Concurrent remodeling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase

  1. Valentin Mitterer  Is a corresponding author
  2. Matthias Thoms
  3. Robert Buschauer
  4. Otto Berninghausen
  5. Ed Hurt  Is a corresponding author
  6. Roland Beckmann  Is a corresponding author
  1. Heidelberg University, Germany
  2. Ludwig-Maximilians-Universität München, Germany

Abstract

Biogenesis intermediates of nucleolar ribosomal 60S precursor particles undergo a number of structural maturation steps before they transit to the nucleoplasm and are finally exported into the cytoplasm. The AAA+-ATPase Rea1 participates in the nucleolar exit by releasing the Ytm1-Erb1 heterodimer from the evolving pre-60S particle. Here, we show that the DEAD-box RNA helicase Spb4 with its interacting partner Rrp17 is further integrated into this maturation event. Spb4 binds to a specific class of late nucleolar pre-60S intermediates, whose cryo-EM structure revealed how its helicase activity facilitates melting and restructuring of 25S rRNA helices H62 and H63/H63a prior to Ytm1-Erb1 release. In vitro maturation of such Spb4-enriched pre-60S particles, incubated with purified Rea1 and its associated pentameric Rix1-complex in the presence of ATP, combined with cryo-EM analysis depicted the details of the Rea1-dependent large-scale pre-ribosomal remodelling. Our structural insights unveil how the Rea1 ATPase and Spb4 helicase remodel late nucleolar pre-60S particles by rRNA restructuring and dismantling of a network of several ribosomal assembly factors.

Data availability

Atomic models reported in this study have been deposited in the Protein Data Bank (PDB) and can be retrieved using the following accession codes: 8BVN, 8BVU, 8BVV, 8BVY. Cryo-EM density maps have been deposited in the Electron Microscopy Data Bank (EMDB) and can be retrieved using the following accession codes: 16267, 16272, 16273, 16275, 16276, 16277, 16278. Yeast strains and plasmids are available from the corresponding authors upon request.

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Article and author information

Author details

  1. Valentin Mitterer

    Biochemistry Center, Heidelberg University, Heidelberg, Germany
    For correspondence
    mitterer.valentin@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1587-1194
  2. Matthias Thoms

    Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Robert Buschauer

    Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Otto Berninghausen

    Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Ed Hurt

    Biochemistry Center, Heidelberg University, Heidelberg, Germany
    For correspondence
    ed.hurt@bzh.uni-heidelberg.de
    Competing interests
    The authors declare that no competing interests exist.
  6. Roland Beckmann

    Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
    For correspondence
    beckmann@genzentrum.lmu.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4291-3898

Funding

European Research Council (885711-Human-Ribogenesis)

  • Roland Beckmann

Deutsche Forschungsgemeinschaft (HU363/15-2)

  • Ed Hurt

European Research Council (ADG 741781 GLOWSOME)

  • Ed Hurt

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

Reviewing Editor

  1. Ruben L Gonzalez, Columbia University, United States

Version history

  1. Received: November 12, 2022
  2. Preprint posted: November 15, 2022 (view preprint)
  3. Accepted: March 16, 2023
  4. Accepted Manuscript published: March 17, 2023 (version 1)
  5. Accepted Manuscript updated: March 21, 2023 (version 2)
  6. Version of Record published: May 2, 2023 (version 3)

Copyright

© 2023, Mitterer 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. Valentin Mitterer
  2. Matthias Thoms
  3. Robert Buschauer
  4. Otto Berninghausen
  5. Ed Hurt
  6. Roland Beckmann
(2023)
Concurrent remodeling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase
eLife 12:e84877.
https://doi.org/10.7554/eLife.84877

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https://doi.org/10.7554/eLife.84877

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