1. Evolutionary Biology
  2. Genetics and Genomics
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Universal and taxon-specific trends in protein sequences as a function of age

  1. Jennifer E James  Is a corresponding author
  2. Sara M Willis
  3. Paul G Nelson
  4. Catherine Weibel
  5. Luke J Kosinski
  6. Joanna Masel  Is a corresponding author
  1. University of Arizona, United States
Research Article
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Cite this article as: eLife 2021;10:e57347 doi: 10.7554/eLife.57347

Abstract

Extant protein-coding sequences span a huge range of ages, from those that emerged only recently, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be 'phylostratigraphy' trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.

Data availability

All scripts used in this work can be accessed at: https://github.com/MaselLab/ProteinEvolution. Our raw data, and homology files used in our analyses, are available at https://doi.org/10.6084/m9.figshare.12037281.

The following previously published data sets were used
    1. NCBI
    (2020) NCBI
    NCBI, https://www.ncbi.nlm.nih.gov/.
    1. Ensembl
    (2020) Ensembl
    Ensembl, https://uswest.ensembl.org/index.html.

Article and author information

Author details

  1. Jennifer E James

    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
    For correspondence
    jejames@arizona.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0518-6783
  2. Sara M Willis

    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Paul G Nelson

    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Catherine Weibel

    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Luke J Kosinski

    Department of Molecular Cell Biology, University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Joanna Masel

    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
    For correspondence
    masel@arizona.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7398-2127

Funding

John Templeton Foundation (60814)

  • Joanna Masel

National Institutes of Health (GM-104040)

  • Joanna Masel

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Christian R Landry, Université Laval, Canada

Publication history

  1. Received: March 28, 2020
  2. Accepted: January 5, 2021
  3. Accepted Manuscript published: January 8, 2021 (version 1)
  4. Version of Record published: January 21, 2021 (version 2)

Copyright

© 2021, James 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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