Systems and methods for host cell improvement utilizing epistatic effects

Patent metadata

Field	Value
Publication number	US-11085040-B2
Application number	US-201916665764-A
Country	US
Kind code	B2
Filing date	Oct 28, 2019
Priority date	Dec 7, 2015
Publication date	Aug 10, 2021
Grant date	Aug 10, 2021

Abstract

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.

First claim

What is claimed is:

1. A computer-implemented method for applying epistatic effects in the iterative improvement of a host cell, the method comprising:
a. providing data representing measured performance in response to a plurality of genetic changes, wherein each genetic change is made to a plurality of host background strains;
b. generating a selected combination of at least two genetic changes based at least in part upon a degree of dissimilarity between the corresponding responsive performance measures of the plurality of genetic changes from the data provided in step (a); wherein the degree of dissimilarity is the degree to which the at least two genetic changes affect their corresponding performance measures differently when compared across the plurality of host background strains;
c. designing genetic changes to a host cell that include the selected combination of genetic changes; and
d. manufacturing the host cell designed in step (c).

2. The method of claim 1 , wherein the degree of dissimilarity is determined by calculating the cosine similarity of the measured performance of the plurality of genetic changes across the plurality of host background strains.

3. The method of claim 1 , wherein the degree of dissimilarity is determined by calculating a distance measure of a cluster of the measured performance of the plurality of genetic changes across the plurality of host background strains, wherein the measured performance is clustered by a k-mean or a hierarchical agglomerative clustering method, and wherein the distance measure is Euclidean, or hamming.

4. The method of claim 1 , wherein the plurality of host background strains comprise host cells that are genetically identical except for the genetic change in step (a) and an added secondary genetic change introduced to create genetic diversity in said plurality of host background strains.

5. The method of claim 4 , wherein the secondary genetic change is 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 4 , wherein the secondary genetic change comprises one or more heterologous promoters from a promoter ladder operably linked to an endogenous target gene.

7. The method of claim 1 , wherein the genetic changes in step (a) are selected from the group consisting of: a single nucleotide polymorphism, nucleotide sequence insertion, nucleotide sequence deletion, and nucleotide sequence replacements.

8. The method of claim 1 , wherein the genetic changes in step (a) comprise one or more heterologous promoters from a promoter ladder operably linked to an endogenous target gene.

9. The method of claim 1 , wherein the combination of at least two genetic changes in step (b) is also selected based on each genetic change's individual ability to improve the measured performance of their host background strains compared to otherwise identical control host strains lacking said genetic change.

10. The method of claim 1 , wherein the manufactured host cell comprising the selected combination of genetic changes exhibits an improved phenotypic performance over an otherwise identical host cell that comprises only one of the selected genetic changes.

11. The method of claim 10 , wherein the improved phenotypic performance is selected from the group consisting of: volumetric productivity of a product of interest, specific productivity of a product of interest, yield of a product of interest, titer of a product of interest, and combinations thereof.

12. The method of claim 10 , 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.

13. The method of claim 10 , wherein the improved phenotypic performance is: increased production of lysine or citric acid or more efficient production of lysine or citric acid.

14. A system for applying epistatic effects in the iterative improvement of candidate microbial strains, the system comprising:
one or more processors; and
one or more memories operatively coupled to at least one of the one or more processors and having instructions stored thereon that, when executed by at least one of the one or more processors, cause the system to:
a. provide data representing measured performance in response to a plurality of genetic changes, wherein each genetic change is made to a plurality of host background strains;
b. generate a selected combination of at least two genetic changes based at least in part upon a degree of dissimilarity between the corresponding performance measures of the plurality of genetic changes from the data provided in step (a); wherein the degree of dissimilarity is the degree to which the at least two genetic changes affect their corresponding responsive performance measures differently when compared across the plurality of host background strains;
c. design genetic changes to a host cell that include the selected combination of genetic changes; and
d. manufacture the host cell designed in step (c).

15. The system of claim 14 , wherein the degree of dissimilarity is determined by calculating the cosine similarity of the measured performance of the plurality of genetic changes across the plurality of host background strains.

16. The system of claim 14 , wherein the degree of dissimilarity is determined by calculating a distance measure of a cluster of the measured performance of the at least two genetic changes across the plurality of host background strains, wherein the measured performance is clustered by a k-mean or a hierarchical agglomerative clustering method, and wherein the distance measure is Euclidean, or hamming.

17. The system of claim 14 , wherein the plurality of host background strains comprise host cells that are genetically identical except for the genetic change in step (a) and an added secondary genetic change introduced to create genetic diversity in said plurality of host background strains.

18. The system of claim 14 , wherein the system manufactures the host cell by contacting DNA effectuating the genetic changes designed by the system in step (c) with a host cell, said contacting effectuated by automated liquid and particle handling robotics in communication with the processor.

19. The system of claim 18 , wherein the system further comprises an electroporator.

20. The system of claim 18 , wherein the system further comprises a thermocycler.

21. The system of claim 14 , wherein the system manufactures the host cell through ballistic transformation of cells via ballistic robotics in communication with the processor.

22. A computer-implemented method for applying epistatic effects in the iterative improvement of a host cell, the method comprising:
a. providing data representing measured performance in response to a plurality of genetic changes, each made to a plurality of host background strains;
b. generating a selected combination of at least two genetic changes based at least in part upon a degree of dissimilarity between the corresponding responsive performance measures of the plurality of genetic changes from the data provided in step (a); wherein the degree of dissimilarity i

Assignees

• Zymergen Inc

Inventors

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

Classifications

• B01L2200/16

  Reagents, handling or storing thereof · CPC title

• G01N35/00871

  Communications between instruments or with remote terminals · 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

• B01L2300/1894

  Cooling means; Cryo cooling · CPC title

• C12M3/00

  Tissue, human, animal or plant cell, or virus culture apparatus · CPC title