1
|
Tanaka S, Oide H, Ikeda S, Tagaya M, Nagai H, Kubori T, Arasaki K. Subversion of the host endocytic pathway by Legionella pneumophila-mediated ubiquitination of Rab5. J Cell Biol 2025; 224:e202406159. [PMID: 40035702 PMCID: PMC11893168 DOI: 10.1083/jcb.202406159] [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: 06/27/2024] [Revised: 11/17/2024] [Accepted: 01/10/2025] [Indexed: 03/06/2025] Open
Abstract
Legionella pneumophila is an intracellular bacterial pathogen that modulates membrane trafficking to survive and proliferate within host cells. After phagocytosis, the L. pneumophila-containing vacuole evades the endocytic pathway by excluding the host GTPase Rab5, a crucial regulator of phagosomal maturation. In this study, we show that the evolutionarily conserved lysine residue K134 of Rab5 undergoes ubiquitination during infection. This modification depends on Lpg2525, an F-box protein from L. pneumophila that acts as a component of the SKP-Cullin-F-box complex. We further demonstrate that Rab5 ubiquitination facilitates the recruitment of RabGAP-5, a Rab5-specific GAP, leading to Rab5 inactivation and subsequent release from the bacterial vacuole. Importantly, the K134 Rab5 mutant limits L. pneumophila replication within host cells. These findings reveal that Lpg2525-mediated Rab5 ubiquitination is a key survival strategy employed by L. pneumophila in infected host cells.
Collapse
Affiliation(s)
- Shino Tanaka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hiromu Oide
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Shumma Ikeda
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Mitsuo Tagaya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Institute for Advanced Study, Gifu University, Gifu, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| |
Collapse
|
2
|
Mount HO, Urbanus ML, Zangari F, Gingras AC, Ensminger AW. The Legionella pneumophila effector PieF modulates mRNA stability through association with eukaryotic CCR4-NOT. mSphere 2025; 10:e0089124. [PMID: 39699231 PMCID: PMC11774319 DOI: 10.1128/msphere.00891-24] [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: 10/23/2024] [Accepted: 11/26/2024] [Indexed: 12/20/2024] Open
Abstract
The eukaryotic CCR4-NOT deadenylase complex is a highly conserved regulator of mRNA metabolism that influences the expression of the complete transcriptome, representing a prime target for a generalist bacterial pathogen. We show that a translocated bacterial effector protein, PieF (Lpg1972) of Legionella pneumophila, directly interacts with the CNOT7/8 nuclease module of CCR4-NOT, with a dissociation constant in the low nanomolar range. PieF is a robust in vitro inhibitor of the DEDD-type nuclease, CNOT7, acting in a stoichiometric, dose-dependent manner. Heterologous expression of PieF phenocopies knockout of the CNOT7 ortholog (POP2) in Saccharomyces cerevisiae, resulting in 6-azauracil sensitivity. In mammalian cells, expression of PieF leads to a variety of quantifiable phenotypes: PieF silences gene expression and reduces mRNA steady-state levels when artificially tethered to a reporter transcript, and its overexpression results in the nuclear exclusion of CNOT7. PieF expression also disrupts the association between CNOT6/6L EEP-type nucleases and CNOT7. Adding to the complexities of PieF activity in vivo, we identified a separate domain of PieF responsible for binding to eukaryotic kinases. Unlike what we observe for CNOT6/6L, we show that these interactions can occur concomitantly with PieF's binding to CNOT7. Collectively, this work reveals a new, highly conserved target of L. pneumophila effectors and suggests a mechanism by which the pathogen may be modulating host mRNA stability and expression during infection. IMPORTANCE The intracellular bacterial pathogen Legionella pneumophila targets conserved eukaryotic pathways to establish a replicative niche inside host cells. With a host range that spans billions of years of evolution (from protists to humans), the interaction between L. pneumophila and its hosts frequently involves conserved eukaryotic pathways (protein translation, ubiquitination, membrane trafficking, autophagy, and the cytoskeleton). Here, we present the identification of a new, highly conserved host target of L. pneumophila effectors: the CCR4-NOT complex. CCR4-NOT modulates mRNA stability in eukaryotes from yeast to humans, making it an attractive target for a generalist pathogen, such as L. pneumophila. We show that the uncharacterized L. pneumophila effector PieF specifically targets one component of this complex, the deadenylase subunit CNOT7/8. We show that the interaction between PieF and CNOT7 is direct, occurs with high affinity, and reshapes the catalytic activity, localization, and composition of the complex across evolutionarily diverse eukaryotic cells.
Collapse
Affiliation(s)
| | - Malene L. Urbanus
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Francesco Zangari
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Alexander W. Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Lopez AE, Mayoral J, Zheng H, Cianciotto NP. Legionella pneumophila IrsA, a novel, iron-regulated exoprotein that facilitates growth in low-iron conditions and modulates biofilm formation. Microbiol Spectr 2025; 13:e0231324. [PMID: 39612475 PMCID: PMC11705809 DOI: 10.1128/spectrum.02313-24] [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: 09/14/2024] [Accepted: 11/07/2024] [Indexed: 12/01/2024] Open
Abstract
To discover new factors that are involved in iron acquisition by Legionella pneumophila, we used RNA-Seq to identify the genes that are most highly induced when virulent strain 130b is cultured in a low-iron chemically defined medium. Among other things, this revealed 14915, a heretofore uncharacterized gene that is predicted to be transcriptionally regulated by Fur and to encode a novel, ~15 kDa protein. 14915 was present in all L. pneumophila strains examined and had homologs in a subset of the other Legionella species. Compatible with it containing a classic signal sequence, the 14915 protein was detected in bacterial culture supernatants in a manner dependent upon the L. pneumophila type II secretion system. Thus, we designated 14915 as IrsA for iron-regulated, secreted protein A. Based on mutant analysis, the irsA gene was not required for optimal growth of strain 130b in low-iron media. However, after discovering that the commonly used laboratory-derived strain Lp02 has a much greater requirement for iron, we uncovered a growth-enhancing role for IrsA after examining an Lp02 mutant that lacked both IrsA and the Fe2+-transporter FeoB. The irsA mutant of 130b, but not its complemented derivative, did, however, display increased biofilm formation on both plastic and agar surfaces, and compatible with this, the mutant hyper-aggregated. Thus, IrsA is a novel, iron-regulated exoprotein that modulates biofilm formation and, under some circumstances, promotes growth in low-iron conditions. For this study, we determined and deposited in the database a complete and fully assembled genome sequence for strain 130b.IMPORTANCEThe bacterium Legionella pneumophila is the principal cause of Legionnaires' disease, a potentially fatal form of pneumonia that is increasing in incidence. L. pneumophila exists in many natural and human-made water systems and can be transmitted to humans through inhalation of contaminated water droplets. L. pneumophila flourishes within its habitats by spreading planktonically, assembling into biofilms, and growing in larger host cells. Iron acquisition is a key determinant for L. pneumophila persistence in water and during infection. We previously demonstrated that L. pneumophila assimilates iron both by secreting a non-protein iron chelator (siderophore) and by importing iron through membrane transporters. In this study, we uncovered a novel, secreted protein that is highly iron-regulated, promotes L. pneumophila's growth in low-iron media, and impacts biofilm formation. We also identified uncharacterized, IrsA-related proteins in other important human and animal pathogens. Thus, our results have important implications for understanding iron assimilation, biofilm formation, and pathogenesis.
Collapse
Affiliation(s)
- Alberto E. Lopez
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| | - Joshua Mayoral
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| |
Collapse
|
4
|
Cameron G, Faucher SP. Copper resistance in Legionella pneumophila: Role of genetic factors and host cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 958:177943. [PMID: 39671930 DOI: 10.1016/j.scitotenv.2024.177943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 11/27/2024] [Accepted: 12/03/2024] [Indexed: 12/15/2024]
Abstract
Copper is frequently found in drinking water due to its presence in the natural environment and the widespread usage of copper pipes. This toxic metal has a well-known antimicrobial activity, an activity harnessed in copper‑silver ionization (CSI) to eliminate the opportunistic pathogen Legionella pneumophila from engineered water systems. Despite utilizing the antimicrobial properties of copper in Legionella control, little is known about how copper containing environments affect L.pneumophila populations. The goal of this study is to understand how L. pneumophila responds to copper within a hot water distribution system (HWDS) environment. To answer this question, different sequence types and regulatory mutants were exposed to copper to compare their survival. L. pneumophila isolates of 4 sequence types from 3 different HWDSs exhibited a wide diversity of phenotypes after copper stress. The ΔletA and ΔletS mutants were sensitive to copper, indicating that the LetAS two component system is important for copper resistance. Additionally, transmissive phase cultures were more resistant to copper than replicative phase cultures. Therefore, the regulation of entry into transmissive phase by the LetAS system is essential for L. pneumophila's ability to survive copper stress. In a water system, L. pneumophila replicates within eukaryotic hosts. When cocultured with the host ciliate Tetrahymena pyriformis, L. pneumophila was more resistant to copper than when the bacteria were in a monoculture. No difference in L. pneumophila replication inside of hosts in cocultures with or without copper was observed. This result confirms that the presence of host cells protects L. pneumophila from copper stress.
Collapse
Affiliation(s)
- Gillian Cameron
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec H9X 3V9, Canada; Centreau - Centre québécois de recherche sur la gestion de l'eau, Université Laval, Québec, Québec, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec H9X 3V9, Canada; Centreau - Centre québécois de recherche sur la gestion de l'eau, Université Laval, Québec, Québec, Canada; Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, Québec, Canada.
| |
Collapse
|
5
|
Schmid C, Hilbi H. Rapid Icm/Dot T4SS Inactivation Prevents Resuscitation of Heat-Induced VBNC Legionella pneumophila by Amoebae. Environ Microbiol 2025; 27:e70035. [PMID: 39810465 DOI: 10.1111/1462-2920.70035] [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: 11/12/2024] [Accepted: 12/23/2024] [Indexed: 01/16/2025]
Abstract
Legionella pneumophila, the causative agent of Legionnaires' disease, employs the Icm/Dot Type IV secretion system (T4SS) to replicate in amoebae and macrophages. The opportunistic pathogen responds to stress by forming 'viable but non-culturable' (VBNC) cells, which cannot be detected by standard cultivation-based techniques. In this study, we document that L. pneumophila enters the VBNC state after exposure to heat stress at 50°C for 30 h, at 55°C for 5 h or at 60°C for 30 min, while still retaining metabolic activity and intact cell membranes. Resuscitation of heat-induced VBNC L. pneumophila neither occurred in amoebae nor in macrophages. VBNC L. pneumophila showed impaired uptake by phagocytes, formation of Legionella-containing vacuoles (LCVs), and Icm/Dot-dependent secretion of effector proteins. The T4SS was rapidly inactivated already upon exposure to 50°C for 3-5 h, while the bacteria were still culturable. The Legionella quorum sensing (Lqs)-LvbR network is implicated in VBNC induction, since the ∆lvbR and ∆lqsR mutant strains showed a more pronounced heat sensitivity than the parental strain, and the ∆lqsA mutant was less heat sensitive. Taken together, our results reveal that heat exposure of L. pneumophila rapidly inactivates the Icm/Dot T4SS before the VBNC state is induced, thus impairing resuscitation by amoebae.
Collapse
Affiliation(s)
- Camille Schmid
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| |
Collapse
|
6
|
Patel DT, Stogios PJ, Jaroszewski L, Urbanus ML, Sedova M, Semper C, Le C, Takkouche A, Ichii K, Innabi J, Patel DH, Ensminger AW, Godzik A, Savchenko A. Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors. Mol Syst Biol 2025; 21:59-89. [PMID: 39562741 PMCID: PMC11696984 DOI: 10.1038/s44320-024-00076-z] [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: 05/21/2024] [Revised: 10/17/2024] [Accepted: 10/31/2024] [Indexed: 11/21/2024] Open
Abstract
Legionella pneumophila utilizes the Dot/Icm type IVB secretion system to deliver hundreds of effector proteins inside eukaryotic cells to ensure intracellular replication. Our understanding of the molecular functions of the largest pathogenic arsenal known to the bacterial world remains incomplete. By leveraging advancements in 3D protein structure prediction, we provide a comprehensive structural analysis of 368 L. pneumophila effectors, representing a global atlas of predicted functional domains summarized in a database ( https://pathogens3d.org/legionella-pneumophila ). Our analysis identified 157 types of diverse functional domains in 287 effectors, including 159 effectors with no prior functional annotations. Furthermore, we identified 35 cryptic domains in 30 effector models that have no similarity with experimentally structurally characterized proteins, thus, hinting at novel functionalities. Using this analysis, we demonstrate the activity of thirteen functional domains, including three cryptic domains, predicted in L. pneumophila effectors to cause growth defects in the Saccharomyces cerevisiae model system. This illustrates an emerging strategy of exploring synergies between predictions and targeted experimental approaches in elucidating novel effector activities involved in infection.
Collapse
Affiliation(s)
- Deepak T Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Peter J Stogios
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Lukasz Jaroszewski
- University of California, Riverside, School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Malene L Urbanus
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Mayya Sedova
- University of California, Riverside, School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Cameron Semper
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Cathy Le
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Abraham Takkouche
- University of California, Riverside, School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Keita Ichii
- University of California, Riverside, School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Julie Innabi
- University of California, Riverside, School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Dhruvin H Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Alexander W Ensminger
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada.
| | - Adam Godzik
- University of California, Riverside, School of Medicine, Biosciences Division, Riverside, CA, USA.
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
| |
Collapse
|
7
|
Mount HO, Urbanus ML, Sheykhkarimli D, Coté AG, Laval F, Coppin G, Kishore N, Li R, Spirohn-Fitzgerald K, Petersen MO, Knapp JJ, Kim DK, Twizere JC, Calderwood MA, Vidal M, Roth FP, Ensminger AW. A comprehensive two-hybrid analysis to explore the Legionella pneumophila effector-effector interactome. mSystems 2024; 9:e0100424. [PMID: 39526800 DOI: 10.1128/msystems.01004-24] [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: 07/24/2024] [Accepted: 10/13/2024] [Indexed: 11/16/2024] Open
Abstract
Legionella pneumophila uses over 300 translocated effector proteins to rewire host cells during infection and create a replicative niche for intracellular growth. To date, several studies have identified L. pneumophila effectors that indirectly and directly regulate the activity of other effectors, providing an additional layer of regulatory complexity. Among these are "metaeffectors," a special class of effectors that regulate the activity of other effectors once inside the host. A defining feature of metaeffectors is direct, physical interaction with a target effector. Metaeffector identification, to date, has depended on phenotypes in heterologous systems and experimental serendipity. Using a multiplexed, recombinant barcode-based yeast two-hybrid technology we screened for protein-protein interactions among all L. pneumophila effectors and 28 components of the Dot/Icm type IV secretion system (>167,000 protein combinations). Of the 52 protein interactions identified by this approach, 44 are novel protein interactions, including 10 novel effector-effector interactions (doubling the number of known effector-effector interactions). IMPORTANCE Secreted bacterial effector proteins are typically viewed as modulators of host activity, entering the host cytosol to physically interact with and modify the activity of one or more host proteins in support of infection. A growing body of evidence suggests that a subset of effectors primarily function to modify the activities of other effectors inside the host. These "effectors of effectors" or metaeffectors are often identified through experimental serendipity during the study of canonical effector function against the host. We previously performed the first global effector-wide genetic interaction screen for metaeffectors within the arsenal of Legionella pneumophila, an intracellular bacterial pathogen with over 300 effectors. Here, using a high-throughput, scalable methodology, we present the first global interaction network of physical interactions between L. pneumophila effectors. This data set serves as a complementary resource to identify and understand both the scope and nature of non-canonical effector activity within this important human pathogen.
Collapse
Affiliation(s)
| | - Malene L Urbanus
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Atina G Coté
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
- Laboratory of Molecular and Cellular Epigenetics, GIGA Institute, University of Liège, Liège, Belgium
| | - Georges Coppin
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Roujia Li
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Morgan O Petersen
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jennifer J Knapp
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Dae-Kyum Kim
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Frederick P Roth
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alexander W Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
8
|
Ge J, Wang Y, Li X, Lu Q, Yu H, Liu H, Ma K, Deng X, Luo ZQ, Liu X, Qiu J. Phosphorylation of caspases by a bacterial kinase inhibits host programmed cell death. Nat Commun 2024; 15:8464. [PMID: 39349471 PMCID: PMC11442631 DOI: 10.1038/s41467-024-52817-1] [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: 03/25/2024] [Accepted: 09/20/2024] [Indexed: 10/02/2024] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila utilizes the Dot/Icm system to translocate over 330 effectors into the host cytosol. These virulence factors modify a variety of cell processes, including pathways involved in cell death and survival, to promote bacterial proliferation. Here, we show that the effector LegK3 is a eukaryotic-like Ser/Thr kinase that functions to suppress host apoptosis. Mechanistically, LegK3 directly phosphorylates multiple caspases involved in apoptosis signaling, including Caspase-3, Caspase-7, and Caspase-9. LegK3-induced phosphorylation of these caspases occurs at serine (Ser29 in Caspase-3 and Ser199 in Caspase-7) or threonine (Thr102 in Caspase-9) residues located in the prodomain or interdomain linkers. These modifications interfere with the suitability of the caspases as the substrates of initiator caspases or upstream regulators without impacting their proteolytic activity. Collectively, our study reveals a novel strategy used by L. pneumophila to maintain the integrity of infected cells for its intracellular growth.
Collapse
Affiliation(s)
- 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, Changchun, China
| | - Ying Wang
- 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
| | - Xueyu Li
- 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, 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, Changchun, China
| | - Hangqian Yu
- 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, 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, Changchun, China
| | - 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, Changchun, China
| | - Xuming Deng
- 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, 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, Changchun, China.
| |
Collapse
|
9
|
Hershkovitz D, Chen EJ, Ensminger AW, Dugan AS, Conway KT, Joyce AC, Segal G, Isberg RR. Genetic evidence for a regulated cysteine protease catalytic triad in LegA7, a Legionella pneumophila protein that impinges on a stress response pathway. mSphere 2024; 9:e0022224. [PMID: 39166849 PMCID: PMC11423584 DOI: 10.1128/msphere.00222-24] [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: 03/21/2024] [Accepted: 06/30/2024] [Indexed: 08/23/2024] Open
Abstract
Legionella pneumophila grows within membrane-bound vacuoles in phylogenetically diverse hosts. Intracellular growth requires the function of the Icm/Dot type-IVb secretion system, which translocates more than 300 proteins into host cells. A screen was performed to identify L. pneumophila proteins that stimulate mitogen-activated protein kinase (MAPK) activation, using Icm/Dot translocated proteins ectopically expressed in mammalian cells. In parallel, a second screen was performed to identify L. pneumophila proteins expressed in yeast that cause growth inhibition in MAPK pathway-stimulatory high-osmolarity medium. LegA7 was shared in both screens, a protein predicted to be a member of the bacterial cysteine protease family that has five carboxyl-terminal ankyrin repeats. Three conserved residues in the predicted catalytic triad of LegA7 were mutated. These mutations abolished the ability of LegA7 to inhibit yeast growth. To identify other residues important for LegA7 function, a generalizable selection strategy in yeast was devised to isolate mutants that have lost function and no longer cause growth inhibition on a high-osmolarity medium. Mutations were isolated in the two carboxyl-terminal ankyrin repeats, as well as an inter-domain region located between the cysteine protease domain and the ankyrin repeats. These mutations were predicted by AlphaFold modeling to localize to the face opposite from the catalytic site, arguing that they interfere with the positive regulation of the catalytic activity. Based on our data, we present a model in which LegA7 harbors a cysteine protease domain with an inter-domain and two carboxyl-terminal ankyrin repeat regions that modulate the function of the catalytic domain. IMPORTANCE Legionella pneumophila grows in a membrane-bound compartment in macrophages during disease. Construction of the compartment requires a dedicated secretion system that translocates virulence proteins into host cells. One of these proteins, LegA7, is shown to activate a stress response pathway in host cells called the mitogen-activated protein kinase (MAPK) pathway. The effects on the mammalian MAPK pathway were reconstructed in yeast, allowing the development of a strategy to identify the role of individual domains of LegA7. A domain similar to cysteine proteases is demonstrated to be critical for impinging on the MAPK pathway, and the catalytic activity of this domain is required for targeting this path. In addition, a conserved series of repeats, called ankyrin repeats, controls this activity. Data are provided that argue the interaction of the ankyrin repeats with unknown targets probably results in activation of the cysteine protease domain.
Collapse
Affiliation(s)
- Dar Hershkovitz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Emy J Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Program in Genetics, Molecular and Cellular Biology, Graduate School of Biomedical Sciences Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alexander W Ensminger
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aisling S Dugan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Kaleigh T Conway
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Program in Genetics, Molecular and Cellular Biology, Graduate School of Biomedical Sciences Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alex C Joyce
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Gil Segal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Urbanus ML, Zheng TM, Khusnutdinova AN, Banh D, O'Connor Mount H, Gupta A, Stogios PJ, Savchenko A, Isberg RR, Yakunin AF, Ensminger AW. A random mutagenesis screen enriched for missense mutations in bacterial effector proteins. G3 (BETHESDA, MD.) 2024; 14:jkae158. [PMID: 39028840 PMCID: PMC11373652 DOI: 10.1093/g3journal/jkae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
To remodel their hosts and escape immune defenses, many pathogens rely on large arsenals of proteins (effectors) that are delivered to the host cell using dedicated translocation machinery. Effectors hold significant insight into the biology of both the pathogens that encode them and the host pathways that they manipulate. One of the most powerful systems biology tools for studying effectors is the model organism, Saccharomyces cerevisiae. For many pathogens, the heterologous expression of effectors in yeast is growth inhibitory at a frequency much higher than housekeeping genes, an observation ascribed to targeting conserved eukaryotic proteins. Abrogation of yeast growth inhibition has been used to identify bacterial suppressors of effector activity, host targets, and functional residues and domains within effector proteins. We present here a yeast-based method for enriching for informative, in-frame, missense mutations in a pool of random effector mutants. We benchmark this approach against three effectors from Legionella pneumophila, an intracellular bacterial pathogen that injects a staggering >330 effectors into the host cell. For each protein, we show how in silico protein modeling (AlphaFold2) and missense-directed mutagenesis can be combined to reveal important structural features within effectors. We identify known active site residues within the metalloprotease RavK, the putative active site in SdbB, and previously unidentified functional motifs within the C-terminal domain of SdbA. We show that this domain has structural similarity with glycosyltransferases and exhibits in vitro activity consistent with this predicted function.
Collapse
Affiliation(s)
- Malene L Urbanus
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thomas M Zheng
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Doreen Banh
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Harley O'Connor Mount
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Alind Gupta
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02115, USA
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Alexander W Ensminger
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| |
Collapse
|
11
|
Schmidt S, Mondino S, Gomez-Valero L, Escoll P, Mascarenhas DPA, Gonçalves A, Camara PHM, Garcia Rodriguez FJ, Rusniok C, Sachse M, Moya-Nilges M, Fontaine T, Zamboni DS, Buchrieser C. The unique Legionella longbeachae capsule favors intracellular replication and immune evasion. PLoS Pathog 2024; 20:e1012534. [PMID: 39259722 PMCID: PMC11419355 DOI: 10.1371/journal.ppat.1012534] [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: 11/28/2023] [Revised: 09/23/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024] Open
Abstract
Legionella longbeachae and Legionella pneumophila are the most common causative agents of Legionnaires' disease. While the clinical manifestations caused by both species are similar, species-specific differences exist in environmental niches, disease epidemiology, and genomic content. One such difference is the presence of a genomic locus predicted to encode a capsule. Here, we show that L. longbeachae indeed expresses a capsule in post-exponential growth phase as evidenced by electron microscopy analyses, and that capsule expression is abrogated when deleting a capsule transporter gene. Capsule purification and its analysis via HLPC revealed the presence of a highly anionic polysaccharide that is absent in the capsule mutant. The capsule is important for replication and virulence in vivo in a mouse model of infection and in the natural host Acanthamoeba castellanii. It has anti-phagocytic function when encountering innate immune cells such as human macrophages and it is involved in the low cytokine responses in mice and in human monocyte derived macrophages, thus dampening the innate immune response. Thus, the here characterized L. longbeachae capsule is a novel virulence factor, unique among the known Legionella species, which may aid L. longbeachae to survive in its specific niches and which partly confers L. longbeachae its unique infection characteristics.
Collapse
Affiliation(s)
- Silke Schmidt
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, CNRS UMR 6047, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Sonia Mondino
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, CNRS UMR 6047, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, CNRS UMR 6047, Paris, France
| | - Pedro Escoll
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, CNRS UMR 6047, Paris, France
| | | | - Augusto Gonçalves
- Department of Cell Biology, Medical School of Ribeirão Preto, FMRP/USP, Ribeirão Preto, Brazil
| | - Pedro H. M. Camara
- Department of Cell Biology, Medical School of Ribeirão Preto, FMRP/USP, Ribeirão Preto, Brazil
| | | | - Christophe Rusniok
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, CNRS UMR 6047, Paris, France
| | - Martin Sachse
- UTechS UBI, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Maryse Moya-Nilges
- UTechS UBI, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Thierry Fontaine
- Biologie et Pathogénicité fongiques, Institut Pasteur, Paris, France
| | - Dario S. Zamboni
- Department of Cell Biology, Medical School of Ribeirão Preto, FMRP/USP, Ribeirão Preto, Brazil
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, CNRS UMR 6047, Paris, France
| |
Collapse
|
12
|
Hershkovitz D, Chen EJ, Ensminger AW, Dugan AS, Conway KT, Joyce AC, Segal G, Isberg RR. Genetic evidence for a regulated cysteine protease catalytic triad in LegA7, a Legionella pneumophila protein that impinges on a stress response pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585421. [PMID: 38562771 PMCID: PMC10983931 DOI: 10.1101/2024.03.17.585421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Legionella pneumophila grows within membrane-bound vacuoles in phylogenetically diverse hosts. Intracellular growth requires the function of the Icm/Dot type-IVb secretion system, which translocates more than 300 proteins into host cells. A screen was performed to identify L. pneumophila proteins that stimulate MAPK activation, using Icm/Dot translocated proteins ectopically expressed in mammalian cells. In parallel, a second screen was performed to identify L. pneumophila proteins expressed in yeast that cause growth inhibition in MAPK pathway-stimulatory high osmolarity medium. LegA7 was shared in both screens, a protein predicted to be a member of the bacterial cysteine protease family that has five carboxyl-terminal ankyrin repeats. Three conserved residues in the predicted catalytic triad of LegA7 were mutated. These mutations abolished the ability of LegA7 to inhibit yeast growth. To identify other residues important for LegA7 function, a generalizable selection strategy in yeast was devised to isolate mutants that have lost function and no longer cause growth inhibition on high osmolarity medium. Mutations were isolated in the two carboxyl-terminal ankyrin repeats, as well as an inter-domain region located between the cysteine protease domain and the ankyrin repeats. These mutations were predicted by AlphaFold modeling to localize to the face opposite from the catalytic site, arguing that they interfere with the positive regulation of the catalytic activity. Based on our data, we present a model in which LegA7 harbors a cysteine protease domain with an inter-domain and two carboxyl-terminal ankyrin repeat regions that modulate the function of the catalytic domain.
Collapse
Affiliation(s)
- Dar Hershkovitz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Emy J. Chen
- Department of Molecular Biology and Microbiology
- Program in Genetics, Molecular and Cellular Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine,150 Harrison Ave., Boston, MA 02115, USA
| | | | - Aisling S. Dugan
- Department of Molecular Biology and Microbiology
- Current Address: Dept. of Biology, Brown University, Providence, RI 02912
| | - Kaleigh T. Conway
- Department of Molecular Biology and Microbiology
- Program in Genetics, Molecular and Cellular Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine,150 Harrison Ave., Boston, MA 02115, USA
| | | | - Gil Segal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | | |
Collapse
|
13
|
Wong Z, Ong EBB. Unravelling bacterial virulence factors in yeast: From identification to the elucidation of their mechanisms of action. Arch Microbiol 2024; 206:303. [PMID: 38878203 DOI: 10.1007/s00203-024-04023-2] [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: 04/19/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Pathogenic bacteria employ virulence factors (VF) to establish infection and cause disease in their host. Yeasts, Saccharomyces cerevisiae and Saccharomyces pombe, are useful model organisms to study the functions of bacterial VFs and their interaction with targeted cellular processes because yeast processes and organelle structures are highly conserved and similar to higher eukaryotes. In this review, we describe the principles and applications of the yeast model for the identification and functional characterisation of bacterial VFs to investigate bacterial pathogenesis. The growth inhibition phenotype caused by the heterologous expression of bacterial VFs in yeast is commonly used to identify candidate VFs. Then, subcellular localisation patterns of bacterial VFs can provide further clues about their target molecules and functions during infection. Yeast knockout and overexpression libraries are also used to investigate VF interactions with conserved eukaryotic cell structures (e.g., cytoskeleton and plasma membrane), and cellular processes (e.g., vesicle trafficking, signalling pathways, and programmed cell death). In addition, the yeast growth inhibition phenotype is also useful for screening new drug leads that target and inhibit bacterial VFs. This review provides an updated overview of new tools, principles and applications to study bacterial VFs in yeast.
Collapse
Affiliation(s)
- ZhenPei Wong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800 USM, Malaysia
| | - Eugene Boon Beng Ong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800 USM, Malaysia.
| |
Collapse
|
14
|
Chatterjee R, Setty SRG, Chakravortty D. SNAREs: a double-edged sword for intravacuolar bacterial pathogens within host cells. Trends Microbiol 2024; 32:477-493. [PMID: 38040624 DOI: 10.1016/j.tim.2023.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
In the tug-of-war between host and pathogen, both evolve to combat each other's defence arsenals. Intracellular phagosomal bacteria have developed strategies to modify the vacuolar niche to suit their requirements best. Conversely, the host tries to target the pathogen-containing vacuoles towards the degradative pathways. The host cells use a robust system through intracellular trafficking to maintain homeostasis inside the cellular milieu. In parallel, intracellular bacterial pathogens have coevolved with the host to harbour strategies to manipulate cellular pathways, organelles, and cargoes, facilitating the conversion of the phagosome into a modified pathogen-containing vacuole (PCV). Key molecular regulators of intracellular traffic, such as changes in the organelle (phospholipid) composition, recruitment of small GTPases and associated effectors, soluble N-ethylmaleimide-sensitive factor-activating protein receptors (SNAREs), etc., are hijacked to evade lysosomal degradation. Legionella, Salmonella, Coxiella, Chlamydia, Mycobacterium, and Brucella are examples of pathogens which diverge from the endocytic pathway by using effector-mediated mechanisms to overcome the challenges and establish their intracellular niches. These pathogens extensively utilise and modulate the end processes of secretory pathways, particularly SNAREs, in repurposing the PCV into specialised compartments resembling the host organelles within the secretory network; at the same time, they avoid being degraded by the host's cellular mechanisms. Here, we discuss the recent research advances on the host-pathogen interaction/crosstalk that involves host SNAREs, conserved cellular processes, and the ongoing host-pathogen defence mechanisms in the molecular arms race against each other. The current knowledge of SNAREs, and intravacuolar bacterial pathogen interactions, enables us to understand host cellular innate immune pathways, maintenance of homeostasis, and potential therapeutic strategies to combat ever-growing antimicrobial resistance.
Collapse
Affiliation(s)
- Ritika Chatterjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Subba Rao Gangi Setty
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka, India.
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka, India; Adjunct Faculty, Indian Institute of Science Research and Education, Thiruvananthapuram, Kerala, India.
| |
Collapse
|
15
|
Lehman SS, Williamson CD, Tucholski T, Ellis NA, Bouchard S, Jarnik M, Allen M, Nita-Lazar A, Machner MP. The Legionella pneumophila effector DenR hijacks the host NRas proto-oncoprotein to downregulate MAPK signaling. Cell Rep 2024; 43:114033. [PMID: 38568811 PMCID: PMC11141579 DOI: 10.1016/j.celrep.2024.114033] [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: 05/18/2023] [Revised: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024] Open
Abstract
Small GTPases of the Ras subfamily are best known for their role as proto-oncoproteins, while their function during microbial infection has remained elusive. Here, we show that Legionella pneumophila hijacks the small GTPase NRas to the Legionella-containing vacuole (LCV) surface. A CRISPR interference screen identifies a single L. pneumophila effector, DenR (Lpg1909), required for this process. Recruitment is specific for NRas, while its homologs KRas and HRas are excluded from LCVs. The C-terminal hypervariable tail of NRas is sufficient for recruitment, and interference with either NRas farnesylation or S-acylation sites abrogates recruitment. Intriguingly, we detect markers of active NRas signaling on the LCV, suggesting it acts as a signaling platform. Subsequent phosphoproteomics analyses show that DenR rewires the host NRas signaling landscape, including dampening of the canonical mitogen-activated protein kinase pathway. These results provide evidence for L. pneumophila targeting NRas and suggest a link between NRas GTPase signaling and microbial infection.
Collapse
Affiliation(s)
- Stephanie S Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chad D Williamson
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Trisha Tucholski
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Ellis
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabrina Bouchard
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michal Jarnik
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan Allen
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - 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, MD 20892, USA.
| |
Collapse
|
16
|
Cabello AL, Wells K, Peng W, Feng HQ, Wang J, Meyer DF, Noroy C, Zhao ES, Zhang H, Li X, Chang H, Gomez G, Mao Y, Patrick KL, Watson RO, Russell WK, Yu A, Zhong J, Guo F, Li M, Zhou M, Qian X, Kobayashi KS, Song J, Panthee S, Mechref Y, Ficht TA, Qin QM, de Figueiredo P. Brucella-driven host N-glycome remodeling controls infection. Cell Host Microbe 2024; 32:588-605.e9. [PMID: 38531364 DOI: 10.1016/j.chom.2024.03.003] [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: 09/14/2022] [Revised: 08/28/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
Many powerful methods have been employed to elucidate the global transcriptomic, proteomic, or metabolic responses to pathogen-infected host cells. However, the host glycome responses to bacterial infection remain largely unexplored, and hence, our understanding of the molecular mechanisms by which bacterial pathogens manipulate the host glycome to favor infection remains incomplete. Here, we address this gap by performing a systematic analysis of the host glycome during infection by the bacterial pathogen Brucella spp. that cause brucellosis. We discover, surprisingly, that a Brucella effector protein (EP) Rhg1 induces global reprogramming of the host cell N-glycome by interacting with components of the oligosaccharide transferase complex that controls N-linked protein glycosylation, and Rhg1 regulates Brucella replication and tissue colonization in a mouse model of brucellosis, demonstrating that Brucella exploits the EP Rhg1 to reprogram the host N-glycome and promote bacterial intracellular parasitism, thereby providing a paradigm for bacterial control of host cell infection.
Collapse
Affiliation(s)
- Ana-Lucia Cabello
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Kelsey Wells
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine, The University of Missouri, Columbia, MO 65211, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Hui-Qiang Feng
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Damien F Meyer
- CIRAD, UMR ASTRE, 97170 Petit-Bourg, Guadeloupe, France; ASTRE, University Montpellier, CIRAD, INRAE, Montpellier, France
| | - Christophe Noroy
- CIRAD, UMR ASTRE, 97170 Petit-Bourg, Guadeloupe, France; ASTRE, University Montpellier, CIRAD, INRAE, Montpellier, France
| | - En-Shuang Zhao
- College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Hao Zhang
- College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Xueqing Li
- College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Haowu Chang
- College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Gabriel Gomez
- Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL), Texas A&M University, College Station, TX 77843, USA
| | - Yuxin Mao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - William K Russell
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0635, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Fengguang Guo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Mingqian Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 78843, USA
| | - Mingyuan Zhou
- Department of Information, Risk, and Operations Management, Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaoning Qian
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 78843, USA; TEES-AgriLife Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Koichi S Kobayashi
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA; Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan; Hokkaido University, Institute for Vaccine Research and Development (HU-IVReD), Sapporo 060-8638, Japan
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Suresh Panthee
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
| | - Thomas A Ficht
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA.
| | - Qing-Ming Qin
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine, The University of Missouri, Columbia, MO 65211, USA.
| | - Paul de Figueiredo
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine, The University of Missouri, Columbia, MO 65211, USA; Department of Veterinary Pathobiology, The University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
17
|
Shapira N, Zusman T, Segal G. The LysR-type transcriptional regulator LelA co-regulates various effectors in different Legionella species. Mol Microbiol 2024; 121:243-259. [PMID: 38153189 DOI: 10.1111/mmi.15214] [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: 10/12/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023]
Abstract
The intracellular pathogen Legionella pneumophila translocates more than 300 effector proteins into its host cells. The expression levels of the genes encoding these effectors are orchestrated by an intricate regulatory network. Here, we introduce LelA, the first L. pneumophila LysR-type transcriptional regulator of effectors. Through bioinformatic and experimental analyses, we identified the LelA target regulatory element and demonstrated that it directly activates the expression of three L. pneumophila effectors (legL7, legL6, and legU1). We further found that the gene encoding LelA is positively regulated by the RpoS sigma factor, thus linking it to the known effector regulatory network. Examination of other species throughout the Legionella genus revealed that this regulatory element is found upstream of 34 genes encoding validated effectors, putative effectors, and hypothetical proteins. Moreover, ten of these genes were examined and found to be activated by the L. pneumophila LelA as well as by their orthologs in the corresponding species. LelA represents a novel type of Legionella effector regulator, which coordinates the expression of both adjacently and distantly located effector-encoding genes, thus forming small groups of co-regulated effectors.
Collapse
Affiliation(s)
- Naomi Shapira
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tal Zusman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Gil Segal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
18
|
Allombert J, Vianney A, Charpentier X. Monitoring Effector Translocation with the TEM-1 Beta-Lactamase Reporter System: From Endpoint to Time Course Analysis. Methods Mol Biol 2024; 2715:563-575. [PMID: 37930552 DOI: 10.1007/978-1-0716-3445-5_35] [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] [Indexed: 11/07/2023]
Abstract
Among the bacterial secretion systems, the Type III, IV, and VI secretion systems enable bacteria to secrete proteins directly into a target cell. This specific form of secretion, referred to as "translocation", is essential for a number of pathogens to alter and/or kill the targeted cell. The translocated proteins, called effector proteins, can directly interfere with the normal processes of the targeted cell, preventing elimination of the pathogen and promoting its multiplication. The function of the effector proteins varies greatly depending on the considered pathogen and the targeted cell. In addition, there is often no magic bullet and the number of effector proteins can range from a handful to hundreds, with, for instance, over 300 effector proteins substrate of the Icm/Dot Type IV secretion system in the human pathogen Legionella pneumophila. Identifying, detecting, and monitoring the translocation of each of the effector proteins represent an active field or research and are key to understanding the bacterial molecular weaponry. Translational fusion of the effector with a reporter protein of known activity remains the best method to monitor effector translocation. The development of a fluorescent substrate for the TEM-1 beta-lactamase has turned this antibiotic-resistance protein into a highly versatile reporter system to investigate protein transfer events associated with microbial infection of host cells. We here described a simple protocol to assay translocation of an effector protein by the Icm/Dot system of the human pathogen Legionella pneumophila. Taking advantage that the protonophore CCCP inhibits the secretion activity, this simple protocol can be derived into a time course analysis to follow the kinetic of effector translocation into target cells.
Collapse
Affiliation(s)
- Julie Allombert
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Anne Vianney
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Lyon, France.
| | - Xavier Charpentier
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Lyon, France.
| |
Collapse
|
19
|
Lin JD, Stogios PJ, Abe KT, Wang A, MacPherson J, Skarina T, Gingras AC, Savchenko A, Ensminger AW. Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila. mBio 2023; 14:e0151023. [PMID: 37819088 PMCID: PMC10653801 DOI: 10.1128/mbio.01510-23] [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: 06/16/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Toxin-antitoxin (TA) systems are parasitic genetic elements found in almost all bacterial genomes. They are exchanged horizontally between cells and are typically poorly conserved across closely related strains and species. Here, we report the characterization of a tripartite TA system in the bacterial pathogen Legionella pneumophila that is highly conserved across Legionella species genomes. This system (denoted HipBSTLp) is a distant homolog of the recently discovered split-HipA system in Escherichia coli (HipBSTEc). We present bioinformatic, molecular, and structural analyses of the divergence between these two systems and the functionality of this newly described TA system family. Furthermore, we provide evidence to refute previous claims that the toxin in this system (HipTLp) possesses bifunctionality as an L. pneumophila virulence protein. Overall, this work expands our understanding of the split-HipA system architecture and illustrates the potential for undiscovered biology in these abundant genetic elements.
Collapse
Affiliation(s)
- Jordan D. Lin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kento T. Abe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Avril Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John MacPherson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, Alberta, Canada
| | - Alexander W. Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
20
|
Liang J, Cameron G, Faucher SP. Development of heat-shock resistance in Legionella pneumophila modeled by experimental evolution. Appl Environ Microbiol 2023; 89:e0066623. [PMID: 37668382 PMCID: PMC10537758 DOI: 10.1128/aem.00666-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/29/2023] [Indexed: 09/06/2023] Open
Abstract
Because it can grow in buildings with complex hot water distribution systems (HWDS), healthcare facilities recognize the waterborne bacterium Legionella pneumophila as a major nosocomial infection threat and often try to clear the systems with a pasteurization process known as superheat-and-flush. After this treatment, many facilities find that the contaminating populations slowly recover, suggesting the possibility of in situ evolution favoring increased survival in high-temperature conditions. To mimic this process in a controlled environment, an adaptive laboratory evolution model was used to select a wild-type strain of L. pneumophila for survival to transient exposures to temperatures characteristic of routine hot water use or failed pasteurization processes in HWDS. Over their evolution, these populations became insensitive to exposure to 55°C and developed the ability to survive short exposures to 59°C heat shock. Heat-adapted lineages maintained a higher expression of heat-shock genes during low-temperature incubation in freshwater, suggesting a pre-adaptation to heat stress. Although there were distinct mutation profiles in each of the heat-adapted lineages, each acquired multiple mutations in the DnaJ/DnaK/ClpB disaggregase complex, as well as mutations in chaperone htpG and protease clpX. These mutations were specific to heat-shock survival and were not seen in control lineages included in the experimental model without exposure to heat shock. This study supports in situ observations of adaptation to heat stress and demonstrates the potential of L. pneumophila to develop resistance to control measures. IMPORTANCE As a bacterium that thrives in warm water ecosystems, Legionella pneumophila is a key factor motivating regulations on hot water systems. Two major measures to control Legionella are high circulating temperatures intended to curtail growth and the use of superheat-and-flush pasteurization processes to eliminate established populations. Facilities often suffer recolonization of their hot water systems; hospitals are particularly at risk due to the severe nosocomial pneumoniae caused by Legionella. To understand these long-term survivors, we have used an adaptive laboratory evolution model to replicate this process. We find major differences between the mutational profiles of heat-adapted and heat-naïve L. pneumophila populations including mutations in major heat-shock genes like chaperones and proteases. This model demonstrates that well-validated treatment protocols are needed to clear contaminated systems and-in an analog to antibiotic resistance-the importance of complete eradication of the resident population to prevent selection for more persistent bacteria.
Collapse
Affiliation(s)
- Jeffrey Liang
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Gillian Cameron
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Sébastien P. Faucher
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| |
Collapse
|
21
|
Kang YS, Kirby JE. A Versatile Nanoluciferase Reporter Reveals Structural Properties Associated with a Highly Efficient, N-Terminal Legionella pneumophila Type IV Secretion Translocation Signal. Microbiol Spectr 2023; 11:e0233822. [PMID: 36815834 PMCID: PMC10100965 DOI: 10.1128/spectrum.02338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Many Gram-negative pathogens rely on type IV secretion systems (T4SS) for infection. One limitation has been the lack of ideal reporters to identify T4SS translocated effectors and study T4SS function. Most reporter systems make use of fusions to reporter proteins, in particular, β-lactamase (TEM) and calmodulin-dependent adenylate cyclase (CYA), that allow detection of translocated enzymatic activity inside host cells. However, both systems require costly reagents and use complex, multistep procedures for loading host cells with substrate (TEM) or for analysis (CYA). Therefore, we have developed and characterized a novel reporter system using nanoluciferase (NLuc) fusions to address these limitations. Serendipitously, we discovered that Nluc itself is efficiently translocated by Legionella pneumophila T4SS in an IcmSW chaperone-dependent manner via an N-terminal translocation signal. Extensive mutagenesis in the NLuc N terminus suggested the importance of an α-helical domain spanning D5 to V9, as mutations predicted to disrupt this structure, with one exception, were translocation defective. Notably, NLuc was capable of translocating several proteins examined when fused to the N or C terminus, while maintaining robust luciferase activity. In particular, it delivered the split GFP11 fragment into J774 macrophages transfected with GFPopt, thereby resulting in in vivo assembly of superfolder green fluorescent protein (GFP). This provided a bifunctional assay in which translocation could be assayed by fluorescence microplate, confocal microscopy, and/or luciferase assays. We further identified an optimal NLuc substrate which allowed a robust, inexpensive, one-step, high-throughput screening assay to identify T4SS translocation substrates and inhibitors. Taken together, these results indicate that NLuc provides both new insight into and also tools for studying T4SS biology. IMPORTANCE Type IV secretion systems (T4SS) are used by Gram-negative pathogens to coopt host cell function. However, the translocation signals recognized by T4SS are not fully explained by primary amino acid sequence, suggesting yet-to-be-defined contributions of secondary and tertiary structure. Here, we unexpectedly identified nanoluciferase (NLuc) as an efficient IcmSW-dependent translocated T4SS substrate, and we provide extensive mutagenesis data suggesting that the first N-terminal, alpha-helix domain is a critical translocation recognition motif. Notably, most existing reporter systems for studying translocated proteins make use of fusions to reporters to permit detection of translocated enzymatic activity inside the host cell. However, existing systems require extremely costly substrates, complex technical procedures to isolate eukaryotic cytoplasm for analysis, and/or are insensitive. Importantly, we found that NLuc provides a powerful, cost-effective new tool to address these limitations and facilitate high-throughput exploration of secretion system biology.
Collapse
Affiliation(s)
- Yoon-Suk Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
22
|
Guzmán-Herrador DL, Fernández-Gómez A, Llosa M. Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation. Front Cell Infect Microbiol 2023; 13:1146000. [PMID: 36949816 PMCID: PMC10025392 DOI: 10.3389/fcimb.2023.1146000] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.
Collapse
|
23
|
VpdC is a ubiquitin-activated phospholipase effector that regulates Legionella vacuole expansion during infection. Proc Natl Acad Sci U S A 2022; 119:e2209149119. [PMID: 36413498 PMCID: PMC9860323 DOI: 10.1073/pnas.2209149119] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intravacuolar pathogens need to gradually expand their surrounding vacuole to accommodate the growing number of bacterial offspring during intracellular replication. Here we found that Legionella pneumophila controls vacuole expansion by fine-tuning the generation of lysophospholipids within the vacuolar membrane. Upon allosteric activation by binding to host ubiquitin, the type IVB (Dot/Icm) effector VpdC converts phospholipids into lysophospholipids which, at moderate concentrations, are known to promote membrane fusion but block it at elevated levels by generating excessive positive membrane curvature. Consequently, L. pneumophila overproducing VpdC were prevented from adequately expanding their surrounding membrane, trapping the replicating bacteria within spatially confined vacuoles and reducing their capability to proliferate intracellularly. Quantitative lipidomics confirmed a VpdC-dependent increase in several types of lysophospholipids during infection, and VpdC production in transiently transfected cells caused tubulation of organelle membranes as well as mitochondria fragmentation, processes that can be phenocopied by supplying cells with exogenous lysophospholipids. Together, these results demonstrate an important role for bacterial phospholipases in vacuolar expansion.
Collapse
|
24
|
Fu M, Liu Y, Wang G, Wang P, Zhang J, Chen C, Zhao M, Zhang S, Jiao J, Ouyang X, Yu Y, Wen B, He C, Wang J, Zhou D, Xiong X. A protein–protein interaction map reveals that the Coxiella burnetii effector CirB inhibits host proteasome activity. PLoS Pathog 2022; 18:e1010660. [PMID: 35816513 PMCID: PMC9273094 DOI: 10.1371/journal.ppat.1010660] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/09/2022] [Indexed: 12/19/2022] Open
Abstract
Coxiella burnetii is the etiological agent of the zoonotic disease Q fever, which is featured by its ability to replicate in acid vacuoles resembling the lysosomal network. One key virulence determinant of C. burnetii is the Dot/Icm system that transfers more than 150 effector proteins into host cells. These effectors function to construct the lysosome-like compartment permissive for bacterial replication, but the functions of most of these effectors remain elusive. In this study, we used an affinity tag purification mass spectrometry (AP-MS) approach to generate a C. burnetii-human protein-protein interaction (PPI) map involving 53 C. burnetii effectors and 3480 host proteins. This PPI map revealed that the C. burnetii effector CBU0425 (designated CirB) interacts with most subunits of the 20S core proteasome. We found that ectopically expressed CirB inhibits hydrolytic activity of the proteasome. In addition, overexpression of CirB in C. burnetii caused dramatic inhibition of proteasome activity in host cells, while knocking down CirB expression alleviated such inhibitory effects. Moreover, we showed that a region of CirB that spans residues 91–120 binds to the proteasome subunit PSMB5 (beta 5). Finally, PSMB5 knockdown promotes C. burnetii virulence, highlighting the importance of proteasome activity modulation during the course of C. burnetii infection. As the causative agent of Q fever, C. burnetii colonizes host cells by transferring effector proteins into the host cytoplasm through its Dot/Icm secretion system to construct a replicative vacuole. The function of effectors remains largely unknown. Here, we performed a large-scale AP-MS screen to analyze the interactions among C. burnetii effectors and human proteins. These analyses found that CirB functions as an inhibitor of host proteasome activity, revealing that proteasome activity is important for intracellular survival of C. burnetii. Our data have laid the foundation for future exploring the molecular mechanisms underlying the roles of C. burnetii effectors in its virulence and for the identification of novel potential drug targets for the development of novel therapeutic treatment for C. burnetii infection.
Collapse
Affiliation(s)
- Mengjiao Fu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Guannan Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Jianing Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Chen Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mingliang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Shan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Xuan Ouyang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Bohai Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
- * E-mail: , (DZ); (XX)
| | - Xiaolu Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medicine Sciences, Fengtai, Beijing,China
- * E-mail: , (DZ); (XX)
| |
Collapse
|
25
|
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: 4.7] [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.
Collapse
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
| |
Collapse
|
26
|
Monteiro IP, Sousa S, Borges V, Gonçalves P, Gomes JP, Mota LJ, Franco IS. A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector. Front Cell Infect Microbiol 2022; 12:864626. [PMID: 35711665 PMCID: PMC9195298 DOI: 10.3389/fcimb.2022.864626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Legionella pneumophila is an accidental human pathogen that causes the potentially fatal Legionnaires’ disease, a severe type of pneumonia. The main virulence mechanism of L. pneumophila is a Type 4B Secretion System (T4SS) named Icm/Dot that transports effector proteins into the host cell cytosol. The concerted action of effectors on several host cell processes leads to the formation of an intracellular Legionella-containing vacuole that is replication competent and avoids phagolysosomal degradation. To date over 300 Icm/Dot substrates have been identified. In this study, we searched the genome of a L. pneumophila strain (Pt/VFX2014) responsible for the second largest L. pneumophila outbreak worldwide (in Vila Franca de Xira, Portugal, in 2014) for genes encoding potential novel Icm/Dot substrates. This strain Pt/VFX2014 belongs to serogroup 1 but phylogenetically segregates from all other serogroup 1 strains previously sequenced, displaying a unique mosaic genetic backbone. The ability of the selected putative effectors to be delivered into host cells by the T4SS was confirmed using the TEM-1 β-lactamase reporter assay. Two previously unknown Icm/Dot effectors were identified, VFX05045 and VFX10045, whose homologs Lpp1450 and Lpp3070 in clinical strain L. pneumophila Paris were also confirmed as T4SS substrates. After delivery into the host cell cytosol, homologs VFX05045/Lpp1450 remained diffused in the cell, similarly to Lpp3070. In contrast, VFX10045 localized to the host cell nucleus. To understand how VFX10045 and Lpp3070 (94% of identity at amino acid level) are directed to distinct sites, we carried out a comprehensive site-directed mutagenesis followed by analyses of the subcellular localization of the mutant proteins. This led to the delineation of region in the C-terminal part (residues 380 to 534) of the 583 amino acid-long VFX10045 as necessary and sufficient for nuclear targeting and highlighted the fundamental function of the VFX10045-specific R440 and I441 residues in this process. These studies revealed a strain-specific nucleotropism for new effector VFX10045/Lpp3070, which anticipates distinct functions between these homologs.
Collapse
Affiliation(s)
- Inês P. Monteiro
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Sofia Sousa
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Vítor Borges
- Núcleo de Bioinformática, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Paulo Gonçalves
- Laboratório Nacional de Referência de Legionella, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - João Paulo Gomes
- Núcleo de Bioinformática, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Luís Jaime Mota
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Irina S. Franco
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- *Correspondence: Irina S. Franco,
| |
Collapse
|
27
|
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: 7] [Impact Index Per Article: 2.3] [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.
Collapse
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.
| |
Collapse
|
28
|
Cheng E, Dorjsuren D, Lehman S, Larson CL, Titus SA, Sun H, Zakharov A, Rai G, Heinzen RA, Simeonov A, Machner MP. A Comprehensive Phenotypic Screening Strategy to Identify Modulators of Cargo Translocation by the Bacterial Type IVB Secretion System. mBio 2022; 13:e0024022. [PMID: 35258332 PMCID: PMC9040768 DOI: 10.1128/mbio.00240-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 02/03/2023] Open
Abstract
Bacterial type IV secretion systems (T4SSs) are macromolecular machines that translocate effector proteins across multiple membranes into infected host cells. Loss of function mutations in genes encoding protein components of the T4SS render bacteria avirulent, highlighting the attractiveness of T4SSs as drug targets. Here, we designed an automated high-throughput screening approach for the identification of compounds that interfere with the delivery of a reporter-effector fusion protein from Legionella pneumophila into RAW264.7 mouse macrophages. Using a fluorescence resonance energy transfer (FRET)-based detection assay in a bacteria/macrophage coculture format, we screened a library of over 18,000 compounds and, upon vetting compound candidates in a variety of in vitro and cell-based secondary screens, isolated several hits that efficiently interfered with biological processes that depend on a functional T4SS, such as intracellular bacterial proliferation or lysosomal avoidance, but had no detectable effect on L. pneumophila growth in culture medium, conditions under which the T4SS is dispensable. Notably, the same hit compounds also attenuated, to varying degrees, effector delivery by the closely related T4SS from Coxiella burnetii, notably without impacting growth of this organism within synthetic media. Together, these results support the idea that interference with T4SS function is a possible therapeutic intervention strategy, and the emerging compounds provide tools to interrogate at a molecular level the regulation and dynamics of these virulence-critical translocation machines. IMPORTANCE Multi-drug-resistant pathogens are an emerging threat to human health. Because conventional antibiotics target not only the pathogen but also eradicate the beneficial microbiota, they often cause additional clinical complications. Thus, there is an urgent need for the development of "smarter" therapeutics that selectively target pathogens without affecting beneficial commensals. The bacterial type IV secretion system (T4SS) is essential for the virulence of a variety of pathogens but dispensable for bacterial viability in general and can, thus, be considered a pathogen's Achilles heel. By identifying small molecules that interfere with cargo delivery by the T4SS from two important human pathogens, Legionella pneumophila and Coxiella burnetii, our study represents the first step in our pursuit toward precision medicine by developing pathogen-selective therapeutics capable of treating the infections without causing harm to commensal bacteria.
Collapse
Affiliation(s)
- Eric Cheng
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Dorjbal Dorjsuren
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Stephanie Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles L. Larson
- Laboratory of Bacteriology, Coxiella Pathogenesis Section, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - Steven A. Titus
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Hongmao Sun
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Alexey Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ganesha Rai
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Robert A. Heinzen
- Laboratory of Bacteriology, Coxiella Pathogenesis Section, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, Hamilton, Montana, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - 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, USA
| |
Collapse
|
29
|
Hochstrasser R, Michaelis S, Brülisauer S, Sura T, Fan M, Maaß S, Becher D, Hilbi H. Migration of Acanthamoeba through Legionella biofilms is regulated by the bacterial Lqs-LvbR network, effector proteins and the flagellum. Environ Microbiol 2022; 24:3672-3692. [PMID: 35415862 PMCID: PMC9544456 DOI: 10.1111/1462-2920.16008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
The environmental bacterium Legionella pneumophila causes the pneumonia Legionnaires' disease. The opportunistic pathogen forms biofilms and employs the Icm/Dot type IV secretion system (T4SS) to replicate in amoebae and macrophages. A regulatory network comprising the Legionella quorum sensing (Lqs) system and the transcription factor LvbR controls bacterial motility, virulence and biofilm architecture. Here we show by comparative proteomics that in biofilms formed by the L. pneumophila ΔlqsR or ΔlvbR regulatory mutants the abundance of proteins encoded by a genomic ‘fitness island’, metabolic enzymes, effector proteins and flagellar components (e.g. FlaA) varies. ∆lqsR or ∆flaA mutants form ‘patchy’ biofilms like the parental strain JR32, while ∆lvbR forms a ‘mat‐like’ biofilm. Acanthamoeba castellanii amoebae migrated more slowly through biofilms of L. pneumophila lacking lqsR, lvbR, flaA, a functional Icm/Dot T4SS (∆icmT), or secreted effector proteins. Clusters of bacteria decorated amoebae in JR32, ∆lvbR or ∆icmT biofilms but not in ∆lqsR or ∆flaA biofilms. The amoeba‐adherent bacteria induced promoters implicated in motility (PflaA) or virulence (PsidC, PralF). Taken together, the Lqs‐LvbR network (quorum sensing), FlaA (motility) and the Icm/Dot T4SS (virulence) regulate migration of A. castellanii through L. pneumophila biofilms, and – apart from the T4SS – govern bacterial cluster formation on the amoebae.
Collapse
Affiliation(s)
- Ramon Hochstrasser
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Sabrina Brülisauer
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Thomas Sura
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Mingzhen Fan
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Sandra Maaß
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| |
Collapse
|
30
|
Sahr T, Escoll P, Rusniok C, Bui S, Pehau-Arnaudet G, Lavieu G, Buchrieser C. Translocated Legionella pneumophila small RNAs mimic eukaryotic microRNAs targeting the host immune response. Nat Commun 2022; 13:762. [PMID: 35140216 PMCID: PMC8828724 DOI: 10.1038/s41467-022-28454-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/26/2022] [Indexed: 02/08/2023] Open
Abstract
Legionella pneumophila is an intracellular bacterial pathogen that can cause a severe form of pneumonia in humans, a phenotype evolved through interactions with aquatic protozoa in the environment. Here, we show that L. pneumophila uses extracellular vesicles to translocate bacterial small RNAs (sRNAs) into host cells that act on host defence signalling pathways. The bacterial sRNA RsmY binds to the UTR of ddx58 (RIG-I encoding gene) and cRel, while tRNA-Phe binds ddx58 and irak1 collectively reducing expression of RIG-I, IRAK1 and cRel, with subsequent downregulation of IFN-β. Thus, RsmY and tRNA-Phe are bacterial trans-kingdom regulatory RNAs downregulating selected sensor and regulator proteins of the host cell innate immune response. This miRNA-like regulation of the expression of key sensors and regulators of immunity is a feature of L. pneumophila host-pathogen communication and likely represents a general mechanism employed by bacteria that interact with eukaryotic hosts.
Collapse
Affiliation(s)
- Tobias Sahr
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France
| | - Pedro Escoll
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France
| | - Christophe Rusniok
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France
| | - Sheryl Bui
- Université de Paris, INSERM ERL U1316, UMR 7057/CNRS, Paris, France
| | - Gérard Pehau-Arnaudet
- Unité de Technologie et Service BioImagerie Ultrastructurale and CNRS UMR 3528, Paris, France
| | - Gregory Lavieu
- Université de Paris, INSERM ERL U1316, UMR 7057/CNRS, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France.
| |
Collapse
|
31
|
Belyi Y, Levanova N, Schroeder GN. Glycosylating Effectors of Legionella pneumophila: Finding the Sweet Spots for Host Cell Subversion. Biomolecules 2022; 12:255. [PMID: 35204756 PMCID: PMC8961657 DOI: 10.3390/biom12020255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023] Open
Abstract
Work over the past two decades clearly defined a significant role of glycosyltransferase effectors in the infection strategy of the Gram-negative, respiratory pathogen Legionella pneumophila. Identification of the glucosyltransferase effectors Lgt1-3, specifically modifying elongation factor eEF1A, disclosed a novel mechanism of host protein synthesis manipulation by pathogens and illuminated its impact on the physiological state of the target cell, in particular cell cycle progression and immune and stress responses. Recent characterization of SetA as a general O-glucosyltransferase with a wide range of targets including the proteins Rab1 and Snx1, mediators of membrane transport processes, and the discovery of new types of glycosyltransferases such as LtpM and SidI indicate that the vast effector arsenal might still hold more so-far unrecognized family members with new catalytic features and substrates. In this article, we review our current knowledge regarding these fascinating biomolecules and discuss their role in introducing new or overriding endogenous post-translational regulatory mechanisms enabling the subversion of eukaryotic cells by L. pneumophila.
Collapse
Affiliation(s)
- Yury Belyi
- Laboratory of Molecular Pathogenesis, Gamaleya Research Centre, 123098 Moscow, Russia
| | | | - Gunnar N. Schroeder
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK
| |
Collapse
|
32
|
Voth K, Pasricha S, Chung IYW, Wibawa RR, Zainudin ENHE, Hartland EL, Cygler M. Structural and Functional Characterization of Legionella pneumophila Effector MavL. Biomolecules 2021; 11:biom11121802. [PMID: 34944446 PMCID: PMC8699189 DOI: 10.3390/biom11121802] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/23/2022] Open
Abstract
Legionella pneumophila is a Gram-negative intracellular pathogen that causes Legionnaires’ disease in elderly or immunocompromised individuals. This bacterium relies on the Dot/Icm (Defective in organelle trafficking/Intracellular multiplication) Type IV Secretion System (T4SS) and a large (>330) set of effector proteins to colonize the host cell. The structural variability of these effectors allows them to disrupt many host processes. Herein, we report the crystal structure of MavL to 2.65 Å resolution. MavL adopts an ADP-ribosyltransferase (ART) fold and contains the distinctive ligand-binding cleft of ART proteins. Indeed, MavL binds ADP-ribose with Kd of 13 µM. Structural overlay of MavL with poly-(ADP-ribose) glycohydrolases (PARGs) revealed a pair of aspartate residues in MavL that align with the catalytic glutamates in PARGs. MavL also aligns with ADP-ribose “reader” proteins (proteins that recognize ADP-ribose). Since no glycohydrolase activity was observed when incubated in the presence of ADP-ribosylated PARP1, MavL may play a role as a signaling protein that binds ADP-ribose. An interaction between MavL and the mammalian ubiquitin-conjugating enzyme UBE2Q1 was revealed by yeast two-hybrid and co-immunoprecipitation experiments. This work provides structural and molecular insights to guide biochemical studies aimed at elucidating the function of MavL. Our findings support the notion that ubiquitination and ADP-ribosylation are global modifications exploited by L. pneumophila.
Collapse
Affiliation(s)
- Kevin Voth
- Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.V.); (I.Y.W.C.)
| | - Shivani Pasricha
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton 3168, Australia; (S.P.); (R.R.W.)
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.V.); (I.Y.W.C.)
| | - Rachelia R. Wibawa
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton 3168, Australia; (S.P.); (R.R.W.)
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia;
| | - Engku Nuraishah Huda E. Zainudin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia;
| | - Elizabeth L. Hartland
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton 3168, Australia; (S.P.); (R.R.W.)
- Department of Molecular and Translational Science, Monash University, Clayton 3168, Australia
- Correspondence: (E.L.H.); (M.C.)
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.V.); (I.Y.W.C.)
- Correspondence: (E.L.H.); (M.C.)
| |
Collapse
|
33
|
Budowa i znaczenie II systemu sekrecji białek w ekologii i patogenezie Legionella pneumophila. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Pałeczki Legionella pneumophila pasożytują w komórkach odległych filogenetycznie gospodarzy, w środowisku wodnym w pierwotniakach, a w organizmie człowieka w makrofagach alweolarnych. Zdolność tych bakterii do wewnątrzkomórkowego namnażania się w komórkach fagocytujących, wyspecjalizowanych do niszczenia mikroorganizmów, ma podstawowe znaczenie dla rozwoju nietypowego zapalenia płuc zwanego chorobą legionistów. Umiejscowione na kilku różnych loci chromosomu bakteryjnego geny II systemu sekrecji L. pneumophila kodują co najmniej 25 białek, w tym enzymy o aktywności lipolitycznej, proteolitycznej, rybonukleazy oraz białka unikalne bakterii Legionella. W środowisku naturalnym T2SS L. pneumophila odgrywa decydującą rolę w ekologii tych drobnoustrojów determinując ich zdolność do przeżycia zarówno w postaci planktonicznej, jak i w strukturach biofilmu w słodkowodnych zbiornikach o niskiej temperaturze. Białka T2SS umożliwiają L. pneumophila zakażenie różnych gatunków pierwotniaków, a substraty tego systemu określają zakres pierwotniaczego gospodarza. Namnażanie się bakterii w różnorodnych pierwotniakach przyczynia się do ich rozsiewania oraz transmisji do antropogenicznych źródeł. Białka wydzielane za pomocą II systemu sekrecji determinują również zdolność L. pneumophila do zakażania mysich makrofagów alweolarnych i szpiku kostnego, ludzkich makrofagów linii U937 i THP-1 oraz komórek nabłonkowych pęcherzyków płucnych. Enzymy wydzielane za pomocą tego systemu, takie jak: proteazy, aminopeptydazy czy fosfolipazy umożliwiają pozyskanie substancji pokarmowych oraz powodują destrukcję tkanki płucnej myszy. W organizmie człowieka białka T2SS przyczyniają się do osłabienia wrodzonej odpowiedzi immunologicznej na zakażenie L. pneumophila przez hamowanie indukcji prozapalnych cytokin (IL-6, TNF-α, IL-1 oraz IL-8).
Collapse
|
34
|
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: 22] [Impact Index Per Article: 5.5] [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.
Collapse
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
| |
Collapse
|
35
|
Noroy C, Meyer DF. The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis. PLoS Comput Biol 2021; 17:e1008788. [PMID: 34252087 PMCID: PMC8274917 DOI: 10.1371/journal.pcbi.1008788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
The identification of bacterial effectors is essential to understand how obligatory intracellular bacteria such as Ehrlichia spp. manipulate the host cell for survival and replication. Infection of mammals–including humans–by the intracellular pathogenic bacteria Ehrlichia spp. depends largely on the injection of virulence proteins that hijack host cell processes. Several hypothetical virulence proteins have been identified in Ehrlichia spp., but one so far has been experimentally shown to translocate into host cells via the type IV secretion system. However, the current challenge is to identify most of the type IV effectors (T4Es) to fully understand their role in Ehrlichia spp. virulence and host adaptation. Here, we predict the T4E repertoires of four sequenced Ehrlichia spp. and four other Anaplasmataceae as comparative models (pathogenic Anaplasma spp. and Wolbachia endosymbiont) using previously developed S4TE 2.0 software. This analysis identified 579 predicted T4Es (228 pT4Es for Ehrlichia spp. only). The effector repertoires of Ehrlichia spp. overlapped, thereby defining a conserved core effectome of 92 predicted effectors shared by all strains. In addition, 69 species-specific T4Es were predicted with non-canonical GC% mostly in gene sparse regions of the genomes and we observed a bias in pT4Es according to host-specificity. We also identified new protein domain combinations, suggesting novel effector functions. This work presenting the predicted effector collection of Ehrlichia spp. can serve as a guide for future functional characterisation of effectors and design of alternative control strategies against these bacteria. A fundamental step for the survival and replication of intravacuolar bacterial pathogens is the establishment of a replicative niche inside host cells by the secretion of bacterial effector proteins in the cytoplasm of the infected cells. These effectors manipulate host signaling pathways, thus allowing to escape the host degradative pathway and uptake nutrients required for intracellular replication of bacteria. In this study, we used S4TE2.0 software for high-throughput computational prediction of bacterial type IV effectors in zoonotic bacteria of the Anaplasmataceae family. The analysis of protein architecture of effectors helped us to identify the cellular pathways targeted during the infection process. The demonstration that effectors are modular components with a broad variety of protein architectures nicely explains their pleotropic mode of action and enlightens their function. We showed that bacterial adaptation to a given host during evolution requires a minimal repertoire of candidate effectors although further experimental determination is needed. T4Es are of increasing interest for basic research, including comprehension of hijacked cellular pathways, manipulated innate immunity, and application for therapeutics. Indeed pathogenomics-driven studies, especially on genetically intractable intracellular bacteria such as Anaplasmataceae, have now a substantial impact for the development of host-targeted antimicrobials, as an alternative to antibiotics.
Collapse
Affiliation(s)
- Christophe Noroy
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRA, Univ Montpellier, Montpellier, France
- Université des Antilles, Fouillole, Pointe-à-Pitre, Guadeloupe, France
| | - Damien F. Meyer
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRA, Univ Montpellier, Montpellier, France
- * E-mail:
| |
Collapse
|
36
|
Glueck NK, O'Brien KM, Seguin DC, Starai VJ. Legionella pneumophila LegC7 effector protein drives aberrant endoplasmic reticulum:endosome contacts in yeast. Traffic 2021; 22:284-302. [PMID: 34184807 DOI: 10.1111/tra.12807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/28/2022]
Abstract
Legionella pneumophila is a facultative intracellular bacterial pathogen, causing the severe form of pneumonia known as Legionnaires' disease. Legionella actively alters host organelle trafficking through the activities of "effector" proteins secreted via a type-IVB secretion system, in order to construct the bacteria-laden Legionella-containing vacuole (LCV) and prevent lysosomal degradation. The LCV is created with membrane derived from host endoplasmic reticulum (ER), secretory vesicles and phagosomes, although the precise molecular mechanisms that drive its synthesis remain poorly understood. In an effort to characterize the in vivo activity of the LegC7/YlfA SNARE-like effector protein from Legionella in the context of eukaryotic membrane trafficking in yeast, we find that LegC7 interacts with the Emp46p/Emp47p ER-to-Golgi glycoprotein cargo adapter complex, alters ER morphology and induces aberrant ER:endosome interactions, as measured by visualization of ER cargo degradation, reconstitution of split-GFP proteins and enhanced oxidation of the ER lumen. LegC7-dependent toxicity, disruption of ER morphology and ER:endosome fusion events were dependent upon endosomal VPS class C tethering complexes and the endosomal t-SNARE, Pep12p. This work establishes a model in which LegC7 functions to recruit host ER material to the bacterial phagosome during infection by driving ER:endosome contacts, potentially through interaction with host membrane tethering complexes and/or cargo adapters.
Collapse
Affiliation(s)
- Nathan K Glueck
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Kevin M O'Brien
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Danielle C Seguin
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Vincent J Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, USA.,Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
37
|
Lettl C, Haas R, Fischer W. Kinetics of CagA type IV secretion by Helicobacter pylori and the requirement for substrate unfolding. Mol Microbiol 2021; 116:794-807. [PMID: 34121254 DOI: 10.1111/mmi.14772] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Accepted: 06/12/2021] [Indexed: 12/27/2022]
Abstract
Type IV secretion of effector proteins is an important principle for interaction of human pathogens with their target cells. The corresponding secretion systems may transport a multitude of effector proteins that have to be deployed in the respective spatiotemporal context, or only a single translocated protein, as in the case of the CagA effector protein produced by the human gastric pathogen Helicobacter pylori. For a more detailed analysis of the kinetics and mode of action of CagA type IV secretion by H. pylori, we describe here, a novel, highly sensitive split luciferase-based translocation reporter which can be easily adapted to different end-point or real-time measurements. Using this reporter, we showed that H. pylori cells are able to rapidly inject a limited amount of their CagA supply into cultured gastric epithelial cells. We have further employed the reporter system to address the question whether CagA has to be unfolded prior to translocation by the type IV secretion system. We showed that protein domains co-translocated with CagA as protein fusions are more readily tolerated as substrates than in other secretion systems, but also provide evidence that unfolding of effector proteins is a prerequisite for their transport.
Collapse
Affiliation(s)
- Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Munich, Germany.,Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Munich, Germany.,Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Munich, Germany.,Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
| |
Collapse
|
38
|
Linsky M, Segal G. A horizontally acquired Legionella genomic island encoding a LuxR type regulator and effector proteins displays variation in gene content and regulation. Mol Microbiol 2021; 116:766-782. [PMID: 34120381 DOI: 10.1111/mmi.14770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/30/2022]
Abstract
The intracellular pathogen Legionella pneumophila translocates >300 effector proteins into host cells, many of which are regulated at the transcriptional level. Here, we describe a novel L. pneumophila genomic island, which undergoes horizontal gene transfer within the Legionella genus. This island encodes two Icm/Dot effectors: LegK3 and a previously uncharacterized effector which we named CegK3, as well as a LuxR type regulator, which we named RegK3. Analysis of this island in different Legionella species revealed a conserved regulatory element located upstream to the effector-encoding genes in the island. Further analyses, including gene expression analysis, mutagenesis of the RegK3 regulatory element, controlled expression studies, and gel-mobility shift assays, all demonstrate that RegK3 directly activates the expression levels of legK3 and cegK3 effector-encoding genes. Additionally, the expression of all the components of the island is silenced by the Fis repressors. Comparison of expression profiles of these three genes among different Legionella species revealed variability in the activation levels mediated by RegK3, which were positively correlated with the Fis-mediated repression. Furthermore, LegK3 and CegK3 effectors moderately inhibit yeast growth, and importantly, they have a strong synergistic inhibitory effect on yeast growth, suggesting these two effectors are not only co-regulated but also might function together.
Collapse
Affiliation(s)
- Marika Linsky
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Gil Segal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
39
|
Allombert J, Jaboulay C, Michard C, Andréa C, Charpentier X, Vianney A, Doublet P. Deciphering Legionella effector delivery by Icm/Dot secretion system reveals a new role for c-di-GMP signaling. J Mol Biol 2021; 433:166985. [PMID: 33845084 DOI: 10.1016/j.jmb.2021.166985] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022]
Abstract
Secretion of bacterial effector proteins into host cells plays a key role in bacterial virulence. Yet, the dynamics of the secretion systems activity remains poorly understood, especially when machineries deal with the export of numerous effectors. We address the question of multi-effector secretion by focusing on the Legionella pneumophila Icm/Dot T4SS that translocates a record number of 300 effectors. We set up a kinetic translocation assay, based on the β-lactamase translocation reporter system combined with the effect of the protonophore CCCP. When used for translocation analysis of Icm/Dot substrates constitutively produced by L. pneumophila, this assay allows a fine monitoring of the secretion activity of the T4SS, independently of the expression control of the effectors. We observed that effectors are translocated with a specific timing, suggesting a control of their docking/translocation by the T4SS. Their delivery is accurately organized to allow effective manipulation of the host cell, as exemplified by the sequential translocation of effectors targeting Rab1, namely SidM/DrrA, LidA, LepB. Remarkably, the timed delivery of effectors does not depend only on their interaction with chaperone proteins but implies cyclic-di-GMP signaling, as the diguanylate cyclase Lpl0780/Lpp0809, contributes to the timing of translocation.
Collapse
Affiliation(s)
- J Allombert
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - C Jaboulay
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - C Michard
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - C Andréa
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - X Charpentier
- CIRI, Centre International de Recherche en Infectiologie, (Team: Horigene), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - A Vianney
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.
| | - P Doublet
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.
| |
Collapse
|
40
|
The Tail-Specific Protease Is Important for Legionella pneumophila To Survive Thermal Stress in Water and inside Amoebae. Appl Environ Microbiol 2021; 87:AEM.02975-20. [PMID: 33608288 DOI: 10.1128/aem.02975-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Legionella pneumophila (Lp) is an inhabitant of natural and human-made water systems, where it replicates within amoebae and ciliates and survives within biofilms. When Lp-contaminated aerosols are breathed in, Lp can enter the lungs and may infect human alveolar macrophages, causing severe pneumonia known as Legionnaires' disease. Lp is often found in hot water distribution systems (HWDS), which are linked to nosocomial outbreaks. Heat treatment is used to disinfect HWDS and reduce the concentration of Lp However, Lp is often able to recolonize these water systems, indicating an efficient heat shock response. Tail-specific proteases (Tsp) are typically periplasmic proteases implicated in degrading aberrant proteins in the periplasm and important for surviving thermal stress. In Lp Philadelphia-1, Tsp is encoded by the lpg0499 gene. In this paper, we show that Tsp is important for surviving thermal stress in water and for optimal infection of amoeba when a shift in temperature occurs during intracellular growth. We also demonstrate that Tsp is expressed in the postexponential phase but repressed in the exponential phase and that the cis-encoded small regulatory RNA Lpr17 shows the opposite expression, suggesting that it represses translation of tsp In addition, our results show that tsp is regulated by CpxR, a major regulator in Lp, in an Lpr17-independent manner. Deletion of CpxR also reduced the ability of Lp to survive heat shock. In conclusion, our study shows that Tsp is likely an important factor for the survival and growth of Lp in water systems.IMPORTANCE Lp is a major cause of nosocomial and community-acquired pneumonia. Lp is found in water systems, including hot water distribution systems. Heat treatment is a method of disinfection often used to limit the presence of Lp in such systems; however, the benefit is usually short term, as Lp is able to quickly recolonize these systems. Presumably, Lp responds efficiently to thermal stress, but so far, not much is known about the genes involved. In this paper, we show that the Tsp and the two-component system CpxRA are required for resistance to thermal stress when Lp is free in water and when it is inside host cells. Our study identifies critical systems for the survival of Lp in its natural environment under thermal stress.
Collapse
|
41
|
Chauhan D, Shames SR. Pathogenicity and Virulence of Legionella: Intracellular replication and host response. Virulence 2021; 12:1122-1144. [PMID: 33843434 PMCID: PMC8043192 DOI: 10.1080/21505594.2021.1903199] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacteria of the genus Legionella are natural pathogens of amoebae that can cause a severe pneumonia in humans called Legionnaires’ Disease. Human disease results from inhalation of Legionella-contaminated aerosols and subsequent bacterial replication within alveolar macrophages. Legionella pathogenicity in humans has resulted from extensive co-evolution with diverse genera of amoebae. To replicate intracellularly, Legionella generates a replication-permissive compartment called the Legionella-containing vacuole (LCV) through the concerted action of hundreds of Dot/Icm-translocated effector proteins. In this review, we present a collective overview of Legionella pathogenicity including infection mechanisms, secretion systems, and translocated effector function. We also discuss innate and adaptive immune responses to L. pneumophila, the implications of Legionella genome diversity and future avenues for the field.
Collapse
Affiliation(s)
- Deepika Chauhan
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | |
Collapse
|
42
|
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: 24] [Impact Index Per Article: 6.0] [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.
Collapse
|
43
|
Abstract
Intracellular proliferation of Legionella pneumophila within a vacuole in human alveolar macrophages is essential for manifestation of Legionnaires’ pneumonia. Intravacuolar growth of the pathogen is totally dependent on remodeling the L. pneumophila-containing vacuole (LCV) by the ER and on its evasion of the endosomal-lysosomal degradation pathway. Diversion of the Legionella pneumophila-containing vacuole (LCV) from the host endosomal-lysosomal degradation pathway is one of the main virulence features essential for manifestation of Legionnaires’ pneumonia. Many of the ∼350 Dot/Icm-injected effectors identified in L. pneumophila have been shown to interfere with various host pathways and processes, but no L. pneumophila effector has ever been identified to be indispensable for lysosomal evasion. While most single effector mutants of L. pneumophila do not exhibit a defective phenotype within macrophages, we show that the MavE effector is essential for intracellular growth of L. pneumophila in human monocyte-derived macrophages (hMDMs) and amoebae and for intrapulmonary proliferation in mice. The mavE null mutant fails to remodel the LCV with endoplasmic reticulum (ER)-derived vesicles and is trafficked to the lysosomes where it is degraded, similar to formalin-killed bacteria. During infection of hMDMs, the MavE effector localizes to the poles of the LCV membrane. The crystal structure of MavE, resolved to 1.8 Å, reveals a C-terminal transmembrane helix, three copies of tyrosine-based sorting motifs, and an NPxY eukaryotic motif, which binds phosphotyrosine-binding domains present on signaling and adaptor eukaryotic proteins. Two point mutations within the NPxY motif result in attenuation of L. pneumophila in both hMDMs and amoeba. The substitution defects of P78 and D64 are associated with failure of vacuoles harboring the mutant to be remodeled by the ER and results in fusion of the vacuole to the lysosomes leading to bacterial degradation. Therefore, the MavE effector of L. pneumophila is indispensable for phagosome biogenesis and lysosomal evasion.
Collapse
|
44
|
Saoud J, Carrier MC, Massé É, Faucher SP. The small regulatory RNA Lpr10 regulates the expression of RpoS in Legionella pneumophila. Mol Microbiol 2020; 115:789-806. [PMID: 33191583 DOI: 10.1111/mmi.14644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
Abstract
Legionella pneumophila (Lp) is a waterborne bacterium able to infect human alveolar macrophages, causing Legionnaires' disease. Lp can survive for several months in water, while searching for host cells to grow in, such as ciliates and amoeba. In Lp, the sigma factor RpoS is essential for survival in water. A previous transcriptomic study showed that RpoS positively regulates the small regulatory RNA Lpr10. In the present study, deletion of lpr10 results in an increased survival of Lp in water. Microarray analysis and RT-qPCR revealed that Lpr10 negatively regulates the expression of RpoS in the postexponential phase. Electrophoretic mobility shift assay and in-line probing showed that Lpr10 binds to a region upstream of the previously identified transcription start sites (TSS) of rpoS. A third putative transcription start site was identified by primer extension analysis, upstream of the Lpr10 binding site. In addition, nlpD TSS produces a polycistronic mRNA including the downstream gene rpoS, indicating a fourth TSS for rpoS. Our results suggest that the transcripts from the third and fourth TSS are negatively regulated by the Lpr10 sRNA. Therefore, we propose that Lpr10 is involved in a negative regulatory feedback loop to maintain expression of RpoS to an optimal level.
Collapse
Affiliation(s)
- Joseph Saoud
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| | - Marie-Claude Carrier
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, QC, Canada
| | - Éric Massé
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, QC, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| |
Collapse
|
45
|
Swart AL, Gomez-Valero L, Buchrieser C, Hilbi H. Evolution and function of bacterial RCC1 repeat effectors. Cell Microbiol 2020; 22:e13246. [PMID: 32720355 DOI: 10.1111/cmi.13246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/10/2020] [Accepted: 07/11/2020] [Indexed: 01/02/2023]
Abstract
Intracellular bacterial pathogens harbour genes, the closest homologues of which are found in eukaryotes. Regulator of chromosome condensation 1 (RCC1) repeat proteins are phylogenetically widespread and implicated in protein-protein interactions, such as the activation of the small GTPase Ran by its cognate guanine nucleotide exchange factor, RCC1. Legionella pneumophila and Coxiella burnetii, the causative agents of Legionnaires' disease and Q fever, respectively, harbour RCC1 repeat coding genes. Legionella pneumophila secretes the RCC1 repeat 'effector' proteins LegG1, PpgA and PieG into eukaryotic host cells, where they promote the activation of the pleiotropic small GTPase Ran, microtubule stabilisation, pathogen vacuole motility and intracellular bacterial growth as well as host cell migration. The RCC1 repeat effectors localise to the pathogen vacuole or the host plasma membrane and target distinct components of the Ran GTPase cycle, including Ran modulators and the small GTPase itself. Coxiella burnetii translocates the RCC1 repeat effector NopA into host cells, where the protein localises to nucleoli. NopA binds to Ran GTPase and promotes the nuclear accumulation of Ran(GTP), thus pertubing the import of the transcription factor NF-κB and innate immune signalling. Hence, divergent evolution of bacterial RCC1 repeat effectors defines the range of Ran GTPase cycle targets and likely allows fine-tuning of Ran GTPase activation by the pathogens at different cellular sites.
Collapse
Affiliation(s)
- Anna Leoni Swart
- Institute of Medical Microbiology, Faculty of Medicine, University of Zurich, Zürich, Switzerland
| | - Laura Gomez-Valero
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
| | - Hubert Hilbi
- Institute of Medical Microbiology, Faculty of Medicine, University of Zurich, Zürich, Switzerland
| |
Collapse
|
46
|
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: 28] [Impact Index Per Article: 5.6] [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.
Collapse
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
| |
Collapse
|
47
|
Burette M, Allombert J, Lambou K, Maarifi G, Nisole S, Di Russo Case E, Blanchet FP, Hassen-Khodja C, Cabantous S, Samuel J, Martinez E, Bonazzi M. Modulation of innate immune signaling by a Coxiella burnetii eukaryotic-like effector protein. Proc Natl Acad Sci U S A 2020; 117:13708-13718. [PMID: 32482853 PMCID: PMC7306807 DOI: 10.1073/pnas.1914892117] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Q fever agent Coxiella burnetii uses a defect in organelle trafficking/intracellular multiplication (Dot/Icm) type 4b secretion system (T4SS) to silence the host innate immune response during infection. By investigating C. burnetii effector proteins containing eukaryotic-like domains, here we identify NopA (nucleolar protein A), which displays four regulator of chromosome condensation (RCC) repeats, homologous to those found in the eukaryotic Ras-related nuclear protein (Ran) guanine nucleotide exchange factor (GEF) RCC1. Accordingly, NopA is found associated with the chromatin nuclear fraction of cells and uses the RCC-like domain to interact with Ran. Interestingly, NopA triggers an accumulation of Ran-GTP, which accumulates at nucleoli of transfected or infected cells, thus perturbing the nuclear import of transcription factors of the innate immune signaling pathway. Accordingly, qRT-PCR analysis on a panel of cytokines shows that cells exposed to the C. burnetii nopA::Tn or a Dot/Icm-defective dotA::Tn mutant strain present a functional innate immune response, as opposed to cells exposed to wild-type C. burnetii or the corresponding nopA complemented strain. Thus, NopA is an important regulator of the innate immune response allowing Coxiella to behave as a stealth pathogen.
Collapse
Affiliation(s)
- Melanie Burette
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Julie Allombert
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Karine Lambou
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Ghizlane Maarifi
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Elizabeth Di Russo Case
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center College of Medicine, Bryan, TX 77807-3260
| | - Fabien P Blanchet
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Cedric Hassen-Khodja
- Montpellier Ressources Imagerie (MRI), BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, 34293 Montpellier, France
| | - Stéphanie Cabantous
- Centre de Recherche en Cancérologie de Toulouse, INSERM, Université Paul Sabatier-Toulouse III, CNRS, 31037 Toulouse, France
| | - James Samuel
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center College of Medicine, Bryan, TX 77807-3260
| | - Eric Martinez
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France
| | - Matteo Bonazzi
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004, CNRS, Université de Montpellier, 34293 Montpellier, France;
| |
Collapse
|
48
|
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: 4.6] [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.
Collapse
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
| |
Collapse
|
49
|
Gomez-Valero L, Buchrieser C. Intracellular parasitism, the driving force of evolution of Legionella pneumophila and the genus Legionella. Microbes Infect 2019; 21:230-236. [PMID: 31252216 DOI: 10.1016/j.micinf.2019.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 12/25/2022]
Abstract
Legionella pneumophila is an intracellular pathogen that causes a severe pneumonia called Legionnaires' disease that is often fatal when not promptly diagnosed and treated. Legionella parasitize aquatic protozoa with which it co-evolved over an evolutionary long time. The close relationship between hosts and pathogens, their co-evolution, led to molecular interactions such as the exchange of genetic material through horizontal gene transfer (HGT). Genome sequencing of L. pneumophila and of the entire genus Legionella that comprises over 60 species revealed that Legionellae have co-opted genes and thus cellular functions from their eukaryotic hosts to a surprisingly high extent. Acquisition and loss of these eukaryotic-like genes and domains is an on-going process underlining the highly dynamic nature of the Legionella genomes. Although the large amount and diversity of HGT in Legionella seems to be unique in the prokaryotic world the analyses of more and more genomes from environmental organisms and symbionts of amoeba revealed that such genetic exchanges occur among all amoeba associated bacteria and also among the different microorganisms that infect amoeba. This dynamic reshuffling and gene-acquisition has led to the emergence of Legionella as human pathogen and may lead to the emergence of new human pathogens from the environment.
Collapse
Affiliation(s)
- Laure Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, 75724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, 75724, Paris, France.
| |
Collapse
|
50
|
Determination of In Vivo Interactomes of Dot/Icm Type IV Secretion System Effectors by Tandem Affinity Purification. Methods Mol Biol 2019. [PMID: 30694500 DOI: 10.1007/978-1-4939-9048-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
The Dot/Icm type IV secretion system (T4SS) is essential for the pathogenesis of Legionella species and translocates a multitude of effector proteins into host cells. The identification of host cell targets of these effectors is often critical to unravel their roles in controlling the host. Here we describe a method to characterize the protein complexes associated with effectors in infected host cells. To achieve this, Legionella expressing an effector of interest fused to a Bio-tag, a combination of hexahistidine tags and a specific recognition sequence for the biotin ligase BirA, are used to infect host cells expressing BirA, which leads to biotinylation of the translocated effector. Following chemical cross-linking, effector interactomes are isolated by tandem affinity purification employing metal affinity and NeutrAvidin resins and identified by western blotting or mass spectrometry.
Collapse
|