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Santos MNM, Pintor KL, Hsieh PY, Cheung YW, Sung LK, Shih YL, Lai EM. Agrobacteria deploy two classes of His-Me finger superfamily nuclease effectors exerting different antibacterial capacities against specific bacterial competitors. Front Microbiol 2024; 15:1351590. [PMID: 38426053 PMCID: PMC10902643 DOI: 10.3389/fmicb.2024.1351590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024] Open
Abstract
The type VI secretion system (T6SS) assembles into a contractile nanomachine to inject effectors across bacterial membranes for secretion. The Agrobacterium tumefaciens species complex is a group of soil inhabitants and phytopathogens that deploys T6SS as an antibacterial weapon against bacterial competitors at both inter-species and intra-species levels. The A. tumefaciens strain 1D1609 genome encodes one main T6SS gene cluster and four vrgG genes (i.e., vgrGa-d), each encoding a spike protein as an effector carrier. A previous study reported that vgrGa-associated gene 2, named v2a, encodes a His-Me finger nuclease toxin (also named HNH/ENDO VII nuclease), contributing to DNase-mediated antibacterial activity. However, the functions and roles of other putative effectors remain unknown. In this study, we identified vgrGc-associated gene 2 (v2c) that encodes another His-Me finger nuclease but with a distinct Serine Histidine Histidine (SHH) motif that differs from the AHH motif of V2a. We demonstrated that the ectopic expression of V2c caused growth inhibition, plasmid DNA degradation, and cell elongation in Escherichia coli using DNAse activity assay and fluorescence microscopy. The cognate immunity protein, V3c, neutralizes the DNase activity and rescues the phenotypes of growth inhibition and cell elongation. Ectopic expression of V2c DNase-inactive variants retains the cell elongation phenotype, while V2a induces cell elongation in a DNase-mediated manner. We also showed that the amino acids of conserved SHH and HNH motifs are responsible for the V2c DNase activity in vivo and in vitro. Notably, V2c also mediated the DNA degradation and cell elongation of the target cell in the context of interbacterial competition. Importantly, V2a and V2c exhibit different capacities against different bacterial species and function synergistically to exert stronger antibacterial activity against the soft rot phytopathogen, Dickeya dadantii.
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Affiliation(s)
- Mary Nia M. Santos
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Aquaculture Research and Development Division, Department of Agriculture-National Fisheries Research and Development Institute (DA-NFRDI), Manila, Philippines
| | | | - Pei-Yu Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yee-Wai Cheung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Li-Kang Sung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
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2
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Weisberg AJ, Wu Y, Chang JH, Lai EM, Kuo CH. Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:1-23. [PMID: 37164023 DOI: 10.1146/annurev-phyto-021622-125009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Yu Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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3
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Chepsergon J, Moleleki LN. Rhizosphere bacterial interactions and impact on plant health. Curr Opin Microbiol 2023; 73:102297. [PMID: 37002974 DOI: 10.1016/j.mib.2023.102297] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 04/01/2023]
Abstract
The rhizosphere is a chemically complex environment that harbors a strikingly diverse microbial community. The past few decades have seen a rapid growth in the body of literature on plant-microbe-microbe interactions and plant health. Thus, the aim of this paper is to review current knowledge on plant-microbe-microbe (specifically bacteria) interactions in the rhizosphere and how these influence rhizosphere microbiomes and impact plant health. This article discusses (i) how the plant recruits beneficial rhizosphere bacteria and ii) how competition between rhizosphere bacteria and mechanisms/weapons employed in bacteria-bacteria competition shapes rhizosphere microbiome and in turn affects plant heath. The discussion mainly focuses on interference competition, characterized by production of specialized metabolites (antibacterial compounds) and exploitative competition where a bacterial strain restricts the competitor's access to nutrients such as through secretion of siderophores that could allude to cooperation. Understanding mechanisms employed in bacteria-bacteria and plant-bacteria interactions could provide insights into how to manipulate microbiomes for improved agricultural outcomes.
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Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome. mBio 2023; 14:e0017723. [PMID: 36877054 PMCID: PMC10128044 DOI: 10.1128/mbio.00177-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
The type VI secretion system (T6SS) is deployed by many proteobacteria to secrete effector proteins into bacterial competitors for competition or eukaryotic cells for pathogenesis. Agrobacteria, a group of soilborne phytopathogens causing crown gall disease on various plant species, deploy the T6SS to attack closely and distantly related bacterial species in vitro and in planta. Current evidence suggests that the T6SS is not essential for pathogenesis under direct inoculation, but it remains unknown whether the T6SS influences natural disease incidence or the microbial community within crown galls (i.e., the gallobiome). To address these two key questions, we established a soil inoculation method on wounded tomato seedlings that mimics natural infections and developed a bacterial 16S rRNA gene amplicon enrichment sequencing platform. By comparing the Agrobacterium wild-type strain C58 with two T6SS mutants, we demonstrate that the T6SS influences both disease occurrence and gallobiome composition. Based on multiple inoculation trials across seasons, all three strains induced tumors, but the mutants had significantly lower disease incidences. The season of inoculation played a more important role than the T6SS in shaping the gallobiome. The influence of the T6SS was evident in summer, during which two Sphingomonadaceae species and the family Burkholderiaceae were enriched in the gallobiome induced by the mutants. Further in vitro competition and colonization assays demonstrated the T6SS-mediated antagonism to a Sphingomonas sp. R1 strain isolated from tomato rhizosphere in this study. In conclusion, this work demonstrates that the Agrobacterium T6SS promotes tumorigenesis in infection processes and provides competitive advantages in gall-associated microbiota. IMPORTANCE The T6SS is widespread among proteobacteria and used for interbacterial competition by agrobacteria, which are soil inhabitants and opportunistic bacterial pathogens causing crown gall disease in a wide range of plants. Current evidence indicates that the T6SS is not required for gall formation when agrobacteria are inoculated directly on plant wounding sites. However, in natural settings, agrobacteria may need to compete with other bacteria in bulk soil to gain access to plant wounds and influence the microbial community inside crown galls. The role of the T6SS in these critical aspects of disease ecology have remained largely unknown. In this study, we successfully developed a soil inoculation method coupled with blocker-mediated enrichment of bacterial 16S rRNA gene amplicon sequencing, named SI-BBacSeq, to address these two important questions. We provided evidence that the T6SS promotes disease occurrence and influences crown gall microbiota composition by interbacterial competition.
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Tang MX, Pei TT, Xiang Q, Wang ZH, Luo H, Wang XY, Fu Y, Dong T. Abiotic factors modulate interspecies competition mediated by the type VI secretion system effectors in Vibrio cholerae. THE ISME JOURNAL 2022; 16:1765-1775. [PMID: 35354946 PMCID: PMC9213406 DOI: 10.1038/s41396-022-01228-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 05/06/2023]
Abstract
Vibrio cholerae, the etiological pathogen of cholera, employs its type VI secretion system (T6SS) as an effective weapon to survive in highly competitive communities. Antibacterial and anti-eukaryotic functions of the T6SS depend on its secreted effectors that target multiple cellular processes. However, the mechanisms that account for effector diversity and different effectiveness during interspecies competition remain elusive. Here we report that environmental cations and temperature play a key role in dictating cellular response and effector effectiveness during interspecies competition mediated by the T6SS of V. cholerae. We found that V. cholerae could employ its cell-wall-targeting effector TseH to outcompete the otherwise resistant Escherichia coli and the V. cholerae immunity deletion mutant ∆tsiH when Mg2+ or Ca2+ was supplemented. Transcriptome and genetic analyses demonstrate that the metal-sensing PhoPQ two-component system is important for Mg2+-dependent sensitivity. Competition analysis in infant mice shows that TseH was active under in vivo conditions. Using a panel of V. cholerae single-effector active mutants, we further show that E. coli also exhibited variable susceptibilities to other T6SS effectors depending on cations and temperatures, respectively. Lastly, V. cholerae effector VasX could sensitize Pseudomonas aeruginosa to its intrinsically resistant antibiotic irgasan in a temperature-dependent manner. Collectively, these findings suggest that abiotic factors, that V. cholerae frequently encounters in natural and host environments, could modulate cellular responses and dictate the competitive fitness conferred by the T6SS effectors in complex multispecies communities.
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Affiliation(s)
- 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
| | - 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
| | - Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - 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, 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
| | - Xing-Yu 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, Shanghai, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 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.
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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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7
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Comparative Transcriptome Analysis of Agrobacterium tumefaciens Reveals the Molecular Basis for the Recalcitrant Genetic Transformation of Camellia sinensis L. Biomolecules 2022; 12:biom12050688. [PMID: 35625616 PMCID: PMC9138961 DOI: 10.3390/biom12050688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis L.), an important economic crop, is recalcitrant to Agrobacterium-mediated transformation (AMT), which has seriously hindered the progress of molecular research on this species. The mechanisms leading to low efficiency of AMT in tea plants, related to the morphology, growth, and gene expression of Agrobacterium tumefaciens during tea-leaf explant infection, were compared to AMT of Nicotiana benthamiana leaves in the present work. Scanning electron microscopy (SEM) images showed that tea leaves induced significant morphological aberrations on bacterial cells and affected pathogen–plant attachment, the initial step of a successful AMT. RNA sequencing and transcriptomic analysis on Agrobacterium at 0, 3 and 4 days after leaf post-inoculation resulted in 762, 1923 and 1656 differentially expressed genes (DEGs) between the tea group and the tobacco group, respectively. The expressions of genes involved in bacterial fundamental metabolic processes, ATP-binding cassette (ABC) transporters, two-component systems (TCSs), secretion systems, and quorum sensing (QS) systems were severely affected in response to the tea-leaf phylloplane. Collectively, these results suggest that compounds in tea leaves, especially gamma-aminobutyrate (GABA) and catechins, interfered with plant–pathogen attachment, essential minerals (iron and potassium) acquisition, and quorum quenching (QQ) induction, which may have been major contributing factors to hinder AMT efficiency of the tea plant.
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8
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Czolkoss S, Safronov X, Rexroth S, Knoke LR, Aktas M, Narberhaus F. Agrobacterium tumefaciens Type IV and Type VI Secretion Systems Reside in Detergent-Resistant Membranes. Front Microbiol 2021; 12:754486. [PMID: 34899640 PMCID: PMC8656257 DOI: 10.3389/fmicb.2021.754486] [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: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cell membranes are not homogenous but compartmentalized into lateral microdomains, which are considered as biochemical reaction centers for various physiological processes in eukaryotes and prokaryotes. Due to their special lipid and protein composition, some of these microdomains are resistant to treatment with non-ionic detergents and can be purified as detergent-resistant membranes (DRMs). Here we report the proteome of DRMs from the Gram-negative phytopathogen Agrobacterium tumefaciens. Using label-free liquid chromatography-tandem mass spectrometry, we identified proteins enriched in DRMs isolated under normal and virulence-mimicking growth conditions. Prominent microdomain marker proteins such as the SPFH (stomatin/prohibitin/flotillin/HflKC) proteins HflK, HflC and Atu3772, along with the protease FtsH were highly enriched in DRMs isolated under any given condition. Moreover, proteins involved in cell envelope biogenesis, transport and secretion, as well as motility- and chemotaxis-associated proteins were overrepresented in DRMs. Most strikingly, we found virulence-associated proteins such as the VirA/VirG two-component system, and the membrane-spanning type IV and type VI secretion systems enriched in DRMs. Fluorescence microscopy of the cellular localization of both secretion systems and of marker proteins was in agreement with the results from the proteomics approach. These findings suggest that virulence traits are micro-compartmentalized into functional microdomains in A. tumefaciens.
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Affiliation(s)
- Simon Czolkoss
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Xenia Safronov
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Sascha Rexroth
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Lisa R Knoke
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Meriyem Aktas
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
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Wu CF, Weisberg AJ, Davis EW, Chou L, Khan S, Lai EM, Kuo CH, Chang JH. Diversification of the Type VI Secretion System in Agrobacteria. mBio 2021; 12:e0192721. [PMID: 34517758 PMCID: PMC8546570 DOI: 10.1128/mbio.01927-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022] Open
Abstract
The type VI secretion system (T6SS) is used by many Gram-negative bacteria to deploy toxic effectors for interbacterial competition. This system provides a competitive advantage in planta to agrobacteria, a diverse group with phytopathogenic members capable of genetically transforming plants. To inform on the ecology and evolution of agrobacteria, we revealed processes that diversify their effector gene collections. From genome sequences of diverse strains, we identified T6SS loci, functionally validated associated effector genes for toxicity, and predicted genes homologous to those that encode proteins known to interact with effectors. The gene loci were analyzed in a phylogenetic framework, and results show that strains of some species-level groups have different patterns of T6SS expression and are enriched in specific sets of T6SS loci. Findings also demonstrate that the modularity of T6SS loci and their associated genes engenders dynamicity, promoting reshuffling of entire loci, fragments therein, and domains to swap toxic effector genes across species. However, diversification is constrained by the need to maintain specific combinations of gene subtypes, congruent with observations that certain genes function together to regulate T6SS loading and activation. Data are consistent with a scenario where species can acquire unique T6SS loci that are then reshuffled across the genus in a restricted manner to generate new combinations of effector genes. IMPORTANCE The T6SS is used by several taxa of Gram-negative bacteria to secrete toxic effector proteins to attack others. Diversification of effector collections shapes bacterial interactions and impacts the health of hosts and ecosystems in which bacteria reside. We uncovered the diversity of T6SS loci across a genus of plant-associated bacteria and show that diversification is driven by the acquisition of new loci and reshuffling among species. However, linkages between specific subtypes of genes need to be maintained to ensure that proteins whose interactions are necessary to activate the T6SS remain together. Results reveal how organization of gene loci and domain structure of genes provides flexibility to diversify under the constraints imposed by the system. Findings inform on the evolution of a mechanism that influences bacterial communities.
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Affiliation(s)
- Chih-Feng Wu
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, USA
| | - Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Surtaz Khan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
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