Proteome partitioning constraints in long-term laboratory evolution

Matteo Mori, Vadim Patsalo, Christian Euler, James R. Williamson and Matthew Scott ()
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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

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-48447-2

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