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Adaptive laboratory evolution reveals significant proteome remodeling in bacteria over 40,000 generations. Increased enzyme efficiency, particularly in lower glycolysis, suggests a link between metabolic regulation and evolutionary adaptation.

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Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Systems Biology

Background:

  • Adaptive laboratory evolution (ALE) allows real-time study of genetic adaptation at the single-nucleotide level.
  • Physiological constraints offer a coarse-grained view of bacterial gene expression on short timescales.
  • Understanding physiological changes on evolutionary timescales remains a challenge.

Purpose of the Study:

  • To investigate if a framework based on physiological constraints informs changes occurring over evolutionary timescales.
  • To analyze proteome remodeling during long-term bacterial adaptation.
  • To identify key physiological shifts driving adaptation.

Main Methods:

  • Utilized adaptive laboratory evolution (ALE) with a bacterial strain adapted to glucose minimal medium.
  • Tracked genetic and proteomic changes over 40,000 generations.
  • Analyzed enzyme efficiency and metabolic flux regulation.

Main Results:

  • Observed substantial proteome remodeling over 40,000 generations.
  • Identified a striking increase in enzyme efficiency, especially in lower glycolysis enzymes.
  • Proposed that early deletion of metabolic flux-sensing regulation drives these changes.

Conclusions:

  • A framework based on physiological constraints can inform evolutionary changes.
  • Proteome remodeling, particularly increased enzyme efficiency, is a key outcome of long-term adaptation.
  • Loss of metabolic flux-sensing regulation contributes to observed proteome changes and increased enzyme saturation.