The GTPase Nog1 co-ordinates assembly, maturation and quality control of distant ribosomal functional centers

Abstract

Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading of their functional centers. In case of the pre-60S, these steps include removal of placeholders Rlp24, Arx1 and Mrt4 that prevent premature loading of the ribosomal protein eL24, the protein-folding machinery at the polypeptide exit tunnel (PET), and the ribosomal stalk, respectively. Here, we reveal that sequential ATPase and GTPase activities license release factors Rei1 and Yvh1 to trigger Arx1 and Mrt4 removal. Drg1-ATPase activity removes Rlp24 from the GTPase Nog1 on the pre-60S; consequently, the C-terminal tail of Nog1 is extracted from the PET. These events enable Rei1 to probe PET integrity, and catalyze Arx1 release. Concomitantly, Nog1 eviction from the pre-60S permits peptidyl transferase center maturation, and Yvh1 to mediate Mrt4 release for stalk assembly. Thus, Nog1 co-ordinates assembly, maturation and quality control of distant functional centers during ribosome formation.

Data availability

The mass spectrometry data reported in this study has been deposited into the ProteomXchange Consortium via the PRIDE partner repository with dataset identifier PXD011382.

The following data sets were generated

Article and author information

Author details

  1. Purnima Klingauf-Nerurkar

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. 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
  3. Daniela Portugal-Calisto

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1591-5812
  4. Michaela Oplova

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0976-4341
  5. Martin Jäger

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. Olga T Schubert

    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:" 0000-0002-2613-0714
  7. Agnese Pisano

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  8. Cohue Peña

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  9. Sanjana Rao

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  10. Martin Altvater

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  11. Yiming Chang

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  12. Ruedi Aebersold

    Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  13. Vikram G Panse

    Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
    For correspondence
    vpanse@imm.uzh.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7950-5746

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

  • Vikram G Panse

H2020 European Research Council (EURIBIO)

  • Vikram G Panse

Novartis Stiftung für Medizinisch-Biologische Forschung

  • Vikram G Panse

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

Reviewing Editor

  1. Robin E Stanley, National Institutes of Health, United States

Publication history

  1. Received: October 5, 2019
  2. Accepted: December 20, 2019
  3. Accepted Manuscript published: January 7, 2020 (version 1)
  4. Version of Record published: January 17, 2020 (version 2)

Copyright

© 2020, Klingauf-Nerurkar 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

  • 2,116
    Page views
  • 255
    Downloads
  • 17
    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)

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

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

  1. Purnima Klingauf-Nerurkar
  2. Ludovic C Gillet
  3. Daniela Portugal-Calisto
  4. Michaela Oplova
  5. Martin Jäger
  6. Olga T Schubert
  7. Agnese Pisano
  8. Cohue Peña
  9. Sanjana Rao
  10. Martin Altvater
  11. Yiming Chang
  12. Ruedi Aebersold
  13. Vikram G Panse
(2020)
The GTPase Nog1 co-ordinates assembly, maturation and quality control of distant ribosomal functional centers
eLife 9:e52474.
https://doi.org/10.7554/eLife.52474

Further reading

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    Laura M Doherty et al.
    Research Article

    Deubiquitinating enzymes (DUBs), ~100 of which are found in human cells, are proteases that remove ubiquitin conjugates from proteins, thereby regulating protein turnover. They are involved in a wide range of cellular activities and are emerging therapeutic targets for cancer and other diseases. Drugs targeting USP1 and USP30 are in clinical development for cancer and kidney disease respectively. However, the majority of substrates and pathways regulated by DUBs remain unknown, impeding efforts to prioritize specific enzymes for research and drug development. To assemble a knowledgebase of DUB activities, co-dependent genes, and substrates, we combined targeted experiments using CRISPR libraries and inhibitors with systematic mining of functional genomic databases. Analysis of the Dependency Map, Connectivity Map, Cancer Cell Line Encyclopedia, and multiple protein-protein interaction databases yielded specific hypotheses about DUB function, a subset of which were confirmed in follow-on experiments. The data in this paper are browsable online in a newly developed DUB Portal and promise to improve understanding of DUBs as a family as well as the activities of incompletely characterized DUBs (e.g. USPL1 and USP32) and those already targeted with investigational cancer therapeutics (e.g. USP14, UCHL5, and USP7).

    1. Biochemistry and Chemical Biology
    Erich J Goebel et al.
    Research Article

    Activin ligands are formed from two disulfide-linked inhibin β (Inhβ) subunit chains. They exist as homodimeric proteins, as in the case of activin A (ActA; InhβA/InhβA) or activin C (ActC; InhβC/InhβC), or as heterodimers, as with activin AC (ActAC; InhβA:InhβC). While the biological functions of ActA and activin B (ActB) have been well characterized, little is known about the biological functions of ActC or ActAC. One thought is that the InhβC chain functions to interfere with ActA production by forming less active ActAC heterodimers. Here, we assessed and characterized the signaling capacity of ligands containing the InhβC chain. ActC and ActAC activated SMAD2/3-dependent signaling via the type I receptor, activin receptor-like kinase 7 (ALK7). Relative to ActA and ActB, ActC exhibited lower affinity for the cognate activin type II receptors and was resistant to neutralization by the extracellular antagonist, follistatin. In mature murine adipocytes, which exhibit high ALK7 expression, ActC elicited a SMAD2/3 response similar to ActB, which can also signal via ALK7. Collectively, these results establish that ActC and ActAC are active ligands that exhibit a distinct signaling receptor and antagonist profile compared to other activins.