1
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Matte LM, Genal AV, Landolt EF, Danka ES. T6SS in plant pathogens: unique mechanisms in complex hosts. Infect Immun 2024; 92:e0050023. [PMID: 39166846 PMCID: PMC11385963 DOI: 10.1128/iai.00500-23] [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] [Indexed: 08/23/2024] Open
Abstract
Type VI secretion systems (T6SSs) are complex molecular machines that allow bacteria to deliver toxic effector proteins to neighboring bacterial and eukaryotic cells. Although initial work focused on the T6SS as a virulence mechanism of human pathogens, the field shifted to examine the use of T6SSs for interbacterial competition in various environments, including in the plant rhizosphere. Genes encoding the T6SS are estimated to be found in a quarter of all Gram-negative bacteria and are especially highly represented in Proteobacteria, a group which includes the most important bacterial phytopathogens. Many of these pathogens encode multiple distinct T6SS gene clusters which can include the core components of the apparatus as well as effector proteins. The T6SS is deployed by pathogens at multiple points as they colonize their hosts and establish an infection. In this review, we describe what is known about the use of T6SS by phytopathogens against plant hosts and non-plant organisms, keeping in mind that the structure of plants requires unique mechanisms of attack that are distinct from the mechanisms used for interbacterial interactions and against animal hosts. While the interactions of specific effectors (such as phospholipases, endonucleases, peptidases, and amidases) with targets have been well described in the context of interbacterial competition and in some eukaryotic interactions, this review highlights the need for future studies to assess the activity of phytobacterial T6SS effectors against plant cells.
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Affiliation(s)
- Lexie M Matte
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Abigail V Genal
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Emily F Landolt
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Elizabeth S Danka
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
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2
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Virgo M, Mostowy S, Ho BT. Use of zebrafish to identify host responses specific to type VI secretion system mediated interbacterial antagonism. PLoS Pathog 2024; 20:e1012384. [PMID: 39024393 PMCID: PMC11288455 DOI: 10.1371/journal.ppat.1012384] [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: 02/26/2024] [Revised: 07/30/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
Interbacterial competition is known to shape the microbial communities found in the host, however the interplay between this competition and host defense are less clear. Here, we use the zebrafish hindbrain ventricle (HBV) as an in vivo platform to investigate host responses to defined bacterial communities with distinct forms of interbacterial competition. We found that antibacterial activity of the type VI secretion system (T6SS) from both Vibrio cholerae and Acinetobacter baylyi can induce host inflammation and sensitize the host to infection independent of any individual effector. Chemical suppression of inflammation could resolve T6SS-dependent differences in host survival, but the mechanism by which this occurred differed between the two bacterial species. By contrast, colicin-mediated antagonism elicited by an avirulent strain of Shigella sonnei induced a negligible host response despite being a more potent bacterial killer, resulting in no impact on A. baylyi or V. cholerae virulence. Altogether, these results provide insight into how different modes of interbacterial competition in vivo affect the host in distinct ways.
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Affiliation(s)
- Mollie Virgo
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Brian T. Ho
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
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3
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Xie H, Huang Y, Wang S, Che J, Luo T, Li L, Bao B. Deletion of speA and aroC genes impacts the pathogenicity of Vibrio anguillarum in spotted sea bass. Microb Pathog 2024; 189:106597. [PMID: 38395316 DOI: 10.1016/j.micpath.2024.106597] [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: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Vibrio anguillarum is one of the major pathogens responsible for bacterial infections in marine environments, causing significant impacts on the aquaculture industry. The misuse of antibiotics leads to bacteria developing multiple drug resistances, which is detrimental to the development of the fisheries industry. In contrast, live attenuated vaccines are gradually gaining acceptance and widespread recognition. In this study, we constructed a double-knockout attenuated strain, V. anguillarum ΔspeA-aroC, to assess its potential for preparing a live attenuated vaccine. The research results indicate a significant downregulation of virulence-related genes, including Type VI secretion system, Type II secretion system, biofilm synthesis, iron uptake system, and other related genes, in the mutant strain. Furthermore, the strain lacking the genes exhibited a 67.47% reduction in biofilm formation ability and increased sensitivity to antibiotics. The mutant strain exhibited significantly reduced capability in evading host immune system defenses and causing in vivo infections in spotted sea bass (Lateolabrax maculatus), with an LD50 that was 13.93 times higher than that of the wild-type V. anguillarum. Additionally, RT-qPCR analysis of immune-related gene expression in spotted sea bass head kidney and spleen showed a weakened immune response triggered by the knockout strain. Compared to the wild-type V. anguillarum, the mutant strain caused reduced levels of tissue damage. The results demonstrate that the deletion of speA and aroC significantly reduces the biosynthesis of biofilms in V. anguillarum, leading to a decrease in its pathogenicity. This suggests a crucial role of biofilms in the survival and invasive capabilities of V. anguillarum.
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Affiliation(s)
- Haisheng Xie
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yajuan Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Shengming Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jingyuan Che
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Tuyan Luo
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Lekang Li
- Jiujiang Academy of Fishery Sciences, Jiujiang, 332000, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, 201306, China.
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4
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Jia F, Peng X, Yang X, Qiu S, Jia S, Ran T, Wang W, Xu D. PqqF inhibits T6SS secretion by decreasing the pH in Serratia marcescens FS14. FEMS Microbiol Lett 2024; 371:fnae047. [PMID: 38908910 DOI: 10.1093/femsle/fnae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 06/24/2024] Open
Abstract
Pyrroloquinoline quinone (PQQ) is a redox cofactor with numerous important physiological functions, and the type VI secretion system (T6SS) is commonly found in Gram-negative bacteria and plays important roles in physiological metabolism of the bacteria. In this study, we found that the deletion of pqqF enhanced the secretion of Hcp-1 in Serratia marcesens FS14 in M9 medium. Transcriptional analysis showed that the deletion of pqqF almost had no effect on the expression of T6SS-1. Further study revealed that the increased secretion of Hcp-1 was altered by the pH changes of the culture medium through the reaction catalyzed by the glucose dehydrogenases in FS14. Finally, we demonstrated that decreased pH of culture medium has similar inhibition effects as PQQ induced on the secretion of T6SS-1. This regulation mode on T6SS by pH in FS14 is different from previously reported in other bacteria. Therefore, our results suggest a novel pH regulation mode of T6SS in S. marcesens FS14, and would broaden our knowledge on the regulation of T6SS secretion.
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Affiliation(s)
- Fengyu Jia
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Xuede Peng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Xiaomei Yang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Shenshen Qiu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Shanshan Jia
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Tingting Ran
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Weiwu Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Dongqing Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
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Alcoforado Diniz J, Earl C, Hernandez RE, Hollmann B, Coulthurst SJ. Quantitative Determination of Antibacterial Activity During Bacterial Coculture. Methods Mol Biol 2024; 2715:593-600. [PMID: 37930554 DOI: 10.1007/978-1-0716-3445-5_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Antibacterial activity assays are an important tool in the assessment of the ability of one bacterium to kill or inhibit the growth of another, for example, during the study of the Type VI secretion system (T6SS) and the antibacterial toxins it secretes. The method we describe here can detect the ability of a bacterial strain to kill or inhibit other bacterial cells in a contact-dependent manner when cocultured on an agar surface. It is particularly useful since it enumerates the recovery of viable target cells and thus enables quantification of the antibacterial activity. We provide a detailed description of how to measure the T6SS-dependent antibacterial activity of a bacterium such as Serratia marcescens against a competitor prokaryotic organism, Escherichia coli, and describe possible variations in the method to allow adaptation to other attacker and target organisms.
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Affiliation(s)
| | - Christopher Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ruth E Hernandez
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Birte Hollmann
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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6
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Reglinski M, Monlezun L, Coulthurst SJ. The accessory protein TagV is required for full Type VI secretion system activity in Serratia marcescens. Mol Microbiol 2023; 119:326-339. [PMID: 36627840 PMCID: PMC7614798 DOI: 10.1111/mmi.15027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
The bacterial Type VI secretion system (T6SS) is a dynamic macromolecular structure that promotes inter- and intra-species competition through the delivery of toxic effector proteins into neighbouring cells. The T6SS contains 14 well-characterised core proteins necessary for effector delivery (TssA-M, PAAR). In this study, we have identified a novel accessory component required for optimal T6SS activity in the opportunistic pathogen Serratia marcescens, which we name TagV. Deletion of tagV, which encodes an outer membrane lipoprotein, caused a reduction in the T6SS-dependent antibacterial activity of S. marcescens Db10. Mutants of S. marcescens lacking the core component TssJ, a distinct outer membrane lipoprotein previously considered essential for T6SS firing, retained a modest T6SS activity that could be abolished through deletion of tagV. TagV did not interact with the T6SS membrane complex proteins TssL or TssM, but is proposed to bind to peptidoglycan, indicating that the mechanism by which TagV promotes T6SS firing differs from that of TssJ. Homologues of tagV were identified in several other bacterial genera, suggesting that the accessory function of TagV is not restricted to S. marcescens. Together, our findings support the existence of a second, TssJ-independent mechanism for T6SS firing that is dependent upon the activity of TagV proteins.
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Affiliation(s)
- Mark Reglinski
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Laura Monlezun
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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7
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Guckes KR, Miyashiro TI. The type-VI secretion system of the beneficial symbiont Vibrio fischeri. MICROBIOLOGY (READING, ENGLAND) 2023; 169:10.1099/mic.0.001302. [PMID: 36809081 PMCID: PMC9972734 DOI: 10.1099/mic.0.001302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The mutualistic symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the marine bacterium Vibrio fischeri is a powerful experimental system for determining how intercellular interactions impact animal-bacterial associations. In nature, this symbiosis features multiple strains of V. fischeri within each adult animal, which indicates that different strains initially colonize each squid. Various studies have demonstrated that certain strains of V. fischeri possess a type-VI secretion system (T6SS), which can inhibit other strains from establishing symbiosis within the same host habitat. The T6SS is a bacterial melee weapon that enables a cell to kill adjacent cells by translocating toxic effectors via a lancet-like apparatus. This review describes the progress that has been made in understanding the factors that govern the structure and expression of the T6SS in V. fischeri and its effect on the symbiosis.
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8
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Colautti J, Bullen NP, Whitney JC. Lack of evidence that Pseudomonas aeruginosa AmpDh3-PA0808 constitute a type VI secretion system effector-immunity pair. Mol Microbiol 2023; 119:262-274. [PMID: 36577706 DOI: 10.1111/mmi.15021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
Type VI secretion systems (T6SSs) are cell envelope-spanning protein complexes that Gram-negative bacteria use to inject a diverse arsenal of antibacterial toxins into competitor cells. Recently, Wang et al. reported that the H2-T6SS of Pseudomonas aeruginosa delivers the peptidoglycan recycling amidase, AmpDh3, into the periplasm of recipient cells where it is proposed to act as a peptidoglycan degrading toxin. They further reported that PA0808, the open reading frame downstream of AmpDh3, encodes an immunity protein that localizes to the periplasm where it binds to and inactivates intercellularly delivered AmpDh3, thus protecting against its toxic activity. Given that AmpDh3 has an established role in cell wall homeostasis and that no precedent exists for cytosolic enzymes moonlighting as T6SS effectors, we attempted to replicate these findings. We found that cells lacking PA0808 are not susceptible to bacterial killing by AmpDh3 and that PA0808 and AmpDh3 do not physically interact in vitro or in vivo. Additionally, we found no evidence that AmpDh3 is exported from cells, including by strains with a constitutively active H2-T6SS. Finally, subcellular fractionation experiments and a 1.97 Å crystal structure reveal that PA0808 does not contain a canonical signal peptide or localize to the correct cellular compartment to confer protection against a cell wall targeting toxin. Taken together, these results cast doubt on the assertion that AmpDh3-PA0808 constitutes an H2-T6SS effector-immunity pair.
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Affiliation(s)
- Jake Colautti
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Center for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
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9
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Huang Y, Han Y, Li Z, Li X, Li Z, Liu P, Liu X, Cheng Q, Fan F, Kan B, Liang W. TssI2-TsiI2 of Vibrio fluvialis VflT6SS2 delivers pesticin domain-containing periplasmic toxin and cognate immunity that modulates bacterial competitiveness. Gut Microbes 2022; 14:2136460. [PMID: 36288406 PMCID: PMC9620997 DOI: 10.1080/19490976.2022.2136460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Vibrio fluvialis is a halophilic Gram-negative bacterium regarded as an emerging unusual enteric pathogen of increasing public health concern. Our previous work has identified two type VI secretion systems (T6SSs) in V. fluvialis, VflT6SS1, and VflT6SS2, and the latter is functional in mediating interbacterial competitiveness. However, its antibacterial effectors remain to be clarified. In this work, we focused on a new potential effector/immunity pair TssI2/TsiI2. Bioinformatics analysis revealed that the C-terminal domain of TssI2 belongs to a widespread family of pesticin, and its antibacterial toxicity and corresponding protection by TsiI2 were proved via bacterial killing assays, and their action sites were localized to the periplasm of bacterial cells. The interaction of TssI2 and TsiI2 was demonstrated by the bacterial adenylate cyclase two-hybrid, protein pull-down and isothermal titration calorimetry assays. Site-directed mutagenesis demonstrated that, in addition to Glu-844, Thr-863, and Asp-869, which correspond to three reported residues in pesticin of Yersinia pestis, additional residues including Phe-837, Gly-845, Tyr-851, Gly-867, Gln-963, Trp-975, and Arg-1000 were also proved to be crucial to the bactericidal activity of TssI2. Muramidase/lysozyme-related peptidoglycan (PG) hydrolase activities of TssI2 and its variants were validated with permeabilized Escherichia coli cells and purified PG substrate. Based on sequence homologies at C-terminals in various V. fluvialis isolates, TssI2 was subdivided into five clusters (12-22% identity among them), and the antibacterial activities of representative effectors from other four Clusters were also confirmed through periplasmic over-expression in E. coli host. Two selected cognate immunities were proved to confer protection against the toxicities of their effectors. Additionally, TsiI2, which belongs to Cluster I, exhibited cross-protection to effector from Cluster V. Together, current findings expand our knowledge of the diversity and consistency of evolved VgrG effectors in V. fluvialis and on how VflT6SS2 mediates a competitive advantage to gain a better survival.
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Affiliation(s)
- Yuanming Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaorui Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhe Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoshu Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fenxia Fan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,CONTACT Biao Kan
| | - Weili Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Weili Liang State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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10
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Lorente Cobo N, Sibinelli-Sousa S, Biboy J, Vollmer W, Bayer-Santos E, Prehna G. Molecular characterization of the type VI secretion system effector Tlde1a reveals a structurally altered LD-transpeptidase fold. J Biol Chem 2022; 298:102556. [PMID: 36183829 PMCID: PMC9638812 DOI: 10.1016/j.jbc.2022.102556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/01/2022] Open
Abstract
The type VI secretion system (T6SS) is a molecular machine that Gram-negative bacteria have adapted for multiple functions, including interbacterial competition. Bacteria use the T6SS to deliver protein effectors into adjacent cells to kill rivals and establish niche dominance. Central to T6SS-mediated bacterial competition is an arms race to acquire diverse effectors to attack and neutralize target cells. The peptidoglycan has a central role in bacterial cell physiology, and effectors that biochemically modify peptidoglycan structure effectively induce cell death. One such T6SS effector is Tlde1a from Salmonella Typhimurium. Tlde1a functions as an LD-carboxypeptidase to cleave tetrapeptide stems and as an LD-transpeptidase to exchange the terminal D-alanine of a tetrapeptide stem with a noncanonical D-amino acid. To understand how Tlde1a exhibits toxicity at the molecular level, we determined the X-ray crystal structure of Tlde1a alone and in complex with D-amino acids. Our structural data revealed that Tlde1a possesses a unique LD-transpeptidase fold consisting of a dual pocket active site with a capping subdomain. This includes an exchange pocket to bind a D-amino acid for exchange and a catalytic pocket to position the D-alanine of a tetrapeptide stem for cleavage. Our toxicity assays in Escherichia coli and in vitro peptidoglycan biochemical assays with Tlde1a variants correlate Tlde1a molecular features directly to its biochemical functions. We observe that the LD-carboxypeptidase and LD-transpeptidase activities of Tlde1a are both structurally and functionally linked. Overall, our data highlight how an LD-transpeptidase fold has been structurally altered to create a toxic effector in the T6SS arms race.
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Affiliation(s)
- Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Stephanie Sibinelli-Sousa
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ethel Bayer-Santos
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Canada.
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11
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Fei N, Ji W, Yang L, Yu C, Qiao P, Yan J, Guan W, Yang Y, Zhao T. Hcp of the Type VI Secretion System (T6SS) in Acidovorax citrulli Group II Strain Aac5 Has a Dual Role as a Core Structural Protein and an Effector Protein in Colonization, Growth Ability, Competition, Biofilm Formation, and Ferric Iron Absorption. Int J Mol Sci 2022; 23:9632. [PMID: 36077040 PMCID: PMC9456162 DOI: 10.3390/ijms23179632] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/06/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
A type VI secretion system (T6SS) gene cluster has been reported in Acidovorax citrulli. Research on the activation conditions, functions, and the interactions between key elements in A. citrulli T6SS is lacking. Hcp (Hemolysin co-regulated protein) is both a structural protein and a secretion protein of T6SS, which makes it a special element. The aims of this study were to determine the role of Hcp and its activated conditions to reveal the functions of T6SS. In virulence and colonization assays of hcp deletion mutant strain Δhcp, tssm (type VI secretion system membrane subunit) deletion mutant strain Δtssm and double mutant ΔhcpΔtssm, population growth was affected but not virulence after injection of cotyledons and seed-to-seedling transmission on watermelon. The population growth of Δhcp and Δtssm were lower than A. citrulli wild type strain Aac5 of A. citrulli group II at early stage but higher at a later stage. Deletion of hcp also affected growth ability in different culture media, and the decline stage of Δhcp was delayed in KB medium. Biofilm formation ability of Δhcp, Δtssm and ΔhcpΔtssm was lower than Aac5 with competition by prey bacteria but higher in KB and M9-Fe3+ medium. Deletion of hcp reduced the competition and survival ability of Aac5. Based on the results of Western blotting and qRT-PCR analyses, Hcp is activated by cell density, competition, ferric irons, and the host plant. The expression levels of genes related to bacterial secretion systems, protein export, and several other pathways, were significantly changed in the Δhcp mutant compared to Aac5 when T6SS was activated at high cell density. Based on transcriptome data, we found that a few candidate effectors need further identification. The phenotypes, activated conditions and transcriptome data all supported the conclusion that although there is only one T6SS gene cluster present in the A. citrulli group II strain Aac5, it related to multiple biological processes, including colonization, growth ability, competition and biofilm formation.
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Affiliation(s)
- Nuoya Fei
- Department of Plant Pathology, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weiqin Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Linlin Yang
- Department of Plant Pathology, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chunyan Yu
- Department of Plant Pathology, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pei Qiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianpei Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Guan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuwen Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tingchang Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Radkov A, Sapiro AL, Flores S, Henderson C, Saunders H, Kim R, Massa S, Thompson S, Mateusiak C, Biboy J, Zhao Z, Starita LM, Hatleberg WL, Vollmer W, Russell AB, Simorre JP, Anthony-Cahill S, Brzovic P, Hayes B, Chou S. Antibacterial potency of Type VI amidase effector toxins is dependent on substrate topology and cellular context. eLife 2022; 11:79796. [PMID: 35762582 PMCID: PMC9270033 DOI: 10.7554/elife.79796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/23/2022] [Indexed: 11/15/2022] Open
Abstract
Members of the bacterial T6SS amidase effector (Tae) superfamily of toxins are delivered between competing bacteria to degrade cell wall peptidoglycan. Although Taes share a common substrate, they exhibit distinct antimicrobial potency across different competitor species. To investigate the molecular basis governing these differences, we quantitatively defined the functional determinants of Tae1 from Pseudomonas aeruginosa PAO1 using a combination of nuclear magnetic resonance and a high-throughput in vivo genetic approach called deep mutational scanning (DMS). As expected, combined analyses confirmed the role of critical residues near the Tae1 catalytic center. Unexpectedly, DMS revealed substantial contributions to enzymatic activity from a much larger, ring-like functional hot spot extending around the entire circumference of the enzyme. Comparative DMS across distinct growth conditions highlighted how functional contribution of different surfaces is highly context-dependent, varying alongside composition of targeted cell walls. These observations suggest that Tae1 engages with the intact cell wall network through a more distributed three-dimensional interaction interface than previously appreciated, providing an explanation for observed differences in antimicrobial potency across divergent Gram-negative competitors. Further binding studies of several Tae1 variants with their cognate immunity protein demonstrate that requirements to maintain protection from Tae activity may be a significant constraint on the mutational landscape of tae1 toxicity in the wild. In total, our work reveals that Tae diversification has likely been shaped by multiple independent pressures to maintain interactions with binding partners that vary across bacterial species and conditions.
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Affiliation(s)
- Atanas Radkov
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Anne L Sapiro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | | | - Hayden Saunders
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Rachel Kim
- Pacific Northwest University of Health Sciences, Yakima, United States
| | - Steven Massa
- Department of Biology, Stanford University, Stanford, United States
| | - Samuel Thompson
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Chase Mateusiak
- Computer Science Department, Washington University in St. Louis, St. Louis, United States
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ziyi Zhao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, United States
| | | | - Waldemar Vollmer
- Center for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alistair B Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
| | | | - Peter Brzovic
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Beth Hayes
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Seemay Chou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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13
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Boak EN, Kirolos S, Pan H, Pierson LS, Pierson EA. The Type VI Secretion Systems in Plant-Beneficial Bacteria Modulate Prokaryotic and Eukaryotic Interactions in the Rhizosphere. Front Microbiol 2022; 13:843092. [PMID: 35464916 PMCID: PMC9022076 DOI: 10.3389/fmicb.2022.843092] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/04/2022] [Indexed: 01/15/2023] Open
Abstract
Rhizosphere colonizing plant growth promoting bacteria (PGPB) increase their competitiveness by producing diffusible toxic secondary metabolites, which inhibit competitors and deter predators. Many PGPB also have one or more Type VI Secretion System (T6SS), for the delivery of weapons directly into prokaryotic and eukaryotic cells. Studied predominantly in human and plant pathogens as a virulence mechanism for the delivery of effector proteins, the function of T6SS for PGPB in the rhizosphere niche is poorly understood. We utilized a collection of Pseudomonas chlororaphis 30-84 mutants deficient in one or both of its two T6SS and/or secondary metabolite production to examine the relative importance of each T6SS in rhizosphere competence, bacterial competition, and protection from bacterivores. A mutant deficient in both T6SS was less persistent than wild type in the rhizosphere. Both T6SS contributed to competitiveness against other PGPB or plant pathogenic strains not affected by secondary metabolite production, but only T6SS-2 was effective against strains lacking their own T6SS. Having at least one T6SS was also essential for protection from predation by several eukaryotic bacterivores. In contrast to diffusible weapons that may not be produced at low cell density, T6SS afford rhizobacteria an additional, more immediate line of defense against competitors and predators.
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Affiliation(s)
- Emily N. Boak
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Sara Kirolos
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Huiqiao Pan
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
| | - Leland S. Pierson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Elizabeth A. Pierson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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14
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Günther P, Quentin D, Ahmad S, Sachar K, Gatsogiannis C, Whitney JC, Raunser S. Structure of a bacterial Rhs effector exported by the type VI secretion system. PLoS Pathog 2022; 18:e1010182. [PMID: 34986192 PMCID: PMC8765631 DOI: 10.1371/journal.ppat.1010182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/18/2022] [Accepted: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread protein export apparatus found in Gram-negative bacteria. The majority of T6SSs deliver toxic effector proteins into competitor bacteria. Yet, the structure, function, and activation of many of these effectors remains poorly understood. Here, we present the structures of the T6SS effector RhsA from Pseudomonas protegens and its cognate T6SS spike protein, VgrG1, at 3.3 Å resolution. The structures reveal that the rearrangement hotspot (Rhs) repeats of RhsA assemble into a closed anticlockwise β-barrel spiral similar to that found in bacterial insecticidal Tc toxins and in metazoan teneurin proteins. We find that the C-terminal toxin domain of RhsA is autoproteolytically cleaved but remains inside the Rhs ‘cocoon’ where, with the exception of three ordered structural elements, most of the toxin is disordered. The N-terminal ‘plug’ domain is unique to T6SS Rhs proteins and resembles a champagne cork that seals the Rhs cocoon at one end while also mediating interactions with VgrG1. Interestingly, this domain is also autoproteolytically cleaved inside the cocoon but remains associated with it. We propose that mechanical force is required to remove the cleaved part of the plug, resulting in the release of the toxin domain as it is delivered into a susceptible bacterial cell by the T6SS. Bacteria have developed a variety of strategies to compete for nutrients and limited resources. One system widely used by Gram-negative bacteria is the T6 secretion system which delivers a plethora of effectors into competing bacterial cells. Known functions of effectors are degradation of the cell wall, the depletion of essential metabolites such as NAD+ or the cleavage of DNA. RhsA is an effector from the widespread plant-protecting bacteria Pseudomonas protegens. We found that RhsA forms a closed cocoon similar to that found in bacterial Tc toxins and metazoan teneurin proteins. The effector cleaves its polypeptide chain by itself in three pieces, namely the N-terminal domain including a seal, the cocoon and the actual toxic component which potentially cleaves DNA. The toxic component is encapsulated in the large cocoon, so that the effector producing bacterium is protected from the toxin. In order for the toxin to exit the cocoon, we propose that the seal, which closes the cocoon at one end, is removed by mechanical forces during injection of the effector by the T6 secretion system. We further hypothesize about different scenarios for the delivery of the toxin into the cytoplasm of the host cell. Together, our findings expand the knowledge of the mechanism of action of the T6 secretion system and its essential role in interbacterial competition.
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Affiliation(s)
- Patrick Günther
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Shehryar Ahmad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Kartik Sachar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
- * E-mail: (J.C.W.); (S.R.)
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- * E-mail: (J.C.W.); (S.R.)
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15
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Liang X, Pei TT, Li H, Zheng HY, Luo H, Cui Y, Tang MX, Zhao YJ, Xu P, Dong T. VgrG-dependent effectors and chaperones modulate the assembly of the type VI secretion system. PLoS Pathog 2021; 17:e1010116. [PMID: 34852023 PMCID: PMC8668125 DOI: 10.1371/journal.ppat.1010116] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/13/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
The type VI secretion system (T6SS) is a spear-like nanomachine found in gram-negative pathogens for delivery of toxic effectors to neighboring bacterial and host cells. Its assembly requires a tip spike complex consisting of a VgrG-trimer, a PAAR protein, and the interacting effectors. However, how the spike controls T6SS assembly remains elusive. Here we investigated the role of three VgrG-effector pairs in Aeromonas dhakensis strain SSU, a clinical isolate with a constitutively active T6SS. By swapping VgrG tail sequences, we demonstrate that the C-terminal ~30 amino-acid tail dictates effector specificity. Double deletion of vgrG1&2 genes (VgrG3+) abolished T6SS secretion, which can be rescued by ectopically expressing chimeric VgrG3 with a VgrG1/2-tail but not the wild type VgrG3. In addition, deletion of effector-specific chaperones also severely impaired T6SS secretion, despite the presence of intact VgrG and effector proteins, in both SSU and Vibrio cholerae V52. We further show that SSU could deliver a V. cholerae effector VasX when expressing a plasmid-borne chimeric VgrG with VasX-specific VgrG tail and chaperone sequences. Pull-down analyses show that two SSU effectors, TseP and TseC, could interact with their cognate VgrGs, the baseplate protein TssK, and the key assembly chaperone TssA. Effectors TseL and VasX could interact with TssF, TssK and TssA in V. cholerae. Collectively, we demonstrate that chimeric VgrG-effector pairs could bypass the requirement of heterologous VgrG complex and propose that effector-stuffing inside the baseplate complex, facilitated by chaperones and the interaction with structural proteins, serves as a crucial structural determinant for T6SS assembly. Effectors of bacterial secretion systems are generally considered as secreted proteins for interspecies interactions rather than components of the secretion apparatus. Our results reveal the complex interactions of effectors, chaperones, and structural proteins are crucial for T6SS assembly, suggesting an integral role of effectors as parts of the apparatus and distinctive from other secretion systems.
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Affiliation(s)
- 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, Shanghai, China
| | - 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, 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, Shanghai, China
| | - Hao-Yu Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Han Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Cui
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Xuan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ya-Jie Zhao
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 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, Shanghai, China
| | - Tao 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, Shanghai, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- * E-mail:
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16
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Abstract
Commensal microbes in animal guts often help to exclude bacterial pathogens. In honey bees, perturbing or depleting the gut microbiota increases host mortality rates upon challenge with the opportunistic pathogen Serratia marcescens, suggesting antagonism between S. marcescens and one or more members of the bee gut microbiota. In laboratory culture, S. marcescens uses a type VI secretion system (T6SS) to kill bacterial competitors, but the role of this T6SS within hosts is unknown. Using infection assays, we determined how the microbiota impacts the abundance and persistence of S. marcescens in the gut and visualized colocalization of S. marcescens with specific community members in situ. Using T6SS-deficient S. marcescens strains, we measured T6SS-dependent killing of gut isolates in vitro and compared the persistence of mutant and wild-type strains in the gut. We found that S. marcescens is rapidly eliminated in the presence of the microbiota but persists in microbiota-free guts. Protection is reduced in monocolonized and antibiotic-treated bees, possibly because different symbionts occupy distinct niches. Serratia marcescens uses a T6SS to antagonize Escherichia coli and other S. marcescens strains but shows limited ability to kill bee symbionts. Furthermore, wild-type and T6SS-deficient S. marcescens strains achieved similar abundance and persistence in bee guts. Thus, an intact gut microbiota offers robust protection against this common pathogen, whose T6SSs do not confer the ability to compete with commensal species. IMPORTANCE Bacteria living within guts of animals can provide protection against infection by pathogens. Some pathogens have been shown to use a molecular weapon known as a T6SS to kill beneficial bacteria during invasion of the mouse gut. In this study, we examined how bacteria native to the honey bee gut work together to exclude the opportunistic pathogen Serratia marcescens. Although S. marcescens has a T6SS that can kill bacteria, bee gut bacteria seem resistant to its effects. This limitation may partially explain why ingestion of S. marcescens is rarely lethal to insects with healthy gut communities.
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17
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Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins. J Bacteriol 2021; 203:e0028121. [PMID: 34398661 DOI: 10.1128/jb.00281-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Competition is a critical aspect of bacterial life, as it enables niche establishment and facilitates the acquisition of essential nutrients. Warfare between Gram-negative bacteria is largely mediated by the type VI secretion system (T6SS), a dynamic nanoweapon that delivers toxic effector proteins from an attacking cell to adjacent bacteria in a contact-dependent manner. Effector-encoding bacteria prevent self-intoxication and kin cell killing by the expression of immunity proteins, which prevent effector toxicity by specifically binding their cognate effector and either occluding its active site or preventing structural rearrangements necessary for effector activation. In this study, we investigate Tsi3, a previously uncharacterized T6SS immunity protein present in multiple strains of the human pathogen Acinetobacter baumannii. We show that Tsi3 is the cognate immunity protein of the antibacterial effector of unknown function Tse3. Our bioinformatic analyses indicate that Tsi3 homologs are widespread among Gram-negative bacteria, often encoded within T6SS effector-immunity modules. Surprisingly, we found that Tsi3 homologs are predicted to possess a characteristic formylglycine-generating enzyme (FGE) domain, which is present in various enzymatic proteins. Our data shows that Tsi3-mediated immunity is dependent on Tse3-Tsi3 protein-protein interactions and that Tsi3 homologs from various bacteria do not provide immunity against non-kin Tse3. Thus, we conclude that Tsi3 homologs are unlikely to be functional enzymes. Collectively, our work identifies FGE domain-containing proteins as important mediators of immunity against T6SS attacks and indicates that the FGE domain can be co-opted as a scaffold in multiple proteins to carry out diverse functions. Importance Despite the wealth of knowledge on the diversity of biochemical activities carried out by T6SS effectors, comparably little is known about the various strategies bacteria employ to prevent susceptibility to T6SS-dependent bacterial killing. Our work establishes a novel family of T6SS immunity proteins with a characteristic FGE domain. This domain is present in enzymatic proteins with various catalytic activities. Our characterization of Tsi3 expands the known functions carried out by FGE-like proteins to include defense during T6SS-mediated bacterial warfare. Moreover, it highlights the evolution of FGE domain-containing proteins to carry out diverse biological functions.
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18
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Robinson L, Liaw J, Omole Z, Xia D, van Vliet AHM, Corcionivoschi N, Hachani A, Gundogdu O. Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction. Front Microbiol 2021; 12:694824. [PMID: 34276628 PMCID: PMC8285248 DOI: 10.3389/fmicb.2021.694824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
The Type VI Secretion System (T6SS) has important roles relating to bacterial antagonism, subversion of host cells, and niche colonisation. Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis worldwide and is a commensal coloniser of birds. Although recently discovered, the T6SS biological functions and identities of its effectors are still poorly defined in C. jejuni. Here, we perform a comprehensive bioinformatic analysis of the C. jejuni T6SS by investigating the prevalence and genetic architecture of the T6SS in 513 publicly available genomes using C. jejuni 488 strain as reference. A unique and conserved T6SS cluster associated with the Campylobacter jejuni Integrated Element 3 (CJIE3) was identified in the genomes of 117 strains. Analyses of the T6SS-positive 488 strain against the T6SS-negative C. jejuni RM1221 strain and the T6SS-positive plasmid pCJDM202 carried by C. jejuni WP2-202 strain defined the “T6SS-containing CJIE3” as a pathogenicity island, thus renamed as Campylobacter jejuni Pathogenicity Island-1 (CJPI-1). Analysis of CJPI-1 revealed two canonical VgrG homologues, CJ488_0978 and CJ488_0998, harbouring distinct C-termini in a genetically variable region downstream of the T6SS operon. CJPI-1 was also found to carry a putative DinJ-YafQ Type II toxin-antitoxin (TA) module, conserved across pCJDM202 and the genomic island CJIE3, as well as several open reading frames functionally predicted to encode for nucleases, lipases, and peptidoglycan hydrolases. This comprehensive in silico study provides a framework for experimental characterisation of T6SS-related effectors and TA modules in C. jejuni.
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Affiliation(s)
- Luca Robinson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Janie Liaw
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Zahra Omole
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dong Xia
- Comparative Biomedical Sciences, Royal Veterinary College, London, United Kingdom
| | - Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Bioengineering of Animal Science Resources, Banat University of Agricultural Sciences and Veterinary Medicine - King Michael the I of Romania, Timisoara, Romania
| | - Abderrahman Hachani
- The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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19
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Evolution of Interbacterial Antagonism in Bee Gut Microbiota Reflects Host and Symbiont Diversification. mSystems 2021; 6:6/3/e00063-21. [PMID: 33975963 PMCID: PMC8125069 DOI: 10.1128/msystems.00063-21] [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] [Indexed: 11/20/2022] Open
Abstract
Antagonistic interactions between bacteria affect diversity and dynamics of host-associated communities, including gut communities that are linked to host health. In many bacterial communities, including human and honey bee gut microbiotas, antagonism is mediated by type VI secretion systems (T6SSs) that deliver lethal toxins to competing strains. Gram-negative bacteria frequently possess type VI secretion systems (T6SSs), protein complexes that are able to inject toxic proteins into nearby cells. Many aspects of T6SS structure and function have been characterized for model species, but less is known about the evolutionary processes that shape T6SS and effector (toxin) diversity in host-associated microbial communities. The bee gut microbiota is a simple community that has codiversified with bees for >80 million years. This study investigated how complements of T6SSs and effectors within the bee microbiota changed as bacteria and their hosts diversified into isolated species. We used protein homology to survey 198 isolate genomes of 9 Gram-negative species for genes encoding T6SS structural components; Rhs toxins, which are common T6SS effectors; and VgrG proteins, which are structural components associated with specific toxins. T6SS loci were present in 5 species clusters found only in bees, namely Apibacter spp., Gilliamella spp., Frischella perrara, “Candidatus Schmidhempelia bombi,” and Snodgrassella alvi. The distribution of T6SS loci suggests that at least 3 were present in the microbiota of the common ancestor of social bees and that loss of these genes in some bacterial lineages was linked to both host and bacterial speciation. Isolates differed enormously in repertoires of Rhs and VgrG proteins. We found that bacterial species employ different mechanisms for toxin acquisition and diversification and that species and strains sometimes lose the T6SS entirely, likely causing shifts in competitive dynamics within these communities. IMPORTANCE Antagonistic interactions between bacteria affect diversity and dynamics of host-associated communities, including gut communities that are linked to host health. In many bacterial communities, including human and honey bee gut microbiotas, antagonism is mediated by type VI secretion systems (T6SSs) that deliver lethal toxins to competing strains. In this study, we explored how T6SSs and associated toxins have evolved in the simple, host-specific gut microbiota of honey bees and bumble bees. Using comparative genomics, we explored the conservation, recombination, horizontal transfer, and loss of T6SSs and effectors during 80 million years of evolution of this bee-associated community. We find that that patterns of T6SS loss and retention are linked to differences in biology across host species, while trends in effector diversification are mostly specific to bacterial lineages.
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20
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Agashe P, Kuzminov A. Catalase inhibition by nitric oxide potentiates hydrogen peroxide to trigger catastrophic chromosome fragmentation in Escherichia coli. Genetics 2021; 218:6214516. [PMID: 34027548 DOI: 10.1093/genetics/iyab057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/02/2021] [Indexed: 01/01/2023] Open
Abstract
Hydrogen peroxide (H2O2, HP) is a universal toxin that organisms deploy to kill competing or invading cells. Bactericidal action of H2O2 presents several questions. First, the lethal H2O2 concentrations in bacterial cultures are 1000x higher than, for example, those calculated for the phagosome. Second, H2O2-alone kills bacteria in cultures either by mode-one, via iron-mediated chromosomal damage, or by mode-two, via unknown targets, but the killing mode in phagosomes is unclear. Third, phagosomal H2O2 toxicity is enhanced by production of nitric oxide (NO), but in vitro studies disagree: some show NO synergy with H2O2 antimicrobial action, others instead report alleviation. To investigate this "NO paradox," we treated Escherichia coli with various concentrations of H2O2-alone or H2O2+NO, measuring survival and chromosome stability. We found that all NO concentrations make sublethal H2O2 treatments highly lethal, via triggering catastrophic chromosome fragmentation (mode-one killing). Yet, NO-alone is not lethal, potentiating H2O2 toxicity by blocking H2O2 scavenging in cultures. Catalases represent obvious targets of NO inhibition, and catalase-deficient mutants are indeed killed equally by H2O2-alone or H2O2+NO treatments, also showing similar levels of chromosome fragmentation. Interestingly, iron chelation blocks chromosome fragmentation in catalase-deficient mutants without blocking H2O2-alone lethality, indicating mode-two killing. In fact, mode-two killing of WT cells by much higher H2O2 concentrations is transiently alleviated by NO, reproducing the "NO paradox." We conclude that NO potentiates H2O2 toxicity by promoting mode-one killing (via catastrophic chromosome fragmentation) by otherwise static low H2O2 concentrations, while transiently suppressing mode-two killing by immediately lethal high H2O2 concentrations.
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Affiliation(s)
- Pooja Agashe
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Sibinelli-Sousa S, Hespanhol JT, Bayer-Santos E. Targeting the Achilles' Heel of Bacteria: Different Mechanisms To Break Down the Peptidoglycan Cell Wall during Bacterial Warfare. J Bacteriol 2021; 203:e00478-20. [PMID: 33139480 PMCID: PMC8088523 DOI: 10.1128/jb.00478-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria commonly live in dense polymicrobial communities and compete for scarce resources. Consequently, they employ a diverse array of mechanisms to harm, inhibit, and kill their competitors. The cell wall is essential for bacterial survival by providing mechanical strength to resist osmotic stress. Because peptidoglycan is the major component of the cell wall and its synthesis is a complex multistep pathway that requires the coordinate action of several enzymes, it provides a target for rival bacteria, which have developed a large arsenal of antibacterial molecules to attack the peptidoglycan of competitors. These molecules include antibiotics, bacteriocins, and contact-dependent effectors that are either secreted into the medium or directly translocated into a target cell. In this minireview, we summarize the diversity of these molecules and highlight distinct mechanisms to disrupt the peptidoglycan, giving special attention to molecules that are known or have the potential to be used during interbacterial competitions.
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Affiliation(s)
- Stephanie Sibinelli-Sousa
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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22
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Declercq AM, Tilleman L, Gansemans Y, De Witte C, Haesebrouck F, Van Nieuwerburgh F, Smet A, Decostere A. Comparative genomics of Flavobacterium columnare unveils novel insights in virulence and antimicrobial resistance mechanisms. Vet Res 2021; 52:18. [PMID: 33579339 PMCID: PMC7881675 DOI: 10.1186/s13567-021-00899-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/18/2021] [Indexed: 11/28/2022] Open
Abstract
This study reports the comparative analyses of four Flavobacterium columnare isolates that have different virulence and antimicrobial resistance patterns. The main research goal was to reveal new insights into possible virulence genes by comparing the genomes of bacterial isolates that could induce tissue damage and mortality versus the genome of a non-virulent isolate. The results indicated that only the genomes of the virulent isolates possessed unique genes encoding amongst others a methyl-accepting chemotaxis protein possibly involved in the initial colonization of tissue, and several VgrG proteins engaged in interbacterial competition. Furthermore, comparisons of genes unique for the genomes of the highly virulent (HV) carp and trout isolates versus the, respectively, low and non-virulent carp and trout isolates were performed. An important part of the identified unique virulence genes of the HV-trout isolate was located in one particular gene region identified as a genomic island. This region contained araC and nodT genes, both linked to pathogenic and multidrug-resistance, and a luxR-gene, functional in bacterial cell-to-cell communication. Furthermore, the genome of the HV-trout isolate possessed unique sugar-transferases possibly important in bacterial adhesion. The second research goal was to obtain insights into the genetic basis of acquired antimicrobial resistance. Several point-mutations were discovered in gyrase-genes of an isolate showing phenotypic resistance towards first and second-generation quinolones, which were absent in isolates susceptible to quinolones. Tetracycline-resistance gene tetA was found in an isolate displaying acquired phenotypic resistance towards oxytetracycline. Although not localized on a prophage, several flanking genes were indicative of the gene’s mobile character.
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Affiliation(s)
- Annelies Maria Declercq
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium. .,Flanders Marine Institute, Wandelaarkaai 7, 8400, Ostend, Belgium. .,Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Annemieke Smet
- Laboratory Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Annemie Decostere
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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23
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Agrobacterium tumefaciens Deploys a Versatile Antibacterial Strategy To Increase Its Competitiveness. J Bacteriol 2021; 203:JB.00490-20. [PMID: 33168638 PMCID: PMC7811202 DOI: 10.1128/jb.00490-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/02/2020] [Indexed: 12/28/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread antibacterial weapon capable of secreting multiple effectors for inhibition of competitor cells. Most of the effectors in the system share the same purpose of target intoxication, but the rationale for maintaining various types of effectors in a species is not well studied. In this study, we showed that a peptidoglycan amidase effector in Agrobacterium tumefaciens, Tae, cleaves d-Ala-meso-diaminopimelic acid (mDAP) and d-Glu bonds in peptidoglycan and is able to suppress the growth of Escherichia coli recipient cells. The growth suppression was effective only under the condition in which E. coli cells are actively growing. In contrast, the Tde DNase effectors in the strain possessed a dominant killing effect under carbon starvation. Microscopic analysis showed that Tde triggers cell elongation and DNA degradation, while Tae causes cell enlargement without DNA damage in E. coli recipient cells. In a rich medium, A. tumefaciens harboring only functional Tae was able to maintain competitiveness among E. coli and its own sibling cells. Growth suppression and the competitive advantage of A. tumefaciens were abrogated when recipient cells produced the Tae-specific immunity protein Tai. Given that Tae is highly conserved among A. tumefaciens strains, the combination of Tae and Tde effectors could allow A. tumefaciens to better compete with various competitors by increasing its survival during changing environmental conditions.IMPORTANCE The T6SS encodes multiple effectors with diverse functions, but little is known about the biological significance of harboring such a repertoire of effectors. We reported that the T6SS antibacterial activity of the plant pathogen Agrobacterium tumefaciens can be enhanced under carbon starvation or when recipient cell wall peptidoglycan is disturbed. This led to a newly discovered role for the T6SS peptidoglycan amidase Tae effector in providing a growth advantage dependent on the growth status of the target cell. This is in contrast to the Tde DNase effectors that are dominant during carbon starvation. Our study suggests that combining Tae and other effectors could allow A. tumefaciens to increase its competitiveness among changing environmental conditions.
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24
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T6SS Mediated Stress Responses for Bacterial Environmental Survival and Host Adaptation. Int J Mol Sci 2021; 22:ijms22020478. [PMID: 33418898 PMCID: PMC7825059 DOI: 10.3390/ijms22020478] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/25/2020] [Accepted: 01/01/2021] [Indexed: 02/07/2023] Open
Abstract
The bacterial type VI secretion system (T6SS) is a protein secretion apparatus widely distributed in Gram-negative bacterial species. Many bacterial pathogens employ T6SS to compete with the host and to coordinate the invasion process. The T6SS apparatus consists of a membrane complex and an inner tail tube-like structure that is surrounded by a contractile sheath and capped with a spike complex. A series of antibacterial or antieukaryotic effectors is delivered by the puncturing device consisting of a Hcp tube decorated by the VgrG/PAAR complex into the target following the contraction of the TssB/C sheath, which often leads to damage and death of the competitor and/or host cells. As a tool for protein secretion and interspecies interactions, T6SS can be triggered by many different mechanisms to respond to various physiological conditions. This review summarizes our current knowledge of T6SS in coordinating bacterial stress responses against the unfavorable environmental and host conditions.
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25
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Stolle AS, Meader BT, Toska J, Mekalanos JJ. Endogenous membrane stress induces T6SS activity in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2021; 118:e2018365118. [PMID: 33443205 PMCID: PMC7817224 DOI: 10.1073/pnas.2018365118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The type 6 secretion system (T6SS) is a dynamic organelle encoded by many gram-negative bacteria that can be used to kill competing bacterial prey species in densely occupied niches. Some predatory species, such as Vibrio cholerae, use their T6SS in an untargeted fashion while in contrast, Pseudomonas aeruginosa assembles and fires its T6SS apparatus only after detecting initial attacks by other bacterial prey cells; this targeted attack strategy has been termed the T6SS tit-for-tat response. Molecules that interact with the P. aeruginosa outer membrane such as polymyxin B can also trigger assembly of T6SS organelles via a signal transduction pathway that involves protein phosphorylation. Recent work suggests that a phospholipase T6SS effector (TseL) of V. cholerae can induce T6SS dynamic activity in P. aeruginosa when delivered to or expressed in the periplasmic space of this organism. Here, we report that inhibiting expression of essential genes involved in outer membrane biogenesis can also trigger T6SS activation in P. aeruginosa Specifically, we developed a CRISPR interference (CRISPRi) system to knock down expression of bamA, tolB, and lptD and found that these knockdowns activated T6SS activity. This increase in T6SS activity was dependent on the same signal transduction pathway that was previously shown to be required for the tit-for-tat response. We conclude that outer membrane perturbation can be sensed by P. aeruginosa to activate the T6SS even when the disruption is generated by aberrant cell envelope biogenesis.
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Affiliation(s)
- Anne-Sophie Stolle
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Institute of Infectiology, Center for Molecular Biology of Inflammation, University of Münster, 48149 Münster, Germany
| | | | - Jonida Toska
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - John J Mekalanos
- Department of Microbiology, Harvard Medical School, Boston, MA 02115;
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26
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Liu Y, Zhang Z, Wang F, Li DD, Li YZ. Identification of type VI secretion system toxic effectors using adaptors as markers. Comput Struct Biotechnol J 2020; 18:3723-3733. [PMID: 33304467 PMCID: PMC7714669 DOI: 10.1016/j.csbj.2020.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022] Open
Abstract
Each class of adaptors can be used as an effective marker to identify T6SS effectors. The PRK06147 homolog may be a novel adaptor. 1356 putative toxic effectors related to adaptors from 92 families were identified.
Toxic effectors secreted by the type VI secretion system (T6SS) facilitate interbacterial warfare, as well as pathogenesis toward humans, animals and plants. However, systematically predicting T6SS effectors remains challenging due to their sequence and functional diversity. In this study, we systematically identified putative T6SS toxic effectors in prokaryotic genomes on the basis of the observation that genes encoding adaptor proteins and genes encoding cognate effector proteins are generally adjacent in the genome. Adaptor proteins are mediators that help to load their cognate effectors onto the T6SS spike complex. The contextual genes of the known adaptor proteins (DUF1795, DUF2169 or DUF4123) all exhibited a high proportion of encoding T6SS spike complex protein (VgrG or PAAR) and effector proteins. On the basis of the genomic context, we found that PRK06147 might be a novel adaptor protein. These four adaptors are widely distributed among the bacterial genomes. From neighbors of 5297 adaptor genes, we identified 1356 putative effector genes from 92 different families, and two-thirds were currently annotated as hypothetical proteins or as having unknown functions. Our results indicate that each class of adaptors can be used as an effective marker to identify T6SS toxic effectors, moreover, this approach can promote the discovery of new effectors.
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Affiliation(s)
- Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.,Suzhou Research Institute, Shandong University, Suzhou 215123, China
| | - Feng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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27
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Lin HH, Filloux A, Lai EM. Role of Recipient Susceptibility Factors During Contact-Dependent Interbacterial Competition. Front Microbiol 2020; 11:603652. [PMID: 33281802 PMCID: PMC7690452 DOI: 10.3389/fmicb.2020.603652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved multiple strategies to survive and develop optimal fitness in their ecological niche. They deployed protein secretion systems for robust and efficient delivery of antibacterial toxins into their target cells, therefore inhibiting their growth or killing them. To maximize antagonism, recipient factors on target cells can be recognized or hijacked to enhance the entry or toxicity of these toxins. To date, knowledge regarding recipient susceptibility (RS) factors and their mode of action is mostly originating from studies on the type Vb secretion system that is also known as the contact-dependent inhibition (CDI) system. Yet, recent studies on the type VI secretion system (T6SS), and the CDI by glycine-zipper protein (Cdz) system, also reported the emerging roles of RS factors in interbacterial competition. Here, we review these RS factors and their mechanistic impact in increasing susceptibility of recipient cells in response to CDI, T6SS, and Cdz. Past and future strategies for identifying novel RS factors are also discussed, which will help in understanding the interplay between attacker and prey upon secretion system-dependent competition. Understanding these mechanisms would also provide insights for developing novel antibacterial strategies to antagonize aggressive bacteria-killing pathogens.
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Affiliation(s)
- Hsiao-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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28
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Wood TE, Howard SA, Förster A, Nolan LM, Manoli E, Bullen NP, Yau HCL, Hachani A, Hayward RD, Whitney JC, Vollmer W, Freemont PS, Filloux A. The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology. Cell Rep 2020; 29:187-201.e7. [PMID: 31577948 PMCID: PMC6899460 DOI: 10.1016/j.celrep.2019.08.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/02/2019] [Accepted: 08/27/2019] [Indexed: 01/10/2023] Open
Abstract
The type VI secretion system (T6SS) is crucial in interbacterial competition and is a virulence determinant of many Gram-negative bacteria. Several T6SS effectors are covalently fused to secreted T6SS structural components such as the VgrG spike for delivery into target cells. In Pseudomonas aeruginosa, the VgrG2b effector was previously proposed to mediate bacterial internalization into eukaryotic cells. In this work, we find that the VgrG2b C-terminal domain (VgrG2bC-ter) elicits toxicity in the bacterial periplasm, counteracted by a cognate immunity protein. We resolve the structure of VgrG2bC-ter and confirm it is a member of the zinc-metallopeptidase family of enzymes. We show that this effector causes membrane blebbing at midcell, which suggests a distinct type of T6SS-mediated growth inhibition through interference with cell division, mimicking the impact of β-lactam antibiotics. Our study introduces a further effector family to the T6SS arsenal and demonstrates that VgrG2b can target both prokaryotic and eukaryotic cells. The structure of the VgrG2b C-terminal domain presents a metallopeptidase fold VgrG2b exerts antibacterial activity in the periplasmic space Toxicity of VgrG2b is counteracted by a cognate periplasmic immunity protein VgrG2bC-ter-intoxicated prey cells bleb at the midcell and lyse
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Affiliation(s)
- Thomas E Wood
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Andreas Förster
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Laura M Nolan
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Hamish C L Yau
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Abderrahman Hachani
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Richard D Hayward
- Division of Microbiology and Parasitology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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29
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A Family of T6SS Antibacterial Effectors Related to l,d-Transpeptidases Targets the Peptidoglycan. Cell Rep 2020; 31:107813. [DOI: 10.1016/j.celrep.2020.107813] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/20/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
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30
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Gangadharappa BS, Rajashekarappa S, Sathe G. Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry. ACTA ACUST UNITED AC 2020; 10:123-135. [PMID: 32363156 PMCID: PMC7186543 DOI: 10.34172/bi.2020.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022]
Abstract
Introduction: Serratia marcescens, an opportunistic human pathogen, is reported as an important cause of nosocomial infection and outbreaks. Although the genome of S. marcescens (ATCC 13880) was completely sequenced by 2014, there are no studies on the proteomic profile of the organism. The objective of the present study is to analyze the protein profile of S. marcescens (ATCC 13880) using a high resolution mass spectrometry (MS). Methods: Serratia marcescens ATCC 13880 strain was grown in Luria-Bertani broth and the protein extracted was subjected to trypsin digestion, followed by basic reverse phase liquid chromatography fractionation. The peptide fractions were then analysed using Orbitrap Fusion Mass Spectrometry and the raw MS data were processed in Proteome Discoverer software. Results: The proteomic analysis identified 15 009 unique peptides mapping to 2541 unique protein groups, which corresponds to approximately 54% of the computationally predicted protein-coding genes. Bioinformatic analysis of these identified proteins showed their involvement in biological processes such as cell wall organization, chaperone-mediated protein folding and ATP binding. Pathway analysis revealed that some of these proteins are associated with bacterial chemotaxis and beta-lactam resistance pathway. Conclusion: To the best of our knowledge, this is the first high-throughput proteomics study of S. marcescens (ATCC 13880). These novel observations provide a crucial baseline molecular profile of the S. marcescens proteome which will prove to be helpful for the future research in understanding the host-pathogen interactions during infection, elucidating the mechanism of multidrug resistance, and developing novel diagnostic markers or vaccine for the disease.
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Affiliation(s)
- Bhavya Somalapura Gangadharappa
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bengaluru-560054, Karnataka, India.,Visvesvaraya Technological University, Belagavi-590018, Karnataka, India
| | | | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore-560066, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore-560029, Karnataka, India
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31
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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: 34] [Impact Index Per Article: 8.5] [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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32
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Fernández-Bravo A, Figueras MJ. An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity. Microorganisms 2020; 8:microorganisms8010129. [PMID: 31963469 PMCID: PMC7022790 DOI: 10.3390/microorganisms8010129] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.
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Wu C, Lien Y, Bondage D, Lin J, Pilhofer M, Shih Y, Chang JH, Lai E. Effector loading onto the VgrG carrier activates type VI secretion system assembly. EMBO Rep 2020; 21:e47961. [PMID: 31808291 PMCID: PMC6945064 DOI: 10.15252/embr.201947961] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 01/08/2023] Open
Abstract
The type VI secretion system (T6SS) is used by many bacteria to engage in social behavior and can affect the health of its host plant or animal. Because activities associated with T6SSs are often costly, T6SSs must be tightly regulated. However, our knowledge regarding how T6SS assembly and contraction are regulated remains limited. Using the plant pathogen Agrobacterium tumefaciens, we show that effectors are not just passengers but also impact on T6SS assembly. The A. tumefaciens strain C58 encodes one T6SS and two Tde DNase toxin effectors used as major weapons for interbacterial competition. Here, we demonstrate that loading of Tde effectors onto their cognate carriers, the VgrG spikes, is required for active T6SS secretion. The assembly of the TssBC contractile sheath occurs only in the presence of Tde effectors. The requirement of effector loading for efficient T6SS secretion was also validated in other A. tumefaciens strains. We propose that such a mechanism is used by bacteria as a strategy for efficacious T6SS firing and to ensure that effectors are loaded onto the T6SS prior to completing its assembly.
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Affiliation(s)
- Chih‐Feng Wu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Department of Botany and Plant PathologyOregon State UniversityCorvallisORUSA
| | - Yun‐Wei Lien
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Department of Plant Pathology and MicrobiologyNational Taiwan UniversityTaipeiTaiwan
- Institute of Molecular Biology & BiophysicsEidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Devanand Bondage
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Present address:
Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMDUSA
| | - Jer‐Sheng Lin
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Present address:
Department of Organismic InteractionsMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Martin Pilhofer
- Institute of Molecular Biology & BiophysicsEidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Yu‐Ling Shih
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Jeff H Chang
- Department of Botany and Plant PathologyOregon State UniversityCorvallisORUSA
- Center for Genome Research and BiocomputingOregon State UniversityCorvallisORUSA
| | - Erh‐Min Lai
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Department of Plant Pathology and MicrobiologyNational Taiwan UniversityTaipeiTaiwan
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Mariano G, Trunk K, Williams DJ, Monlezun L, Strahl H, Pitt SJ, Coulthurst SJ. A family of Type VI secretion system effector proteins that form ion-selective pores. Nat Commun 2019; 10:5484. [PMID: 31792213 PMCID: PMC6889166 DOI: 10.1038/s41467-019-13439-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/05/2019] [Indexed: 12/25/2022] Open
Abstract
Type VI secretion systems (T6SSs) are nanomachines widely used by bacteria to deliver toxic effector proteins directly into neighbouring cells. However, the modes of action of many effectors remain unknown. Here we report that Ssp6, an anti-bacterial effector delivered by a T6SS of the opportunistic pathogen Serratia marcescens, is a toxin that forms ion-selective pores. Ssp6 inhibits bacterial growth by causing depolarisation of the inner membrane in intoxicated cells, together with increased outer membrane permeability. Reconstruction of Ssp6 activity in vitro demonstrates that it forms cation-selective pores. A survey of bacterial genomes reveals that genes encoding Ssp6-like effectors are widespread in Enterobacteriaceae and often linked with T6SS genes. We conclude that Ssp6 and similar proteins represent a new family of T6SS-delivered anti-bacterial effectors.
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Affiliation(s)
- Giuseppina Mariano
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Katharina Trunk
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - David J Williams
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Laura Monlezun
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Newcastle University, Richardson Road, Newcastle-upon-Tyne, NE2 4AX, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK.
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Fernández-Bravo A, Kilgore PB, Andersson JA, Blears E, Figueras MJ, Hasan NA, Colwell RR, Sha J, Chopra AK. T6SS and ExoA of flesh-eating Aeromonas hydrophila in peritonitis and necrotizing fasciitis during mono- and polymicrobial infections. Proc Natl Acad Sci U S A 2019; 116:24084-24092. [PMID: 31712444 PMCID: PMC6883842 DOI: 10.1073/pnas.1914395116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An earlier report described a human case of necrotizing fasciitis (NF) caused by mixed infection with 4 Aeromonas hydrophila strains (NF1-NF4). While the NF2, NF3, and NF4 strains were clonal and possessed exotoxin A (ExoA), the NF1 strain was determined to be phylogenetically distinct, harboring a unique type 6 secretion system (T6SS) effector (TseC). During NF1 and NF2 mixed infection, only NF1 disseminated, while NF2 was rapidly killed by a contact-dependent mechanism and macrophage phagocytosis, as was demonstrated by using in vitro models. To confirm these findings, we developed 2 NF1 mutants (NF1ΔtseC and NF1ΔvasK); vasK encodes an essential T6SS structural component. NF1 VasK and TseC were proven to be involved in contact-dependent killing of NF2 in vitro, as well as in its elimination at the intramuscular injection site in vivo during mixed infection, with overall reduced mouse mortality. ExoA was shown to have an important role in NF by both NF1-exoA (with cis exoA) and NF2 during monomicrobial infection. However, the contribution of ExoA was more important for NF2 than NF1 in the murine peritonitis model. The NF2∆exoA mutant did not significantly alter animal mortality or NF1 dissemination during mixed infection in the NF model, suggesting that the ExoA activity was significant at the injection site. Immunization of mice to ExoA protected animals from NF2 monomicrobial challenge, but not from polymicrobial infection because of NF2 clearance. This study clarified the roles of T6SS and ExoA in pathogenesis caused by A. hydrophila NF strains in both mouse peritonitis and NF models in monomicrobial and polymicrobial infections.
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Affiliation(s)
- Ana Fernández-Bravo
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, Instituto de Investigación Sanitaria Pere Virgili, Universidad Rovira i Virgili, 43201 Reus, Spain
| | - Paul B Kilgore
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555
| | - Jourdan A Andersson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555
- Department of Pathology and Immunology and Texas Children's Microbiome Center, Baylor College of Medicine, Houston, TX, 77030
| | - Elizabeth Blears
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555
| | - Maria José Figueras
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, Instituto de Investigación Sanitaria Pere Virgili, Universidad Rovira i Virgili, 43201 Reus, Spain
| | - Nur A Hasan
- Research and Development Department, CosmosID Inc., Rockville, MD 20850
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742
| | - Rita R Colwell
- Research and Development Department, CosmosID Inc., Rockville, MD 20850
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742
- Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205
| | - Jian Sha
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555;
| | - Ashok K Chopra
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555;
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36
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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: 6.4] [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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37
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Lewis JM, Deveson Lucas D, Harper M, Boyce JD. Systematic Identification and Analysis of Acinetobacter baumannii Type VI Secretion System Effector and Immunity Components. Front Microbiol 2019; 10:2440. [PMID: 31736890 PMCID: PMC6833914 DOI: 10.3389/fmicb.2019.02440] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022] Open
Abstract
Many Gram-negative bacteria use a type VI secretion system (T6SS) for microbial warfare and/or host manipulation. Acinetobacter baumannii is an important nosocomial pathogen and many A. baumannii strains utilize a T6SS to deliver toxic effector proteins to surrounding bacterial cells. These toxic effectors are usually delivered together with VgrG proteins, which form part of the T6SS tip complex. All previously identified A. baumannii T6SS effectors are encoded within a three- or four-gene locus that also encodes a cognate VgrG and immunity protein, and sometimes a chaperone. In order to characterize the diversity and distribution of T6SS effectors and immunity proteins in this species, we first identified all vgrG genes in 97 A. baumannii strains via the presence of the highly conserved VgrG domain. Most strains encoded between two and four different VgrG proteins. We then analyzed the regions downstream of the identified vgrG genes and identified more than 240 putative effectors. The presence of conserved domains in these effectors suggested a range of functions, including peptidoglycan hydrolases, lipases, nucleases, and nucleic acid deaminases. However, 10 of the effector groups had no functionally characterized domains. Phylogenetic analysis of these putative effectors revealed that they clustered into 32 distinct groups that appear to have been acquired from a diverse set of ancestors. Corresponding immunity proteins were identified for all but two of the effector groups. Effectors from eight of the 32 groups contained N-terminal rearrangement hotspot (RHS) domains. The C-terminal regions of these RHS proteins, which are predicted to confer the toxic effector function, were very diverse, but the N-terminal RHS domains clustered into just two groups. While the majority of A. baumannii strains contained an RHS type effector, no strains encoded two RHS effectors with similar N-terminal sequences, suggesting that the presence of similar N-terminal RHS domains leads to competitive exclusion. Together, these analyses define the extreme diversity of T6SS effectors within A. baumannii and, as many have unknown functions, future detailed characterization of these effectors may lead to the identification of proteins with novel antibacterial properties.
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Affiliation(s)
- Jessica M Lewis
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Marina Harper
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - John D Boyce
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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38
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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: 60] [Impact Index Per Article: 12.0] [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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39
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Mariano G, Monlezun L, Coulthurst SJ. Dual Role for DsbA in Attacking and Targeted Bacterial Cells during Type VI Secretion System-Mediated Competition. Cell Rep 2019; 22:774-785. [PMID: 29346773 PMCID: PMC5792426 DOI: 10.1016/j.celrep.2017.12.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 01/23/2023] Open
Abstract
Incorporation of disulfide bonds into proteins can be critical for function or stability. In bacterial cells, the periplasmic enzyme DsbA is responsible for disulfide incorporation into many extra-cytoplasmic proteins. The type VI secretion system (T6SS) is a widely occurring nanomachine that delivers toxic effector proteins directly into rival bacterial cells, playing a key role in inter-bacterial competition. We report that two redundant DsbA proteins are required for virulence and for proper deployment of the T6SS in the opportunistic pathogen Serratia marcescens, with several T6SS components being subject to the action of DsbA in secreting cells. Importantly, we demonstrate that DsbA also plays a critical role in recipient target cells, being required for the toxicity of certain incoming effector proteins. Thus we reveal that target cell functions can be hijacked by T6SS effectors for effector activation, adding a further level of complexity to the T6SS-mediated inter-bacterial interactions which define varied microbial communities. Type VI secretion systems (T6SSs) are used by bacteria to attack competitors Disulfide bond formation by DsbA promotes assembly of an active T6SS in Serratia DsbA in the target cell is needed for activation of certain incoming T6SS effectors This work reveals that T6SS-delivered effectors can hijack target cell functions
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Affiliation(s)
- Giuseppina Mariano
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Laura Monlezun
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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40
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Trunk K, Peltier J, Liu YC, Dill BD, Walker L, Gow NAR, Stark MJR, Quinn J, Strahl H, Trost M, Coulthurst SJ. The type VI secretion system deploys antifungal effectors against microbial competitors. Nat Microbiol 2018; 3:920-931. [PMID: 30038307 PMCID: PMC6071859 DOI: 10.1038/s41564-018-0191-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Interactions between bacterial and fungal cells shape many polymicrobial communities. Bacteria elaborate diverse strategies to interact and compete with other organisms, including the deployment of protein secretion systems. The type VI secretion system (T6SS) delivers toxic effector proteins into host eukaryotic cells and competitor bacterial cells, but, surprisingly, T6SS-delivered effectors targeting fungal cells have not been reported. Here we show that the 'antibacterial' T6SS of Serratia marcescens can act against fungal cells, including pathogenic Candida species, and identify the previously undescribed effector proteins responsible. These antifungal effectors, Tfe1 and Tfe2, have distinct impacts on the target cell, but both can ultimately cause fungal cell death. 'In competition' proteomics analysis revealed that T6SS-mediated delivery of Tfe2 disrupts nutrient uptake and amino acid metabolism in fungal cells, and leads to the induction of autophagy. Intoxication by Tfe1, in contrast, causes a loss of plasma membrane potential. Our findings extend the repertoire of the T6SS and suggest that antifungal T6SSs represent widespread and important determinants of the outcome of bacterial-fungal interactions.
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Affiliation(s)
- Katharina Trunk
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Yi-Chia Liu
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Louise Walker
- Aberdeen Fungal Group, Institute of Medical Sciences, MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | - Neil A R Gow
- Aberdeen Fungal Group, Institute of Medical Sciences, MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | - Michael J R Stark
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle-upon-Tyne, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK.
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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41
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Identification of Novel Acinetobacter baumannii Type VI Secretion System Antibacterial Effector and Immunity Pairs. Infect Immun 2018; 86:IAI.00297-18. [PMID: 29735524 DOI: 10.1128/iai.00297-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022] Open
Abstract
The type VI secretion system (T6SS) is a macromolecular machine that delivers protein effectors into host cells and/or competing bacteria. The effectors may be delivered as noncovalently bound cargo of T6SS needle proteins (VgrG/Hcp/PAAR) or as C-terminal extensions of these proteins. Many Acinetobacter baumannii strains produce a T6SS, but little is known about the specific effectors or how they are delivered. In this study, we show that A. baumannii AB307-0294 encodes three vgrG loci, each containing a vgrG gene, a T6SS toxic effector gene, and an antitoxin/immunity gene. Each of the T6SS toxic effectors could kill Escherichia coli when produced in trans unless the cognate immunity protein was coproduced. To determine the role of each VgrG in effector delivery, we performed interbacterial competitive killing assays using A. baumannii AB307-0294 vgrG mutants, together with Acinetobacter baylyi prey cells expressing pairs of immunity genes that protected against two toxic effectors but not a third. Using this approach, we showed that AB307-0294 produces only three T6SS toxic effectors capable of killing A. baylyi and that each VgrG protein is specific for the carriage of one effector. Finally, we analyzed a number of A. baumannii genomes and identified significant diversity in the range of encoded T6SS VgrG and effector proteins, with correlations between effector types and A. baumannii global clone lineages.
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42
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Diverse toxic effectors are harbored by vgrG islands for interbacterial antagonism in type VI secretion system. Biochim Biophys Acta Gen Subj 2018; 1862:1635-1643. [DOI: 10.1016/j.bbagen.2018.04.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 12/26/2022]
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Ostrowski A, Cianfanelli FR, Porter M, Mariano G, Peltier J, Wong JJ, Swedlow JR, Trost M, Coulthurst SJ. Killing with proficiency: Integrated post-translational regulation of an offensive Type VI secretion system. PLoS Pathog 2018; 14:e1007230. [PMID: 30052683 PMCID: PMC6082577 DOI: 10.1371/journal.ppat.1007230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/08/2018] [Accepted: 07/17/2018] [Indexed: 11/20/2022] Open
Abstract
The Type VI secretion system (T6SS) is widely used by bacterial pathogens as an effective weapon against bacterial competitors and is also deployed against host eukaryotic cells in some cases. It is a contractile nanomachine which delivers toxic effector proteins directly into target cells by dynamic cycles of assembly and firing. Bacterial cells adopt distinct post-translational regulatory strategies for deployment of the T6SS. 'Defensive' T6SSs assemble and fire in response to incoming attacks from aggressive neighbouring cells, and can utilise the Threonine Protein Phosphorylation (TPP) regulatory pathway to achieve this control. However, many T6SSs are 'offensive', firing at all-comers without the need for incoming attack or other cell contact-dependent signal. Post-translational control of the offensive mode has been less well defined but can utilise components of the same TPP pathway. Here, we used the anti-bacterial T6SS of Serratia marcescens to elucidate post-translational regulation of offensive T6SS deployment, using single-cell microscopy and genetic analyses. We show that the integration of the TPP pathway with the negative regulator TagF to control core T6SS machine assembly is conserved between offensive and defensive T6SSs. Signal-dependent PpkA-mediated phosphorylation of Fha is required to overcome inhibition of membrane complex assembly by TagF, whilst PppA-mediated dephosphorylation promotes spatial reorientation and efficient killing. In contrast, the upstream input of the TPP pathway defines regulatory strategy, with a new periplasmic regulator, RtkS, shown to interact with the PpkA kinase in S. marcescens. We propose a model whereby the opposing actions of the TPP pathway and TagF impose a delay on T6SS re-assembly after firing, providing an opportunity for spatial re-orientation of the T6SS in order to maximise the efficiency of competitor cell targeting. Our findings provide a better understanding of how bacterial cells deploy competitive weapons effectively, with implications for the structure and dynamics of varied polymicrobial communities.
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Affiliation(s)
- Adam Ostrowski
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Francesca R. Cianfanelli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael Porter
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Giuseppina Mariano
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Julien Peltier
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jun Jie Wong
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Matthias Trost
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sarah J. Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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44
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Effector⁻Immunity Pairs Provide the T6SS Nanomachine its Offensive and Defensive Capabilities. Molecules 2018; 23:molecules23051009. [PMID: 29701633 PMCID: PMC6099711 DOI: 10.3390/molecules23051009] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 01/23/2023] Open
Abstract
Type VI protein secretion systems (T6SSs) are specialized transport apparatus which can target both eukaryotic and prokaryotic cells and play key roles in host⁻pathogen⁻microbiota interactions. Therefore, T6SSs have attracted much attention as a research topic during the past ten years. In this review, we particularly summarized the T6SS antibacterial function, which involves an interesting offensive and defensive mechanism of the effector⁻immunity (E⁻I) pairs. The three main categories of effectors that target the cell wall, membranes, and nucleic acids during bacterial interaction, along with their corresponding immunity proteins are presented. We also discuss structural analyses of several effectors and E⁻I pairs, which explain the offensive and defensive mechanisms underpinning T6SS function during bacterial competition for niche-space, as well as the bioinformatics, proteomics, and protein⁻protein interaction (PPI) methods used to identify and characterize T6SS mediated E⁻I pairs. Additionally, we described PPI methods for verifying E⁻I pairs.
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45
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Alcoforado Diniz J, Hollmann B, Coulthurst SJ. Quantitative Determination of Anti-bacterial Activity During Bacterial Co-culture. Methods Mol Biol 2018; 1615:517-524. [PMID: 28667634 DOI: 10.1007/978-1-4939-7033-9_36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Anti-bacterial activity assays are an important tool in the assessment of the ability of one bacterium to kill or inhibit the growth of another, for example during the study of the Type VI secretion system (T6SS) and the anti-bacterial toxins it secretes. The method we describe here can detect the ability of a bacterial strain to kill or inhibit other bacterial cells in a contact-dependent manner when co-cultured on an agar surface. It is particularly useful since it enumerates the recovery of viable target cells and thus enables quantification of the anti-bacterial activity. We provide a detailed description of how to measure the T6SS-dependent anti-bacterial activity of a bacterium such as Serratia marcescens against a competitor prokaryotic organism, Escherichia coli, and also describe possible variations in the method to allow adaptation to other attacker and target organisms.
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Affiliation(s)
- Juliana Alcoforado Diniz
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Birte Hollmann
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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46
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Wu CF, Smith DA, Lai EM, Chang JH. The Agrobacterium Type VI Secretion System: A Contractile Nanomachine for Interbacterial Competition. Curr Top Microbiol Immunol 2018; 418:215-231. [PMID: 29992360 DOI: 10.1007/82_2018_99] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The bacterial type VI secretion system (T6SS) is a contractile nanomachine dedicated to delivering molecules out of bacterial cells. T6SS-encoding loci are in the genome sequences of many Gram-negative bacteria, and T6SS has been implicated in a plethora of roles. In the majority of cases, the T6SSs deliver effector proteins in a contact-dependent manner to antagonize other bacteria. Current models suggest that the effectors are deployed to influence social interactions in microbial communities. In this chapter, we describe the structure, function, and regulation of the T6SS and its effectors. We provide focus on the T6SS of Agrobacterium tumefaciens, the causative agent of crown gall disease, and relate the role of the T6SS to the ecology of A. tumefaciens.
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Affiliation(s)
- Chih-Feng Wu
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Delaney A Smith
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
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47
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Chen X, Hitchings MD, Mendoza JE, Balanza V, Facey PD, Dyson PJ, Bielza P, Del Sol R. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association. Front Microbiol 2017; 8:1969. [PMID: 29067021 PMCID: PMC5641365 DOI: 10.3389/fmicb.2017.01969] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2022] Open
Abstract
Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.
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Affiliation(s)
- Xiaorui Chen
- Institute of Life Science 1, Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - Matthew D Hitchings
- Institute of Life Science 1, Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - José E Mendoza
- Departamento de Producción Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Virginia Balanza
- Departamento de Producción Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Paul D Facey
- Institute of Life Science 1, Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - Paul J Dyson
- Institute of Life Science 1, Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - Pablo Bielza
- Departamento de Producción Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Ricardo Del Sol
- Institute of Life Science 1, Swansea University Medical School, Swansea University, Swansea, United Kingdom
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A Transcriptional Regulatory Mechanism Finely Tunes the Firing of Type VI Secretion System in Response to Bacterial Enemies. mBio 2017; 8:mBio.00559-17. [PMID: 28830939 PMCID: PMC5565961 DOI: 10.1128/mbio.00559-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ability to detect and measure danger from an environmental signal is paramount for bacteria to respond accordingly, deploying strategies that halt or counteract potential cellular injury and maximize survival chances. Type VI secretion systems (T6SSs) are complex bacterial contractile nanomachines able to target toxic effectors into neighboring bacteria competing for the same colonization niche. Previous studies support the concept that either T6SSs are constitutively active or they fire effectors in response to various stimuli, such as high bacterial density, cell-cell contact, nutrient depletion, or components from dead sibling cells. For Serratia marcescens, it has been proposed that its T6SS is stochastically expressed, with no distinction between harmless or aggressive competitors. In contrast, we demonstrate that the Rcs regulatory system is responsible for finely tuning Serratia T6SS expression levels, behaving as a transcriptional rheostat. When confronted with harmless bacteria, basal T6SS expression levels suffice for Serratia to eliminate the competitor. A moderate T6SS upregulation is triggered when, according to the aggressor-prey ratio, an unbalanced interplay between homologous and heterologous effectors and immunity proteins takes place. Higher T6SS expression levels are achieved when Serratia is challenged by a contender like Acinetobacter, which indiscriminately fires heterologous effectors able to exert lethal cellular harm, threatening the survival of the Serratia population. We also demonstrate that Serratia’s RcsB-dependent T6SS regulatory mechanism responds not to general stress signals but to the action of specific effectors from competitors, displaying an exquisite strategy to weigh risks and keep the balance between energy expenditure and fitness costs. Serratia marcescens is among the health-threatening pathogens categorized by the WHO as research priorities to develop alternative antimicrobial strategies, and it was also recently identified as one major component of the gut microbiome in familial Crohn disease dysbiosis. Type VI secretion systems (T6SSs) stand among the array of survival strategies that Serratia displays. They are contractile multiprotein complexes able to deliver toxic effectors directed to kill bacterial species sharing the same niche and, thus, competing for vital resources. Here, we show that Serratia is able to detect and measure the extent of damage generated through T6SS-delivered toxins from neighboring bacteria and responds by transcriptionally adjusting the expression level of its own T6SS machinery to counterattack the rival. This strategy allows Serratia to finely tune the production of costly T6SS devices to maximize the chances of successfully fighting against enemies and minimize energy investment. The knowledge of this novel mechanism provides insight to better understand bacterial interactions and design alternative treatments for polymicrobial infections.
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49
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Interbacterial predation as a strategy for DNA acquisition in naturally competent bacteria. Nat Rev Microbiol 2017; 15:621-629. [PMID: 28690319 DOI: 10.1038/nrmicro.2017.66] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Natural competence enables bacteria to take up exogenous DNA. The evolutionary function of natural competence remains controversial, as imported DNA can act as a source of substrates or can be integrated into the genome. Exogenous homologous DNA can also be used for genome repair. In this Opinion article, we propose that predation of non-related neighbouring bacteria coupled with competence regulation might function as an active strategy for DNA acquisition. Competence-dependent kin-discriminated killing has been observed in the unrelated bacteria Vibrio cholerae and Streptococcus pneumoniae. Importantly, both the regulatory networks and the mode of action of neighbour predation differ between these organisms, with V. cholerae using a type VI secretion system and S. pneumoniae secreting bacteriocins. We argue that the forced release of DNA from killed bacteria and the transfer of non-clonal genetic material have important roles in bacterial evolution.
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50
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Abstract
Bacterial type VI secretion systems (T6SSs) function as contractile nanomachines to puncture target cells and deliver lethal effectors. In the 10 years since the discovery of the T6SS, much has been learned about the structure and function of this versatile protein secretion apparatus. Most of the conserved protein components that comprise the T6SS apparatus itself have been identified and ascribed specific functions. In addition, numerous effector proteins that are translocated by the T6SS have been identified and characterized. These protein effectors usually represent toxic cargoes that are delivered by the attacker cell to a target cell. Researchers in the field are beginning to better understand the lifestyle or physiology that dictates when bacteria normally express their T6SS. In this article, we consider what is known about the structure and regulation of the T6SS, the numerous classes of antibacterial effector T6SS substrates, and how the action of the T6SS relates to a given lifestyle or behavior in certain bacteria.
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