1. Biochemistry and Chemical Biology

The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains

  1. Alan Rodriguez Carvajal
  2. Irina Grishkovskaya
  3. Carlos Gomez Diaz
  4. Antonia Vogel
  5. Adar Sonn-Segev
  6. Manish S Kushwah
  7. Katrin Schodl
  8. Luiza Deszcz
  9. Zsuzsanna Orban-Nemeth
  10. Shinji Sakamoto
  11. Karl Mechtler
  12. Philipp Kukura
  13. Tim Clausen
  14. David Haselbach  Is a corresponding author
  15. Fumiyo Ikeda  Is a corresponding author
  1. Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Austria
  2. Research Institute of Molecular Pathology, Austria
  3. University of Oxford, United Kingdom
  4. JT Inc., Japan
  5. Medical Institute of Bioregulation (MIB), Kyushu University, Japan
https://doi.org/10.7554/eLife.60660
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  1. Alan Rodriguez Carvajal
  2. Irina Grishkovskaya
  3. Carlos Gomez Diaz
  4. Antonia Vogel
  5. Adar Sonn-Segev
  6. Manish S Kushwah
  7. Katrin Schodl
  8. Luiza Deszcz
  9. Zsuzsanna Orban-Nemeth
  10. Shinji Sakamoto
  11. Karl Mechtler
  12. Philipp Kukura
  13. Tim Clausen
  14. David Haselbach
  15. Fumiyo Ikeda
(2021)
The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains
eLife 10:e60660.
https://doi.org/10.7554/eLife.60660
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Abstract

The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear/Met1-linked ubiquitin chain formation. One of the LUBAC components, HOIL-1L, was recently shown to catalyse oxyester bond formation between ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. Here, we present the first 3D reconstruction of human LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that this event depends on HOIL-1L catalytic activity. By cross-linking mass spectrometry showing proximity between the catalytic RBR domains, a coordinated ubiquitin relay mechanism between the HOIP and HOIL-1L ligases is suggested. In mouse embryonic fibroblasts, these heterotypic chains were induced by TNF, which is reduced in cells expressing an HOIL-1L catalytic inactive mutant. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains by the concerted action of HOIP and HOIL-1L.

Data availability

All data besides the structural data and the mass spec data (see below) generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Supplementary Tables 1-3.wwPDB deposition with dataset ID: D_1292108794ProteomeXchange with identifier PXD019771.

Article and author information

Author details

  1. Alan Rodriguez Carvajal

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
    Competing interests
    No competing interests declared.

  2. Irina Grishkovskaya

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    No competing interests declared.

  3. Carlos Gomez Diaz

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6416-806X

  4. Antonia Vogel

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    No competing interests declared.

  5. Adar Sonn-Segev

    Department of Chemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.

  6. Manish S Kushwah

    Department of Chemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.

  7. Katrin Schodl

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
    Competing interests
    No competing interests declared.

  8. Luiza Deszcz

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
    Competing interests
    No competing interests declared.

  9. Zsuzsanna Orban-Nemeth

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    No competing interests declared.

  10. Shinji Sakamoto

    Pharmaceutical Frontier Research Labs, JT Inc., Yokohama, Japan
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2480-2940

  11. Karl Mechtler

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    No competing interests declared.

  12. Philipp Kukura

    Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    Philipp Kukura, academic founder, consultant, and shareholder in Refeyn Ltd..

  13. Tim Clausen

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1582-6924

  14. David Haselbach

    Research Institute of Molecular Pathology, Vienna, Austria
    For correspondence
    david.haselbach@IMP.AC.AT
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5276-5633

  15. Fumiyo Ikeda

    Department of Molecular and Cellular Biology, Medical Institute of Bioregulation (MIB), Kyushu University, Fukuoka, Japan
    For correspondence
    fumiyo.ikeda@bioreg.kyushu-u.ac.jp
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0407-2768

Funding

Japan Society for the Promotion of Science (JP 18K19959)

  • Fumiyo Ikeda

Japan Society for the Promotion of Science (JP 21H04777)

  • Fumiyo Ikeda

Japan Society for the Promotion of Science (JP 21H00288)

  • Fumiyo Ikeda

Austrian Academy of Sciences

  • Fumiyo Ikeda

Boehringer Ingelheim

  • David Haselbach

FFG (Headquarter Grant 852936)

  • Tim Clausen

Boehringer Ingelheim

  • Tim Clausen

European Research Counsil (PHOTOMASS 819593)

  • Philipp Kukura

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

Reviewing Editor

  1. Andreas Martin, University of California, Berkeley, United States

Ethics

Animal experimentation: All mice were bred and maintained in accordance with ethical animal license protocols complying with the Austrian and European legislation. Animal procedures were covered by the license 568809/2013/18.

Version history

  1. Received: July 2, 2020
  2. Accepted: June 17, 2021
  3. Accepted Manuscript published: June 18, 2021 (version 1)
  4. Version of Record published: June 30, 2021 (version 2)

Copyright

© 2021, Rodriguez Carvajal 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. Alan Rodriguez Carvajal
  2. Irina Grishkovskaya
  3. Carlos Gomez Diaz
  4. Antonia Vogel
  5. Adar Sonn-Segev
  6. Manish S Kushwah
  7. Katrin Schodl
  8. Luiza Deszcz
  9. Zsuzsanna Orban-Nemeth
  10. Shinji Sakamoto
  11. Karl Mechtler
  12. Philipp Kukura
  13. Tim Clausen
  14. David Haselbach
  15. Fumiyo Ikeda
(2021)
The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains
eLife 10:e60660.
https://doi.org/10.7554/eLife.60660

Share this article

https://doi.org/10.7554/eLife.60660

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