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Genomic analysis of a key innovation in an experimental Escherichia coli population

Author

Listed:
  • Zachary D. Blount

    (Michigan State University
    BEACON Center for the Study of Evolution in Action, Michigan State University)

  • Jeffrey E. Barrick

    (BEACON Center for the Study of Evolution in Action, Michigan State University
    The University of Texas
    Institute for Cellular and Molecular Biology, The University of Texas)

  • Carla J. Davidson

    (Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada)

  • Richard E. Lenski

    (Michigan State University
    BEACON Center for the Study of Evolution in Action, Michigan State University)

Abstract

Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit+), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations before its emergence. The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population’s history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

Suggested Citation

  • Zachary D. Blount & Jeffrey E. Barrick & Carla J. Davidson & Richard E. Lenski, 2012. "Genomic analysis of a key innovation in an experimental Escherichia coli population," Nature, Nature, vol. 489(7417), pages 513-518, September.
    • Handle: RePEc:nat:nature:v:489:y:2012:i:7417:d:10.1038_nature11514
    DOI: 10.1038/nature11514
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    Cited by:

    1. Richard E. Lenski & Terence C. Burnham, 2018. "Experimental evolution of bacteria across 60,000 generations, and what it might mean for economics and human decision-making," Journal of Bioeconomics, Springer, vol. 20(1), pages 107-124, April.
    2. 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.
    3. Terence C. Burnham & Jay Phelan, 2020. "Ordinaries," Journal of Bioeconomics, Springer, vol. 22(3), pages 137-154, October.
    4. Ryo Mizuuchi & Taro Furubayashi & Norikazu Ichihashi, 2022. "Evolutionary transition from a single RNA replicator to a multiple replicator network," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    5. James S. Horton & Louise M. Flanagan & Robert W. Jackson & Nicholas K. Priest & Tiffany B. Taylor, 2021. "A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    6. Milva Pepi & Silvano Focardi, 2021. "Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area," IJERPH, MDPI, vol. 18(11), pages 1-31, May.

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