The multi-subunit GID/CTLH E3 ligase promotes proliferation and targets the transcription factor Hbp1 for degradation

Abstract

In yeast, the glucose-induced degradation-deficient (GID) E3 ligase selectively degrades superfluous gluconeogenic enzymes. Here we identified all subunits of the mammalian GID/CTLH complex and provide a comprehensive map of its hierarchical organization and step-wise assembly. Biochemical reconstitution demonstrates that the mammalian complex possesses inherent E3 ubiquitin ligase activity, using Ube2H as its cognate E2. Deletions of multiple GID subunits compromise cell proliferation, and this defect is accompanied by deregulation of critical cell cycle markers such as the retinoblastoma (Rb) tumor suppressor, phospho-Histone H3 and Cyclin A. We identify the negative regulator of pro-proliferative genes Hbp1 as a bonafide GID/CTLH proteolytic substrate. Indeed, Hbp1 accumulates in cells lacking GID/CTLH activity, and Hbp1 physically interacts and is ubiquitinated in vitro by reconstituted GID/CTLH complexes. Our biochemical and cellular analysis thus demonstrates that the GID/CTLH complex prevents cell cycle exit in G1, at least in part by degrading Hbp1.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files contain the complete lists of mass spectrometry results and SAINT scores

Article and author information

Author details

  1. Fabienne Lampert

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    For correspondence
    fabienne.lampert@bc.biol.ethz.ch
    Competing interests
    The authors declare that no competing interests exist.
  2. Diana Stafa

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Algera Goga

    Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Martin Varis Soste

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. Samuel Gilberto

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. Natacha Olieric

    Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  7. Paola Picotti

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  8. Markus Stoffel

    Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  9. Matthias Peter

    Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
    For correspondence
    matthias.peter@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:" 0000-0002-2160-6824

Funding

Swiss National Science Foundation

  • Markus Stoffel
  • Matthias Peter

Human Frontier Science Program (LT- 000376/2014-L)

  • Fabienne Lampert

European Research Council

  • Matthias Peter

ETH Zurich

  • Paola Picotti
  • Markus Stoffel
  • Matthias Peter

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

Reviewing Editor

  1. Ivan Dikic, Goethe University Frankfurt, Germany

Ethics

Animal experimentation: All animal experiments were approved by the Kantonale Veterinäramt Zürich.

Version history

  1. Received: January 30, 2018
  2. Accepted: June 16, 2018
  3. Accepted Manuscript published: June 18, 2018 (version 1)
  4. Version of Record published: July 9, 2018 (version 2)

Copyright

© 2018, Lampert 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

  • 5,427
    views
  • 897
    downloads
  • 81
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Fabienne Lampert
  2. Diana Stafa
  3. Algera Goga
  4. Martin Varis Soste
  5. Samuel Gilberto
  6. Natacha Olieric
  7. Paola Picotti
  8. Markus Stoffel
  9. Matthias Peter
(2018)
The multi-subunit GID/CTLH E3 ligase promotes proliferation and targets the transcription factor Hbp1 for degradation
eLife 7:e35528.
https://doi.org/10.7554/eLife.35528

Share this article

https://doi.org/10.7554/eLife.35528

Further reading

    1. Biochemistry and Chemical Biology
    Boglarka Zambo, Evelina Edelweiss ... Gergo Gogl
    Research Article

    Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventional in vitro and cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
    Ramona Weber, Chung-Te Chang
    Research Article

    Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.