1. Evolutionary Biology
  2. Plant Biology
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Origin and evolution of the nuclear auxin response system

  1. Sumanth K Mutte
  2. Hirotaka Kato
  3. Carl Rothfels
  4. Michael Melkonian
  5. Gane Ka-Shu Wong
  6. Dolf Weijers  Is a corresponding author
  1. Wageningen University, Netherlands
  2. University of California, Berkeley, United States
  3. University of Cologne, Germany
  4. University of Alberta, Canada
Research Article
  • Cited 80
  • Views 7,890
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Cite this article as: eLife 2018;7:e33399 doi: 10.7554/eLife.33399

Abstract

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

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The following previously published data sets were used

Article and author information

Author details

  1. Sumanth K Mutte

    Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  2. Hirotaka Kato

    Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8521-1450
  3. Carl Rothfels

    Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Michael Melkonian

    Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Gane Ka-Shu Wong

    Department of Biological Sciences, University of Alberta, Edmonton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Dolf Weijers

    Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
    For correspondence
    dolf.weijers@wur.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4378-141X

Funding

Netherlands Organisation for Scientific Research (VICI 865.14.001)

  • Sumanth K Mutte
  • Dolf Weijers

European Molecular Biology Organization (ALTF 415-2016)

  • Hirotaka Kato

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

Reviewing Editor

  1. Hao Yu, National University of Singapore & Temasek Life Sciences Laboratory, Singapore

Publication history

  1. Received: November 7, 2017
  2. Accepted: March 6, 2018
  3. Accepted Manuscript published: March 27, 2018 (version 1)
  4. Version of Record published: March 28, 2018 (version 2)

Copyright

© 2018, Mutte 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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