1
|
Lee Y, Jin Y, Wu W, Ha UH. Elongation factor-G1A identified as a novel effector protein translocated into cells and a key modulator of Pseudomonas aeruginosa physiology and host cellular responses. Microb Pathog 2025; 205:107720. [PMID: 40403987 DOI: 10.1016/j.micpath.2025.107720] [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: 01/16/2025] [Revised: 05/07/2025] [Accepted: 05/18/2025] [Indexed: 05/24/2025]
Abstract
Pseudomonas aeruginosa has two closely related elongation factors, EF-G1A and EF-G1B, which share 90 % sequence similarity. Despite their high sequence homology, the role of EF-G in P. aeruginosa pathogenesis remains not fully understood. In our study, we found that compared to EF-G1B, EF-G1A expression reduced bacterial growth and twitching motility, while increasing swimming motility. Notably, EF-G1A was translocated into host cells in a T6SS-dependent manner. This translocation was significantly reduced, though not completely abolished, in strains with mutations in both the T6SS spike protein VgrG1a and the tube protein Hcp1, suggesting that while EF-G1A translocation is influenced by T6SS, additional components are also involved. Moreover, EF-G1A expression reduced T3SS-mediated morphological alterations, as evidenced by the downregulation of T3SS effectors such as ExoS and ExoT. EF-G1A was also found to suppress activation of the NF-κB signaling pathway, leading to decreased production of inflammatory cytokines including IL-6, IL-8, and TNFα. These findings highlight EF-G1A as a key modulator, affecting both P. aeruginosa physiology and host cellular responses, thereby providing new insights into the complex role of EF-G1A in bacterial pathogenesis.
Collapse
Affiliation(s)
- Yeji Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, Nankai University, Tianjin, 300071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, Nankai University, Tianjin, 300071, China
| | - Un-Hwan Ha
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea.
| |
Collapse
|
2
|
Silva UCM, da Silva DRC, Cuadros-Orellana S, Moreira LM, Leite LR, Medeiros JD, Felestrino EB, Caneschi WL, Almeida NF, Silva RS, Oliveira-Paiva CA, Dos Santos VL. Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective. Braz J Microbiol 2025; 56:1219-1239. [PMID: 40131635 PMCID: PMC12095751 DOI: 10.1007/s42770-025-01652-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 02/13/2025] [Indexed: 03/27/2025] Open
Abstract
We investigated the plant growth-promoting potential of two endophytic strains of Serratia marcescens, namely SmCNPMS2112 and SmUFMG85, which were isolated from the roots of the same maize (Zea mays) plant. The strains were evaluated in vitro for their ability to produce siderophores and indoleacetic acid, form biofilm, solubilize iron phosphate (Fe-P) and Araxá rock phosphate (RP), mineralize phytate, and for their ability to adhere and colonize host roots. Additionally, their plant growth-promoting potential was tested in vivo under greenhouse conditions using millet grown in soil under two fertilization schemes (triple superphosphate, TSP, or commercial rock phosphate, cRP). Both strains improved at least five physiological traits of millet or P content in soil. In order to elucidate the genetic basis of the plant growth-promoting ability of these strains, their genomes were compared. While both genomes exhibited a similar overall functional profile, each strain had unique features. SmCNPMS2112 contained genes related to arsenic and aromatic hydrocarbons degradation, whereas SmUFMG85 harbored genes related to rhamnolipid biosynthesis and chromium bioremediation. Also, we observe a unique repertoire of genes related to plant growth-promotion (PGP) in the SmUFMG85 genome, including oxalate decarboxylase (OxdC), associated with the catabolism of oxalic acid, and aerobactin siderophore (lucD) in the genome of SmCNPMS2112. The alkaline phosphatase was observed on two strains, but acid phosphatase was exclusive to SmUFMG85. Eighteen secondary metabolic gene clusters, such as those involved in the biosynthesis of macrolides and bacillomycin, among others, occur in both strains. Moreover, both genomes contained prophages, suggesting that viral-mediated horizontal gene transfer may be a key mechanism driving genomic variability in the endophytic environment. Indeed, the most genes unique and accessory of SmUFMG85 and SmCNPMS2112 were localized in genomic islands, highlighting genome plasticity and its underlying drivers. To investigate the ecological distribution of plant-interaction traits in the genus Serratia, the genomes of SmUFMG85 and SmCNPMS2112 strains were compared with those of other 19 Serratia strains of different species, which were isolated from different environments. We observe that many features for PGP are present in all genomes, regardless of niche, for instance: formation of flagella, fimbriae and pili, chemotaxis, biosynthesis of siderophores, indole-3-acetic acid (IAA) and volatile organic (VOC) and inorganic (VIC) compounds, such as acetoin and HCN. Also, all the analyzed genomes show an antimicrobial resistance repertoire of genes that confer resistance to several antibiotics belonging to the groups of aminoglycosides and quinolones, for instance. Also, from a niche partitioning perspective, secretion system preference and the ability to produce exopolysaccharides involved in biofilm formation are among the features that vary the most among strains, and most likely influence niche adaptation in Serratia spp., even though only the latter seems to be a feature specifically associated with virulence in the analyzed strains. Our results show that populations of bacteria sharing the same niche can present significant physiological and genomic differences, and reveal the intraspecific metabolic plasticity that underlie plant-bacteria interactions. Also, this study reveals the potential of two Serratia marcescens strains as bioinoculants in agriculture. Considering that Serratia spp. are regarded as low risk biological agents, despite the fact that they can be associated with human disease, we suggest that strain biosafety be evaluated using a combination of genome and phenotypic analyses, as presented herein.
Collapse
Affiliation(s)
- Ubiana C Mourão Silva
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Av. Antônio CarlosBelo Horizonte, Pampulha, MG, 662731270901, Brazil
| | - Daliane R C da Silva
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Av. Antônio CarlosBelo Horizonte, Pampulha, MG, 662731270901, Brazil
| | - Sara Cuadros-Orellana
- Centro de Biotecnología de los Recursos Naturales, Universidad Católica del Maule, Talca, Chile
| | - Leandro M Moreira
- Núcleo de Pesquisas Em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Laura R Leite
- Grupo de Pesquisa Em Genômica E Informática de Biossistemas, Centro de Pesquisa René Rachou Research, Belo Horizonte, Fiocruz, MG, Brazil
- Grupo Fleury S. A, Belo Horizonte, MG, Brazil
| | - Julliane D Medeiros
- Laboratório de Genômica e Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Erica B Felestrino
- Núcleo de Pesquisas Em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Washington L Caneschi
- Núcleo de Pesquisas Em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Robson S Silva
- Faculdade de Computação, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | | | - Vera Lúcia Dos Santos
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Av. Antônio CarlosBelo Horizonte, Pampulha, MG, 662731270901, Brazil.
| |
Collapse
|
3
|
Yang F, Li M, Wu H, Yu C, Liu W, Chen H. Comparative genomics-based insights into Pantoea ananatis strains, isolated from white spot diseased leaves of maize with plant growth-promoting attributes. Appl Environ Microbiol 2025:e0032925. [PMID: 40387325 DOI: 10.1128/aem.00329-25] [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: 02/14/2025] [Accepted: 04/13/2025] [Indexed: 05/20/2025] Open
Abstract
Pantoea ananatis is a member of the Enterobacteriaceae family known for its broad host adaptability. This study isolated 10 P. ananatis strains from white spot (MWS)-diseased leaves of maize (Zea mays) grown in Yunnan Province, China, and analyzed their putative functions, genomic diversity, and variation. The inoculation tests revealed that none of the 10 isolates caused MWS symptoms in maize. Nine maize isolates, except for S47, induced a hypersensitive response (HR) in tobacco and caused rot symptoms in onion. Most isolates exhibited plant growth-promoting characteristics, with strains JCC14, JCY1, and S47 significantly enhancing maize seedling growth parameters. Genomic sequencing of 10 maize isolates and two rice isolates revealed that 12 isolates clustered into three groups, with an open pan-genome identified. Ancestral reconstruction indicated that the genome size increased in Group A and then decreased in Group B, with significant gains in orthologous groups at Node 14, the most recent common ancestor (MRCA) of Group A and Group B, and at Node 19, the MRCA of seven maize-isolated strains and other Group B strains. Additionally, 11 single-copy orthologous groups were under positive selection. Furthermore, the HIVir (high virulence, also known as PASVIL, P. ananatis-specific virulence locus) cluster and type VI secretion system-related genes were conserved in certain P. ananatis strains but were not related to their group divergences. This study not only reveals the diverse functions of MWS-diseased maize P. ananatis isolates, but also enhances our understanding of divergent genome evolution and environmental adaptation across P. ananatis species.IMPORTANCEPantoea ananatis is a bacterium commonly found in various agronomic crops. Maize white spot (MWS) has been one of the most destructive diseases affecting maize, leading to significant economic losses. This study clarified that P. ananatis strains colonized maize leaves but were not the causal agents of MWS in Yunnan Province, China. Moreover, most of these P. ananatis strains exhibited plant growth-promoting (PGP) activities, induced hypersensitive response (HR) activity on tobacco, and caused rot symptoms in onion. Notably, the analysis of divergence throughout the evolutionary process revealed significant genomic evolution and environmental adaptation in these P. ananatis strains. This highlights the genetic exchange that has shaped the genome of P. ananatis. These findings improve our understanding of the functional diversity of P. ananatis strains across different hosts and their positions within the evolutionary lineages of P. ananatis species.
Collapse
Affiliation(s)
- Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miao Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hanxiang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
4
|
Liu Y, Shan X, Liu C, Chen H. Microcosm experiments deciphered resistome coalescence, risks and source-sink relationship of antibiotic resistance in the soil irrigated with reclaimed water. JOURNAL OF HAZARDOUS MATERIALS 2025; 488:137398. [PMID: 39874760 DOI: 10.1016/j.jhazmat.2025.137398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 01/02/2025] [Accepted: 01/25/2025] [Indexed: 01/30/2025]
Abstract
Reclaimed water is widely used in agriculture irrigation to alleviate water scarcity, whereas the dissemination of antibiotic resistance genes (ARGs) in the soil it introduces has attracted widespread attention. Currently, few studies have systematically elucidated the coalescence of the resistome originating from reclaimed water with the soil's native community. Also, the effects and mechanisms of irrigation on the dissemination of ARGs in soils have yet to be demonstrated. To address this gap, microcosm experiments have been conducted in this study to decipher the resistome coalescence, risks and source-sink relationship of ARGs in soils irrigated with reclaimed water. The results show 237 ARGs, 55 mobile genetic elements (MGEs) and 28 virulence factors were identified in the irrigated soils. Irrigation increased the abundance and diversity of ARGs in the soil by introducing antibiotic-resistant bacteria, altering the microbial community and facilitating horizontal transfer of ARGs via MGEs, and ultimately exacerbated resistome risks in the environment. Relatively, a larger volume of irrigation water led to a more complex propagation network of the resistome. Source apportionment analysis suggested reclaimed water contributed less than 15 % of ARGs in the irrigated soils, whereas its contribution proportion increased with a larger volume of irrigation water.
Collapse
Affiliation(s)
- Yiyi Liu
- College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Xin Shan
- College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Chang Liu
- College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Haiyang Chen
- College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing, 100875, China.
| |
Collapse
|
5
|
Pérez-Lorente AI, Araujo-Garrido M, de Vicente A, Romero D, Molina-Santiago C. Engineering the T6SS of Pseudomonas for targeted delivery of antibacterial and antifungal effectors. J Biol Eng 2025; 19:28. [PMID: 40176102 PMCID: PMC11966926 DOI: 10.1186/s13036-025-00497-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 03/26/2025] [Indexed: 04/04/2025] Open
Abstract
BACKGROUND Bacteria employ diverse molecular systems, such as the type VI secretion system (T6SS) to outcompete other microorganisms and adapt to ecological niches. The T6SS is a versatile nanomachine capable of delivering toxic effectors into neighboring cells, providing advantages in bacterial interactions. In recent years, T6SSs have been proposed as promising tools for engineering selective antimicrobial platforms. RESULTS In this study, we successfully engineered Pseudomonas putida KT2440 to heterologously express and release T6SS effectors. The expression of Tse1, an effector from Pseudomonas chlororaphis, induced sporulation in plant-beneficial Bacillus strains via a T6SS-dependent mechanism, particularly when Tse1 was paired with a PAAR protein. Similarly, the engineered strain effectively inhibited Aeromonas hydrophila growth using the phospholipase toxin TplE from Pseudomonas aeruginosa. Furthermore, antifungal activity was achieved by coexpressing Tfe2, an effector from Serratia marcescens, with VgrGs, resulting in increased reactive oxygen species levels and cellular damage in Botrytis cinerea. Importantly, the T6SS was also employed to deliver non-T6SS effectors such as chitosanase, demonstrating its versatility in degrading fungal cell walls. CONCLUSIONS Our findings demonstrate that the T6SS can be engineered to deliver both canonical and noncanonical effectors, providing a robust platform for targeted antibacterial and antifungal applications. The modularity of the system enables precise pairing of effectors with structural components such as VgrG and PAAR proteins, optimizing delivery efficiency. These engineered systems provide new opportunities for the development of biocontrol strategies in agriculture, microbiome modulation, and potential therapeutic applications. Future advancements in bioinformatics and protein engineering will further increase the specificity and functionality of T6SS-based delivery systems, offering innovative tools for managing microbial ecosystems and addressing global challenges in health and agriculture.
Collapse
Affiliation(s)
- Alicia Isabel Pérez-Lorente
- Departamento de Microbiologia, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Mario Araujo-Garrido
- Departamento de Microbiologia, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Diego Romero
- Departamento de Microbiologia, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Departamento de Microbiologia, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain.
| |
Collapse
|
6
|
Luo C, Gu H, Pan D, Zhao Y, Zheng A, Zhu H, Zhang C, Li C, Zhang J, Chen C, Xu L, Pan J, Shen X, Wang Y. Pseudomonas aeruginosa T6SS secretes an oxygen-binding hemerythrin to facilitate competitive growth under microaerobic conditions. Microbiol Res 2025; 293:128052. [PMID: 39813750 DOI: 10.1016/j.micres.2025.128052] [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: 11/24/2024] [Revised: 12/26/2024] [Accepted: 01/04/2025] [Indexed: 01/18/2025]
Abstract
Pseudomonas aeruginosa is a prominent respiratory pathogen in cystic fibrosis (CF) patients, thriving in the hypoxic airway mucus. Previous studies have established the role of the oxygen-binding hemerythrin, Mhr, in enhancing P. aeruginosa's fitness under microaerobic conditions. However, the specific mechanisms by which Mhr operates remain unclear. This study uniquely identifies Mhr as an effector of the H2-Type VI Secretion System (H2-T6SS) and elucidates its role in the transport and interaction mechanisms that confer a growth advantage under microaerobic conditions. Our findings demonstrate that mhr expression is directly regulated by Anr and Dnr. Western blot analysis confirms that Mhr is secreted extracellularly via the H2-T6SS. The oxygen-binding Mhr re-enters P. aeruginosa through the OprG porin. Then, Mhr interacts with cbb3-type cytochrome c oxidase (cbb3-CcO) subunits CcoP1/CcoP2, significantly impacting intracellular NADH/NAD+ levels. These insights suggest that the T6SS-mediated secretion and transport of Mhr represent a novel mechanism by which P. aeruginosa acquires and delivers oxygen, potentially enhancing microaerobic respiration, energy production, and growth under microaerobic conditions.
Collapse
Affiliation(s)
- Chunhui Luo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huawei Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Damin Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Anqi Zheng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hai Zhu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chen Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chen Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhang
- College of Life Sciences, Tarim University, Alar,Xinjiang 843300, China
| | - Can Chen
- Institute of Food and Drug Inspection, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Lei Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junfeng Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
7
|
Dyrma S, Pei TT, Liang X, Dong T. Not just passengers: effectors contribute to the assembly of the type VI secretion system as structural building blocks. J Bacteriol 2025; 207:e0045524. [PMID: 39902958 PMCID: PMC11925235 DOI: 10.1128/jb.00455-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2025] Open
Abstract
Protein secretion systems are critical macromolecular machines employed by bacteria to interact with diverse environments and hosts during their life cycle. Cytosolically produced protein effectors are translocated across at least one membrane to the outside of the cells or directly into target cells. In most secretion systems, these effectors are mere passengers in unfolded or folded states. However, the type VI secretion system (T6SS) stands out as a powerful contractile device that requires some of its effectors as structural components. This review aims to provide an updated view of the diverse functions of effectors, especially focusing on their roles in T6SS assembly, the implications for T6SS engineering, and the potential of recently developed T6SS models to study effector-T6SS association.
Collapse
Affiliation(s)
- Sherina Dyrma
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Tong-Tong Pei
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiaoye Liang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| |
Collapse
|
8
|
Wang ZH, An Y, Zhao T, Pei TT, Wang DY, Liang X, Qin W, Dong T. Amidase and lysozyme dual functions in TseP reveal a new family of chimeric effectors in the type VI secretion system. eLife 2025; 13:RP101125. [PMID: 40063082 PMCID: PMC11893102 DOI: 10.7554/elife.101125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2025] Open
Abstract
Peptidoglycan (PG) serves as an essential target for antimicrobial development. An overlooked reservoir of antimicrobials lies in the form of PG-hydrolyzing enzymes naturally produced for polymicrobial competition, particularly those associated with the type VI secretion system (T6SS). Here, we report that a T6SS effector TseP, from Aeromonas dhakensis, represents a family of effectors with dual amidase-lysozyme activities. In vitro PG-digestion coupled with LC-MS analysis revealed the N-domain's amidase activity, which is neutralized by either catalytic mutations or the presence of the immunity protein TsiP. The N-domain, but not the C-domain, of TseP is sufficient to restore T6SS secretion in T6SS-defective mutants, underscoring its critical structural role. Using pull-down and secretion assays, we showed that these two domains interact directly with a carrier protein VgrG2 and can be secreted separately. Homologs in Aeromonas hydrophila and Pseudomonas syringae exhibited analogous dual functions. Additionally, N- and C-domains display distinctive GC contents, suggesting an evolutionary fusion event. By altering the surface charge through structural-guided design, we engineered the TsePC4+ effector that successfully lyses otherwise resistant Bacillus subtilis cells, enabling the T6SS to inhibit B. subtilis in a contact-independent manner. This research uncovers TseP as a new family of bifunctional chimeric effectors targeting PG, offering a potential strategy to harness these proteins in the fight against antimicrobial resistance.
Collapse
Affiliation(s)
- 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 UniversityShanghaiChina
- Department of Immunology and Microbiology, School of Life Sciences, Guangming Advanced Research Institute, Southern University of Science and TechnologyShenzhenChina
| | - Ying An
- Department of Immunology and Microbiology, School of Life Sciences, Guangming Advanced Research Institute, Southern University of Science and TechnologyShenzhenChina
| | - Ting Zhao
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghaiChina
- School of Pharmaceutical Sciences, Wuhan UniversityWuhanChina
| | - Tong-Tong Pei
- Department of Immunology and Microbiology, School of Life Sciences, Guangming Advanced Research Institute, Southern University of Science and TechnologyShenzhenChina
| | - Dora Yuping Wang
- Department of Immunology and Microbiology, School of Life Sciences, Guangming Advanced Research Institute, Southern University of Science and TechnologyShenzhenChina
- Department of Physiology, University of TorontoTorontoCanada
| | - Xiaoye Liang
- Department of Immunology and Microbiology, School of Life Sciences, Guangming Advanced Research Institute, Southern University of Science and TechnologyShenzhenChina
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghaiChina
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Guangming Advanced Research Institute, Southern University of Science and TechnologyShenzhenChina
| |
Collapse
|
9
|
Brüderlin M, Kolesnikov M, Röthlin F, Lim RYH, Basler M. Pseudomonas aeruginosa assembles H1-T6SS in response to physical and chemical damage of the outer membrane. SCIENCE ADVANCES 2025; 11:eadr1713. [PMID: 40043119 PMCID: PMC11881912 DOI: 10.1126/sciadv.adr1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 01/30/2025] [Indexed: 05/13/2025]
Abstract
Bacteria respond to environmental stimuli and attacks from competing organisms. Pseudomonas aeruginosa assembles the type VI secretion system (H1-T6SS) to precisely retaliate against aggressive competing bacteria. However, we lack an understanding of how the H1-T6SS assembly dynamically responds to nanomechanical forces. To address this, we analyzed live cells using correlative atomic force microscopy (AFM) and fluorescence microscopy. We show that indentation forces above 7 nanonewtons trigger local, repeated and targeted H1-T6SS assemblies within seconds of impact by the AFM tip. Analysis of the corresponding AFM force curves shows that a breach of a single layer of the cell envelope is necessary and sufficient for triggering H1-T6SS assembly. Accordingly, polymyxin B nonapeptide, which damages the outer membrane, also triggers H1-T6SS assembly. This suggests that P. aeruginosa has evolved a danger-sensing mechanism that enables rapid and precise deployment of its antibacterial H1-T6SS in response to breaches in the outer membrane.
Collapse
Affiliation(s)
- Mitchell Brüderlin
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Maxim Kolesnikov
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Florian Röthlin
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Marek Basler
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| |
Collapse
|
10
|
Duan Z, Liao L, Lai T, Yang R, Zhang J, Chen B. Dynamic and intricate regulation by the Csr sRNAs in the Arctic Pseudoalteromonas fuliginea. Commun Biol 2025; 8:369. [PMID: 40044903 PMCID: PMC11882849 DOI: 10.1038/s42003-025-07780-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 02/19/2025] [Indexed: 03/09/2025] Open
Abstract
The Csr (Carbon Storage Regulator) system is pivotal in controlling various cellular functions in most bacteria, primarily through the CsrA protein and its antagonistic sRNAs. However, riboregulatory networks are less explored in non-model organisms, particularly those in extreme environments. In this study, we discovered two new sRNAs of the Csr system, Pf2 and Pf3, in the Arctic bacterium Pseudoalteromonas fuliginea BSW20308, along with the previously known Pf1. By studying the impact of these Pf sRNAs on CsrA targetomes and physiological processes, we found a significant influence on various cellular functions and a collective effect on the interaction dynamics between CsrA and RNAs. Furthermore, we identified additional sRNAs that can interact with CsrA and mRNAs. Overall, our results emphasize the growing influence of the Csr system on cellular physiology through intricate sRNA regulation of CsrA, revealing riboregulatory network complexity and significance in non-model organisms.
Collapse
Affiliation(s)
- Zedong Duan
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; Shanghai Key Laboratory of Polar Life and Environment Sciences; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Li Liao
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; Shanghai Key Laboratory of Polar Life and Environment Sciences; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China.
| | - Tingyi Lai
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; Shanghai Key Laboratory of Polar Life and Environment Sciences; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Ruyi Yang
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jin Zhang
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Bo Chen
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| |
Collapse
|
11
|
Pan TL, Cha JL, Wang H, Zhang JS, Xiao JL, Shen J, Zhou M, Li Y, Ma JZ, Zhao KY, Zhang YK, Xiao P, Gao H. The CRISPR/Cas9-Mediated Knockout of VgrG2 in Wild Pathogenic E. coli to Alleviate the Effects on Cell Damage and Autophagy. Vet Sci 2025; 12:249. [PMID: 40266908 PMCID: PMC11945575 DOI: 10.3390/vetsci12030249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 02/17/2025] [Accepted: 02/18/2025] [Indexed: 04/25/2025] Open
Abstract
CRISPR/Cas9, as a well-established gene editing technology, has been applied in numerous model organisms, but its application in wild-type E. coli remains limited. Pathogenic wild-type E. coli, a major cause of foodborne illnesses and intestinal inflammation in humans and animals, poses a significant global public health threat. The valine-glycine repeat protein G (VgrG) is a key virulence factor that enhances E. coli pathogenicity. In this study, PCR was used to identify 50 strains carrying the virulence gene VgrG2 out of 83 wild pathogenic E. coli strains, with only one strain sensitive to kanamycin and spectinomycin. A homologous repair template for VgrG2 was constructed using overlap PCR. A dual-plasmid CRISPR/Cas9 system, combining pTarget (spectinomycin resistance) and pCas (kanamycin resistance) with Red homologous recombination, was then used to induce genomic cleavage and knock out VgrG2. PCR and sequencing confirmed the deletion of a 1708 bp fragment of the VgrG2 gene in wild-type E. coli. IPEC-J2 cells were infected with E. coli-WT and E. coli ∆VgrG2, and treated with the mTOR inhibitor rapamycin to study the effects of VgrG2 on the mTOR signaling pathway. The qPCR results showed that VgrG2 activated the mTOR pathway, suppressed mTOR and p62 mRNA levels, and upregulated the autophagy-related genes and LC3-II protein expression. In conclusion, we utilized CRISPR/Cas9 technology to achieve large-fragment deletions in wild-type E. coli, revealing that VgrG2 activates the mTOR signaling pathway and upregulates autophagy markers. These findings offer new insights into E. coli genome editing and clarifies the pathogenic mechanisms through which VgrG2 induces cellular damage.
Collapse
Affiliation(s)
- Tian-Ling Pan
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Jin-Long Cha
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Hao Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (M.Z.)
| | - Jing-Song Zhang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Jin-Long Xiao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Jue Shen
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Meng Zhou
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (M.Z.)
| | - Yue Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Jin-Zhi Ma
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Kai-Yuan Zhao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Yong-Kang Zhang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Peng Xiao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| | - Hong Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China; (T.-L.P.); (J.-L.C.); (J.-S.Z.); (J.-L.X.); (J.S.); (Y.L.); (J.-Z.M.); (K.-Y.Z.); (Y.-K.Z.)
| |
Collapse
|
12
|
Fridman CM, Keppel K, Rudenko V, Altuna-Alvarez J, Albesa-Jové D, Bosis E, Salomon D. A new class of type VI secretion system effectors can carry two toxic domains and are recognized through the WHIX motif for export. PLoS Biol 2025; 23:e3003053. [PMID: 40096082 DOI: 10.1371/journal.pbio.3003053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 03/28/2025] [Accepted: 02/05/2025] [Indexed: 03/19/2025] Open
Abstract
Gram-negative bacteria employ the type VI secretion system (T6SS) to deliver toxic effectors into neighboring cells and outcompete rivals. Although many effectors have been identified, their secretion mechanism often remains unknown. Here, we describe WHIX, a domain sufficient to mediate the secretion of effectors via the T6SS. Remarkably, we find WHIX in T6SS effectors that contain a single toxic domain, as well as in effectors that contain two distinct toxic domains fused to either side of WHIX. We demonstrate that the latter, which we name double-blade effectors, require two cognate immunity proteins to antagonize their toxicity. Furthermore, we show that WHIX can be used as a chassis for T6SS-mediated secretion of multiple domains. Our findings reveal a new class of polymorphic T6SS cargo effectors with a unique secretion domain that can deploy two toxic domains in one shot, possibly reducing recipients' ability to defend themselves.
Collapse
Affiliation(s)
- Chaya Mushka Fridman
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kinga Keppel
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Vladislav Rudenko
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jon Altuna-Alvarez
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Leioa, Spain
| | - David Albesa-Jové
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Leioa, Spain
- Departamento de Bioquímica y Biología Molecular, University of the Basque Country, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
13
|
Rojas-Palomino J, Altuna-Alvarez J, González-Magaña A, Queralt-Martín M, Albesa-Jové D, Alcaraz A. Electrophysiological dissection of the ion channel activity of the Pseudomonas aeruginosa ionophore protein toxin Tse5. Chem Phys Lipids 2025; 267:105472. [PMID: 39778700 DOI: 10.1016/j.chemphyslip.2025.105472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 12/19/2024] [Accepted: 01/05/2025] [Indexed: 01/11/2025]
Abstract
We present an in-depth electrophysiological analysis of Tse5, a pore-forming toxin (PFT) delivered by the type VI secretion system (T6SS) of Pseudomonas aeruginosa. The T6SS is a sophisticated bacterial secretion system that injects toxic effector proteins into competing bacteria or host cells, providing a competitive advantage by disabling other microbes and modulating their environment. Our findings highlight the dependency of Tse5 insertion on membrane charge and electrolyte concentration, suggesting an in vivo effect from the periplasmic space. Conductance and selectivity experiments reveal a predominant and reproducible pore architecture of Tse5, characterized by a weak cation selectivity without chemical specificity. pH titration experiments suggest a proteolipidic pore structure influenced by both protein and lipid charges, a hypothesis further supported by experiments involving engineered mutants of Tse5 with altered glycine zippers. These results significantly advance our understanding of Tse5's molecular mechanism of toxicity, paving the way for potential applications in biosensing and macromolecular delivery.
Collapse
Affiliation(s)
- Jessica Rojas-Palomino
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, Castellón 12071, Spain
| | - Jon Altuna-Alvarez
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, Leioa 48940, Spain
| | - Amaia González-Magaña
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, Leioa 48940, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, Castellón 12071, Spain
| | - David Albesa-Jové
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, Leioa 48940, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain.
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, Castellón 12071, Spain.
| |
Collapse
|
14
|
Sachar K, Kanarek K, Colautti J, Kim Y, Bosis E, Prehna G, Salomon D, Whitney JC. A conserved chaperone protein is required for the formation of a noncanonical type VI secretion system spike tip complex. J Biol Chem 2025; 301:108242. [PMID: 39880087 PMCID: PMC11883445 DOI: 10.1016/j.jbc.2025.108242] [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: 12/03/2024] [Revised: 01/17/2025] [Accepted: 01/20/2025] [Indexed: 01/31/2025] Open
Abstract
Type VI secretion systems (T6SSs) are dynamic protein nanomachines found in Gram-negative bacteria that deliver toxic effector proteins into target cells in a contact-dependent manner. Prior to secretion, many T6SS effector proteins require chaperones and/or accessory proteins for proper loading onto the structural components of the T6SS apparatus. However, despite their established importance, the precise molecular function of several T6SS accessory protein families remains unclear. In this study, we set out to characterize the DUF2169 family of T6SS accessory proteins. Using gene co-occurrence analyses, we find that DUF2169-encoding genes strictly co-occur with genes encoding T6SS spike complexes formed by valine-glycine repeat protein G (VgrG) and DUF4150 domains. Although structurally similar to Pro-Ala-Ala-Arg (PAAR) domains, "PAAR-like" DUF4150 domains lack PAAR motifs and instead contain a conserved PIPY motif, leading us to designate them PIPY domains. Next, we present both genetic and biochemical evidence that PIPY domains require a cognate DUF2169 protein to form a functional T6SS spike complex with VgrG. This contrasts with canonical PAAR proteins, which bind VgrG on their own to form functional spike complexes. By solving the first crystal structure of a DUF2169 protein, we show that this T6SS accessory protein adopts a novel protein fold. Furthermore, biophysical and structural modeling data suggest that DUF2169 contains a dynamic loop that physically interacts with a hydrophobic patch on the surface of its cognate PIPY domain. Based on these findings, we propose a model whereby DUF2169 proteins function as molecular chaperones that maintain VgrG-PIPY spike complexes in a secretion-competent state prior to their export by the T6SS apparatus.
Collapse
Affiliation(s)
- Kartik Sachar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Katarzyna Kanarek
- Department of Clinical Microbiology and Immunology, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jake Colautti
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Youngchang Kim
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
| |
Collapse
|
15
|
Reyes‐Pérez PJ, Jiménez‐Guerrero I, Sánchez‐Reina A, Civantos C, Castro NM, Ollero FJ, Gandullo J, Bernal P, Pérez‐Montaño F. The Type VI Secretion System of Sinorhizobium fredii USDA257 Is Required for Successful Nodulation With Glycine max cv Pekin. Microb Biotechnol 2025; 18:e70112. [PMID: 40025656 PMCID: PMC11872809 DOI: 10.1111/1751-7915.70112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/29/2025] [Accepted: 02/03/2025] [Indexed: 03/04/2025] Open
Abstract
The symbiotic relationship between rhizobia and legumes is critical for sustainable agriculture and has important economic and environmental implications. In this intricate process, rhizobial bacteria colonise plant roots and induce the formation of specialised plant organs, the nodules. Within these structures, rhizobia fix environmental nitrogen into ammonia, significantly reducing the demand for synthetic fertilisers. Multiple bacterial secretion systems (TXSS, Type X Secretion System) are involved in establishing this symbiosis, with T3SS being the most studied. While the Type 6 Secretion System (T6SS) is known as a "nanoweapon" commonly used by diderm (formerly gram-negative) bacteria for inter-bacterial competition and potentially manipulating eukaryotic cells, its precise role in legume symbiosis remains unclear. Sinorhizobium fredii USDA257, a fast-growing rhizobial strain capable of nodulating diverse legume plants, possesses a single T6SS cluster containing genes encoding structural components and potential effectors that could target plant cells and/or act as effector-immunity pairs. Our research reveals that this T6SS can be induced in nutrient-limited conditions and, more importantly, is essential for successful nodulation and competitive colonisation of Glycine max cv Pekin. Although the system did not demonstrate effectiveness in eliminating competing bacteria in vitro, its active presence within root nodules suggests a sophisticated role in symbiotic interactions that extends beyond traditional interbacterial competition.
Collapse
Affiliation(s)
| | | | - Ana Sánchez‐Reina
- Departamento de Microbiología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Cristina Civantos
- Departamento de Microbiología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | | | | | - Jacinto Gandullo
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | | |
Collapse
|
16
|
Qian Y, Liu Q, Cheng X, Wang C, Kong C, Li M, Ren C, Jiang D, Wang S, Xia P. A VgrG2b fragment cleaved by caspase-11/4 promotes Pseudomonas aeruginosa infection through suppressing the NLRP3 inflammasome. eLife 2025; 13:RP99939. [PMID: 39998486 PMCID: PMC11856931 DOI: 10.7554/elife.99939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2025] Open
Abstract
The T6SS of Pseudomonas aeruginosa plays an essential role in the establishment of chronic infections. Inflammasome-mediated inflammatory cytokines are crucial for host defense against bacterial infections. We found that P. aeruginosa infection activates the non-canonical inflammasome in macrophages, yet it inhibits the downstream activation of the NLRP3 inflammasome. The VgrG2b of P. aeruginosa is recognized and cleaved by caspase-11, generating a free C-terminal fragment. The VgrG2b C-terminus can bind to NLRP3, inhibiting the activation of the NLRP3 inflammasome by rejecting NEK7 binding to NLRP3. Administration of a specific peptide that inhibits caspase-11 cleavage of VgrG2b significantly improves mouse survival during infection. Our discovery elucidates a mechanism by which P. aeruginosa inhibits host immune response, providing a new approach for the future clinical treatment of P. aeruginosa infections.
Collapse
Affiliation(s)
- Yan Qian
- Department of Immunology, School of Basic Medical Sciences, Peking UniversityBeijingChina
- NHC Key Laboratory of Medical Immunology, Peking UniversityBeijingChina
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical SciencesBeijingChina
| | - Qiannv Liu
- Department of Immunology, School of Basic Medical Sciences, Peking UniversityBeijingChina
- NHC Key Laboratory of Medical Immunology, Peking UniversityBeijingChina
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical SciencesBeijingChina
| | - Xiangyun Cheng
- Department of Sports Medicine, Peking University Third HospitalBeijingChina
- Beijing Key Laboratory of Sports Injuries, Institute of Sports Medicine of Peking UniversityBeijingChina
| | - Chunlei Wang
- Department of Immunology, School of Basic Medical Sciences, Peking UniversityBeijingChina
- NHC Key Laboratory of Medical Immunology, Peking UniversityBeijingChina
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical SciencesBeijingChina
| | - Chun Kong
- Department of Immunology, School of Basic Medical Sciences, Peking UniversityBeijingChina
- NHC Key Laboratory of Medical Immunology, Peking UniversityBeijingChina
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical SciencesBeijingChina
| | - Mengqian Li
- Department of Immunology, School of Basic Medical Sciences, Peking UniversityBeijingChina
- NHC Key Laboratory of Medical Immunology, Peking UniversityBeijingChina
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical SciencesBeijingChina
| | - Chao Ren
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical UniversityBeijingChina
| | - Dong Jiang
- Department of Sports Medicine, Peking University Third HospitalBeijingChina
- Beijing Key Laboratory of Sports Injuries, Institute of Sports Medicine of Peking UniversityBeijingChina
| | - Shuo Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Pengyan Xia
- Department of Immunology, School of Basic Medical Sciences, Peking UniversityBeijingChina
- NHC Key Laboratory of Medical Immunology, Peking UniversityBeijingChina
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical SciencesBeijingChina
| |
Collapse
|
17
|
Williams DJ, Hawkins A, Hernandez RE, Mariano G, Mathers K, Buchanan G, Stonier BJ, Inkster T, Leanord A, Chalmers JD, Thomson NR, Holden MTG, Coulthurst SJ. Competitive behaviors in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment. Cell Host Microbe 2025; 33:252-266.e5. [PMID: 39884275 DOI: 10.1016/j.chom.2025.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 12/02/2024] [Accepted: 01/06/2025] [Indexed: 02/01/2025]
Abstract
Opportunistic bacterial pathogens must compete with other bacteria and switch between host- and environment-adapted states. Type VI secretion systems (T6SSs) occur widely in gram-negative bacteria and can efficiently kill neighboring competitors. We determined the distribution of T6SSs across the genus Serratia and observed that a highly conserved antibacterial T6SS is differentially active between closely related clinical isolates of Serratia marcescens. By combining genomic and experimental approaches, we identified a genus-core two-component system, BetR-Reg1-Reg2, that controls T6SS activity and exhibits frequent inactivating mutations, exclusively in S. marcescens isolates of clinical origin. This regulatory system controls a number of lifestyle-related traits at transcriptional and post-translational levels, including T6SS activity, antibiotic production, motility, and adhesion, with loss of BetR increasing virulence in an in vivo infection model. Our data support a model whereby this system represents a conserved, modular switch from sessile to pioneering and aggressive behavior, which is subject to selection pressure in clinical environments.
Collapse
Affiliation(s)
- David J Williams
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Ruth E Hernandez
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | | | - Grant Buchanan
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Teresa Inkster
- Antimicrobial Resistance and Healthcare Associated Infection (ARHAI), Glasgow, Scotland
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK; Scottish Microbiology Reference Laboratories, Glasgow G31 2ER, UK
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | | |
Collapse
|
18
|
Liu S, Wu Z, Yan W, Liu Q, Zhao Y, Gao T, Yang Y, Cao L, Tao R, Li M, Liu L, Zhang Y, Wang T. Regulation of the H1 Type VI Secretion System by the Transcriptional Regulator NfxB in Pseudomonas aeruginosa. Int J Mol Sci 2025; 26:1472. [PMID: 40003937 PMCID: PMC11855083 DOI: 10.3390/ijms26041472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Revised: 01/25/2025] [Accepted: 02/04/2025] [Indexed: 02/27/2025] Open
Abstract
The type VI secretion system (T6SS) is a widely distributed molecular apparatus found in most Gram-negative bacteria. Studies show that T6SSs have functions in bacterial virulence, inter- and intra-bacterial competition, and environmental adaptation. Pseudomonas aeruginosa, an opportunistic pathogen, harbors three T6SS gene clusters that perform diverse roles in clinical infection. Herein, using DNA affinity chromatography of the H1-T6SS promoter, the fluoroquinolone antibiotic resistance regulator NfxB was identified. Further studies demonstrated that NfxB negatively regulates the expression of H1-T6SS by directly binding to its promoter region. T6SS expression and effector secretion are regulated by the fluoroquinolone antibiotic via NfxB, which enhances inter-bacterial competition in the complex bacterial ecology. Meanwhile, the deletion of nfxB alters carbenicillin resistance through an unknown pathway. This study provides new insights into the regulation of T6SS by environmental signals, and it provides data support for antibiotic resistance and inter-bacterial competition due to T6SSs.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yani Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Tietao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| |
Collapse
|
19
|
Bhowmik S, Pathak A, Pandey S, Devnath K, Sett A, Jyoti N, Bhando T, Akhter J, Chugh S, Singh R, Sharma TK, Pathania R. Acinetobacter baumannii represses type VI secretion system through a manganese-dependent small RNA-mediated regulation. mBio 2025; 16:e0302524. [PMID: 39704509 PMCID: PMC11796373 DOI: 10.1128/mbio.03025-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 12/02/2024] [Indexed: 12/21/2024] Open
Abstract
Type VI secretion system (T6SS) is utilized by many Gram-negative bacteria to eliminate competing bacterial species and manipulate host cells. Acinetobacter baumannii ATCC 17978 utilizes T6SS at the expense of losing pAB3 plasmid to induce contact-dependent killing of competitor microbes, resulting in the loss of antibiotic resistance carried by pAB3. However, the regulatory network associated with T6SS in A. baumannii remains poorly understood. Here, we identified an Mn2+-dependent post-transcriptional regulation of T6SS mediated by a bonafide small RNA, AbsR28. A. baumannii utilizes MumT, an Mn2+-uptake inner membrane transporter, for the uptake of extracellular Mn2+ during oxidative stress. We demonstrate that the abundance of intracellular Mn2+ enables complementary base pairing of AbsR28-tssM mRNA (that translates to TssM, one of the vital inner membrane components of T6SS), inducing RNase E-mediated degradation of tssM mRNA and resulting in T6SS repression. Thus, AbsR28 mediates a crosstalk between MumT and T6SS in A. baumannii.IMPORTANCESmall RNAs (sRNAs) are identified as critical components within the bacterial regulatory networks involved in fine regulation of virulence-associated factors. The sRNA-mediated regulation of type VI secretion system (T6SS) in Acinetobacter baumannii was unchartered. Previously, it was demonstrated that A. baumannii ATCC 17978 cells switch from T6- to T6+ phenotype, resulting in the loss of antibiotic resistance conferred by plasmid pAB3. Furthermore, the derivatives of pAB3 found in recent clinical isolates of A. baumannii harbor expanded antibiotic resistance genes and multiple determinants for virulence factors. Hence, the loss of this plasmid for T6SS activity renders A. baumannii T6+ cells susceptible to antibiotics and compromises their virulence. Our findings show how A. baumannii tends to inactivate T6SS through an sRNA-mediated regulation that relies on Mn2+ and retains pAB3 during infection to retain antibiotic resistance genes carried on the plasmid.
Collapse
Affiliation(s)
- Somok Bhowmik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Avik Pathak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Shivam Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldip Devnath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Abhiroop Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Nishant Jyoti
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Timsy Bhando
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Jawed Akhter
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Saurabh Chugh
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
- Center of Excellence in Disaster Mitigation and Management, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| |
Collapse
|
20
|
Liu Y, Geng Y, Jiang Y, Sun J, Li P, Li YZ, Zhang Z. Global biogeography and projection of antimicrobial toxin genes. MICROBIOME 2025; 13:40. [PMID: 39905479 PMCID: PMC11796102 DOI: 10.1186/s40168-025-02038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 01/15/2025] [Indexed: 02/06/2025]
Abstract
BACKGROUND Antimicrobial toxin genes (ATGs) encode potent antimicrobial weapons in nature that rival antibiotics, significantly impacting microbial survival and offering potential benefits for human health. However, the drivers of their global diversity and biogeography remain unknown. RESULTS Here, we identified 4400 ATG clusters from 149 families by correlating 10,000 samples worldwide with over 200,000 microbial genome data. We demonstrated that global microbial communities universally encode complex and diverse ATGs, with widespread differences across various habitats. Most ATG clusters were rare within habitats but were shared among habitats. Compared with those in animal-associated habitats, ATG clusters in human-associated habitats exhibit greater diversity and a greater proportion of sharing with natural habitats. We generated a global atlas of ATG distribution, identifying anthropogenic factors as crucial in explaining ATG diversity hotspots. CONCLUSIONS Our study provides baseline information on the global distribution of antimicrobial toxins by combining community samples, genome sequences, and environmental constraints. Our results highlight the natural environment as a reservoir of antimicrobial toxins, advance the understanding of the global distribution of these antimicrobial weapons, and aid their application in clinical, agricultural, and industrial fields. Video Abstract.
Collapse
Affiliation(s)
- Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
- Suzhou Research Institute, Shandong University, Suzhou, 215123, China
| | - Yu Geng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jingyu Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng 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.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
21
|
Habich A, Chaves Vargas V, Robinson LA, Allsopp LP, Unterweger D. Distribution of the four type VI secretion systems in Pseudomonas aeruginosa and classification of their core and accessory effectors. Nat Commun 2025; 16:888. [PMID: 39837841 PMCID: PMC11751169 DOI: 10.1038/s41467-024-54649-5] [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: 12/18/2023] [Accepted: 11/14/2024] [Indexed: 01/23/2025] Open
Abstract
Bacterial type VI secretion systems (T6SSs) are puncturing molecular machines that transport effector proteins to kill microbes, manipulate eukaryotic cells, or facilitate nutrient uptake. How and why T6SS machines and effectors differ within a species is not fully understood. Here, we applied molecular population genetics to the T6SSs in a global population of the opportunistic pathogen Pseudomonas aeruginosa. We reveal varying occurrence of up to four distinct T6SS machines. Moreover, we define conserved core T6SS effectors, likely critical for the biology of P. aeruginosa, and accessory effectors that can exhibit mutual exclusivity between strains. By ancestral reconstruction, we observed dynamic changes in the gain and loss of effector genes in the species' evolutionary history. Our work highlights the potential importance of T6SS intraspecific diversity in bacterial ecology and evolution.
Collapse
Affiliation(s)
- Antonia Habich
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Verónica Chaves Vargas
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Luca A Robinson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Luke P Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
| |
Collapse
|
22
|
Colautti J, Kelly SD, Whitney JC. Specialized killing across the domains of life by the type VI secretion systems of Pseudomonas aeruginosa. Biochem J 2025; 482:1-15. [PMID: 39774785 DOI: 10.1042/bcj20230240] [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: 08/09/2024] [Revised: 12/05/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025]
Abstract
Type VI secretion systems (T6SSs) are widespread bacterial protein secretion machines that inject toxic effector proteins into nearby cells, thus facilitating both bacterial competition and virulence. Pseudomonas aeruginosa encodes three evolutionarily distinct T6SSs that each export a unique repertoire of effectors. Owing to its genetic tractability, P. aeruginosa has served as a model organism for molecular studies of the T6SS. However, P. aeruginosa is also an opportunistic pathogen and ubiquitous environmental organism that thrives in a wide range of habitats. Consequently, studies of its T6SSs have provided insight into the role these systems play in the diverse lifestyles of this species. In this review, we discuss recent advances in understanding the regulation and toxin repertoire of each of the three P. aeruginosa T6SSs. We argue that these T6SSs serve distinct physiological functions; whereas one system is a dedicated defensive weapon for interbacterial antagonism, the other two T6SSs appear to function primarily during infection. We find support for this model in examining the signalling pathways that control the expression of each T6SS and co-ordinate the activity of these systems with other P. aeruginosa behaviours. Furthermore, we discuss the effector repertoires of each T6SS and connect the mechanisms by which these effectors kill target cells to the ecological conditions under which their respective systems are activated. Understanding the T6SSs of P. aeruginosa in the context of this organism's diverse lifestyles will provide insight into the physiological roles these secretion systems play in this remarkably adaptable bacterium.
Collapse
Affiliation(s)
- Jake Colautti
- 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 4K1, Canada
| | - Steven D Kelly
- 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 4K1, Canada
| | - 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 4K1, Canada
- David Braley Center for Antibiotic Discovery, McMaster University, Hamilton, ON, L8S 4K1, Canada
| |
Collapse
|
23
|
Long D, Li M, Ma L, Huang J, Lv C, Chen Y, Cheng Z, Liu C, Huang H, Guo X, Yang C, Zhu Y. Epidemiological and genetic charateristics of Vibrio vulnificus from diverse sources in China during 2012-2023. Commun Biol 2025; 8:9. [PMID: 39755764 DOI: 10.1038/s42003-024-07426-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 12/18/2024] [Indexed: 01/06/2025] Open
Abstract
Vibrio vulnificus is a significant zoonotic pathogen that causes severe vibriosis in humans and fish. The lack of a national annual surveillance program in China has hindered understanding of its epidemiological characteristics and genetic diversity. This study characterized 150 V. vulnificus isolates collected from diverse sources in China during 2012-2023, including seafood, aquaculture water, migratory birds, marine animals, and clinical patients. Most seafood-derived isolates and all 15 clinical isolates harbored the virulence-related gene vcgC and 16S rRNA type B. The isolates exhibited diverse virulence factors (VFs), including flagella, outer membrane components, RTX toxins, and multiple secretion systems. Genes associated with the Type III secretion system were identified in migratory bird isolates, while a unique Type VI secretion system (T6SS1) were identified exclusively within a specific phylogenetic sub-lineage. T6SS1-positive strains demonstrated an increased number of genomic islands (GIs) and VFs compared to T6SS1-negative strains. Enrichment of genes related to secretion systems and biofilm formation likely facilitated the expansion of the T6SS1-positive population. The novel association between T6SS1 and a specific sub-lineage underscores potential ecological and adaptive advantages. These findings provide new insights into the ecological and evolutionary dynamics of V. vulnificus.
Collapse
Affiliation(s)
- Dongling Long
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Min Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China.
| | - Lingchao Ma
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Lv
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Yiwen Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Zile Cheng
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Chang Liu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huitao Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
| | - Yongzhang Zhu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China.
| |
Collapse
|
24
|
Sun H, Ju X, Wang H, Ma X, Shi B. Ammonia nitrogen affects bacterial virulence and conditional pathogenic bacterial growth by regulating biofilm microbial metabolism and EPS secretion in laboratory scale distribution systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 958:178150. [PMID: 39705953 DOI: 10.1016/j.scitotenv.2024.178150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 12/11/2024] [Accepted: 12/14/2024] [Indexed: 12/23/2024]
Abstract
The control of conditional pathogenic bacteria and inhibition of their virulence factors (VFs) in drinking water distribution systems (DWDSs) is vital for drinking water safety. This study adopted two groups of DWDSs to investigate how ammonia nitrogen affects bacterial VFs and conditional pathogenic bacterial growth in biofilms. Our results indicated that Acidimicrobium (95,916.62 ± 119.24 TPM), Limnohabitans (30,338.81 ± 139.14 TPM), and Sediminibacterium (10,658.01 ± 48.94 TPM) were predominant in the biofilm bacterial community of DWDSs with NH3-N addition. Under these conditions, the abundances of various bacterial metabolites, such as L-glutamate (1.45-fold), 2-oxoglutarate (1.24-fold), pyruvate (2.10-fold), and adenosine monophosphate (AMP, 5.29-fold), were significantly upregulated, which suggested the upregulation of amino acid, carbohydrate, nucleotide, lipid, pyrimidine and purine metabolism. These metabolic pathways accelerated extracellular polymeric substance (EPS) secretion. The protein concentration in EPS also increased to 187.59 ± 0.58 μg/cm2. The increased EPS secretion promoted the amide I CO group of the EPS protein to interact with the surface of the DWDSs, thus enhancing the ability of bacteria (especially conditional pathogenic bacteria) to adhere to the pipe surface to form biofilms. Due to EPS protection, the abundance of the adherence subtype of VFs and the plate counts of Pseudomonas aeruginosa increased to 5912.8 ± 21.89 TPM and 655.78 ± 27.10 CFU/cm2, respectively. Therefore, NH3-N in DWDSs increased bacterial VFs levels and promoted the growth of some conditional pathogenic bacteria by regulating biofilm microbial metabolic pathways and EPS secretion, ultimately impacting the interaction between EPS and the pipe surface.
Collapse
Affiliation(s)
- Huifang Sun
- Institute of Resources and Environmental Engineering, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Xiurong Ju
- Institute of Resources and Environmental Engineering, Shanxi University, Taiyuan 030006, Shanxi, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haibo Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xu Ma
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Baoyou Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
25
|
Tandhavanant S, Yimthin T, Sengyee S, Charoenwattanasatien R, Lebedev AA, Lafontaine ER, Hogan RJ, Chewapreecha C, West TE, Brett PJ, Burtnick MN, Chantratita N. Genetic variation of hemolysin co-regulated protein 1 affects the immunogenicity and pathogenicity of Burkholderia pseudomallei. PLoS Negl Trop Dis 2025; 19:e0012758. [PMID: 39761280 PMCID: PMC11737846 DOI: 10.1371/journal.pntd.0012758] [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: 06/07/2024] [Revised: 01/16/2025] [Accepted: 12/04/2024] [Indexed: 01/18/2025] Open
Abstract
Hemolysin co-regulated protein 1 (Hcp1) is a component of the cluster 1 Type VI secretion system (T6SS1) that plays a key role during the intracellular lifecycle of Burkholderia pseudomallei. Hcp1 is recognized as a promising target antigen for developing melioidosis diagnostics and vaccines. While the gene encoding Hcp1 is retained across B. pseudomallei strains, variants of hcp1 have recently been identified. This study aimed to examine the prevalence of hcp1 variants in clinical isolates of B. pseudomallei, assess the antigenicity of the Hcp1 variants, and the ability of strains expressing these variants to stimulate multinucleated giant cell (MNGC) formation in comparison to strains expressing wild-type Hcp1 (Hcp1wt). Sequence analysis of 1,283 primary clinical isolates of B. pseudomallei demonstrated the presence of 8 hcp1 alleles encoding three types of Hcp1 proteins, including Hcp1wt (98.05%), Hcp1variant A (1.87%) and Hcp1variant B (0.08%). Compared to strains expressing Hcp1wt, those expressing the dominant variant, Hcp1variant A, stimulated lower levels of Hcp1variant A-specific antibody responses in melioidosis patients. Interestingly, when Hcp1variant A was expressed in B. pseudomallei K96243, this strain retained the ability to stimulate MNGC formation in A549 cells. In contrast, however, similar experiments with the Hcp1variant B demonstrated a decreased ability of B. pseudomallei to stimulate MNGC formation. Collectively, these results show that B. pseudomallei strains expressing variants of Hcp1 elicit variable antibody responses in melioidosis patients and differ in their ability to promote MNGC formation in cell culture.
Collapse
Affiliation(s)
- Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Bacteriology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Thatcha Yimthin
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sineenart Sengyee
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Ratana Charoenwattanasatien
- Beamline Division, Synchrotron Light Research Institute, (Public Organization), Nakhon Ratchasima, Thailand
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchsima, Thailand
| | - Andrey A. Lebedev
- CCP4, Research Complex at Harwell, UKRI–STFC Rutherford Appleton Laboratory, Harwell, Didcot, United Kingdom
| | - Eric R. Lafontaine
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Hogan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Paul J. Brett
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Mary N. Burtnick
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
26
|
Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [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: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
Collapse
Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
27
|
Wu S, Huang Y, Wu M, Chen H, Wang B, Amoah K, Cai J, Jian J. Identification of a cellular role of hemolysin co-regulatory protein (Hcp) in Vibrio alginolyticus modulating substrate metabolism and biofilm formation by cAMP-CRP. Int J Biol Macromol 2024; 282:136656. [PMID: 39423969 DOI: 10.1016/j.ijbiomac.2024.136656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/14/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
Abstract
Cyclic AMP (cAMP) and cAMP receptor protein (CRP) system controls catabolic enzyme expression based on metabolite concentrations in bacteria. Hemolysin co-regulatory protein (Hcp) is well known as a molecular chaperone for virulence factor secretion of the type VI secretion system (T6SS). However, the intracellular role of Hcp involving in bacterial physiological processes remains unknown. To clarify that, we constructed a single hcp mutant strain and analyzed their effects on the physiological processes of Vibrio alginolyticus. The omics results revealed the extensive involvement of Hcp in the catabolic metabolism in bacteria. Simultaneously, Hcp1 and Hcp2 played opposing regulatory roles on the bacterial growth, biofilm formation, and intracellular cAMP-CRP levels during cultivation in a glucose medium. Furthermore, the interacting protein screening and co-immunoprecipitation (Co-IP) assays confirmed that the glucose-specific phosphoenolpyruvate (PEP)-phosphotransferase system (PTS) enzyme IIA component (EIIAglc) was a key interacting partner with Hcp proteins as well as class I adenylyl cyclase (AC-I) in Vibrio alginolyticus. These results indicated that, to achieve cellular homeostasis, Hcp1 and Hcp2 might exert antagonistic and synergistic effects, respectively, on the interaction between EIIAglc and AC thus cooperatively regulating intracellular cAMP-CRP production.
Collapse
Affiliation(s)
- Shuilong Wu
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yu Huang
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Minhui Wu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang 524045, China
| | - Huapu Chen
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Bei Wang
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Kwaku Amoah
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jia Cai
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Jichang Jian
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education Institutions, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China.
| |
Collapse
|
28
|
Alattas H, Glick BR, Murphy DV, Scott C. Harnessing Pseudomonas spp. for sustainable plant crop protection. Front Microbiol 2024; 15:1485197. [PMID: 39640850 PMCID: PMC11617545 DOI: 10.3389/fmicb.2024.1485197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 11/04/2024] [Indexed: 12/07/2024] Open
Abstract
This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and integration with other management practices, are discussed. The advantages of Pseudomonas-based biocontrol for sustainable agriculture include reduced reliance on chemical pesticides, enhanced crop productivity, and improved environmental sustainability. Future research directions should focus on understanding the complex interactions within the plant microbiome, optimizing delivery systems, and addressing regulatory hurdles for commercial deployment. This review underscores the significant potential of Pseudomonas spp. in sustainable crop protection while acknowledging the need for further research to fully harness their capabilities in agricultural systems.
Collapse
Affiliation(s)
- Hussain Alattas
- Bioplastics Innovation Hub, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- School of Medical, Molecular, and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Daniel V. Murphy
- Bioplastics Innovation Hub, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Colin Scott
- Bioplastics Innovation Hub, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| |
Collapse
|
29
|
Mashruwala AA, Bassler BL. Quorum sensing orchestrates parallel cell death pathways in Vibrio cholerae via Type 6 secretion-dependent and -independent mechanisms. Proc Natl Acad Sci U S A 2024; 121:e2412642121. [PMID: 39499633 PMCID: PMC11573629 DOI: 10.1073/pnas.2412642121] [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: 06/23/2024] [Accepted: 10/07/2024] [Indexed: 11/07/2024] Open
Abstract
Quorum sensing (QS) is a cell-to-cell communication process that enables bacteria to coordinate group behaviors. In Vibrio cholerae colonies, a program of spatial-temporal cell death is among the QS-controlled traits. Cell death occurs in two phases, first along the colony rim, and subsequently, at the colony center. Both cell death phases are driven by the type 6 secretion system (T6SS). Here, we show that HapR, the master QS regulator, does not control t6ss gene expression nor T6SS-mediated killing activity. Nonetheless, a ΔhapR strain displays no cell death at the colony rim. RNA-Sequencing (RNA-Seq) analyses reveal that HapR activates expression of an operon containing four genes of unknown function, vca0646-0649. Epistasis and overexpression studies show that two of the genes, vca0646 and vca0647, are required to drive cell death in both a ΔhapR and a ΔhapR Δt6ss strain. Thus, vca0646-0649 are regulated by HapR but act independently of the T6SS machinery to cause cell death, suggesting that a second, parallel pathway to cell death exists in V. cholerae.
Collapse
Affiliation(s)
- Ameya A. Mashruwala
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- HHMI, Chevy Chase, MD20815
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- HHMI, Chevy Chase, MD20815
| |
Collapse
|
30
|
Mihályi C, Iordanov I, Szollosi A, Csanády L. Structural determinants of protein kinase A essential for CFTR channel activation. Proc Natl Acad Sci U S A 2024; 121:e2407728121. [PMID: 39495914 PMCID: PMC11573668 DOI: 10.1073/pnas.2407728121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/30/2024] [Indexed: 11/06/2024] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), the anion channel mutated in cystic fibrosis (CF) patients, is activated by the catalytic subunit of protein kinase A (PKA-C). PKA-C activates CFTR both noncatalytically, through binding, and catalytically, through phosphorylation of multiple serines in CFTR's regulatory (R) domain. Here, we identify key molecular determinants of the CFTR/PKA-C interaction essential for these processes. By comparing CFTR current activation in the presence of ATP or an ATP analog unsuitable for phosphotransfer, as well as pseudosubstrate peptides of various lengths, we identify two distinct specific regions of the PKA-C surface which interact with CFTR to cause noncatalytic and catalytic CFTR stimulation, respectively. Whereas the "substrate site" mediates CFTR phosphorylation, a distinct hydrophobic patch (the "docking site") is responsible for noncatalytic CFTR activation, achieved by stabilizing the R domain in a "released" conformation permissive to channel gating. Furthermore, by comparing PKA-C variants with different posttranslational modification patterns, we find that direct membrane tethering of the kinase through its N-terminal myristoyl group is an unappreciated fundamental requirement for CFTR activation: PKA-C demyristoylation abolishes noncatalytic, and profoundly slows catalytic, CFTR stimulation. For the F508del CFTR mutant, present in ~90% of CF patients, maximal activation by demyristoylated PKA-C is reduced by ~10-fold compared to that by myristoylated PKA-C. Finally, in bacterial genera that contain common CF pathogens, we identify virulence factors that demyristoylate PKA-C in vitro, raising the possibility that during recurrent bacterial infections in CF patients, PKA-C demyristoylation may contribute to the exacerbation of lung disease.
Collapse
Affiliation(s)
- Csaba Mihályi
- Department of Biochemistry, Semmelweis University, Budapest H-1094, Hungary
- Molecular Channelopathies Research Group, Hungarian Centre of Excellence for Molecular Medicine - Semmelweis University, Budapest H-1094, Hungary
- Ion Channel Research Group, Hungarian Research Network - Semmelweis University, Budapest H-1094, Hungary
| | - Iordan Iordanov
- Department of Biochemistry, Semmelweis University, Budapest H-1094, Hungary
- Molecular Channelopathies Research Group, Hungarian Centre of Excellence for Molecular Medicine - Semmelweis University, Budapest H-1094, Hungary
- Ion Channel Research Group, Hungarian Research Network - Semmelweis University, Budapest H-1094, Hungary
| | - Andras Szollosi
- Department of Biochemistry, Semmelweis University, Budapest H-1094, Hungary
- Molecular Channelopathies Research Group, Hungarian Centre of Excellence for Molecular Medicine - Semmelweis University, Budapest H-1094, Hungary
- Ion Channel Research Group, Hungarian Research Network - Semmelweis University, Budapest H-1094, Hungary
| | - László Csanády
- Department of Biochemistry, Semmelweis University, Budapest H-1094, Hungary
- Molecular Channelopathies Research Group, Hungarian Centre of Excellence for Molecular Medicine - Semmelweis University, Budapest H-1094, Hungary
- Ion Channel Research Group, Hungarian Research Network - Semmelweis University, Budapest H-1094, Hungary
| |
Collapse
|
31
|
Chen Z, Mao Y, Song Y, Dou M, Shang K, Yu Z, Ding K, Chen S. Refined egoist: The toxin-antitoxin immune system of T6SS. Microb Pathog 2024; 196:106991. [PMID: 39369755 DOI: 10.1016/j.micpath.2024.106991] [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: 05/28/2024] [Revised: 09/30/2024] [Accepted: 10/01/2024] [Indexed: 10/08/2024]
Abstract
The Type VI secretory system (T6SS) is a key regulatory network in the bacterial system, which plays an important role in host-pathogen interactions and maintains cell homeostasis by regulating the release of effector proteins in specific competition. T6SS causes cell lysis or competitive inhibition by delivering effector molecules, such as toxic proteins and nucleic acids, directly from donor bacterial cells to eukaryotic or prokaryotic targets. Additionally, it orchestrates synthesis of immune effectors that counteract toxins thus preventing self-intoxication or antagonistic actions by competing microbes. Even so, the mechanism of toxin-antitoxin regulation in bacteria remains unclear. In response, this review discusses the bacterial T6SS's structure and function and the mechanism behind toxin-antitoxin secretion and the T6SS's expression in order to guide the further exploration of the pathogenic mechanism of the T6SS and the development of novel preparations for reducing and replacing toxins and antitoxins.
Collapse
Affiliation(s)
- Ziduo Chen
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yikai Mao
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yinzhou Song
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China
| | - Mengxuan Dou
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ke Shang
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China
| | - Zuhua Yu
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ke Ding
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Songbiao Chen
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang, 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang, 471023, China.
| |
Collapse
|
32
|
Li J, Huang W, Li Q. New insights into pathogenic performances during peroxydisulfate composting: sources, pathways, and influencing factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:58093-58108. [PMID: 39306820 DOI: 10.1007/s11356-024-35040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 09/16/2024] [Indexed: 10/11/2024]
Abstract
Livestock manure treatment technology and composting and its products have been widely used in agricultural soil. However, little was known about the variations in the fate of pathogens and the factors affecting their pathogenic ability during this process, which posed threats to ecological safety and public health globally. This study used a metagenomic approach to profile the behaviors of pathogens during peroxydisulfate composting. Results showed that Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Burkholderia pseudomallei, and Mycobacterium tuberculosis were the main secretors of virulence factors (VFs) in composting system; their abundance and the virulence factor-related genes they carried were better downregulated under the role of peroxydisulfate. In addition, peroxydisulfate composting ensured the lower moisture, weakening the swimming mobility behavior of pathogens through suppressing the abundance of genes associated with flagellar formation, and impaired the communication between pathogens by regulating quorum sensing (QS)- and quorum quenching (QQ)-related genes. Moreover, reduced abundance of resistomes restricted pathogens disseminating infection. In summary, this study provided useful strategies in managing pathogen pathogenic ability during composting based on pathogenic source (pathogens), pathway (VFs), influencing factors (QS/QQ, physicochemical habitats), and resistomes.
Collapse
Affiliation(s)
- Jixuan Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Wenyu Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
| |
Collapse
|
33
|
Mashruwala AA, Bassler BL. Quorum sensing orchestrates parallel cell death pathways in Vibrio cholerae via Type 6 secretion dependent and independent mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.23.614608. [PMID: 39386452 PMCID: PMC11463680 DOI: 10.1101/2024.09.23.614608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Quorum sensing (QS) is a cell-to-cell communication process that enables bacteria to coordinate group behaviors. In Vibrio cholerae colonies, a program of spatial-temporal cell death is among the QS-controlled traits. Cell death occurs in two phases, first along the colony rim, and subsequently, at the colony center. Both cell death phases are driven by the type VI secretion system (T6SS). Here, we show that HapR, the master QS regulator, does not control t6ss gene expression nor T6SS-mediated killing activity. Nonetheless, a ΔhapR strain displays no cell death at the colony rim. RNA-Seq analyses reveal that HapR activates expression of an operon containing four genes of unknown function, vca0646-0649. Epistasis and overexpression studies show that two of the genes, vca0646 and vca0647, are required to drive cell death in both a ΔhapR and a ΔhapR Δt6ss strain. Thus, vca0646-0649 are regulated by HapR but act independently of the T6SS machinery to cause cell death, suggesting that a second, parallel pathway to cell death exists in V. cholerae.
Collapse
Affiliation(s)
- Ameya A. Mashruwala
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Current address: The Stowers Institute for Medical Research, Kansas City, MO, 64110
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
George M, Narayanan S, Tejada-Arranz A, Plack A, Basler M. Initiation of H1-T6SS dueling between Pseudomonas aeruginosa. mBio 2024; 15:e0035524. [PMID: 38990002 PMCID: PMC11323562 DOI: 10.1128/mbio.00355-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
The Type VI secretion system (T6SS) is a multicomponent apparatus, present in many Gram-negative bacteria, which can inhibit bacterial prey in various ecological niches. Pseudomonas aeruginosa assembles one of its three T6SS (H1-T6SS) to respond to attacks from adjacent competing bacteria. Surprisingly, repeated assemblies of the H1-T6SS, termed dueling, were described in a monoculture in the absence of an attacker strain; however, the underlying mechanism was unknown. Here, we explored the role of H2-T6SS of P. aeruginosa in triggering H1-T6SS assembly. We show that H2-T6SS inactivation in P. aeruginosa causes a significant reduction in H1-T6SS dueling and that H2-T6SS activity directly triggers retaliation by the H1-T6SS. Intraspecific competition experiments revealed that elimination of H2-T6SS in non-immune prey cells conferred protection from H1-T6SS. Moreover, we show that the H1-T6SS response is triggered independently of the characterized lipase effectors of the H2-T6SS, as well as those of Acinetobacter baylyi and Vibrio cholerae. Our results suggest that H1-T6SS response to H2-T6SS in P. aeruginosa can impact intraspecific competition, particularly when the H1-T6SS effector-immunity pairs differ between strains, and could determine the outcome of multistrain colonization.IMPORTANCEThe opportunistic pathogen Pseudomonas aeruginosa harbors three different Type VI secretion systems (H1, H2, and H3-T6SS), which can translocate toxins that can inhibit bacterial competitors or inflict damage to eukaryotic host cells. Unlike the unregulated T6SS assembly in other Gram-negative bacteria, the H1-T6SS in P. aeruginosa is precisely assembled as a response to various cell damaging attacks from neighboring bacterial cells. Surprisingly, it was observed that neighboring P. aeruginosa cells repeatedly assemble their H1-T6SS toward each other. Mechanisms triggering this "dueling" behavior between sister cells were unknown. In this report, we used a combination of microscopy, genetic and intraspecific competition experiments to show that H2-T6SS initiates H1-T6SS dueling. Our study highlights the interplay between different T6SS clusters in P. aeruginosa, which may influence the outcomes of multistrain competition in various ecological settings such as biofilm formation and colonization of cystic fibrosis lungs.
Collapse
Affiliation(s)
- M. George
- Biozentrum, University of Basel, Basel, Switzerland
| | - S. Narayanan
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - A. Plack
- Biozentrum, University of Basel, Basel, Switzerland
| | - M. Basler
- Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|
36
|
Das S, Das S, Rath PP, Banerjee A, Gourinath S, Mukhopadhyay AK, Maiti S. Hemolysin Coregulated Protein (HCP) from Vibrio Cholerae Interacts with the Host Cell Actin Cytoskeleton. ACS Infect Dis 2024; 10:2886-2898. [PMID: 39079033 DOI: 10.1021/acsinfecdis.4c00265] [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: 08/10/2024]
Abstract
Vibrio cholerae (V. cholerae), the etiological agent of cholera, employs various virulence factors to adapt and thrive within both aquatic and human host environments. Among these factors, the type VI secretion system (T6SS) stands out as one of the crucial determinants of its pathogenicity. Valine glycine repeat protein G1 (VgrG1) and hemolysin coregulated protein (HCP) are considered major effector molecules of T6SS. Previous studies have highlighted that VgrG1 interacts with HCP proteins. Additionally, it has been shown that VgrG1 possesses an actin cross-linking domain (ACD) with actin-binding activity. Interestingly, it was reported that purified HCP protein treatment increased the stress fibers within cells. Therefore, we hypothesize that HCP may interact with host cell actin, potentially playing a role in the cytoskeletal rearrangement during V. cholerae infection. To test this hypothesis, we characterized HCP from the V. cholerae O139 serotype and demonstrated its interaction with actin monomers. In silico analysis and experimental validation revealed the presence of an actin-binding site within HCP. Furthermore, overexpression of HCP resulted in its colocalization with actin stress fibers in host cells. Our findings establish HCP as an effector molecule for potent host cell actin cytoskeleton remodeling during V. cholerae infection, providing new insights into bacterial pathogenicity mechanisms. Understanding the interplay between bacterial effectors and host cell components is crucial for developing targeted therapeutic interventions against cholera and related infectious diseases.
Collapse
Affiliation(s)
- Shubham Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246, India
| | - Saikat Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246, India
| | | | - Aishwarya Banerjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246, India
| | - Samudrala Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Sankar Maiti
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246, India
| |
Collapse
|
37
|
Bier SB, Toska J, Zhao W, Suthianthong P, Proespraiwong P, Robins WP, Mekalanos J. A coordinated attack by a bacterial secretion system and a small molecule drives prey specificity. Commun Biol 2024; 7:958. [PMID: 39117895 PMCID: PMC11310501 DOI: 10.1038/s42003-024-06637-0] [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: 02/15/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Vibrio species are recognized for their role in food- and water-borne diseases in humans, fish, and aquatic invertebrates. We screened bacterial strains isolated from raw food shrimp for those that are bactericidal to Vibrio strains. Here we identify and characterize Aeromonas dhakensis strain A603 which shows robust bactericidal activity specifically towards Vibrio and related taxa but less potency toward other Gram-negative species. Using the A603 genome and genetic analysis, we show that two antibacterial mechanisms account for its vibriocidal activity -- a highly potent Type Six Secretion System (T6SS) and biosynthesis of a vibriocidal phenazine-like small molecule, named here as Ad-Phen. Further analysis indicates coregulation between Ad-Phen and a pore-forming T6SS effector TseC, which potentiates V. cholerae to killing by Ad-Phen.
Collapse
Affiliation(s)
- S B Bier
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - J Toska
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - W Zhao
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease. The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - P Suthianthong
- Charoen Pokphand Foods PCL. Aquatic Animal Health Research Center, Samutsakorn, Thailand
| | - P Proespraiwong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - W P Robins
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - J Mekalanos
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
38
|
Huang Q, Zhang M, Zhang Y, Li X, Luo X, Ji S, Lu R. IcmF2 of the type VI secretion system 2 plays a role in biofilm formation of Vibrio parahaemolyticus. Arch Microbiol 2024; 206:321. [PMID: 38907796 DOI: 10.1007/s00203-024-04060-x] [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: 05/09/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
Vibrio parahaemolyticus possesses two distinct type VI secretion systems (T6SS), namely T6SS1 and T6SS2. T6SS1 is predominantly responsible for adhesion to Caco-2 and HeLa cells and for the antibacterial activity of V. parahaemolyticus, while T6SS2 mainly contributes to HeLa cell adhesion. However, it remains unclear whether the T6SS systems have other physiological roles in V. parahaemolyticus. In this study, we demonstrated that the deletion of icmF2, a structural gene of T6SS2, reduced the biofilm formation capacity of V. parahaemolyticus under low salt conditions, which was also influenced by the incubation time. Nonetheless, the deletion of icmF2 did not affect the biofilm formation capacity in marine-like growth conditions, nor did it impact the flagella-driven swimming and swarming motility of V. parahaemolyticus. IcmF2 was found to promote the production of the main components of the biofilm matrix, including extracellular DNA (eDNA) and extracellular proteins, and cyclic di-GMP (c-di-GMP) in V. parahaemolyticus. Additionally, IcmF2 positively influenced the transcription of cpsA, mfpA, and several genes involved in c-di-GMP metabolism, including scrJ, scrL, vopY, tpdA, gefA, and scrG. Conversely, the transcription of scrA was negatively impacted by IcmF2. Therefore, IcmF2-dependent biofilm formation was mediated through its effects on the production of eDNA, extracellular proteins, and c-di-GMP, as well as its impact on the transcription of cpsA, mfpA, and genes associated with c-di-GMP metabolism. This study confirmed new physiological roles for IcmF2 in promoting biofilm formation and c-di-GMP production in V. parahaemolyticus.
Collapse
Affiliation(s)
- Qinglian Huang
- Department of Clinical Laboratory, Qidong People's Hospital, Qidong, Jiangsu, 226200, China
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Miaomiao Zhang
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Yiquan Zhang
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China.
| | - Xue Li
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Xi Luo
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Shenjie Ji
- Department of Clinical Laboratory, Qidong People's Hospital, Qidong, Jiangsu, 226200, China.
| | - Renfei Lu
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China.
| |
Collapse
|
39
|
Yang L, Jia S, Sun S, Wang L, Zhao B, Zhang M, Yin Y, Yang M, Fulano AM, Shen X, Pan J, Wang Y. A pyocin-like T6SS effector mediates bacterial competition in Yersinia pseudotuberculosis. Microbiol Spectr 2024; 12:e0427823. [PMID: 38712967 PMCID: PMC11237486 DOI: 10.1128/spectrum.04278-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Within the realm of Gram-negative bacteria, bacteriocins are secreted almost everywhere, and the most representative are colicin and pyocin, which are secreted by Escherichia coli and Pseudomonas aeruginosa, respectively. Signal peptides at the amino terminus of bacteriocins or ABC transporters can secrete bacteriocins, which then enter bacteria through cell membrane receptors and exert toxicity. In general, the bactericidal spectrum is usually narrow, killing only the kin or closely related species. Our previous research indicates that YPK_0952 is an effector of the third Type VI secretion system (T6SS-3) in Yersinia pseudotuberculosis. Next, we sought to determine its identity and characterize its toxicity. We found that YPK_0952 (a pyocin-like effector) can achieve intra-species and inter-species competitive advantages through both contact-dependent and contact-independent mechanisms mediated by the T6SS-3 while enhancing the intestinal colonization capacity of Y. pseudotuberculosis. We further identified YPK_0952 as a DNase dependent on Mg2+, Ni2+, Mn2+, and Co2+ bivalent metal ions, and the homologous immune protein YPK_0953 can inhibit its activity. In summary, YPK_0952 exerts toxicity by degrading nucleic acids from competing cells, and YPK_0953 prevents self-attack in Y. pseudotuberculosis.IMPORTANCEBacteriocins secreted by Gram-negative bacteria generally enter cells through specific interactions on the cell surface, resulting in a narrow bactericidal spectrum. First, we identified a new pyocin-like effector protein, YPK_0952, in the third Type VI secretion system (T6SS-3) of Yersinia pseudotuberculosis. YPK_0952 is secreted by T6SS-3 and can exert DNase activity through contact-dependent and contact-independent entry into nearby cells of the same and other species (e.g., Escherichia coli) to help Y. pseudotuberculosis to exert a competitive advantage and promote intestinal colonization. This discovery lays the foundation for an in-depth study of the different effector protein types within the T6SS and their complexity in competing interactions. At the same time, this study provides a new development for the toolbox of toxin/immune pairs for studying Gram-negative bacteriocin translocation.
Collapse
Affiliation(s)
- Leilei Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuangkai Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Sihuai Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Bobo Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mengsi Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanling Yin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Mingming Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Alex M. Fulano
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Junfeng Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
40
|
Chourashi R, Oglesby AG. Iron starvation increases the production of the Pseudomonas aeruginosa RsmY and RsmZ sRNAs in static conditions. J Bacteriol 2024; 206:e0027823. [PMID: 38624234 PMCID: PMC11112995 DOI: 10.1128/jb.00278-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that induces virulence gene expression in response to host-mediated iron starvation. Recently, our laboratory showed that some virulence factors are responsive to iron limitation in static but not shaking growth conditions. One of these is the HSI-2-type six secretion system (T6SS), which is also induced during chronic infection. Iron regulation of T6SS was partially impacted by the iron-responsive PrrF sRNA and completely dependent upon the Pseudomonas quinolone signal (PQS) biosynthetic gene pqsA. Here, we analyzed the impact of iron on the expression of two small regulatory RNAs (sRNAs), RsmY and RsmZ, that activate the expression of T6SS by sequestering the RsmA translation inhibitor. Our results demonstrate that iron starvation induces the expression of RsmY and RsmZ in static but not shaking cultures. We further show that this induction occurs through the rsmY and rsmZ promoters and is dependent upon PqsA. Disruption of either the pqsR gene also eliminated iron-dependent regulation of rsmY and rsmZ promoter activity. Taken together, our results show novel targets of iron regulation that are specific to static growth, highlighting the importance of studying regulatory mechanisms in static communities that may be more representative of growth during chronic infection.IMPORTANCEIron is a central component of various bacterial metabolic pathways making it an important host-acquired nutrient for pathogens to establish infection. Previous iron regulatory studies primarily relied on shaking bacterial cultures; while these ensure cultural homogeneity, they do not reflect growth conditions during infection. We recently showed that static growth of Pseudomonas aeruginosa promotes iron-dependent regulation of a type six secretion system (T6SS), a virulence factor that is induced during chronic infections. In the current study, we found that static growth also promotes iron-dependent regulation of the RsmY and RsmZ sRNAs, which are global regulators that affect T6SS during chronic P. aeruginosa lung infection. Hence, our work demonstrates the Rsm sRNAs as potential effectors of iron regulation during static growth that may also be relevant in chronic infection.
Collapse
Affiliation(s)
- Rhishita Chourashi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Amanda G. Oglesby
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| |
Collapse
|
41
|
Fecht S, Paracuellos P, Subramoni S, Tan CAZ, Ilangovan A, Costa TRD, Filloux A. Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains. Nat Commun 2024; 15:4283. [PMID: 38769318 PMCID: PMC11106082 DOI: 10.1038/s41467-024-48487-8] [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: 03/19/2023] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.
Collapse
Affiliation(s)
- Selina Fecht
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Patricia Paracuellos
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Aravindan Ilangovan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Tiago R D Costa
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Alain Filloux
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
| |
Collapse
|
42
|
Casiano González A, Pacheco Villanueva A, Castro-Alarcón N, Méndez J, Oropeza R, Martínez-Santos VI. A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026. PeerJ 2024; 12:e17336. [PMID: 38784397 PMCID: PMC11114119 DOI: 10.7717/peerj.17336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Background Urinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75-95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs. Aim To analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins. Methods The frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools. Results The ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 but not in all the clinical isolates. Strain UMN026 had antibacterial activity against UPEC clinical isolate 4014 (ECUMN-) and E. faecalis but not against isolate 4012 (ECUMN+). Bioinformatics analysis suggested that the ECUMN genes encode a chaperone/effector/immunity system. Conclusions The ECUMN genes are conserved in clinical isolates from symptomatic and asymptomatic patients and are not related to UTI symptoms. However, these genes encode a putative chaperone/effector/immunity system that seems to be involved in the antibacterial activity of strain UMN026.
Collapse
Affiliation(s)
- América Casiano González
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Arantxa Pacheco Villanueva
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Natividad Castro-Alarcón
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Julio Méndez
- Department of Molecular Microbiology, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ricardo Oropeza
- Department of Molecular Microbiology, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | |
Collapse
|
43
|
Oscarsson J, Bao K, Shiratsuchi A, Grossmann J, Wolski W, Aung KM, Lindholm M, Johansson A, Mowsumi FR, Wai SN, Belibasakis GN, Bostanci N. Bacterial symbionts in oral niche use type VI secretion nanomachinery for fitness increase against pathobionts. iScience 2024; 27:109650. [PMID: 38650989 PMCID: PMC11033201 DOI: 10.1016/j.isci.2024.109650] [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: 12/18/2023] [Revised: 02/09/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
Microbial ecosystems experience spatial and nutrient restrictions leading to the coevolution of cooperation and competition among cohabiting species. To increase their fitness for survival, bacteria exploit machinery to antagonizing rival species upon close contact. As such, the bacterial type VI secretion system (T6SS) nanomachinery, typically expressed by pathobionts, can transport proteins directly into eukaryotic or prokaryotic cells, consequently killing cohabiting competitors. Here, we demonstrate for the first time that oral symbiont Aggregatibacter aphrophilus possesses a T6SS and can eliminate its close relative oral pathobiont Aggregatibacter actinomycetemcomitans using its T6SS. These findings bring nearer the anti-bacterial prospects of symbionts against cohabiting pathobionts while introducing the presence of an active T6SS in the oral cavity.
Collapse
Affiliation(s)
- Jan Oscarsson
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
| | - Kai Bao
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Alfred Nobels Allé 8, 14104 Huddinge, Stockholm, Sweden
| | - Akiko Shiratsuchi
- Department of Liberal Arts and Sciences, Graduate School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Jonas Grossmann
- Functional Genomics Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics (SIB) Quartier Sorge-Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Witold Wolski
- Functional Genomics Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics (SIB) Quartier Sorge-Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Kyaw Min Aung
- Department of Molecular Biology and the Umeå Centre for Microbial Research (UCMR), and the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Mark Lindholm
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Alfred Nobels Allé 8, 14104 Huddinge, Stockholm, Sweden
| | - Anders Johansson
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
| | | | - Sun Nyunt Wai
- Department of Molecular Biology and the Umeå Centre for Microbial Research (UCMR), and the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Georgios N. Belibasakis
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Alfred Nobels Allé 8, 14104 Huddinge, Stockholm, Sweden
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Alfred Nobels Allé 8, 14104 Huddinge, Stockholm, Sweden
| |
Collapse
|
44
|
Plum MTW, Cheung HC, Iscar PR, Chen Y, Gan YH, Basler M. Burkholderia thailandensis uses a type VI secretion system to lyse protrusions without triggering host cell responses. Cell Host Microbe 2024; 32:676-692.e5. [PMID: 38640929 DOI: 10.1016/j.chom.2024.03.013] [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: 03/01/2023] [Revised: 08/01/2023] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
To spread within a host, intracellular Burkholderia form actin tails to generate membrane protrusions into neighboring host cells and use type VI secretion system-5 (T6SS-5) to induce cell-cell fusions. Here, we show that B. thailandensis also uses T6SS-5 to lyse protrusions to directly spread from cell to cell. Dynamin-2 recruitment to the membrane near a bacterium was followed by a short burst of T6SS-5 activity. This resulted in the polymerization of the actin of the newly invaded host cell and disruption of the protrusion membrane. Most protrusion lysis events were dependent on dynamin activity, caused no cell-cell fusion, and failed to be recognized by galectin-3. T6SS-5 inactivation decreased protrusion lysis but increased galectin-3, LC3, and LAMP1 accumulation in host cells. Our results indicate that B. thailandensis specifically activates T6SS-5 assembly in membrane protrusions to disrupt host cell membranes and spread without alerting cellular responses, such as autophagy.
Collapse
Affiliation(s)
| | - Hoi Ching Cheung
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | | | - Yahua Chen
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117596, Singapore
| | - Yunn-Hwen Gan
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117596, Singapore
| | - Marek Basler
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
| |
Collapse
|
45
|
Mikhailovich V, Heydarov R, Zimenkov D, Chebotar I. Stenotrophomonas maltophilia virulence: a current view. Front Microbiol 2024; 15:1385631. [PMID: 38741741 PMCID: PMC11089167 DOI: 10.3389/fmicb.2024.1385631] [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: 02/14/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen intrinsically resistant to multiple and broad-spectrum antibiotics. Although the bacterium is considered a low-virulence pathogen, it can cause various severe diseases and contributes significantly to the pathogenesis of multibacterial infections. During the COVID-19 pandemic, S. maltophilia has been recognized as one of the most common causative agents of respiratory co-infections and bacteremia in critically ill COVID-19 patients. The high ability to adapt to unfavorable environments and new habitat niches, as well as the sophisticated switching of metabolic pathways, are unique mechanisms that attract the attention of clinical researchers and experts studying the fundamental basis of virulence. In this review, we have summarized the current knowledge on the molecular aspects of S. maltophilia virulence and putative virulence factors, partially touched on interspecific bacterial interactions and iron uptake systems in the context of virulence, and have not addressed antibiotic resistance.
Collapse
Affiliation(s)
- Vladimir Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Rustam Heydarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Danila Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor Chebotar
- Pirogov Russian National Research Medical University, Moscow, Russia
| |
Collapse
|
46
|
Sung K, Park M, Chon J, Kweon O, Khan S. Unraveling the molecular dynamics of Pseudomonas aeruginosa biofilms at the air-liquid interface. Future Microbiol 2024; 19:681-696. [PMID: 38661712 PMCID: PMC11259063 DOI: 10.2217/fmb-2023-0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/31/2024] [Indexed: 04/26/2024] Open
Abstract
Aim: The aim of this study was to probe the dynamics of Pseudomonas aeruginosa PA14 air-liquid interface (ALI) biofilms over time through global proteomic analysis. Materials & methods: P. aeruginosa PA14 ALI biofilm samples, collected over 48-144 h, underwent differential expression analysis to identify varying proteins at each time point. Results: A consistent set of 778 proteins was identified, with variable expression over time. Upregulated proteins were mainly linked to 'amino acid transport and metabolism'. Biofilm-related pathways, including cAMP/Vfr and QS, underwent significant changes. Flagella were more influential than pili, especially in early biofilm development. Proteins associated with virulence, transporters and iron showed differential expression throughout. Conclusion: The findings enhance our understanding of ALI biofilm development.
Collapse
Affiliation(s)
- Kidon Sung
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Miseon Park
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Jungwhan Chon
- Department of Companion Animal Health, Inje University, Gimhae, South Korea
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Saeed Khan
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| |
Collapse
|
47
|
Carobbi A, Leo K, Di Nepi S, Bosis E, Salomon D, Sessa G. PIX is an N-terminal delivery domain that defines a class of polymorphic T6SS effectors in Enterobacterales. Cell Rep 2024; 43:114015. [PMID: 38568810 DOI: 10.1016/j.celrep.2024.114015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
The type VI secretion system (T6SS), a widespread protein delivery apparatus, plays a role in bacterial competition by delivering toxic effectors into neighboring cells. Identifying new T6SS effectors and deciphering the mechanism that governs their secretion remain major challenges. Here, we report two orphan antibacterial T6SS effectors in the pathogen Pantoea agglomerans (Pa). These effectors share an N-terminal domain, Pantoea type six (PIX), that defines a widespread class of polymorphic T6SS effectors in Enterobacterales. We show that the PIX domain is necessary and sufficient for T6SS-mediated effector secretion and that PIX binds to a specialized Pa VgrG protein outside its C-terminal toxic domain. Our findings underline the importance of identifying and characterizing delivery domains in polymorphic toxin classes as a tool to reveal effectors and shed light on effector delivery mechanisms.
Collapse
Affiliation(s)
- Andrea Carobbi
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ksenia Leo
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Simone Di Nepi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
48
|
Zhou Y, Yu L, Liu M, Liang W, Li Z, Nan Z, Kan B. Virulence, antibiotic resistance phenotypes and molecular characterisation of Vibrio furnissii isolates from patients with diarrhoea. BMC Infect Dis 2024; 24:412. [PMID: 38641583 PMCID: PMC11027346 DOI: 10.1186/s12879-024-09273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/29/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Vibrio furnissii is an emerging human pathogen closely related to V. fluvialis that causes acute gastroenteritis. V. furnissii infection has been reported to be rarer than V. fluvialis, but a multi-drug resistance plasmid has recently been discovered in V. furnissii. METHODS During daily monitoring at a general hospital in Beijing, China, seven V. furnissii strains were collected from patients aged over 14 years who presented with acute diarrhoea between April and October 2018. Genome analysis and comparison were performed for virulence and antimicrobial resistance genes, plasmids and transposon islands, together with phylogenetic analysis. Antimicrobial resistance to 19 antibiotics was investigated using the microbroth dilution method. Virulence phenotypes were investigated based on type VI secretion system (T6SS) expression and using a bacterial killing assay and a haemolysin assay. RESULTS Phylogenetic analysis based on single-nucleotide polymorphisms revealed a closer relationship between V. furnissii and V. fluvialis than between other Vibrio spp. The seven V. furnissii isolates were in different monophyletic clades in the phylogenetic tree, suggesting that the seven cases of gastroenteritis were independent. High resistance to cefazolin, tetracycline and streptomycin was found in the V. furnissii isolates at respective rates of 100.0%, 57.1% and 42.9%, and intermediate resistance to ampicillin/sulbactam and imipenem was observed at respective rates of 85.7% and 85.7%. Of the tested strains, VFBJ02 was resistant to both imipenem and meropenem, while VFBJ01, VFBJ02, VFBJ05 and VFBJ07 were multi-drug resistant. Transposon islands containing antibiotic resistance genes were found on the multi-drug resistance plasmid in VFBJ05. Such transposon islands also occurred in VFBJ07 but were located on the chromosome. The virulence-related genes T6SS, vfh, hupO, vfp and ilpA were widespread in V. furnissii. The results of the virulence phenotype assays demonstrated that our isolated V. furnissii strains encoded an activated T6SS and grew in large colonies with strong beta-haemolysis on blood agar. CONCLUSION This study showed that diarrhoea associated with V. furnissii occurred sporadically and was more common than expected in the summer in Beijing, China. The antibiotic resistance of V. furnissii has unique characteristics compared with that of V. fluvialis. Fluoroquinolones and third-generation cephalosporins, such as ceftazidime and doxycycline, were effective at treating V. furnissii infection. Continua laboratory-based surveillance is needed for the prevention and control of V. furnissii infection, especially the dissemination of the antibiotic resistance genes in this pathogen.
Collapse
Affiliation(s)
- Yanyan Zhou
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100052, China
| | - Li Yu
- Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, China
| | - Ming Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Weili Liang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Zhenpeng Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Zheng Nan
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100052, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China.
| |
Collapse
|
49
|
Dessartine MM, Kosta A, Doan T, Cascales É, Côté JP. Type 1 fimbriae-mediated collective protection against type 6 secretion system attacks. mBio 2024; 15:e0255323. [PMID: 38497656 PMCID: PMC11005336 DOI: 10.1128/mbio.02553-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/25/2024] [Indexed: 03/19/2024] Open
Abstract
Bacterial competition may rely on secretion systems such as the type 6 secretion system (T6SS), which punctures and releases toxic molecules into neighboring cells. To subsist, bacterial targets must counteract the threats posed by T6SS-positive competitors. In this study, we used a comprehensive genome-wide high-throughput screening approach to investigate the dynamics of interbacterial competition. Our primary goal was to identify deletion mutants within the well-characterized E. coli K-12 single-gene deletion library, the Keio collection, that demonstrated resistance to T6SS-mediated killing by the enteropathogenic bacterium Cronobacter malonaticus. We identified 49 potential mutants conferring resistance to T6SS and focused our interest on a deletion mutant (∆fimE) exhibiting enhanced expression of type 1 fimbriae. We demonstrated that the presence of type 1 fimbriae leads to the formation of microcolonies and thus protects against T6SS-mediated assaults. Collectively, our study demonstrated that adhesive structures such as type 1 fimbriae confer collective protective behavior against T6SS attacks.IMPORTANCEType 6 secretion systems (T6SS) are molecular weapons employed by gram-negative bacteria to eliminate neighboring microbes. T6SS plays a pivotal role as a virulence factor, enabling pathogenic gram-negative bacteria to compete with the established communities to colonize hosts and induce infections. Gaining a deeper understanding of bacterial interactions will allow the development of strategies to control the action of systems such as the T6SS that can manipulate bacterial communities. In this context, we demonstrate that bacteria targeted by T6SS attacks from the enteric pathogen Cronobacter malonaticus, which poses a significant threat to infants, can develop a collective protective mechanism centered on the production of type I fimbriae. These adhesive structures promote the aggregation of bacterial preys and the formation of microcolonies, which protect the cells from T6SS attacks.
Collapse
Affiliation(s)
- Margot Marie Dessartine
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Artemis Kosta
- Plateforme de microscopie, Institut de Microbiologie de la Méditerranée (IMM, FR3479), Aix-Marseille Univ, CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, CNRS, Marseille, France
| | - Éric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, CNRS, Marseille, France
| | - Jean-Philippe Côté
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
50
|
Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum. Microbiol Spectr 2024; 12:e0315723. [PMID: 38385740 PMCID: PMC10986534 DOI: 10.1128/spectrum.03157-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Chronic Pseudomonas aeruginosa lung infections are a feature of cystic fibrosis (CF) that many patients experience even with the advent of highly effective modulator therapies. Identifying factors that impact P. aeruginosa in the CF lung could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement published P. aeruginosa studies using laboratory models or RNA isolated from sputum, we analyzed transcripts of strain PAO1 after incubation in sputum from different CF donors prior to RNA extraction. We compared PAO1 gene expression in this "spike-in" sputum model to that for P. aeruginosa grown in synthetic cystic fibrosis sputum medium to determine key genes, which are among the most differentially expressed or most highly expressed. Using the key genes, gene sets with correlated expression were determined using the gene expression analysis tool eADAGE. Gene sets were used to analyze the activity of specific pathways in P. aeruginosa grown in sputum from different individuals. Gene sets that we found to be more active in sputum showed similar activation in published data that included P. aeruginosa RNA isolated from sputum relative to corresponding in vitro reference cultures. In the ex vivo samples, P. aeruginosa had increased levels of genes related to zinc and iron acquisition which were suppressed by metal amendment of sputum. We also found a significant correlation between expression of the H1-type VI secretion system and CFTR corrector use by the sputum donor. An ex vivo sputum model or synthetic sputum medium formulation that imposes metal restriction may enhance future CF-related studies.IMPORTANCEIdentifying the gene expression programs used by Pseudomonas aeruginosa to colonize the lungs of people with cystic fibrosis (CF) will illuminate new therapeutic strategies. To capture these transcriptional programs, we cultured the common P. aeruginosa laboratory strain PAO1 in expectorated sputum from CF patient donors. Through bioinformatic analysis, we defined sets of genes that are more transcriptionally active in real CF sputum compared to a synthetic cystic fibrosis sputum medium. Many of the most differentially active gene sets contained genes related to metal acquisition, suggesting that these gene sets play an active role in scavenging for metals in the CF lung environment which may be inadequately represented in some models. Future studies of P. aeruginosa transcript abundance in CF may benefit from the use of an expectorated sputum model or media supplemented with factors that induce metal restriction.
Collapse
Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Georgia Doing
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Taylor Reiter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|