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Ma K, Xian W, Liu H, Shu R, Ge J, Luo ZQ, Liu X, Qiu J. Bacterial ubiquitin ligases hijack the host deubiquitinase OTUB1 to inhibit MTORC1 signaling and promote autophagy. Autophagy 2024; 20:1968-1983. [PMID: 38818749 PMCID: PMC11346569 DOI: 10.1080/15548627.2024.2353492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/21/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024] Open
Abstract
Many bacterial pathogens have evolved effective strategies to interfere with the ubiquitination network to evade clearance by the innate immune system. Here, we report that OTUB1, one of the most abundant deubiquitinases (DUBs) in mammalian cells, is subjected to both canonical and noncanonical ubiquitination during Legionella pneumophila infection. The effectors SidC and SdcA catalyze OTUB1 ubiquitination at multiple lysine residues, resulting in its association with a Legionella-containing vacuole. Lysine ubiquitination by SidC and SdcA promotes interactions between OTUB1 and DEPTOR, an inhibitor of the MTORC1 pathway, thus suppressing MTORC1 signaling. The inhibition of MTORC1 leads to suppression of host protein synthesis and promotion of host macroautophagy/autophagy during L. pneumophila infection. In addition, members of the SidE family effectors (SidEs) induce phosphoribosyl (PR)-linked ubiquitination of OTUB1 at Ser16 and Ser18 and block its DUB activity. The levels of the lysine and serine ubiquitination of OTUB1 are further regulated by effectors that function to antagonize the activities of SidC, SdcA and SidEs, including Lem27, DupA, DupB, SidJ and SdjA. Our study reveals an effectors-mediated complicated mechanism in regulating the activity of a host DUB.Abbreviations: BafA1: bafilomycin A1; BMDMs: bone marrow-derived macrophages; DUB: deubiquitinase; Dot/Icm: defective for organelle trafficking/intracellular multiplication; DEPTOR: DEP domain containing MTOR interacting protein; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; L. pneumophila: Legionella pneumophila; LCV: Legionella-containing vacuole; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTORC1: mechanistic target of rapamycin kinase complex 1; OTUB1: OTU deubiquitinase, ubiquitin aldehyde binding 1; PR-Ub: phosphoribosyl (PR)-linked ubiquitin; PTM: posttranslational modification; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SidEs: SidE family effectors; Ub: ubiquitin.
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Affiliation(s)
- Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Rundong Shu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
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Choi M, Jeong M, Kang S, Jeon H, Shin D. Legionella pneumophila evades host-autophagic clearance using phosphoribosyl-polyubiquitin chains. Nat Commun 2024; 15:7480. [PMID: 39214961 PMCID: PMC11364748 DOI: 10.1038/s41467-024-51277-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Affiliation(s)
- Minhyeong Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 03722, Seoul, Republic of Korea
| | - Minwoo Jeong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 03722, Seoul, Republic of Korea
| | - Sangwoo Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 03722, Seoul, Republic of Korea
| | - Hayoung Jeon
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 03722, Seoul, Republic of Korea
| | - Donghyuk Shin
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 03722, Seoul, Republic of Korea.
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Ma K, Shu R, Liu H, Ge J, Liu J, Lu Q, Fu J, Liu X, Qiu J. Legionella effectors SidC/SdcA ubiquitinate multiple small GTPases and SNARE proteins to promote phagosomal maturation. Cell Mol Life Sci 2024; 81:249. [PMID: 38836877 PMCID: PMC11335287 DOI: 10.1007/s00018-024-05271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024]
Abstract
Protein ubiquitination is one of the most important posttranslational modifications (PTMs) in eukaryotes and is involved in the regulation of almost all cellular signaling pathways. The intracellular bacterial pathogen Legionella pneumophila translocates at least 26 effectors to hijack host ubiquitination signaling via distinct mechanisms. Among these effectors, SidC/SdcA are novel E3 ubiquitin ligases with the adoption of a Cys-His-Asp catalytic triad. SidC/SdcA are critical for the recruitment of endoplasmic reticulum (ER)-derived vesicles to the Legionella-containing vacuole (LCV). However, the ubiquitination targets of SidC/SdcA are largely unknown, which restricts our understanding of the mechanisms used by these effectors to hijack the vesicle trafficking pathway. Here, we demonstrated that multiple Rab small GTPases and target soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) proteins are bona fide ubiquitination substrates of SidC/SdcA. SidC/SdcA-mediated ubiquitination of syntaxin 3 and syntaxin 4 promotes their unconventional pairing with the vesicle-SNARE protein Sec22b, thereby contributing to the membrane fusion of ER-derived vesicles with the phagosome. In addition, our data reveal that ubiquitination of Rab7 by SidC/SdcA is critical for its association with the LCV membrane. Rab7 ubiquitination could impair its binding with the downstream effector Rab-interacting lysosomal protein (RILP), which partially explains why LCVs avoid fusion with lysosomes despite the acquisition of Rab7. Taken together, our study reveals the biological mechanisms employed by SidC/SdcA to promote the maturation of the LCVs.
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Affiliation(s)
- Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Rundong Shu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jiayang Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Qian Lu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jiaqi Fu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China.
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Kubori T, Arasaki K, Oide H, Kitao T, Nagai H. Multi-tiered actions of Legionella effectors to modulate host Rab10 dynamics. eLife 2024; 12:RP89002. [PMID: 38771316 PMCID: PMC11108646 DOI: 10.7554/elife.89002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Rab GTPases are representative targets of manipulation by intracellular bacterial pathogens for hijacking membrane trafficking. Legionella pneumophila recruits many Rab GTPases to its vacuole and exploits their activities. Here, we found that infection-associated regulation of Rab10 dynamics involves ubiquitin signaling cascades mediated by the SidE and SidC families of Legionella ubiquitin ligases. Phosphoribosyl-ubiquitination of Rab10 catalyzed by the SidE ligases is crucial for its recruitment to the bacterial vacuole. SdcB, the previously uncharacterized SidC-family effector, resides on the vacuole and contributes to retention of Rab10 at the late stages of infection. We further identified MavC as a negative regulator of SdcB. By the transglutaminase activity, MavC crosslinks ubiquitin to SdcB and suppresses its function, resulting in elimination of Rab10 from the vacuole. These results demonstrate that the orchestrated actions of many L. pneumophila effectors fine-tune the dynamics of Rab10 during infection.
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Affiliation(s)
- Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Hiromu Oide
- School of Life Sciences, Tokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu UniversityGifuJapan
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Chadha A, Yanai Y, Oide H, Wakana Y, Inoue H, Saha S, Tagaya M, Arasaki K, Mukherjee S. Legionella uses host Rab GTPases and BAP31 to create a unique ER niche. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593622. [PMID: 38765994 PMCID: PMC11100814 DOI: 10.1101/2024.05.10.593622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Upon entry into host cells, the facultative intracellular bacterium Legionella pneumophila ( L.p .) uses its type IV secretion system, Dot/Icm, to secrete ~330 bacterial effector proteins into the host cell. Some of these effectors hijack endoplasmic reticulum (ER)-derived vesicles to form the Legionella -containing vacuole (LCV). Despite extensive investigation over decades, the fundamental question persists: Is the LCV membrane distinct from or contiguous with the host ER network? Here, we employ advanced photobleaching techniques, revealing a temporal acquisition of both smooth and rough ER (sER and rER) markers on the LCV. In the early stages of infection, the sER intimately associates with the LCV. Remarkably, as the infection progresses, the LCV evolves into a distinct niche comprising an rER membrane that is independent of the host ER network. We discover that the L.p. effector LidA binds to and recruits two host proteins of the Rab superfamily, Rab10, and Rab4, that play significant roles in acquiring sER and rER membranes, respectively. Additionally, we identify the pivotal role of a host ER-resident protein, BAP31, in orchestrating the transition from sER to rER. While previously recognized for shuttling between sER and rER, we demonstrate BAP31's role as a Rab effector, mediating communication between these ER sub-compartments. Furthermore, using genomic deletion strains, we uncover a novel L.p. effector, Lpg1152, essential for recruiting BAP31 to the LCV and facilitating its transition from sER to rER. Depletion of BAP31 or infection with an isogenic L.p. strain lacking Lpg1152 results in a growth defect. Collectively, our findings illuminate the intricate interplay between molecular players from both host and pathogen, elucidating how L.p. orchestrates the transformation of its residing vacuole membrane from a host-associated sER to a distinct rER membrane that is not contiguous with the host ER network.
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Hollingsworth LR, Veeraraghavan P, Paulo JA, Harper JW, Rauch I. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590338. [PMID: 38659763 PMCID: PMC11042255 DOI: 10.1101/2024.04.19.590338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript on pubpub.org (https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
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Affiliation(s)
- L. Robert Hollingsworth
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University
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7
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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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Yang Y, Mei L, Chen J, Chen X, Wang Z, Liu L, Yang A. Legionella pneumophila-mediated host posttranslational modifications. J Mol Cell Biol 2023; 15:mjad032. [PMID: 37156500 PMCID: PMC10720952 DOI: 10.1093/jmcb/mjad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023] Open
Abstract
Legionella pneumophila is a Gram-negative bacterium ubiquitously present in freshwater environments and causes a serious type of pneumonia called Legionnaires' disease. During infections, L. pneumophila releases over 300 effector proteins into host cells through an Icm/Dot type IV secretion system to manipulate the host defense system for survival within the host. Notably, certain effector proteins mediate posttranslational modifications (PTMs), serving as useful approaches exploited by L. pneumophila to modify host proteins. Some effectors catalyze the addition of host protein PTMs, while others mediate the removal of PTMs from host proteins. In this review, we summarize L. pneumophila effector-mediated PTMs of host proteins, including phosphorylation, ubiquitination, glycosylation, AMPylation, phosphocholination, methylation, and ADP-ribosylation, as well as dephosphorylation, deubiquitination, deAMPylation, deADP-ribosylation, dephosphocholination, and delipidation. We describe their molecular mechanisms and biological functions in the regulation of bacterial growth and Legionella-containing vacuole biosynthesis and in the disruption of host immune and defense machinery.
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Affiliation(s)
- Yi Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
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Anand A, Mazur AC, Rosell-Arevalo P, Franzkoch R, Breitsprecher L, Listian SA, Hüttel SV, Müller D, Schäfer DG, Vormittag S, Hilbi H, Maniak M, Gutierrez MG, Barisch C. ER-dependent membrane repair of mycobacteria-induced vacuole damage. mBio 2023; 14:e0094323. [PMID: 37676004 PMCID: PMC10653851 DOI: 10.1128/mbio.00943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Tuberculosis still remains a global burden and is one of the top infectious diseases from a single pathogen. Mycobacterium tuberculosis, the causative agent, has perfected many ways to replicate and persist within its host. While mycobacteria induce vacuole damage to evade the toxic environment and eventually escape into the cytosol, the host recruits repair machineries to restore the MCV membrane. However, how lipids are delivered for membrane repair is poorly understood. Using advanced fluorescence imaging and volumetric correlative approaches, we demonstrate that this involves the recruitment of the endoplasmic reticulum (ER)-Golgi lipid transfer protein OSBP8 in the Dictyostelium discoideum/Mycobacterium marinum system. Strikingly, depletion of OSBP8 affects lysosomal function accelerating mycobacterial growth. This indicates that an ER-dependent repair pathway constitutes a host defense mechanism against intracellular pathogens such as M. tuberculosis.
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Affiliation(s)
- Aby Anand
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Anna-Carina Mazur
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Patricia Rosell-Arevalo
- Host–Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Rico Franzkoch
- Integrated Bioimaging Facility, Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Leonhard Breitsprecher
- Integrated Bioimaging Facility, Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Stevanus A. Listian
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Sylvana V. Hüttel
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Danica Müller
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Deise G. Schäfer
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Simone Vormittag
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Markus Maniak
- Department of Cell Biology, University of Kassel, Kassel, Germany
| | - Maximiliano G. Gutierrez
- Host–Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Caroline Barisch
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
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10
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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11
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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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12
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Vormittag S, Ende RJ, Derré I, Hilbi H. Pathogen vacuole membrane contact sites - close encounters of the fifth kind. MICROLIFE 2023; 4:uqad018. [PMID: 37223745 PMCID: PMC10117887 DOI: 10.1093/femsml/uqad018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/25/2023]
Abstract
Vesicular trafficking and membrane fusion are well-characterized, versatile, and sophisticated means of 'long range' intracellular protein and lipid delivery. Membrane contact sites (MCS) have been studied in far less detail, but are crucial for 'short range' (10-30 nm) communication between organelles, as well as between pathogen vacuoles and organelles. MCS are specialized in the non-vesicular trafficking of small molecules such as calcium and lipids. Pivotal MCS components important for lipid transfer are the VAP receptor/tether protein, oxysterol binding proteins (OSBPs), the ceramide transport protein CERT, the phosphoinositide phosphatase Sac1, and the lipid phosphatidylinositol 4-phosphate (PtdIns(4)P). In this review, we discuss how these MCS components are subverted by bacterial pathogens and their secreted effector proteins to promote intracellular survival and replication.
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Affiliation(s)
| | | | - Isabelle Derré
- Corresponding author. Department of Microbiology, Immunology and Cancer Biology, University of Virginia, 1340 Jefferson Park Ave, Charlottesville, VA 22908, United States. Tel: +1-434-924-2330; E-mail:
| | - Hubert Hilbi
- Corresponding author. Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006 Zürich, Switzerland. Tel: +41-44-634-2650; E-mail:
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13
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Vormittag S, Hüsler D, Haneburger I, Kroniger T, Anand A, Prantl M, Barisch C, Maaß S, Becher D, Letourneur F, Hilbi H. Legionella- and host-driven lipid flux at LCV-ER membrane contact sites promotes vacuole remodeling. EMBO Rep 2023; 24:e56007. [PMID: 36588479 PMCID: PMC9986823 DOI: 10.15252/embr.202256007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/03/2023] Open
Abstract
Legionella pneumophila replicates in macrophages and amoeba within a unique compartment, the Legionella-containing vacuole (LCV). Hallmarks of LCV formation are the phosphoinositide lipid conversion from PtdIns(3)P to PtdIns(4)P, fusion with ER-derived vesicles and a tight association with the ER. Proteomics of purified LCVs indicate the presence of membrane contact sites (MCS) proteins possibly implicated in lipid exchange. Using dually fluorescence-labeled Dictyostelium discoideum amoeba, we reveal that VAMP-associated protein (Vap) and the PtdIns(4)P 4-phosphatase Sac1 localize to the ER, and Vap also localizes to the LCV membrane. Furthermore, Vap as well as Sac1 promote intracellular replication of L. pneumophila and LCV remodeling. Oxysterol binding proteins (OSBPs) preferentially localize to the ER (OSBP8) or the LCV membrane (OSBP11), respectively, and restrict (OSBP8) or promote (OSBP11) bacterial replication and LCV expansion. The sterol probes GFP-D4H* and filipin indicate that sterols are rapidly depleted from LCVs, while PtdIns(4)P accumulates. In addition to Sac1, the PtdIns(4)P-subverting L. pneumophila effector proteins LepB and SidC also support LCV remodeling. Taken together, the Legionella- and host cell-driven PtdIns(4)P gradient at LCV-ER MCSs promotes Vap-, OSBP- and Sac1-dependent pathogen vacuole maturation.
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Affiliation(s)
- Simone Vormittag
- Institute of Medical MicrobiologyUniversity of ZürichZürichSwitzerland
| | - Dario Hüsler
- Institute of Medical MicrobiologyUniversity of ZürichZürichSwitzerland
| | - Ina Haneburger
- Institute of Medical MicrobiologyUniversity of ZürichZürichSwitzerland
| | - Tobias Kroniger
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Aby Anand
- Division of Molecular Infection Biology and Center for Cellular NanoanalyticsUniversity of OsnabrückOsnabrückGermany
| | - Manuel Prantl
- Institute of Medical MicrobiologyUniversity of ZürichZürichSwitzerland
| | - Caroline Barisch
- Division of Molecular Infection Biology and Center for Cellular NanoanalyticsUniversity of OsnabrückOsnabrückGermany
| | - Sandra Maaß
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Dörte Becher
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - François Letourneur
- Laboratory of Pathogen Host InteractionsUniversité de Montpellier, CNRS, INSERMMontpellierFrance
| | - Hubert Hilbi
- Institute of Medical MicrobiologyUniversity of ZürichZürichSwitzerland
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14
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Hay A, Rolland S, Bernard C, Héchard Y, Villéger R, Samba-Louaka A. Proteomic analysis of Acanthamoeba castellanii response to Legionella pneumophila infection. FEMS Microbiol Lett 2023; 370:fnad086. [PMID: 37653467 DOI: 10.1093/femsle/fnad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Legionella pneumophila is an opportunistic pathogen responsible for Legionnaires' disease or Legionellosis. This bacterium is found in the environment interacting with free-living amoebae such as Acanthamoeba castellanii. Until now, proteomic analyses have been done in amoebae infected with L. pneumophila but focused on the Legionella-containing vacuole. In this study, we propose a global proteomic analysis of the A. castellanii proteome following infection with L. pneumophila wild-type (WT) or with an isogenic ΔdotA mutant strain, which is unable to replicate intracellularly. We found that infection with L. pneumophila WT leads to reduced levels of A. castellanii proteins associated with lipid homeostasis/metabolism, GTPase regulation, and kinase. The levels of organelle-associated proteins were also decreased during infection. Legionellapneumophila WT infection leads to increased levels of proteins associated with polyubiquitination, folding or degradation, and antioxidant activities. This study reinforces our knowledge of this too little explored but so fundamental interaction between L. pneumophila and A. castellanii, to understand how the bacterium could resist amoeba digestion.
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Affiliation(s)
- Alban Hay
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 86073 Poitiers, France
| | - Steven Rolland
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 86073 Poitiers, France
| | - Clément Bernard
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 86073 Poitiers, France
| | - Yann Héchard
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 86073 Poitiers, France
| | - Romain Villéger
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 86073 Poitiers, France
| | - Ascel Samba-Louaka
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 86073 Poitiers, France
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15
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Welin A, Hüsler D, Hilbi H. Imaging Flow Cytometry of Legionella-Containing Vacuoles in Intact and Homogenized Wild-Type and Mutant Dictyostelium. Methods Mol Biol 2023; 2635:63-85. [PMID: 37074657 DOI: 10.1007/978-1-0716-3020-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The causative agent of a severe pneumonia termed "Legionnaires' disease", Legionella pneumophila, replicates within protozoan and mammalian phagocytes in a specialized intracellular compartment called the Legionella-containing vacuole (LCV). This compartment does not fuse with bactericidal lysosomes but communicates extensively with several cellular vesicle trafficking pathways and eventually associates tightly with the endoplasmic reticulum. In order to comprehend in detail the complex process of LCV formation, the identification and kinetic analysis of cellular trafficking pathway markers on the pathogen vacuole are crucial. This chapter describes imaging flow cytometry (IFC)-based methods for the objective, quantitative and high-throughput analysis of different fluorescently tagged proteins or probes on the LCV. To this end, we use the haploid amoeba Dictyostelium discoideum as an infection model for L. pneumophila, to analyze either fixed intact infected host cells or LCVs from homogenized amoebae. Parental strains and isogenic mutant amoebae are compared in order to determine the contribution of a specific host factor to LCV formation. The amoebae simultaneously produce two different fluorescently tagged probes enabling tandem quantification of two LCV markers in intact amoebae or the identification of LCVs using one probe and quantification of the other probe in host cell homogenates. The IFC approach allows rapid generation of statistically robust data from thousands of pathogen vacuoles and can be applied to other infection models.
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Affiliation(s)
- Amanda Welin
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Dario Hüsler
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland.
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16
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Tomaskovic I, Gonzalez A, Dikic I. Ubiquitin and Legionella: From bench to bedside. Semin Cell Dev Biol 2022; 132:230-241. [PMID: 35177348 DOI: 10.1016/j.semcdb.2022.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
Legionella pneumophila, a Gram-negative intracellular bacterium, is one of the major causes of Legionnaires' disease, a specific type of atypical pneumonia. Despite intensive research efforts that elucidated many relevant structural, molecular and medical insights into Legionella's pathogenicity, Legionnaires' disease continues to present an ongoing public health concern. Legionella's virulence is based on its ability to simultaneously hijack multiple molecular pathways of the host cell to ensure its fast replication and dissemination. Legionella usurps the host ubiquitin system through multiple effector proteins, using the advantage of both conventional and unconventional (phosphoribosyl-linked) ubiquitination, thus providing optimal conditions for its replication. In this review, we summarize the current understanding of L. pneumophila from medical, biochemical and molecular perspectives. We describe the clinical disease presentation, its diagnostics and treatment, as well as host-pathogen interactions, with the emphasis on the ability of Legionella to target the host ubiquitin system upon infection. Furthermore, the interdisciplinary use of innovative technologies enables better insights into the pathogenesis of Legionnaires' disease and provides new opportunities for its treatment and prevention.
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Affiliation(s)
- Ines Tomaskovic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany.
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17
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Legionella pneumophila Infection of Human Macrophages Retains Golgi Structure but Reduces O-Glycans. Pathogens 2022; 11:pathogens11080908. [PMID: 36015029 PMCID: PMC9415278 DOI: 10.3390/pathogens11080908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Abstract
Legionella pneumophila is an accidental pathogen that replicates intracellularly within the Legionella-containing vacuole (LCV) in macrophages. Within an hour of infection, L. pneumophila secretes effectors to manipulate Rab1 and intercept ER-derived vesicles to the LCV. The downstream consequences of interrupted ER trafficking on the Golgi of macrophages are not clear. We examined the Golgi structure and function in L. pneumophila-infected human U937 macrophages. Intriguingly, the size of the Golgi in infected macrophages remained similar to uninfected macrophages. Furthermore, TEM analysis also did not reveal any significant changes in the ultrastructure of the Golgi in L. pneumophila-infected cells. Drug-induced Golgi disruption impacted bacterial replication in human macrophages, suggesting that an intact organelle is important for bacteria growth. To probe for Golgi functionality after L. pneumophila infection, we assayed glycosylation levels using fluorescent lectins. Golgi O-glycosylation levels, visualized by the fluorescent cis-Golgi lectin, Helix pomatia agglutinin (HPA), significantly decreased over time as infection progressed, compared to control cells. N-glycosylation levels in the Golgi, as measured by L-PHA lectin staining, were not impacted by L. pneumophila infection. To understand the mechanism of reduced O-glycans in the Golgi we monitored UDP-GalNAc transporter levels in infected macrophages. The solute carrier family 35 membrane A2 (SLC35A2) protein levels were significantly reduced in L. pneumophila-infected U937 and HeLa cells and L. pneumophila growth in human macrophages benefitted from GalNAc supplementation. The pronounced reduction in Golgi HPA levels was dependent on the translocation apparatus DotA expression in bacteria and occurred in a ubiquitin-independent manner. Thus, L. pneumophila infection of human macrophages maintains and requires an intact host Golgi ultrastructure despite known interference of ER–Golgi trafficking. Finally, L. pneumophila infection blocks the formation of O-linked glycans and reduces SLC35A2 protein levels in infected human macrophages.
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18
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Lockwood DC, Amin H, Costa TRD, Schroeder GN. The Legionella pneumophila Dot/Icm type IV secretion system and its effectors. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35639581 DOI: 10.1099/mic.0.001187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To prevail in the interaction with eukaryotic hosts, many bacterial pathogens use protein secretion systems to release virulence factors at the host–pathogen interface and/or deliver them directly into host cells. An outstanding example of the complexity and sophistication of secretion systems and the diversity of their protein substrates, effectors, is the Defective in organelle trafficking/Intracellular multiplication (Dot/Icm) Type IVB secretion system (T4BSS) of
Legionella pneumophila
and related species.
Legionella
species are facultative intracellular pathogens of environmental protozoa and opportunistic human respiratory pathogens. The Dot/Icm T4BSS translocates an exceptionally large number of effectors, more than 300 per
L. pneumophila
strain, and is essential for evasion of phagolysosomal degradation and exploitation of protozoa and human macrophages as replicative niches. Recent technological advancements in the imaging of large protein complexes have provided new insight into the architecture of the T4BSS and allowed us to propose models for the transport mechanism. At the same time, significant progress has been made in assigning functions to about a third of
L. pneumophila
effectors, discovering unprecedented new enzymatic activities and concepts of host subversion. In this review, we describe the current knowledge of the workings of the Dot/Icm T4BSS machinery and provide an overview of the activities and functions of the to-date characterized effectors in the interaction of
L. pneumophila
with host cells.
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Affiliation(s)
- Daniel C Lockwood
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
| | - Himani Amin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Gunnar N Schroeder
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
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19
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Ge Z, Yuan P, Chen L, Chen J, Shen D, She Z, Lu Y. New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila. Mol Cell Proteomics 2022; 21:100233. [PMID: 35427813 PMCID: PMC9112007 DOI: 10.1016/j.mcpro.2022.100233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 01/11/2023] Open
Abstract
Legionella pneumophila, an environmental bacterium that parasitizes protozoa, causes Legionnaires’ disease in humans that is characterized by severe pneumonia. This bacterium adopts a distinct biphasic life cycle consisting of a nonvirulent replicative phase and a virulent transmissive phase in response to different environmental conditions. Hence, the timely and fine-tuned expression of growth and virulence factors in a life cycle–dependent manner is crucial for survival and replication. Here, we report that the completion of the biphasic life cycle and bacterial pathogenesis is greatly dependent on the protein homeostasis regulated by caseinolytic protease P (ClpP)-dependent proteolysis. We characterized the ClpP-dependent dynamic profiles of the regulatory and substrate proteins during the biphasic life cycle of L. pneumophila using proteomic approaches and discovered that ClpP-dependent proteolysis specifically and conditionally degraded the substrate proteins, thereby directly playing a regulatory role or indirectly controlling cellular events via the regulatory proteins. We further observed that ClpP-dependent proteolysis is required to monitor the abundance of fatty acid biosynthesis–related protein Lpg0102/Lpg0361/Lpg0362 and SpoT for the normal regulation of L. pneumophila differentiation. We also found that the control of the biphasic life cycle and bacterial virulence is independent. Furthermore, the ClpP-dependent proteolysis of Dot/Icm (defect in organelle trafficking/intracellular multiplication) type IVB secretion system and effector proteins at a specific phase of the life cycle is essential for bacterial pathogenesis. Therefore, our findings provide novel insights on ClpP-dependent proteolysis, which spans a broad physiological spectrum involving key metabolic pathways that regulate the transition of the biphasic life cycle and bacterial virulence of L. pneumophila, facilitating adaptation to aquatic and intracellular niches. ClpP is the major determinant of biphasic life cycle–dependent protein turnover. ClpP-dependent proteolysis monitors SpoT abundance for cellular differentiation. ClpP-dependent regulation of life cycle and bacterial virulence is independent. ClpP-dependent proteolysis of T4BSS and effector proteins is vital for virulence.
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Affiliation(s)
- Zhenhuang Ge
- School of Chemistry, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China
| | - Peibo Yuan
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lingming Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junyi Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China
| | - Dong Shen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhigang She
- School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China.
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20
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Luo J, Wang L, Song L, Luo ZQ. Exploitation of the Host Ubiquitin System: Means by Legionella pneumophila. Front Microbiol 2022; 12:790442. [PMID: 35003021 PMCID: PMC8727461 DOI: 10.3389/fmicb.2021.790442] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/30/2021] [Indexed: 01/12/2023] Open
Abstract
Ubiquitination is a commonly used post-translational modification (PTM) in eukaryotic cells, which regulates a wide variety of cellular processes, such as differentiation, apoptosis, cell cycle, and immunity. Because of its essential role in immunity, the ubiquitin network is a common target of infectious agents, which have evolved various effective strategies to hijack and co-opt ubiquitin signaling for their benefit. The intracellular pathogen Legionella pneumophila represents one such example; it utilizes a large cohort of virulence factors called effectors to modulate diverse cellular processes, resulting in the formation a compartment called the Legionella-containing vacuole (LCV) that supports its replication. Many of these effectors function to re-orchestrate ubiquitin signaling with distinct biochemical activities. In this review, we highlight recent progress in the mechanism of action of L. pneumophila effectors involved in ubiquitination and discuss their roles in bacterial virulence and host cell biology.
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Affiliation(s)
- Jingjing Luo
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lidong Wang
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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21
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Coronas-Serna JM, del Val E, Kagan JC, Molina M, Cid VJ. Heterologous Expression and Assembly of Human TLR Signaling Components in Saccharomyces cerevisiae. Biomolecules 2021; 11:1737. [PMID: 34827735 PMCID: PMC8615643 DOI: 10.3390/biom11111737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Toll-like receptor (TLR) signaling is key to detect pathogens and initiating inflammation. Ligand recognition triggers the assembly of supramolecular organizing centers (SMOCs) consisting of large complexes composed of multiple subunits. Building such signaling hubs relies on Toll Interleukin-1 Receptor (TIR) and Death Domain (DD) protein-protein interaction domains. We have expressed TIR domain-containing components of the human myddosome (TIRAP and MyD88) and triffosome (TRAM and TRIF) SMOCs in Saccharomyces cerevisiae, as a platform for their study. Interactions between the TLR4 TIR domain, TIRAP, and MyD88 were recapitulated in yeast. Human TIRAP decorated the yeast plasma membrane (PM), except for the bud neck, whereas MyD88 was found at cytoplasmic spots, which were consistent with endoplasmic reticulum (ER)-mitochondria junctions, as evidenced by co-localization with Mmm1 and Mdm34, components of the ER and Mitochondria Encounter Structures (ERMES). The formation of MyD88-TIRAP foci at the yeast PM was reinforced by co-expression of a membrane-bound TLR4 TIR domain. Mutations in essential residues of their TIR domains aborted MyD88 recruitment by TIRAP, but their respective subcellular localizations were unaltered. TRAM and TRIF, however, did not co-localize in yeast. TRAM assembled long PM-bound filaments that were disrupted by co-expression of the TLR4 TIR domain. Our results evidence that the yeast model can be exploited to study the interactions and subcellular localization of human SMOC components in vivo.
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Affiliation(s)
- Julia María Coronas-Serna
- Departament of Microbiology and Parasitology, Faculty of Pharmacy, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRyCIS), Pza. Ramón y Cajal s/n, 28040 Madrid, Spain; (J.M.C.-S.); (E.d.V.)
| | - Elba del Val
- Departament of Microbiology and Parasitology, Faculty of Pharmacy, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRyCIS), Pza. Ramón y Cajal s/n, 28040 Madrid, Spain; (J.M.C.-S.); (E.d.V.)
| | - Jonathan C. Kagan
- Division of Gastroenterology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA;
| | - María Molina
- Departament of Microbiology and Parasitology, Faculty of Pharmacy, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRyCIS), Pza. Ramón y Cajal s/n, 28040 Madrid, Spain; (J.M.C.-S.); (E.d.V.)
| | - Víctor J. Cid
- Departament of Microbiology and Parasitology, Faculty of Pharmacy, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRyCIS), Pza. Ramón y Cajal s/n, 28040 Madrid, Spain; (J.M.C.-S.); (E.d.V.)
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Abstract
Legionella pneumophila, the causative agent of Legionnaires' disease, is a facultative intracellular pathogen that survives inside phagocytic host cells by establishing a protected replication niche, termed the "Legionella-containing vacuole" (LCV). To form an LCV and subvert pivotal host pathways, L. pneumophila employs a type IV secretion system (T4SS), which translocates more than 300 different effector proteins into the host cell. The L. pneumophila T4SS complex has been shown to span the bacterial cell envelope at the bacterial poles. However, the interactions between the T4SS and the LCV membrane are not understood. Using cryo-focused ion beam milling, cryo-electron tomography, and confocal laser scanning fluorescence microscopy, we show that up to half of the intravacuolar L. pneumophila bacteria tether their cell pole to the LCV membrane. Tethering coincides with the presence and function of T4SSs and likely promotes the establishment of distinct contact sites between T4SSs and the LCV membrane. Contact sites are characterized by indentations in the limiting LCV membrane and localize juxtaposed to T4SS machineries. The data are in agreement with the notion that effector translocation occurs by close membrane contact rather than by an extended pilus. Our findings provide novel insights into the interactions of the L. pneumophila T4SS with the LCV membrane in situ. IMPORTANCE Legionnaires' disease is a life-threatening pneumonia, which is characterized by high fever, coughing, shortness of breath, muscle pain, and headache. The disease is caused by the amoeba-resistant bacterium L. pneumophila found in various soil and aquatic environments and is transmitted to humans via the inhalation of small bacteria-containing droplets. An essential virulence factor of L. pneumophila is a so-called "type IV secretion system" (T4SS), which, by injecting a plethora of "effector proteins" into the host cell, determines pathogen-host interactions and the formation of a distinct intracellular compartment, the "Legionella-containing vacuole" (LCV). It is unknown how the T4SS makes contact to the LCV membrane to deliver the effectors. In this study, we identify indentations in the host cell membrane in close proximity to functional T4SSs localizing at the bacterial poles. Our work reveals first insights into the architecture of Legionella-LCV contact sites.
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Striednig B, Lanner U, Niggli S, Katic A, Vormittag S, Brülisauer S, Hochstrasser R, Kaech A, Welin A, Flieger A, Ziegler U, Schmidt A, Hilbi H, Personnic N. Quorum sensing governs a transmissive Legionella subpopulation at the pathogen vacuole periphery. EMBO Rep 2021; 22:e52972. [PMID: 34314090 PMCID: PMC8419707 DOI: 10.15252/embr.202152972] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 01/24/2023] Open
Abstract
The Gram‐negative bacterium Legionella pneumophila is the causative agent of Legionnaires' disease and replicates in amoebae and macrophages within a distinct compartment, the Legionella‐containing vacuole (LCV). The facultative intracellular pathogen switches between a replicative, non‐virulent and a non‐replicating, virulent/transmissive phase. Here, we show on a single‐cell level that at late stages of infection, individual motile (PflaA‐GFP‐positive) and virulent (PralF‐ and PsidC‐GFP‐positive) L. pneumophila emerge in the cluster of non‐growing bacteria within an LCV. Comparative proteomics of PflaA‐GFP‐positive and PflaA‐GFP‐negative L. pneumophila subpopulations reveals distinct proteomes with flagellar proteins or cell division proteins being preferentially produced by the former or the latter, respectively. Toward the end of an infection cycle (˜ 48 h), the PflaA‐GFP‐positive L. pneumophila subpopulation emerges at the cluster periphery, predominantly escapes the LCV, and spreads from the bursting host cell. These processes are mediated by the Legionella quorum sensing (Lqs) system. Thus, quorum sensing regulates the emergence of a subpopulation of transmissive L. pneumophila at the LCV periphery, and phenotypic heterogeneity underlies the intravacuolar bi‐phasic life cycle of L. pneumophila.
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Affiliation(s)
- Bianca Striednig
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Ulrike Lanner
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Selina Niggli
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Ana Katic
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Simone Vormittag
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Sabrina Brülisauer
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Ramon Hochstrasser
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zürich, Zürich, Switzerland
| | - Amanda Welin
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Urs Ziegler
- Center for Microscopy and Image Analysis, University of Zürich, Zürich, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Nicolas Personnic
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
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Legionella hijacks the host Golgi-to-ER retrograde pathway for the association of Legionella-containing vacuole with the ER. PLoS Pathog 2021; 17:e1009437. [PMID: 33760868 PMCID: PMC8021152 DOI: 10.1371/journal.ppat.1009437] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/05/2021] [Accepted: 03/01/2021] [Indexed: 11/19/2022] Open
Abstract
Legionella pneumophila (L. pneumophila) is a gram-negative bacterium that replicates in a compartment that resembles the host endoplasmic reticulum (ER). To create its replicative niche, L. pneumophila manipulates host membrane traffic and fusion machineries. Bacterial proteins called Legionella effectors are translocated into the host cytosol and play a crucial role in these processes. In an early stage of infection, Legionella subverts ER-derived vesicles (ERDVs) by manipulating GTPase Rab1 to facilitate remodeling of the Legionella-containing vacuole (LCV). Subsequently, the LCV associates with the ER in a mechanism that remains elusive. In this study, we show that L. pneumophila recruits GTPases Rab33B and Rab6A, which regulate vesicle trafficking from the Golgi to the ER, to the LCV to promote the association of LCV with the ER. We found that recruitment of Rab6A to the LCV depends on Rab33B. Legionella effector SidE family proteins, which phosphoribosyl-ubiquitinate Rab33B, were found to be necessary for the recruitment of Rab33B to the LCV. Immunoprecipitation experiments revealed that L. pneumophila facilitates the interaction of Rab6 with ER-resident SNAREs comprising syntaxin 18, p31, and BNIP1, but not tethering factors including NAG, RINT-1, and ZW10, which are normally required for syntaxin 18-mediated fusion of Golgi-derived vesicles with the ER. Our results identified a Rab33B-Rab6A cascade on the LCV and the interaction of Rab6 with ER-resident SNARE proteins for the association of LCV with the ER and disclosed the unidentified physiological role of SidE family proteins. Legionella pneumophila causes a sever pneumonia called Legionnaires’ disease and a threat of this disease has increased on a world-wide scale. As a feature of L. pneumophila, it secrets over 300 bacterial effectors to adapt and survive inside the host and many of effectors modify the host proteins in a unique manner. L. pneumophila is known to travel inside the host and final destination of this pathogens is the host ER. In the initial step of this travel, L. pneumophila subverts host early vesicular trafficking to remodel the membrane composition of Legionella-containing vacuole (LCV). Although this remodeling process has been well characterized, the molecular machinery of association of remodeled vacuoles with the ER is still obscure. This paper shows that the host GTPases Rab6A and Rab33B, both of which control Golgi-to-ER traffic, are recruited to the LCV in a cascade manner and are required for the association of LCVs with the ER through the interaction between Rab6A and ER-resident t-SNARE proteins. Of note, we demonstrate that a bacteria-specific Rab33B modification called phosphoribosyl-ubiquitination by Legionella effectors proteins of the SidE family is essential for the recruitment of Rab33B to the LCV.
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Nguyen JA, Yates RM. Better Together: Current Insights Into Phagosome-Lysosome Fusion. Front Immunol 2021; 12:636078. [PMID: 33717183 PMCID: PMC7946854 DOI: 10.3389/fimmu.2021.636078] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Following phagocytosis, the nascent phagosome undergoes maturation to become a phagolysosome with an acidic, hydrolytic, and often oxidative lumen that can efficiently kill and digest engulfed microbes, cells, and debris. The fusion of phagosomes with lysosomes is a principal driver of phagosomal maturation and is targeted by several adapted intracellular pathogens. Impairment of this process has significant consequences for microbial infection, tissue inflammation, the onset of adaptive immunity, and disease. Given the importance of phagosome-lysosome fusion to phagocyte function and the many virulence factors that target it, it is unsurprising that multiple molecular pathways have evolved to mediate this essential process. While the full range of these pathways has yet to be fully characterized, several pathways involving proteins such as members of the Rab GTPases, tethering factors and SNAREs have been identified. Here, we summarize the current state of knowledge to clarify the ambiguities in the field and construct a more comprehensive phagolysosome formation model. Lastly, we discuss how other cellular pathways help support phagolysosome biogenesis and, consequently, phagocyte function.
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Affiliation(s)
- Jenny A Nguyen
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Robin M Yates
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, Snyder Institute of Chronic Disease, University of Calgary, Calgary, AB, Canada
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26
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Price CT, Abu Kwaik Y. Evolution and Adaptation of Legionella pneumophila to Manipulate the Ubiquitination Machinery of Its Amoebae and Mammalian Hosts. Biomolecules 2021; 11:biom11010112. [PMID: 33467718 PMCID: PMC7830128 DOI: 10.3390/biom11010112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin pathway is highly conserved across the eukaryotic domain of life and plays an essential role in a plethora of cellular processes. It is not surprising that many intracellular bacterial pathogens often target the essential host ubiquitin pathway. The intracellular bacterial pathogen Legionella pneumophila injects into the host cell cytosol multiple classes of classical and novel ubiquitin-modifying enzymes that modulate diverse ubiquitin-related processes in the host cell. Most of these pathogen-injected proteins, designated as effectors, mimic known E3-ubiquitin ligases through harboring F-box or U-box domains. The classical F-box effector, AnkB targets host proteins for K48-linked polyubiquitination, which leads to excessive proteasomal degradation that is required to generate adequate supplies of amino acids for metabolism of the pathogen. In contrast, the SidC and SdcA effectors share no structural similarity to known eukaryotic ligases despite having E3-ubiquitin ligase activity, suggesting that the number of E3-ligases in eukaryotes is under-represented. L. pneumophila also injects into the host many novel ubiquitin-modifying enzymes, which are the SidE family of effectors that catalyze phosphoribosyl-ubiquitination of serine residue of target proteins, independently of the canonical E1-2-3 enzymatic cascade. Interestingly, the environmental bacterium, L. pneumophila, has evolved within a diverse range of amoebal species, which serve as the natural hosts, while accidental transmission through contaminated aerosols can cause pneumonia in humans. Therefore, it is likely that the novel ubiquitin-modifying enzymes of L. pneumophila were acquired by the pathogen through interkingdom gene transfer from the diverse natural amoebal hosts. Furthermore, conservation of the ubiquitin pathway across eukaryotes has enabled these novel ubiquitin-modifying enzymes to function similarly in mammalian cells. Studies on the biological functions of these effectors are likely to reveal further novel ubiquitin biology and shed further lights on the evolution of ubiquitin.
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Affiliation(s)
- Christopher T.D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, KY 40202, USA
- Correspondence:
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Kitao T, Nagai H, Kubori T. Divergence of Legionella Effectors Reversing Conventional and Unconventional Ubiquitination. Front Cell Infect Microbiol 2020; 10:448. [PMID: 32974222 PMCID: PMC7472693 DOI: 10.3389/fcimb.2020.00448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila employs bacteria-derived effector proteins in a variety of functions to exploit host cellular systems. The ubiquitination machinery constitutes a crucial eukaryotic system for the regulation of numerous cellular processes, and is a representative target for effector-mediated bacterial manipulation. L. pneumophila transports over 300 effector proteins into host cells through its Dot/Icm type IV secretion system. Among these, several effector proteins have been found to function as ubiquitin ligases, including unprecedented enzymes that catalyze ubiquitination through unconventional mechanisms. Recent studies have identified many L. pneumophila effector proteins that can interfere with ubiquitination. These effectors include proteins that are distantly related to the ovarian tumor protein superfamily described as deubiquitinases (DUBs), which regulate important signaling cascades in human cells. Intriguingly, L. pneumophila DUBs are not limited to enzymes that exhibit canonical DUB activity. Some L. pneumophila DUBs can catalyze the cleavage of the unconventional linkage between ubiquitin and substrates. Furthermore, novel mechanisms have been found that adversely affect the function of specific ubiquitin ligases; for instance, effector-mediated posttranslational modifications of ubiquitin ligases result in the inhibition of their activity. In the context of L. pneumophila infection, the existence of enzymes that reverse ubiquitination primarily relates to a fine tuning of biogenesis and remodeling of the Legionella-containing vacuole as a replicative niche. The complexity of the effector arrays reflects sophisticated strategies that bacteria have adopted to adapt their host environment and enable their survival in host cells. This review summarizes the current state of knowledge on the divergent mechanisms of the L. pneumophila effectors that can reverse ubiquitination, which is mediated by other effectors as well as the host ubiquitin machinery.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
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Berglund J, Gjondrekaj R, Verney E, Maupin-Furlow JA, Edelmann MJ. Modification of the host ubiquitome by bacterial enzymes. Microbiol Res 2020; 235:126429. [PMID: 32109687 PMCID: PMC7369425 DOI: 10.1016/j.micres.2020.126429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 12/14/2022]
Abstract
Attachment of ubiquitin molecules to protein substrates is a reversible post-translational modification (PTM), which occurs ubiquitously in eukaryotic cells and controls most cellular processes. As a consequence, ubiquitination is an attractive target of pathogen-encoded virulence factors. Pathogenic bacteria have evolved multiple mechanisms to hijack the host's ubiquitin system to their advantage. In this review, we discuss the bacteria-encoded E3 ligases and deubiquitinases translocated to the host for an addition or removal of eukaryotic ubiquitin modification, effectively hijacking the host's ubiquitination processes. We review bacterial enzymes homologous to host proteins in sequence and functions, as well as enzymes with novel mechanisms in ubiquitination, which have significant structural differences in comparison to the mammalian E3 ligases. Finally, we will also discuss examples of molecular "counter-weapons" - eukaryotic proteins, which counteract pathogen-encoded E3 ligases. The many examples of the pathogen effector molecules that catalyze eukaryotic ubiquitin modification bring to light the intricate pathways involved in the pathogenesis of some of the most virulent bacterial infections with human pathogens. The role of these effector molecules remains an essential determinant of bacterial virulence in terms of infection, invasion, and replication. A comprehensive understanding of the mechanisms dictating the mimicry employed by bacterial pathogens is of vital importance in developing new strategies for therapeutic approaches.
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Affiliation(s)
- Jennifer Berglund
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Rafaela Gjondrekaj
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Ellen Verney
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA.
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Divergent Evolution of Legionella RCC1 Repeat Effectors Defines the Range of Ran GTPase Cycle Targets. mBio 2020; 11:mBio.00405-20. [PMID: 32209684 PMCID: PMC7157520 DOI: 10.1128/mbio.00405-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Legionella pneumophila is a ubiquitous environmental bacterium which, upon inhalation, causes a life-threatening pneumonia termed Legionnaires’ disease. The opportunistic pathogen grows in amoebae and macrophages by employing a “type IV” secretion system, which secretes more than 300 different “effector” proteins into the host cell, where they subvert pivotal processes. The function of many of these effector proteins is unknown, and their evolution has not been studied. L. pneumophila RCC1 repeat effectors target the small GTPase Ran, a molecular switch implicated in different cellular processes such as nucleocytoplasmic transport and microtubule cytoskeleton dynamics. We provide evidence that one or more RCC1 repeat genes are distributed in two main clusters of L. pneumophila strains and have divergently evolved to target different components of the Ran GTPase activation cycle at different subcellular sites. Thus, L. pneumophila employs a sophisticated strategy to subvert host cell Ran GTPase during infection. Legionella pneumophila governs its interactions with host cells by secreting >300 different “effector” proteins. Some of these effectors contain eukaryotic domains such as the RCC1 (regulator of chromosome condensation 1) repeats promoting the activation of the small GTPase Ran. In this report, we reveal a conserved pattern of L. pneumophila RCC1 repeat genes, which are distributed in two main clusters of strains. Accordingly, strain Philadelphia-1 contains two RCC1 genes implicated in bacterial virulence, legG1 (Legionella eukaryotic gene 1), and ppgA, while strain Paris contains only one, pieG. The RCC1 repeat effectors localize to different cellular compartments and bind distinct components of the Ran GTPase cycle, including Ran modulators and the small GTPase itself, and yet they all promote the activation of Ran. The pieG gene spans the corresponding open reading frames of legG1 and a separate adjacent upstream gene, lpg1975. legG1 and lpg1975 are fused upon addition of a single nucleotide to encode a protein that adopts the binding specificity of PieG. Thus, a point mutation in pieG splits the gene, altering the effector target. These results indicate that divergent evolution of RCC1 repeat effectors defines the Ran GTPase cycle targets and that modulation of different components of the cycle might fine-tune Ran activation during Legionella infection.
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Hostile Takeover: Hijacking of Endoplasmic Reticulum Function by T4SS and T3SS Effectors Creates a Niche for Intracellular Pathogens. Microbiol Spectr 2020; 7. [PMID: 31198132 DOI: 10.1128/microbiolspec.psib-0027-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
After entering a cell, intracellular pathogens must evade destruction and generate a niche for intracellular replication. A strategy shared by multiple intracellular pathogens is the deployment of type III secretion system (T3SS)- and type IV secretion system (T4SS)-injected proteins (effectors) that subvert cellular functions. A subset of these effectors targets activities of the host cell's endoplasmic reticulum (ER). Effectors are now appreciated to interfere with the ER in multiple ways, including capture of secretory vesicles, tethering of pathogen vacuoles to the ER, and manipulation of ER-based autophagy initiation and the unfolded-protein response. These strategies enable pathogens to generate a niche with access to cellular nutrients and to evade the host cell's defenses.
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31
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Swart AL, Hilbi H. Phosphoinositides and the Fate of Legionella in Phagocytes. Front Immunol 2020; 11:25. [PMID: 32117224 PMCID: PMC7025538 DOI: 10.3389/fimmu.2020.00025] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/08/2020] [Indexed: 01/28/2023] Open
Abstract
Legionella pneumophila is the causative agent of a severe pneumonia called Legionnaires' disease. The environmental bacterium replicates in free-living amoebae as well as in lung macrophages in a distinct compartment, the Legionella-containing vacuole (LCV). The LCV communicates with a number of cellular vesicle trafficking pathways and is formed by a plethora of secreted bacterial effector proteins, which target host cell proteins and lipids. Phosphoinositide (PI) lipids are pivotal determinants of organelle identity, membrane dynamics and vesicle trafficking. Accordingly, eukaryotic cells tightly regulate the production, turnover, interconversion, and localization of PI lipids. L. pneumophila modulates the PI pattern in infected cells for its own benefit by (i) recruiting PI-decorated vesicles, (ii) producing effectors acting as PI interactors, phosphatases, kinases or phospholipases, and (iii) subverting host PI metabolizing enzymes. The PI conversion from PtdIns(3)P to PtdIns(4)P represents a decisive step during LCV maturation. In this review, we summarize recent progress on elucidating the strategies, by which L. pneumophila subverts host PI lipids to promote LCV formation and intracellular replication.
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Affiliation(s)
- A Leoni Swart
- Faculty of Medicine, Institute of Medical Microbiology, University of Zürich, Zurich, Switzerland
| | - Hubert Hilbi
- Faculty of Medicine, Institute of Medical Microbiology, University of Zürich, Zurich, Switzerland
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Mondino S, Schmidt S, Rolando M, Escoll P, Gomez-Valero L, Buchrieser C. Legionnaires’ Disease: State of the Art Knowledge of Pathogenesis Mechanisms of Legionella. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:439-466. [DOI: 10.1146/annurev-pathmechdis-012419-032742] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Legionella species are environmental gram-negative bacteria able to cause a severe form of pneumonia in humans known as Legionnaires’ disease. Since the identification of Legionella pneumophila in 1977, four decades of research on Legionella biology and Legionnaires’ disease have brought important insights into the biology of the bacteria and the molecular mechanisms that these intracellular pathogens use to cause disease in humans. Nowadays, Legionella species constitute a remarkable model of bacterial adaptation, with a genus genome shaped by their close coevolution with amoebae and an ability to exploit many hosts and signaling pathways through the secretion of a myriad of effector proteins, many of which have a eukaryotic origin. This review aims to discuss current knowledge of Legionella infection mechanisms and future research directions to be taken that might answer the many remaining open questions. This research will without a doubt be a terrific scientific journey worth taking.
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Affiliation(s)
- Sonia Mondino
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Silke Schmidt
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
- Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Monica Rolando
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Pedro Escoll
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
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Personnic N, Striednig B, Lezan E, Manske C, Welin A, Schmidt A, Hilbi H. Quorum sensing modulates the formation of virulent Legionella persisters within infected cells. Nat Commun 2019; 10:5216. [PMID: 31740681 PMCID: PMC6861284 DOI: 10.1038/s41467-019-13021-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
The facultative intracellular bacterium Legionella pneumophila replicates in environmental amoebae and in lung macrophages, and causes Legionnaires' disease. Here we show that L. pneumophila reversibly forms replicating and nonreplicating subpopulations of similar size within amoebae. The nonreplicating bacteria are viable and metabolically active, display increased antibiotic tolerance and a distinct proteome, and show high virulence as well as the capacity to form a degradation-resistant compartment. Upon infection of naïve or interferon-γ-activated macrophages, the nonreplicating subpopulation comprises ca. 10% or 50%, respectively, of the total intracellular bacteria; hence, the nonreplicating subpopulation is of similar size in amoebae and activated macrophages. The numbers of nonreplicating bacteria within amoebae are reduced in the absence of the autoinducer synthase LqsA or other components of the Lqs quorum-sensing system. Our results indicate that virulent, antibiotic-tolerant subpopulations of L. pneumophila are formed during infection of evolutionarily distant phagocytes, in a process controlled by the Lqs system.
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Affiliation(s)
- Nicolas Personnic
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland.
| | - Bianca Striednig
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Emmanuelle Lezan
- Proteomics Core Facility, Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Christian Manske
- Max von Pettenkofer Institute, Ludwig-Maximilians University Munich, Pettenkoferstrasse 9a, 80336, Munich, Germany
| | - Amanda Welin
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Hubert Hilbi
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
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Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. Cell Host Microbe 2019; 26:551-563.e6. [PMID: 31540829 DOI: 10.1016/j.chom.2019.08.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/26/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022]
Abstract
During infection, Legionella pneumophila translocates over 300 effector proteins into the host cytosol, allowing the pathogen to establish an endoplasmic reticulum (ER)-like Legionella-containing vacuole (LCV) that supports bacterial replication. Here, we perform a genome-wide CRISPR-Cas9 screen and secondary targeted screens in U937 human monocyte/macrophage-like cells to systematically identify host factors that regulate killing by L. pneumophila. The screens reveal known host factors hijacked by L. pneumophila, as well as genes spanning diverse trafficking and signaling pathways previously not linked to L. pneumophila pathogenesis. We further characterize C1orf43 and KIAA1109 as regulators of phagocytosis and show that RAB10 and its chaperone RABIF are required for optimal L. pneumophila replication and ER recruitment to the LCV. Finally, we show that Rab10 protein is recruited to the LCV and ubiquitinated by the effectors SidC/SdcA. Collectively, our results provide a wealth of previously undescribed insights into L. pneumophila pathogenesis and mammalian cell function.
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Affiliation(s)
- Edwin E Jeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Varun Bhadkamkar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nnejiuwa U Ibe
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Haley Gause
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanne Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David Jimenez-Morales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Lau N, Haeberle AL, O’Keeffe BJ, Latomanski EA, Celli J, Newton HJ, Knodler LA. SopF, a phosphoinositide binding effector, promotes the stability of the nascent Salmonella-containing vacuole. PLoS Pathog 2019; 15:e1007959. [PMID: 31339948 PMCID: PMC6682159 DOI: 10.1371/journal.ppat.1007959] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 08/05/2019] [Accepted: 07/02/2019] [Indexed: 12/19/2022] Open
Abstract
The enteric bacterial pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), utilizes two type III secretion systems (T3SSs) to invade host cells, survive and replicate intracellularly. T3SS1 and its dedicated effector proteins are required for bacterial entry into non-phagocytic cells and establishment and trafficking of the nascent Salmonella-containing vacuole (SCV). Here we identify the first T3SS1 effector required to maintain the integrity of the nascent SCV as SopF. SopF associates with host cell membranes, either when translocated by bacteria or ectopically expressed. Recombinant SopF binds to multiple phosphoinositides in protein-lipid overlays, suggesting that it targets eukaryotic cell membranes via phospholipid interactions. In yeast, the subcellular localization of SopF is dependent on the activity of Mss4, a phosphatidylinositol 4-phosphate 5-kinase that generates PI(4,5)P2 from PI(4)P, indicating that membrane recruitment of SopF requires specific phospholipids. Ectopically expressed SopF partially colocalizes with specific phosphoinositide pools present on the plasma membrane in mammalian cells and with cytoskeletal-associated markers at the leading edge of cells. Translocated SopF concentrates on plasma membrane ruffles and around intracellular bacteria, presumably on the SCV. SopF is not required for bacterial invasion of non-phagocytic cells but is required for maintenance of the internalization vacuole membrane as infection with a S. Typhimurium ΔsopF mutant led to increased lysis of the SCV compared to wild type bacteria. Our structure-function analysis shows that the carboxy-terminal seven amino acids of SopF are essential for its membrane association in host cells and to promote SCV membrane stability. We also describe that SopF and another T3SS1 effector, SopB, act antagonistically to modulate nascent SCV membrane dynamics. In summary, our study highlights that a delicate balance of type III effector activities regulates the stability of the Salmonella internalization vacuole.
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Affiliation(s)
- Nicole Lau
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Amanda L. Haeberle
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Brittany J. O’Keeffe
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Eleanor A. Latomanski
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Celli
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
| | - Hayley J. Newton
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (LAK); (HJN)
| | - Leigh A. Knodler
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States of America
- * E-mail: (LAK); (HJN)
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Study of Legionella Effector Domains Revealed Novel and Prevalent Phosphatidylinositol 3-Phosphate Binding Domains. Infect Immun 2019; 87:IAI.00153-19. [PMID: 30962397 DOI: 10.1128/iai.00153-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022] Open
Abstract
Legionella pneumophila and other Legionella species replicate intracellularly using the Icm/Dot type IV secretion system. In L. pneumophila this system translocates >300 effectors into host cells and in the Legionella genus thousands of effectors were identified, the function of most of which is unknown. Fourteen L. pneumophila effectors were previously shown to specifically bind phosphoinositides (PIs) using dedicated domains. We found that PI-binding domains of effectors are usually not homologous to one another; they are relatively small and located at the effectors' C termini. We used the previously identified Legionella effector domains (LEDs) with unknown function and the above characteristics of effector PI-binding domains to discover novel PI-binding LEDs. We identified three predicted PI-binding LEDs that are present in 14 L. pneumophila effectors and in >200 effectors in the Legionella genus. Using an in vitro protein-lipid overlay assay, we found that 11 of these L. pneumophila effectors specifically bind phosphatidylinositol 3-phosphate (PI3P), almost doubling the number of L. pneumophila effectors known to bind PIs. Further, we identified in each of these newly discovered PI3P-binding LEDs conserved, mainly positively charged, amino acids that are essential for PI3P binding. Our results indicate that Legionella effectors harbor unique domains, shared by many effectors, which directly mediate PI3P binding.
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Hilbi H, Nagai H, Kubori T, Roy CR. Subversion of Host Membrane Dynamics by the Legionella Dot/Icm Type IV Secretion System. Curr Top Microbiol Immunol 2019. [PMID: 29536361 DOI: 10.1007/978-3-319-75241-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Legionella species are Gram-negative ubiquitous environmental bacteria, which thrive in biofilms and parasitize protozoa. Employing an evolutionarily conserved mechanism, the opportunistic pathogens also replicate intracellularly in mammalian macrophages. This feature is a prerequisite for the pathogenicity of Legionella pneumophila, which causes the vast majority of clinical cases of a severe pneumonia, termed "Legionnaires' disease." In macrophages as well as in amoeba, L. pneumophila grows in a distinct membrane-bound compartment, the Legionella-containing vacuole (LCV). Formation of this replication-permissive pathogen compartment requires the bacterial Dot/Icm type IV secretion system (T4SS). Through the T4SS as many as 300 different "effector" proteins are injected into host cells, where they presumably subvert pivotal processes. Less than 40 Dot/Icm substrates have been characterized in detail to date, a number of which show unprecedented biological activities. Some of these effector proteins target host cell small GTPases, phosphoinositide lipids, the chelator phytate, the ubiquitination machinery, the retromer complex, the actin cytoskeleton, or the autophagy pathway. A recently discovered class of L. pneumophila effectors modulates the activity of other effectors and is termed "metaeffectors." Here, we summarize recent insight into the cellular functions and biochemical activities of L. pneumophila effectors and metaeffectors targeting the host's endocytic, retrograde, or autophagic pathways.
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Affiliation(s)
- Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zurich, Switzerland.
| | - Hiroki Nagai
- School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1194, Japan.
| | - Tomoko Kubori
- School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1194, Japan.
| | - Craig R Roy
- Department of Microbial Pathogenesis, Yale University, 295 Congress Avenue, BCMM 354B, New Haven, CT, 06536-0812, USA.
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Hochstrasser R, Kessler A, Sahr T, Simon S, Schell U, Gomez-Valero L, Buchrieser C, Hilbi H. The pleiotropic Legionella transcription factor LvbR links the Lqs and c-di-GMP regulatory networks to control biofilm architecture and virulence. Environ Microbiol 2019; 21:1035-1053. [PMID: 30623561 DOI: 10.1111/1462-2920.14523] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/05/2019] [Indexed: 11/29/2022]
Abstract
The causative agent of Legionnaires' disease, Legionella pneumophila, colonizes amoebae and biofilms in the environment. The opportunistic pathogen employs the Lqs (Legionella quorum sensing) system and the signalling molecule LAI-1 (Legionella autoinducer-1) to regulate virulence, motility, natural competence and expression of a 133 kb genomic "fitness island", including a putative novel regulator. Here, we show that the regulator termed LvbR is an LqsS-regulated transcription factor that binds to the promoter of lpg1056/hnox1 (encoding an inhibitor of the diguanylate cyclase Lpg1057), and thus, regulates proteins involved in c-di-GMP metabolism. LvbR determines biofilm architecture, since L. pneumophila lacking lvbR accumulates less sessile biomass and forms homogeneous mat-like structures, while the parental strain develops more compact bacterial aggregates. Comparative transcriptomics of sessile and planktonic ΔlvbR or ΔlqsR mutant strains revealed concerted (virulence, fitness island, metabolism) and reciprocally (motility) regulated genes in biofilm and broth respectively. Moreover, ΔlvbR is hyper-competent for DNA uptake, defective for phagocyte infection, outcompeted by the parental strain in amoebae co-infections and impaired for cell migration inhibition. Taken together, our results indicate that L. pneumophila LvbR is a novel pleiotropic transcription factor, which links the Lqs and c-di-GMP regulatory networks to control biofilm architecture and pathogen-host cell interactions.
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Affiliation(s)
- Ramon Hochstrasser
- Institute of Medical Microbiology, Faculty of Medicine, University of Zürich, Gloriastrasse 30, 8006 Zürich, Switzerland
| | - Aline Kessler
- Max von Pettenkofer Institute, Faculty of Medicine, Ludwig-Maximilians University, Pettenkoferstrasse 9a, 80336 Munich, Germany
| | - Tobias Sahr
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, 28 Rue du Dr Roux, 75724 Paris, France.,CNRS UMR 3525, 28 Rue du Dr Roux, 75724 Paris, France
| | - Sylvia Simon
- Institute of Medical Microbiology, Faculty of Medicine, University of Zürich, Gloriastrasse 30, 8006 Zürich, Switzerland
| | - Ursula Schell
- Max von Pettenkofer Institute, Faculty of Medicine, Ludwig-Maximilians University, Pettenkoferstrasse 9a, 80336 Munich, Germany
| | - Laura Gomez-Valero
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, 28 Rue du Dr Roux, 75724 Paris, France.,CNRS UMR 3525, 28 Rue du Dr Roux, 75724 Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, 28 Rue du Dr Roux, 75724 Paris, France.,CNRS UMR 3525, 28 Rue du Dr Roux, 75724 Paris, France
| | - Hubert Hilbi
- Institute of Medical Microbiology, Faculty of Medicine, University of Zürich, Gloriastrasse 30, 8006 Zürich, Switzerland
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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40
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Welin A, Weber S, Hilbi H. Quantitative Imaging Flow Cytometry of Legionella-Containing Vacuoles in Dually Fluorescence-Labeled Dictyostelium. Methods Mol Biol 2019; 1921:161-177. [PMID: 30694491 DOI: 10.1007/978-1-4939-9048-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Legionella pneumophila enters and replicates within protozoan and mammalian phagocytes by forming through a conserved mechanism a specialized intracellular compartment termed the Legionella-containing vacuole (LCV). This compartment avoids fusion with bactericidal lysosomes but communicates extensively with different cellular vesicle trafficking pathways and ultimately interacts closely with the endoplasmic reticulum. In order to delineate the process of pathogen vacuole formation and to better understand L. pneumophila virulence, an analysis of markers of the different trafficking pathways on the pathogen vacuole is crucial. Here, we describe a method for rapid, objective and quantitative analysis of different fluorescently tagged proteins or probes on the LCV. To this end, we employ an imaging flow cytometry approach and use the D. discoideum -L. pneumophila infection model. Imaging flow cytometry enables quantification of many different parameters by fluorescence microscopy of cells in flow, rapidly producing statistically robust data from thousands of cells. We also describe the generation of D. discoideum strains simultaneously producing two different fluorescently tagged probes that enable visualization of compartments and processes in parallel. The quantitative imaging flow technique can be corroborated and enhanced by laser scanning confocal microscopy.
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Affiliation(s)
- Amanda Welin
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland.
| | - Stephen Weber
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
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41
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Martinez E, Siadous FA, Bonazzi M. Tiny architects: biogenesis of intracellular replicative niches by bacterial pathogens. FEMS Microbiol Rev 2018; 42:425-447. [PMID: 29596635 DOI: 10.1093/femsre/fuy013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/26/2018] [Indexed: 11/13/2022] Open
Abstract
Co-evolution of bacterial pathogens with their hosts led to the emergence of a stunning variety of strategies aiming at the evasion of host defences, colonisation of host cells and tissues and, ultimately, the establishment of a successful infection. Pathogenic bacteria are typically classified as extracellular and intracellular; however, intracellular lifestyle comes in many different flavours: some microbes rapidly escape to the cytosol whereas other microbes remain within vacuolar compartments and harness membrane trafficking pathways to generate their host-derived, pathogen-specific replicative niche. Here we review the current knowledge on a variety of vacuolar lifestyles, the effector proteins used by bacteria as tools to take control of the host cell and the main membrane trafficking signalling pathways targeted by vacuolar pathogens as source of membranes and nutrients. Finally, we will also discuss how host cells have developed countermeasures to sense the biogenesis of the aberrant organelles harbouring bacteria. Understanding the dialogue between bacterial and eukaryotic proteins is the key to unravel the molecular mechanisms of infection and in turn, this may lead to the identification of new targets for the development of new antimicrobials.
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Affiliation(s)
- Eric Martinez
- IRIM, University of Montpellier, CNRS, 34293 Montpellier, France
| | | | - Matteo Bonazzi
- IRIM, University of Montpellier, CNRS, 34293 Montpellier, France
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42
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Abstract
Legionella pneumophila is the causative agent of a pneumonia termed Legionnaires' disease. The facultative intracellular bacterium employs the Icm/Dot type IV secretion system (T4SS) and a plethora of translocated "effector" proteins to interfere with host vesicle trafficking pathways and establish a replicative niche, the Legionella-containing vacuole (LCV). Internalization of the pathogen and the events immediately ensuing are accompanied by host cell-mediated phosphoinositide (PI) lipid changes and the Icm/Dot-controlled conversion of the LCV from a PtdIns(3)P-positive vacuole into a PtdIns(4)P-positive replication-permissive compartment, which tightly associates with the endoplasmic reticulum. The source and formation of PtdIns(4)P are ill-defined. Using dually labeled Dictyostelium discoideum amoebae and real-time high-resolution confocal laser scanning microscopy (CLSM), we show here that nascent LCVs continuously capture and accumulate PtdIns(4)P-positive vesicles from the host cell. Trafficking of these PtdIns(4)P-positive vesicles to LCVs occurs independently of the Icm/Dot system, but their sustained association requires a functional T4SS. During the infection, PtdIns(3)P-positive membranes become compacted and segregated from the LCV, and PtdIns(3)P-positive vesicles traffic to the LCV but do not fuse. Moreover, using eukaryotic and prokaryotic PtdIns(4)P probes (2×PHFAPP-green fluorescent protein [2×PHFAPP-GFP] and P4CSidC-GFP, respectively) along with Arf1-GFP, we show that PtdIns(4)P-rich membranes of the trans-Golgi network associate with the LCV. Intriguingly, the interaction dynamics of 2×PHFAPP-GFP and P4CSidC-GFP are spatially separable and reveal the specific PtdIns(4)P pool from which the LCV PI originates. These findings provide high-resolution real-time insights into how L. pneumophila exploits the cellular dynamics of membrane-bound PtdIns(4)P for LCV formation.IMPORTANCE The environmental bacterium Legionella pneumophila causes a life-threatening pneumonia termed Legionnaires' disease. The bacteria grow intracellularly in free-living amoebae as well as in respiratory tract macrophages. To this end, L. pneumophila forms a distinct membrane-bound compartment called the Legionella-containing vacuole (LCV). Phosphoinositide (PI) lipids are crucial regulators of the identity and dynamics of host cell organelles. The PI lipid PtdIns(4)P is a hallmark of the host cell secretory pathway, and decoration of LCVs with this PI is required for pathogen vacuole maturation. The source, dynamics, and mode of accumulation of PtdIns(4)P on LCVs are largely unknown. Using Dictyostelium amoebae producing different fluorescent probes as host cells, we show here that LCVs rapidly acquire PtdIns(4)P through the continuous interaction with PtdIns(4)P-positive host vesicles derived from the Golgi apparatus. Thus, the PI lipid pattern of the secretory pathway contributes to the formation of the replication-permissive pathogen compartment.
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Wasilko DJ, Huang Q, Mao Y. Insights into the ubiquitin transfer cascade catalyzed by the Legionella effector SidC. eLife 2018; 7:36154. [PMID: 30015617 PMCID: PMC6063727 DOI: 10.7554/elife.36154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022] Open
Abstract
The causative agent of Legionnaires’ disease, Legionella pneumophila, delivers more than 330 virulent effectors to its host to establish an intracellular membrane-bound organelle called the Legionella containing vacuole. Among the army of Legionella effectors, SidC and its paralog SdcA have been identified as novel bacterial ubiquitin (Ub) E3 ligases. To gain insight into the molecular mechanism of SidC/SdcA as Ub ligases, we determined the crystal structures of a binary complex of the N-terminal catalytic SNL domain of SdcA with its cognate E2 UbcH5C and a ternary complex consisting of the SNL domain of SidC with the Ub-linked E2 UbcH7. These two structures reveal the molecular determinants governing the Ub transfer cascade catalyzed by SidC. Together, our data support a common mechanism in the Ub transfer cascade in which the donor Ub is immobilized with its C-terminal tail locked in an extended conformation, priming the donor Ub for catalysis.
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Affiliation(s)
- David Jon Wasilko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
| | | | - Yuxin Mao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
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44
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Quantitative Imaging Flow Cytometry of Legionella-Infected Dictyostelium Amoebae Reveals the Impact of Retrograde Trafficking on Pathogen Vacuole Composition. Appl Environ Microbiol 2018; 84:AEM.00158-18. [PMID: 29602783 DOI: 10.1128/aem.00158-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/27/2018] [Indexed: 01/15/2023] Open
Abstract
The ubiquitous environmental bacterium Legionella pneumophila survives and replicates within amoebae and human macrophages by forming a Legionella-containing vacuole (LCV). In an intricate process governed by the bacterial Icm/Dot type IV secretion system and a plethora of effector proteins, the nascent LCV interferes with a number of intracellular trafficking pathways, including retrograde transport from endosomes to the Golgi apparatus. Conserved retrograde trafficking components, such as the retromer coat complex or the phosphoinositide (PI) 5-phosphatase D. discoideum 5-phosphatase 4 (Dd5P4)/oculocerebrorenal syndrome of Lowe (OCRL), restrict intracellular replication of L. pneumophila by an unknown mechanism. Here, we established an imaging flow cytometry (IFC) approach to assess in a rapid, unbiased, and large-scale quantitative manner the role of retrograde-linked PI metabolism and actin dynamics in the LCV composition. Exploiting Dictyostelium discoideum genetics, we found that Dd5P4 modulates the acquisition of fluorescently labeled LCV markers, such as calnexin, the small GTPase Rab1 (but not Rab7 and Rab8), and retrograde trafficking components (Vps5, Vps26, Vps35). The actin-nucleating protein and retromer interactor WASH (Wiskott-Aldrich syndrome protein [WASP] and suppressor of cAMP receptor [SCAR] homologue) promotes the accumulation of Rab1 and Rab8 on LCVs. Collectively, our findings validate IFC for the quantitative and unbiased analysis of the pathogen vacuole composition and reveal the impact of retrograde-linked PI metabolism and actin dynamics on the LCV composition. The IFC approach employed here can be adapted for a molecular analysis of the pathogen vacuole composition of other amoeba-resistant pathogens.IMPORTANCELegionella pneumophila is an amoeba-resistant environmental bacterium which can cause a life-threatening pneumonia termed Legionnaires' disease. In order to replicate intracellularly, the opportunistic pathogen forms a protective compartment, the Legionella-containing vacuole (LCV). An in-depth analysis of the LCV composition and the complex process of pathogen vacuole formation is crucial for understanding the virulence of L. pneumophila Here, we established an imaging flow cytometry (IFC) approach to assess in a rapid, unbiased, and quantitative manner the accumulation of fluorescently labeled markers and probes on LCVs. Using IFC and L. pneumophila-infected Dictyostelium discoideum or defined mutant amoebae, a role for phosphoinositide (PI) metabolism, retrograde trafficking, and the actin cytoskeleton in the LCV composition was revealed. In principle, the powerful IFC approach can be used to analyze the molecular composition of any cellular compartment harboring bacterial pathogens.
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45
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Steiner B, Weber S, Kaech A, Ziegler U, Hilbi H. The large GTPase atlastin controls ER remodeling around a pathogen vacuole. Commun Integr Biol 2018; 11:1-5. [PMID: 30083282 PMCID: PMC6067846 DOI: 10.1080/19420889.2018.1440880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/04/2018] [Indexed: 12/22/2022] Open
Abstract
The ubiquitous environmental bacterium Legionella pneumophila is the causative agent of Legionnaires' pneumonia and replicates in free-living protozoa and mammalian macrophages in a specific compartment, the Legionella-containing vacuole (LCV). LCVs communicate with the endosomal, retrograde and secretory vesicle trafficking pathway, and eventually tightly interact with the endoplasmic reticulum (ER). In Dictyostelium discoideum amoebae and macrophages, the ER tubule-resident large GTPase Sey1/atlastin3 (Atl3) accumulates on LCVs and promotes LCV expansion and intracellular replication of L. pneumophila. Fluorescence microscopy of D. discoideum infected with L. pneumophila indicated that Sey1 is involved in extensive ER remodeling around LCVs. An ultrastructural analysis confirmed these findings. Moreover, dominant negative Sey1_K154A compromises ER accumulation on LCVs and causes an aberrant ER morphology in uninfected D. discoideum as well as in amoebae infected with avirulent L. pneumophila that lack a functional type IV secretion system. Thus, the large, dynamin-like GTPase Sey1/Atl3 controls circumferential ER remodeling during LCV maturation.
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Affiliation(s)
- Bernhard Steiner
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Stephen Weber
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zürich, Zürich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
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46
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Swart AL, Harrison CF, Eichinger L, Steinert M, Hilbi H. Acanthamoeba and Dictyostelium as Cellular Models for Legionella Infection. Front Cell Infect Microbiol 2018; 8:61. [PMID: 29552544 PMCID: PMC5840211 DOI: 10.3389/fcimb.2018.00061] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
Environmental bacteria of the genus Legionella naturally parasitize free-living amoebae. Upon inhalation of bacteria-laden aerosols, the opportunistic pathogens grow intracellularly in alveolar macrophages and can cause a life-threatening pneumonia termed Legionnaires' disease. Intracellular replication in amoebae and macrophages takes place in a unique membrane-bound compartment, the Legionella-containing vacuole (LCV). LCV formation requires the bacterial Icm/Dot type IV secretion system, which translocates literally hundreds of "effector" proteins into host cells, where they modulate crucial cellular processes for the pathogen's benefit. The mechanism of LCV formation appears to be evolutionarily conserved, and therefore, amoebae are not only ecologically significant niches for Legionella spp., but also useful cellular models for eukaryotic phagocytes. In particular, Acanthamoeba castellanii and Dictyostelium discoideum emerged over the last years as versatile and powerful models. Using genetic, biochemical and cell biological approaches, molecular interactions between amoebae and Legionella pneumophila have recently been investigated in detail with a focus on the role of phosphoinositide lipids, small and large GTPases, autophagy components and the retromer complex, as well as on bacterial effectors targeting these host factors.
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Affiliation(s)
- A Leoni Swart
- Institute of Medical Microbiology, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Christopher F Harrison
- Max von Pettenkofer Institute, Medical Faculty, Ludwig-Maximilians University Munich, Munich, Germany
| | - Ludwig Eichinger
- Institute for Biochemistry I, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Michael Steinert
- Department of Life Sciences, Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Hubert Hilbi
- Institute of Medical Microbiology, Medical Faculty, University of Zurich, Zurich, Switzerland
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Lin YH, Lucas M, Evans TR, Abascal-Palacios G, Doms AG, Beauchene NA, Rojas AL, Hierro A, Machner MP. RavN is a member of a previously unrecognized group of Legionella pneumophila E3 ubiquitin ligases. PLoS Pathog 2018; 14:e1006897. [PMID: 29415051 PMCID: PMC5819833 DOI: 10.1371/journal.ppat.1006897] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/20/2018] [Accepted: 01/23/2018] [Indexed: 11/18/2022] Open
Abstract
The eukaryotic ubiquitylation machinery catalyzes the covalent attachment of the small protein modifier ubiquitin to cellular target proteins in order to alter their fate. Microbial pathogens exploit this post-translational modification process by encoding molecular mimics of E3 ubiquitin ligases, eukaryotic enzymes that catalyze the final step in the ubiquitylation cascade. Here, we show that the Legionella pneumophila effector protein RavN belongs to a growing class of bacterial proteins that mimic host cell E3 ligases to exploit the ubiquitylation pathway. The E3 ligase activity of RavN was located within its N-terminal region and was dependent upon interaction with a defined subset of E2 ubiquitin-conjugating enzymes. The crystal structure of the N-terminal region of RavN revealed a U-box-like motif that was only remotely similar to other U-box domains, indicating that RavN is an E3 ligase relic that has undergone significant evolutionary alteration. Substitution of residues within the predicted E2 binding interface rendered RavN inactive, indicating that, despite significant structural changes, the mode of E2 recognition has remained conserved. Using hidden Markov model-based secondary structure analyses, we identified and experimentally validated four additional L. pneumophila effectors that were not previously recognized to possess E3 ligase activity, including Lpg2452/SdcB, a new paralog of SidC. Our study provides strong evidence that L. pneumophila is dedicating a considerable fraction of its effector arsenal to the manipulation of the host ubiquitylation pathway. Bacterial pathogens often hijack conserved host pathways by encoding proteins that are molecular mimics of eukaryotic enzymes, thus tricking the host cell into surrendering its resources to the bacteria. Here, we show that the intracellular pathogen Legionella pneumophila uses such a strategy to exploit ubiquitylation, a conserved post-translational modification that is mediated by E3 ubiquitin ligases. L. pneumophila encodes molecular mimics of host E3 ligases, including the effector protein RavN, thereby subverting the ubiquitylation pathway for its own benefit during infection. Using protein crystallography, we show that the fold of RavN has only residual resemblance to conventional eukaryotic E3s, yet its mode of interaction with E2 enzymes, host proteins that are important for the ubiquitin transfer reaction, has been preserved throughout evolution. Inspired by the discovery of RavN, we performed an in silico fold homology search and discovered several additional E3 ligase candidates within the effector repertoire of L. pneumophila that, until now, had remained hidden due to lack of primary sequence similarity. Our study supports the hypothesis that E3 ligases are a vital part of the virulence program of L. pneumophila, and that these effectors, despite having undergone extensive evolutionary changes, have retained features that are critical for their biological function, including the ability to hijack host factors that are part of the ubiquitylation machinery.
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Affiliation(s)
- Yi-Han Lin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - María Lucas
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Timothy R. Evans
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Alexandra G. Doms
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicole A. Beauchene
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adriana L. Rojas
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Aitor Hierro
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail: (AH); (MPM)
| | - Matthias P. Machner
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (AH); (MPM)
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48
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Grohmann E, Christie PJ, Waksman G, Backert S. Type IV secretion in Gram-negative and Gram-positive bacteria. Mol Microbiol 2018; 107:455-471. [PMID: 29235173 PMCID: PMC5796862 DOI: 10.1111/mmi.13896] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 02/06/2023]
Abstract
Type IV secretion systems (T4SSs) are versatile multiprotein nanomachines spanning the entire cell envelope in Gram-negative and Gram-positive bacteria. They play important roles through the contact-dependent secretion of effector molecules into eukaryotic hosts and conjugative transfer of mobile DNA elements as well as contact-independent exchange of DNA with the extracellular milieu. In the last few years, many details on the molecular mechanisms of T4SSs have been elucidated. Exciting structures of T4SS complexes from Escherichia coli plasmids R388 and pKM101, Helicobacter pylori and Legionella pneumophila have been solved. The structure of the F-pilus was also reported and surprisingly revealed a filament composed of pilin subunits in 1:1 stoichiometry with phospholipid molecules. Many new T4SSs have been identified and characterized, underscoring the structural and functional diversity of this secretion superfamily. Complex regulatory circuits also have been shown to control T4SS machine production in response to host cell physiological status or a quorum of bacterial recipient cells in the vicinity. Here, we summarize recent advances in our knowledge of 'paradigmatic' and emerging systems, and further explore how new basic insights are aiding in the design of strategies aimed at suppressing T4SS functions in bacterial infections and spread of antimicrobial resistances.
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Affiliation(s)
- Elisabeth Grohmann
- Beuth University of Applied Sciences Berlin, Life Sciences and Technology, D-13347 Berlin, Germany
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, The University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, USA
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom
| | - Steffen Backert
- Friedrich Alexander University Erlangen-Nuremberg, Department of Biology, Division of Microbiology, Staudtstrasse 5, D-91058 Erlangen, Germany
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49
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Intracellular Growth of Bacterial Pathogens: The Role of Secreted Effector Proteins in the Control of Phagocytosed Microorganisms. Microbiol Spectr 2018; 3. [PMID: 27337278 DOI: 10.1128/microbiolspec.vmbf-0003-2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The ability of intracellular pathogens to subvert the host response, to facilitate invasion and subsequent infection, is the hallmark of microbial pathogenesis. Bacterial pathogens produce and secrete a variety of effector proteins, which are the primary means by which they exert control over the host cell. Secreted effectors work independently, yet in concert with each other, to facilitate microbial invasion, replication, and intracellular survival in host cells. In this review we focus on defined host cell processes targeted by bacterial pathogens. These include phagosome maturation and its subprocesses: phagosome-endosome and phagosome-lysosome fusion events, as well as phagosomal acidification, cytoskeleton remodeling, and lysis of the phagosomal membrane. We further describe the mode of action for selected effectors from six pathogens: the Gram-negative Legionella, Salmonella, Shigella, and Yersinia, the Gram-positive Listeria, and the acid-fast actinomycete Mycobacterium.
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50
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Buracco S, Peracino B, Andreini C, Bracco E, Bozzaro S. Differential Effects of Iron, Zinc, and Copper on Dictyostelium discoideum Cell Growth and Resistance to Legionella pneumophila. Front Cell Infect Microbiol 2018; 7:536. [PMID: 29379774 PMCID: PMC5770829 DOI: 10.3389/fcimb.2017.00536] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/26/2017] [Indexed: 12/29/2022] Open
Abstract
Iron, zinc, and copper play fundamental roles in eucaryotes and procaryotes, and their bioavailability regulates host-pathogen interactions. For intracellular pathogens, the source of metals is the cytoplasm of the host, which in turn manipulates intracellular metal traffic following pathogen recognition. It is established that iron is withheld from the pathogen-containing vacuole, whereas for copper and zinc the evidence is unclear. Most infection studies in mammals have concentrated on effects of metal deficiency/overloading at organismal level. Thus, zinc deficiency or supplementation correlate with high risk of respiratory tract infection or recovery from severe infection, respectively. Iron, zinc, and copper deficiency or overload affects lymphocyte proliferation/maturation, and thus the adaptive immune response. Whether they regulate innate immunity at macrophage level is open, except for iron. The early identification in a mouse mutant susceptible to mycobacterial infection of the iron transporter Nramp1 allowed dissecting Nramp1 role in phagocytes, from the social amoeba Dictyostelium to macrophages. Nramp1 regulates iron efflux from the phagosomes, thus starving pathogenic bacteria for iron. Similar studies for zinc or copper are scant, due to the large number of copper and zinc transporters. In Dictyostelium, zinc and copper transporters include 11 and 6 members, respectively. To assess the role of zinc or copper in Dictyostelium, cells were grown under conditions of metal depletion or excess and tested for resistance to Legionella pneumophila infection. Iron shortage or overload inhibited Dictyostelium cell growth within few generations. Surprisingly, zinc or copper depletion failed to affect growth. Zinc or copper overloading inhibited cell growth at, respectively, 50- or 500-fold the physiological concentration, suggesting very efficient control of their homeostasis, as confirmed by Inductively Coupled Plasma Mass Spectrometry quantification of cellular metals. Legionella infection was inhibited or enhanced in cells grown under iron shortage or overload, respectively, confirming a major role for iron in controlling resistance to pathogens. In contrast, zinc and copper depletion or excess during growth did not affect Legionella infection. Using Zinpyr-1 as fluorescent sensor, we show that zinc accumulates in endo-lysosomal vesicles, including phagosomes, and the contractile vacuole. Furthermore, we provide evidence for permeabilization of the Legionella-containing vacuole during bacterial proliferation.
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Affiliation(s)
- Simona Buracco
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - Barbara Peracino
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Enrico Bracco
- Department of Oncology, University of Torino, Turin, Italy
| | - Salvatore Bozzaro
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
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