1. Chromosomes and Gene Expression
  2. Structural Biology and Molecular Biophysics
Download icon

The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

  1. Laura Plassart
  2. Ramtin Shayan
  3. Christian Montellese
  4. Dana Rinaldi
  5. Natacha Larburu
  6. Carole Pichereaux
  7. Carine Froment
  8. Simon Lebaron
  9. Marie-Françoise O'Donohue
  10. Ulrike Kutay
  11. Julien Marcoux
  12. Pierre-Emmanuel Gleizes  Is a corresponding author
  13. Celia Plisson-Chastang  Is a corresponding author
  1. Centre de Biologie Integrative, University of Toulouse, France
  2. ETH Zürich, Switzerland
  3. Institut de Pharmacologie et de Biologie Structurale, France
  4. CNRS, France
Research Article
  • Cited 1
  • Views 1,066
  • Annotations
Cite this article as: eLife 2021;10:e61254 doi: 10.7554/eLife.61254

Abstract

Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-EM analysis of late human pre-40S particles purified using a catalytically-inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.

Data availability

Mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD019270. Cryo-EM maps have been deposited in the Electron Microscopy Data Bank (EMDB), under the accession codes : EMD-11440 (State A multi-body composite map); EMD-11441 (State B multi-body composite map); EMD-11446 (State A, head); EMD-11445 (State A, body); EMD-11447 (State A, platform); EMD-11443 (State B, head); EMD-11442 (State B, body); EMD-11444 (State B, platform). Atomic coordinate models of State A and State B RIO1(kd)-StHA pre-40S particles have been deposited in the Protein Data Bank (PDB), with respective PDB accession codes 6ZUO and 6ZV6.

Article and author information

Author details

  1. Laura Plassart

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Ramtin Shayan

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Christian Montellese

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

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Natacha Larburu

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Carole Pichereaux

    Department of Biophysics, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Carine Froment

    Institute of Pharmacology and Structural Biology, CNRS, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Simon Lebaron

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  9. Marie-Françoise O'Donohue

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  10. Ulrike Kutay

    Institute of Biochemistry, ETH Zürich, Zurich, Switzerland
    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
  11. Julien Marcoux

    Institute of Pharmacology and Structural Biology, CNRS, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7321-7436
  12. Pierre-Emmanuel Gleizes

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    For correspondence
    pierre-emmanuel.gleizes@univ-tlse3.fr
    Competing interests
    The authors declare that no competing interests exist.
  13. Celia Plisson-Chastang

    Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative, University of Toulouse, Toulouse, France
    For correspondence
    celia.plisson-chastang@univ-tlse3.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8439-8428

Funding

Agence Nationale de la Recherche (16-CE11-0029)

  • Laura Plassart
  • Ramtin Shayan
  • Natacha Larburu
  • Simon Lebaron
  • Julien Marcoux
  • Pierre-Emmanuel Gleizes
  • Celia Plisson-Chastang

Swiss National Science Fundation (31003A_166565)

  • Christian Montellese

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

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Publication history

  1. Received: July 20, 2020
  2. Accepted: April 19, 2021
  3. Accepted Manuscript published: April 28, 2021 (version 1)
  4. Version of Record published: May 11, 2021 (version 2)

Copyright

© 2021, Plassart 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.

Metrics

  • 1,066
    Page views
  • 141
    Downloads
  • 1
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease
    Michele Felletti et al.
    Research Article

    The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.

    1. Chromosomes and Gene Expression
    2. Developmental Biology
    Benoit Roch et al.
    Research Article

    We developed a Xrcc4M61R separation of function mouse line to overcome the embryonic lethality of Xrcc4 deficient mice. XRCC4M61R protein does not interact with Xlf, thus obliterating XRCC4-Xlf filament formation while preserving the ability to stabilize DNA Ligase IV. X4M61R mice, which are DNA repair deficient, phenocopy the Nhej1-/- (known as Xlf -/-) setting with a minor impact on the development of the adaptive immune system. The core NHEJ DNA repair factor XRCC4 is therefore not mandatory for V(D)J recombination aside from its role in stabilizing DNA ligase IV. In contrast, Xrcc4M61R mice crossed on Paxx-/-, Nhej1-/-, or Atm-/- backgrounds are severely immunocompromised, owing to aborted V(D)J recombination as in Xlf-Paxx and Xlf-Atm double KO settings. Furthermore, massive apoptosis of post-mitotic neurons causes embryonic lethality of Xrcc4M61R -Nhej1-/- double mutants. These in vivo results reveal new functional interplays between XRCC4 and PAXX, ATM and Xlf in mouse development and provide new insights in the understanding of the clinical manifestations of human XRCC4 deficient condition, in particular its absence of immune deficiency.