Decoys provide a scalable platform for identification of plant E3 ubiquitin ligases that regulate circadian function

  1. Ann Feke
  2. Wei Liu
  3. Jing Hong
  4. Man-Wah Li
  5. Chin-Mei Lee
  6. Elton K Zhou
  7. Joshua M Gendron  Is a corresponding author
  1. Yale University, United States
  2. South China University of Technology, China

Abstract

The circadian clock relies on regulated degradation of clock proteins to maintain rhythmicity. Despite this, we know few components that mediate protein degradation. This is due to high levels of functional redundancy within plant E3 ubiquitin ligase families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian function, we generated a library of transgenic Arabidopsis plants expressing dominant-negative 'decoy' E3 ubiquitin ligases. We determined their effects on the circadian clock and identified dozens of new potential regulators of circadian function. To demonstrate the potency of the decoy screening methodology to overcome redundancy and identify bona fide clock regulators, we performed follow-up studies on MAC3A (PUB59) and MAC3B (PUB60). We show that they redundantly control circadian period by regulating splicing. This work demonstrates the viability of ubiquitin ligase decoys as a screening platform to overcome genetic challenges and discover E3 ubiquitin ligases that regulate plant development.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Source data is provided for Figures 2,3,4,6, S1 and S2.

The following previously published data sets were used

Article and author information

Author details

  1. Ann Feke

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Wei Liu

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Jing Hong

    School of Food Science and Engineering, South China University of Technology, Guangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Man-Wah Li

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Chin-Mei Lee

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3870-4268
  6. Elton K Zhou

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Joshua M Gendron

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    For correspondence
    joshua.gendron@yale.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8605-3047

Funding

National Science Foundation (EAGER #1548538)

  • Joshua M Gendron

National Institutes of Health (R35 GM128670)

  • Joshua M Gendron

Gruber Foundation

  • Ann Feke

Rudolph J. Anderson Fund

  • Chin-Mei Lee

Forest B.H. and Elizabeth D.W. Brown Fund

  • Wei Liu
  • Chin-Mei Lee

National Science Foundation (GRFP DGE-1122492)

  • Ann Feke

National Institutes of Health (T32 GM007499)

  • Ann Feke

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

Reviewing Editor

  1. Jürgen Kleine-Vehn, University of Natural Resources and Life Sciences, Austria

Publication history

  1. Received: December 20, 2018
  2. Accepted: April 4, 2019
  3. Accepted Manuscript published: April 5, 2019 (version 1)
  4. Version of Record published: April 25, 2019 (version 2)

Copyright

© 2019, Feke 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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  1. Ann Feke
  2. Wei Liu
  3. Jing Hong
  4. Man-Wah Li
  5. Chin-Mei Lee
  6. Elton K Zhou
  7. Joshua M Gendron
(2019)
Decoys provide a scalable platform for identification of plant E3 ubiquitin ligases that regulate circadian function
eLife 8:e44558.
https://doi.org/10.7554/eLife.44558

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