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Appl Environ Microbiol. 2018 Sep 17;84(19). pii: e00823-18. doi: 10.1128/AEM.00823-18. Print 2018 Oct 1.

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions.

Author information

1
Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
2
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
3
Department of Bioengineering, University of California, San Diego, La Jolla, California, USA palsson@ucsd.edu.

Abstract

A mechanistic understanding of how new phenotypes develop to overcome the loss of a gene product provides valuable insight on both the metabolic and regulatory functions of the lost gene. The pgi gene, whose product catalyzes the second step in glycolysis, was deleted in a growth-optimized Escherichia coli K-12 MG1655 strain. The initial knockout (KO) strain exhibited an 80% drop in growth rate that was largely recovered in eight replicate, but phenotypically distinct, cultures after undergoing adaptive laboratory evolution (ALE). Multi-omic data sets showed that the loss of pgi substantially shifted pathway usage, leading to a redox and sugar phosphate stress response. These stress responses were overcome by unique combinations of innovative mutations selected for by ALE. Thus, the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after the loss of a major gene product were revealed.IMPORTANCE A mechanistic understanding of how microbes are able to overcome the loss of a gene through regulatory and metabolic changes is not well understood. Eight independent adaptive laboratory evolution (ALE) experiments with pgi knockout strains resulted in eight phenotypically distinct endpoints that were able to overcome the gene loss. Utilizing multi-omics analysis, the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after the loss of a major gene product were revealed.

KEYWORDS:

Escherichia coli; adaptive laboratory evolution; multi-omics analysis; mutation analysis; pgi gene knockout; systems biology

PMID:
30054360
PMCID:
PMC6146989
DOI:
10.1128/AEM.00823-18
[Indexed for MEDLINE]
Free PMC Article

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