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Proteome partitioning constraints in long-term laboratory evolution

Author

Listed:
  • Matteo Mori

    (University of California at San Diego)

  • Vadim Patsalo

    (The Scripps Research Institute)

  • Christian Euler

    (University of Waterloo)

  • James R. Williamson

    (The Scripps Research Institute)

  • Matthew Scott

    (University of Waterloo)

Abstract

Adaptive laboratory evolution experiments provide a controlled context in which the dynamics of selection and adaptation can be followed in real-time at the single-nucleotide level. And yet this precision introduces hundreds of degrees-of-freedom as genetic changes accrue in parallel lineages over generations. On short timescales, physiological constraints have been leveraged to provide a coarse-grained view of bacterial gene expression characterized by a small set of phenomenological parameters. Here, we ask whether this same framework, operating at a level between genotype and fitness, informs physiological changes that occur on evolutionary timescales. Using a strain adapted to growth in glucose minimal medium, we find that the proteome is substantially remodeled over 40 000 generations. The most striking change is an apparent increase in enzyme efficiency, particularly in the enzymes of lower-glycolysis. We propose that deletion of metabolic flux-sensing regulation early in the adaptation results in increased enzyme saturation and can account for the observed proteome remodeling.

Suggested Citation

  • Matteo Mori & Vadim Patsalo & Christian Euler & James R. Williamson & Matthew Scott, 2024. "Proteome partitioning constraints in long-term laboratory evolution," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48447-2
    DOI: 10.1038/s41467-024-48447-2
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    References listed on IDEAS

    as
    1. Nicholas Leiby & Christopher J Marx, 2014. "Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli," PLOS Biology, Public Library of Science, vol. 12(2), pages 1-10, February.
    2. Jeffrey E. Barrick & Dong Su Yu & Sung Ho Yoon & Haeyoung Jeong & Tae Kwang Oh & Dominique Schneider & Richard E. Lenski & Jihyun F. Kim, 2009. "Genome evolution and adaptation in a long-term experiment with Escherichia coli," Nature, Nature, vol. 461(7268), pages 1243-1247, October.
    3. Conghui You & Hiroyuki Okano & Sheng Hui & Zhongge Zhang & Minsu Kim & Carl W. Gunderson & Yi-Ping Wang & Peter Lenz & Dalai Yan & Terence Hwa, 2013. "Coordination of bacterial proteome with metabolism by cyclic AMP signalling," Nature, Nature, vol. 500(7462), pages 301-306, August.
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