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Keck C, Enninga J, Swistak L. Caught in the act: In situ visualization of bacterial secretion systems by cryo-electron tomography. Mol Microbiol 2024; 121:636-645. [PMID: 37975530 DOI: 10.1111/mmi.15186] [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: 07/31/2023] [Revised: 10/09/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
Bacterial secretion systems, such as the type 3, 4, and 6 are multiprotein nanomachines expressed at the surface of pathogens with Gram-negative like envelopes. They are known to be crucial for virulence and to translocate bacteria-encoded effector proteins into host cells to manipulate cellular functions. This facilitates either pathogen attachment or invasion of the targeted cell. Effector proteins also promote evasion of host immune recognition. Imaging by cryo-electron microscopy in combination with structure determination has become a powerful approach to understand how these nanomachines work. Still, questions on their assembly, the precise secretion mechanisms, and their direct involvement in pathogenicity remain unsolved. Here, we present an overview of the recent developments in in situ cryo-electron microscopy. We discuss its potential for the investigation of the role of bacterial secretion systems during the host-bacterial crosstalk at the molecular level. These in situ studies open new perspectives for our understanding of secretion system structure and function.
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Affiliation(s)
- Camille Keck
- Dynamics of Host-Pathogen Interactions, Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Paris, France
| | - Jost Enninga
- Dynamics of Host-Pathogen Interactions, Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Paris, France
| | - Léa Swistak
- Dynamics of Host-Pathogen Interactions, Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Paris, France
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PopB-PcrV Interactions Are Essential for Pore Formation in the Pseudomonas aeruginosa Type III Secretion System Translocon. mBio 2022; 13:e0238122. [PMID: 36154276 PMCID: PMC9600203 DOI: 10.1128/mbio.02381-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type III secretion system (T3SS) is a syringe-like virulence factor that delivers bacterial proteins directly into the cytoplasm of host cells. An essential component of the system is the translocon, which creates a pore in the host cell membrane through which proteins are injected. In Pseudomonas aeruginosa, the translocation pore is formed by proteins PopB and PopD and attaches to the T3SS needle via the needle tip protein PcrV. The structure and stoichiometry of the multimeric pore are unknown. We took a genetic approach to map contact points within the system by taking advantage of the fact that the translocator proteins of P. aeruginosa and the related Aeromonas hydrophila T3SS are incompatible and cannot be freely exchanged. We created chimeric versions of P. aeruginosa PopB and A. hydrophila AopB to intentionally disrupt and restore protein-protein interactions. We identified a chimeric B-translocator that specifically disrupts an interaction with the needle tip protein. This disruption did not affect membrane insertion of the B-translocator but did prevent formation of the translocation pore, arguing that the needle tip protein drives the formation of the translocation pore. IMPORTANCE Type III secretion systems are integral to the pathogenesis of many Gram-negative bacterial pathogens. A hallmark of these secretion systems is that they deliver effector proteins vectorially into the targeted host cell via a translocation pore. The translocon is crucial for T3SS function, but it has proven difficult to study biochemically and structurally. Here, we used a genetic approach to identify protein-protein contacts among translocator proteins that are important for function. This genetic approach allowed us to specifically break a contact between the translocator PopB and the T3SS needle tip protein PcrV. Breaking this contact allowed us to determine, for the first time, that the needle tip actively participates in the assembly of the translocation pore by the membrane-bound pore-forming translocator proteins. Our study therefore both expands our knowledge of the network of functionally important interactions among translocator proteins and illuminates a new step in the assembly of this critical host cell interface.
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Special Issue: Type III Secretion Systems in Human/Animal Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10071461. [PMID: 35889180 PMCID: PMC9319260 DOI: 10.3390/microorganisms10071461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
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Raymond BBA. Bacterial macromolecular machineries. Mol Microbiol 2022; 118:1-2. [PMID: 35811503 DOI: 10.1111/mmi.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022]
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Ortega D, Beeby M. How Did the Archaellum Get Its Rotation? Front Microbiol 2022; 12:803720. [PMID: 35558523 PMCID: PMC9087265 DOI: 10.3389/fmicb.2021.803720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
How new functions evolve fascinates many evolutionary biologists. Particularly captivating is the evolution of rotation in molecular machines, as it evokes familiar machines that we have made ourselves. The archaellum, an archaeal analog of the bacterial flagellum, is one of the simplest rotary motors. It features a long helical propeller attached to a cell envelope-embedded rotary motor. Satisfyingly, the archaellum is one of many members of the large type IV filament superfamily, which includes pili, secretion systems, and adhesins, relationships that promise clues as to how the rotating archaellum evolved from a non-rotary ancestor. Nevertheless, determining exactly how the archaellum got its rotation remains frustratingly elusive. Here we review what is known about how the archaellum got its rotation, what clues exist, and what more is needed to address this question.
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Affiliation(s)
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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Jenkins J, Worrall L, Strynadka N. Recent structural advances towards understanding of the bacterial type III secretion injectisome. Trends Biochem Sci 2022; 47:795-809. [DOI: 10.1016/j.tibs.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022]
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VirB4- and VirD4-Like ATPases, Components of a Putative Type 4C Secretion System in Clostridioides difficile. J Bacteriol 2021; 203:e0035921. [PMID: 34424036 DOI: 10.1128/jb.00359-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The type 4 secretion system (T4SS) represents a bacterial nanomachine capable of trans-cell wall transportation of proteins and DNA and has attracted intense interest due to its roles in the pathogenesis of infectious diseases. In the current investigation, we uncovered three distinct gene clusters in Clostridioides difficile strain 630 encoding proteins structurally related to components of the VirB4/D4 type 4C secretion system from Streptococcus suis strain 05ZYH33 and located within sequences of conjugative transposons (CTn). Phylogenic analysis revealed that VirB4- and VirD4-like proteins of the CTn4 locus, on the one hand, and those of the CTn2 and CTn5 loci, on the other hand, fit into separate clades, suggesting specific roles of identified secretion system variants in the physiology of C. difficile. Our further study on VirB4- and VirD4-like products encoded by CTn4 revealed that both proteins possess Mg2+-dependent ATPase activity, form oligomers (most likely hexamers) in aqueous solutions, and rely on potassium but not sodium ions for the highest catalytic rate. VirD4 binds nonspecifically to DNA and RNA. The DNA-binding activity of VirD4 strongly decreased with the W241A variant. Mutations in the nucleotide sequences encoding presumable Walker A and Walker B motifs decreased the stability of the oligomers and significantly but not completely attenuated the enzymatic activity of VirB4. In VirD4, substitutions of amino acid residues in the peptides reminiscent of Walker structural motifs neither attenuated the enzymatic activity of the protein nor influenced the oligomerization state of the ATPase. IMPORTANCE C. difficile is a Gram-positive, anaerobic, spore-forming bacterium that causes life-threatening colitis in humans. Major virulence factors of the microorganism include the toxins TcdA, TcdB, and CDT. However, other bacterial products, including a type 4C secretion system, have been hypothesized to contribute to the pathogenesis of the infection and are considered possible virulence factors of C. difficile. In the current paper, we describe the structural organization of putative T4SS machinery in C. difficile and characterize its VirB4- and VirD4-like components. Our studies, in addition to its significance for basic science, can potentially aid the development of antivirulence drugs suitable for the treatment of C. difficile infection.
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Matthews-Palmer TRS, Gonzalez-Rodriguez N, Calcraft T, Lagercrantz S, Zachs T, Yu XJ, Grabe GJ, Holden DW, Nans A, Rosenthal PB, Rouse SL, Beeby M. Structure of the cytoplasmic domain of SctV (SsaV) from the Salmonella SPI-2 injectisome and implications for a pH sensing mechanism. J Struct Biol 2021; 213:107729. [PMID: 33774138 PMCID: PMC8223533 DOI: 10.1016/j.jsb.2021.107729] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/22/2022]
Abstract
CryoEM of a full-length type III secretion system SctV resolves cytoplasmic but not transmembrane domains. MD simulations show SctV protomers flexibly hinge. Acidification expands the SctV ring by altering interprotomer interactions.
Bacterial type III secretion systems assemble the axial structures of both injectisomes and flagella. Injectisome type III secretion systems subsequently secrete effector proteins through their hollow needle into a host, requiring co-ordination. In the Salmonella enterica serovar Typhimurium SPI-2 injectisome, this switch is triggered by sensing the neutral pH of the host cytoplasm. Central to specificity switching is a nonameric SctV protein with an N-terminal transmembrane domain and a toroidal C-terminal cytoplasmic domain. A ‘gatekeeper’ complex interacts with the SctV cytoplasmic domain in a pH dependent manner, facilitating translocon secretion while repressing effector secretion through a poorly understood mechanism. To better understand the role of SctV in SPI-2 translocon-effector specificity switching, we purified full-length SctV and determined its toroidal cytoplasmic region’s structure using cryo-EM. Structural comparisons and molecular dynamics simulations revealed that the cytoplasmic torus is stabilized by its core subdomain 3, about which subdomains 2 and 4 hinge, varying the flexible outside cleft implicated in gatekeeper and substrate binding. In light of patterns of surface conservation, deprotonation, and structural motion, the location of previously identified critical residues suggest that gatekeeper binds a cleft buried between neighboring subdomain 4s. Simulations suggest that a local pH change from 5 to 7.2 stabilizes the subdomain 3 hinge and narrows the central aperture of the nonameric torus. Our results are consistent with a model of local pH sensing at SctV, where pH-dependent dynamics of SctV cytoplasmic domain affect binding of gatekeeper complex.
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Affiliation(s)
| | | | - Thomas Calcraft
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Signe Lagercrantz
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tobias Zachs
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiu-Jun Yu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Grzegorz J Grabe
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - David W Holden
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
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