Abstract

Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential connection between 40S maturation and protein synthesis.

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD016458 (http://www.ebi.ac.uk/pride/archive/projects/PXD016458).

The following data sets were generated

Article and author information

Author details

  1. Christian Montellese

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. Jasmin van den Heuvel

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Caroline Ashiono

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Kerstin Dörner

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. André Melnik

    Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. Stefanie Jonas

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  7. Ivo Zemp

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  8. Paola Picotti

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  9. Ludovic C Gillet

    Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1001-3265
  10. Ulrike Kutay

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    For correspondence
    ulrike.kutay@bc.biol.ethz.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8257-7465

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_166565)

  • Ulrike Kutay

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (NCCR RNA and disease)

  • Ulrike Kutay

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

Copyright

© 2020, Montellese 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. Christian Montellese
  2. Jasmin van den Heuvel
  3. Caroline Ashiono
  4. Kerstin Dörner
  5. André Melnik
  6. Stefanie Jonas
  7. Ivo Zemp
  8. Paola Picotti
  9. Ludovic C Gillet
  10. Ulrike Kutay
(2020)
USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit
eLife 9:e54435.
https://doi.org/10.7554/eLife.54435

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https://doi.org/10.7554/eLife.54435

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