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

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.

Data availability

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

The following data sets were generated

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.

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.

Metrics

  • 4,119
    views
  • 681
    downloads
  • 61
    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. 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
(2021)
Chemical genetics and proteome-wide site mapping reveal cysteine MARylation by PARP-7 on immune-relevant protein targets
eLife 10:e60480.
https://doi.org/10.7554/eLife.60480

Share this article

https://doi.org/10.7554/eLife.60480

Further reading

    1. Biochemistry and Chemical Biology
    Nelson García-Vázquez, Tania J González-Robles ... Michele Pagano
    Research Article

    In healthy cells, cyclin D1 is expressed during the G1 phase of the cell cycle, where it activates CDK4 and CDK6. Its dysregulation is a well-established oncogenic driver in numerous human cancers. The cancer-related function of cyclin D1 has been primarily studied by focusing on the phosphorylation of the retinoblastoma (RB) gene product. Here, using an integrative approach combining bioinformatic analyses and biochemical experiments, we show that GTSE1 (G-Two and S phases expressed protein 1), a protein positively regulating cell cycle progression, is a previously unrecognized substrate of cyclin D1–CDK4/6 in tumor cells overexpressing cyclin D1 during G1 and subsequent phases. The phosphorylation of GTSE1 mediated by cyclin D1–CDK4/6 inhibits GTSE1 degradation, leading to high levels of GTSE1 across all cell cycle phases. Functionally, the phosphorylation of GTSE1 promotes cellular proliferation and is associated with poor prognosis within a pan-cancer cohort. Our findings provide insights into cyclin D1’s role in cell cycle control and oncogenesis beyond RB phosphorylation.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Mai Nguyen, Elda Bauda ... Cecile Morlot
    Research Article

    Teichoic acids (TA) are linear phospho-saccharidic polymers and important constituents of the cell envelope of Gram-positive bacteria, either bound to the peptidoglycan as wall teichoic acids (WTA) or to the membrane as lipoteichoic acids (LTA). The composition of TA varies greatly but the presence of both WTA and LTA is highly conserved, hinting at an underlying fundamental function that is distinct from their specific roles in diverse organisms. We report the observation of a periplasmic space in Streptococcus pneumoniae by cryo-electron microscopy of vitreous sections. The thickness and appearance of this region change upon deletion of genes involved in the attachment of TA, supporting their role in the maintenance of a periplasmic space in Gram-positive bacteria as a possible universal function. Consequences of these mutations were further examined by super-resolved microscopy, following metabolic labeling and fluorophore coupling by click chemistry. This novel labeling method also enabled in-gel analysis of cell fractions. With this approach, we were able to titrate the actual amount of TA per cell and to determine the ratio of WTA to LTA. In addition, we followed the change of TA length during growth phases, and discovered that a mutant devoid of LTA accumulates the membrane-bound polymerized TA precursor.