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

Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. Palsson*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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.
Original languageEnglish
Article numbere00823-18
JournalApplied and Environmental Microbiology
Volume84
Issue number19
Number of pages17
ISSN0099-2240
DOIs
Publication statusPublished - 2018

Keywords

  • Escherichia coli
  • Adaptive laboratory evolution
  • Multi-omics analysis
  • Mutation analysis
  • pgi gene knockout
  • Systems biology

Cite this

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title = "Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions",
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.",
keywords = "Escherichia coli, Adaptive laboratory evolution, Multi-omics analysis, Mutation analysis, pgi gene knockout, Systems biology",
author = "Douglas McCloskey and Sibei Xu and Sandberg, {Troy E.} and Elizabeth Brunk and Ying Hefner and Richard Szubin and Feist, {Adam M.} and Palsson, {Bernhard O.}",
year = "2018",
doi = "10.1128/AEM.00823-18",
language = "English",
volume = "84",
journal = "Applied and Environmental Microbiology",
issn = "0099-2240",
publisher = "American Society for Microbiology",
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}

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. / McCloskey, Douglas; Xu, Sibei; Sandberg, Troy E.; Brunk, Elizabeth; Hefner, Ying; Szubin, Richard; Feist, Adam M.; Palsson, Bernhard O.

In: Applied and Environmental Microbiology, Vol. 84, No. 19, e00823-18, 2018.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

AU - McCloskey, Douglas

AU - Xu, Sibei

AU - Sandberg, Troy E.

AU - Brunk, Elizabeth

AU - Hefner, Ying

AU - Szubin, Richard

AU - Feist, Adam M.

AU - Palsson, Bernhard O.

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - Escherichia coli

KW - Adaptive laboratory evolution

KW - Multi-omics analysis

KW - Mutation analysis

KW - pgi gene knockout

KW - Systems biology

U2 - 10.1128/AEM.00823-18

DO - 10.1128/AEM.00823-18

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VL - 84

JO - Applied and Environmental Microbiology

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