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Fridman CM, Keppel K, Rudenko V, Altuna-Alvarez J, Albesa-Jové D, Bosis E, Salomon D. A new class of type VI secretion system effectors can carry two toxic domains and are recognized through the WHIX motif for export. PLoS Biol 2025; 23:e3003053. [PMID: 40096082 DOI: 10.1371/journal.pbio.3003053] [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: 08/22/2024] [Revised: 03/28/2025] [Accepted: 02/05/2025] [Indexed: 03/19/2025] Open
Abstract
Gram-negative bacteria employ the type VI secretion system (T6SS) to deliver toxic effectors into neighboring cells and outcompete rivals. Although many effectors have been identified, their secretion mechanism often remains unknown. Here, we describe WHIX, a domain sufficient to mediate the secretion of effectors via the T6SS. Remarkably, we find WHIX in T6SS effectors that contain a single toxic domain, as well as in effectors that contain two distinct toxic domains fused to either side of WHIX. We demonstrate that the latter, which we name double-blade effectors, require two cognate immunity proteins to antagonize their toxicity. Furthermore, we show that WHIX can be used as a chassis for T6SS-mediated secretion of multiple domains. Our findings reveal a new class of polymorphic T6SS cargo effectors with a unique secretion domain that can deploy two toxic domains in one shot, possibly reducing recipients' ability to defend themselves.
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Affiliation(s)
- Chaya Mushka Fridman
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kinga Keppel
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Vladislav Rudenko
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jon Altuna-Alvarez
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Leioa, Spain
| | - David Albesa-Jové
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Leioa, Spain
- Departamento de Bioquímica y Biología Molecular, University of the Basque Country, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
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2
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Mahata T, Kanarek K, Goren MG, Marimuthu Ragavan R, Bosis E, Qimron U, Salomon D. Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools. Nat Microbiol 2024; 9:3268-3283. [PMID: 39443754 DOI: 10.1038/s41564-024-01840-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 09/25/2024] [Indexed: 10/25/2024]
Abstract
The evolutionary arms race between bacteria and phages led to the emergence of bacterial immune systems whose diversity and dynamics remain poorly understood. Here we use comparative genomics to describe a widespread genetic element, defined by the presence of the Gamma-Mobile-Trio (GMT) proteins, that serves as a reservoir of offensive and defensive tools. We demonstrate, using Vibrio parahaemolyticus as a model, that GMT-containing genomic islands are active mobile elements. Furthermore, we show that GMT islands' cargoes contain various anti-phage defence systems, antibacterial type VI secretion system (T6SS) effectors and antibiotic-resistance genes. We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy. Our findings underscore the need to broaden the concept of 'defence islands' to include defensive and offensive tools, as both share the same mobile elements for dissemination.
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Affiliation(s)
- Tridib Mahata
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Katarzyna Kanarek
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moran G Goren
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rameshkumar Marimuthu Ragavan
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel.
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
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3
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van Kessel JC, Camilli A. Vibrio cholerae: a fundamental model system for bacterial genetics and pathogenesis research. J Bacteriol 2024; 206:e0024824. [PMID: 39405459 PMCID: PMC11580405 DOI: 10.1128/jb.00248-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2024] Open
Abstract
Species of the Vibrio genus occupy diverse aquatic environments ranging from brackish water to warm equatorial seas to salty coastal regions. More than 80 species of Vibrio have been identified, many of them as pathogens of marine organisms, including fish, shellfish, and corals, causing disease and wreaking havoc on aquacultures and coral reefs. Moreover, many Vibrio species associate with and thrive on chitinous organisms abundant in the ocean. Among the many diverse Vibrio species, the most well-known and studied is Vibrio cholerae, discovered in the 19th century to cause cholera in humans when ingested. The V. cholerae field blossomed in the late 20th century, with studies broadly examining V. cholerae evolution as a human pathogen, natural competence, biofilm formation, and virulence mechanisms, including toxin biology and virulence gene regulation. This review discusses some of the historic discoveries of V. cholerae biology and ecology as one of the fundamental model systems of bacterial genetics and pathogenesis.
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Affiliation(s)
| | - Andrew Camilli
- Tufts University, School of Medicine, Boston, Massachusetts, USA
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4
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Mass S, Cohen H, Podicheti R, Rusch DB, Gerlic M, Ushijima B, van Kessel JC, Bosis E, Salomon D. The coral pathogen Vibrio coralliilyticus uses a T6SS to secrete a group of novel anti-eukaryotic effectors that contribute to virulence. PLoS Biol 2024; 22:e3002734. [PMID: 39226241 PMCID: PMC11371242 DOI: 10.1371/journal.pbio.3002734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/03/2024] [Indexed: 09/05/2024] Open
Abstract
Vibrio coralliilyticus is a pathogen of coral and shellfish, leading to devastating economic and ecological consequences worldwide. Although rising ocean temperatures correlate with increased V. coralliilyticus pathogenicity, the specific molecular mechanisms and determinants contributing to virulence remain poorly understood. Here, we systematically analyzed the type VI secretion system (T6SS), a contact-dependent toxin delivery apparatus, in V. coralliilyticus. We identified 2 omnipresent T6SSs that are activated at temperatures in which V. coralliilyticus becomes virulent; T6SS1 is an antibacterial system mediating interbacterial competition, whereas T6SS2 mediates anti-eukaryotic toxicity and contributes to mortality during infection of an aquatic model organism, Artemia salina. Using comparative proteomics, we identified the T6SS1 and T6SS2 toxin arsenals of 3 V. coralliilyticus strains with distinct disease etiologies. Remarkably, T6SS2 secretes at least 9 novel anti-eukaryotic toxins comprising core and accessory repertoires. We propose that T6SSs differently contribute to V. coralliilyticus's virulence: T6SS2 plays a direct role by targeting the host, while T6SS1 plays an indirect role by eliminating competitors.
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Affiliation(s)
- Shir Mass
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hadar Cohen
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ram Podicheti
- Center for Genomics and Bioinformatics Indiana University, Bloomington, Indiana, United States of America
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics Indiana University, Bloomington, Indiana, United States of America
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
| | - Julia C. van Kessel
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
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5
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Otto SB, Servajean R, Lemopoulos A, Bitbol AF, Blokesch M. Interactions between pili affect the outcome of bacterial competition driven by the type VI secretion system. Curr Biol 2024; 34:2403-2417.e9. [PMID: 38749426 DOI: 10.1016/j.cub.2024.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
The bacterial type VI secretion system (T6SS) is a widespread, kin-discriminatory weapon capable of shaping microbial communities. Due to the system's dependency on contact, cellular interactions can lead to either competition or kin protection. Cell-to-cell contact is often accomplished via surface-exposed type IV pili (T4Ps). In Vibrio cholerae, these T4Ps facilitate specific interactions when the bacteria colonize natural chitinous surfaces. However, it has remained unclear whether and, if so, how these interactions affect the bacterium's T6SS-mediated killing. In this study, we demonstrate that pilus-mediated interactions can be harnessed by T6SS-equipped V. cholerae to kill non-kin cells under liquid growth conditions. We also show that the naturally occurring diversity of pili determines the likelihood of cell-to-cell contact and, consequently, the extent of T6SS-mediated competition. To determine the factors that enable or hinder the T6SS's targeted reduction of competitors carrying pili, we developed a physics-grounded computational model for autoaggregation. Collectively, our research demonstrates that T4Ps involved in cell-to-cell contact can impose a selective burden when V. cholerae encounters non-kin cells that possess an active T6SS. Additionally, our study underscores the significance of T4P diversity in protecting closely related individuals from T6SS attacks through autoaggregation and spatial segregation.
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Affiliation(s)
- Simon B Otto
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Richard Servajean
- Laboratory of Computational Biology and Theoretical Biophysics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Lemopoulos
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anne-Florence Bitbol
- Laboratory of Computational Biology and Theoretical Biophysics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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6
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Carobbi A, Leo K, Di Nepi S, Bosis E, Salomon D, Sessa G. PIX is an N-terminal delivery domain that defines a class of polymorphic T6SS effectors in Enterobacterales. Cell Rep 2024; 43:114015. [PMID: 38568810 DOI: 10.1016/j.celrep.2024.114015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
The type VI secretion system (T6SS), a widespread protein delivery apparatus, plays a role in bacterial competition by delivering toxic effectors into neighboring cells. Identifying new T6SS effectors and deciphering the mechanism that governs their secretion remain major challenges. Here, we report two orphan antibacterial T6SS effectors in the pathogen Pantoea agglomerans (Pa). These effectors share an N-terminal domain, Pantoea type six (PIX), that defines a widespread class of polymorphic T6SS effectors in Enterobacterales. We show that the PIX domain is necessary and sufficient for T6SS-mediated effector secretion and that PIX binds to a specialized Pa VgrG protein outside its C-terminal toxic domain. Our findings underline the importance of identifying and characterizing delivery domains in polymorphic toxin classes as a tool to reveal effectors and shed light on effector delivery mechanisms.
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Affiliation(s)
- Andrea Carobbi
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ksenia Leo
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Simone Di Nepi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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7
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Restrepo-Benavides M, Lozano-Arce D, Gonzalez-Garcia LN, Báez-Aguirre F, Ariza-Aranguren G, Faccini D, Zambrano MM, Jiménez P, Fernández-Bravo A, Restrepo S, Guevara-Suarez M. Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses. Microbiol Spectr 2024; 12:e0292823. [PMID: 38189292 PMCID: PMC10846245 DOI: 10.1128/spectrum.02928-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024] Open
Abstract
The genus Vibrio includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on Vibrio in several marine organisms, no specific studies have been conducted on Anadara tuberculosa. This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast. Therefore, this study aimed to identify and characterize the genomes of Vibrio isolates obtained from A. tuberculosa. Bacterial isolates were obtained from 14 A. tuberculosa specimens collected from two locations along the Colombian Pacific coast, of which 17 strains were identified as Vibrio: V. parahaemolyticus (n = 12), V. alginolyticus (n = 3), V. fluvialis (n = 1), and V. natriegens (n = 1). Whole genome sequence of these isolates was done using Oxford Nanopore Technologies (ONT). The analysis revealed the presence of genes conferring resistance to β-lactams, tetracyclines, chloramphenicol, and macrolides, indicating potential resistance to these antimicrobial agents. Genes associated with virulence were also found, suggesting the potential pathogenicity of these Vibrio isolates, as well as genes for Type III Secretion Systems (T3SS) and Type VI Secretion Systems (T6SS), which play crucial roles in delivering virulence factors and in interbacterial competition. This study represents the first genomic analysis of bacteria within A. tuberculosa, shedding light on Vibrio genetic factors and contributing to a comprehensive understanding of the pathogenic potential of these Vibrio isolates.IMPORTANCEThis study presents the first comprehensive report on the whole genome analysis of Vibrio isolates obtained from Anadara tuberculosa, a bivalve species of great significance for social and economic matters on the Pacific coast of Colombia. Research findings have significant implications for the field, as they provide crucial information on the genetic factors and possible pathogenicity of Vibrio isolates associated with A. tuberculosa. The identification of antimicrobial resistance genes and virulence factors within these isolates emphasizes the potential risks they pose to both human and animal health. Furthermore, the presence of genes associated with Type III and Type VI Secretion Systems suggests their critical role in virulence and interbacterial competition. Understanding the genetic factors that contribute to Vibrio bacterial virulence and survival strategies within their ecological niche is of utmost importance for the effective prevention and management of diseases in aquaculture practices.
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Affiliation(s)
- Mariana Restrepo-Benavides
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Daniela Lozano-Arce
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Laura Natalia Gonzalez-Garcia
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá, Colombia
- UMR DIADE, Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, France
| | - Felipe Báez-Aguirre
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Gabriela Ariza-Aranguren
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Daniel Faccini
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | | | - Pedro Jiménez
- Laboratorio de Fitopatología, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Ana Fernández-Bravo
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Silvia Restrepo
- Departamento de Ingeniería Química y de Alimentos, Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Marcela Guevara-Suarez
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
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8
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Wu S, Tang J, Wang B, Cai J, Jian J. Roles of Hcp2, a Hallmark of T6SS2 in Motility, Adhesive Capacity, and Pathogenicity of Vibrio alginolyticus. Microorganisms 2023; 11:2893. [PMID: 38138037 PMCID: PMC10745990 DOI: 10.3390/microorganisms11122893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
The type VI secretion system (T6SS) is a large secretory device, widely found in Gram-negative bacteria, which plays important roles in virulence, bacterial competition, and environmental adaptation. Vibrio alginolyticus (V. alginolyticus) is an opportunistic pathogen that causes vibriosis in aquaculture animals. V. alginolyticus possesses two type VI secretion systems (named the T6SS1 and T6SS2), but their functions remain largely unclear. In this paper, the roles of the core component of the T6SS2 cluster of V. alginolyticus HY9901, hemolysin-coregulated protein2 coding gene hcp2, are reported. Deletion of hcp2 clearly impaired the swarming motility, adhesive capacity, and pathogenicity of V. alginolyticus against zebrafish. Furthermore, transmission electron microscopy (TEM) found that the abnormal morphology of flagellum filament in the hcp2 mutant strain could be partially restored by hcp2 complementarity. By proteomic and RT-qPCR analysis, we confirmed that the expression levels of flagellar flagellin and assembly-associated proteins were remarkably decreased in an hcp2 mutant strain, compared with the wild-type strain, and could be partially restored with a supply of hcp2. Accordingly, hcp2 had a positive influence on the transcription of flagellar regulons rpoN, rpoS, and fliA; this was verified by RT-qPCR. Taken together, these results suggested that hcp2 was involved in mediating the motility, adhesion, and pathogenicity of Vibrio alginolyticus through positively impacting its flagellar system.
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Affiliation(s)
- Shuilong Wu
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
- Central People’s Hospital of Zhanjiang, Zhanjiang 524045, China
| | - Jufen Tang
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Bei Wang
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jia Cai
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jichang Jian
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
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9
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Cummins EA, Moran RA, Snaith AE, Hall RJ, Connor CH, Dunn SJ, McNally A. Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages. Microb Genom 2023; 9. [PMID: 37970873 DOI: 10.1099/mgen.0.001133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann E Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christopher H Connor
- Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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10
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Kanarek K, Fridman CM, Bosis E, Salomon D. The RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors. Nat Commun 2023; 14:4983. [PMID: 37591831 PMCID: PMC10435454 DOI: 10.1038/s41467-023-40659-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Bacteria use the type VI secretion system (T6SS) to deliver toxic effectors into bacterial or eukaryotic cells during interbacterial competition, host colonization, or when resisting predation. Identifying effectors is a challenging task, as they lack canonical secretion signals or universally conserved domains. Here, we identify a protein domain, RIX, that defines a class of polymorphic T6SS cargo effectors. RIX is widespread in the Vibrionaceae family and is located at N-termini of proteins containing diverse antibacterial and anti-eukaryotic toxic domains. We demonstrate that RIX-containing proteins are delivered via T6SS into neighboring cells and that RIX is necessary and sufficient for T6SS-mediated secretion. In addition, RIX-containing proteins can enable the T6SS-mediated delivery of other cargo effectors by a previously undescribed mechanism. The identification of RIX-containing proteins significantly enlarges the repertoire of known T6SS effectors, especially those with anti-eukaryotic activities. Furthermore, our findings also suggest that T6SSs may play an underappreciated role in the interactions between vibrios and eukaryotes.
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Affiliation(s)
- Katarzyna Kanarek
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chaya Mushka Fridman
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel.
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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11
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Singh RP, Kumari K. Bacterial type VI secretion system (T6SS): an evolved molecular weapon with diverse functionality. Biotechnol Lett 2023; 45:309-331. [PMID: 36683130 DOI: 10.1007/s10529-023-03354-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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12
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Type VI Secretion Systems: Environmental and Intra-host Competition of Vibrio cholerae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:41-63. [PMID: 36792870 DOI: 10.1007/978-3-031-22997-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Vibrio Type VI Secretion System (T6SS) is a harpoon-like nanomachine that serves as a defense system and is encoded by approximately 25% of all gram-negative bacteria. In this chapter, we describe the structure of the T6SS in different Vibrio species and outline how the use of different T6SS effector and immunity proteins control kin selection. We summarize the genetic loci that encode the structural elements that make up the Vibrio T6SSs and how these gene clusters are regulated. Finally, we provide insights into T6SS-based competitive dynamics, the role of T6SS genetic exchange in those competitive dynamics, and roles for the Vibrio T6SS in virulence.
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13
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Santoriello FJ, Kirchberger PC, Boucher Y, Pukatzki S. Pandemic Vibrio cholerae acquired competitive traits from an environmental Vibrio species. Life Sci Alliance 2023; 6:e202201437. [PMID: 36446527 PMCID: PMC9711863 DOI: 10.26508/lsa.202201437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
Vibrio cholerae is a human pathogen that thrives in estuarine environments. Within the environment and human host, V. cholerae uses the type VI secretion system (T6SS) to inject toxic effectors into neighboring microbes and to establish its replicative niche. V. cholerae strains encode a wide variety of horizontally shared effectors, but pandemic isolates encode an identical set of distinct effectors. Effector set retention in pandemic strains despite mobility between disparate strains suggests that horizontal acquisition of these effectors was crucial for evolving pandemic V. cholerae We attempted to locate the donor of the pandemic effectors to V. cholerae To this end, we identified potential gene transfer events of the pandemic-associated T6SS clusters between a fish pathogen, Vibrio anguillarum, and V. cholerae We supported the likelihood of interaction between these species by demonstrating that homologous effector-immunity pairs from V. cholerae and V. anguillarum can cross-neutralize one another. Thus, V. anguillarum constitutes an environmental reservoir of pandemic-associated V. cholerae T6SS effectors that may have initially facilitated competition between pre-pandemic V. cholerae and V. anguillarum for an environmental niche.
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Affiliation(s)
- Francis J Santoriello
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Biology, The City College of New York, New York, NY, USA
| | - Paul C Kirchberger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Yann Boucher
- Saw Swee Hock School of Public Health and National University Hospital System, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Hospital System, Singapore, Singapore
| | - Stefan Pukatzki
- Department of Biology, The City College of New York, New York, NY, USA
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Tchelet D, Keppel K, Bosis E, Salomon D. Vibrio parahaemolyticus T6SS2 effector repertoires. Gut Microbes 2023; 15:2178795. [PMID: 36803660 PMCID: PMC9980498 DOI: 10.1080/19490976.2023.2178795] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/07/2023] [Indexed: 02/23/2023] Open
Abstract
All strains of the marine bacterium Vibrio parahaemolyticus harbor a type VI secretion system (T6SS) named T6SS2, suggesting that this system plays an important role in the life cycle of this emerging pathogen. Although T6SS2 was recently shown to play a role in interbacterial competition, its effector repertoire remains unknown. Here, we employed proteomics to investigate the T6SS2 secretome of two V. parahaemolyticus strains, and we identified several antibacterial effectors encoded outside of the main T6SS2 gene cluster. We revealed two T6SS2-secreted proteins that are conserved in this species, indicating that they belong to the core secretome of T6SS2; other identified effectors are found only in subsets of strains, suggesting that they comprise an accessory effector arsenal of T6SS2. Remarkably, a conserved Rhs repeat-containing effector serves as a quality control checkpoint and is required for T6SS2 activity. Our results reveal effector repertoires of a conserved T6SS, including effectors that have no known activity and that have not been previously associated with T6SSs.
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Affiliation(s)
- Daniel Tchelet
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kinga Keppel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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15
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Zha F, Pang R, Huang S, Zhang J, Wang J, Chen M, Xue L, Ye Q, Wu S, Yang M, Gu Q, Ding Y, Zhang H, Wu Q. Evaluation of the pathogenesis of non-typical strain with α-hemolysin, Vibrio parahaemolyticus 353, isolated from Chinese seafood through comparative genome and transcriptome analysis. MARINE POLLUTION BULLETIN 2023; 186:114276. [PMID: 36437125 DOI: 10.1016/j.marpolbul.2022.114276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/21/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Vibrio parahaemolyticus outbreaks frequently occur, causing gastrointestinal sickness owing to the consumption of aquatic foods by various virulence factors; however, the mechanism of pathogenesis is still unknown. In this study, a non-typical strain of V. parahaemolyticus, named VP353, was isolated from shrimp in China. Its comparative genome and transcriptome after infection with Caco-2 cells were examined to illustrate the mechanisms of its pathogenesis. VP353 was a tdh-trh- strain but uncommonly manifested robust cytotoxicity towards Caco-2 cells. Compared with the standard strain RIMD2210633, VP353 harbored alpha-hemolysins (hlyA, hlyB, hlyC, and hlyD) was first reported in V. parahaemolyticus and showed high diversity in the T3SS2 gene cluster. Moreover, the expression of flagella, T2SS, quorum sensing-related genes, hlyA, hlyC were up-regulated, and hlyB, hlyD were down-regulated. In summary, our results demonstrate that some novel virulence factors contribute to the pathogenesis of V. parahaemolyticus infection.
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Affiliation(s)
- Fei Zha
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Shixuan Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Meiyan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Yu Ding
- Department of Food Science and Engineering, Institute of Food Safety & Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China.
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16
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Wang R, Xiao J, Wang Q, Zhao W, Liu X, Liu Y, Fu S. Genomic analysis of a new type VI secretion system in Vibrio parahaemolyticus and its implications for environmental adaptation in shrimp ponds. Can J Microbiol 2023; 69:53-61. [PMID: 36343341 DOI: 10.1139/cjm-2022-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The type VI secretion system (T6SS) in Vibrio spp. is often used to kill heteroclonal neighbors by direct injection of toxic effectors, but its strategies in aquacultural environments receive limited attention. In this study, we conducted genomic analysis for a T6SS-harboring plasmid in V. parahaemolyticus strain VP157. Coculture assays were further conducted to verify its antibacterial function. The results showed that strain VP157 harbored a 132-kb plasmid, pVP157-1, which consists of two fragments: an 87.8-kb fragment identical to plasmid pTJ114-1 and a 44.2-kb T6SS gene cluster with only 4% DNA identity to T6SS1 in the V. parahaemolyticus reference genome. Gene-by-gene analysis of six genes representing core T6SS components suggested that each gene has distinct evolutionary origins. In vitro experimental evolution revealed that pVP157-1 can excise from the VP157 genome with an excision rate of 4%. A coculture assay suggested that strain VP157 had significantly higher antibacterial activity against Bacillus pumilus and V. cholerae than the strain without pVP157-1(VP157∆T6SS). In contrast, a rapid decline was observed for the proportion of VP157∆ T6SS in a mock microbial community, which decreased from 10.7% to 2.1% in 5 days. The results highlighted that the acquisition of T6SS fostered the fitness of V . parahaemolyticus in a complex environment.
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Affiliation(s)
- Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China.,Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Ministry of Education, Dalian 116023, China
| | - Jinzhou Xiao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qingyao Wang
- Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Ministry of Education, Dalian 116023, China
| | - Wenyu Zhao
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Xinyue Liu
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Ministry of Education, Dalian 116023, China
| | - Songzhe Fu
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, Xi'an 710069, China
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Multiple T6SSs, Mobile Auxiliary Modules, and Effectors Revealed in a Systematic Analysis of the Vibrio parahaemolyticus Pan-Genome. mSystems 2022; 7:e0072322. [PMID: 36226968 PMCID: PMC9765294 DOI: 10.1128/msystems.00723-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Type VI secretion systems (T6SSs) play a major role in interbacterial competition and in bacterial interactions with eukaryotic cells. The distribution of T6SSs and the effectors they secrete vary between strains of the same bacterial species. Therefore, a pan-genome investigation is required to better understand the T6SS potential of a bacterial species of interest. Here, we performed a comprehensive, systematic analysis of T6SS gene clusters and auxiliary modules found in the pan-genome of Vibrio parahaemolyticus, an emerging pathogen widespread in marine environments. We identified 4 different T6SS gene clusters within genomes of this species; two systems appear to be ancient and widespread, whereas the other 2 systems are rare and appear to have been more recently acquired via horizontal gene transfer. In addition, we identified diverse T6SS auxiliary modules containing putative effectors with either known or predicted toxin domains. Many auxiliary modules are possibly horizontally shared between V. parahaemolyticus genomes, since they are flanked by DNA mobility genes. We further investigated a DUF4225-containing protein encoded on an Hcp auxiliary module, and we showed that it is an antibacterial T6SS effector that exerts its toxicity in the bacterial periplasm, leading to cell lysis. Computational analyses of DUF4225 revealed a widespread toxin domain associated with various toxin delivery systems. Taken together, our findings reveal a diverse repertoire of T6SSs and auxiliary modules in the V. parahaemolyticus pan-genome, as well as novel T6SS effectors and toxin domains that can play a major role in the interactions of this species with other cells. IMPORTANCE Gram-negative bacteria employ toxin delivery systems to mediate their interactions with neighboring cells. Vibrio parahaemolyticus, an emerging pathogen of humans and marine animals, was shown to deploy antibacterial toxins into competing bacteria via the type VI secretion system (T6SS). Here, we analyzed 1,727 V. parahaemolyticus genomes and revealed the pan-genome T6SS repertoire of this species, including the T6SS gene clusters, horizontally shared auxiliary modules, and toxins. We also identified a role for a previously uncharacterized domain, DUF4225, as a widespread antibacterial toxin associated with diverse toxin delivery systems.
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Abstract
Gram-negative bacteria often employ the type VI secretion system (T6SS) to deliver diverse cocktails of antibacterial effectors into rival bacteria. In many cases, even when the identity of the delivered effectors is known, their toxic activity and mechanism of secretion are not. Here, we investigate VPA1263, a Vibrio parahaemolyticus T6SS effector that belongs to a widespread class of polymorphic effectors containing a MIX domain. We reveal a C-terminal DNase toxin domain belonging to the HNH nuclease superfamily, and we show that it mediates the antibacterial toxicity of this effector during bacterial competition. Furthermore, we demonstrate that the VPA1263 MIX domain is necessary for T6SS-mediated secretion and intoxication of recipient bacteria. These results are the first indication of a functional role for MIX domains in T6SS secretion. IMPORTANCE Specialized protein delivery systems are used during bacterial competition to deploy cocktails of toxins that target conserved cellular components. Although numerous toxins have been revealed, the activity of many remains unknown. In this study, we investigated such a toxin from the pathogen Vibrio parahaemolyticus. Our findings indicate that the toxin employs a DNase domain to intoxicate competitors. We also show that a domain used as a marker for secreted toxins is required for secretion of the toxin via a type VI secretion system.
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19
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Skåne A, Edvardsen PK, Cordara G, Loose JSM, Leitl KD, Krengel U, Sørum H, Askarian F, Vaaje-Kolstad G. Chitinolytic enzymes contribute to the pathogenicity of Aliivibrio salmonicida LFI1238 in the invasive phase of cold-water vibriosis. BMC Microbiol 2022; 22:194. [PMID: 35941540 PMCID: PMC9361615 DOI: 10.1186/s12866-022-02590-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background Aliivibrio salmonicida is the causative agent of cold-water vibriosis in salmonids (Oncorhynchus mykiss and Salmo salar L.) and gadidae (Gadus morhua L.). Virulence-associated factors that are essential for the full spectrum of A. salmonicida pathogenicity are largely unknown. Chitin-active lytic polysaccharide monooxygenases (LPMOs) have been indicated to play roles in both chitin degradation and virulence in a variety of pathogenic bacteria but are largely unexplored in this context. Results In the present study we investigated the role of LPMOs in the pathogenicity of A. salmonicida LFI238 in Atlantic salmon (Salmo salar L.). In vivo challenge experiments using isogenic deletion mutants of the two LPMOs encoding genes AsLPMO10A and AsLPMO10B, showed that both LPMOs, and in particular AsLPMO10B, were important in the invasive phase of cold-water vibriosis. Crystallographic analysis of the AsLPMO10B AA10 LPMO domain (to 1.4 Å resolution) revealed high structural similarity to viral fusolin, an LPMO known to enhance the virulence of insecticidal agents. Finally, exposure to Atlantic salmon serum resulted in substantial proteome re-organization of the A. salmonicida LPMO deletion variants compared to the wild type strain, indicating the struggle of the bacterium to adapt to the host immune components in the absence of the LPMOs. Conclusion The present study consolidates the role of LPMOs in virulence and demonstrates that such enzymes may have more than one function.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02590-2.
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Affiliation(s)
- Anna Skåne
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Per Kristian Edvardsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gabriele Cordara
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Jennifer Sarah Maria Loose
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Kira Daryl Leitl
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Henning Sørum
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Fatemeh Askarian
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, San Diego, CA, USA.
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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Horizontal Transfer of Virulence Factors by Pathogenic Enterobacteria to Marine Saprotrophic Bacteria during Co-Cultivation in Biofilm. BIOTECH 2022; 11:biotech11020017. [PMID: 35822790 PMCID: PMC9264390 DOI: 10.3390/biotech11020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
Environmental problems associated with marine pollution and climate warming create favorable conditions for the penetration and survival of pathogenic bacteria in marine ecosystems. These microorganisms have interspecific competitive interactions with marine bacteria. Co-culture, as an important research strategy that mimics the natural environment of bacteria, can activate silent genes or clusters through interspecies interactions. The authors used modern biotechnology of co-cultivation to dynamically study intercellular interactions between different taxa of bacteria—pathogenic enterobacteria Yersinia pseudotuberculosis and Listeria monocytogenes and saprotrophic marine bacteria Bacillus sp. and Pseudomonas japonica isolated in summer from the coastal waters of the recreational areas of the Sea of Japan. The results of the experiments showed that during the formation of polycultural biofilms, horizontal transfer of genes encoding some pathogenicity factors from Y. pseudotuberculosis and L. monocytogenes to marine saprotrophic bacteria with different secretion systems is possible. It was previously thought that this was largely prevented by the type VI secretion system (T6SS) found in marine saprotrophic bacteria. The authors showed for the first time the ability of marine bacteria Bacillus sp. and P. japonica to biofilm formation with pathogenic enterobacteria Y. pseudotuberculosis and L. monocytogenes, saprophytic bacteria with type III secretion system (T3SS). For the first time, a marine saprotrophic strain of Bacillus sp. Revealed manifestations of hyaluronidase, proteolytic and hemolytic activity after cultivation in a polycultural biofilm with listeria. Saprotrophic marine bacteria that have acquired virulence factors from pathogenic enterobacteria, including antibiotic resistance genes, could potentially play a role in altering the biological properties of other members of the marine microbial community. In addition, given the possible interdomain nature of intercellular gene translocation, acquired virulence factors can be transferred to marine unicellular and multicellular eukaryotes. The results obtained contribute to the paradigm of the epidemiological significance and potential danger of anthropogenic pollution of marine ecosystems, which creates serious problems for public health and the development of marine culture as an important area of economic activity in coastal regions.
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Unni R, Pintor KL, Diepold A, Unterweger D. Presence and absence of type VI secretion systems in bacteria. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35467500 DOI: 10.1099/mic.0.001151] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.
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Affiliation(s)
- Rahul Unni
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105 Kiel, Germany
| | - Katherine L Pintor
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniel Unterweger
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105 Kiel, Germany
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22
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Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N. Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas. Front Microbiol 2022; 13:840308. [PMID: 35495725 PMCID: PMC9048695 DOI: 10.3389/fmicb.2022.840308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) present in many Gram-negative bacteria is a contact-dependent apparatus that can directly deliver secreted effectors or toxins into diverse neighboring cellular targets including both prokaryotic and eukaryotic organisms. Recent reverse genetics studies with T6 core gene loci have indicated the importance of functional T6SS toward overall competitive fitness in various pathogenic Xanthomonas spp. To understand the contribution of T6SS toward ecology and evolution of Xanthomonas spp., we explored the distribution of the three distinguishable T6SS clusters, i3*, i3***, and i4, in approximately 1,740 Xanthomonas genomes, along with their conservation, genetic organization, and their evolutionary patterns in this genus. Screening genomes for core genes of each T6 cluster indicated that 40% of the sequenced strains possess two T6 clusters, with combinations of i3*** and i3* or i3*** and i4. A few strains of Xanthomonas citri, Xanthomonas phaseoli, and Xanthomonas cissicola were the exception, possessing a unique combination of i3* and i4. The findings also indicated clade-specific distribution of T6SS clusters. Phylogenetic analysis demonstrated that T6SS clusters i3* and i3*** were probably acquired by the ancestor of the genus Xanthomonas, followed by gain or loss of individual clusters upon diversification into subsequent clades. T6 i4 cluster has been acquired in recent independent events by group 2 xanthomonads followed by its spread via horizontal dissemination across distinct clades across groups 1 and 2 xanthomonads. We also noted reshuffling of the entire core T6 loci, as well as T6SS spike complex components, hcp and vgrG, among different species. Our findings indicate that gain or loss events of specific T6SS clusters across Xanthomonas phylogeny have not been random.
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Affiliation(s)
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
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23
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Dar Y, Jana B, Bosis E, Salomon D. A binary effector module secreted by a type VI secretion system. EMBO Rep 2022; 23:e53981. [PMID: 34752000 PMCID: PMC8728615 DOI: 10.15252/embr.202153981] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/22/2023] Open
Abstract
Gram-negative bacteria use type VI secretion systems (T6SSs) to deliver toxic effector proteins into neighboring cells. Cargo effectors are secreted by binding noncovalently to the T6SS apparatus. Occasionally, effector secretion is assisted by an adaptor protein, although the adaptor itself is not secreted. Here, we report a new T6SS secretion mechanism, in which an effector and a co-effector are secreted together. Specifically, we identify a novel periplasm-targeting effector that is secreted together with its co-effector, which contains a MIX (marker for type sIX effector) domain previously reported only in polymorphic toxins. The effector and co-effector directly interact, and they are dependent on each other for secretion. We term this new secretion mechanism "a binary effector module," and we show that it is widely distributed in marine bacteria.
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Affiliation(s)
- Yasmin Dar
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Biswanath Jana
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Eran Bosis
- Department of Biotechnology EngineeringORT Braude College of EngineeringKarmielIsrael
| | - Dor Salomon
- Department of Clinical Microbiology and ImmunologySackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
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24
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Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
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Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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25
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Gallegos-Monterrosa R, Coulthurst SJ. The ecological impact of a bacterial weapon: microbial interactions and the Type VI secretion system. FEMS Microbiol Rev 2021; 45:fuab033. [PMID: 34156081 PMCID: PMC8632748 DOI: 10.1093/femsre/fuab033] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria inhabit all known ecological niches and establish interactions with organisms from all kingdoms of life. These interactions are mediated by a wide variety of mechanisms and very often involve the secretion of diverse molecules from the bacterial cells. The Type VI secretion system (T6SS) is a bacterial protein secretion system that uses a bacteriophage-like machinery to secrete a diverse array of effectors, usually translocating them directly into neighbouring cells. These effectors display toxic activity in the recipient cell, making the T6SS an effective weapon during inter-bacterial competition and interactions with eukaryotic cells. Over the last two decades, microbiology research has experienced a shift towards using systems-based approaches to study the interactions between diverse organisms and their communities in an ecological context. Here, we focus on this aspect of the T6SS. We consider how our perspective of the T6SS has developed and examine what is currently known about the impact that bacteria deploying the T6SS can have in diverse environments, including niches associated with plants, insects and mammals. We consider how T6SS-mediated interactions can affect host organisms by shaping their microbiota, as well as the diverse interactions that can be established between different microorganisms through the deployment of this versatile secretion system.
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Affiliation(s)
| | - Sarah J Coulthurst
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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26
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Jana B, Keppel K, Salomon D. Engineering a customizable antibacterial T6SS-based platform in Vibrio natriegens. EMBO Rep 2021; 22:e53681. [PMID: 34494702 PMCID: PMC8567230 DOI: 10.15252/embr.202153681] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 01/22/2023] Open
Abstract
Bacterial pathogens are a major risk to human, animal, and plant health. To counteract the spread of antibiotic resistance, alternative antibacterial strategies are urgently needed. Here, we construct a proof‐of‐concept customizable, modular, and inducible antibacterial toxin delivery platform. By engineering a type VI secretion system (T6SS) that is controlled by an externally induced on/off switch, we transform the safe bacterium, Vibrio natriegens, into an effective antibacterial weapon. Furthermore, we demonstrate that the delivered effector repertoire, and thus the toxicity range of this platform, can be easily manipulated and tested. We believe that this platform can serve as a foundation for novel antibacterial bio‐treatments, as well as a unique tool to study antibacterial toxins.
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Affiliation(s)
- Biswanath Jana
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kinga Keppel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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27
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Wu CF, Weisberg AJ, Davis EW, Chou L, Khan S, Lai EM, Kuo CH, Chang JH. Diversification of the Type VI Secretion System in Agrobacteria. mBio 2021; 12:e0192721. [PMID: 34517758 PMCID: PMC8546570 DOI: 10.1128/mbio.01927-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022] Open
Abstract
The type VI secretion system (T6SS) is used by many Gram-negative bacteria to deploy toxic effectors for interbacterial competition. This system provides a competitive advantage in planta to agrobacteria, a diverse group with phytopathogenic members capable of genetically transforming plants. To inform on the ecology and evolution of agrobacteria, we revealed processes that diversify their effector gene collections. From genome sequences of diverse strains, we identified T6SS loci, functionally validated associated effector genes for toxicity, and predicted genes homologous to those that encode proteins known to interact with effectors. The gene loci were analyzed in a phylogenetic framework, and results show that strains of some species-level groups have different patterns of T6SS expression and are enriched in specific sets of T6SS loci. Findings also demonstrate that the modularity of T6SS loci and their associated genes engenders dynamicity, promoting reshuffling of entire loci, fragments therein, and domains to swap toxic effector genes across species. However, diversification is constrained by the need to maintain specific combinations of gene subtypes, congruent with observations that certain genes function together to regulate T6SS loading and activation. Data are consistent with a scenario where species can acquire unique T6SS loci that are then reshuffled across the genus in a restricted manner to generate new combinations of effector genes. IMPORTANCE The T6SS is used by several taxa of Gram-negative bacteria to secrete toxic effector proteins to attack others. Diversification of effector collections shapes bacterial interactions and impacts the health of hosts and ecosystems in which bacteria reside. We uncovered the diversity of T6SS loci across a genus of plant-associated bacteria and show that diversification is driven by the acquisition of new loci and reshuffling among species. However, linkages between specific subtypes of genes need to be maintained to ensure that proteins whose interactions are necessary to activate the T6SS remain together. Results reveal how organization of gene loci and domain structure of genes provides flexibility to diversify under the constraints imposed by the system. Findings inform on the evolution of a mechanism that influences bacterial communities.
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Affiliation(s)
- Chih-Feng Wu
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, USA
| | - Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Surtaz Khan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
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28
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Janecko N, Bloomfield SJ, Palau R, Mather AE. Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail. Microb Genom 2021; 7. [PMID: 34586050 PMCID: PMC8715430 DOI: 10.1099/mgen.0.000647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Consumption of prawns as a protein source has been on the rise worldwide with seafood identified as the predominant attributable source of human vibriosis. However, surveillance of non-cholera Vibrio is limited both in public health and in food. Using a population- and market share-weighted study design, 211 prawn samples were collected and cultured for Vibrio spp. Contamination was detected in 46 % of samples, and multiple diverse Vibrio isolates were obtained from 34 % of positive samples. Whole genome sequencing (WGS) and phylogenetic analysis illustrated a comprehensive view of Vibrio species diversity in prawns available at retail, with no known pathogenicity markers identified in Vibrio parahaemolyticus and V. cholerae. Antimicrobial resistance genes were found in 77 % of isolates, and 12 % carried genes conferring resistance to three or more drug classes. Resistance genes were found predominantly in V. parahaemolyticus, though multiple resistance genes were also identified in V. cholerae and V. vulnificus. This study highlights the large diversity in Vibrio derived from prawns at retail, even within a single sample. Although there was little evidence in this study that prawns are a major source of vibriosis in the UK, surveillance of non-cholera Vibrio is very limited. This study illustrates the value of expanding WGS surveillance efforts of non-cholera Vibrios in the food chain to identify critical control points for food safety through the production system and to determine the full extent of the public health impact.
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Affiliation(s)
- Nicol Janecko
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | | | - Raphaëlle Palau
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.,Faculty of Medicine and Health Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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29
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Defending against the Type Six Secretion System: beyond Immunity Genes. Cell Rep 2021; 33:108259. [PMID: 33053336 DOI: 10.1016/j.celrep.2020.108259] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/10/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
The bacterial type six secretion system (T6SS) delivers toxic effector proteins into neighboring cells, but bacteria must protect themselves against their own T6SS. Immunity genes are the best-characterized defenses, protecting against specific cognate effectors. However, the prevalence of the T6SS and the coexistence of species with heterologous T6SSs suggest evolutionary pressure selecting for additional defenses against it. Here we review defenses against the T6SS beyond self-associated immunity genes, such as diverse stress responses that can recognize T6SS-inflicted damage and coordinate induction of molecular armor, repair pathways, and overall survival. Some of these stress responses are required for full survival even in the presence of immunity genes. Finally, we propose that immunity gene-independent protection is, mechanistically, bacterial innate immunity and that such defenses and the T6SS have co-evolved and continue to shape one another in polymicrobial communities.
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30
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Abstract
Genetic editing has revolutionized biotechnology, but delivery of endonuclease genes as DNA can lead to aberrant integration or overexpression, leading to off-target effects. Here, we develop a mechanism to deliver Cre recombinase as a protein by engineering the bacterial type six secretion system (T6SS). Using multiple T6SS fusion proteins, Aeromonas dhakensis or attenuated Vibrio cholerae donor strains, and a gain-of-function cassette for detecting Cre recombination, we demonstrate successful delivery of active Cre directly into recipient cells. The most efficient transfer was achieved using a truncated version of PAAR2 from V. cholerae, resulting in a relatively small (118-amino-acid) delivery tag. We further demonstrate the versatility of this system by delivering an exogenous effector, TseC, enabling V. cholerae to kill Pseudomonas aeruginosa. This implies that P. aeruginosa is naturally resistant to all native effectors of V. cholerae and that the TseC chaperone protein is not required for its activity. Moreover, it demonstrates that the engineered system can improve T6SS efficacy against specific pathogens, proposing future application in microbiome manipulation or as a next-generation antimicrobial. Inexpensive and easy to produce, this protein delivery system has many potential applications, ranging from studying T6SS effectors to genetic editing.
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31
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Drebes Dörr NC, Blokesch M. Interbacterial competition and anti-predatory behaviour of environmental Vibrio cholerae strains. Environ Microbiol 2020; 22:4485-4504. [PMID: 32885535 PMCID: PMC7702109 DOI: 10.1111/1462-2920.15224] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae isolates responsible for cholera pandemics represent only a small portion of the diverse strains belonging to this species. Indeed, most V. cholerae are encountered in aquatic environments. To better understand the emergence of pandemic lineages, it is crucial to discern what differentiates pandemic strains from their environmental relatives. Here, we studied the interaction of environmental V. cholerae with eukaryotic predators or competing bacteria and tested the contributions of the haemolysin and the type VI secretion system (T6SS) to those interactions. Both of these molecular weapons are constitutively active in environmental isolates but subject to tight regulation in the pandemic clade. We showed that several environmental isolates resist amoebal grazing and that this anti‐grazing defense relies on the strains' T6SS and its actincross‐linking domain (ACD)‐containing tip protein. Strains lacking the ACD were unable to defend themselves against grazing amoebae but maintained high levels of T6SS‐dependent interbacterial killing. We explored the latter phenotype through whole‐genome sequencing of 14 isolates, which unveiled a wide array of novel T6SS effector and (orphan) immunity proteins. By combining these in silico predictions with experimental validations, we showed that highly similar but non‐identical immunity proteins were insufficient to provide cross‐immunity among those wild strains.
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Affiliation(s)
- Natália C Drebes Dörr
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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32
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Peng J, Lelis T, Chen R, Barphagha I, Osti S, Ham JH. tepR encoding a bacterial enhancer-binding protein orchestrates the virulence and interspecies competition of Burkholderia glumae through qsmR and a type VI secretion system. MOLECULAR PLANT PATHOLOGY 2020; 21:1042-1054. [PMID: 32608174 PMCID: PMC7368122 DOI: 10.1111/mpp.12947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/23/2020] [Accepted: 05/04/2020] [Indexed: 05/05/2023]
Abstract
The pathogenesis of the rice pathogenic bacterium Burkholderia glumae is under the tight regulation of the tofI/tofR quorum-sensing (QS) system. tepR, encoding a group I bacterial enhancer-binding protein, negatively regulates the production of toxoflavin, the phytotoxin acting as a major virulence factor in B. glumae. In this study, through a transcriptomic analysis, we identified the genes that were modulated by tepR and/or the tofI/tofR QS system. More than half of the differentially expressed genes, including the genes for the biosynthesis and transport of toxoflavin, were significantly more highly expressed in the ΔtepR mutant but less expressed in the ΔtofI-tofR (tofI/tofR QS-defective) mutant. In consonance with the transcriptome data, other virulence-related functions of B. glumae, extracellular protease activity and flagellum-dependent motility, were also negatively regulated by tepR, and this negative regulatory function of tepR was dependent on the IclR-type transcriptional regulator gene qsmR. Likewise, the ΔtepR mutant exhibited a higher level of heat tolerance in congruence with the higher transcription levels of heat shock protein genes in the mutant. Interestingly, tepR also exhibited its positive regulatory function on a previously uncharacterized type VI secretion system (denoted as BgT6SS-1). The survival of the both ΔtepR and ΔtssD (BgT6SS-1-defective) mutants was significantly compromised compared to the wild-type parent strain 336gr-1 in the presence of the natural rice-inhabiting bacterium, Pantoea sp. RSPAM1. Taken together, this study revealed pivotal regulatory roles of tepR in orchestrating multiple biological functions of B. glumae, including pathogenesis, heat tolerance, and bacterial interspecies competition.
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Affiliation(s)
- Jingyu Peng
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMI48824USA
| | - Tiago Lelis
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Tropical Research and Education CenterInstitute of Food and Agriculture SciencesUniversity of FloridaHomesteadFLUSA
| | - Ruoxi Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
1501 Capitol AvenueSacramentoCA95814USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Surendra Osti
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Agricultural Economics and AgribusinessLouisiana State UniversityBaton RougeLA70803USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
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33
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Marasini D, Karki AB, Bryant JM, Sheaff RJ, Fakhr MK. Molecular characterization of megaplasmids encoding the type VI secretion system in Campylobacter jejuni isolated from chicken livers and gizzards. Sci Rep 2020; 10:12514. [PMID: 32719325 PMCID: PMC7385129 DOI: 10.1038/s41598-020-69155-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
Megaplasmids in Campylobacter spp. likely play important roles in antibiotic resistance, virulence, and horizontal gene transfer. In this study, megaplasmids pCJDM202 (119 kb) and pCJDM67L (116 kb) from C. jejuni strains WP2-202 and OD2-67, respectively, were sequenced and characterized. These megaplasmids contained genes for tetracycline resistance [tet(O)], the Type IV secretion system, conjugative transfer and the Type VI secretion system (T6SS). The T6SS genes in Campylobacter plasmids encoded genes and proteins that were similar to those identified in Campylobacter chromosomal DNA. When the megaplasmid pCJDM202 from C. jejuni WP2-202 was transferred via conjugation to C. jejuni NCTC11168 Nal+, transconconjugants acquired tetracycline resistance and enhanced cytotoxicity towards red blood cells. A T6SS mutant of strain WP2-202 was generated and designated Δhcp3; the mutant was significantly impaired in its ability to lyse red blood cells and survive in defibrinated blood. The cytotoxicity of Campylobacter strains towards the human embryonic kidney cell line HEK 293 was not impacted by the T6SS. In summary, the T6SS encoded by Campylobacter megaplasmids mediates lysis of RBCs and likely contributes to survival on retail meats where blood cells are abundant.
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Affiliation(s)
- Daya Marasini
- Department of Biological Science, The University of Tulsa, Tulsa, OK, USA
| | - Anand B Karki
- Department of Biological Science, The University of Tulsa, Tulsa, OK, USA
| | - John M Bryant
- Department of Biological Science, The University of Tulsa, Tulsa, OK, USA
| | - Robert J Sheaff
- Department of Chemistry and Biochemistry, The University of Tulsa, Tulsa, OK, USA
| | - Mohamed K Fakhr
- Department of Biological Science, The University of Tulsa, Tulsa, OK, USA.
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34
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Ruhe ZC, Low DA, Hayes CS. Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery. Annu Rev Microbiol 2020; 74:497-520. [PMID: 32680451 DOI: 10.1146/annurev-micro-020518-115638] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often deploy closely related toxin domains. Thus, diverse competition systems are linked through a common reservoir of toxin-immunity pairs that is shared via horizontal gene transfer. These toxin-immunity protein pairs are extraordinarily diverse in sequence, and this polymorphism underpins an important mechanism of self/nonself discrimination in bacteria. This review focuses on the structures, functions, and delivery mechanisms of polymorphic toxin effectors that mediate bacterial competition.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
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35
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Hubert CL, Michell SL. A universal oyster infection model demonstrates that
Vibrio vulnificus
Type 6
secretion systems have antibacterial activity
in vivo. Environ Microbiol 2020; 22:4381-4393. [DOI: 10.1111/1462-2920.15123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Cameron L. Hubert
- College of Life and Environmental Sciences University of Exeter Exeter EX4 4QD UK
| | - Stephen Ll. Michell
- College of Life and Environmental Sciences University of Exeter Exeter EX4 4QD UK
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36
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Chien CF, Liu CY, Lu YY, Sung YH, Chen KY, Lin NC. HSI-II Gene Cluster of Pseudomonas syringae pv. tomato DC3000 Encodes a Functional Type VI Secretion System Required for Interbacterial Competition. Front Microbiol 2020; 11:1118. [PMID: 32582082 PMCID: PMC7283901 DOI: 10.3389/fmicb.2020.01118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/05/2020] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread bacterial nanoweapon used for delivery of toxic proteins into cell targets and contributes to virulence, anti-inflammatory processes, and interbacterial competition. In the model phytopathogenic bacterium Pseudomonas syringae pv. tomato (Pst) DC3000, two T6SS gene clusters, HSI-I and HSI-II, were identified, but their functions remain unclear. We previously reported that hcp2, located in HSI-II, is involved in competition with enterobacteria and yeast. Here, we demonstrated that interbacterial competition of Pst DC3000 against several Gram-negative plant-associated bacteria requires mainly HSI-II activity. By means of a systematic approach using in-frame deletion mutants for each gene in the HSI-II cluster, we identified genes indispensable for Hcp2 expression, Hcp2 secretion and interbacterial competition ability. Deletion of PSPTO_5413 only affected growth in interbacterial competition assays but not Hcp2 secretion, which suggests that PSPTO_5413 might be a putative effector. Moreover, PSPTO_5424, encoding a putative σ54-dependent transcriptional regulator, positively regulated the expression of all three operons in HSI-II. Our discovery that the HSI-II gene cluster gives Pst DC3000 the ability to compete with other plant-associated bacteria could help in understanding a possible mechanism of how phytopathogenic bacteria maintain their ecological niches.
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Affiliation(s)
- Ching-Fang Chien
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Cheng-Ying Liu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yew-Yee Lu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - You-Hsing Sung
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Kuo-Yau Chen
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Nai-Chun Lin
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
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37
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Pei TT, Li H, Liang X, Wang ZH, Liu G, Wu LL, Kim H, Xie Z, Yu M, Lin S, Xu P, Dong TG. Intramolecular chaperone-mediated secretion of an Rhs effector toxin by a type VI secretion system. Nat Commun 2020; 11:1865. [PMID: 32313027 PMCID: PMC7170923 DOI: 10.1038/s41467-020-15774-z] [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: 10/26/2019] [Accepted: 03/27/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial Rhs proteins containing toxic domains are often secreted by type VI secretion systems (T6SSs) through unclear mechanisms. Here, we show that the T6SS Rhs-family effector TseI of Aeromonas dhakensis is subject to self-cleavage at both the N- and the C-terminus, releasing the middle Rhs core and two VgrG-interacting domains (which we name VIRN and VIRC). VIRC is an endonuclease, and the immunity protein TsiI protects against VIRC toxicity through direct interaction. Proteolytic release of VIRC and VIRN is mediated, respectively, by an internal aspartic protease activity and by two conserved glutamic residues in the Rhs core. Mutations abolishing self-cleavage do not block secretion, but reduce TseI toxicity. Deletion of VIRN or the Rhs core abolishes secretion. TseI homologs from Pseudomonas syringae, P. aeruginosa, and Vibrio parahaemolyticus are also self-cleaved. VIRN and VIRC interact with protein VgrG1, while the Rhs core interacts with protein TecI. We propose that VIRN and the Rhs core act as T6SS intramolecular chaperones to facilitate toxin secretion and function.
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Affiliation(s)
- Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaoye Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.,Department of Ecosystem and Public Health, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N4Z6, Canada
| | - Zeng-Hang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Li-Li Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Haeun Kim
- Department of Ecosystem and Public Health, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N4Z6, Canada
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Ming Yu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Tao G Dong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China. .,Department of Ecosystem and Public Health, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N4Z6, Canada.
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38
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A comparative genomics methodology reveals a widespread family of membrane-disrupting T6SS effectors. Nat Commun 2020; 11:1085. [PMID: 32109231 PMCID: PMC7046647 DOI: 10.1038/s41467-020-14951-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 01/01/2023] Open
Abstract
Gram-negative bacteria deliver effectors via the type VI secretion system (T6SS) to outcompete their rivals. Each bacterial strain carries a different arsenal of effectors; the identities of many remain unknown. Here, we present an approach to identify T6SS effectors encoded in bacterial genomes of interest, without prior knowledge of the effectors’ domain content or genetic neighborhood. Our pipeline comprises a comparative genomics analysis followed by screening using a surrogate T6SS+ strain. Using this approach, we identify an antibacterial effector belonging to the T6SS1 of Vibrio parahaemolyticus, representing a widespread family of T6SS effectors sharing a C-terminal domain that we name Tme (Type VI membrane-disrupting effector). Tme effectors function in the periplasm where they intoxicate bacteria by disrupting membrane integrity. We believe our approach can be scaled up to identify additional T6SS effectors in various bacterial genera. Gram-negative bacteria deliver effectors via the type VI secretion system (T6SS) to outcompete their rivals. Here, Fridman et al. present an approach to identify T6SS effectors encoded in bacterial genomes without prior knowledge of their domain content or genetic neighbourhood, and identify a new family of membrane-disrupting effectors.
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39
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Guillemette R, Ushijima B, Jalan M, Häse CC, Azam F. Insight into the resilience and susceptibility of marine bacteria to T6SS attack by Vibrio cholerae and Vibrio coralliilyticus. PLoS One 2020; 15:e0227864. [PMID: 31990915 PMCID: PMC6986712 DOI: 10.1371/journal.pone.0227864] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/31/2019] [Indexed: 11/19/2022] Open
Abstract
The type VI secretion system (T6SS) is a nanomachine capable of killing adjacent microbial cells in a contact-dependent manner. Due to limited studies, relatively little is known about the range of marine bacteria that are susceptible to T6SS attack. Here, 15 diverse marine bacterial isolates from the phyla Bacteroidetes and Ɣ-Proteobacteria were challenged against the marine bacterium and human pathogen, Vibrio cholerae, which has a well described T6SS. V. cholerae killed several of the tested Ɣ-Proteobacteria, including members of the orders Vibrionales, Alteromonadales, Oceanospirillales, and Pseudomonadales. In contrast, V. cholerae co-existed with multiple Bacteroidetes and Ɣ-Proteobacteria isolates, but was killed by Vibrio coralliilyticus. Follow-up experiments revealed that five V. coralliilyticus strains, including known coral and shellfish pathogens survived the T6SS challenge and killed V. cholerae. By using predicted protein comparisons and mutagenesis, we conclude that V. coralliilyticus protected itself in the challenge by using its own T6SS to kill V. cholerae. This study provides valuable insight into the resilience and susceptibility of marine bacteria to the V. cholerae T6SS, and provides the first evidence for a functional T6SS in V. coralliilyticus, both of which have implications for human and ocean health.
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Affiliation(s)
- Ryan Guillemette
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Blake Ushijima
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Mihika Jalan
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Claudia C. Häse
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Farooq Azam
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, San Diego, CA, United States of America
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40
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Jana B, Salomon D. Type VI secretion system: a modular toolkit for bacterial dominance. Future Microbiol 2019; 14:1451-1463. [DOI: 10.2217/fmb-2019-0194] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria use toxin delivery systems, such as the type VI secretion system (T6SS), to antagonize competitors. The T6SS transports toxins, called effectors, directly into recipient cells. In the absence of cognate immunity proteins that protect against kin-intoxication, these effectors target conserved and essential cell components resulting in growth arrest or cell death. Here, we focus on antibacterial T6SS effectors and explore their different activities, modes of delivery, and the domains and proteins that are associated with them to provide a modular and dynamic toxin arsenal. We conclude that these natural machines present a lucrative pool and platform for future antibacterial treatments.
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Affiliation(s)
- Biswanath Jana
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dor Salomon
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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41
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Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T. Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinformatics 2019; 34:2546-2555. [PMID: 29547915 DOI: 10.1093/bioinformatics/bty155] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022] Open
Abstract
Motivation Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data. Results We extracted a wide range of features from T6SE protein sequences and comprehensively analyzed the prediction performance of these features through unsupervised and supervised learning. By integrating these features, we subsequently developed a two-layer SVM-based ensemble model with fine-grain optimized parameters, to identify potential T6SEs. We further validated the predictive model using an independent dataset, which showed that the proposed model achieved an impressive performance in terms of ACC (0.943), F-value (0.946), MCC (0.892) and AUC (0.976). To demonstrate applicability, we employed this method to correctly identify two very recently validated T6SE proteins, which represent challenging prediction targets because they significantly differed from previously known T6SEs in terms of their sequence similarity and cellular function. Furthermore, a genome-wide prediction across 12 bacterial species, involving in total 54 212 protein sequences, was carried out to distinguish 94 putative T6SE candidates. We envisage both this information and our publicly accessible web server will facilitate future discoveries of novel T6SEs. Availability and implementation http://bastion6.erc.monash.edu/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiawei Wang
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Bingjiao Yang
- Bioinformatics Group, School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tatiana T Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Morihiro Hayashida
- National Institute of Technology, Matsue College, Matsue, Shimane, Japan
| | - Andrea Rocker
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Yanju Zhang
- Bioinformatics Group, School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard A Strugnell
- Department of Microbiology and Immunology and Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology.,Monash Centre for Data Science, Faculty of Information Technolog, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Trevor Lithgow
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
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42
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Jana B, Fridman CM, Bosis E, Salomon D. A modular effector with a DNase domain and a marker for T6SS substrates. Nat Commun 2019; 10:3595. [PMID: 31399579 PMCID: PMC6688995 DOI: 10.1038/s41467-019-11546-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteria deliver toxic effectors via type VI secretion systems (T6SSs) to dominate competitors, but the identity and function of many effectors remain unknown. Here we identify a Vibrio antibacterial T6SS effector that contains a previously undescribed, widespread DNase toxin domain that we call PoNe (Polymorphic Nuclease effector). PoNe belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. In addition to PoNe, the effector contains a domain of unknown function (FIX domain) that is also found N-terminal to known toxin domains and is genetically and functionally linked to T6SS. FIX sequences can be used to identify T6SS effector candidates with potentially novel toxin domains. Our findings underline the modular nature of bacterial effectors harboring delivery or marker domains, specific to a secretion system, fused to interchangeable toxins. Bacteria deliver toxic effectors via type VI secretion systems (T6SSs) to dominate competitors. Here, the authors identify a Vibrio antibacterial effector that contains a new DNase toxin domain and a domain of unknown function that can be used as a marker to identify new T6SS effectors.
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Affiliation(s)
- Biswanath Jana
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Chaya M Fridman
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, 2161002, Karmiel, Israel.
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.
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43
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Metzger LC, Matthey N, Stoudmann C, Collas EJ, Blokesch M. Ecological implications of gene regulation by TfoX and TfoY among diverse Vibrio species. Environ Microbiol 2019; 21:2231-2247. [PMID: 30761714 PMCID: PMC6618264 DOI: 10.1111/1462-2920.14562] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/16/2019] [Accepted: 02/10/2019] [Indexed: 01/26/2023]
Abstract
Bacteria of the genus Vibrio are common members of aquatic environments where they compete with other prokaryotes and defend themselves against grazing predators. A macromolecular protein complex called the type VI secretion system (T6SS) is used for both purposes. Previous research showed that the sole T6SS of the human pathogen V. cholerae is induced by extracellular (chitin) or intracellular (low c‐di‐GMP levels) cues and that these cues lead to distinctive signalling pathways for which the proteins TfoX and TfoY serve as master regulators. In this study, we tested whether the TfoX‐ and TfoY‐mediated regulation of T6SS, concomitantly with natural competence or motility, was conserved in non‐cholera Vibrio species, and if so, how these regulators affected the production of individual T6SSs in double‐armed vibrios. We show that, alongside representative competence genes, TfoX regulates at least one T6SS in all tested Vibrio species. TfoY, on the other hand, fostered motility in all vibrios but had a more versatile T6SS response in that it did not foster T6SS‐mediated killing in all tested vibrios. Collectively, our data provide evidence that the TfoX‐ and TfoY‐mediated signalling pathways are mostly conserved in diverse Vibrio species and important for signal‐specific T6SS induction.
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Affiliation(s)
- Lisa C Metzger
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Noémie Matthey
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Candice Stoudmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Esther J Collas
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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44
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Vonaesch P, Anderson M, Sansonetti PJ. Pathogens, microbiome and the host: emergence of the ecological Koch's postulates. FEMS Microbiol Rev 2018; 42:273-292. [PMID: 29325027 DOI: 10.1093/femsre/fuy003] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Indexed: 02/07/2023] Open
Abstract
Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the 'traditional Koch's postulates', which state that a given pathogen leads to a distinct disease, are not valid for all 'infectious' diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term 'ecological Koch's postulates'.
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Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| | - Mark Anderson
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
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45
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Dar Y, Salomon D, Bosis E. The Antibacterial and Anti-Eukaryotic Type VI Secretion System MIX-Effector Repertoire in Vibrionaceae. Mar Drugs 2018; 16:md16110433. [PMID: 30400344 PMCID: PMC6267618 DOI: 10.3390/md16110433] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
Vibrionaceae is a widespread family of aquatic bacteria that includes emerging pathogens and symbionts. Many Vibrionaceae harbor a type VI secretion system (T6SS), which is a secretion apparatus used to deliver toxins, termed effectors, into neighboring cells. T6SSs mediate both antibacterial and anti-eukaryotic activities. Notably, antibacterial effectors are encoded together with a gene that encodes a cognate immunity protein so as to antagonize the toxicity of the effector. The MIX (Marker for type sIX effectors) domain has been previously defined as a marker of T6SS effectors carrying polymorphic C-terminal toxins. Here, we set out to identify the Vibrionaceae MIX-effector repertoire and to analyze the various toxin domains they carry. We used a computational approach to search for the MIX-effectors in the Vibrionaceae genomes, and grouped them into clusters based on the C-terminal toxin domains. We classified MIX-effectors as either antibacterial or anti-eukaryotic, based on the presence or absence of adjacent putative immunity genes, respectively. Antibacterial MIX-effectors carrying pore-forming, phospholipase, nuclease, peptidoglycan hydrolase, and protease activities were found. Furthermore, we uncovered novel virulence MIX-effectors. These are encoded by “professional MIXologist” strains that employ a cocktail of antibacterial and anti-eukaryotic MIX-effectors. Our findings suggest that certain Vibrionaceae adapted their antibacterial T6SS to mediate interactions with eukaryotic hosts or predators.
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Affiliation(s)
- Yasmin Dar
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel.
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46
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Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host. Proc Natl Acad Sci U S A 2018; 115:E8528-E8537. [PMID: 30127013 PMCID: PMC6130350 DOI: 10.1073/pnas.1808302115] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Competition among cooccurring bacteria can change the structure and function of a microbial community. However, little is known about the molecular mechanisms that impact such interactions in vivo. We used the association between bioluminescent bacteria and their squid host to study how environmentally transmitted bacteria compete for a limited number of host colonization sites. Our work suggests that Vibrio fischeri use a type VI secretion system, acting as a contact-dependent interbacterial “weapon,” to eliminate competing strains from cooccupying sites in the host. This work illuminates a mechanism by which strain-specific differences drive closely related bacteria to engage in lethal battles as they establish a beneficial symbiosis, revealing how genetic variation among potential colonizers directly impacts the spatial structure of the host-associated population. Intraspecific competition describes the negative interaction that occurs when different populations of the same species attempt to fill the same niche. Such competition is predicted to occur among host-associated bacteria but has been challenging to study in natural biological systems. Although many bioluminescent Vibrio fischeri strains exist in seawater, only a few strains are found in the light-organ crypts of an individual wild-caught Euprymna scolopes squid, suggesting a possible role for intraspecific competition during early colonization. Using a culture-based assay to investigate the interactions of different V. fischeri strains, we found “lethal” and “nonlethal” isolates that could kill or not kill the well-studied light-organ isolate ES114, respectively. The killing phenotype of these lethal strains required a type VI secretion system (T6SS) encoded in a 50-kb genomic island. Multiple lethal and nonlethal strains could be cultured from the light organs of individual wild-caught adult squid. Although lethal strains eliminate nonlethal strains in vitro, two lethal strains could coexist in interspersed microcolonies that formed in a T6SS-dependent manner. This coexistence was destabilized upon physical mixing, resulting in one lethal strain consistently eliminating the other. When juvenile squid were coinoculated with lethal and nonlethal strains, they occupied different crypts, yet they were observed to coexist within crypts when T6SS function was disrupted. These findings, using a combination of natural isolates and experimental approaches in vitro and in the animal host, reveal the importance of T6SS in spatially separating strains during the establishment of host colonization in a natural symbiosis.
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47
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Gao X, Wang X, Mao Q, Xu R, Zhou X, Ma Y, Liu Q, Zhang Y, Wang Q. VqsA, a Novel LysR-Type Transcriptional Regulator, Coordinates Quorum Sensing (QS) and Is Controlled by QS To Regulate Virulence in the Pathogen Vibrio alginolyticus. Appl Environ Microbiol 2018; 84:e00444-18. [PMID: 29625990 PMCID: PMC5981076 DOI: 10.1128/aem.00444-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/30/2018] [Indexed: 12/12/2022] Open
Abstract
The quorum sensing (QS) system controls bacterial group behaviors in response to cell density. In vibrios, LuxR and AphA are two master QS regulators (MQSRs) controlling gene expression in response to high or low cell density. Other regulators involved in the regulation of these two MQSRs and QS pathways remain to be determined. Here, we performed bacterial one-hybrid (B1H)-assay-based screens of transcriptional factors (TFs) to identify TFs that can directly regulate the expression of luxR and aphA from a library of 285 TFs encoded by the fish pathogen Vibrio alginolyticus A total of 7 TFs were identified to bind to the promoters of both luxR and aphA Among these TFs, the novel LysR-type transcriptional regulator (LTTR) VqsA could activate LuxR and repress AphA transcription. Meanwhile, LuxR and AphA exerted feedback inhibition and activation of vqsA expression, respectively, indicating that VqsA coordinates QS and is also regulated by QS. In addition, VqsA inhibited its own expression by directly binding to its own promoter region. The VqsA-binding sites in the promoter regions of luxR and aphA as well as the binding sites of LuxR, AphA, and VqsA in the vqsA gene were uncovered by electrophoretic mobility shift assays (EMSAs) and DNase I footprinting analysis. Finally, VqsA was verified to play essential roles in QS-regulated phenotypes, i.e., type VI secretion system 2 (T6SS2)-dependent interbacterial competition, biofilm formation, exotoxin production, and in vivo virulence of V. alginolyticus Collectively, our data showed that VqsA is an important QS regulator in V. alginolyticusIMPORTANCE Investigation of the mechanism of regulation of quorum sensing (QS) systems will facilitate an understanding of bacterial pathogenesis and the identification of effective QS interference (QSI) targets. Here, we systematically screened transcriptional factors (TFs) that modulate the expression of the master QS regulators (MQSRs) LuxR and AphA, and a novel LysR-type transcriptional regulator, VqsA, was identified. Our data illuminated the mechanisms mediating the interaction among LuxR, AphA, and VqsA as well as the effects of these regulators on the expression and output of QS. The impaired expression of virulence genes as a result of vqsA disruption demonstrated that VqsA is an important player in QS regulation and pathogenesis and may be the third MQSR involved in sensing environmental signals by vibrios to coordinate QS responses. This study will facilitate the development of strategies to interfere with QS and effectively control this pathogen that plagues the aquaculture industry.
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Affiliation(s)
- Xiating Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xuetong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qiaoqiao Mao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Rongjing Xu
- Yantai Tianyuan Aquatic Co. Ltd., Shandong, Yantai, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, Connecticut, USA
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
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Abstract
Vibrio is a genus of ubiquitous heterotrophic bacteria found in aquatic environments. Although they are a small percentage of the bacteria in these environments, vibrios can predominate during blooms. Vibrios also play important roles in the degradation of polymeric substances, such as chitin, and in other biogeochemical processes. Vibrios can be found as free-living bacteria, attached to particles, or associated with other organisms in a mutualistic, commensal, or pathogenic relationship. This review focuses on vibrio ecology and genome plasticity, which confers an ability to adapt to new niches and is driven, at least in part, by horizontal gene transfer (HGT). The extent of HGT and its role in pathogen emergence are discussed based on genomic studies of environmental and pathogenic vibrios, mobile genetically encoded virulence factors, and mechanistic studies on the different modes of HGT.
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Affiliation(s)
- Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, F-29280 Plouzané, France.,Laboratoire de Biologie Intégrative des Modèles Marins, Station Biologique de Roscoff, CNRS UMR 8227, UPMC Paris 06, Sorbonne Universités, F-29688 Roscoff CEDEX, France;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland;
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49
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Phosphorylation of PppA at threonine 253 controls T6SS2 expression and bacterial killing capacity in the marine pathogen Vibrio alginolyticus. Microbiol Res 2018; 209:70-78. [DOI: 10.1016/j.micres.2018.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/05/2018] [Accepted: 02/17/2018] [Indexed: 12/30/2022]
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50
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Yang Z, Zhou X, Ma Y, Zhou M, Waldor MK, Zhang Y, Wang Q. Serine/threonine kinase PpkA coordinates the interplay between T6SS2 activation and quorum sensing in the marine pathogen Vibrio alginolyticus. Environ Microbiol 2018; 20:903-919. [PMID: 29314504 DOI: 10.1111/1462-2920.14039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/31/2017] [Accepted: 12/31/2017] [Indexed: 11/30/2022]
Abstract
Type VI secretion systems (T6SS) are multiprotein secretion machines that can mediate killing of bacterial cells and thereby modify the composition of bacterial communities. The mechanisms that control the production of and secretion of these killing machines are incompletely understood, although quorum sensing (QS) and the PpkA kinase modulate T6SS activity in some organisms. Here we investigated control the T6S in the marine organism Vibrio alginolyticus EPGS, which encodes two T6SS systems (T6SS1 and T6SS2). We found that the organism principally relies on T6SS2 for interbacterial competition. We further carried out a phosphoproteomic screen to identify substrates of the T6SS2-linked PpkA2 kinase. Substrates of PpkA2 encoded within the T6SS2 cluster as well proteins that are apparently not linked to T6SS-related processes were identified. Similar to other organisms, PpkA2 autophosphorylation was critical for T6SS2 function. Notably, phosphorylation of a polypeptide encoded outside of the T6SS2 cluster, VtsR, was critical for T6SS2 expression and function because it augments the expression of luxR, a key regulator of QS that also promotes T6SS2 gene expression. Thus, PpkA2 controls a phosphorylation cascade that mediates a positive regulatory loop entwining T6SS and QS, thereby coordinating these pathways to enhance the competitive fitness of V. alginolyticus.
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Affiliation(s)
- Zhen Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT 06269, USA.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Matthew K Waldor
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
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