UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling

  1. Stéphanie Torrino  Is a corresponding author
  2. Victor Tiroille
  3. Bastien Dolfi
  4. Maeva Dufies
  5. Charlotte Hinault
  6. Laurent Bonesso
  7. Sonia Dagnino
  8. Jennifer Uhler
  9. Marie Irondelle
  10. Anne-sophie Gay
  11. Lucile Fleuriot
  12. Delphine Debayle
  13. Sandra Lacas-Gervais
  14. Mireille Cormont
  15. Thomas Bertero
  16. Frederic Bost
  17. Jerome Gilleron
  18. Stephan Clavel  Is a corresponding author
  1. IPMC, France
  2. C3M, France
  3. Centre Scientifique de Monaco, Monaco
  4. CHU, France
  5. Imperial College London, United Kingdom
  6. University of Gothenburg, Sweden
  7. UFR Sciences, Université Côte d'Azur, France

Abstract

To adapt in an ever-changing environment, cells must integrate physical and chemical signals and translate them into biological meaningful information through complex signaling pathways. By combining lipidomic and proteomic approaches with functional analysis, we have shown that UBTD1 (Ubiquitin domain-containing protein 1) plays a crucial role in both the EGFR (Epidermal Growth Factor Receptor) self-phosphorylation and its lysosomal degradation. On the one hand, by modulating the cellular level of ceramides through ASAH1 (N-Acylsphingosine Amidohydrolase 1) ubiquitination, UBTD1 controls the ligand-independent phosphorylation of EGFR. On the other hand, UBTD1, via the ubiquitination of SQSTM1/p62 (Sequestosome 1) by RNF26 and endolysosome positioning, participates in the lysosomal degradation of EGFR. The coordination of these two ubiquitin-dependent processes contributes to the control of the duration of the EGFR signal. Moreover, we showed that UBTD1 depletion exacerbates EGFR signaling and induces cell proliferation emphasizing a hitherto unknown function of UBTD1 in EGFR-driven human cell proliferation.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided.

Article and author information

Author details

  1. Stéphanie Torrino

    CNRS, IPMC, VALBONNE, France
    For correspondence
    stephanie.torrino@unice.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8280-5907
  2. Victor Tiroille

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Bastien Dolfi

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Maeva Dufies

    Biomedical Department, Centre Scientifique de Monaco, Monaco, Monaco
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1732-0388
  5. Charlotte Hinault

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Laurent Bonesso

    Biochemistry Laboratory, CHU, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Sonia Dagnino

    MRC-PHE Centre for Environment & Health, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6846-7190
  8. Jennifer Uhler

    Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  9. Marie Irondelle

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  10. Anne-sophie Gay

    CNRS, IPMC, VALBONNE, France
    Competing interests
    The authors declare that no competing interests exist.
  11. Lucile Fleuriot

    CNRS, IPMC, VALBONNE, France
    Competing interests
    The authors declare that no competing interests exist.
  12. Delphine Debayle

    CNRS, IPMC, VALBONNE, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2807-9198
  13. Sandra Lacas-Gervais

    CCMA, UFR Sciences, Université Côte d'Azur, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  14. Mireille Cormont

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  15. Thomas Bertero

    CNRS, IPMC, VALBONNE, France
    Competing interests
    The authors declare that no competing interests exist.
  16. Frederic Bost

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4509-4701
  17. Jerome Gilleron

    INSERM, C3M, Nice, France
    Competing interests
    The authors declare that no competing interests exist.
  18. Stephan Clavel

    INSERM, C3M, Nice, France
    For correspondence
    Stephan.CLAVEL@univ-cotedazur.fr
    Competing interests
    The authors declare that no competing interests exist.

Funding

Agence Nationale de la Recherche (ANR-15-IDEX-01)

  • Stephan Clavel

Agence Nationale de la Recherche (ANR18-CE14-0035-01-GILLERON)

  • Jerome Gilleron

Fondation de France

  • Stéphanie Torrino

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

Reviewing Editor

  1. Roger J Davis, University of Massachusetts Medical School, United States

Publication history

  1. Received: March 12, 2021
  2. Accepted: April 20, 2021
  3. Accepted Manuscript published: April 22, 2021 (version 1)
  4. Version of Record published: May 13, 2021 (version 2)

Copyright

© 2021, Torrino 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

  • 867
    Page views
  • 181
    Downloads
  • 2
    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. Stéphanie Torrino
  2. Victor Tiroille
  3. Bastien Dolfi
  4. Maeva Dufies
  5. Charlotte Hinault
  6. Laurent Bonesso
  7. Sonia Dagnino
  8. Jennifer Uhler
  9. Marie Irondelle
  10. Anne-sophie Gay
  11. Lucile Fleuriot
  12. Delphine Debayle
  13. Sandra Lacas-Gervais
  14. Mireille Cormont
  15. Thomas Bertero
  16. Frederic Bost
  17. Jerome Gilleron
  18. Stephan Clavel
(2021)
UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling
eLife 10:e68348.
https://doi.org/10.7554/eLife.68348

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Morgan L Pimm et al.
    Research Article Updated

    Profilin-1 (PFN1) is a cytoskeletal protein that regulates the dynamics of actin and microtubule assembly. Thus, PFN1 is essential for the normal division, motility, and morphology of cells. Unfortunately, conventional fusion and direct labeling strategies compromise different facets of PFN1 function. As a consequence, the only methods used to determine known PFN1 functions have been indirect and often deduced in cell-free biochemical assays. We engineered and characterized two genetically encoded versions of tagged PFN1 that behave identical to each other and the tag-free protein. In biochemical assays purified proteins bind to phosphoinositide lipids, catalyze nucleotide exchange on actin monomers, stimulate formin-mediated actin filament assembly, and bound tubulin dimers (kD = 1.89 µM) to impact microtubule dynamics. In PFN1-deficient mammalian cells, Halo-PFN1 or mApple-PFN1 (mAp-PEN1) restored morphological and cytoskeletal functions. Titrations of self-labeling Halo-ligands were used to visualize molecules of PFN1. This approach combined with specific function-disrupting point-mutants (Y6D and R88E) revealed PFN1 bound to microtubules in live cells. Cells expressing the ALS-associated G118V disease variant did not associate with actin filaments or microtubules. Thus, these tagged PFN1s are reliable tools for studying the dynamic interactions of PFN1 with actin or microtubules in vitro as well as in important cell processes or disease-states.

    1. Cell Biology
    Lu Zhu et al.
    Research Article

    Nedd4/Rsp5 family E3 ligases mediate numerous cellular processes, many of which require the E3 ligase to interact with PY-motif containing adaptor proteins. Several Arrestin-Related Trafficking adaptors (ARTs) of Rsp5 were self-ubiquitinated for activation, but the regulation mechanism remains elusive. Remarkably, we demonstrate that Art1, Art4, and Art5 undergo K63 linked di-Ubiquitination by Rsp5. This modification enhances the PM recruitment of Rsp5 by Art1 or Art5 upon substrate induction, required for cargo protein ubiquitination. In agreement with these observations, we find that di-ubiquitin strengthens the interaction between the Pombe orthologs of Rsp5 and Art1, Pub1 and Any1. Further, we discover that the HECT domain exosite protects the K63 linked di-Ubiquitin on the adaptors from cleavage by the deubiquitination enzyme Ubp2. Together, our study uncovers a novel ubiquitination modification implemented by Rsp5 adaptor proteins, underscoring the regulatory mechanism of how adaptor proteins control the recruitment and activity of Rsp5 for the turnover of membrane proteins.