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Chen H, Gao Q, Liu B, Zhang Y, Fang J, Wang S, Chen Y, Chen C. Identification of the global regulatory roles of RraA via the integrative transcriptome and proteome in Vibrio alginolyticus. mSphere 2024:e0002024. [PMID: 38934599 DOI: 10.1128/msphere.00020-24] [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: 01/08/2024] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Bacterial ribonuclease E (RNase E) is vital for posttranscriptional regulation by degrading and processing RNA. The RraA protein inhibits RNase E activity through protein-protein interactions, exerting a global regulatory effect on gene expression. However, the specific role of RraA remains unclear. In this study, we investigated rraA expression in Vibrio alginolyticus ZJ-T and identified three promoters responsible for its expression, resulting in transcripts with varying 5'-UTR lengths. During the stationary phase, rraA was significantly posttranscriptionally inhibited. Deletion of rraA had no impact on bacterial growth in rich medium Luria-Bertani broth with salt (LBS) but resulted in decreased biofilm formation and increased resistance to polymyxin B. Transcriptome analysis revealed 350 differentially expressed genes (DEGs) between the wild type and the rraA mutant, while proteome analysis identified 267 differentially expressed proteins (DEPs). Integrative analysis identified 55 genes common to both DEGs and DEPs, suggesting that RraA primarily affects gene expression at the posttranscriptional level. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis demonstrated that RraA facilitates the conversion of fatty acids, propionic acid, and branched-chain amino acids to acetyl-CoA while enhancing amino acid and peptide uptake. Notably, RraA positively regulates the expression of virulence-associated genes, including those involved in biofilm formation and the type VI secretion system. This study expands the understanding of the regulatory network of RraA through transcriptome analysis, emphasizing the importance of proteomic analysis in investigating posttranscriptional regulation.IMPORTANCERraA is an inhibitor protein of ribonuclease E that interacts with and suppresses its endonucleolytic activity, thereby playing a widespread regulatory role in the degradation and maturation of diverse mRNAs and noncoding small RNAs. However, the physiological functions and associated regulon of RraA in Vibrio alginolyticus have not been fully elucidated. Here, we report that RraA impacts virulence-associated physiological processes, namely, antibiotic resistance and biofilm formation, in V. alginolyticus. By conducting an integrative analysis of both the transcriptome and proteome, we revealed the involvement of RraA in carbon metabolism, amino acid catabolism, and transport, as well as in the type VI secretion system. Collectively, these findings elucidate the regulatory influence of RraA on multiple pathways associated with metabolism and pathogenesis in V. alginolyticus.
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Affiliation(s)
- Huizhen Chen
- South China Sea Institute of Oceanology, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Gao
- South China Sea Institute of Oceanology, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Liu
- South China Sea Institute of Oceanology, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- South China Sea Institute of Oceanology, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jianxiang Fang
- South China Sea Institute of Oceanology, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Songbiao Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Youqi Chen
- Guangzhou College of Technology and Business, Guangzhou, China
| | - Chang Chen
- South China Sea Institute of Oceanology, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Xisha Marine Environmental National Observation and Research Station, Sansha, China
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Hajdú G, Szathmári C, Sőti C. Modeling Host-Pathogen Interactions in C. elegans: Lessons Learned from Pseudomonas aeruginosa Infection. Int J Mol Sci 2024; 25:7034. [PMID: 39000143 PMCID: PMC11241598 DOI: 10.3390/ijms25137034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Infections, such as that by the multiresistant opportunistic bacterial pathogen Pseudomonas aeruginosa, may pose a serious health risk, especially on vulnerable patient populations. The nematode Caenorhabditis elegans provides a simple organismal model to investigate both pathogenic mechanisms and the emerging role of innate immunity in host protection. Here, we review the virulence and infection strategies of P. aeruginosa and host defenses of C. elegans. We summarize the recognition mechanisms of patterns of pathogenesis, including novel pathogen-associated molecular patterns and surveillance immunity of translation, mitochondria, and lysosome-related organelles. We also review the regulation of antimicrobial and behavioral defenses by the worm's neuroendocrine system. We focus on how discoveries in this rich field align with well-characterized evolutionary conserved protective pathways, as well as on potential crossovers to human pathogenesis and innate immune responses.
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Affiliation(s)
- Gábor Hajdú
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Csenge Szathmári
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Csaba Sőti
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
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Yu X, Yan Y, Zeng J, Liu Y, Sun X, Wang Z, Li L. T6SS nuclease effectors in Pseudomonas syringae act as potent antimicrobials in interbacterial competition. J Bacteriol 2024; 206:e0027323. [PMID: 38717111 DOI: 10.1128/jb.00273-23] [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: 08/16/2023] [Accepted: 04/09/2024] [Indexed: 06/21/2024] Open
Abstract
Type VI secretion system (T6SS) is a potent weapon employed by various Pseudomonas species to compete with neighboring microorganisms for limited nutrients and ecological niches. However, the involvement of T6SS effectors in interbacterial competition within the phytopathogen Pseudomonas syringae remains unknown. In this study, we examined two T6SS clusters in a wild-type P. syringae MB03 and verified the involvement of one cluster, namely, T6SS-1, in interbacterial competition. Additionally, our results showed that two T6SS DNase effectors, specifically Tde1 and Tde4, effectively outcompeted antagonistic bacteria, with Tde4 playing a prominent role. Furthermore, we found several cognate immunity proteins, including Tde1ia, Tde1ib, and Tde4i, which are located in the downstream loci of their corresponding effector protein genes and worked synergistically to protect MB03 cells from self-intoxication. Moreover, expression of either Tde1 or C-terminus of Tde4 in Escherichia coli cells induced DNA degradation and changes in cell morphology. Thus, our results provide new insights into the role of the T6SS effectors of P. syringae in the interbacterial competition in the natural environment. IMPORTANCE The phytopathogen Pseudomonas syringae employs an active type VI secretion system (T6SS) to outcompete other microorganisms in the natural environment, particularly during the epiphytic growth in the phyllosphere. By examining two T6SS clusters in P. syringae MB03, T6SS-1 is found to be effective in killing Escherichia coli cells. We highlight the excellent antibacterial effect of two T6SS DNase effectors, namely, Tde1 and Tde4. Both of them function as nuclease effectors, leading to DNA degradation and cell filamentation in prey cells, ultimately resulting in cell death. Our findings deepen our understanding of the T6SS effector repertoires used in P. syringae and will facilitate the development of effective antibacterial strategies.
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Affiliation(s)
- Xun Yu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei University of Technology, Wuhan, China
| | - Yubo Yan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jie Zeng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yongxuan Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xiaowen Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zhiyong Wang
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Lin Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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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 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.
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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
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Geller AM, Shalom M, Zlotkin D, Blum N, Levy A. Identification of type VI secretion system effector-immunity pairs using structural bioinformatics. Mol Syst Biol 2024; 20:702-718. [PMID: 38658795 PMCID: PMC11148199 DOI: 10.1038/s44320-024-00035-8] [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: 01/02/2024] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
The type VI secretion system (T6SS) is an important mediator of microbe-microbe and microbe-host interactions. Gram-negative bacteria use the T6SS to inject T6SS effectors (T6Es), which are usually proteins with toxic activity, into neighboring cells. Antibacterial effectors have cognate immunity proteins that neutralize self-intoxication. Here, we applied novel structural bioinformatic tools to perform systematic discovery and functional annotation of T6Es and their cognate immunity proteins from a dataset of 17,920 T6SS-encoding bacterial genomes. Using structural clustering, we identified 517 putative T6E families, outperforming sequence-based clustering. We developed a logistic regression model to reliably quantify protein-protein interaction of new T6E-immunity pairs, yielding candidate immunity proteins for 231 out of the 517 T6E families. We used sensitive structure-based annotation which yielded functional annotations for 51% of the T6E families, again outperforming sequence-based annotation. Next, we validated four novel T6E-immunity pairs using basic experiments in E. coli. In particular, we showed that the Pfam domain DUF3289 is a homolog of Colicin M and that DUF943 acts as its cognate immunity protein. Furthermore, we discovered a novel T6E that is a structural homolog of SleB, a lytic transglycosylase, and identified a specific glutamate that acts as its putative catalytic residue. Overall, this study applies novel structural bioinformatic tools to T6E-immunity pair discovery, and provides an extensive database of annotated T6E-immunity pairs.
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Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maor Shalom
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Zlotkin
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noam Blum
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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Mannaa M, Lee D, Lee HH, Han G, Kang M, Kim TJ, Park J, Seo YS. Exploring the comparative genome of rice pathogen Burkholderia plantarii: unveiling virulence, fitness traits, and a potential type III secretion system effector. FRONTIERS IN PLANT SCIENCE 2024; 15:1416253. [PMID: 38845849 PMCID: PMC11153758 DOI: 10.3389/fpls.2024.1416253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Duyoung Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Minhee Kang
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Tae-Jin Kim
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
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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.
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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
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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.
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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.
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9
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Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024; 629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [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: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
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Affiliation(s)
- Qinqin Zhao
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Savannah Bertolli
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yongjun Tan
- Department of Biology, St Louis University, St Louis, MO, USA
| | - Kevin J Cutler
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Pooja Srinivas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle L Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Citlali Fonesca-García
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dapeng Zhang
- Department of Biology, St Louis University, St Louis, MO, USA
- Program of Bioinformatic and Computational Biology, St Louis University, St Louis, MO, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA.
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10
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Gordils-Valentin L, Ouyang H, Qian L, Hong J, Zhu X. Conjugative type IV secretion systems enable bacterial antagonism that operates independently of plasmid transfer. Commun Biol 2024; 7:499. [PMID: 38664513 PMCID: PMC11045733 DOI: 10.1038/s42003-024-06192-8] [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: 06/20/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Bacterial cooperation and antagonism mediated by secretion systems are among the ways in which bacteria interact with one another. Here we report the discovery of an antagonistic property of a type IV secretion system (T4SS) sourced from a conjugative plasmid, RP4, using engineering approaches. We scrutinized the genetic determinants and suggested that this antagonistic activity is independent of molecular cargos, while we also elucidated the resistance genes. We further showed that a range of Gram-negative bacteria and a mixed bacterial population can be eliminated by this T4SS-dependent antagonism. Finally, we showed that such an antagonistic property is not limited to T4SS sourced from RP4, rather it can also be observed in a T4SS originated from another conjugative plasmid, namely R388. Our results are the first demonstration of conjugative T4SS-dependent antagonism between Gram-negative bacteria on the genetic level and provide the foundation for future mechanistic studies.
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Affiliation(s)
- Lois Gordils-Valentin
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US
- Interdisciplinary Graduate Program in Genetics & Genomics, Texas A&M University, College Station, 77843, TX, US
| | - Huanrong Ouyang
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US
| | - Liangyu Qian
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US
| | - Joshua Hong
- Department of Biology, Texas A&M University, College Station, 77843, TX, US
| | - Xuejun Zhu
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US.
- Interdisciplinary Graduate Program in Genetics & Genomics, Texas A&M University, College Station, 77843, TX, US.
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11
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Carobbi A, Leo K, Di Nepi S, Bosis E, Salomon D, Sessa G. PIX is an N-terminal delivery domain that defines a class of polymorphic T6SS effectors in Enterobacterales. Cell Rep 2024; 43:114015. [PMID: 38568810 DOI: 10.1016/j.celrep.2024.114015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
The type VI secretion system (T6SS), a widespread protein delivery apparatus, plays a role in bacterial competition by delivering toxic effectors into neighboring cells. Identifying new T6SS effectors and deciphering the mechanism that governs their secretion remain major challenges. Here, we report two orphan antibacterial T6SS effectors in the pathogen Pantoea agglomerans (Pa). These effectors share an N-terminal domain, Pantoea type six (PIX), that defines a widespread class of polymorphic T6SS effectors in Enterobacterales. We show that the PIX domain is necessary and sufficient for T6SS-mediated effector secretion and that PIX binds to a specialized Pa VgrG protein outside its C-terminal toxic domain. Our findings underline the importance of identifying and characterizing delivery domains in polymorphic toxin classes as a tool to reveal effectors and shed light on effector delivery mechanisms.
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Affiliation(s)
- Andrea Carobbi
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ksenia Leo
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Simone Di Nepi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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12
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Bray AS, Zafar MA. Deciphering the gastrointestinal carriage of Klebsiella pneumoniae. Infect Immun 2024:e0048223. [PMID: 38597634 DOI: 10.1128/iai.00482-23] [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] [Indexed: 04/11/2024] Open
Abstract
Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.
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Affiliation(s)
- Andrew S Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - M Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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13
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Liu X, Yang Y, Takizawa S, Graham NJD, Chen C, Pu J, Ng HY. New insights into the concentration-dependent regulation of membrane biofouling formation via continuous nanoplastics stimulation. WATER RESEARCH 2024; 253:121268. [PMID: 38340700 DOI: 10.1016/j.watres.2024.121268] [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: 12/07/2023] [Revised: 01/17/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
The release of nanoplastics (NPs) into the environment is growing due to the extensive use of plastic products. Numerous studies have confirmed the negative effects of NPs on microorganisms, which poses uncertainties concerning their impact on nanofiltration (NF) membrane biofouling. This study investigated the initial cell adhesion process, NF membrane biofouling kinetic processes and bacterial responses of Pseudomonas aeruginosa (P. aeruginosa) exposed to varied NPs concentrations (0-50 mg·L-1). Transcriptome analysis demonstrated that low concentration of NPs (0.1 mg·L-1) promoted bacterial quorum sensing, energy metabolism, exopolysaccharide biosynthesis and bacterial secretion systems. Correspondingly, the polysaccharide content increased remarkably to 2.77 times the unexposed control, which served as a protective barrier for bacteria to avoid the impact of NPs-induced stress. Suppressed homologous recombination, microbial metabolic potentials and flagellar assembly were detected in bacteria exposed to a high concentration (50 mg·L-1) of NPs, mainly due to the triggered reactive oxygen species (ROS) generation, genomic DNA damage, and decreased energy production. Overall, enhanced formation of the extracellular polymeric substances (EPS) and aggravated membrane flux decline were observed when NPs interacted with the membrane surface by cell secretions (low NPs levels) or cell lysis (high NPs levels). These findings shed light on understanding the microbial metabolism mechanism and membrane biofouling propensity with NPs stress at both the molecular and gene levels.
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Affiliation(s)
- Xinhui Liu
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yu Yang
- School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Satoshi Takizawa
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Chao Chen
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jian Pu
- Institute for the Advanced Study of Sustainability, United Nations University, Jingumae 5-53-70, Shibuya-ku, Tokyo 150-8925, Japan; Institute for Future Initiatives, The University of Tokyo, Tokyo 113-0033, Japan
| | - How Yong Ng
- Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, Singapore 117411, Singapore
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14
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Lu L, Qi Z, Chen Z, Wang H, Wei X, Zhao B, Wang Z, Shao Y, Tu J, Song X. Avian pathogenic Escherichia coli T6SS effector protein Hcp2a causes mitochondrial dysfunction through interaction with LETM1 protein in DF-1 cells. Poult Sci 2024; 103:103514. [PMID: 38367471 PMCID: PMC10879833 DOI: 10.1016/j.psj.2024.103514] [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: 12/05/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/19/2024] Open
Abstract
The type VI secretion system (T6SS) of avian pathogenic Escherichia coli (APEC) can affect the functions of eukaryotic cells by secreting or injecting effectors. Hemolysin co-regulatory protein (Hcp), one of the markers of the T6SS, is both a structural protein and an effector protein of the T6SS. According to previous studies, mitochondria in eukaryotic cells are targeted by pathogenic bacteria. However, little is known about the regulation of mitochondria in eukaryotic host cells by the T6SS effector protein Hcp of APEC. In our study, DF-1 cells co-incubated with Hcp2a protein for 6 h showed decreased mitochondrial membrane potential, increased Ca2+ concentration, and increased cellular reactive oxygen species (ROS) levels. We therefore conclude that Hcp2a protein causes dysfunction to mitochondria in DF-1 cells. To explain the mechanism that causes mitochondrial dysfunction, we reanalyzed the Hcp2a interaction protein dataset in DF-1 cells, and the Leucine zipper EF-hand-containing transmembrane protein 1 (LETM1), which is associated with mitochondria, was screened. The protein and molecular docking results showed that Hcp2a protein and LETM1 protein have better binding. Finally, subcellular localization results showed that Hcp2a was localized to mitochondria. In summary, Hcp2a effector proteins caused dysfunction to DF-1 cellular mitochondria, and we hypothesize that the interaction of Hcp2a protein with LETM1 protein induces mitochondrial dysfunction and promotes mitochondrial localization of Hcp2a in DF-1 cells.
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Affiliation(s)
- Liting Lu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Zhao Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Zhe Chen
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Haiyang Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Xiyang Wei
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Bingyu Zhao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Zhenyu Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei, PR China
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Joint Research Center for Food Nutrition and Health of IHM, Anhui Agricultural University, Hefei, PR China.
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15
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Oka GU, Souza DP, Sgro GG, Guzzo CR, Dunger G, Farah CS. Xanthomonas immunity proteins protect against the cis-toxic effects of their cognate T4SS effectors. EMBO Rep 2024; 25:1436-1452. [PMID: 38332152 PMCID: PMC10933484 DOI: 10.1038/s44319-024-00060-6] [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: 09/07/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
Many bacteria kill rival species by translocating toxic effectors into target cells. Effectors are often encoded along with cognate immunity proteins that could (i) protect against "friendly-fire" (trans-intoxication) from neighboring sister cells and/or (ii) protect against internal cis-intoxication (suicide). Here, we distinguish between these two mechanisms in the case of the bactericidal Xanthomonas citri Type IV Secretion System (X-T4SS). We use a set of X. citri mutants lacking multiple effector/immunity protein (X-Tfe/X-Tfi) pairs to show that X-Tfis are not absolutely required to protect against trans-intoxication by wild-type cells. Our investigation then focused on the in vivo function of the lysozyme-like effector X-TfeXAC2609 and its cognate immunity protein X-TfiXAC2610. In the absence of X-TfiXAC2610, we observe X-TfeXAC2609-dependent and X-T4SS-independent accumulation of damage in the X. citri cell envelope, cell death, and inhibition of biofilm formation. While immunity proteins in other systems have been shown to protect against attacks by sister cells (trans-intoxication), this is an example of an antibacterial secretion system in which the immunity proteins are dedicated to protecting cells against cis-intoxication.
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Affiliation(s)
- Gabriel U Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Structure and Function of Bacterial Nanomachines, Institut Européen de Chimie et Biologie-CNRS, UMR 5234 Microbiologie Fondamentale et Pathogénicité University of Bordeaux, Pessac, France
| | - Diorge P Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Germán G Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Cristiane R Guzzo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - German Dunger
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto de Ciencias Agropecuarias del Litoral (ICiAgro Litoral), Universidad Nacional del Litoral, CONICET, Facultad de Ciencias Agrarias, Esperanza, Argentina
| | - Chuck S Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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16
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Zhao X, Gao L, Ali Q, Yu C, Yuan B, Huang H, Long J, Gu Q, Wu H, Gao X. A type VI secretion system effector TseG of Pantoea ananatis is involved in virulence and antibacterial activity. MOLECULAR PLANT PATHOLOGY 2024; 25:e13442. [PMID: 38476100 DOI: 10.1111/mpp.13442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
The type VI secretion system (T6SS) of many gram-negative bacteria injects toxic effectors into adjacent cells to manipulate host cells during pathogenesis or to kill competing bacteria. However, the identification and function of the T6SS effectors remains only partly known. Pantoea ananatis, a gram-negative bacterium, is commonly found in various plants and natural environments, including water and soil. In the current study, genomic analysis of P. ananatis DZ-12 causing brown stalk rot on maize demonstrated that it carries three T6SS gene clusters, namely, T6SS-1, T6SS-2, and T6SS-3. Interestingly, only T6SS-1 secretion systems are involved in pathogenicity and bacterial competition. The study also investigated the T6SS-1 system in detail and identified an unknown T6SS-1-secreted effector TseG by using the upstream T6SS effector chaperone TecG containing a conserved domain of DUF2169. TseG can directly interact with the chaperone TecG for delivery and with a downstream immunity protein TsiG for protection from its toxicity. TseG, highly conserved in the Pantoea genus, is involved in virulence in maize, potato, and onion. Additionally, P. ananatis uses TseG to target Escherichia coli, gaining a competitive advantage. This study provides the first report on the T6SS-1-secreted effector from P. ananatis, thereby enriching our understanding of the various types and functions of type VI effector proteins.
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Affiliation(s)
- Xiaozhen Zhao
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Lu Gao
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Qurban Ali
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Bingqin Yuan
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Hai Huang
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Juying Long
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Qin Gu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
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17
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Yin R, Cheng J, Lin J. The role of the type VI secretion system in the stress resistance of plant-associated bacteria. STRESS BIOLOGY 2024; 4:16. [PMID: 38376647 PMCID: PMC10879055 DOI: 10.1007/s44154-024-00151-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024]
Abstract
The type VI secretion system (T6SS) is a powerful bacterial molecular weapon that can inject effector proteins into prokaryotic or eukaryotic cells, thereby participating in the competition between bacteria and improving bacterial environmental adaptability. Although most current studies of the T6SS have focused on animal bacteria, this system is also significant for the adaptation of plant-associated bacteria. This paper briefly introduces the structure and biological functions of the T6SS. We summarize the role of plant-associated bacterial T6SS in adaptability to host plants and the external environment, including resistance to biotic stresses such as host defenses and competition from other bacteria. We review the role of the T6SS in response to abiotic factors such as acid stress, oxidation stress, and osmotic stress. This review provides an important reference for exploring the functions of the T6SS in plant-associated bacteria. In addition, characterizing these anti-stress functions of the T6SS may provide new pathways toward eliminating plant pathogens and controlling agricultural losses.
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Affiliation(s)
- Rui Yin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Juanli Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Jinshui Lin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China.
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18
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Restrepo-Benavides M, Lozano-Arce D, Gonzalez-Garcia LN, Báez-Aguirre F, Ariza-Aranguren G, Faccini D, Zambrano MM, Jiménez P, Fernández-Bravo A, Restrepo S, Guevara-Suarez M. Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses. Microbiol Spectr 2024; 12:e0292823. [PMID: 38189292 PMCID: PMC10846245 DOI: 10.1128/spectrum.02928-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024] Open
Abstract
The genus Vibrio includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on Vibrio in several marine organisms, no specific studies have been conducted on Anadara tuberculosa. This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast. Therefore, this study aimed to identify and characterize the genomes of Vibrio isolates obtained from A. tuberculosa. Bacterial isolates were obtained from 14 A. tuberculosa specimens collected from two locations along the Colombian Pacific coast, of which 17 strains were identified as Vibrio: V. parahaemolyticus (n = 12), V. alginolyticus (n = 3), V. fluvialis (n = 1), and V. natriegens (n = 1). Whole genome sequence of these isolates was done using Oxford Nanopore Technologies (ONT). The analysis revealed the presence of genes conferring resistance to β-lactams, tetracyclines, chloramphenicol, and macrolides, indicating potential resistance to these antimicrobial agents. Genes associated with virulence were also found, suggesting the potential pathogenicity of these Vibrio isolates, as well as genes for Type III Secretion Systems (T3SS) and Type VI Secretion Systems (T6SS), which play crucial roles in delivering virulence factors and in interbacterial competition. This study represents the first genomic analysis of bacteria within A. tuberculosa, shedding light on Vibrio genetic factors and contributing to a comprehensive understanding of the pathogenic potential of these Vibrio isolates.IMPORTANCEThis study presents the first comprehensive report on the whole genome analysis of Vibrio isolates obtained from Anadara tuberculosa, a bivalve species of great significance for social and economic matters on the Pacific coast of Colombia. Research findings have significant implications for the field, as they provide crucial information on the genetic factors and possible pathogenicity of Vibrio isolates associated with A. tuberculosa. The identification of antimicrobial resistance genes and virulence factors within these isolates emphasizes the potential risks they pose to both human and animal health. Furthermore, the presence of genes associated with Type III and Type VI Secretion Systems suggests their critical role in virulence and interbacterial competition. Understanding the genetic factors that contribute to Vibrio bacterial virulence and survival strategies within their ecological niche is of utmost importance for the effective prevention and management of diseases in aquaculture practices.
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Affiliation(s)
- Mariana Restrepo-Benavides
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Daniela Lozano-Arce
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Laura Natalia Gonzalez-Garcia
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá, Colombia
- UMR DIADE, Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, France
| | - Felipe Báez-Aguirre
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Gabriela Ariza-Aranguren
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Daniel Faccini
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | | | - Pedro Jiménez
- Laboratorio de Fitopatología, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Ana Fernández-Bravo
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Silvia Restrepo
- Departamento de Ingeniería Química y de Alimentos, Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Marcela Guevara-Suarez
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
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19
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Gudeta DD, Foley SL. Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation. Microbiol Spectr 2024; 12:e0338723. [PMID: 37991378 PMCID: PMC10782977 DOI: 10.1128/spectrum.03387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.
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Affiliation(s)
- Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
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20
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Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E. Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota. Nat Commun 2024; 15:429. [PMID: 38200008 PMCID: PMC10781749 DOI: 10.1038/s41467-023-44426-1] [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: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
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Affiliation(s)
- Thibault R Bongiovanni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Casey J Latario
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Youn Le Cras
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Danica Schmidtke
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA
| | - Maxence Vincent
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Artemis Kosta
- Microscopy Core Facility, Institut de Microbiologie de la Méditerranée (IMM), FR3479, CNRS, Aix-Marseille University, Marseille, France
| | - Jan Orth
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007, Lyon, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA.
| | - Eric Durand
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
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21
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Song L, Xu L, Wu T, Shi Z, Kareem HA, Wang Z, Dai Q, Guo C, Pan J, Yang M, Wei X, Wang Y, Wei G, Shen X. Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition. THE ISME JOURNAL 2024; 18:wrad028. [PMID: 38365238 PMCID: PMC10833071 DOI: 10.1093/ismejo/wrad028] [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: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 02/18/2024]
Abstract
The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.
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Affiliation(s)
- Li Song
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Xu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tong Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenkun Shi
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hafiz Abdul Kareem
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuo Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingyun Dai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenghao Guo
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junfeng Pan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomeng Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihui Shen
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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22
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Kjellin J, Lee D, Steinsland H, Dwane R, Barth Vedoy O, Hanevik K, Koskiniemi S. Colicins and T6SS-based competition systems enhance enterotoxigenic E. coli (ETEC) competitiveness. Gut Microbes 2024; 16:2295891. [PMID: 38149626 PMCID: PMC10761095 DOI: 10.1080/19490976.2023.2295891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023] Open
Abstract
Diarrheal diseases are still a significant problem for humankind, causing approximately half a million deaths annually. To cause diarrhea, enteric bacterial pathogens must first colonize the gut, which is a niche occupied by the normal bacterial microbiota. Therefore, the ability of pathogenic bacteria to inhibit the growth of other bacteria can facilitate the colonization process. Although enterotoxigenic Escherichia coli (ETEC) is one of the major causative agents of diarrheal diseases, little is known about the competition systems found in and used by ETEC and how they contribute to the ability of ETEC to colonize a host. Here, we collected a set of 94 fully assembled ETEC genomes by performing whole-genome sequencing and mining the NCBI RefSeq database. Using this set, we performed a comprehensive search for delivered bacterial toxins and investigated how these toxins contribute to ETEC competitiveness in vitro. We found that type VI secretion systems (T6SS) were widespread among ETEC (n = 47). In addition, several closely related ETEC strains were found to encode Colicin Ia and T6SS (n = 8). These toxins provide ETEC competitive advantages during in vitro competition against other E. coli, suggesting that the role of T6SS as well as colicins in ETEC biology has until now been underappreciated.
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Affiliation(s)
- Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Danna Lee
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Hans Steinsland
- CISMAC, Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rachel Dwane
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Oda Barth Vedoy
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National centre for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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23
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Flaugnatti N, Journet L. Identification of Effectors: Precipitation of Supernatant Material. Methods Mol Biol 2024; 2715:533-538. [PMID: 37930549 DOI: 10.1007/978-1-0716-3445-5_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems allow the transport of proteins, called effectors, as well as external machine components in the extracellular medium or directly into target cells. Comparison of the secretome, i.e., the proteins released in the culture medium, of wild-type and mutant cells provides information on the secretion profile. In addition, mass spectrometry analyses of the culture supernatant of bacteria grown in liquid culture under secreting conditions allow the identification of secretion systems substrates. Upon identification of the substrates, the secretion profile serves as a tool to test the functionality of secretion systems. Here, we present a classical method used to concentrate the culture supernatant, based on TCA precipitation.
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Affiliation(s)
- Nicolas Flaugnatti
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, CNRS, Marseille, France
- Laboratory of Molecular Microbiology, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laure Journet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, CNRS, Marseille, France.
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24
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Alcoforado Diniz J, Earl C, Hernandez RE, Hollmann B, Coulthurst SJ. Quantitative Determination of Antibacterial Activity During Bacterial Coculture. Methods Mol Biol 2024; 2715:593-600. [PMID: 37930554 DOI: 10.1007/978-1-0716-3445-5_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Antibacterial activity assays are an important tool in the assessment of the ability of one bacterium to kill or inhibit the growth of another, for example, during the study of the Type VI secretion system (T6SS) and the antibacterial toxins it secretes. The method we describe here can detect the ability of a bacterial strain to kill or inhibit other bacterial cells in a contact-dependent manner when cocultured on an agar surface. It is particularly useful since it enumerates the recovery of viable target cells and thus enables quantification of the antibacterial activity. We provide a detailed description of how to measure the T6SS-dependent antibacterial activity of a bacterium such as Serratia marcescens against a competitor prokaryotic organism, Escherichia coli, and describe possible variations in the method to allow adaptation to other attacker and target organisms.
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Affiliation(s)
| | - Christopher Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ruth E Hernandez
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Birte Hollmann
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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25
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Luo Y, Chen Z, Lian S, Ji X, Zhu C, Zhu G, Xia P. The Love and Hate Relationship between T5SS and Other Secretion Systems in Bacteria. Int J Mol Sci 2023; 25:281. [PMID: 38203452 PMCID: PMC10778856 DOI: 10.3390/ijms25010281] [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: 12/04/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Bacteria have existed on Earth for billions of years, exhibiting ubiquity and involvement in various biological activities. To ensure survival, bacteria usually release and secrete effector proteins to acquire nutrients and compete with other microorganisms for living space during long-term evolution. Consequently, bacteria have developed a range of secretion systems, which are complex macromolecular transport machines responsible for transporting proteins across the bacterial cell membranes. Among them, one particular secretion system that stands out from the rest is the type V secretion system (T5SS), known as the "autotransporter". Bacterial activities mediated by T5SS include adherence to host cells or the extracellular matrix, invasion of host cells, immune evasion and serum resistance, contact-dependent growth inhibition, cytotoxicity, intracellular flow, protease activity, autoaggregation, and biofilm formation. In a bacterial body, it is not enough to rely on T5SS alone; in most cases, T5SS cooperates with other secretion systems to carry out bacterial life activities, but regardless of how good the relationship is, there is friction between the secretion systems. T5SS and T1SS/T2SS/T3SS/T6SS all play a synergistic role in the pathogenic processes of bacteria, such as nutrient acquisition, pathogenicity enhancement, and immune modulation, but T5SS indirectly inhibits the function of T4SS. This could be considered a love-hate relationship between secretion systems. This paper uses the systematic literature review methodology to review 117 journal articles published within the period from 1995 to 2024, which are all available from the PubMed, Web of Science, and Scopus databases and aim to elucidate the link between T5SS and other secretion systems, providing clues for future prevention and control of bacterial diseases.
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Affiliation(s)
- Yi Luo
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, Yangzhou 225009, China; (Y.L.); (Z.C.); (S.L.); (X.J.); (G.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
| | - Ziyue Chen
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, Yangzhou 225009, China; (Y.L.); (Z.C.); (S.L.); (X.J.); (G.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
| | - Siqi Lian
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, Yangzhou 225009, China; (Y.L.); (Z.C.); (S.L.); (X.J.); (G.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
| | - Xingduo Ji
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, Yangzhou 225009, China; (Y.L.); (Z.C.); (S.L.); (X.J.); (G.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
| | - Chunhong Zhu
- Jiangsu Institute of Poultry Science, Yangzhou 225009, China;
| | - Guoqiang Zhu
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, Yangzhou 225009, China; (Y.L.); (Z.C.); (S.L.); (X.J.); (G.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
| | - Pengpeng Xia
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, Yangzhou 225009, China; (Y.L.); (Z.C.); (S.L.); (X.J.); (G.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
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26
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Neff SL, Hampton TH, Koeppen K, Sarkar S, Latario CJ, Ross BD, Stanton BA. Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development. mSystems 2023; 8:e0065323. [PMID: 37975659 PMCID: PMC10734502 DOI: 10.1128/msystems.00653-23] [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: 06/22/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Antimicrobial-resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The application's target audience are microbiologists that have the laboratory resources to test the application's predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including cystic fibrosis, chronic obstructive pulmonary disease (COPD), urinary tract infections, and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Casey J. Latario
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Benjamin D. Ross
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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27
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Dogsa I, Mandic-Mulec I. Multiscale spatial segregation analysis in digital images of biofilms. Biofilm 2023; 6:100157. [PMID: 37790733 PMCID: PMC10542597 DOI: 10.1016/j.bioflm.2023.100157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Quantifying the degree of spatial segregation of two bacterial strains in mixed biofilms is an important topic in microbiology. Spatial segregation is dependent on spatial scale as two strains may appear to be well mixed if observed from a distance, but a closer look can reveal strong separation. Typically, this information is encoded in a digital image that represents the binary system, e.g., a microscopy image of a two species biofilm. To decode spatial segregation information, we have developed quantitative measures for evaluating the degree of the spatial scale-dependent segregation of two bacterial strains in a digital image. The constructed algorithm is based on the new segregation measures and overcomes drawbacks of existing approaches for biofilm segregation analysis. The new approach is implemented in a freely available software and was successfully applied to biofilms of two strains and bacterial suspensions for detection of the different spatial scale-dependent segregation levels.
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Affiliation(s)
- Iztok Dogsa
- Chair of Microbiology, Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, EU, Slovenia
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, EU, Slovenia
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28
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Robitaille S, Simmons EL, Verster AJ, McClure EA, Royce DB, Trus E, Swartz K, Schultz D, Nadell CD, Ross BD. Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria. Nat Ecol Evol 2023; 7:2092-2107. [PMID: 37884689 PMCID: PMC11099977 DOI: 10.1038/s41559-023-02230-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of great importance; however, knowledge of the biogeographical and ecological relationships between physically interacting taxa is limited. Interbacterial antagonism may play an important role in gut community dynamics, yet the conditions under which antagonistic behaviour is favoured or disfavoured by selection in the gut are not well understood. Here, using genomics, we show that a species-specific type VI secretion system (T6SS) repeatedly acquires inactivating mutations in Bacteroides fragilis in the human gut. This result implies a fitness cost to the T6SS, but we could not identify laboratory conditions under which such a cost manifests. Strikingly, experiments in mice illustrate that the T6SS can be favoured or disfavoured in the gut depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use ecological modelling to explore the conditions that could underlie these results and find that community spatial structure modulates interaction patterns among bacteria, thereby modulating the costs and benefits of T6SS activity. Our findings point towards new integrative models for interrogating the evolutionary dynamics of type VI secretion and other modes of antagonistic interaction in microbiomes.
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Affiliation(s)
- Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Emilia L Simmons
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Emily Ann McClure
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Darlene B Royce
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA.
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Wang C, Chen M, Shao Y, Jiang M, Li Q, Chen L, Wu Y, Cen S, Waterfield NR, Yang J, Yang G. Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system. Commun Biol 2023; 6:1195. [PMID: 38001377 PMCID: PMC10673891 DOI: 10.1038/s42003-023-05580-w] [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: 05/31/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Type VI secretion systems (T6SSs) deliver effectors into target cells. Besides structural and effector proteins, many other proteins, such as adaptors, co-effectors and accessory proteins, are involved in this process. MIX domains can assist in the delivery of T6SS effectors when encoded as a stand-alone gene or fused at the N-terminal of the effector. However, whether there are other conserved domains exhibiting similar encoding forms to MIX in T6SS remains obscure. Here, we scanned publicly available bacterial genomes and established a database which include 130,825 T6SS vgrG loci from 45,041 bacterial genomes. Based on this database, we revealed six domain families encoded within vgrG loci, which are either fused at the C-terminus of VgrG/N-terminus of T6SS toxin or encoded by an independent gene. Among them, DUF2345 was further validated and shown to be indispensable for the T6SS effector delivery and LysM was confirmed to assist the interaction between VgrG and the corresponding effector. Together, our results implied that these widely distributed domain families with similar genetic configurations may be required for the T6SS effector recruitment process.
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Affiliation(s)
- Caihong Wang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Mingxing Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China
| | - Yuhan Shao
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Mengyuan Jiang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China
| | - Yun Wu
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- CAMS Key Laboratory of Antiviral Drug Research, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
| | - Guowei Yang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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30
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Warsi OM, Gedda L, Edwards K, Andersson DI. Vesicle-enriched secretomes alter bacterial competitive abilities and are drivers of evolution in microbial communities. FEMS Microbiol Ecol 2023; 99:fiad141. [PMID: 37884450 PMCID: PMC10653989 DOI: 10.1093/femsec/fiad141] [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: 07/31/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial membrane vesicles can carry compounds that inhibit bacterial growth, but how they impact the fitness of the vesicle-producing bacterial species and influence community dynamics remain unexplored questions. To address these questions, we examined the effect of vesicle-enriched secretomes (VESs) in different single-species and multi-species systems. Effects of VESs on single-species growth dynamics were determined for nine bacterial species belonging to four genera (Escherichia, Salmonella, Pseudomonas and Bacillus) in nutrient-rich and poor growth media. Results showed both species-specific and nutrient-dependent effects of the VESs on bacterial growth. The strongest antagonistic effects were observed for VES isolated from the natural isolates of E. coli, while those isolated from P. aeruginosa PA14 affected the highest number of species. We further demonstrated that these VESs altered the competitive abilities of the species involved in two-species (S. Typhimurium LT2 and S. arizonae) and three-species systems (E. coli, S. Typhimurium LT2 and B. subtilis). Finally, using experimental evolution we showed that different bacterial species could rapidly acquire mutations that abrogated the antagonistic effects of VESs. This study demonstrates how VESs can contribute in shaping microbial communities, both by increasing the competitive ability of a given bacterial species and as a driver of genetic adaptation.
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Affiliation(s)
- Omar M Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Lars Gedda
- Department of Chemistry-Ångström, Uppsala University, Uppsala 75237, Sweden
| | - Katarina Edwards
- Department of Chemistry-Ångström, Uppsala University, Uppsala 75237, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
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31
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Navarro-Monserrat ED, Taylor CG. T6SS: A Key to Pseudomonas's Success in Biocontrol? Microorganisms 2023; 11:2718. [PMID: 38004732 PMCID: PMC10673566 DOI: 10.3390/microorganisms11112718] [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: 09/25/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteria from the genus Pseudomonas have been extensively studied for their capacity to act as biological control agents of disease and pests and for their ability to enhance and promote crop production in agricultural systems. While initial research primarily focused on the human pathogenic bacteria Pseudomonas aeruginosa, recent studies indicate the significance of type VI secretion (T6SS) in other Pseudomonas strains for biocontrol purposes. This system possibly plays a pivotal role in restricting the biological activity of target microorganisms and may also contribute to the bolstering of the survival capabilities of the bacteria within their applied environment. The type VI secretion system is a phage-like structure used to translocate effectors into both prokaryotic and eukaryotic target cells. T6SSs are involved in a myriad of interactions, some of which have direct implications in the success of Pseudomonas as biocontrol agents. The prevalence of T6SSs in the genomes of Pseudomonas species is notably greater than the estimated 25% occurrence rate found in Gram-negative bacteria. This observation implies that T6SS likely plays a pivotal role in the survival and fitness of Pseudomonas. This review provides a brief overview of T6SS, its role in Pseudomonas with biocontrol applications, and future avenues of research within this subject matter.
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Affiliation(s)
| | - Christopher G. Taylor
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA;
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Durán D, Vazquez-Arias D, Blanco-Romero E, Garrido-Sanz D, Redondo-Nieto M, Rivilla R, Martín M. An Orphan VrgG Auxiliary Module Related to the Type VI Secretion Systems from Pseudomonas ogarae F113 Mediates Bacterial Killing. Genes (Basel) 2023; 14:1979. [PMID: 38002922 PMCID: PMC10671463 DOI: 10.3390/genes14111979] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The model rhizobacterium Pseudomonas ogarae F113, a relevant plant growth-promoting bacterium, encodes three different Type VI secretion systems (T6SS) in its genome. In silico analysis of its genome revealed the presence of a genetic auxiliary module containing a gene encoding an orphan VgrG protein (VgrG5a) that is not genetically linked to any T6SS structural cluster, but is associated with genes encoding putative T6SS-related proteins: a possible adaptor Tap protein, followed by a putative effector, Tfe8, and its putative cognate immunity protein, Tfi8. The bioinformatic analysis of the VgrG5a auxiliary module has revealed that this cluster is only present in several subgroups of the P. fluorescens complex of species. An analysis of the mutants affecting the vgrG5a and tfe8 genes has shown that the module is involved in bacterial killing. To test whether Tfe8/Tfi8 constitute an effector-immunity pair, the genes encoding Tfe8 and Tfi8 were cloned and expressed in E. coli, showing that the ectopic expression of tfe8 affected growth. The growth defect was suppressed by tfi8 ectopic expression. These results indicate that Tfe8 is a bacterial killing effector, while Tfi8 is its cognate immunity protein. The Tfe8 protein sequence presents homology to the proteins of the MATE family involved in drug extrusion. The Tfe8 effector is a membrane protein with 10 to 12 transmembrane domains that could destabilize the membranes of target cells by the formation of pores, revealing the importance of these effectors for bacterial interaction. Tfe8 represents a novel type of a T6SS effector present in pseudomonads.
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Affiliation(s)
- David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - David Vazquez-Arias
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
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33
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Khan S, Marathe SA, Jha PN. Characterizing the type 6 secretion system (T6SS) of E. cloacae SBP-8 and its role in pathogenesis and bacterial competition. Microb Pathog 2023; 183:106268. [PMID: 37536636 DOI: 10.1016/j.micpath.2023.106268] [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: 05/25/2023] [Revised: 07/06/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Despite the relevance of E. cloacae as an opportunistic pathogen, very little is known about its pathogenicity mechanism and the factors influencing its virulence. The mechanism of E. cloacae pathogenicity appears to be complex and multifactorial, with the presence of different putative virulence factors whose role is still not clear in the development of the disease. In this study, we systematically investigated the role of T6SS (type six secretion system) of E. cloacae SBP-8, an environmental isolate, in eukaryotic and bacterial cell interaction. Analysis of the genome sequence of E. cloacae SBP-8 revealed the presence of sets of genes coding for the expression of one complete T6SS cluster, which is similar to T6SS-1 cluster of E. cloacae ATCC 13047 (clinical isolates). In addition, an Hcp effector protein was detected in the secretome, and this secretion depended on ClpV, an Atpase of T6SS, confirming that strain SBP-8 produces functional T6SS. Deletion of T6SS-associated gene clpV did not induce any significant change in the life span and rate of colonization in C. elegans. No major significant change was observed in the expression profiling of antimicrobial genes (clec-60, clec-85, clec-87 and lys-1) and toll-like receptor (toll-1) gene, involved in stimulating an immune response against the pathogen. No difference in the ability to invade and proliferate in intestinal cells and phagocytosis by macrophages was observed. In addition, we demonstrated that the ability of E. cloacae SBP-8 to out-compete Escherichia coli was reliant upon its T6SS in contact-dependent manner. Our results show that T6SS of the environmental isolates is required for interbacterial competition but not for invasion and proliferation inside host cells.
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Affiliation(s)
- Shahid Khan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA; Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani, 333031, Rajasthan, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani, 333031, Rajasthan, India.
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani, 333031, Rajasthan, India.
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Meacock OJ, Durham WM. Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker. PLoS Comput Biol 2023; 19:e1011524. [PMID: 37812642 PMCID: PMC10586697 DOI: 10.1371/journal.pcbi.1011524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 10/19/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023] Open
Abstract
Most bacteria live attached to surfaces in densely-packed communities. While new experimental and imaging techniques are beginning to provide a window on the complex processes that play out in these communities, resolving the behaviour of individual cells through time and space remains a major challenge. Although a number of different software solutions have been developed to track microorganisms, these typically require users either to tune a large number of parameters or to groundtruth a large volume of imaging data to train a deep learning model-both manual processes which can be very time consuming for novel experiments. To overcome these limitations, we have developed FAST, the Feature-Assisted Segmenter/Tracker, which uses unsupervised machine learning to optimise tracking while maintaining ease of use. Our approach, rooted in information theory, largely eliminates the need for users to iteratively adjust parameters manually and make qualitative assessments of the resulting cell trajectories. Instead, FAST measures multiple distinguishing 'features' for each cell and then autonomously quantifies the amount of unique information each feature provides. We then use these measurements to determine how data from different features should be combined to minimize tracking errors. Comparing our algorithm with a naïve approach that uses cell position alone revealed that FAST produced 4 to 10 fold fewer tracking errors. The modular design of FAST combines our novel tracking method with tools for segmentation, extensive data visualisation, lineage assignment, and manual track correction. It is also highly extensible, allowing users to extract custom information from images and seamlessly integrate it into downstream analyses. FAST therefore enables high-throughput, data-rich analyses with minimal user input. It has been released for use either in Matlab or as a compiled stand-alone application, and is available at https://bit.ly/3vovDHn, along with extensive tutorials and detailed documentation.
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Affiliation(s)
- Oliver J. Meacock
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - William M. Durham
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
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35
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Smith JA, Holmes DE, Woodard TL, Li Y, Liu X, Wang LY, Meier D, Schwarz IA, Lovley DR. Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer. Microbiol Spectr 2023; 11:e0094123. [PMID: 37650614 PMCID: PMC10580878 DOI: 10.1128/spectrum.00941-23] [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: 03/02/2023] [Accepted: 07/02/2023] [Indexed: 09/01/2023] Open
Abstract
Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular-activated carbon (GAC), consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasizes the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCE Direct interspecies electron transfer is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity of establishing syntrophic relationships.
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Affiliation(s)
- Jessica A. Smith
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Yang Li
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, Liaoning, China
| | - Xinying Liu
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - David Meier
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
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Kan Y, Zhang Y, Lin W, Dong T. Differential plant cell responses to Acidovorax citrulli T3SS and T6SS reveal an effective strategy for controlling plant-associated pathogens. mBio 2023; 14:e0045923. [PMID: 37288971 PMCID: PMC10470598 DOI: 10.1128/mbio.00459-23] [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: 02/27/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
Acidovorax citrulli is a gram-negative plant pathogen that employs the type Ⅲ secretion system (T3SS) to infect cucurbit crops and cause bacterial fruit blotch. This bacterium also possesses an active type Ⅵ secretion system (T6SS) with strong antibacterial and antifungal activities. However, how plant cells respond to these two secretion systems and whether there is any cross talk between T3SS and T6SS during infection remain unknown. Here, we employ transcriptomic analysis to compare cellular responses to the T3SS and the T6SS during in planta infection and report distinctive effects on multiple pathways. The T3SS-mediated differentially expressed genes were enriched in the pathways of phenylpropanoid biosynthesis, plant-pathogen interaction, MAPK signaling pathway, and glutathione metabolism, while the T6SS uniquely affected genes were related to photosynthesis. The T6SS does not contribute to the in planta virulence of A. citrulli but is critical for the survival of the bacterium when mixed with watermelon phyllosphere bacteria. In addition, T3SS-mediated virulence is independent of the T6SS, and the inactivation of the T3SS does not affect the T6SS-mediated competition against a diverse set of bacterial pathogens that commonly contaminate edible plants or directly infect plants. A T6SS-active T3SS-null mutant (Acav) could inhibit the growth of Xanthomonas oryzae pv. oryzae significantly both in vitro and in vivo and also reduce symptoms of rice bacterial blight. In conclusion, our data demonstrate the T6SS in A. citrulli is nonpathogenic to the plant host and can be harnessed as a pathogen killer against plant-associated bacteria. IMPORTANCE Chemical pesticides are widely used to protect crops from various pathogens. Still, their extensive use has led to severe consequences, including drug resistance and environmental contamination. Here, we show that an engineered T6SS-active, but avirulent mutant of Acidovorax citrulli has strong inhibition capabilities against several pathogenic bacteria, demonstrating an effective strategy that is an alternative to chemical pesticides for sustainable agricultural practices.
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Affiliation(s)
- Yumin Kan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhui Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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37
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Wein P, Dornblut K, Herkersdorf S, Krüger T, Molloy EM, Brakhage AA, Hoffmeister D, Hertweck C. Bacterial secretion systems contribute to rapid tissue decay in button mushroom soft rot disease. mBio 2023; 14:e0078723. [PMID: 37486262 PMCID: PMC10470514 DOI: 10.1128/mbio.00787-23] [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: 03/28/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023] Open
Abstract
The soft rot pathogen Janthinobacterium agaricidamnosum causes devastating damage to button mushrooms (Agaricus bisporus), one of the most cultivated and commercially relevant mushrooms. We previously discovered that this pathogen releases the membrane-disrupting lipopeptide jagaricin. This bacterial toxin, however, could not solely explain the rapid decay of mushroom fruiting bodies, indicating that J. agaricidamnosum implements a more sophisticated infection strategy. In this study, we show that secretion systems play a crucial role in soft rot disease. By mining the genome of J. agaricidamnosum, we identified gene clusters encoding a type I (T1SS), a type II (T2SS), a type III (T3SS), and two type VI secretion systems (T6SSs). We targeted the T2SS and T3SS for gene inactivation studies, and subsequent bioassays implicated both in soft rot disease. Furthermore, through a combination of comparative secretome analysis and activity-guided fractionation, we identified a number of secreted lytic enzymes responsible for mushroom damage. Our findings regarding the contribution of secretion systems to the disease process expand the current knowledge of bacterial soft rot pathogens and represent a significant stride toward identifying targets for their disarmament with secretion system inhibitors. IMPORTANCE The button mushroom (Agaricus bisporus) is the most popular edible mushroom in the Western world. However, mushroom crops can fall victim to serious bacterial diseases that are a major threat to the mushroom industry, among them being soft rot disease caused by Janthinobacterium agaricidamnosum. Here, we show that the rapid dissolution of mushroom fruiting bodies after bacterial invasion is due to degradative enzymes and putative effector proteins secreted via the type II secretion system (T2SS) and the type III secretion system (T3SS), respectively. The ability to degrade mushroom tissue is significantly attenuated in secretion-deficient mutants, which establishes that secretion systems are key factors in mushroom soft rot disease. This insight is of both ecological and agricultural relevance by shedding light on the disease processes behind a pathogenic bacterial-fungal interaction which, in turn, serves as a starting point for the development of secretion system inhibitors to control disease progression.
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Affiliation(s)
- Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Katharina Dornblut
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Sebastian Herkersdorf
- Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University Jena, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A. Brakhage
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University Jena, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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38
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Kanarek K, Fridman CM, Bosis E, Salomon D. The RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors. Nat Commun 2023; 14:4983. [PMID: 37591831 PMCID: PMC10435454 DOI: 10.1038/s41467-023-40659-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Bacteria use the type VI secretion system (T6SS) to deliver toxic effectors into bacterial or eukaryotic cells during interbacterial competition, host colonization, or when resisting predation. Identifying effectors is a challenging task, as they lack canonical secretion signals or universally conserved domains. Here, we identify a protein domain, RIX, that defines a class of polymorphic T6SS cargo effectors. RIX is widespread in the Vibrionaceae family and is located at N-termini of proteins containing diverse antibacterial and anti-eukaryotic toxic domains. We demonstrate that RIX-containing proteins are delivered via T6SS into neighboring cells and that RIX is necessary and sufficient for T6SS-mediated secretion. In addition, RIX-containing proteins can enable the T6SS-mediated delivery of other cargo effectors by a previously undescribed mechanism. The identification of RIX-containing proteins significantly enlarges the repertoire of known T6SS effectors, especially those with anti-eukaryotic activities. Furthermore, our findings also suggest that T6SSs may play an underappreciated role in the interactions between vibrios and eukaryotes.
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Affiliation(s)
- Katarzyna Kanarek
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chaya Mushka Fridman
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel.
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Hespanhol JT, Nóbrega-Silva L, Bayer-Santos E. Regulation of type VI secretion systems at the transcriptional, posttranscriptional and posttranslational level. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001376. [PMID: 37552221 PMCID: PMC10482370 DOI: 10.1099/mic.0.001376] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Bacteria live in complex polymicrobial communities and are constantly competing for resources. The type VI secretion system (T6SS) is a widespread antagonistic mechanism used by Gram-negative bacteria to gain an advantage over competitors. T6SSs translocate toxic effector proteins inside target prokaryotic cells in a contact-dependent manner. In addition, some T6SS effectors can be secreted extracellularly and contribute to the scavenging scarce metal ions. Bacteria deploy their T6SSs in different situations, categorizing these systems into offensive, defensive and exploitative. The great variety of bacterial species and environments occupied by such species reflect the complexity of regulatory signals and networks that control the expression and activation of the T6SSs. Such regulation is tightly controlled at the transcriptional, posttranscriptional and posttranslational level by abiotic (e.g. pH, iron) or biotic (e.g. quorum-sensing) cues. In this review, we provide an update on the current knowledge about the regulatory networks that modulate the expression and activity of T6SSs across several species, focusing on systems used for interbacterial competition.
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Affiliation(s)
- Julia Takuno Hespanhol
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Luize Nóbrega-Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Ethel Bayer-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
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40
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Liu H, Wei Z, Li J, Liu X, Zhu L, Wang Y, Wang T, Li C, Shen X. A Yersinia T6SS Effector YezP Engages the Hemin Uptake Receptor HmuR and ZnuABC for Zn 2+ Acquisition. Appl Environ Microbiol 2023; 89:e0024023. [PMID: 37338394 PMCID: PMC10370319 DOI: 10.1128/aem.00240-23] [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: 02/15/2023] [Accepted: 05/25/2023] [Indexed: 06/21/2023] Open
Abstract
Metal ions are essential nutrients for all life forms, and restriction of metal ion availability is an effective host defense against bacterial infection. Meanwhile, bacterial pathogens have developed equally effective means to secure their metal ion supply. The enteric pathogen Yersinia pseudotuberculosis was found to uptake zinc using the T6SS4 effector YezP, which is essential for Zn2+ acquisition and bacterial survival under oxidative stress. However, the mechanism of this zinc uptake pathway has not been fully elucidated. Here, we identified the hemin uptake receptor HmuR for YezP, which can mediate import of Zn2+ into the periplasm by the YezP-Zn2+ complex and demonstrated that YezP functions extracellularly. This study also confirmed that the ZnuCB transporter is the inner membrane transporter for Zn2+ from the periplasm to cytoplasm. Overall, our results reveal the complete T6SS/YezP/HmuR/ZnuABC pathway, wherein multiple systems are coupled to support zinc uptake by Y. pseudotuberculosis under oxidative stress. IMPORTANCE Identifying the transporters involved in import of metal ions under normal physiological growth conditions in bacterial pathogens will clarify its pathogenic mechanism. Y. pseudotuberculosis YPIII, a common foodborne pathogen that infects animals and humans, uptake zinc via the T6SS4 effector YezP. However, the outer and inner transports involved in Zn2+ acquisition remain unknown. The important outcomes of this study are the identification of the hemin uptake receptor HmuR and inner membrane transporter ZnuCB that import Zn2+ into the cytoplasm via the YezP-Zn2+ complex, and elucidation of the complete Zn2+ acquisition pathway consisting of T6SS, HmuRSTUV, and ZnuABC, thereby providing a comprehensive view of T6SS-mediated ion transport and its functions.
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Affiliation(s)
- Hai Liu
- Qingyang Longfeng Sponge City Construction Management & Operation Co., Ltd, Qingyang, Gansu, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiyan Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiali Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingyu Liu
- State Key Laboratory of Geological Processes and Mineral Resources, Institute of Earth Sciences, China University of Geosciences, Beijing, China
| | - Lingfang Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Tietao Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Changfu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Olbrecht M, Echahidi F, Piérard D, Peeters C, Vandamme P, Wybo I, Demuyser T. In Vitro Susceptibility of Achromobacter Species Isolated from Cystic Fibrosis Patients: a 6-Year Survey. Antimicrob Agents Chemother 2023; 67:e0037923. [PMID: 37310234 PMCID: PMC10353363 DOI: 10.1128/aac.00379-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
We conducted in vitro antimicrobial susceptibility testing of 267 Achromobacter isolates for 16 antibiotics from 2017 to 2022. The highest susceptibility was found for piperacillin-tazobactam (70%) and ceftazidime-avibactam (62%). Between 30% and 49% of strains were susceptible to tigecycline, ceftazidime, and meropenem. We applied species-specific Achromobacter xylosoxidans breakpoints for piperacillin-tazobactam, meropenem, and trimethoprim-sulfamethoxazole and EUCAST pharmacokinetic/pharmacodynamic (PK/PD) breakpoints for the others. A. xylosoxidans was the most frequently isolated species, followed by Achromobacter insuavis and Achromobacter ruhlandii.
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Affiliation(s)
- Margo Olbrecht
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Fedoua Echahidi
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Denis Piérard
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Ingrid Wybo
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Thomas Demuyser
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- AIMS lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Taillefer B, Grandjean MM, Herrou J, Robert D, Mignot T, Sebban-Kreuzer C, Cascales E. Qualitative and Quantitative Methods to Measure Antibacterial Activity Resulting from Bacterial Competition. Bio Protoc 2023; 13:e4706. [PMID: 37449039 PMCID: PMC10336571 DOI: 10.21769/bioprotoc.4706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/06/2023] [Accepted: 04/16/2023] [Indexed: 07/18/2023] Open
Abstract
In the environment, bacteria compete for niche occupancy and resources; they have, therefore, evolved a broad variety of antibacterial weapons to destroy competitors. Current laboratory techniques to evaluate antibacterial activity are usually labor intensive, low throughput, costly, and time consuming. Typical assays rely on the outgrowth of colonies of prey cells on selective solid media after competition. Here, we present fast, inexpensive, and complementary optimized protocols to qualitatively and quantitively measure antibacterial activity. The first method is based on the degradation of a cell-impermeable chromogenic substrate of the β-galactosidase, a cytoplasmic enzyme released during lysis of the attacked reporter strain. The second method relies on the lag time required for the attacked cells to reach a defined optical density after the competition, which is directly dependent on the initial number of surviving cells. Key features First method utilizes the release of β-galactosidase as a proxy for bacterial lysis. Second method is based on the growth timing of surviving cells. Combination of two methods discriminates between cell death and lysis, cell death without lysis, or survival to quasi-lysis. Methods optimized to various bacterial species such as Escherichia coli, Pseudomonas aeruginosa, and Myxococcus xanthus. Graphical overview.
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Affiliation(s)
- Boris Taillefer
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Marie M. Grandjean
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Julien Herrou
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7283, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Donovan Robert
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7283, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7283, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Corinne Sebban-Kreuzer
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
| | - Eric Cascales
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Univ–CNRS, UMR7255, 31 Chemin Joseph Aiguier CS7071, 13402 Marseille Cedex 09, France
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43
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Rathnapala JMSN, Ragab W, Kawato S, Furukawa M, Nozaki R, Kondo H, Hirono I. Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei. JOURNAL OF FISH DISEASES 2023; 46:779-790. [PMID: 36989191 DOI: 10.1111/jfd.13786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 06/07/2023]
Abstract
Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.
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Affiliation(s)
- Jayasundara Mudiyanselage Sajani Nisansala Rathnapala
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
- Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Wafaa Ragab
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Satoshi Kawato
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Miho Furukawa
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
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44
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Allsopp LP, Bernal P. Killing in the name of: T6SS structure and effector diversity. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001367. [PMID: 37490402 PMCID: PMC10433429 DOI: 10.1099/mic.0.001367] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
The life of bacteria is challenging, to endure bacteria employ a range of mechanisms to optimize their environment, including deploying the type VI secretion system (T6SS). Acting as a bacterial crossbow, this system delivers effectors responsible for subverting host cells, killing competitors and facilitating general secretion to access common goods. Due to its importance, this lethal machine has been evolutionarily maintained, disseminated and specialized to fulfil these vital functions. In fact, T6SS structural clusters are present in over 25 % of Gram-negative bacteria, varying in number from one to six different genetic clusters per organism. Since its discovery in 2006, research on the T6SS has rapidly progressed, yielding remarkable breakthroughs. The identification and characterization of novel components of the T6SS, combined with biochemical and structural studies, have revealed fascinating mechanisms governing its assembly, loading, firing and disassembly processes. Recent findings have also demonstrated the efficacy of this system against fungal and Gram-positive cells, expanding its scope. Ongoing research continues to uncover an extensive and expanding repertoire of T6SS effectors, the genuine mediators of T6SS function. These studies are shedding light on new aspects of the biology of prokaryotic and eukaryotic organisms. This review provides a comprehensive overview of the T6SS, highlighting recent discoveries of its structure and the diversity of its effectors. Additionally, it injects a personal perspective on avenues for future research, aiming to deepen our understanding of this combative system.
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Affiliation(s)
- Luke P. Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
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45
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Jensen SJ, Ruhe ZC, Williams AF, Nhan DQ, Garza-Sánchez F, Low DA, Hayes CS. Paradoxical Activation of a Type VI Secretion System Phospholipase Effector by Its Cognate Immunity Protein. J Bacteriol 2023; 205:e0011323. [PMID: 37212679 PMCID: PMC10294671 DOI: 10.1128/jb.00113-23] [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: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
Type VI secretion systems (T6SSs) deliver cytotoxic effector proteins into target bacteria and eukaryotic host cells. Antibacterial effectors are invariably encoded with cognate immunity proteins that protect the producing cell from self-intoxication. Here, we identify transposon insertions that disrupt the tli immunity gene of Enterobacter cloacae and induce autopermeabilization through unopposed activity of the Tle phospholipase effector. This hyperpermeability phenotype is T6SS dependent, indicating that the mutants are intoxicated by Tle delivered from neighboring sibling cells rather than by internally produced phospholipase. Unexpectedly, an in-frame deletion of tli does not induce hyperpermeability because Δtli null mutants fail to deploy active Tle. Instead, the most striking phenotypes are associated with disruption of the tli lipoprotein signal sequence, which prevents immunity protein localization to the periplasm. Immunoblotting reveals that most hyperpermeable mutants still produce Tli, presumably from alternative translation initiation codons downstream of the signal sequence. These observations suggest that cytosolic Tli is required for the activation and/or export of Tle. We show that Tle growth inhibition activity remains Tli dependent when phospholipase delivery into target bacteria is ensured through fusion to the VgrG β-spike protein. Together, these findings indicate that Tli has distinct functions, depending on its subcellular localization. Periplasmic Tli acts as a canonical immunity factor to neutralize incoming effector proteins, while a cytosolic pool of Tli is required to activate the phospholipase domain of Tle prior to T6SS-dependent export. IMPORTANCE Gram-negative bacteria use type VI secretion systems deliver toxic effector proteins directly into neighboring competitors. Secreting cells also produce specific immunity proteins that neutralize effector activities to prevent autointoxication. Here, we show the Tli immunity protein of Enterobacter cloacae has two distinct functions, depending on its subcellular localization. Periplasmic Tli acts as a canonical immunity factor to block Tle lipase effector activity, while cytoplasmic Tli is required to activate the lipase prior to export. These results indicate Tle interacts transiently with its cognate immunity protein to promote effector protein folding and/or packaging into the secretion apparatus.
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Affiliation(s)
- Steven J. Jensen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Zachary C. Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - August F. Williams
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Dinh Q. Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - David A. Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, USA
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46
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Rossi M, Galetto L, Bodino N, Beltramo J, Gamalero S, Pegoraro M, Bosco D, Marzachì C. Competition among Flavescence Dorée Phytoplasma Strains in the Experimental Insect Vector Euscelidius variegatus. INSECTS 2023; 14:575. [PMID: 37504582 PMCID: PMC10380400 DOI: 10.3390/insects14070575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Phytoplasmas are plant pathogenic wall-less bacteria transmitted in a persistent propagative manner by hemipteran insects, mainly belonging to the suborder Auchenorrhyncha (Fulgoromorpha and Cicadomorpha). Flavescence dorée (FD) is a quarantine disease of grapevine, causing great damage to European viticulture and associated with phytoplasmas belonging to 16SrV-C (FD-C) and -D (FD-D) subgroups. FD-C and FD-D strains share similar pathogenicity, but mixed infections are rare in nature. To investigate the competition among FDp strains, specimens of the laboratory vector Euscelidius variegatus (Hemiptera: Cicadellidae) were forced to acquire both phytoplasma haplotypes upon feeding on FD-C- and FD-D-infected plants or after the injection of both strains. The pathogen colonization of insect bodies and heads was monitored with multiplex qPCR, and the efficiencies of phytoplasma transmission were estimated. Single infection, irrespective of strain type, was more frequent than expected, indicating that competition among FD strains occurs. Hypotheses of competition for resources and/or host active sites or the direct antibiosis of one strain against the other are discussed, based on the genetic complexity of FDp populations and on the high genome variability of the FD-D strain. As FD management still mainly relies on insecticides against vectors, the characterization of FDp haplotypes and the description of their epidemiology also have practical implications.
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Affiliation(s)
- Marika Rossi
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Luciana Galetto
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Nicola Bodino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Jessica Beltramo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Silvia Gamalero
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
- Dipartimento di Scienze dell'Ambiente e della Vita, Università del Piemonte Orientale "Amedeo Avogadro", Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Mattia Pegoraro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
- Metrologia dei Materiali Innovativi e Scienze della Vita, Istituto Nazionale di Ricerca Metrologica, INRiM, Strada delle Cacce 91, 10135 Torino, Italy
| | - Domenico Bosco
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Cristina Marzachì
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73, 10135 Torino, Italy
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47
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Caballero-Flores G, Pickard JM, Núñez G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat Rev Microbiol 2023; 21:347-360. [PMID: 36539611 PMCID: PMC10249723 DOI: 10.1038/s41579-022-00833-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 12/24/2022]
Abstract
A dense and diverse microbial community inhabits the gut and many epithelial surfaces. Referred to as the microbiota, it co-evolved with the host and is beneficial for many host physiological processes. A major function of these symbiotic microorganisms is protection against pathogen colonization and overgrowth of indigenous pathobionts. Dysbiosis of the normal microbial community increases the risk of pathogen infection and overgrowth of harmful pathobionts. The protective mechanisms conferred by the microbiota are complex and include competitive microbial-microbial interactions and induction of host immune responses. Pathogens, in turn, have evolved multiple strategies to subvert colonization resistance conferred by the microbiota. Understanding the mechanisms by which microbial symbionts limit pathogen colonization should guide the development of new therapeutic approaches to prevent or treat disease.
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Affiliation(s)
- Gustavo Caballero-Flores
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Joseph M Pickard
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA.
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48
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Trotta KL, Hayes BM, Schneider JP, Wang J, Todor H, Rockefeller Grimes P, Zhao Z, Hatleberg WL, Silvis MR, Kim R, Koo BM, Basler M, Chou S. Lipopolysaccharide transport regulates bacterial sensitivity to a cell wall-degrading intermicrobial toxin. PLoS Pathog 2023; 19:e1011454. [PMID: 37363922 PMCID: PMC10328246 DOI: 10.1371/journal.ppat.1011454] [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: 05/02/2023] [Revised: 07/07/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Gram-negative bacteria can antagonize neighboring microbes using a type VI secretion system (T6SS) to deliver toxins that target different essential cellular features. Despite the conserved nature of these targets, T6SS potency can vary across recipient species. To understand the functional basis of intrinsic T6SS susceptibility, we screened for essential Escherichia coli (Eco) genes that affect its survival when antagonized by a cell wall-degrading T6SS toxin from Pseudomonas aeruginosa, Tae1. We revealed genes associated with both the cell wall and a separate layer of the cell envelope, lipopolysaccharide, that modulate Tae1 toxicity in vivo. Disruption of genes in early lipopolysaccharide biosynthesis provided Eco with novel resistance to Tae1, despite significant cell wall degradation. These data suggest that Tae1 toxicity is determined not only by direct substrate damage, but also by indirect cell envelope homeostasis activities. We also found that Tae1-resistant Eco exhibited reduced cell wall synthesis and overall slowed growth, suggesting that reactive cell envelope maintenance pathways could promote, not prevent, self-lysis. Together, our study reveals the complex functional underpinnings of susceptibility to Tae1 and T6SS which regulate the impact of toxin-substrate interactions in vivo.
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Affiliation(s)
- Kristine L. Trotta
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | - Beth M. Hayes
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | | | - Jing Wang
- Biozentrum, University of Basel, Basel, Switzerland
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California–San Francisco, San Francisco, California, United States of America
| | - Patrick Rockefeller Grimes
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | - Ziyi Zhao
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | | | - Melanie R. Silvis
- Department of Cell and Tissue Biology, University of California–San Francisco, San Francisco, California, United States of America
| | - Rachel Kim
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
| | - Byoung Mo Koo
- Department of Cell and Tissue Biology, University of California–San Francisco, San Francisco, California, United States of America
| | - Marek Basler
- Biozentrum, University of Basel, Basel, Switzerland
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, United States of America
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49
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Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [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: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
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Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
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50
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Trotta KL, Hayes BM, Schneider JP, Wang J, Todor H, Grimes PR, Zhao Z, Hatleberg WL, Silvis MR, Kim R, Koo BM, Basler M, Chou S. Lipopolysaccharide integrity primes bacterial sensitivity to a cell wall-degrading intermicrobial toxin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524922. [PMID: 36747731 PMCID: PMC9900751 DOI: 10.1101/2023.01.20.524922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Gram-negative bacteria can antagonize neighboring microbes using a type VI secretion system (T6SS) to deliver toxins that target different essential cellular features. Despite the conserved nature of these targets, T6SS potency can vary across recipient species. To understand the molecular basis of intrinsic T6SS susceptibility, we screened for essential Escherichia coli genes that affect its survival when antagonized by a cell wall-degrading T6SS toxin from Pseudomonas aeruginosa , Tae1. We revealed genes associated with both the cell wall and a separate layer of the cell envelope, surface lipopolysaccharide, that modulate Tae1 toxicity in vivo . Disruption of lipopolysaccharide synthesis provided Escherichia coli (Eco) with novel resistance to Tae1, despite significant cell wall degradation. These data suggest that Tae1 toxicity is determined not only by direct substrate damage, but also by indirect cell envelope homeostasis activities. We also found that Tae1-resistant Eco exhibited reduced cell wall synthesis and overall slowed growth, suggesting that reactive cell envelope maintenance pathways could promote, not prevent, self-lysis. Together, our study highlights the consequences of co-regulating essential pathways on recipient fitness during interbacterial competition, and how antibacterial toxins leverage cellular vulnerabilities that are both direct and indirect to their specific targets in vivo .
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Affiliation(s)
- Kristine L Trotta
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Beth M Hayes
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Johannes P Schneider
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel, Switzerland
| | - Jing Wang
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel, Switzerland
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California – San Francisco, San Francisco, CA, USA
| | - Patrick Rockefeller Grimes
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Ziyi Zhao
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | | | - Melanie R Silvis
- Department of Cell and Tissue Biology, University of California – San Francisco, San Francisco, CA, USA
| | - Rachel Kim
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
| | - Byoung Mo Koo
- Department of Cell and Tissue Biology, University of California – San Francisco, San Francisco, CA, USA
| | - Marek Basler
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel, Switzerland
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California – San Francisco, San Francisco, CA, USA
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