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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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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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Fang N, Wu L, Duan S, Li J. The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins. Molecules 2024; 29:2058. [PMID: 38731549 PMCID: PMC11085428 DOI: 10.3390/molecules29092058] [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: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.
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Affiliation(s)
- Ning Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Lingyun Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Shuyan Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
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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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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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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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Crisan CV, Van Tyne D, Goldberg JB. The type VI secretion system of the emerging pathogen Stenotrophomonas maltophilia complex has antibacterial properties. mSphere 2023; 8:e0058423. [PMID: 37975665 PMCID: PMC10732056 DOI: 10.1128/msphere.00584-23] [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: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Infections with the opportunistic pathogen Stenotrophomonas maltophilia complex can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the type VI secretion system (T6SS) allows S. maltophilia complex to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia complex. The T6SS may confer survival advantages to S. maltophilia complex isolates in polymicrobial communities in both environmental settings and during infections.
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Affiliation(s)
- Cristian V. Crisan
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joanna B. Goldberg
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
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Anderson AJG, Morrell B, Lopez Campos G, Valvano MA. Distribution and diversity of type VI secretion system clusters in Enterobacter bugandensis and Enterobacter cloacae. Microb Genom 2023; 9:001148. [PMID: 38054968 PMCID: PMC10763514 DOI: 10.1099/mgen.0.001148] [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: 09/06/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
Gram-negative bacteria use type VI secretion systems (T6SSs) to antagonize neighbouring cells. Although primarily involved in bacterial competition, the T6SS is also implicated in pathogenesis, biofilm formation and ion scavenging. Enterobacter species belong to the ESKAPE pathogens, and while their antibiotic resistance has been well studied, less is known about their pathogenesis. Here, we investigated the distribution and diversity of T6SS components in isolates of two clinically relevant Enterobacter species, E. cloacae and E. bugandensis. T6SS clusters are grouped into four types (T6SSi-T6SSiv), of which type i can be further divided into six subtypes (i1, i2, i3, i4a, i4b, i5). Analysis of a curated dataset of 31 strains demonstrated that most of them encode T6SS clusters belonging to the T6SSi type. All T6SS-positive strains possessed a conserved i3 cluster, and many harboured one or two additional i2 clusters. These clusters were less conserved, and some strains displayed evidence of deletion. We focused on a pathogenic E. bugandensis clinical isolate for comprehensive in silico effector prediction, with comparative analyses across the 31 isolates. Several new effector candidates were identified, including an evolved VgrG with a metallopeptidase domain and a Tse6-like protein. Additional effectors included an anti-eukaryotic catalase (KatN), M23 peptidase, PAAR and VgrG proteins. Our findings highlight the diversity of Enterobacter T6SSs and reveal new putative effectors that may be important for the interaction of these species with neighbouring cells and their environment.
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Affiliation(s)
- Amy J. G. Anderson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, BT9 7BL, UK
| | - Becca Morrell
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, BT9 7BL, UK
| | - Guillermo Lopez Campos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, BT9 7BL, UK
| | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, BT9 7BL, UK
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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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11
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Hagan M, Pankov G, Gallegos-Monterrosa R, Williams DJ, Earl C, Buchanan G, Hunter WN, Coulthurst SJ. Rhs NADase effectors and their immunity proteins are exchangeable mediators of inter-bacterial competition in Serratia. Nat Commun 2023; 14:6061. [PMID: 37770429 PMCID: PMC10539506 DOI: 10.1038/s41467-023-41751-3] [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: 02/13/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Many bacterial species use Type VI secretion systems (T6SSs) to deliver anti-bacterial effector proteins into neighbouring bacterial cells, representing an important mechanism of inter-bacterial competition. Specific immunity proteins protect bacteria from the toxic action of their own effectors, whilst orphan immunity proteins without a cognate effector may provide protection against incoming effectors from non-self competitors. T6SS-dependent Rhs effectors contain a variable C-terminal toxin domain (CT), with the cognate immunity protein encoded immediately downstream of the effector. Here, we demonstrate that Rhs1 effectors from two strains of Serratia marcescens, the model strain Db10 and clinical isolate SJC1036, possess distinct CTs which both display NAD(P)+ glycohydrolase activity but belong to different subgroups of NADase from each other and other T6SS-associated NADases. Comparative structural analysis identifies conserved functions required for NADase activity and reveals that unrelated NADase immunity proteins utilise a common mechanism of effector inhibition. By replicating a natural recombination event, we show successful functional exchange of CTs and demonstrate that Db10 encodes an orphan immunity protein which provides protection against T6SS-delivered SJC1036 NADase. Our findings highlight the flexible use of Rhs effectors and orphan immunity proteins during inter-strain competition and the repeated adoption of NADase toxins as weapons against bacterial cells.
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Affiliation(s)
- Martin Hagan
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Genady Pankov
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | | | - David J Williams
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Christopher Earl
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Grant Buchanan
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - William N Hunter
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | - Sarah J Coulthurst
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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12
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Meir A, Macé K, Vegunta Y, Williams SM, Waksman G. Substrate recruitment mechanism by gram-negative type III, IV, and VI bacterial injectisomes. Trends Microbiol 2023; 31:916-932. [PMID: 37085348 DOI: 10.1016/j.tim.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/23/2023]
Abstract
Bacteria use a wide arsenal of macromolecular substrates (DNA and proteins) to interact with or infect prokaryotic and eukaryotic cells. To do so, they utilize substrate-injecting secretion systems or injectisomes. However, prior to secretion, substrates must be recruited to specialized recruitment platforms and then handed over to the secretion apparatus for secretion. In this review, we provide an update on recent advances in substrate recruitment and delivery by gram-negative bacterial recruitment platforms associated with Type III, IV, and VI secretion systems.
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Affiliation(s)
- Amit Meir
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Current address: MRC Centre for Virus Research, School of Infection and Immunity, University of Glasgow, Glasgow, UK.
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Yogesh Vegunta
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Sunanda M Williams
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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13
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Blondel CJ, Amaya FA, Bustamante P, Santiviago CA, Pezoa D. Identification and distribution of new candidate T6SS effectors encoded in Salmonella Pathogenicity Island 6. Front Microbiol 2023; 14:1252344. [PMID: 37664116 PMCID: PMC10469887 DOI: 10.3389/fmicb.2023.1252344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
The type VI secretion system (T6SS) is a contact-dependent contractile multiprotein apparatus widely distributed in Gram-negative bacteria. These systems can deliver different effector proteins into target bacterial and/or eukaryotic cells, contributing to the environmental fitness and virulence of many bacterial pathogens. Salmonella harbors five different T6SSs encoded in different genomic islands. The T6SS encoded in Salmonella Pathogenicity Island 6 (SPI-6) contributes to Salmonella competition with the host microbiota and its interaction with infected host cells. Despite its relevance, information regarding the total number of effector proteins encoded within SPI-6 and its distribution among different Salmonella enterica serotypes is limited. In this work, we performed bioinformatic and comparative genomics analyses of the SPI-6 T6SS gene cluster to expand our knowledge regarding the T6SS effector repertoire and the global distribution of these effectors in Salmonella. The analysis of a curated dataset of 60 Salmonella enterica genomes from the Secret6 database revealed the presence of 23 new putative T6SS effector/immunity protein (E/I) modules. These effectors were concentrated in the variable regions 1 to 3 (VR1-3) of the SPI-6 T6SS gene cluster. VR1-2 were enriched in candidate effectors with predicted peptidoglycan hydrolase activity, while VR3 was enriched in candidate effectors of the Rhs family with C-terminal extensions with predicted DNase, RNase, deaminase, or ADP-ribosyltransferase activity. A global analysis of known and candidate effector proteins in Salmonella enterica genomes from the NCBI database revealed that T6SS effector proteins are differentially distributed among Salmonella serotypes. While some effectors are present in over 200 serotypes, others are found in less than a dozen. A hierarchical clustering analysis identified Salmonella serotypes with distinct profiles of T6SS effectors and candidate effectors, highlighting the diversity of T6SS effector repertoires in Salmonella enterica. The existence of different repertoires of effector proteins suggests that different effector protein combinations may have a differential impact on the environmental fitness and pathogenic potential of these strains.
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Affiliation(s)
- Carlos J. Blondel
- Facultad de Medicina y Facultad de Ciencias de la Vida, Instituto de Ciencias Biomédicas, Universidad Andrés Bello, Santiago, Chile
| | - Fernando A. Amaya
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Paloma Bustamante
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - David Pezoa
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago, Chile
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14
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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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15
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Ahmad S, Whitney JC. Location, Location, Location: an Antidote That Both Activates and Neutralizes a Toxin Used in Bacterial Warfare. J Bacteriol 2023; 205:e0016123. [PMID: 37366633 DOI: 10.1128/jb.00161-23] [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: 06/28/2023] Open
Abstract
S.J. Jensen, Z.C. Ruhe, A.F. Williams, D.Q. Nhan, et al. (J Bacteriol 205:e00113-23, 2023, https://doi.org/10.1128/jb.00113-23) demonstrate that a type VI secretion system (T6SS) immunity protein, Tli, functions to both neutralize and activate its cognate toxin, Tle, in Enterobacter cloacae. Their results reveal the surprising finding that Tli function differs, depending on its subcellular localization. Overall, this study enhances our understanding of T6SS immunity proteins, which are commonly viewed as monofunctional toxin-neutralizing antidotes.
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Affiliation(s)
- Shehryar Ahmad
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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16
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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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17
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Crisan CV, Van Tyne D, Goldberg JB. The Type VI Secretion System of the Emerging Pathogen Stenotrophomonas maltophilia has Antibacterial Properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542968. [PMID: 37398041 PMCID: PMC10312562 DOI: 10.1101/2023.05.30.542968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Antagonistic behaviors between bacterial cells can have profound effects on microbial populations and disease outcomes. Polymicrobial interactions may be mediated by contact-dependent proteins with antibacterial properties. The Type VI Secretion System (T6SS) is a macromolecular weapon used by Gram-negative bacteria to translocate proteins into adjacent cells. The T6SS is used by pathogens to escape immune cells, eliminate commensal bacteria, and facilitate infection. Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that causes a wide range of infections in immunocompromised patients and infects the lungs of patients with cystic fibrosis. Infections with the bacterium can be deadly and are challenging to treat because many isolates are multidrug-resistant. We found that globally dispersed S. maltophilia clinical and environmental strains possess T6SS genes. We demonstrate that the T6SS of an S. maltophilia patient isolate is active and can eliminate other bacteria. Furthermore, we provide evidence that the T6SS contributes to the competitive fitness of S. maltophilia against a co-infecting Pseudomonas aeruginosa isolate, and that the T6SS alters the cellular organization of S. maltophilia and P. aeruginosa co-cultures. This study expands our knowledge of the mechanisms employed by S. maltophilia to secrete antibacterial proteins and compete against other bacteria. IMPORTANCE Infections with the opportunistic pathogen Stenotrophomonas maltophilia can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the T6SS allows S. maltophilia to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia . The T6SS may confer survival advantages to S. maltophilia isolates in polymicrobial communities in both environmental settings and during infections.
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18
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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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19
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Rudzite M, Subramoni S, Endres RG, Filloux A. Effectiveness of Pseudomonas aeruginosa type VI secretion system relies on toxin potency and type IV pili-dependent interaction. PLoS Pathog 2023; 19:e1011428. [PMID: 37253075 PMCID: PMC10281587 DOI: 10.1371/journal.ppat.1011428] [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: 11/30/2022] [Revised: 06/20/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023] Open
Abstract
The type VI secretion system (T6SS) is an antibacterial weapon that is used by numerous Gram-negative bacteria to gain competitive advantage by injecting toxins into adjacent prey cells. Predicting the outcome of a T6SS-dependent competition is not only reliant on presence-absence of the system but instead involves a multiplicity of factors. Pseudomonas aeruginosa possesses 3 distinct T6SSs and a set of more than 20 toxic effectors with diverse functions including disruption of cell wall integrity, degradation of nucleic acids or metabolic impairment. We generated a comprehensive collection of mutants with various degrees of T6SS activity and/or sensitivity to each individual T6SS toxin. By imaging whole mixed bacterial macrocolonies, we then investigated how these P. aeruginosa strains gain a competitive edge in multiple attacker/prey combinations. We observed that the potency of single T6SS toxin varies significantly from one another as measured by monitoring the community structure, with some toxins acting better in synergy or requiring a higher payload. Remarkably the degree of intermixing between preys and attackers is also key to the competition outcome and is driven by the frequency of contact as well as the ability of the prey to move away from the attacker using type IV pili-dependent twitching motility. Finally, we implemented a computational model to better understand how changes in T6SS firing behaviours or cell-cell contacts lead to population level competitive advantages, thus providing conceptual insight applicable to all types of contact-based competition.
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Affiliation(s)
- Marta Rudzite
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Robert G. Endres
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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20
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Singh RP, Kumari K. Bacterial type VI secretion system (T6SS): an evolved molecular weapon with diverse functionality. Biotechnol Lett 2023; 45:309-331. [PMID: 36683130 DOI: 10.1007/s10529-023-03354-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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21
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Hou Y, Zeng H, Li Z, Feng N, Meng F, Xu Y, Li L, Shao F, Ding J. Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Nat Struct Mol Biol 2023; 30:261-272. [PMID: 36624349 DOI: 10.1038/s41594-022-00888-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/03/2022] [Indexed: 01/11/2023]
Abstract
The caspase-4/11-GSDMD pyroptosis axis recognizes cytosolic lipopolysaccharide for antibacterial defenses. Shigella flexneri employs an OspC3 effector to block pyroptosis by catalyzing NAD+-dependent arginine ADP-riboxanation of caspase-4/11. Here, we identify Ca2+-free calmodulin (CaM) that binds and stimulates OspC3 ADP-riboxanase activity. Crystal structures of OspC3-CaM and OspC3-caspase-4 binary complexes reveal unique CaM binding to an OspC3 N-terminal domain featuring an ADP-ribosyltransferase-like fold and specific recognition of caspase-4 by an OspC3 ankryin repeat domain, respectively. CaM-OspC3-caspase-4 ternary complex structures show that NAD+ binding reorganizes the catalytic pocket, in which D231 and D177 activate the substrate arginine for initial ADP-ribosylation and ribosyl 2'-OH in the ADP-ribosylated arginine, respectively, for subsequent deamination. We also determine structures of unmodified and OspC3-ADP-riboxanated caspase-4. Mechanisms derived from this series of structures covering the entire process of OspC3 action are supported by biochemical analyses in vitro and functional validation in S. flexneri-infected mice.
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Affiliation(s)
- Yanjie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huan Zeng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Zilin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China
| | - Na Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fanyi Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Xu
- National Institute of Biological Sciences, Beijing, Beijing, China
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Feng Shao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, Beijing, China.
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
| | - Jingjin Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, Beijing, China.
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22
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VgrG Spike Dictates PAAR Requirement for the Assembly of the Type VI Secretion System. J Bacteriol 2023; 205:e0035622. [PMID: 36655996 PMCID: PMC9945574 DOI: 10.1128/jb.00356-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Widely employed by Gram-negative pathogens for competition and pathogenesis, the type six protein secretion system (T6SS) can inject toxic effectors into neighboring cells through the penetration of a spear-like structure comprising a long Hcp tube and a VgrG-PAAR spike complex. The cone-shaped PAAR is believed to sharpen the T6SS spear for penetration but it remains unclear why PAAR is required for T6SS functions in some bacteria but dispensable in others. Here, we report the conditional requirement of PAAR for T6SS functions in Aeromonas dhakensis, an emerging human pathogen that may cause severe bacteremia. By deleting the two PAAR paralogs, we show that PAAR is not required for T6SS secretion, bacterial killing, or specific effector delivery in A. dhakensis. By constructing combinatorial PAAR and vgrG deletions, we demonstrate that deletion of individual PAAR moderately reduced T6SS functions but double or triple deletions of PAAR in the vgrG deletion mutants severely impaired T6SS functions. Notably, the auxiliary-cluster-encoded PAAR2 and VgrG3 are less critical than the main-cluster-encoded PAAR1 and VgrG1&2 proteins to T6SS functions. In addition, PAAR1 but not PAAR2 contributes to antieukaryotic virulence in amoeba. Our data suggest that, for a multi-PAAR T6SS, the variable role of PAAR paralogs correlates with the VgrG-spike composition that collectively dictates T6SS assembly. IMPORTANCE Gram-negative bacteria often encode multiple paralogs of the cone-shaped PAAR that sits atop the VgrG-spike and is thought to sharpen the spear-like T6SS puncturing device. However, it is unclear why PAAR is required for the assembly of some but not all T6SSs and why there are multiple PAARs if they are not required. Our data delineate a VgrG-mediated conditional requirement for PAAR and suggest a core-auxiliary relationship among different PAAR-VgrG modules that may have been acquired sequentially by the T6SS during evolution.
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Wu LL, Yan S, Pei TT, Tang MX, Li H, Liang X, Sun S, Dong T. A Dueling-Competent Signal-Sensing Module Guides Precise Delivery of Cargo Proteins into Target Cells by Engineered Pseudomonas aeruginosa. ACS Synth Biol 2023; 12:360-368. [PMID: 36662232 DOI: 10.1021/acssynbio.2c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
To recognize and manipulate a specific microbe of a crowded community is a highly challenging task in synthetic biology. Here we introduce a highly selective protein delivery platform, termed DUEC, which responds to direct contact of attacking cells by engineering the tit-for-tat/dueling response of H1-T6SS (type VI secretion system) in Pseudomonas aeruginosa. Using a Cre-recombinase-dependent reporter, we screened H1-T6SS-secreted substrates and developed Tse6N as the most effective secretion tag for Cre delivery. DUEC cells can discriminately deliver the Tse6N-Cre cargo into the cytosol of T6SS+ but not T6SS- Vibrio cholerae cells. DUEC could also deliver a nuclease cargo, Tse6N-NucSe1, to selectively kill provoking cells in a mixed community. These data demonstrate that the DUEC cell not only is a prototypical physical-contact sensor and delivery platform but also may be coupled with recombination-based circuits with the potential for complex tasks in mixed microbial communities.
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Affiliation(s)
- Li-Li Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuangquan Yan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming-Xuan Tang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoye Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Pangenomic analysis reveals plant NAD + manipulation as an important virulence activity of bacterial pathogen effectors. Proc Natl Acad Sci U S A 2023; 120:e2217114120. [PMID: 36753463 PMCID: PMC9963460 DOI: 10.1073/pnas.2217114120] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) has emerged as a key component in prokaryotic and eukaryotic immune systems. The recent discovery that Toll/interleukin-1 receptor (TIR) proteins function as NAD+ hydrolases (NADase) links NAD+-derived small molecules with immune signaling. We investigated pathogen manipulation of host NAD+ metabolism as a virulence strategy. Using the pangenome of the model bacterial pathogen Pseudomonas syringae, we conducted a structure-based similarity search from 35,000 orthogroups for type III effectors (T3Es) with potential NADase activity. Thirteen T3Es, including five newly identified candidates, were identified that possess domain(s) characteristic of seven NAD+-hydrolyzing enzyme families. Most Pseudomonas syringae strains that depend on the type III secretion system to cause disease, encode at least one NAD+-manipulating T3E, and many have several. We experimentally confirmed the type III-dependent secretion of a novel T3E, named HopBY, which shows structural similarity to both TIR and adenosine diphosphate ribose (ADPR) cyclase. Homologs of HopBY were predicted to be type VI effectors in diverse bacterial species, indicating potential recruitment of this activity by microbial proteins secreted during various interspecies interactions. HopBY efficiently hydrolyzes NAD+ and specifically produces 2'cADPR, which can also be produced by TIR immune receptors of plants and by other bacteria. Intriguingly, this effector promoted bacterial virulence, indicating that 2'cADPR may not be the signaling molecule that directly initiates immunity. This study highlights a host-pathogen battleground centered around NAD+ metabolism and provides insight into the NAD+-derived molecules involved in plant immunity.
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Colautti J, Bullen NP, Whitney JC. Lack of evidence that Pseudomonas aeruginosa AmpDh3-PA0808 constitute a type VI secretion system effector-immunity pair. Mol Microbiol 2023; 119:262-274. [PMID: 36577706 DOI: 10.1111/mmi.15021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
Type VI secretion systems (T6SSs) are cell envelope-spanning protein complexes that Gram-negative bacteria use to inject a diverse arsenal of antibacterial toxins into competitor cells. Recently, Wang et al. reported that the H2-T6SS of Pseudomonas aeruginosa delivers the peptidoglycan recycling amidase, AmpDh3, into the periplasm of recipient cells where it is proposed to act as a peptidoglycan degrading toxin. They further reported that PA0808, the open reading frame downstream of AmpDh3, encodes an immunity protein that localizes to the periplasm where it binds to and inactivates intercellularly delivered AmpDh3, thus protecting against its toxic activity. Given that AmpDh3 has an established role in cell wall homeostasis and that no precedent exists for cytosolic enzymes moonlighting as T6SS effectors, we attempted to replicate these findings. We found that cells lacking PA0808 are not susceptible to bacterial killing by AmpDh3 and that PA0808 and AmpDh3 do not physically interact in vitro or in vivo. Additionally, we found no evidence that AmpDh3 is exported from cells, including by strains with a constitutively active H2-T6SS. Finally, subcellular fractionation experiments and a 1.97 Å crystal structure reveal that PA0808 does not contain a canonical signal peptide or localize to the correct cellular compartment to confer protection against a cell wall targeting toxin. Taken together, these results cast doubt on the assertion that AmpDh3-PA0808 constitutes an H2-T6SS effector-immunity pair.
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Affiliation(s)
- Jake Colautti
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Center for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
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Wang GZ, Warren EA, Haas AL, Peña AS, Kiedrowski MR, Lomenick B, Chou TF, Bomberger JM, Tirrell DA, Limoli DH. Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526047. [PMID: 36747623 PMCID: PMC9900984 DOI: 10.1101/2023.01.29.526047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Coinfection with two notorious opportunistic pathogens, the Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus , dominates chronic pulmonary infections. While coinfection is associated with poor patient outcomes, the interspecies interactions responsible for such decline remain unknown. Here, we dissected molecular mechanisms of interspecies sensing between P. aeruginosa and S. aureus . We discovered that P. aeruginosa senses S. aureus secreted peptides and, counterintuitively, moves towards these toxins. P. aeruginosa tolerates such a strategy through "competition sensing", whereby it preempts imminent danger/competition by arming cells with type six secretion (T6S) and iron acquisition systems. Intriguingly, while T6S is predominantly described as weaponry targeting Gram-negative and eukaryotic cells, we find that T6S is essential for full P. aeruginosa competition with S. aureus , a previously undescribed role for T6S. Importantly, competition sensing was activated during coinfection of bronchial epithelia, including T6S islands targeting human cells. This study reveals critical insight into both interspecies competition and how antagonism may cause collateral damage to the host environment.
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Li P, Zhang S, Wang J, Al-Shamiri MM, Han B, Chen Y, Han S, Han L. Uncovering the Secretion Systems of Acinetobacter baumannii: Structures and Functions in Pathogenicity and Antibiotic Resistance. Antibiotics (Basel) 2023; 12:antibiotics12020195. [PMID: 36830106 PMCID: PMC9952577 DOI: 10.3390/antibiotics12020195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Infections led by Acinetobacter baumannii strains are of great concern in healthcare environments due to the strong ability of the bacteria to spread through different apparatuses and develop drug resistance. Severe diseases can be caused by A. baumannii in critically ill patients, but its biological process and mechanism are not well understood. Secretion systems have recently been demonstrated to be involved in the pathogenic process, and five types of secretion systems out of the currently known six from Gram-negative bacteria have been found in A. baumannii. They can promote the fitness and pathogenesis of the bacteria by releasing a variety of effectors. Additionally, antibiotic resistance is found to be related to some types of secretion systems. In this review, we describe the genetic and structural compositions of the five secretion systems that exist in Acinetobacter. In addition, the function and molecular mechanism of each secretion system are summarized to explain how they enable these critical pathogens to overcome eukaryotic hosts and prokaryotic competitors to cause diseases.
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Affiliation(s)
- Pu Li
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Sirui Zhang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Jingdan Wang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Mona Mohamed Al-Shamiri
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Bei Han
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Yanjiong Chen
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Shaoshan Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Lei Han
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Correspondence:
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Robinson LA, Collins ACZ, Murphy RA, Davies JC, Allsopp LP. Diversity and prevalence of type VI secretion system effectors in clinical Pseudomonas aeruginosa isolates. Front Microbiol 2023; 13:1042505. [PMID: 36687572 PMCID: PMC9846239 DOI: 10.3389/fmicb.2022.1042505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and a major driver of morbidity and mortality in people with Cystic Fibrosis (CF). The Type VI secretion system (T6SS) is a molecular nanomachine that translocates effectors across the bacterial membrane into target cells or the extracellular environment enabling intermicrobial interaction. P. aeruginosa encodes three T6SS clusters, the H1-, H2- and H3-T6SS, and numerous orphan islands. Genetic diversity of T6SS-associated effectors in P. aeruginosa has been noted in reference strains but has yet to be explored in clinical isolates. Here, we perform a comprehensive bioinformatic analysis of the pangenome and T6SS effector genes in 52 high-quality clinical P. aeruginosa genomes isolated from CF patients and housed in the Personalised Approach to P. aeruginosa strain repository. We confirm that the clinical CF isolate pangenome is open and principally made up of accessory and unique genes that may provide strain-specific advantages. We observed genetic variability in some effector/immunity encoding genes and show that several well-characterised vgrG and PAAR islands are absent from numerous isolates. Our analysis shows clear evidence of disruption to T6SS genomic loci through transposon, prophage, and mobile genetic element insertions. We identified an orphan vgrG island in P. aeruginosa strain PAK and five clinical isolates using in silico analysis which we denote vgrG7, predicting a gene within this cluster to encode a Tle2 lipase family effector. Close comparison of T6SS loci in clinical isolates compared to reference P. aeruginosa strain PAO1 revealed the presence of genes encoding eight new T6SS effectors with the following putative functions: cytidine deaminase, lipase, metallopeptidase, NADase, and pyocin. Finally, the prevalence of characterised and putative T6SS effectors were assessed in 532 publicly available P. aeruginosa genomes, which suggests the existence of accessory effectors. Our in silico study of the P. aeruginosa T6SS exposes a level of genetic diversity at T6SS genomic loci not seen to date within P. aeruginosa, particularly in CF isolates. As understanding the effector repertoire is key to identifying the targets of T6SSs and its efficacy, this comprehensive analysis provides a path for future experimental characterisation of these mediators of intermicrobial competition and host manipulation.
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Affiliation(s)
- Luca A. Robinson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Alice C. Z. Collins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ronan A. Murphy
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jane C. Davies
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom
| | - Luke P. Allsopp
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Guzmán-Herrador DL, Fernández-Gómez A, Llosa M. Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation. Front Cell Infect Microbiol 2023; 13:1146000. [PMID: 36949816 PMCID: PMC10025392 DOI: 10.3389/fcimb.2023.1146000] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.
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Multiple T6SSs, Mobile Auxiliary Modules, and Effectors Revealed in a Systematic Analysis of the Vibrio parahaemolyticus Pan-Genome. mSystems 2022; 7:e0072322. [PMID: 36226968 PMCID: PMC9765294 DOI: 10.1128/msystems.00723-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Type VI secretion systems (T6SSs) play a major role in interbacterial competition and in bacterial interactions with eukaryotic cells. The distribution of T6SSs and the effectors they secrete vary between strains of the same bacterial species. Therefore, a pan-genome investigation is required to better understand the T6SS potential of a bacterial species of interest. Here, we performed a comprehensive, systematic analysis of T6SS gene clusters and auxiliary modules found in the pan-genome of Vibrio parahaemolyticus, an emerging pathogen widespread in marine environments. We identified 4 different T6SS gene clusters within genomes of this species; two systems appear to be ancient and widespread, whereas the other 2 systems are rare and appear to have been more recently acquired via horizontal gene transfer. In addition, we identified diverse T6SS auxiliary modules containing putative effectors with either known or predicted toxin domains. Many auxiliary modules are possibly horizontally shared between V. parahaemolyticus genomes, since they are flanked by DNA mobility genes. We further investigated a DUF4225-containing protein encoded on an Hcp auxiliary module, and we showed that it is an antibacterial T6SS effector that exerts its toxicity in the bacterial periplasm, leading to cell lysis. Computational analyses of DUF4225 revealed a widespread toxin domain associated with various toxin delivery systems. Taken together, our findings reveal a diverse repertoire of T6SSs and auxiliary modules in the V. parahaemolyticus pan-genome, as well as novel T6SS effectors and toxin domains that can play a major role in the interactions of this species with other cells. IMPORTANCE Gram-negative bacteria employ toxin delivery systems to mediate their interactions with neighboring cells. Vibrio parahaemolyticus, an emerging pathogen of humans and marine animals, was shown to deploy antibacterial toxins into competing bacteria via the type VI secretion system (T6SS). Here, we analyzed 1,727 V. parahaemolyticus genomes and revealed the pan-genome T6SS repertoire of this species, including the T6SS gene clusters, horizontally shared auxiliary modules, and toxins. We also identified a role for a previously uncharacterized domain, DUF4225, as a widespread antibacterial toxin associated with diverse toxin delivery systems.
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Zhang K, Peng T, Tao X, Tian M, Li Y, Wang Z, Ma S, Hu S, Pan X, Xue J, Luo J, Wu Q, Fu Y, Li S. Structural insights into caspase ADPR deacylization catalyzed by a bacterial effector and host calmodulin. Mol Cell 2022; 82:4712-4726.e7. [PMID: 36423631 DOI: 10.1016/j.molcel.2022.10.032] [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: 05/09/2022] [Revised: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
Programmed cell death and caspase proteins play a pivotal role in host innate immune response combating pathogen infections. Blocking cell death is employed by many bacterial pathogens as a universal virulence strategy. CopC family type III effectors, including CopC from an environmental pathogen Chromobacterium violaceum, utilize calmodulin (CaM) as a co-factor to inactivate caspases by arginine ADPR deacylization. However, the molecular basis of the catalytic and substrate/co-factor binding mechanism is unknown. Here, we determine successive cryo-EM structures of CaM-CopC-caspase-3 ternary complex in pre-reaction, transition, and post-reaction states, which elucidate a multistep enzymatic mechanism of CopC-catalyzed ADPR deacylization. Moreover, we capture a snapshot of the detachment of modified caspase-3 from CopC. These structural insights are validated by mutagenesis analyses of CopC-mediated ADPR deacylization in vitro and animal infection in vivo. Our study offers a structural framework for understanding the molecular basis of arginine ADPR deacylization catalyzed by the CopC family.
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Affiliation(s)
- Kuo Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ting Peng
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xinyuan Tao
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yanxin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Zhao Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shuaifei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Shufan Hu
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jiwei Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiulan Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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González-Magaña A, Altuna J, Queralt-Martín M, Largo E, Velázquez C, Montánchez I, Bernal P, Alcaraz A, Albesa-Jové D. The P. aeruginosa effector Tse5 forms membrane pores disrupting the membrane potential of intoxicated bacteria. Commun Biol 2022; 5:1189. [PMID: 36335275 PMCID: PMC9637101 DOI: 10.1038/s42003-022-04140-y] [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: 11/25/2021] [Accepted: 10/20/2022] [Indexed: 11/08/2022] Open
Abstract
The type VI secretion system (T6SS) of Pseudomonas aeruginosa injects effector proteins into neighbouring competitors and host cells, providing a fitness advantage that allows this opportunistic nosocomial pathogen to persist and prevail during the onset of infections. However, despite the high clinical relevance of P. aeruginosa, the identity and mode of action of most P. aeruginosa T6SS-dependent effectors remain to be discovered. Here, we report the molecular mechanism of Tse5-CT, the toxic auto-proteolytic product of the P. aeruginosa T6SS exported effector Tse5. Our results demonstrate that Tse5-CT is a pore-forming toxin that can transport ions across the membrane, causing membrane depolarisation and bacterial death. The membrane potential regulates a wide range of essential cellular functions; therefore, membrane depolarisation is an efficient strategy to compete with other microorganisms in polymicrobial environments. The Pseudomonas aeruginosa Type 6 secretion effector Tse5 forms pores in the cytoplasmic membrane when ectopically produced and hence has a bacteriolytic effect by depolarising the inner membrane potential.
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Affiliation(s)
- Amaia González-Magaña
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Jon Altuna
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - Eneko Largo
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain.,Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940, Leioa, Spain
| | - Carmen Velázquez
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Itxaso Montánchez
- Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940, Leioa, Spain
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012, Sevilla, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - David Albesa-Jové
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain. .,Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain.
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Crisan CV, Goldberg JB. Antibacterial contact-dependent proteins secreted by Gram-negative cystic fibrosis respiratory pathogens. Trends Microbiol 2022; 30:986-996. [PMID: 35487848 PMCID: PMC9474641 DOI: 10.1016/j.tim.2022.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 01/11/2023]
Abstract
Cystic fibrosis (CF) is a genetic disease that affects almost 100 000 people worldwide. CF patients suffer from chronic bacterial airway infections that are often polymicrobial and are the leading cause of mortality. Interactions between pathogens modulate expression of genes responsible for virulence and antibiotic resistance. One of the ways bacteria can interact is through contact-dependent systems, which secrete antibacterial proteins (effectors) that confer advantages to cells that harbor them. Here, we highlight recent work that describes effectors used by Gram-negative CF pathogens to eliminate competitor bacteria. Understanding the mechanisms of secreted effectors may lead to novel insights into the ecology of bacteria that colonize respiratory tracts and could also pave the way for the design of new therapeutics.
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Affiliation(s)
- Cristian V Crisan
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA, USA; Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, USA
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA, USA; Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, USA.
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An ADP-ribosyltransferase toxin kills bacterial cells by modifying structured non-coding RNAs. Mol Cell 2022; 82:3484-3498.e11. [PMID: 36070765 DOI: 10.1016/j.molcel.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/25/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
ADP-ribosyltransferases (ARTs) were among the first identified bacterial virulence factors. Canonical ART toxins are delivered into host cells where they modify essential proteins, thereby inactivating cellular processes and promoting pathogenesis. Our understanding of ARTs has since expanded beyond protein-targeting toxins to include antibiotic inactivation and DNA damage repair. Here, we report the discovery of RhsP2 as an ART toxin delivered between competing bacteria by a type VI secretion system of Pseudomonas aeruginosa. A structure of RhsP2 reveals that it resembles protein-targeting ARTs such as diphtheria toxin. Remarkably, however, RhsP2 ADP-ribosylates 2'-hydroxyl groups of double-stranded RNA, and thus, its activity is highly promiscuous with identified cellular targets including the tRNA pool and the RNA-processing ribozyme, ribonuclease P. Consequently, cell death arises from the inhibition of translation and disruption of tRNA processing. Overall, our data demonstrate a previously undescribed mechanism of bacterial antagonism and uncover an unprecedented activity catalyzed by ART enzymes.
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Lorente Cobo N, Sibinelli-Sousa S, Biboy J, Vollmer W, Bayer-Santos E, Prehna G. Molecular characterization of the type VI secretion system effector Tlde1a reveals a structurally altered LD-transpeptidase fold. J Biol Chem 2022; 298:102556. [PMID: 36183829 PMCID: PMC9638812 DOI: 10.1016/j.jbc.2022.102556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/01/2022] Open
Abstract
The type VI secretion system (T6SS) is a molecular machine that Gram-negative bacteria have adapted for multiple functions, including interbacterial competition. Bacteria use the T6SS to deliver protein effectors into adjacent cells to kill rivals and establish niche dominance. Central to T6SS-mediated bacterial competition is an arms race to acquire diverse effectors to attack and neutralize target cells. The peptidoglycan has a central role in bacterial cell physiology, and effectors that biochemically modify peptidoglycan structure effectively induce cell death. One such T6SS effector is Tlde1a from Salmonella Typhimurium. Tlde1a functions as an LD-carboxypeptidase to cleave tetrapeptide stems and as an LD-transpeptidase to exchange the terminal D-alanine of a tetrapeptide stem with a noncanonical D-amino acid. To understand how Tlde1a exhibits toxicity at the molecular level, we determined the X-ray crystal structure of Tlde1a alone and in complex with D-amino acids. Our structural data revealed that Tlde1a possesses a unique LD-transpeptidase fold consisting of a dual pocket active site with a capping subdomain. This includes an exchange pocket to bind a D-amino acid for exchange and a catalytic pocket to position the D-alanine of a tetrapeptide stem for cleavage. Our toxicity assays in Escherichia coli and in vitro peptidoglycan biochemical assays with Tlde1a variants correlate Tlde1a molecular features directly to its biochemical functions. We observe that the LD-carboxypeptidase and LD-transpeptidase activities of Tlde1a are both structurally and functionally linked. Overall, our data highlight how an LD-transpeptidase fold has been structurally altered to create a toxic effector in the T6SS arms race.
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Affiliation(s)
- Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Stephanie Sibinelli-Sousa
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ethel Bayer-Santos
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Canada.
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36
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Tang MX, Pei TT, Xiang Q, Wang ZH, Luo H, Wang XY, Fu Y, Dong T. Abiotic factors modulate interspecies competition mediated by the type VI secretion system effectors in Vibrio cholerae. THE ISME JOURNAL 2022; 16:1765-1775. [PMID: 35354946 PMCID: PMC9213406 DOI: 10.1038/s41396-022-01228-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 05/06/2023]
Abstract
Vibrio cholerae, the etiological pathogen of cholera, employs its type VI secretion system (T6SS) as an effective weapon to survive in highly competitive communities. Antibacterial and anti-eukaryotic functions of the T6SS depend on its secreted effectors that target multiple cellular processes. However, the mechanisms that account for effector diversity and different effectiveness during interspecies competition remain elusive. Here we report that environmental cations and temperature play a key role in dictating cellular response and effector effectiveness during interspecies competition mediated by the T6SS of V. cholerae. We found that V. cholerae could employ its cell-wall-targeting effector TseH to outcompete the otherwise resistant Escherichia coli and the V. cholerae immunity deletion mutant ∆tsiH when Mg2+ or Ca2+ was supplemented. Transcriptome and genetic analyses demonstrate that the metal-sensing PhoPQ two-component system is important for Mg2+-dependent sensitivity. Competition analysis in infant mice shows that TseH was active under in vivo conditions. Using a panel of V. cholerae single-effector active mutants, we further show that E. coli also exhibited variable susceptibilities to other T6SS effectors depending on cations and temperatures, respectively. Lastly, V. cholerae effector VasX could sensitize Pseudomonas aeruginosa to its intrinsically resistant antibiotic irgasan in a temperature-dependent manner. Collectively, these findings suggest that abiotic factors, that V. cholerae frequently encounters in natural and host environments, could modulate cellular responses and dictate the competitive fitness conferred by the T6SS effectors in complex multispecies communities.
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Affiliation(s)
- Ming-Xuan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zeng-Hang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Han Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Yu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Tao Dong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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37
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Kostow N, Welch MD. Plasma membrane protrusions mediate host cell-cell fusion induced by Burkholderia thailandensis. Mol Biol Cell 2022; 33:ar70. [PMID: 35594178 DOI: 10.1091/mbc.e22-02-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cell-cell fusion is important for biological processes including fertilization, development, immunity, and microbial pathogenesis. Bacteria in the pseudomallei group of the Burkholderia species, including B. thailandensis, spread between host cells by inducing cell-cell fusion. Previous work showed that B. thailandensis-induced cell-cell fusion requires intracellular bacterial motility and a bacterial protein secretion apparatus called the type VI secretion system-5 (T6SS-5), including the T6SS-5 protein VgrG5. However, the cellular-level mechanism of and T6SS-5 proteins important for bacteria-induced cell-cell fusion remained incompletely described. Using live-cell imaging, we found bacteria used actin-based motility to push on the host cell plasma membrane to form plasma membrane protrusions that extended into neighboring cells. Then, membrane fusion occurred within membrane protrusions either proximal to the bacterium at the tip or elsewhere within protrusions. Expression of VgrG5 by bacteria within membrane protrusions was required to promote cell-cell fusion. Furthermore, a second predicted T6SS-5 protein, TagD5, was also required for cell-cell fusion. In the absence of VgrG5 or TagD5, bacteria in plasma membrane protrusions were engulfed into neighboring cells. Our results suggest that the T6SS-5 effectors VgrG5 and TagD5 are secreted within membrane protrusions and act locally to promote membrane fusion.
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Affiliation(s)
- Nora Kostow
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Matthew D Welch
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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38
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Jiang F, Shen J, Cheng J, Wang X, Yang J, Li N, Gao N, Jin Q. N-terminal signal peptides facilitate the engineering of PVC complex as a potent protein delivery system. SCIENCE ADVANCES 2022; 8:eabm2343. [PMID: 35486720 PMCID: PMC9054023 DOI: 10.1126/sciadv.abm2343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Extracellular contractile injection systems (eCISs) are widespread bacterial nanomachines that resemble T4 phage tail. As a typical eCIS, Photorhabdus virulence cassette (PVC) was proposed to inject toxins into eukaryotic cells by puncturing the cell membrane from outside. This makes it an ideal tool for protein delivery in biomedical research. However, how to manipulate this nanocomplex as a molecular syringe is still undetermined. Here, we identify that one group of N-terminal signal peptide (SP) sequences are crucial for the effector loading into the inner tube of PVC complex. By application of genetic operation, cryo-electron microscopy, in vitro translocation assays, and animal experiments, we show that, under the guidance of the SP, numerous prokaryotic and eukaryotic proteins can be loaded into PVC to exert their functions across cell membranes. We therefore might customize PVC as a potent protein delivery nanosyringe for biotherapy by selecting cargo proteins in a broad spectrum, regardless of their species, sizes, and charges.
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Affiliation(s)
- Feng Jiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jiawei Shen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jiaxuan Cheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, P. R. China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, P. R. China
| | - Xia Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, P. R. China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, P. R. China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, P. R. China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
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Weagley JS, Zaydman M, Venkatesh S, Sasaki Y, Damaraju N, Yenkin A, Buchser W, Rodionov DA, Osterman A, Ahmed T, Barratt MJ, DiAntonio A, Milbrandt J, Gordon JI. Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition. Cell Rep 2022; 39:110738. [PMID: 35476981 PMCID: PMC9092222 DOI: 10.1016/j.celrep.2022.110738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/05/2022] [Accepted: 04/04/2022] [Indexed: 12/04/2022] Open
Abstract
Perturbed gut microbiome development has been linked to childhood malnutrition. Here, we characterize bacterial Toll/interleukin-1 receptor (TIR) protein domains that metabolize nicotinamide adenine dinucleotide (NAD), a co-enzyme with far-reaching effects on human physiology. A consortium of 26 human gut bacterial strains, representing the diversity of TIRs observed in the microbiome and the NAD hydrolase (NADase) activities of a subset of 152 bacterial TIRs assayed in vitro, was introduced into germ-free mice. Integrating mass spectrometry and microbial RNA sequencing (RNA-seq) with consortium membership manipulation disclosed that a variant of cyclic-ADPR (v-cADPR-x) is a specific product of TIR NADase activity and a prominent, colonization-discriminatory, taxon-specific metabolite. Guided by bioinformatic analyses of biochemically validated TIRs, we find that acute malnutrition is associated with decreased fecal levels of genes encoding TIRs known or predicted to generate v-cADPR-x, as well as decreased levels of the metabolite itself. These results underscore the need to consider microbiome TIR NADases when evaluating NAD metabolism in the human holobiont.
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Affiliation(s)
- James S Weagley
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mark Zaydman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddarth Venkatesh
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Neha Damaraju
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alex Yenkin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - William Buchser
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Andrei Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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40
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Li Y, Yan X, Tao Z. Two Type VI Secretion DNase Effectors are Utilized for Interbacterial Competition in the Fish Pathogen Pseudomonas plecoglossicida. Front Microbiol 2022; 13:869278. [PMID: 35464968 PMCID: PMC9020831 DOI: 10.3389/fmicb.2022.869278] [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: 02/04/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas plecoglossicida is a facultative fish pathogen that possesses three distinct type VI secretion systems (named T6SS-1, T6SS-2, and T6SS-3). Our previous work indicated that only T6SS-2 of P. plecoglossicida mediates interbacterial competition. However, the antibacterial T6SS effectors and their functions are unclear. Here, we reported two T6SS effectors that mediate antibacterial activity. We first identified four putative antibacterial effectors (denoted as Txe1, Txe2, Txe3, and Txe4) and their cognate immunity proteins encoded in P. plecoglossicida strain XSDHY-P by analyzing the regions downstream of three vgrG genes. We showed that the growth of Escherichia coli cells expressing Txe1, Txe2, and Txe4 was inhibited, and these three effectors exhibited nuclease activity in vivo. The interbacterial competition assays with single- or multi-effector deletion mutants as attackers revealed that Txe1 was the predominant T6SS toxin of P. plecoglossicida strain XSDHY-P mediating the interbacterial killing. This work contributes to our understanding of bacterial effectors involved in the interbacterial competition.
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Affiliation(s)
- Yanyan Li
- School of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Xiaojun Yan
- School of Fisheries, Zhejiang Ocean University, Zhoushan, China
| | - Zhen Tao
- School of Fisheries, Zhejiang Ocean University, Zhoushan, China
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41
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Abstract
Blocking host cell death is an important virulence strategy employed by many bacterial pathogens. We recently reported that Shigella flexneri inhibits host pyroptosis by delivering a type III secretion system (T3SS) effector OspC3 that catalyzes a novel arginine ADP-riboxanation modification on caspase-4/11. Here, we investigated the OspC3 homologue CopC from Chromobacterium violaceum, an opportunistic but sometimes deadly bacterial pathogen. CopC bears the same arginine ADP-riboxanase activity as OspC3, but with a different substrate specificity. Through proteomic analysis, we first identified host calmodulin (CaM) as a binding partner of CopC. The analyses additionally revealed that CopC preferably modifies apoptotic caspases including caspase-7, -8 and -9. This results in suppression of both extrinsic and intrinsic apoptosis programs in C. violaceum-infected cells. Biochemical reconstitution showed that CopC requires binding to CaM, specifically in the calcium-free state, to achieve efficient ADP-riboxanation of the caspases. We determined crystal structure of the CaM-CopC-CASP7 ternary complex, which illustrates the caspase recognition mechanism and a unique CaM-binding mode in CopC. Structure-directed mutagenesis validated the functional significance of CaM binding for stimulating CopC modification of its caspase substrates. CopC adopts an ADP-ribosyltransferase-like fold with a unique His-Phe-Glu catalytic triad, featuring two acidic residues critical for site-specific arginine ADP-riboxanation. Our study expands and deepens our understanding of the OspC family of ADP-riboxanase effectors.
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NrtR Mediated Regulation of H1-T6SS in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0185821. [PMID: 35196795 PMCID: PMC8865458 DOI: 10.1128/spectrum.01858-21] [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] [Indexed: 12/02/2022] Open
Abstract
NrtR is a Nudix-related transcriptional regulator that is distributed among diverse bacteria and plays an important role in modulating bacterial intracellular NAD homeostasis. Previously, we showed that NrtR influences the T3SS expression and pathogenesis of Pseudomonas aeruginosa and demonstrated that NrtR mediates T3SS regulation through the cAMP/Vfr pathway. In the present study, we found that mutation of the nrtR gene leads to upregulation of the Hcp secretion island-I type VI secretion system (H1-T6SS). Further analysis revealed that mutation of the nrtR gene results in upregulation of regulatory RNAs (RsmY/RsmZ) that are known to control the H1-T6SS by sequestration of RsmA or RsmN. Simultaneous deletion of rsmY/rsmZ reduced the expression of H1-T6SS in the ΔnrtR mutant. In addition, overexpression of either rsmA or rsmN in ΔnrtR decreased H1-T6SS expression. Chromatin immunoprecipitation (ChIP)-Seq and electrophoretic mobility shift assay (EMSA) analyses revealed that NrtR directly binds to the promoters of rsmY, rsmZ and tssA1 (first gene of the H1-T6SS operon). Overall, the results from this study reveal the molecular details of NrtR-mediated regulation of H1-T6SS in P. aeruginosa. IMPORTANCE NrtR is a Nudix-related transcriptional regulator and controls the NAD cofactor biosynthesis in bacteria. P. aeruginosa NrtR binds to the intergenic region between nadD2 and pcnA to repress the expression of the two operons, therefore controlling the NAD biosynthesis. We have previously reported that NrtR controls T3SS expression via the cAMP/Vfr pathway in P. aeruginosa. However, the global regulatory function and direct binding targets of the NrtR remain elusive in P. aeruginosa. This study reveals novel direct regulatory targets of the NrtR in P. aeruginosa, elucidating the molecular mechanism of NrtR-mediated regulation of H1-T6SS.
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Amaya FA, Blondel CJ, Barros-Infante MF, Rivera D, Moreno-Switt AI, Santiviago CA, Pezoa D. Identification of Type VI Secretion Systems Effector Proteins That Contribute to Interbacterial Competition in Salmonella Dublin. Front Microbiol 2022; 13:811932. [PMID: 35222335 PMCID: PMC8867033 DOI: 10.3389/fmicb.2022.811932] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
The Type VI Secretion System (T6SS) is a multiprotein device that has emerged as an important fitness and virulence factor for many Gram-negative bacteria through the injection of effector proteins into prokaryotic or eukaryotic cells via a contractile mechanism. While some effector proteins specifically target bacterial or eukaryotic cells, others can target both types of cells (trans-kingdom effectors). In Salmonella, five T6SS gene clusters have been identified within pathogenicity islands SPI-6, SPI-19, SPI-20, SPI-21, and SPI-22, which are differentially distributed among serotypes. Salmonella enterica serotype Dublin (S. Dublin) is a cattle-adapted pathogen that harbors both T6SSSPI-6 and T6SSSPI-19. Interestingly, while both systems have been linked to virulence and host colonization in S. Dublin, an antibacterial activity has not been detected for T6SSSPI-6 in this serotype. In addition, there is limited information regarding the repertoire of effector proteins encoded within T6SSSPI-6 and T6SSSPI-19 gene clusters in S. Dublin. In the present study, we demonstrate that T6SSSPI-6 and T6SSSPI-19 of S. Dublin CT_02021853 contribute to interbacterial competition. Bioinformatic and comparative genomic analyses allowed us to identify genes encoding three candidate antibacterial effectors located within SPI-6 and two candidate effectors located within SPI-19. Each antibacterial effector gene is located upstream of a gene encoding a hypothetic immunity protein, thus conforming an effector/immunity (E/I) module. Of note, the genes encoding these effectors and immunity proteins are widely distributed in Salmonella genomes, suggesting a relevant role in interbacterial competition and virulence. Finally, we demonstrate that E/I modules SED_RS01930/SED_RS01935 (encoded in SPI-6), SED_RS06235/SED_RS06230, and SED_RS06335/SED_RS06340 (both encoded in SPI-19) contribute to interbacterial competition in S. Dublin CT_02021853.
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Affiliation(s)
- Fernando A. Amaya
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos J. Blondel
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Dácil Rivera
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Andrea I. Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative on Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- *Correspondence: Carlos A. Santiviago, David Pezoa,
| | - David Pezoa
- Escuela de Medicina Veterinaria, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- *Correspondence: Carlos A. Santiviago, David Pezoa,
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Werum V, Ehrmann M, Vogel R, Hilgarth M. Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat. Microbiol Res 2022; 258:126982. [DOI: 10.1016/j.micres.2022.126982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
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Zhao H, Clevenger AL, Coburn PS, Callegan MC, Rybenkov V. Condensins are essential for Pseudomonas aeruginosa corneal virulence through their control of lifestyle and virulence programs. Mol Microbiol 2022; 117:937-957. [PMID: 35072315 PMCID: PMC9512581 DOI: 10.1111/mmi.14883] [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: 09/30/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/01/2022]
Abstract
Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for numerous human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required for P. aeruginosa virulence during corneal infection. The reduction in virulence was traced to broad changes in gene expression. Transcriptional signatures of smc and mksB mutants were largely dissimilar and non-additive, with the double mutant displaying a distinct gene expression profile. Affected regulons included those responsible for lifestyle control, primary metabolism, surface adhesion and biofilm growth, iron and sulfur assimilation, and numerous virulence factors, including type 3 and type 6 secretion systems. The in vitro phenotypes of condensin mutants mirrored their transcriptional profiles and included impaired production and secretion of multiple virulence factors, growth deficiencies under nutrient limiting conditions, and altered c-di-GMP signaling. Notably, c-di-GMP mediated some but not all transcriptional responses of the mutants. Thus, condensins are integrated into the control of multiple genetic programs related to epigenetic and virulent behavior of P. aeruginosa.
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Affiliation(s)
- Hang Zhao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, USA
| | - April L Clevenger
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, USA
| | - Phillip S Coburn
- Department of Ophthalmology, the University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, USA
| | - Michelle C Callegan
- Department of Ophthalmology, the University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, USA
| | - Valentin Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, USA
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Xu Y, Cheng S, Zeng H, Zhou P, Ma Y, Li L, Liu X, Shao F, Ding J. ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy. Nat Struct Mol Biol 2022; 29:67-77. [PMID: 35046574 DOI: 10.1038/s41594-021-00710-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022]
Abstract
Selective autophagy helps eukaryotes to cope with endogenous dangers or foreign invaders; its initiation often involves membrane damage. By studying a Salmonella effector SopF, we recently identified the vacuolar ATPase (V-ATPase)-ATG16L1 axis that initiates bacteria-induced autophagy. Here we show that SopF is an ADP-ribosyltransferase specifically modifying Gln124 of ATP6V0C in V-ATPase. We identify GTP-bound ADP-ribosylation factor (ARF) GTPases as a cofactor required for SopF functioning. Crystal structures of SopF-ARF1 complexes not only reveal structural basis of SopF ADP-ribosyltransferase activity but also a unique effector-binding mode adopted by ARF GTPases. Further, the N terminus of ARF1, although dispensable for high-affinity binding to SopF, is critical for activating SopF to modify ATP6V0C. Moreover, lysosome or Golgi damage-induced autophagic LC3 activation is inhibited by SopF or Q124A mutation of ATP6V0C, thus also mediated by the V-ATPase-ATG16L1 axis. In this process, the V-ATPase functions to sense membrane damages, which can be uncoupled from its proton-pumping activity.
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Affiliation(s)
- Yue Xu
- National Institute of Biological Sciences, Beijing, China.,Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sen Cheng
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Huan Zeng
- National Institute of Biological Sciences, Beijing, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ping Zhou
- National Institute of Biological Sciences, Beijing, China
| | - Yan Ma
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences, Beijing, China. .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
| | - Jingjin Ding
- National Institute of Biological Sciences, Beijing, China. .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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Antimicrobial Weapons of Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:223-256. [DOI: 10.1007/978-3-031-08491-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Günther P, Quentin D, Ahmad S, Sachar K, Gatsogiannis C, Whitney JC, Raunser S. Structure of a bacterial Rhs effector exported by the type VI secretion system. PLoS Pathog 2022; 18:e1010182. [PMID: 34986192 PMCID: PMC8765631 DOI: 10.1371/journal.ppat.1010182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/18/2022] [Accepted: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread protein export apparatus found in Gram-negative bacteria. The majority of T6SSs deliver toxic effector proteins into competitor bacteria. Yet, the structure, function, and activation of many of these effectors remains poorly understood. Here, we present the structures of the T6SS effector RhsA from Pseudomonas protegens and its cognate T6SS spike protein, VgrG1, at 3.3 Å resolution. The structures reveal that the rearrangement hotspot (Rhs) repeats of RhsA assemble into a closed anticlockwise β-barrel spiral similar to that found in bacterial insecticidal Tc toxins and in metazoan teneurin proteins. We find that the C-terminal toxin domain of RhsA is autoproteolytically cleaved but remains inside the Rhs ‘cocoon’ where, with the exception of three ordered structural elements, most of the toxin is disordered. The N-terminal ‘plug’ domain is unique to T6SS Rhs proteins and resembles a champagne cork that seals the Rhs cocoon at one end while also mediating interactions with VgrG1. Interestingly, this domain is also autoproteolytically cleaved inside the cocoon but remains associated with it. We propose that mechanical force is required to remove the cleaved part of the plug, resulting in the release of the toxin domain as it is delivered into a susceptible bacterial cell by the T6SS. Bacteria have developed a variety of strategies to compete for nutrients and limited resources. One system widely used by Gram-negative bacteria is the T6 secretion system which delivers a plethora of effectors into competing bacterial cells. Known functions of effectors are degradation of the cell wall, the depletion of essential metabolites such as NAD+ or the cleavage of DNA. RhsA is an effector from the widespread plant-protecting bacteria Pseudomonas protegens. We found that RhsA forms a closed cocoon similar to that found in bacterial Tc toxins and metazoan teneurin proteins. The effector cleaves its polypeptide chain by itself in three pieces, namely the N-terminal domain including a seal, the cocoon and the actual toxic component which potentially cleaves DNA. The toxic component is encapsulated in the large cocoon, so that the effector producing bacterium is protected from the toxin. In order for the toxin to exit the cocoon, we propose that the seal, which closes the cocoon at one end, is removed by mechanical forces during injection of the effector by the T6 secretion system. We further hypothesize about different scenarios for the delivery of the toxin into the cytoplasm of the host cell. Together, our findings expand the knowledge of the mechanism of action of the T6 secretion system and its essential role in interbacterial competition.
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Affiliation(s)
- Patrick Günther
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Shehryar Ahmad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Kartik Sachar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
- * E-mail: (J.C.W.); (S.R.)
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- * E-mail: (J.C.W.); (S.R.)
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Abstract
Protein toxins secreted by prokaryotes have been found to affect the pathogenicity of pathogens or directly mediate antagonistic interactions between prokaryotes. PAAR proteins are important carriers of toxic effectors and are located at the forefront of either the type VI secretion system (T6SS) or the extracellular contractile injection system (eCIS). This study systematically investigated PAAR homologues and related toxic effectors. We found that PAAR homologues were divided into 8 types and 16 subtypes and distributed in 23.1% of bacterial genomes and 7.8% of archaeal genomes. PAAR proteins of all types fold into a highly similar conical structure, even from relatively diverse underlying sequences. PAAR homologues associated with different secretion systems display a mixed phylogenetic relationship, indicating that PAAR proteins from such a subtype can be assembled on either a T6SS or an eCIS. More than 1,300 PAAR-related toxic effector genes were identified; one PAAR subtype can be associated with toxins of over 40 families, and toxins from one family can be associated with more than 10 PAAR subtypes. A large-scale comparison of Earth Microbiome Project data and prokaryotic genomes revealed that prokaryotes encoding PAAR genes are widely present in diverse environments worldwide, and taxa encoding multiple PAAR gene copies exhibit a wider distribution in environments than other taxa. Overall, our studies highlighted that PAAR proteins are versatile clips loaded with antimicrobial toxin bullets for secretion weapons (T6SS and eCIS), greatly enriching the weapon arsenal of prokaryotes, which, often together with VgrG, help prokaryotes fight for survival advantages in crowded environments. IMPORTANCE Infectious diseases caused by microbial pathogens are severe threats to human health and economic development. To respond to these threats, it is necessary to understand how microorganisms survive in and adapt to complex environments. Microorganic toxins, which are widely distributed in nature, are the key weapons in life domain interactions. PAAR proteins are important carriers of prokaryotic toxic effectors. We reveal the versatility of PAAR proteins between secretory systems and the massive diversity of toxic effectors carried by PAAR proteins, which helps prokaryotes enrich their arsenal and expand their ability to attack their neighbors. A large number of PAAR homologues and related toxic effectors enhance the survival competitiveness of prokaryotic populations. In conclusion, our work provides an example for large-scale analysis of the global distribution and ecological functions of prokaryotic functional genes.
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