1. Biochemistry and Chemical Biology
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Chemical genetics and proteome-wide site mapping reveal cysteine MARylation by PARP-7 on immune-relevant protein targets

  1. Kelsie M Rodriguez
  2. Sara C Buch-Larsen
  3. Ilsa T Kirby
  4. Ivan Siordia
  5. David Hutin
  6. Marit Rasmussen
  7. Denis M Grant
  8. Larry L David
  9. Jason Matthews
  10. Michael Lund Nielsen
  11. Michael S Cohen  Is a corresponding author
  1. Oregon Health and Science University, United States
  2. University of Copenhagen, Denmark
  3. University of California, San Francisco, United States
  4. University of Toronto, Canada
  5. University of Oslo, Norway
Research Article
  • Cited 2
  • Views 1,290
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Cite this article as: eLife 2021;10:e60480 doi: 10.7554/eLife.60480

Abstract

Poly(ADP-ribose) polymerase 7 (PARP-7) has emerged as a critically important member of a large enzyme family that catalyzes ADP-ribosylation in mammalian cells. PARP-7 is a critical regulator of the innate immune response. What remains unclear is the mechanism by which PARP-7 regulates this process, namely because the protein targets of PARP-7 mono-ADP-ribosylation (MARylation) are largely unknown. Here, we combine chemical genetics, proximity labeling, and proteome-wide amino acid ADP-ribosylation site profiling for identifying the direct targets and sites of PARP-7-mediated MARylation in a cellular context. We found that the inactive PARP family member, PARP-13—a critical regulator of the antiviral innate immune response—is a major target of PARP-7. PARP-13 is preferentially MARylated on cysteine residues in its RNA binding zinc finger domain. Proteome-wide ADP-ribosylation analysis reveals cysteine as a major MARylation acceptor of PARP-7. This study provides insight into PARP-7 targeting and MARylation site preference.

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All RAW proteomics files have been uploaded to PRIDE. This is related to all Supplementary Tables.

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Article and author information

Author details

  1. Kelsie M Rodriguez

    Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sara C Buch-Larsen

    Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6250-5467
  3. Ilsa T Kirby

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ivan Siordia

    Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. David Hutin

    Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Marit Rasmussen

    Department of Nutrition, University of Oslo, Oslo, Norway
    Competing interests
    The authors declare that no competing interests exist.
  7. Denis M Grant

    Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Larry L David

    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Jason Matthews

    Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
    Competing interests
    The authors declare that no competing interests exist.
  10. Michael Lund Nielsen

    The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  11. Michael S Cohen

    Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
    For correspondence
    cohenmic@ohsu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7636-4156

Funding

National Institute of Neurological Disorders and Stroke (NIH 2R01NS088629)

  • Michael S Cohen

Pew Charitable Trusts (NA)

  • Michael S Cohen

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

Reviewing Editor

  1. Anthony K. L. Leung

Publication history

  1. Received: June 27, 2020
  2. Accepted: January 15, 2021
  3. Accepted Manuscript published: January 21, 2021 (version 1)
  4. Version of Record published: February 12, 2021 (version 2)
  5. Version of Record updated: March 2, 2021 (version 3)

Copyright

© 2021, Rodriguez 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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