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.
1. A promoter swap method of genomic engineering to evolve a host cell to acquire a desired phenotype, comprising the steps of:
a. providing a plurality of target genes endogenous to a base host cell, and a promoter ladder, wherein said promoter ladder comprises a plurality of promoters exhibiting different expression profiles in the base host cell;
b. engineering the genome of the base host cell, to create an initial promoter swap host cell library comprising a plurality of individual host cells with a genetic variation found within each host cell of said plurality of host cells, wherein each genetic variation comprises one or more of the promoters from the promoter ladder operably linked to a target gene endogenous to the host cell;
c. screening and selecting individual host cells of the initial promoter swap host cell library for the desired phenotype;
d. providing a subsequent plurality of host cells that each comprise a combination of genetic variation, said genetic variation selected from the genetic variation present in at least two individual host cells screened in a preceding step, to thereby create a subsequent host cell library;
e. screening and selecting individual host cells of the subsequent host cell library for the desired phenotype; and
f. repeating steps d)-e) one or more times, until a resultant host cell has acquired the desired phenotype.
2. The method according to claim 1 , wherein each subsequent iteration of repeating steps d)-e) creates a new host cell library comprising individual host cells harboring genetic variations that are a combination of genetic variation selected from amongst at least two individual host cells of a preceding host cell library.
3. The method according to claim 1 , wherein the promoter ladder comprises one or more heterologous promoters.
4. The method according to claim 1 , wherein the promoter ladder comprises a constitutive promoter.
5. The method according to claim 1 , wherein the promoter ladder is derived from Corynebacterium promoters.
6. The method according to claim 1 , wherein the promoter ladder comprises a plurality of promoters selected from the group consisting of SEQ ID NOs: 1-8.
7. The method according to claim 1 , wherein in step (b) one or more of the promoters from the promoter ladder are operably linked to a target endogenous gene from a metabolic pathway associated with the production of an amino acid.
8. The method according to claim 1 , wherein in step (b) one or more of the promoters from the promoter ladder are operably linked to a target endogenous gene from the lysine metabolic pathway.
9. The method according to claim 1 , wherein in step (b) one or more of the promoters from the promoter ladder are operably linked to a target endogenous gene selected from the group consisting of: PTS, zwf, pgi, tkt, fbp, ppc, pyc, aspB, ask, asd, dapA, dapB, dapD, cg0931, dapE, dapF, ddh, lysA, lysE, hom, odx, pck, and icd.
10. The method according to claim 1 , wherein the combination of genetic variation present in each of the subsequent plurality of host cells in the subsequent host cell library is selected from a combination of two or more promoters operably linked to their respective target endogenous genes chosen from the initial promoter swap host cell library.
11. The method according to claim 1 , wherein the combination of genetic variation present in each of the subsequent plurality of host cells in the subsequent host cell library is selected from a single nucleotide polymorphism, DNA insertion, or DNA deletion, chosen from a subsequent host cell library screened in a preceding step.
12. The method according to claim 1 , wherein the resultant host cell exhibits at least a 10% increase in a measured phenotypic variable compared to that of a base host cell.
13. The method according to claim 1 , wherein the resultant host cell exhibits at least a one-fold increase in a measured phenotypic variable compared to that of a base host cell.
14. The method according to claim 1 , wherein the desired phenotype of step f) is selected from the group consisting of: increased volumetric productivity of a product of interest, increased specific productivity of a product of interest, increased yield of a product of interest, increased titer of a product of interest, and combinations thereof.
15. The method according to claim 1 , wherein the desired phenotype of step f) 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.
16. The method according to claim 1 , wherein said host cell is a Prokaryotic cell.
17. The method according to claim 1 , wherein said host cell is from Corynebacterium glutamicum.
18. The method according to claim 1 , wherein said host cell is a Eukaryotic cell.
19. The method according to claim 1 , wherein said host cell is from Aspergillus niger.
20. A genomic engineering system to evolve a host cell through promoter swapping to acquire a desired phenotype, 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 a plurality of target genes endogenous to a base host cell, and a promoter ladder, wherein said promoter ladder comprises a plurality of promoters exhibiting different expression profiles in the base host cell;
b. engineer the genome of the base host cell, to create an initial promoter swap host cell library comprising a plurality of individual host cells with a genetic variation found within each host cell of said plurality of host cells, wherein each genetic variation comprises one or more of the promoters from the promoter ladder operably linked to a target gene endogenous to the host cell;
c. screen and select individual host cells of the initial promoter swap host cell library for the desired phenotype;
d. provide a subsequent plurality of host cells that each comprise a unique combination of genetic variation, said genetic variation selected from the genetic variation present in at least two individual host cells screened in a preceding step, to thereby create a subsequent host cell library;
e. screen and select individual host cells of the subsequent host cell library for the desired phenotype; and
f. repeat steps d)-e) one or more times, until a resultant host cell has acquired the desired phenotype.