1. Biochemistry and Chemical Biology
  2. Evolutionary Biology
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Reverse evolution leads to genotypic incompatibility despite functional and active-site convergence

  1. Miriam Kaltenbach
  2. Colin J Jackson
  3. Eleanor C Campbell
  4. Florian Hollfelder
  5. Nobuhiko Tokuriki  Is a corresponding author
  1. University of British Columbia, Canada
  2. Australian National University, Australia
  3. University of Cambridge, United Kingdom
Research Article
  • Cited 31
  • Views 2,641
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Cite this article as: eLife 2015;4:e06492 doi: 10.7554/eLife.06492

Abstract

Understanding to which extent enzyme evolution is reversible can shed light on the fundamental relationship between protein sequence, structure, and function. Here, we perform an experimental test of evolutionary reversibility using directed evolution from a phosphotriesterase to an arylesterase, and back, and examine the underlying molecular basis. We find that wild-type phosphotriesterase function could be restored (>104-fold activity increase), but via an alternative set of mutations. The enzyme active site converged towards its original state, indicating evolutionary constraints imposed by catalytic requirements. We reveal that extensive epistasis prevents reversions and necessitates fixation of new mutations, leading to a functionally identical sequence in which many amino acid exchanges between the two sequences are not tolerated, implying sequence incompatibility. Therefore, the evolution was phenotypically reversible, but genotypically irreversible. Our study illustrates that the enzyme's adaptive landscape is highly rugged, and different functional sequences may constitute separate fitness peaks.

Article and author information

Author details

  1. Miriam Kaltenbach

    Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Colin J Jackson

    Research School of Chemistry, Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  3. Eleanor C Campbell

    Research School of Chemistry, Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  4. Florian Hollfelder

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Nobuhiko Tokuriki

    Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
    For correspondence
    tokuriki@msl.ubc.ca
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Michael Laub, Massachusetts Institute of Technology, United States

Publication history

  1. Received: January 15, 2015
  2. Accepted: August 13, 2015
  3. Accepted Manuscript published: August 14, 2015 (version 1)
  4. Version of Record published: September 23, 2015 (version 2)

Copyright

© 2015, Kaltenbach et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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