one genetic alteration;
c) utilizing the predictive machine learning model to predict the expected phenotypic performance of members of the pool of design candidate host cells that comprise a combination of genetic alterations selected from step (a) that are uncharacterized for improving phenotypic performance at the time of carrying out step (c); and
d) manufacturing a member of the pool of design candidate host cells of step (c);

wherein the improved phenotypic performance is increased or more efficient production of a product of interest, said product of interest selected from the group consisting of: a small molecule, enzyme, protein, peptide, amino acid, organic acid, synthetic compound, fuel, alcohol, primary extracellular metabolite, secondary extracellular metabolite, intracellular component molecule, and combinations thereof.

11. The method of claim 10 , wherein the predictive machine learning model incorporates at least one of the following: linear regression, kernel ridge regression, logistic regression, neural networks, support vector machines (SVMs), decision trees, hidden Markov models, Bayesian networks, a Gram-Schmidt process, reinforcement-based learning, cluster-based learning, hierarchical clustering, genetic algorithms, or combinations thereof.

12. The method of claim 10 , wherein the predictive machine learning model incorporates epistatic effects.

13. The method of claim 10 , wherein the predictive machine learning model is supervised, semi-supervised, or unsupervised.

14. The method of claim 10 , wherein the at least one genetic alteration is selected from the group consisting of: a single nucleotide polymorphism, nucleotide sequence insertion, nucleotide sequence deletion, and nucleotide sequence replacements.

15. The method of claim 10 , wherein the at least one genetic alteration comprises one or more heterologous promoters from a promoter ladder operably linked to an endogenous target gene.

16. The method of claim 11 , wherein the improved phenotypic performance is increased or more efficient production of lysine or citric acid.

17. The method of claim 10 , wherein (a)-(d) are repeated until a manufactured member of the pool of design candidate host cells exhibits a desired level of improved phenotypic performance.

Assignees

• Zymergen Inc

Inventors

• Serber Zach
• Dean Erik Jedediah
• Manchester Shawn
• Gora Katherine
• Flashman Michael
• Shellman Erin
• Kimball Aaron
• Szyjka Shawn
• Frewen Barbara
• Treynor Thomas
• Bruno Kenneth S

Classifications

• C12N15/80

  for fungi · CPC title

• C12N15/1058 Primary

  Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms · CPC title

• G16B5/00

  ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks · CPC title

• C12N15/1079

  Screening libraries by altering the phenotype or phenotypic trait of the host (reporter assays C12N15/1086) · CPC title

• C12N15/77

  for Corynebacterium; for Brevibacterium · CPC title