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The adaptive landscape of a metallo-enzyme is shaped by environment-dependent epistasis

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  • Dave W. Anderson

    (University of British Columbia
    University of Calgary)

  • Florian Baier

    (University of British Columbia)

  • Gloria Yang

    (University of British Columbia)

  • Nobuhiko Tokuriki

    (University of British Columbia)

Abstract

Enzymes can evolve new catalytic activity when environmental changes present them with novel substrates. Despite this seemingly straightforward relationship, factors other than the direct catalytic target can also impact adaptation. Here, we characterize the catalytic activity of a recently evolved bacterial methyl-parathion hydrolase for all possible combinations of the five functionally relevant mutations under eight different laboratory conditions (in which an alternative divalent metal is supplemented). The resultant adaptive landscapes across this historical evolutionary transition vary in terms of both the number of “fitness peaks” as well as the genotype(s) at which they are found as a result of genotype-by-environment interactions and environment-dependent epistasis. This suggests that adaptive landscapes may be fluid and molecular adaptation is highly contingent not only on obvious factors (such as catalytic targets), but also on less obvious secondary environmental factors that can direct it towards distinct outcomes.

Suggested Citation

  • Dave W. Anderson & Florian Baier & Gloria Yang & Nobuhiko Tokuriki, 2021. "The adaptive landscape of a metallo-enzyme is shaped by environment-dependent epistasis," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23943-x
    DOI: 10.1038/s41467-021-23943-x
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    Cited by:

    1. Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Karol Buda & Charlotte M. Miton & Nobuhiko Tokuriki, 2023. "Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Yeonwoo Park & Brian P. H. Metzger & Joseph W. Thornton, 2024. "The simplicity of protein sequence-function relationships," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Christos S. Karamitros & Kyle Murray & Yoichi Kumada & Kenneth A. Johnson & Sheena D’Arcy & George Georgiou, 2024. "Mechanistic conformational and substrate selectivity profiles emerging in the evolution of enzymes via parallel trajectories," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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