Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM

  1. Andrés López-Perrote
  2. Nele Hug
  3. Ana González-Corpas
  4. Carlos F Rodríguez
  5. Marina Serna
  6. Carmen García-Martín
  7. Jasminka Boskovic
  8. Rafael Fernandez-Leiro
  9. Javier F Caceres
  10. Oscar Llorca  Is a corresponding author
  1. Spanish National Cancer Research Center, CNIO, Spain
  2. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom

Abstract

Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases form an hetero-hexameric ring that is part of several macromolecular complexes such as INO80, SWR1 and R2TP. Interestingly, RUVBL1-RUVBL2 ATPase activity is required for NMD activation by an unknown mechanism. Here, we show that DHX34, an RNA helicase regulating NMD initiation, directly interacts with RUVBL1-RUVBL2 in vitro and in cells. Cryo-EM reveals that DHX34 induces extensive changes in the N-termini of every RUVBL2 subunit in the complex, stabilizing a conformation that does not bind nucleotide and thereby down-regulates ATP hydrolysis of the complex. Using ATPase-deficient mutants, we find that DHX34 acts exclusively on the RUVBL2 subunits. We propose a model, where DHX34 acts to couple RUVBL1-RUVBL2 ATPase activity to the assembly of factors required to initiate the NMD response.

Data availability

The cryo-EM maps of the RUVBL1-RUVBL2-DHX34 complex and the RUVBL1-RUVBL2 ring have been deposited in the EM database with accession codes EMD-11788 and EMD-11789 respectively. The structure of RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34 has been deposited as PDB ID 7AHO.

The following data sets were generated

Article and author information

Author details

  1. Andrés López-Perrote

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  2. Nele Hug

    Genome Regulation Section, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Ana González-Corpas

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  4. Carlos F Rodríguez

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  5. Marina Serna

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  6. Carmen García-Martín

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  7. Jasminka Boskovic

    Structural Biology and Biocomputing Programme, Electron Microscopy Unit, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  8. Rafael Fernandez-Leiro

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  9. Javier F Caceres

    Genome Regulation Section, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8025-6169
  10. Oscar Llorca

    Structural Biology Programme, Spanish National Cancer Research Center, CNIO, Madrid, Spain
    For correspondence
    ollorca@cnio.es
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5705-0699

Funding

Spanish Ministry of Science and Innovation (SAF2017-82632-P)

  • Andrés López-Perrote
  • Carlos F Rodríguez
  • Marina Serna
  • Oscar Llorca

Autonomous Government of Madrid (Y2018/BIO4747)

  • Ana González-Corpas
  • Oscar Llorca

Autonomous Government of Madrid (P2018/NMT4443)

  • Ana González-Corpas
  • Oscar Llorca

Core funding to the MRC Human Genetics Unit

  • Javier F Caceres

Spanish Ministry of Science and Innovation (BES-2015-071348)

  • Carlos F Rodríguez

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

Reviewing Editor

  1. Andreas Martin, University of California, Berkeley, United States

Version history

  1. Received: September 12, 2020
  2. Accepted: November 12, 2020
  3. Accepted Manuscript published: November 18, 2020 (version 1)
  4. Version of Record published: December 1, 2020 (version 2)

Copyright

© 2020, López-Perrote 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. Andrés López-Perrote
  2. Nele Hug
  3. Ana González-Corpas
  4. Carlos F Rodríguez
  5. Marina Serna
  6. Carmen García-Martín
  7. Jasminka Boskovic
  8. Rafael Fernandez-Leiro
  9. Javier F Caceres
  10. Oscar Llorca
(2020)
Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM
eLife 9:e63042.
https://doi.org/10.7554/eLife.63042

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