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Lin L. The expanding universe of contractile injection systems in bacteria. Curr Opin Microbiol 2024; 79:102465. [PMID: 38520915 DOI: 10.1016/j.mib.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Contractile injection systems (CISs) are phage tail-like machineries found in a wide range of bacteria. They are often deployed by bacteria to translocate effectors into the extracellular space or into target cells. CISs are classified into intracellular type VI secretion systems (T6SSs) and extracellular CIS (eCISs). eCISs are assembled in cytoplasm and released into the extracellular milieu upon cell lysis, while T6SSs are the secretion systems widespread among Gram-negative bacteria and actively translocate effectors into the environment or into the adjacent cell, without lysis of T6SS-producing cells. Recently, several noncanonical CISs that exhibit distinct characteristics have been discovered. This review will provide an overview on these noncanonical CISs and their unique features, as well as new advances in reprogramming CISs for therapeutic protein delivery.
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Affiliation(s)
- Lin Lin
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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2
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Woudstra C, Sørensen AN, Sørensen MCH, Brøndsted L. Strategies for developing phages into novel antimicrobial tailocins. Trends Microbiol 2024:S0966-842X(24)00069-6. [PMID: 38580606 DOI: 10.1016/j.tim.2024.03.003] [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: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
Tailocins are high-molecular-weight bacteriocins produced by bacteria to kill related environmental competitors by binding and puncturing their target. Tailocins are promising alternative antimicrobials, yet the diversity of naturally occurring tailocins is limited. The structural similarities between phage tails and tailocins advocate using phages as scaffolds for developing new tailocins. This article reviews three strategies for producing tailocins: disrupting the capsid-tail junction of phage particles, blocking capsid assembly during phage propagation, and creating headless phage particles synthetically. Particularly appealing is the production of tailocins through synthetic biology using phages with contractile tails as scaffolds to unlock the antimicrobial potential of tailocins.
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Affiliation(s)
- Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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3
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Taillefer B, Giraud JF, Cascales E. No fitness cost entailed by type VI secretion system synthesis, assembly, contraction, or disassembly in enteroaggregative Escherichia coli. J Bacteriol 2023; 205:e0035723. [PMID: 37971272 PMCID: PMC10729742 DOI: 10.1128/jb.00357-23] [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: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Bacteria use weapons to deliver effectors into target cells. One of these weapons, the type VI secretion system (T6SS), assembles a contractile tail acting as a spring to propel a toxin-loaded needle. Due to its size and mechanism of action, the T6SS was intuitively thought to be energetically costly. Here, using a combination of mutants and growth measurements in liquid medium, on plates, and in competition experiments, we show that the T6SS does not entail a growth cost to enteroaggregative Escherichia coli.
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Affiliation(s)
- Boris Taillefer
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Univ, CNRS, Marseille, France
| | - Julien F. Giraud
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Univ, CNRS, Marseille, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Univ, CNRS, Marseille, France
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4
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Bourigault Y, Dupont CA, Desjardins JB, Doan T, Bouteiller M, Le Guenno H, Chevalier S, Barbey C, Latour X, Cascales E, Merieau A. Pseudomonas fluorescens MFE01 delivers a putative type VI secretion amidase that confers biocontrol against the soft-rot pathogen Pectobacterium atrosepticum. Environ Microbiol 2023; 25:2564-2579. [PMID: 37622480 DOI: 10.1111/1462-2920.16492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
The type VI secretion system (T6SS) is a contractile nanomachine widespread in Gram-negative bacteria. The T6SS injects effectors into target cells including eukaryotic hosts and competitor microbial cells and thus participates in pathogenesis and intermicrobial competition. Pseudomonas fluorescens MFE01 possesses a single T6SS gene cluster that confers biocontrol properties by protecting potato tubers against the phytopathogen Pectobacterium atrosepticum (Pca). Here, we demonstrate that a functional T6SS is essential to protect potato tuber by reducing the pectobacteria population. Fluorescence microscopy experiments showed that MFE01 displays an aggressive behaviour with an offensive T6SS characterized by continuous and intense T6SS firing activity. Interestingly, we observed that T6SS firing is correlated with rounding of Pectobacterium cells, suggesting delivery of a potent cell wall targeting effector. Mutagenesis coupled with functional assays then revealed that a putative T6SS secreted amidase, Tae3Pf , is mainly responsible for MFE01 toxicity towards Pca. Further studies finally demonstrated that Tae3Pf is toxic when produced in the periplasm, and that its toxicity is counteracted by the Tai3Pf inner membrane immunity protein.
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Affiliation(s)
- Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Charly A Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Jonas B Desjardins
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Mathilde Bouteiller
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Hugo Le Guenno
- Plateforme de Microscopie, Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Sylvie Chevalier
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
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Dupont CA, Bourigault Y, Osmond T, Nier M, Barbey C, Latour X, Konto-Ghiorghi Y, Verdon J, Merieau A. Pseudomonas fluorescens MFE01 uses 1-undecene as aerial communication molecule. Front Microbiol 2023; 14:1264801. [PMID: 37908545 PMCID: PMC10614000 DOI: 10.3389/fmicb.2023.1264801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
Bacterial communication is a fundamental process used to synchronize gene expression and collective behavior among the bacterial population. The most studied bacterial communication system is quorum sensing, a cell density system, in which the concentration of inductors increases to a threshold level allowing detection by specific receptors. As a result, bacteria can change their behavior in a coordinated way. While in Pseudomonas quorum sensing based on the synthesis of N-acyl homoserine lactone molecules is well studied, volatile organic compounds, although considered to be communication signals in the rhizosphere, are understudied. The Pseudomonas fluorescens MFE01 strain has a very active type six secretion system that can kill some competitive bacteria. Furthermore, MFE01 emits numerous volatile organic compounds, including 1-undecene, which contributes to the aerial inhibition of Legionella pneumophila growth. Finally, MFE01 appears to be deprived of N-acyl homoserine lactone synthase. The main objective of this study was to explore the role of 1-undecene in the communication of MFE01. We constructed a mutant affected in undA gene encoding the enzyme responsible for 1-undecene synthesis to provide further insight into the role of 1-undecene in MFE01. First, we studied the impacts of this mutation both on volatile organic compounds emission, using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry and on L. pneumophila long-range inhibition. Then, we analyzed influence of 1-undecene on MFE01 coordinated phenotypes, including type six secretion system activity and biofilm formation. Next, to test the ability of MFE01 to synthesize N-acyl homoserine lactones in our conditions, we investigated in silico the presence of corresponding genes across the MFE01 genome and we exposed its biofilms to an N-acyl homoserine lactone-degrading enzyme. Finally, we examined the effects of 1-undecene emission on MFE01 biofilm maturation and aerial communication using an original experimental set-up. This study demonstrated that the ΔundA mutant is impaired in biofilm maturation. An exposure of the ΔundA mutant to the volatile compounds emitted by MFE01 during the biofilm development restored the biofilm maturation process. These findings indicate that P. fluorescens MFE01 uses 1-undecene emission for aerial communication, reporting for the first time this volatile organic compound as bacterial intraspecific communication signal.
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Affiliation(s)
- Charly A. Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Théo Osmond
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Maëva Nier
- Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Yoan Konto-Ghiorghi
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Julien Verdon
- Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
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Hug S, Heiniger B, Bolli K, Paszti S, Eberl L, Ahrens CH, Pessi G. Paraburkholderia sabiae Uses One Type VI Secretion System (T6SS-1) as a Powerful Weapon against Notorious Plant Pathogens. Microbiol Spectr 2023; 11:e0162223. [PMID: 37439699 PMCID: PMC10434147 DOI: 10.1128/spectrum.01622-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023] Open
Abstract
Paraburkholderia sabiae LMG24235 is a nitrogen-fixing betaproteobacterium originally isolated from a root nodule of Mimosa caesalpiniifolia in Brazil. We show here that this strain effectively kills strains from several bacterial families (Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae) which include important plant pathogens in a contact-dependent manner. De novo assembly of the first complete genome of P. sabiae using long sequencing reads and subsequent annotation revealed two gene clusters predicted to encode type VI secretion systems (T6SS), which we named T6SS-1 and T6SS-3 according to previous classification methods (G. Shalom, J. G. Shaw, and M. S. Thomas, Microbiology, 153:2689-2699, 2007, https://doi.org/10.1099/mic.0.2007/006585-0). We created P. sabiae with mutations in each of the two T6SS gene clusters that abrogated their function, and the T6SS-1 mutant was no longer able to outcompete other strains in a contact-dependent manner. Notably, our analysis revealed that T6SS-1 is essential for competition against several important plant pathogens in vitro, including Burkholderia plantarii, Ralstonia solanacearum, Pseudomonas syringae, and Pectobacterium carotovorum. The 9-log reduction in P. syringae cells in the presence of P. sabiae was particularly remarkable. Importantly, in an in vivo assay, P. sabiae was able to protect potato tubers from bacterial soft rot disease caused by P. carotovorum, and this protection was partly dependent on T6SS-1. IMPORTANCE Rhizobia often display additional beneficial traits such as the production of plant hormones and the acquisition of limited essential nutrients that improve plant growth and enhance plant yields. Here, we show that the rhizobial strain P. sabiae antagonizes important phytopathogens such as P. carotovorum, P. syringae, and R. solanacearum and that this effect is due to contact-dependent killing mediated by one of two T6SS systems identified in the complete, de novo assembled genome sequence of P. sabiae. Importantly, co-inoculation of Solanum tuberosum tubers with P. sabiae also resulted in a drastic reduction of soft rot caused by P. carotovorum in an in vivo model system. This result highlights the protective potential of P. sabiae against important bacterial plant diseases, which makes it a valuable candidate for application as a biocontrol agent. It also emphasizes the particular potential of rhizobial inoculants that combine several beneficial effects such as plant growth promotion and biocontrol for sustainable agriculture.
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Affiliation(s)
- Sebastian Hug
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Benjamin Heiniger
- Agroscope – Molecular Ecology, Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Kim Bolli
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Sarah Paszti
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Christian H. Ahrens
- Agroscope – Molecular Ecology, Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
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Schlimpert S, Elliot MA. The Best of Both Worlds-Streptomyces coelicolor and Streptomyces venezuelae as Model Species for Studying Antibiotic Production and Bacterial Multicellular Development. J Bacteriol 2023; 205:e0015323. [PMID: 37347176 PMCID: PMC10367585 DOI: 10.1128/jb.00153-23] [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] [Indexed: 06/23/2023] Open
Abstract
Streptomyces bacteria have been studied for more than 80 years thanks to their ability to produce an incredible array of antibiotics and other specialized metabolites and their unusual fungal-like development. Their antibiotic production capabilities have ensured continual interest from both academic and industrial sectors, while their developmental life cycle has provided investigators with unique opportunities to address fundamental questions relating to bacterial multicellular growth. Much of our understanding of the biology and metabolism of these fascinating bacteria, and many of the tools we use to manipulate these organisms, have stemmed from investigations using the model species Streptomyces coelicolor and Streptomyces venezuelae. Here, we explore the pioneering work in S. coelicolor that established foundational genetic principles relating to specialized metabolism and development, alongside the genomic and cell biology developments that led to the emergence of S. venezuelae as a new model system. We highlight key discoveries that have stemmed from studies of these two systems and discuss opportunities for future investigations that leverage the power and understanding provided by S. coelicolor and S. venezuelae.
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Affiliation(s)
- Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marie A. Elliot
- Department of Biology and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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Taillefer B, Grandjean MM, Herrou J, Robert D, Mignot T, Sebban-Kreuzer C, Cascales E. Qualitative and Quantitative Methods to Measure Antibacterial Activity Resulting from Bacterial Competition. Bio Protoc 2023; 13:e4706. [PMID: 37449039 PMCID: PMC10336571 DOI: 10.21769/bioprotoc.4706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/06/2023] [Accepted: 04/16/2023] [Indexed: 07/18/2023] Open
Abstract
In the environment, bacteria compete for niche occupancy and resources; they have, therefore, evolved a broad variety of antibacterial weapons to destroy competitors. Current laboratory techniques to evaluate antibacterial activity are usually labor intensive, low throughput, costly, and time consuming. Typical assays rely on the outgrowth of colonies of prey cells on selective solid media after competition. Here, we present fast, inexpensive, and complementary optimized protocols to qualitatively and quantitively measure antibacterial activity. The first method is based on the degradation of a cell-impermeable chromogenic substrate of the β-galactosidase, a cytoplasmic enzyme released during lysis of the attacked reporter strain. The second method relies on the lag time required for the attacked cells to reach a defined optical density after the competition, which is directly dependent on the initial number of surviving cells. Key features First method utilizes the release of β-galactosidase as a proxy for bacterial lysis. Second method is based on the growth timing of surviving cells. Combination of two methods discriminates between cell death and lysis, cell death without lysis, or survival to quasi-lysis. Methods optimized to various bacterial species such as Escherichia coli, Pseudomonas aeruginosa, and Myxococcus xanthus. Graphical overview.
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Affiliation(s)
- Boris Taillefer
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Marie M. Grandjean
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Julien Herrou
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7283, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Donovan Robert
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7283, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7283, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Corinne Sebban-Kreuzer
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Eric Cascales
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
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9
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Yang F, Wang L, Zhou J, Xiao H, Liu H. In Situ Structures of the Ultra-Long Extended and Contracted Tail of Myoviridae Phage P1. Viruses 2023; 15:1267. [PMID: 37376567 DOI: 10.3390/v15061267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/20/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The Myoviridae phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the Myoviridae tail have been extensively studied, but the dynamic conformational changes before and after contraction and the associated molecular mechanism are still unclear. Here, we present the extended and contracted intact tail-structures of Myoviridae phage P1 by cryo-EM. The ultra-long tail of P1, 2450 Å in length, consists of a neck, a tail terminator, 53 repeated tail sheath rings, 53 repeated tube rings, and a baseplate. The sheath of the contracted tail shrinks by approximately 55%, resulting in the separation of the inner rigid tail tube from the sheath. The extended and contracted tails were further resolved by local reconstruction at 3.3 Å and 3.9 Å resolutions, respectively, allowing us to build the atomic models of the tail terminator protein gp24, the tube protein BplB, and the sheath protein gp22 for the extended tail, and of the sheath protein gp22 for the contracted tail. Our atomic models reveal the complex interaction network in the ultra-long Myoviridae tail and the novel conformational changes of the tail sheath between extended and contracted states. Our structures provide insights into the contraction and stabilization mechanisms of the Myoviridae tail.
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Affiliation(s)
- Fan Yang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
| | - Liwen Wang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
| | - Junquan Zhou
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
| | - Hao Xiao
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Hongrong Liu
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
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10
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Ericson CF, Pilhofer M. Mix-and-match tools for protein injection into cells. Nature 2023; 616:254-255. [PMID: 36991045 DOI: 10.1038/d41586-023-00847-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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11
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Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature 2023; 616:357-364. [PMID: 36991127 PMCID: PMC10097599 DOI: 10.1038/s41586-023-05870-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/21/2023] [Indexed: 03/31/2023]
Abstract
Endosymbiotic bacteria have evolved intricate delivery systems that enable these organisms to interface with host biology. One example, the extracellular contractile injection systems (eCISs), are syringe-like macromolecular complexes that inject protein payloads into eukaryotic cells by driving a spike through the cellular membrane. Recently, eCISs have been found to target mouse cells1-3, raising the possibility that these systems could be harnessed for therapeutic protein delivery. However, whether eCISs can function in human cells remains unknown, and the mechanism by which these systems recognize target cells is poorly understood. Here we show that target selection by the Photorhabdus virulence cassette (PVC)-an eCIS from the entomopathogenic bacterium Photorhabdus asymbiotica-is mediated by specific recognition of a target receptor by a distal binding element of the PVC tail fibre. Furthermore, using in silico structure-guided engineering of the tail fibre, we show that PVCs can be reprogrammed to target organisms not natively targeted by these systems-including human cells and mice-with efficiencies approaching 100%. Finally, we show that PVCs can load diverse protein payloads, including Cas9, base editors and toxins, and can functionally deliver them into human cells. Our results demonstrate that PVCs are programmable protein delivery devices with possible applications in gene therapy, cancer therapy and biocontrol.
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Affiliation(s)
- Joseph Kreitz
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mirco J Friedrich
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akash Guru
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blake Lash
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Saito
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Linares R, Arnaud CA, Effantin G, Darnault C, Epalle NH, Boeri Erba E, Schoehn G, Breyton C. Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation. SCIENCE ADVANCES 2023; 9:eade9674. [PMID: 36961893 PMCID: PMC10038345 DOI: 10.1126/sciadv.ade9674] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a long flexible tail (Siphoviridae) at the tip of which receptor binding proteins (RBPs) specifically interact with their host, triggering infection. In siphophage T5, the unique RBP is located at the extremity of a central fiber. We present the structures of T5 tail tip, determined by cryo-electron microscopy before and after interaction with its E. coli receptor, FhuA, reconstituted into nanodisc. These structures bring out the important conformational changes undergone by T5 tail tip upon infection, which include bending of T5 central fiber on the side of the tail tip, tail anchoring to the membrane, tail tube opening, and formation of a transmembrane channel. The data allow to detail the first steps of an otherwise undescribed infection mechanism.
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13
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Cytoplasmic contractile injection systems mediate cell death in Streptomyces. Nat Microbiol 2023; 8:711-726. [PMID: 36894633 PMCID: PMC10066040 DOI: 10.1038/s41564-023-01341-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Contractile injection systems (CIS) are bacteriophage tail-like structures that mediate bacterial cell-cell interactions. While CIS are highly abundant across diverse bacterial phyla, representative gene clusters in Gram-positive organisms remain poorly studied. Here we characterize a CIS in the Gram-positive multicellular model organism Streptomyces coelicolor and show that, in contrast to most other CIS, S. coelicolor CIS (CISSc) mediate cell death in response to stress and impact cellular development. CISSc are expressed in the cytoplasm of vegetative hyphae and are not released into the medium. Our cryo-electron microscopy structure enabled the engineering of non-contractile and fluorescently tagged CISSc assemblies. Cryo-electron tomography showed that CISSc contraction is linked to reduced cellular integrity. Fluorescence light microscopy furthermore revealed that functional CISSc mediate cell death upon encountering different types of stress. The absence of functional CISSc had an impact on hyphal differentiation and secondary metabolite production. Finally, we identified three putative effector proteins, which when absent, phenocopied other CISSc mutants. Our results provide new functional insights into CIS in Gram-positive organisms and a framework for studying novel intracellular roles, including regulated cell death and life-cycle progression in multicellular bacteria.
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14
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Vanlioğlu E, Santin YG, Filella-Merce I, Pellarin R, Cascales E. Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface. J Mol Biol 2023; 435:167918. [PMID: 36509161 DOI: 10.1016/j.jmb.2022.167918] [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: 10/25/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
The type VI secretion system (T6SS) is a multiprotein weapon evolved by Gram-negative bacteria to deliver effectors into eukaryotic cells or bacterial rivals. The T6SS uses a contractile mechanism to propel an effector-loaded needle into its target. The contractile tail is built on an assembly platform, the baseplate, which is anchored to a membrane complex. Baseplate-membrane complex interactions are mainly mediated by contacts between the C-terminal domain of the TssK baseplate component and the cytoplasmic domain of the TssL inner membrane protein. Currently, the structural details of this interaction are unknown due to the marginal stability of the TssK-TssL complex. Here we conducted a mutagenesis study based on putative TssK-TssL contact pairs identified by co-evolution analyses. We then evaluated the impact of these mutations on T6SS activity, TssK-TssL interaction and sheath assembly and dynamics in enteroaggregative Escherichia coli. Finally, we probed the TssK-TssL interface by disulfide cross-linking, allowing to propose a model for the baseplate-membrane complex interface.
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Affiliation(s)
- Etienne Vanlioğlu
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), CNRS - Aix-Marseille Université UMR7255, 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Yoann G Santin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), CNRS - Aix-Marseille Université UMR7255, 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Isaac Filella-Merce
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), CNRS - Aix-Marseille Université UMR7255, 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France.
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15
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R-Type Fonticins Produced by Pragia fontium Form Large Pores with High Conductance. J Bacteriol 2023; 205:e0031522. [PMID: 36541812 PMCID: PMC9879110 DOI: 10.1128/jb.00315-22] [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: 12/24/2022] Open
Abstract
Fonticins are phage tail-like bacteriocins produced by the Gram-negative bacterium Pragia fontium from the family Budviciaceae. This bacterium produces contractile-type particles that adsorb on the surface of sensitive bacteria and penetrate the cell wall, probably during contraction, in a way similar to the type VI secretion system. We characterized the pore-forming activity of fonticins using both living cells and in vitro model membranes. Using a potassium leakage assay, we show that fonticins are able to permeabilize sensitive cells. On black lipid membranes, single-pore conductance is about 0.78 nS in 1 M NaCl and appears to be linearly dependent on the increasing molar strength of NaCl solution, which is a property of considerably large pores. In agreement with these findings, fonticins are not ion selective for Na+, K+, and Cl-. Polyethylene glycol 3350 (PEG 3350) molecules of about 3.5 nm in diameter can enter the fonticin pore lumen, whereas the larger molecules cannot pass the pore. The size of fonticin pores was confirmed by transmission electron microscopy. The terminal membrane-piercing complex of the fonticin tube probably creates a selective barrier restricting passage of macromolecules. IMPORTANCE Phage tail-like bacteriocins are now the subject of research as potent antibacterial agents due to their narrow host specificity and single-hit mode of action. In this work, we focused on the structure and mode of action of fonticins. According to some theories, related particles were initially adapted for passage of double-stranded DNA (dsDNA) molecules, but fonticins changed their function during the evolution; they are able to form large pores through the bacterial envelope of Gram-negative bacteria. As various pore-forming proteins are extensively used for nanopore sequencing and stochastic sensing, we decided to investigate the pore-forming properties of fonticin protein complexes on artificial lipid membranes. Our research revealed remarkable structural properties of these particles that may have a potential application as a nanodevice.
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Jurėnas D, Rey M, Byrne D, Chamot-Rooke J, Terradot L, Cascales E. Salmonella antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of EF-Tu P-loop. Nucleic Acids Res 2022; 50:13114-13127. [PMID: 36484105 PMCID: PMC9825190 DOI: 10.1093/nar/gkac1162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 11/11/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Rearrangement hot spot (Rhs) proteins are members of the broad family of polymorphic toxins. Polymorphic toxins are modular proteins composed of an N-terminal region that specifies their mode of secretion into the medium or into the target cell, a central delivery module, and a C-terminal domain that has toxic activity. Here, we structurally and functionally characterize the C-terminal toxic domain of the antibacterial Rhsmain protein, TreTu, which is delivered by the type VI secretion system of Salmonella enterica Typhimurium. We show that this domain adopts an ADP-ribosyltransferase fold and inhibits protein synthesis by transferring an ADP-ribose group from NAD+ to the elongation factor Tu (EF-Tu). This modification is specifically placed on the side chain of the conserved D21 residue located on the P-loop of the EF-Tu G-domain. Finally, we demonstrate that the TriTu immunity protein neutralizes TreTu activity by acting like a lid that closes the catalytic site and traps the NAD+.
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Affiliation(s)
- Dukas Jurėnas
- Correspondence may also be addressed to Dukas Jurėnas.
| | - Martial Rey
- Mass Spectrometry for Biology Unit, Université Paris Cité, Institut Pasteur, CNRS, UAR 2024, 75015 Paris, France
| | - Deborah Byrne
- Protein Expression Facility, Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, 13009 Marseille, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Université Paris Cité, Institut Pasteur, CNRS, UAR 2024, 75015 Paris, France
| | - Laurent Terradot
- Laboratory of Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique, Université de Lyon, UMR 5086, 69367 Lyon, France
| | - Eric Cascales
- To whom correspondence should be addressed. Tel: +33 491164462; Fax: +33 491712124;
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17
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A Quorum Sensing-Regulated Type VI Secretion System Containing Multiple Nonredundant VgrG Proteins Is Required for Interbacterial Competition in Chromobacterium violaceum. Microbiol Spectr 2022; 10:e0157622. [PMID: 35876575 PMCID: PMC9430734 DOI: 10.1128/spectrum.01576-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environmental pathogenic bacterium Chromobacterium violaceum kills Gram-positive bacteria by delivering violacein packed into outer membrane vesicles, but nothing is known about its contact-dependent competition mechanisms. In this work, we demonstrate that C. violaceum utilizes a type VI secretion system (T6SS) containing multiple VgrG proteins primarily for interbacterial competition. The single T6SS of C. violaceum contains six vgrG genes, which are located in the main T6SS cluster and four vgrG islands. Using T6SS core component-null mutant strains, Western blotting, fluorescence microscopy, and competition assays, we showed that the C. violaceum T6SS is active and required for competition against Gram-negative bacteria such as Pseudomonas aeruginosa but dispensable for C. violaceum infection in mice. Characterization of single and multiple vgrG mutants revealed that, despite having high sequence similarity, the six VgrGs show little functional redundancy, with VgrG3 showing a major role in T6SS function. Our coimmunoprecipitation data support a model of VgrG3 interacting directly with the other VgrGs. Moreover, we determined that the promoter activities of T6SS genes increased at high cell density, but the produced Hcp protein was not secreted under such condition. This T6SS growth phase-dependent regulation was dependent on CviR but not on CviI, the components of a C. violaceum quorum sensing (QS) system. Indeed, a ΔcviR but not a ΔcviI mutant was completely defective in Hcp secretion, T6SS activity, and interbacterial competition. Overall, our data reveal that C. violaceum relies on a QS-regulated T6SS to outcompete other bacteria and expand our knowledge about the redundancy of multiple VgrGs. IMPORTANCE The type VI secretion system (T6SS) is a contractile nanomachine used by many Gram-negative bacteria to inject toxic effectors into adjacent cells. The delivered effectors are bound to the components of a puncturing apparatus containing the protein VgrG. The T6SS has been implicated in pathogenesis and, more commonly, in competition among bacteria. Chromobacterium violaceum is an environmental bacterium that causes deadly infections in humans. In this work, we characterized the single T6SS of C. violaceum ATCC 12472, including its six VgrG proteins, regarding its function and regulation. This previously undescribed C. violaceum T6SS is active, regulated by QS, and required for interbacterial competition instead of acute infection in mice. Among the VgrGs, VgrG3, encoded outside the main T6SS cluster, showed a major contribution to T6SS function. These results shed light on a key contact-dependent killing mechanism used by C. violaceum to antagonize other bacteria.
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18
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A Putative Lipoprotein Mediates Cell-Cell Contact for Type VI Secretion System-Dependent Killing of Specific Competitors. mBio 2022; 13:e0308521. [PMID: 35404117 PMCID: PMC9040878 DOI: 10.1128/mbio.03085-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Interbacterial competition is prevalent in host-associated microbiota, where it can shape community structure and function, impacting host health in both positive and negative ways. However, the factors that permit bacteria to discriminate among their various neighbors for targeted elimination of competitors remain elusive. We identified a putative lipoprotein (TasL) in Vibrio species that mediates cell-cell attachment with a subset of target strains, allowing inhibitors to target specific competitors for elimination. Here, we describe this putative lipoprotein, which is associated with the broadly distributed type VI secretion system (T6SS), by studying symbiotic Vibrio fischeri, which uses the T6SS to compete for colonization sites in their squid host. We demonstrate that TasL allows V. fischeri cells to restrict T6SS-dependent killing to certain genotypes by selectively integrating competitor cells into aggregates while excluding other cell types. TasL is also required for T6SS-dependent competition within juvenile squid, indicating that the adhesion factor is active in the host. Because TasL homologs are found in other host-associated bacterial species, this newly described cell-cell attachment mechanism has the potential to impact microbiome structure within diverse hosts. IMPORTANCE T6SSs are broadly distributed interbacterial weapons that share an evolutionary history with bacteriophage. Because the T6SS can be used to kill neighboring cells, it can impact the spatial distribution and biological function of both free-living and host-associated microbial communities. Like their phage relatives, T6SS+ cells must sufficiently bind competitor cells to deliver their toxic effector proteins through the syringe-like apparatus. Although phage use receptor-binding proteins (RBPs) and tail fibers to selectively bind prey cells, the biophysical properties that mediate this cell-cell contact for T6SS-mediated killing remain unknown. Here, we identified a large, predicted lipoprotein that is coordinately expressed with T6SS proteins and facilitates the contact that is necessary for the T6SS-dependent elimination of competitors in a natural host. Similar to phage RBPs and tail fibers, this lipoprotein is required for T6SS+ cells to discriminate between prey and nonprey cell types, revealing new insight into prey selection during T6SS-mediated competition.
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Xu J, Ericson CF, Lien YW, Rutaganira FUN, Eisenstein F, Feldmüller M, King N, Pilhofer M. Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol 2022; 7:397-410. [PMID: 35165385 PMCID: PMC8894135 DOI: 10.1038/s41564-022-01059-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 12/11/2022]
Abstract
Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell–cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a ‘cap adaptor’ located at the distal end, a ‘plug’ exposed to the tube lumen, and a ‘cage’ formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re−engineering CISs. The characterization of an extracellular contractile injection system (eCIS) from the marine bacterium Algoriphagus machipongonensis (AlgoCIS) reveals structural features linked to the assembly and function of this nanomachine.
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20
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Kim N, Han G, Jung H, Lee HH, Park J, Seo YS. T6SS Accessory Proteins, Including DUF2169 Domain-Containing Protein and Pentapeptide Repeats Protein, Contribute to Bacterial Virulence in T6SS Group_5 of Burkholderia glumae BGR1. PLANTS 2021; 11:plants11010034. [PMID: 35009038 PMCID: PMC8747328 DOI: 10.3390/plants11010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/23/2022]
Abstract
Burkholderia glumae are bacteria pathogenic to rice plants that cause a disease called bacterial panicle blight (BPB) in rice panicles. BPB, induced by B. glumae, causes enormous economic losses to the rice agricultural industry. B. glumae also causes bacterial disease in other crops because it has various virulence factors, such as toxins, proteases, lipases, extracellular polysaccharides, bacterial motility, and bacterial secretion systems. In particular, B. glumae BGR1 harbors type VI secretion system (T6SS) with functionally distinct roles: the prokaryotic targeting system and the eukaryotic targeting system. The functional activity of T6SS requires 13 core components and T6SS accessory proteins, such as adapters containing DUF2169, DUF4123, and DUF1795 domains. There are two genes, bglu_1g23320 and bglu_2g07420, encoding the DUF2169 domain-containing protein in the genome of B. glumae BGR1. bglu_2g07420 belongs to the gene cluster of T6SS group_5 in B. glumae BGR1, whereas bglu_1g23320 does not belong to any T6SS gene cluster in B. glumae BGR1. T6SS group_5 of B. glumae BGR1 is involved in bacterial virulence in rice plants. The DUF2169 domain-containing protein with a single domain can function by itself; however, Δu1g23320 showed no attenuated virulence in rice plants. In contrast, Δu2g07420DUF2169 and Δu2g07420PPR did exhibit attenuated virulence in rice plants. These results suggest that the pentapeptide repeats region of the C-terminal additional domain, as well as the DUF2169 domain, is required for complete functioning of the DUF2169 domain-containing protein encoded by bglu_2g07420. bglu_2g07410, which encodes the pentapeptide repeats protein, composed of only the pentapeptide repeats region, is located downstream of bglu_2g07420. Δu2g07410 also shows attenuated virulence in rice plants. This finding suggests that the pentapeptide repeats protein, encoded by bglu_2g07410, is involved in bacterial virulence. This study is the first report that the DUF2169 domain-containing protein and pentapeptide repeats protein are involved in bacterial virulence to the rice plants as T6SS accessory proteins, encoded in the gene cluster of the T6SS group_5.
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Affiliation(s)
- Namgyu Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (N.K.); (G.H.); (H.J.); (H.-H.L.)
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (N.K.); (G.H.); (H.J.); (H.-H.L.)
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (N.K.); (G.H.); (H.J.); (H.-H.L.)
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (N.K.); (G.H.); (H.J.); (H.-H.L.)
| | - Jungwook Park
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological, Resources (NNIBR), Sangju 37242, Korea;
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (N.K.); (G.H.); (H.J.); (H.-H.L.)
- Correspondence:
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21
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Mounting, structure and autocleavage of a type VI secretion-associated Rhs polymorphic toxin. Nat Commun 2021; 12:6998. [PMID: 34853317 PMCID: PMC8636562 DOI: 10.1038/s41467-021-27388-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Bacteria have evolved toxins to outcompete other bacteria or to hijack host cell pathways. One broad family of bacterial polymorphic toxins gathers multidomain proteins with a modular organization, comprising a C-terminal toxin domain fused to a N-terminal domain that adapts to the delivery apparatus. Polymorphic toxins include bacteriocins, contact-dependent growth inhibition systems, and specialized Hcp, VgrG, PAAR or Rhs Type VI secretion (T6SS) components. We recently described and characterized Tre23, a toxin domain fused to a T6SS-associated Rhs protein in Photorhabdus laumondii, Rhs1. Here, we show that Rhs1 forms a complex with the T6SS spike protein VgrG and the EagR chaperone. Using truncation derivatives and cross-linking mass spectrometry, we demonstrate that VgrG-EagR-Rhs1 complex formation requires the VgrG C-terminal β-helix and the Rhs1 N-terminal region. We then report the cryo-electron-microscopy structure of the Rhs1-EagR complex, demonstrating that the Rhs1 central region forms a β-barrel cage-like structure that encapsulates the C-terminal toxin domain, and provide evidence for processing of the Rhs1 protein through aspartyl autoproteolysis. We propose a model for Rhs1 loading on the T6SS, transport and delivery into the target cell.
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22
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Jurėnas D, Cascales E. T6SS: killing two bugs with one stone. Trends Microbiol 2021; 30:1-2. [PMID: 34753653 DOI: 10.1016/j.tim.2021.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
Bacteria deploy the type VI secretion system (T6SS) to inject effectors into bacterial rivals. Contrary to the prevailing model, a recent study (Le et al.) expands the target range of the T6SS by demonstrating that it delivers and potentializes a peptidoglycan-targeting bifunctional toxin into Gram-positive bacteria.
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Affiliation(s)
- Dukas Jurėnas
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France.
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France.
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23
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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Cassan FD, Coniglio A, Amavizca E, Maroniche G, Cascales E, Bashan Y, de-Bashan LE. The Azospirillum brasilense type VI secretion system promotes cell aggregation, biocontrol protection against phytopathogens and attachment to the microalgae Chlorella sorokiniana. Environ Microbiol 2021; 23:6257-6274. [PMID: 34472164 DOI: 10.1111/1462-2920.15749] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 01/26/2023]
Abstract
The plant-growth-promoting bacterium Azospirillum brasilense is able to associate with the microalgae Chlorella sorokiniana. Attachment of A. brasilense increases the metabolic performances of the microalgae. Recent genome analyses have revealed that the A. brasilense Az39 genome contains two complete sets of genes encoding type VI secretion systems (T6SS), including the T6SS1 that is induced by the indole-3-acetic acid (IAA) phytohormone. The T6SS is a multiprotein machine, widespread in Gram-negative bacteria, that delivers protein effectors in both prokaryotic and eukaryotic cells. Here we show that the A. brasilense T6SS is required for Chlorella-Azospirillum synthetic mutualism. Our data demonstrate that the T6SS is an important determinant to promote production of lipids, carbohydrates and photosynthetic pigments by the microalgae. We further show that this is likely due to the role of the T6SS during the attachment stage and for the production of IAA phytohormones. Finally, we demonstrate that the A. brasilense T6SS provides antagonistic activities against a number of plant pathogens such as Agrobacterium, Pectobacterium, Dickeya and Ralstonia species in vitro, suggesting that, in addition to promoting growth, A. brasilense might confer T6SS-dependent bio-control protection to microalgae and plants against bacterial pathogens.
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Affiliation(s)
- Fabricio D Cassan
- Laboratorio de Fisiología Vegetal y de la interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB), Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Anahí Coniglio
- Laboratorio de Fisiología Vegetal y de la interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB), Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Edgar Amavizca
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
| | - Guillermo Maroniche
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Buenos Aires, Argentina
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, Aix-Marseille Université - CNRS UMR7255, Marseille, France
| | - Yoav Bashan
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico.,The Bashan Institute of Science, Auburn, AL, USA
| | - Luz E de-Bashan
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico.,The Bashan Institute of Science, Auburn, AL, USA.,Department of Entomology and Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL, USA
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25
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Jurėnas D, Payelleville A, Roghanian M, Turnbull KJ, Givaudan A, Brillard J, Hauryliuk V, Cascales E. Photorhabdus antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of 23S ribosomal RNA. Nucleic Acids Res 2021; 49:8384-8395. [PMID: 34255843 PMCID: PMC8661411 DOI: 10.1093/nar/gkab608] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/10/2021] [Accepted: 07/01/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteria have evolved sophisticated mechanisms to deliver potent toxins into bacterial competitors or into eukaryotic cells in order to destroy rivals and gain access to a specific niche or to hijack essential metabolic or signaling pathways in the host. Delivered effectors carry various activities such as nucleases, phospholipases, peptidoglycan hydrolases, enzymes that deplete the pools of NADH or ATP, compromise the cell division machinery, or the host cell cytoskeleton. Effectors categorized in the family of polymorphic toxins have a modular structure, in which the toxin domain is fused to additional elements acting as cargo to adapt the effector to a specific secretion machinery. Here we show that Photorhabdus laumondii, an entomopathogen species, delivers a polymorphic antibacterial toxin via a type VI secretion system. This toxin inhibits protein synthesis in a NAD+-dependent manner. Using a biotinylated derivative of NAD, we demonstrate that translation is inhibited through ADP-ribosylation of the ribosomal 23S RNA. Mapping of the modification further showed that the adduct locates on helix 44 of the thiostrepton loop located in the GTPase-associated center and decreases the GTPase activity of the EF-G elongation factor.
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Affiliation(s)
- Dukas Jurėnas
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
| | - Amaury Payelleville
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France.,DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden
| | | | | | | | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
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26
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Mohamed AA, Elshawadfy AM, Amin G, Askora A. Characterization of R-pyocin activity against Gram-positive pathogens for the first time with special focus on Staphylococcus aureus. J Appl Microbiol 2021; 131:2780-2792. [PMID: 33977611 DOI: 10.1111/jam.15134] [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: 09/23/2020] [Revised: 02/23/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
AIM This study is aimed at characterization of both antimicrobial and anti-biofilm activity of R-pyocin from clinical Pseudomonas aeruginosa against Gram-positive pathogens including Staphylococcus aureus. METHODS AND RESULTS Pyocinogenic P. aeruginosa was detected using reverse-side method, and pyocinogeny typing was confirmed using revised-spotting method. Transmission electron microscopy (TEM) was used for morphological characterization of R-pyocin and for detection of changes in membrane of R-pyocin-treated S. aureus. SDS-PAGE analysis was used for detection of the molecular weight of R-pyocin protein-subunits and Poisson-killing-distribution assay for burst-size calculation. Lipotechoic-acid (LTA) adsorption-assay was used to confirm whether LTA in Gram-positive bacteria served as R-pyocin receptor. Moreover, R-pyocin production at 10-60°C was assessed herein. Host-range of activity of R-pyocin was tested against antimicrobial resistant (AMR) pathogens. The anti-biofilm activity of R-pyocin was detected against sensitive bacterial strains. Chemical, enzymatic, pH and thermo-stability of R-pyocin were evaluated. TEM micrographs revealed a typical morphology of myotailocins indicating the production of R-pyocin designated as RPU15. TEM revealed pores formation in S. aureus membrane, and bacteriophage-like plaques were obvious on plates of R-pyocin-treated S. aureus. R-pyocin activity was neutralized by LTA of S. aureus and Listeria monocytogenes. Pseudomonas aeruginosa PU15 produced ~428 non-inducible R-pyocin particles. RPU15 sheath and tube protein-subunits exhibited a molecular weight of 38 and 23 kDa, respectively. RPU15 possessed activity against S. aureus, L. monocytogenes, Bacillus cereus and Candida albicans and reduced biofilm-biomasses of tested AMR strains. CONCLUSION Our results show the potential therapeutic use of R-pyocin due to its effectiveness on tested bacterial biofilms. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study that investigates antimicrobial and anti-biofilm activity of R-pyocin activity against S. aureus. R-pyocin shows new phenomenon of bacteriophage-like plaques. Our findings represent a future therapeutic agent targeting both methicillin-resistant and vancomycin-resistant S. aureus.
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Affiliation(s)
- A A Mohamed
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - A M Elshawadfy
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - G Amin
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - A Askora
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
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27
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Liu Y, Zhang Z, Wang F, Li DD, Li YZ. Identification of type VI secretion system toxic effectors using adaptors as markers. Comput Struct Biotechnol J 2020; 18:3723-3733. [PMID: 33304467 PMCID: PMC7714669 DOI: 10.1016/j.csbj.2020.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022] Open
Abstract
Each class of adaptors can be used as an effective marker to identify T6SS effectors. The PRK06147 homolog may be a novel adaptor. 1356 putative toxic effectors related to adaptors from 92 families were identified.
Toxic effectors secreted by the type VI secretion system (T6SS) facilitate interbacterial warfare, as well as pathogenesis toward humans, animals and plants. However, systematically predicting T6SS effectors remains challenging due to their sequence and functional diversity. In this study, we systematically identified putative T6SS toxic effectors in prokaryotic genomes on the basis of the observation that genes encoding adaptor proteins and genes encoding cognate effector proteins are generally adjacent in the genome. Adaptor proteins are mediators that help to load their cognate effectors onto the T6SS spike complex. The contextual genes of the known adaptor proteins (DUF1795, DUF2169 or DUF4123) all exhibited a high proportion of encoding T6SS spike complex protein (VgrG or PAAR) and effector proteins. On the basis of the genomic context, we found that PRK06147 might be a novel adaptor protein. These four adaptors are widely distributed among the bacterial genomes. From neighbors of 5297 adaptor genes, we identified 1356 putative effector genes from 92 different families, and two-thirds were currently annotated as hypothetical proteins or as having unknown functions. Our results indicate that each class of adaptors can be used as an effective marker to identify T6SS toxic effectors, moreover, this approach can promote the discovery of new effectors.
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Affiliation(s)
- Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.,Suzhou Research Institute, Shandong University, Suzhou 215123, China
| | - Feng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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Smith WPJ, Brodmann M, Unterweger D, Davit Y, Comstock LE, Basler M, Foster KR. The evolution of tit-for-tat in bacteria via the type VI secretion system. Nat Commun 2020; 11:5395. [PMID: 33106492 PMCID: PMC7589516 DOI: 10.1038/s41467-020-19017-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
Tit-for-tat is a familiar principle from animal behavior: individuals respond in kind to being helped or harmed by others. Remarkably some bacteria appear to display tit-for-tat behavior, but how this evolved is not understood. Here we combine evolutionary game theory with agent-based modelling of bacterial tit-for-tat, whereby cells stab rivals with poisoned needles (the type VI secretion system) after being stabbed themselves. Our modelling shows tit-for-tat retaliation is a surprisingly poor evolutionary strategy, because tit-for-tat cells lack the first-strike advantage of preemptive attackers. However, if cells retaliate strongly and fire back multiple times, we find that reciprocation is highly effective. We test our predictions by competing Pseudomonas aeruginosa (a tit-for-tat species) with Vibrio cholerae (random-firing), revealing that P. aeruginosa does indeed fire multiple times per incoming attack. Our work suggests bacterial competition has led to a particular form of reciprocation, where the principle is that of strong retaliation, or 'tits-for-tat'.
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Affiliation(s)
- William P J Smith
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Maj Brodmann
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Yohan Davit
- Institut de Mécanique des Fluides de Toulouse, CNRS and Université de Toulouse, 31400, Toulouse, France
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Marek Basler
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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The evolution of the type VI secretion system as a disintegration weapon. PLoS Biol 2020; 18:e3000720. [PMID: 32453732 PMCID: PMC7274471 DOI: 10.1371/journal.pbio.3000720] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/05/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well understood. Here we present a new agent-based model that enables detailed study of the evolutionary costs and benefits of T6SS weaponry during competition with other bacteria. Our model identifies a key problem with the T6SS. Because of its short range, T6SS activity becomes self-limiting, as dead cells accumulate in its way, forming “corpse barriers” that block further attacks. However, further exploration with the model presented a solution to this problem: if injected toxins can quickly lyse target cells in addition to killing them, the T6SS becomes a much more effective weapon. We tested this prediction with single-cell analysis of combat between T6SS-wielding Acinetobacter baylyi and T6SS-sensitive Escherichia coli. As predicted, delivery of lytic toxins is highly effective, whereas nonlytic toxins leave large patches of E. coli alive. We then analyzed hundreds of bacterial species using published genomic data, which suggest that the great majority of T6SS-wielding species do indeed use lytic toxins, indicative of a general principle underlying weapon evolution. Our work suggests that, in the T6SS, bacteria have evolved a disintegration weapon whose effectiveness often rests upon the ability to break up competitors. Understanding the evolutionary function of bacterial weapons can help in the design of probiotics that can both establish well and eliminate problem species. Bacteria attack each other with poison-tipped spears. This study combines theory and experiments to show that these spears (Type VI Secretion Systems) have evolved to break their targets apart with lytic toxins, as this then clears the way to rapidly stab new victims.
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Salinero-Lanzarote A, Pacheco-Moreno A, Domingo-Serrano L, Durán D, Ormeño-Orrillo E, Martínez-Romero E, Albareda M, Palacios JM, Rey L. The Type VI secretion system of Rhizobium etli Mim1 has a positive effect in symbiosis. FEMS Microbiol Ecol 2020; 95:5449006. [PMID: 30977796 DOI: 10.1093/femsec/fiz054] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/11/2019] [Indexed: 12/18/2022] Open
Abstract
The Type VI secretion systems (T6SSs) allow bacteria to translocate effector proteins to other bacteria or to eukaryotic cells. However, little is known about the role of T6SS in endosymbiotic bacteria. In this work we describe the T6SS of Rhizobium etli Mim1, a bacteria able to effectively nodulate common beans. Structural genes and those encoding possible effectors have been identified in a 28-gene DNA region of R. etli Mim1 pRetMIM1f plasmid. Immunodetection of Hcp protein, a conserved key structural component of T6SS systems, indicates that this secretion system is active at high cell densities, in the presence of root exudates, and in bean nodules. Rhizobium etli mutants affected in T6SS structural genes produced plants with lower dry weight and smaller nodules than the wild-type strain, indicating for the first time that the T6SS plays a positive role in Rhizobium-legume symbiosis.
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Affiliation(s)
- Alvaro Salinero-Lanzarote
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alba Pacheco-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Lucía Domingo-Serrano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | | | | | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - José Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223 Madrid, Spain.,Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Fur-Dam Regulatory Interplay at an Internal Promoter of the Enteroaggregative Escherichia coli Type VI Secretion sci1 Gene Cluster. J Bacteriol 2020; 202:JB.00075-20. [PMID: 32152218 DOI: 10.1128/jb.00075-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 02/28/2020] [Indexed: 12/17/2022] Open
Abstract
The type VI secretion system (T6SS) is a weapon for delivering effectors into target cells that is widespread in Gram-negative bacteria. The T6SS is a highly versatile machine, as it can target both eukaryotic and prokaryotic cells, and it has been proposed that T6SSs are adapted to the specific needs of each bacterium. The expression of T6SS gene clusters and the activation of the secretion apparatus are therefore tightly controlled. In enteroaggregative Escherichia coli (EAEC), the sci1 T6SS gene cluster is subject to a complex regulation involving both the ferric uptake regulator (Fur) and DNA adenine methylase (Dam)-dependent DNA methylation. In this study, an additional, internal, promoter was identified within the sci1 gene cluster using +1 transcriptional mapping. Further analyses demonstrated that this internal promoter is controlled by a mechanism strictly identical to that of the main promoter. The Fur binding box overlaps the -10 transcriptional element and a Dam methylation site, GATC-32. Hence, the expression of the distal sci1 genes is repressed and the GATC-32 site is protected from methylation in iron-rich conditions. The Fur-dependent protection of GATC-32 was confirmed by an in vitro methylation assay. In addition, the methylation of GATC-32 negatively impacted Fur binding. The expression of the sci1 internal promoter is therefore controlled by iron availability through Fur regulation, whereas Dam-dependent methylation maintains a stable ON expression in iron-limited conditions.IMPORTANCE Bacteria use weapons to deliver effectors into target cells. One of these weapons, the type VI secretion system (T6SS), assembles a contractile tail acting as a spring to propel a toxin-loaded needle. Its expression and activation therefore need to be tightly regulated. Here, we identified an internal promoter within the sci1 T6SS gene cluster in enteroaggregative E. coli We show that this internal promoter is controlled by Fur and Dam-dependent methylation. We further demonstrate that Fur and Dam compete at the -10 transcriptional element to finely tune the expression of T6SS genes. We propose that this elegant regulatory mechanism allows the optimum production of the T6SS in conditions where enteroaggregative E. coli encounters competing species.
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Double Tubular Contractile Structure of the Type VI Secretion System Displays Striking Flexibility and Elasticity. J Bacteriol 2019; 202:JB.00425-19. [PMID: 31636107 DOI: 10.1128/jb.00425-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial treatment can induce many bacterial pathogens to enter a cell wall-deficient state that contributes to persistent infections. The effect of this physiological state on the assembly of transenvelope-anchored organelles is not well understood. The type VI secretion system (T6SS) is a widespread molecular weapon for interspecies interactions and virulence, comprising a long double tubular structure and a transenvelope/baseplate complex. Here, we report that cell wall-deficient spheroplasts assembled highly flexible and elastic T6SS structures forming U, O, or S shapes. Upon contacting the inner membrane, the T6SS tubes did not contract but rather continued to grow along the membrane. Such deformation likely results from continual addition of sheath/tube subunits at the distal end. Induction of TagA repressed curved sheath formation. Curved sheaths could also contract and deliver T6SS substrates and were readily disassembled by the ClpV ATPase after contraction. Our data highlight the dramatic effect of cell wall deficiency on the shape of the T6SS structures and reveal the elastic nature of this double tubular contractile injection nanomachine.IMPORTANCE The cell wall is a physical scaffold that all transenvelope complexes have to cross for assembly. However, the cell wall-deficient state has been described as a common condition found in both Gram-negative and Gram-positive pathogens during persistent infections. Loss of cell wall is known to have pleiotropic physiological effects, but how membrane-anchored large cellular organelles adapt to this unique state is less completely understood. Our study examined the assembly of the T6SS in cell wall-deficient spheroplast cells. We report the elastic nature of contractile T6SS tubules under such conditions, providing key insights for understanding how large intracellular structures such as the T6SS accommodate the multifaceted changes in cell wall-deficient cells.
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Mariano G, Trunk K, Williams DJ, Monlezun L, Strahl H, Pitt SJ, Coulthurst SJ. A family of Type VI secretion system effector proteins that form ion-selective pores. Nat Commun 2019; 10:5484. [PMID: 31792213 PMCID: PMC6889166 DOI: 10.1038/s41467-019-13439-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/05/2019] [Indexed: 12/25/2022] Open
Abstract
Type VI secretion systems (T6SSs) are nanomachines widely used by bacteria to deliver toxic effector proteins directly into neighbouring cells. However, the modes of action of many effectors remain unknown. Here we report that Ssp6, an anti-bacterial effector delivered by a T6SS of the opportunistic pathogen Serratia marcescens, is a toxin that forms ion-selective pores. Ssp6 inhibits bacterial growth by causing depolarisation of the inner membrane in intoxicated cells, together with increased outer membrane permeability. Reconstruction of Ssp6 activity in vitro demonstrates that it forms cation-selective pores. A survey of bacterial genomes reveals that genes encoding Ssp6-like effectors are widespread in Enterobacteriaceae and often linked with T6SS genes. We conclude that Ssp6 and similar proteins represent a new family of T6SS-delivered anti-bacterial effectors.
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Affiliation(s)
- Giuseppina Mariano
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Katharina Trunk
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - David J Williams
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Laura Monlezun
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Newcastle University, Richardson Road, Newcastle-upon-Tyne, NE2 4AX, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK.
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35
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Ericson CF, Eisenstein F, Medeiros JM, Malter KE, Cavalcanti GS, Zeller RW, Newman DK, Pilhofer M, Shikuma NJ. A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector. eLife 2019; 8:46845. [PMID: 31526475 PMCID: PMC6748791 DOI: 10.7554/elife.46845] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022] Open
Abstract
The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe–animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm Hydroides elegans is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium Pseudoalteromonas luteoviolacea. Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the mif1 gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe–animal interactions in diverse contexts. Many marine animals, including corals and tubeworms, begin life as larvae swimming in open water before transforming into adults that anchor themselves to the seabed. These transformations, known as metamorphoses, are often triggered by certain types of bacteria that form friendly relationships (or “symbioses”) with the animals. One such symbiosis forms between a bacterium called Pseudoalteromonas luteoviolacea and a tubeworm known as Hydroides elegans. Previous studies have shown that P. luteoviolacea produces syringe-like structures known as Metamorphosis Associated Contractile structures (or MACs for short) that are responsible for stimulating metamorphosis in the tubeworm larvae. Some viruses that infect bacteria use similar structures to inject molecules into their host cells. However, it was not clear whether MACs were also able to inject molecules into cells. Here, Ericson, Eisenstein et al. used a technique called cryo-electron tomography combined with genetic and biochemical approaches to study how the MACs of P. luteoviolacea trigger metamorphosis in tubeworms. The experiments identified a protein in the bacteria named Mif1 that was required for the tubeworms to transform. The bacteria loaded Mif1 into the tube of the MAC structure and then injected it into the tubeworms. Further experiments showed that inserting Mif1 alone into tubeworms was sufficient to activate metamorphosis. Mif1 is the first protein from bacteria to be shown to activate metamorphosis, but it is likely that many more remain to be discovered. Since other marine animals also form symbioses with bacteria, understanding how Mif1 and other similar proteins work may inform efforts to restore coral reefs and other fragile ecosystems, and increase the production of oysters and other shellfish. Furthermore, MACs and related structures may have the potential to be developed into biotechnology tools that deliver drugs and other molecules directly into animal cells.
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Affiliation(s)
- Charles F Ericson
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States.,Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Fabian Eisenstein
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - João M Medeiros
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Kyle E Malter
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Giselle S Cavalcanti
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Robert W Zeller
- Department of Biology, San Diego State University, San Diego, United States
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, United States
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Nicholas J Shikuma
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
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36
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Schneider JP, Nazarov S, Adaixo R, Liuzzo M, Ringel PD, Stahlberg H, Basler M. Diverse roles of TssA-like proteins in the assembly of bacterial type VI secretion systems. EMBO J 2019; 38:e100825. [PMID: 31403721 PMCID: PMC6745524 DOI: 10.15252/embj.2018100825] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 01/01/2023] Open
Abstract
Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or TagA-like proteins with a conserved N-terminal domain and varying C-terminal domains can be grouped into at least three distinct classes based on their role in sheath assembly. The proteins of the first class increase speed and frequency of sheath assembly and form a stable dodecamer at the distal end of a polymerizing sheath. The proteins of the second class localize to the cell membrane and block sheath polymerization upon extension across the cell. This prevents excessive sheath polymerization and bending, which may result in sheath destabilization and detachment from its membrane anchor and thus result in failed secretion. The third class of these proteins localizes to the baseplate and is required for initiation of sheath assembly. Our work shows that while various proteins share a conserved N-terminal domain, their roles in T6SS biogenesis are fundamentally different.
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Affiliation(s)
| | - Sergey Nazarov
- BiozentrumUniversity of BaselBaselSwitzerland
- Present address:
Interdisciplinary Center for Electron Microscopy (CIME)EPFLLausanneSwitzerland
| | - Ricardo Adaixo
- Center for Cellular Imaging and NanoAnalytics (C‐CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | | | - Peter David Ringel
- BiozentrumUniversity of BaselBaselSwitzerland
- Present address:
Institute of Forensic MedicineJustus‐Liebig‐University GiessenGiessenGermany
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C‐CINA), BiozentrumUniversity of BaselBaselSwitzerland
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37
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Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019; 87:1037-1057. [PMID: 31442339 PMCID: PMC6851490 DOI: 10.1002/prot.25805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
Abstract
The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.
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Affiliation(s)
- Rosalba Lepore
- BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Harshul A Veraszto
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Joshua C Bufton
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Alex N Bullock
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Hongnan Cao
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | | | - Celia W Goulding
- Department of Molecular Biology and Biochemistry; Pharmaceutical Sciences, University of California Irvine, Irvine, California
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Karolina Michalska
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - A K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, Rockville, Maryland, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Daniel M Pinkas
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK
| | - Jonathan D Walton
- Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - Torsten Schwede
- Biozentrum University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland
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38
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Wang J, Brodmann M, Basler M. Assembly and Subcellular Localization of Bacterial Type VI Secretion Systems. Annu Rev Microbiol 2019; 73:621-638. [DOI: 10.1146/annurev-micro-020518-115420] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria need to deliver large molecules out of the cytosol to the extracellular space or even across membranes of neighboring cells to influence their environment, prevent predation, defeat competitors, or communicate. A variety of protein-secretion systems have evolved to make this process highly regulated and efficient. The type VI secretion system (T6SS) is one of the largest dynamic assemblies in gram-negative bacteria and allows for delivery of toxins into both bacterial and eukaryotic cells. The recent progress in structural biology and live-cell imaging shows the T6SS as a long contractile sheath assembled around a rigid tube with associated toxins anchored to a cell envelope by a baseplate and membrane complex. Rapid sheath contraction releases a large amount of energy used to push the tube and toxins through the membranes of neighboring target cells. Because reach of the T6SS is limited, some bacteria dynamically regulate its subcellular localization to precisely aim at their targets and thus increase efficiency of toxin translocation.
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Affiliation(s)
- Jing Wang
- Biozentrum, University of Basel, CH 4056 Basel, Switzerland
| | - Maj Brodmann
- Biozentrum, University of Basel, CH 4056 Basel, Switzerland
| | - Marek Basler
- Biozentrum, University of Basel, CH 4056 Basel, Switzerland
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39
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An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy. Proc Natl Acad Sci U S A 2019; 116:18597-18606. [PMID: 31439817 PMCID: PMC6744847 DOI: 10.1073/pnas.1906388116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei, the etiologic agent of melioidosis, is an environmental organism that inhabits tropical soils and kills an estimated 90,000 people each year. Caused by an intracellular and often drug-resistant pathogen, melioidosis is notoriously difficult to treat, with mortality rates approaching 50% in some settings despite appropriate diagnosis and clinical management. Using a high-throughput, cell-based phenotypic screen we have discovered 2 antibiotic candidates with improved in vivo efficacy compared to the current standard of care: a fluoroquinolone analog, burkfloxacin, and an FDA-approved antifungal drug, flucytosine. As a widely used antifungal with a well-known safety profile, the potential to repurpose flucytosine for treating melioidosis may represent a rapid route to clinical translation. Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) are Tier-1 Select Agents that cause melioidosis and glanders, respectively. These are highly lethal human infections with limited therapeutic options. Intercellular spread is a hallmark of Burkholderia pathogenesis, and its prominent ties to virulence make it an attractive therapeutic target. We developed a high-throughput cell-based phenotypic assay and screened ∼220,000 small molecules for their ability to disrupt intercellular spread by Burkholderia thailandensis, a closely related BSL-2 surrogate. We identified 268 hits, and cross-species validation found 32 hits that also disrupt intercellular spread by Bp and/or Bm. Among these were a fluoroquinolone analog, which we named burkfloxacin (BFX), which potently inhibits growth of intracellular Burkholderia, and flucytosine (5-FC), an FDA-approved antifungal drug. We found that 5-FC blocks the intracellular life cycle at the point of type VI secretion system 5 (T6SS-5)-mediated cell–cell spread. Bacterial conversion of 5-FC to 5-fluorouracil and subsequently to fluorouridine monophosphate is required for potent and selective activity against intracellular Burkholderia. In a murine model of fulminant respiratory melioidosis, treatment with BFX or 5-FC was significantly more effective than ceftazidime, the current antibiotic of choice, for improving survival and decreasing bacterial counts in major organs. Our results demonstrate the utility of cell-based phenotypic screening for Select Agent drug discovery and warrant the advancement of BFX and 5-FC as candidate therapeutics for melioidosis in humans.
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40
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Desfosses A, Venugopal H, Joshi T, Felix J, Jessop M, Jeong H, Hyun J, Heymann JB, Hurst MRH, Gutsche I, Mitra AK. Atomic structures of an entire contractile injection system in both the extended and contracted states. Nat Microbiol 2019; 4:1885-1894. [PMID: 31384001 PMCID: PMC6817355 DOI: 10.1038/s41564-019-0530-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023]
Abstract
Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. While the amount of atomic resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information about contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here we characterise the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localisation variants and perform specific structural comparisons with related systems. We analyse intersubunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents.
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Affiliation(s)
- Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Hariprasad Venugopal
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Melbourne, Victoria, Australia
| | - Tapan Joshi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jan Felix
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Jessop
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Hyengseop Jeong
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju-si, Republic of Korea
| | - Jaekyung Hyun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju-si, Republic of Korea.,Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - J Bernard Heymann
- Laboratory for Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mark R H Hurst
- Forage Science, AgResearch, Lincoln Research Centre, Christchurch, New Zealand. .,Bio-Protection Research Centre, Christchurch, New Zealand.
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Alok K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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41
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Lennings J, Makhlouf M, Olejnik P, Mayer C, Brötz-Oesterhelt H, Schwarz S. Environmental and cellular factors affecting the localization of T6SS proteins in Burkholderia thailandensis. Int J Med Microbiol 2019; 309:151335. [PMID: 31378704 DOI: 10.1016/j.ijmm.2019.151335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 01/22/2023] Open
Abstract
The type VI secretion system (T6SS) injects effector proteins into neighboring bacteria and host cells. Effector translocation is driven by contraction of a tubular sheath in the cytoplasm that expels an inner needle across the cell envelope. The AAA + ATPase ClpV disassembles and recycles the contracted sheath. While ClpV-1-GFP of the Burkholderia T6SS-1, which targets prokaryotic cells, assembles into randomly localized foci, ClpV-5-GFP of the virulence-associated T6SS-5 displays a polar distribution. The mechanisms underlying the localization of T6SSs to a particular site in the bacterial cell are currently unknown. We recently showed that ClpV-5-GFP retains its polar localization in the absence of all T6SS-5 components during infection of host cells. Herein, we set out to identify factors involved in the distribution of ClpV-5 and ClpV-1 in Burkholderia thailandensis. We show that focal assembly and polar localization of ClpV-5-GFP is not dependent on the intracellular host cell environment, known to contain the signal to induce T6SS-5 gene expression. In contrast to ClpV-5-GFP, localization of ClpV-1-GFP was dependent on the cognate T6SS. Foci formation of both ClpV5-GFP and ClpV-1-GFP was decreased by D cycloserine-mediated inhibition of peptidoglycan synthesis while treatment of B. thailandensis with A22 blocking the cytoskeletal protein MreB did not affect assembly of ClpV-5 and ClpV-1 into single discrete foci. Furthermore, we found that surface contact promotes but is not essential for localization of ClpV-5-GFP to the pole whereas expression of clpV-1-gfp appears to be induced by surface contact. In summary, the study provides novel insights into the localization of ClpV ATPases of T6SSs targeting prokaryotic and eukaryotic cells.
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Affiliation(s)
- Jan Lennings
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Munira Makhlouf
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Przemyslaw Olejnik
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Christian Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Sandra Schwarz
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
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42
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Cherrak Y, Flaugnatti N, Durand E, Journet L, Cascales E. Structure and Activity of the Type VI Secretion System. Microbiol Spectr 2019; 7:10.1128/microbiolspec.psib-0031-2019. [PMID: 31298206 PMCID: PMC10957189 DOI: 10.1128/microbiolspec.psib-0031-2019] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 12/16/2022] Open
Abstract
The type VI secretion system (T6SS) is a multiprotein machine that uses a spring-like mechanism to inject effectors into target cells. The injection apparatus is composed of a baseplate on which is built a contractile tail tube/sheath complex. The inner tube, topped by the spike complex, is propelled outside of the cell by the contraction of the sheath. The injection system is anchored to the cell envelope and oriented towards the cell exterior by a trans-envelope complex. Effectors delivered by the T6SS are loaded within the inner tube or on the spike complex and can target prokaryotic and/or eukaryotic cells. Here we summarize the structure, assembly, and mechanism of action of the T6SS. We also review the function of effectors and their mode of recruitment and delivery.
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Affiliation(s)
- Yassine Cherrak
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, UMR 7255, 13402 Marseille Cedex 20, France
- Y.C. and N.F. contributed equally to this review
| | - Nicolas Flaugnatti
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, UMR 7255, 13402 Marseille Cedex 20, France
- Y.C. and N.F. contributed equally to this review
- Present address: Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Eric Durand
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, UMR 7255, 13402 Marseille Cedex 20, France
| | - Laure Journet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, UMR 7255, 13402 Marseille Cedex 20, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, UMR 7255, 13402 Marseille Cedex 20, France
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43
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Trunk K, Coulthurst SJ, Quinn J. A New Front in Microbial Warfare-Delivery of Antifungal Effectors by the Type VI Secretion System. J Fungi (Basel) 2019; 5:jof5020050. [PMID: 31197124 PMCID: PMC6617251 DOI: 10.3390/jof5020050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022] Open
Abstract
Microbes typically exist in mixed communities and display complex synergistic and antagonistic interactions. The Type VI secretion system (T6SS) is widespread in Gram-negative bacteria and represents a contractile nano-machine that can fire effector proteins directly into neighbouring cells. The primary role assigned to the T6SS is to function as a potent weapon during inter-bacterial competition, delivering antibacterial effectors into rival bacterial cells. However, it has recently emerged that the T6SS can also be used as a powerful weapon against fungal competitors, and the first fungal-specific T6SS effector proteins, Tfe1 and Tfe2, have been identified. These effectors act via distinct mechanisms against a variety of fungal species to cause cell death. Tfe1 intoxication triggers plasma membrane depolarisation, whilst Tfe2 disrupts nutrient uptake and induces autophagy. Based on the frequent coexistence of bacteria and fungi in microbial communities, we propose that T6SS-dependent antifungal activity is likely to be widespread and elicited by a suite of antifungal effectors. Supporting this hypothesis, homologues of Tfe1 and Tfe2 are found in other bacterial species, and a number of T6SS-elaborating species have been demonstrated to interact with fungi. Thus, we envisage that antifungal T6SS will shape many polymicrobial communities, including the human microbiota and disease-causing infections.
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Affiliation(s)
- Katharina Trunk
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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Abundance of bacterial Type VI secretion system components measured by targeted proteomics. Nat Commun 2019; 10:2584. [PMID: 31197144 PMCID: PMC6565705 DOI: 10.1038/s41467-019-10466-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 05/13/2019] [Indexed: 12/31/2022] Open
Abstract
The Type VI secretion system (T6SS) is important for bacterial competition as well as virulence in many Gram-negative bacteria and its dynamics and regulation varies significantly between species. To gain insights into the mechanisms regulating T6SS assembly, we apply targeted proteomics to determine the abundance of the key T6SS components in Vibrio cholerae, Pseudomonas aeruginosa and Acinetobacter baylyi. We show that while there are species specific exceptions, the abundance of most components is similar in all three bacteria and ranges from less than hundred to tens of thousands of copies per cell. The comparison of T6SS dynamics and protein abundance in V. cholerae grown under various conditions suggests that the critical component TssE and the secreted protein VasX are unstable and this diminishes T6SS assembly when protein synthesis is limited. Our quantitative analysis opens possibilities to build realistic models of T6SS assembly and to identify principles of T6SS regulation in various species. Type VI secretion systems (T6SS) are important for bacterial interaction, competition and virulence, but the abundance and assembly of their components is still not well understood. Here, the authors apply targeted proteomics to measure the abundance of T6SS components across different species and conditions.
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Role and Recruitment of the TagL Peptidoglycan-Binding Protein during Type VI Secretion System Biogenesis. J Bacteriol 2019; 201:JB.00173-19. [PMID: 30910811 DOI: 10.1128/jb.00173-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/19/2019] [Indexed: 12/29/2022] Open
Abstract
The type VI secretion system (T6SS) is an injection apparatus that uses a springlike mechanism for effector delivery. The contractile tail is composed of a needle tipped by a sharpened spike and wrapped by the sheath that polymerizes in an extended conformation on the assembly platform, or baseplate. Contraction of the sheath propels the needle and effectors associated with it into target cells. The passage of the needle through the cell envelope of the attacker is ensured by a dedicated trans-envelope channel complex. This membrane complex (MC) comprises the TssJ lipoprotein and the TssL and TssM inner membrane proteins. MC assembly is a hierarchized mechanism in which the different subunits are recruited in a specific order: TssJ, TssM, and then TssL. Once assembled, the MC serves as a docking station for the baseplate. In enteroaggregative Escherichia coli, the MC is accessorized by TagL, a peptidoglycan-binding (PGB) inner membrane-anchored protein. Here, we show that the PGB domain is the only functional domain of TagL and that the N-terminal transmembrane region mediates contact with the TssL transmembrane helix. Finally, we conduct fluorescence microscopy experiments to position TagL in the T6SS biogenesis pathway, demonstrating that TagL is recruited to the membrane complex downstream of TssL and is not required for baseplate docking.IMPORTANCE Bacteria use weapons to deliver effectors into target cells. One of these weapons, called the type VI secretion system (T6SS), could be compared to a nano-spear gun using a springlike mechanism for effector injection. By targeting bacteria and eukaryotic cells, the T6SS reshapes bacterial communities and hijacks host cell defenses. In enteroaggregative Escherichia coli, the T6SS is a multiprotein machine that comprises a cytoplasmic tail and a peptidoglycan-anchored trans-envelope channel. In this work, we show that TagL comprises an N-terminal domain that mediates contact with the channel and a peptidoglycan-binding domain that binds the cell wall. We then determine at which stage of T6SS biogenesis TagL is recruited and how TagL absence impacts the assembly pathway.
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Coulthurst S. The Type VI secretion system: a versatile bacterial weapon. Microbiology (Reading) 2019; 165:503-515. [DOI: 10.1099/mic.0.000789] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Sarah Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Abstract
The Type VI secretion system (T6SS) is a protein nanomachine that is widespread in Gram-negative bacteria and is used to translocate effector proteins directly into neighbouring cells. It represents a versatile bacterial weapon that can deliver effectors into distinct classes of target cells, playing key roles in inter-bacterial competition and bacterial interactions with eukaryotic cells. This versatility is underpinned by the ability of the T6SS to deliver a vast array of effector proteins, with many distinct activities and modes of interaction with the secretion machinery. Recent work has highlighted the importance and diversity of interactions mediated by T6SSs within polymicrobial communities, and offers new molecular insights into effector delivery and action in target cells.
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Affiliation(s)
- Sarah Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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48
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Bidirectional contraction of a type six secretion system. Nat Commun 2019; 10:1565. [PMID: 30952865 PMCID: PMC6450956 DOI: 10.1038/s41467-019-09603-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/20/2019] [Indexed: 12/31/2022] Open
Abstract
Contractile injection systems (CISs) mediate cell-cell interactions by a phage tail-like apparatus. Their conserved mechanism relies on the anchoring of the proximal end of a sheath-tube module to a membrane, followed by contraction of the sheath towards the attachment site and ejection of the inner tube. Here we reveal a major variation of the CIS mechanism in the type six secretion system (T6SS) of enteroaggregative Escherichia coli (EAEC). We show that both ends of the sheath-tube module are attached to opposite sides of the cell, enabling the structure to contract in two opposite directions. The protein TssA1 mediates the interaction of the distal end with the cell envelope, the termination of tail elongation, and non-canonical contraction towards the distal end. We provide a framework for the molecular processes at the T6SS distal end. Further research will address whether bidirectional contraction allows for bidirectional effector secretion. The unrecognized concept of non-canonical contractions could be relevant to biofilms of the human intestine.
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Jiang F, Li N, Wang X, Cheng J, Huang Y, Yang Y, Yang J, Cai B, Wang YP, Jin Q, Gao N. Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Cell 2019; 177:370-383.e15. [PMID: 30905475 DOI: 10.1016/j.cell.2019.02.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. Here, we report the cryo-EM structure of an intact PVC from P. asymbiotica. This over 10-MDa device resembles a simplified T4 phage tail, containing a hexagonal baseplate complex with six fibers and a capped 117-nanometer sheath-tube trunk. One distinct feature of the PVC is the presence of three variants for both tube and sheath proteins, indicating a functional specialization of them during evolution. The terminal hexameric cap docks onto the topmost layer of the inner tube and locks the outer sheath in pre-contraction state with six stretching arms. Our results on the PVC provide a framework for understanding the general mechanism of widespread CISs and pave the way for using them as delivery tools in biological or therapeutic applications.
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Affiliation(s)
- Feng Jiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC
| | - Xia Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC
| | - Jiaxuan Cheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, PRC
| | - Yaoguang Huang
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PRC
| | - Yun Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Bin Cai
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC.
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50
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Agnetti J, Seth-Smith HMB, Ursich S, Reist J, Basler M, Nickel C, Bassetti S, Ritz N, Tschudin-Sutter S, Egli A. Clinical impact of the type VI secretion system on virulence of Campylobacter species during infection. BMC Infect Dis 2019; 19:237. [PMID: 30845966 PMCID: PMC6407262 DOI: 10.1186/s12879-019-3858-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/28/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The clinical course of Campylobacter infection varies in symptoms and severity depending on host factors, virulence of the pathogen and initiated therapy. The type VI secretion system (T6SS) has been identified as a novel virulence factor, which mediates contact-dependent injection of enzymes and toxins into competing bacteria or host cells and facilitates the colonisation of a host organism. We aimed to compare the clinical course of Campylobacter infection caused by strains with and without the T6SS and identify possible associations between this putative virulence factor and the clinical manifestations of disease. METHODS From April 2015 to January 2017, patients with detection of Campylobacter spp. were identified at the University Hospital of Basel and the University Children's Hospital of Basel and included in this case-control study. Presence of the T6SS gene cluster was assayed by PCR targeting the hcp gene, confirmed with whole genome sequencing. Pertinent clinical data was collected by medical record review. Differences in disease- and host-characteristics between T6SS-positive (case) and -negative (control) were compared in a uni- and multi-variable analysis. Hospital admission, antibiotic therapy, admission to intensive care unit, development of bacteraemia and in-hospital mortality were considered as clinical endpoints. RESULTS We identified 138 cases of Campylobacter jejuni infections and 18 cases of Campylobacter coli infections from a paediatric and adult population. Analyses were focused on adult patients with C. jejuni (n = 119) of which 16.8% were T6SS-positive. Comparisons between T6SS-positive and -negative C. jejuni isolates did not reveal significant differences regarding clinical manifestations or course of disease. All clinical endpoints showed a similar distribution in both groups. A higher score in the Charlson Comorbidity Index was associated with T6SS-positive C. jejuni isolates (p < 0.001) and patients were more likely to have a solid organ transplant and to be under immunosuppressive therapy. CONCLUSIONS Our study does not provide evidence that T6SS is associated with a more severe clinical course. Interestingly, T6SS-positive isolates are more commonly found in immunocompromised patients: an observation which merits further investigation.
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Affiliation(s)
- Jessica Agnetti
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland
| | - Sebastian Ursich
- Biozentrum, University of Basel, Basel, Switzerland
- Current address: Institute for Molecular Cancer Research IMCR, University of Zürich, Zürich, Switzerland
| | - Josiane Reist
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland
| | - Marek Basler
- Biozentrum, University of Basel, Basel, Switzerland
| | - Christian Nickel
- Emergency Department, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Nicole Ritz
- Paediatric Infectious Diseases and Vaccinology, University Children Hospital Basel, Basel, Switzerland
- Department of Pediatrics, Royal Children’s Hospital Melbourne, University of Melbourne, Parkville, Australia
| | - Sarah Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Current address: Institute for Molecular Cancer Research IMCR, University of Zürich, Zürich, Switzerland
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