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Steinbach A, Bhadkamkar V, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. Mol Biol Cell 2024; 35:ar27. [PMID: 38117589 PMCID: PMC10916871 DOI: 10.1091/mbc.e23-06-0260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila (L.p.) manipulates eukaryotic host ubiquitination machinery to form its replicative vacuole. While nearly 10% of L.p.'s ∼330 secreted effector proteins are ubiquitin ligases or deubiquitinases, a comprehensive measure of temporally resolved changes in the endogenous host ubiquitinome during infection has not been undertaken. To elucidate how L.p. hijacks host cell ubiquitin signaling, we generated a proteome-wide analysis of changes in protein ubiquitination during infection. We discover that L.p. infection increases ubiquitination of host regulators of subcellular trafficking and membrane dynamics, most notably ∼40% of mammalian Ras superfamily small GTPases. We determine that these small GTPases undergo nondegradative ubiquitination at the Legionella-containing vacuole (LCV) membrane. Finally, we find that the bacterial effectors SidC/SdcA play a central role in cross-family small GTPase ubiquitination, and that these effectors function upstream of SidE family ligases in the polyubiquitination and retention of GTPases in the LCV membrane. This work highlights the extensive reconfiguration of host ubiquitin signaling by bacterial effectors during infection and establishes simultaneous ubiquitination of small GTPases across the Ras superfamily as a novel consequence of L.p. infection. Our findings position L.p. as a tool to better understand how small GTPases can be regulated by ubiquitination in uninfected contexts.
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Affiliation(s)
- Adriana Steinbach
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- George Williams Hooper Foundation, University of California, San Francisco, CA 94143
| | - Varun Bhadkamkar
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- George Williams Hooper Foundation, University of California, San Francisco, CA 94143
| | - David Jimenez-Morales
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, CA 94309
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Gwendolyn M. Jang
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Nevan J. Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Danielle L. Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- George Williams Hooper Foundation, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551750. [PMID: 37577546 PMCID: PMC10418220 DOI: 10.1101/2023.08.03.551750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The intracellular bacterial pathogen Legionella pneumophila (L.p.) manipulates eukaryotic host ubiquitination machinery to form its replicative vacuole. While nearly 10% of L.p.'s arsenal of ~330 secreted effector proteins have been biochemically characterized as ubiquitin ligases or deubiquitinases, a comprehensive measure of temporally resolved changes in the endogenous host ubiquitinome during infection has not been undertaken. To elucidate how L.p hijacks ubiquitin signaling within the host cell, we undertook a proteome-wide analysis of changes in protein ubiquitination during infection. We discover that L.p. infection results in increased ubiquitination of host proteins regulating subcellular trafficking and membrane dynamics, most notably 63 of ~160 mammalian Ras superfamily small GTPases. We determine that these small GTPases predominantly undergo non-degradative monoubiquitination, and link ubiquitination to recruitment to the Legionella-containing vacuole membrane. Finally, we find that the bacterial effectors SidC/SdcA play a central, but likely indirect, role in cross-family small GTPase ubiquitination. This work highlights the extensive reconfiguration of host ubiquitin signaling by bacterial effectors during infection and establishes simultaneous ubiquitination of small GTPases across the Ras superfamily as a novel consequence of L.p. infection. This work positions L.p. as a tool to better understand how small GTPases can be regulated by ubiquitination in uninfected contexts.
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Affiliation(s)
- Adriana M. Steinbach
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - Varun L. Bhadkamkar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - David Jimenez-Morales
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, California, United States of America
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Gwendolyn M. Jang
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Danielle L. Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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