Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages

  1. Jonathan M Budzik
  2. Danielle L Swaney
  3. David Jimenez-Morales
  4. Jeffrey R Johnson
  5. Nicholas E Garelis
  6. Teresa Repasy
  7. Allison W Roberts
  8. Lauren M Popov
  9. Trevor J Parry
  10. Dexter Pratt
  11. Trey Ideker
  12. Nevan J Krogan
  13. Jeffery S Cox  Is a corresponding author
  1. University of California, San Francisco, United States
  2. University of California, Berkeley, United States
  3. University of California, San Diego, United States

Abstract

Macrophages are highly plastic cells with critical roles in immunity, cancer, and tissue homeostasis, but how these distinct cellular fates are triggered by environmental cues is poorly understood. To uncover how primary murine macrophages respond to bacterial pathogens, we globally assessed changes in post-translational modifications of proteins during infection with Mycobacterium tuberculosis, a notorious intracellular pathogen. We identified hundreds of dynamically regulated phosphorylation and ubiquitylation sites, indicating that dramatic remodeling of multiple host pathways, both expected and unexpected, occurred during infection. Most of these cellular changes were not captured by mRNA profiling, and included activation of ubiquitin-mediated autophagy, an evolutionarily ancient cellular antimicrobial system. This analysis also revealed that a particular autophagy receptor, TAX1BP1, mediates clearance of ubiquitylated Mtb and targets bacteria to LC3-positive phagophores. These studies provide a new resource for understanding how macrophages shape their proteome to meet the challenge of infection.

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD015361.

The following data sets were generated

Article and author information

Author details

  1. Jonathan M Budzik

    Department of Medicine, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Danielle L Swaney

    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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6119-6084
  3. David Jimenez-Morales

    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. Jeffrey R Johnson

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francsico, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Nicholas E Garelis

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Teresa Repasy

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Allison W Roberts

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6681-4144
  8. Lauren M Popov

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Trevor J Parry

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Dexter Pratt

    Department of Medicine, University of California, San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Trey Ideker

    Department of Medicine, University of California, San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Nevan J Krogan

    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.
  13. Jeffery S Cox

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    jeff.cox@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5061-6618

Funding

National Institute of Allergy and Infectious Diseases (P01 AI063302)

  • Jeffery S Cox

Cystic Fibrosis Foundation (Harry Shwachman Award)

  • Jonathan M Budzik

National Institute of Allergy and Infectious Diseases (P01 AI063302)

  • Nevan J Krogan

National Institute of General Medical Sciences (P50 GM082250)

  • Nevan J Krogan

National Institute of Allergy and Infectious Diseases (U19 AI106754)

  • Nevan J Krogan

National Institute of Allergy and Infectious Diseases (U19 AI106754)

  • Jeffery S Cox

National Institute of Allergy and Infectious Diseases (DP1 AI124619)

  • Jeffery S Cox

National Institute of Allergy and Infectious Diseases (R01 AI120694)

  • Jeffery S Cox

National Institute of Allergy and Infectious Diseases (R01 AI120694)

  • Nevan J Krogan

National Institute of Allergy and Infectious Diseases (1K08AI146267)

  • Jonathan M Budzik

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

Ethics

Animal experimentation: An animal use protocol (AUP-2015-11-8096) for mouse use was approved by the Office of Laboratory and Animal Care at the University of California, Berkeley, in adherence with guidelines from the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health.

Reviewing Editor

  1. Bavesh D Kana, University of the Witwatersrand, South Africa

Publication history

  1. Received: August 29, 2019
  2. Accepted: January 16, 2020
  3. Accepted Manuscript published: January 17, 2020 (version 1)
  4. Version of Record published: February 19, 2020 (version 2)

Copyright

© 2020, Budzik 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. Jonathan M Budzik
  2. Danielle L Swaney
  3. David Jimenez-Morales
  4. Jeffrey R Johnson
  5. Nicholas E Garelis
  6. Teresa Repasy
  7. Allison W Roberts
  8. Lauren M Popov
  9. Trevor J Parry
  10. Dexter Pratt
  11. Trey Ideker
  12. Nevan J Krogan
  13. Jeffery S Cox
(2020)
Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages
eLife 9:e51461.
https://doi.org/10.7554/eLife.51461

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