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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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2
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Hespanhol JT, Sanchez-Limache DE, Nicastro GG, Mead L, Llontop EE, Chagas-Santos G, Farah CS, de Souza RF, Galhardo RDS, Lovering AL, Bayer-Santos E. Antibacterial T6SS effectors with a VRR-Nuc domain are structure-specific nucleases. eLife 2022; 11:e82437. [PMID: 36226828 PMCID: PMC9635880 DOI: 10.7554/elife.82437] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/09/2022] [Indexed: 11/21/2022] Open
Abstract
The type VI secretion system (T6SS) secretes antibacterial effectors into target competitors. Salmonella spp. encode five phylogenetically distinct T6SSs. Here, we characterize the function of the SPI-22 T6SS of Salmonella bongori showing that it has antibacterial activity and identify a group of antibacterial T6SS effectors (TseV1-4) containing an N-terminal PAAR-like domain and a C-terminal VRR-Nuc domain encoded next to cognate immunity proteins with a DUF3396 domain (TsiV1-4). TseV2 and TseV3 are toxic when expressed in Escherichia coli and bacterial competition assays confirm that TseV2 and TseV3 are secreted by the SPI-22 T6SS. Phylogenetic analysis reveals that TseV1-4 are evolutionarily related to enzymes involved in DNA repair. TseV3 recognizes specific DNA structures and preferentially cleave splayed arms, generating DNA double-strand breaks and inducing the SOS response in target cells. The crystal structure of the TseV3:TsiV3 complex reveals that the immunity protein likely blocks the effector interaction with the DNA substrate. These results expand our knowledge on the function of Salmonella pathogenicity islands, the evolution of toxins used in biological conflicts, and the endogenous mechanisms regulating the activity of these toxins.
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Affiliation(s)
- Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São PauloSão PauloBrazil
| | | | | | - Liam Mead
- Department of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Edgar Enrique Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão PauloBrazil
| | - Gustavo Chagas-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São PauloSão PauloBrazil
| | - Chuck Shaker Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão PauloBrazil
| | - Robson Francisco de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São PauloSão PauloBrazil
| | - Rodrigo da Silva Galhardo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São PauloSão PauloBrazil
| | - Andrew L Lovering
- Department of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São PauloSão PauloBrazil
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3
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A Novel Antimicrobial Metabolite Produced by Paenibacillus apiarius Isolated from Brackish Water of Lake Balkhash in Kazakhstan. Microorganisms 2022; 10:microorganisms10081519. [PMID: 36013937 PMCID: PMC9416454 DOI: 10.3390/microorganisms10081519] [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: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
Four aerobic bacteria with bacteriolytic capabilities were isolated from the brackish water site Strait Uzynaral of Lake Balkhash in Kazakhstan. The morphology and physiology of the bacterial isolates have subsequently been analyzed. Using matrix assisted laser desorption ionization-time of flight mass spectrum and partial 16S rRNA gene sequence analyses, three of the isolates have been identified as Pseudomonas veronii and one as Paenibacillus apiarius. We determined the capability of both species to lyse pre-grown cells of the Gram-negative strains Pseudomonas putida SBUG 24 and Escherichia coli SBUG 13 as well as the Gram-positive strains Micrococcus luteus SBUG 16 and Arthrobacter citreus SBUG 321 on solid media. The bacteriolysis process was analyzed by creating growth curves and electron micrographs of co-cultures with the bacteriolytic isolates and the lysis sensitive strain Arthrobacter citreus SBUG 321 in nutrient-poor liquid media. One metabolite of Paenibacillus apiarius was isolated and structurally characterized by various chemical structure determination methods. It is a novel antibiotic substance.
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4
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Yu H, Bai XC, Wang W. Characterization of the subunit composition and structure of adult human glycine receptors. Neuron 2021; 109:2707-2716.e6. [PMID: 34473954 DOI: 10.1016/j.neuron.2021.08.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/23/2021] [Accepted: 08/16/2021] [Indexed: 11/27/2022]
Abstract
The strychnine-sensitive pentameric glycine receptor (GlyR) mediates fast inhibitory neurotransmission in the mammalian nervous system. Only heteromeric GlyRs mediate synaptic transmission, as they contain the β subunit that permits clustering at the synapse through its interaction with scaffolding proteins. Here, we show that α2 and β subunits assemble with an unexpected 4:1 stoichiometry to produce GlyR with native electrophysiological properties. We determined structures in multiple functional states at 3.6-3.8 Å resolutions and show how 4:1 stoichiometry is consistent with the structural features of α2β GlyR. Furthermore, we show that one single β subunit in each GlyR gives rise to the characteristic electrophysiological properties of heteromeric GlyR, while more β subunits render GlyR non-conductive. A single β subunit ensures a univalent GlyR-scaffold linkage, which means the scaffold alone regulates the cluster properties.
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Affiliation(s)
- Hailong Yu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weiwei Wang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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5
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Wang S, Geng Z, Zhang H, She Z, Dong Y. The Pseudomonas aeruginosa PAAR2 cluster encodes a putative VRR-NUC domain-containing effector. FEBS J 2021; 288:5755-5767. [PMID: 33838074 DOI: 10.1111/febs.15870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 01/10/2023]
Abstract
The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in inter-bacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from the virulence of their own effectors. The T6SS injects its inner-needle Hcp tube, the sharpening tip complex -consisting of VgrG and proline-alanine-alanine-arginine repeats (PAAR) proteins- and toxic effectors into neighboring cells. Its functions are largely determined by the activities of its delivered effectors. Five PAAR proteins were found in the Pseudomonas aeruginosa PAO1 genome with three of them shown to facilitate the delivery of various effectors. Here, we report a putative virus-type replication-repair nuclease domain-containing effector TseV encoded by the least investigated P. aeruginosa PAAR2 cluster. The crystal structure of its putative cognate effector TsiV is presented at 1.6 Å resolution. Through structure and sequence comparisons, we propose TseV-TsiV to be a putative novel effector-immunity (E-I) pair and we discuss the roles of other PAAR2 cluster encoded proteins.
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Affiliation(s)
- Shuangyue Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Zhi Geng
- Multidiscipline Research Center, Institte of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhang
- Multidiscipline Research Center, Institte of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Zhun She
- Multidiscipline Research Center, Institte of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Dong
- Multidiscipline Research Center, Institte of High Energy Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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6
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González-Magaña A, Sainz-Polo MÁ, Pretre G, Çapuni R, Lucas M, Altuna J, Montánchez I, Fucini P, Albesa-Jové D. Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8. J Struct Biol 2020; 212:107651. [PMID: 33096229 DOI: 10.1016/j.jsb.2020.107651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Recent reports indicate that the Type six secretion system exported effector 8 (Tse8) is a cytoactive effector secreted by the Type VI secretion system (T6SS) of the human pathogen Pseudomonas aeruginosa. The T6SS is a nanomachine that assembles inside of the bacteria and injects effectors/toxins into target cells, providing a fitness advantage over competing bacteria and facilitating host colonisation. Here we present the first crystal structure of Tse8 revealing that it conserves the architecture of the catalytic triad Lys84-transSer162-Ser186 that characterises members of the Amidase Signature superfamily. Furthermore, using binding affinity experiments, we show that the interaction of phenylmethylsulfonyl fluoride (PMSF) to Tse8 is dependent on the putative catalytic residue Ser186, providing support for its nucleophilic reactivity. This work thus demonstrates that Tse8 belongs to the Amidase Signature (AS) superfamily. Furthermore, it highlights Tse8 similarity to two family members: the Stenotrophomonas maltophilia Peptide Amidase and the Glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus.
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Affiliation(s)
- Amaia González-Magaña
- Instituto Biofisika (UPV/EHU, CSIC), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940 Leioa, Spain
| | - M Ángela Sainz-Polo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Gabriela Pretre
- Instituto Biofisika (UPV/EHU, CSIC), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940 Leioa, Spain
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - María Lucas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, 39011 Cantabria, Spain
| | - Jon Altuna
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Itxaso Montánchez
- Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940 Leioa, Spain
| | - Paola Fucini
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David Albesa-Jové
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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7
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Barretto LAF, Fowler CC. Identification of A Putative T6SS Immunity Islet in Salmonella Typhi. Pathogens 2020; 9:pathogens9070559. [PMID: 32664482 PMCID: PMC7400221 DOI: 10.3390/pathogens9070559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Typhoid fever is a major global health problem and is the result of systemic infections caused by the human-adapted bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi). The pathology underlying S. Typhi infections significantly differ from infections caused by broad host range serovars of the same species, which are a common cause of gastroenteritis. Accordingly, identifying S. Typhi genetic factors that impart functionality absent from broad host range serovars offers insights into its unique biology. Here, we used an in-silico approach to explore the function of an uncharacterized 14-gene S. Typhi genomic islet. Our results indicated that this islet was specific to the S. enterica species, where it was encoded by the Typhi and Paratyphi A serovars, but was generally absent from non-typhoidal serovars. Evidence was gathered using comparative genomics and sequence analysis tools, and indicated that this islet was comprised of Type VI secretion system (T6SS) and contact-dependent growth inhibition (CDI) genes, the majority of which appeared to encode orphan immunity proteins that protected against the activities of effectors and toxins absent from the S. Typhi genome. We herein propose that this islet represents an immune system that protects S. Typhi against competing bacteria within the human gut.
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8
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Klein TA, Ahmad S, Whitney JC. Contact-Dependent Interbacterial Antagonism Mediated by Protein Secretion Machines. Trends Microbiol 2020; 28:387-400. [PMID: 32298616 DOI: 10.1016/j.tim.2020.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/18/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022]
Abstract
To establish and maintain an ecological niche, bacteria employ a wide range of pathways to inhibit the growth of their microbial competitors. Some of these pathways, such as those that produce antibiotics or bacteriocins, exert toxicity on nearby cells in a cell contact-independent manner. More recently, however, several mechanisms of interbacterial antagonism requiring cell-to-cell contact have been identified. This form of microbial competition is mediated by antibacterial protein toxins whose delivery to target bacteria uses protein secretion apparatuses embedded within the cell envelope of toxin-producing bacteria. In this review, we discuss recent work implicating the bacterial Type I, IV, VI, and VII secretion systems in the export of antibacterial 'effector' proteins that mediate contact-dependent interbacterial antagonism.
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Affiliation(s)
- Timothy A Klein
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada L8S 4K1; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8S 4K1
| | - Shehryar Ahmad
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada L8S 4K1; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8S 4K1
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada L8S 4K1; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8S 4K1; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada L8S 4K1.
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9
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She Z, Geng Z, Xu JH, Li YH, Dong YH. Structural characterization of the Imm52 family protein TsiT in Pseudomonas aeruginosa. Protein Sci 2019; 28:971-975. [PMID: 30834616 DOI: 10.1002/pro.3597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/26/2019] [Indexed: 11/08/2022]
Abstract
The bacterial type VI secretion system (T6SS) utilizes many toxic effectors to gain advantage over interbacterial competition and eukaryotic host infection. Meanwhile, the cognate immunity proteins of these effectors are employed to protect themselves from the virulence. TseT and TsiT form an effector-immunity (E-I) protein pair secreted by T6SS of Pseudomonas aeruginosa. TseT is toxic for other bacteria, whereas TsiT can suppress the virulence of TseT. Here, we report the crystal structure of TsiT at 1.6 Å resolution. TsiT is a typical α + β class protein and belongs to a novel Imm52 protein family of the polymorphic toxin system. Apart from TsiT, only one structure of the Imm52 family proteins is present in the Protein Data Bank (PDB), but that structure is not characterized and shares low sequence identity with TsiT. We characterized the basic features of TsiT structure and identified conserved residues of the Imm52 family proteins according to homology comparison. Our work provided structural information of a new protein family and should aid future functional studies.
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Affiliation(s)
- Zhun She
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Hua Xu
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Hua Li
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Hui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
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10
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Yang XY, Li ZQ, Gao ZQ, Wang WJ, Geng Z, Xu JH, She Z, Dong YH. Structural and SAXS analysis of Tle5-Tli5 complex reveals a novel inhibition mechanism of H2-T6SS in Pseudomonas aeruginosa. Protein Sci 2017; 26:2083-2091. [PMID: 28758353 DOI: 10.1002/pro.3246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 11/11/2022]
Abstract
Widely spread in Gram-negative bacteria, the type VI secretion system (T6SS) secretes many effector-immunity protein pairs to help the bacteria compete against other prokaryotic rivals, and infect their eukaryotic hosts. Tle5 and Tle5B are two phospholipase effector protein secreted by T6SS of Pseudomonas aeruginosa. They can facilitate the bacterial internalization process into human epithelial cells by interacting with Akt protein of the PI3K-Akt signal pathway. Tli5 and PA5086-5088 are cognate immunity proteins of Tle5 and Tle5B, respectively. They can interact with their cognate effector proteins to suppress their virulence. Here, we report the crystal structure of Tli5 at 2.8Å resolution and successfully fit it into the Small angle X-ray scattering (SAXS) model of the complete Tle5-Tli5 complex. We identified two important motifs in Tli5 through sequence and structural analysis. One is a conserved loop-β-hairpin motif that exists in the Tle5 immunity homologs, the other is a long and sharp α-α motif that directly interacts with Tle5 according to SAXS data. We also distinguished the structural features of Tle5 and Tle5B family immunity proteins. Together, our work provided insights into a novel inhibition mechanism that may enhance our understanding of phospholipase D family proteins.
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Affiliation(s)
- Xiao-Yun Yang
- Key Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zong-Qiang Li
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zeng-Qiang Gao
- Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China
| | - Wen-Jia Wang
- Department of Optoelectronic Information, School of Science, Qilu University of Technology, Jinan, China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Xu
- Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China
| | - Zhun She
- Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China
| | - Yu-Hui Dong
- Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China
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11
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Abstract
Bacterial type VI secretion systems (T6SSs) function as contractile nanomachines to puncture target cells and deliver lethal effectors. In the 10 years since the discovery of the T6SS, much has been learned about the structure and function of this versatile protein secretion apparatus. Most of the conserved protein components that comprise the T6SS apparatus itself have been identified and ascribed specific functions. In addition, numerous effector proteins that are translocated by the T6SS have been identified and characterized. These protein effectors usually represent toxic cargoes that are delivered by the attacker cell to a target cell. Researchers in the field are beginning to better understand the lifestyle or physiology that dictates when bacteria normally express their T6SS. In this article, we consider what is known about the structure and regulation of the T6SS, the numerous classes of antibacterial effector T6SS substrates, and how the action of the T6SS relates to a given lifestyle or behavior in certain bacteria.
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12
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Yang XY, Li ZQ, She Z, Geng Z, Xu JH, Gao ZQ, Dong YH. Structural analysis of Pseudomonas aeruginosa H3-T6SS immunity proteins. FEBS Lett 2016; 590:2787-96. [PMID: 27397502 DOI: 10.1002/1873-3468.12291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/31/2016] [Accepted: 06/27/2016] [Indexed: 01/13/2023]
Abstract
The Pseudomonas aeruginosa PldB protein is a transkingdom effector secreted by the Type VI Secretion System (T6SS). PA5088, PA5087, and PA5086 are three immunity proteins that can suppress the virulence of PldB. We report the crystal structures of PA5088 and PA5087 at 2.0 and 2.1 Å resolution, respectively. PA5088 and PA5087 both consist of several Sel1-like Repeats (SLRs) and form super-ring folds. Our structural analysis of these proteins revealed key differences among PA5088, PA5087, and their homologs. Our docking experiments have shed light on the putative interaction mechanism of their function as phospholipase D inhibitors.
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Affiliation(s)
- Xiao-Yun Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zong-Qiang Li
- College of Life Science and Technology, Huazhong Agriculture University, Wuhan, China
| | - Zhun She
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Xu
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Zeng-Qiang Gao
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yu-Hui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
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13
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Lu D, Zheng Y, Liao N, Wei L, Xu B, Liu X, Liu J. The structural basis of the Tle4–Tli4 complex reveals the self-protection mechanism of H2-T6SS inPseudomonas aeruginosa. ACTA ACUST UNITED AC 2014; 70:3233-43. [DOI: 10.1107/s1399004714023967] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/30/2014] [Indexed: 01/02/2023]
Abstract
The type VI secretion system (T6SS) has recently been demonstrated to mediate interbacterial competition and to discriminate between self and nonself. T6SS+bacteria employ toxic effectors to inhibit rival cells and concurrently use effector cognate immunity proteins to protect their sibling cells. The effector and immunity pairs (E–I pairs) endow the bacteria with a great advantage in niche competition. Tle4–Tli4 (PA1510–PA1509) is a newly identified E–I pair that is controlled by H2-T6SS inPseudomonas aeruginosa. Tle4 exhibits phospholipase activity, which destroys the cell membrane of rival cells, and the periplasm-located Tli4 in donor cells eliminates this toxic effect of Tle4. In this paper, the structure of the Tle4–Tli4 complex is reported at 1.75 Å resolution. Tle4 consists of two domains: a conserved α/β-hydrolase domain and an unusual cap domain in which two lid regions (lid1 and lid2) display a closed conformation that buries the catalytic triad in a deep funnel. Tli4 also displays a two-domain structure, in which a large lobe and a small lobe form a crab claw-like conformation. Tli4 uses this crab claw to grasp the cap domain of Tle4, especially the lid2 region, which prevents the interfacial activation of Tle4 and thus causes enzymatic dysfunction of Tle4 in sister cells.
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Durand E, Cambillau C, Cascales E, Journet L. VgrG, Tae, Tle, and beyond: the versatile arsenal of Type VI secretion effectors. Trends Microbiol 2014; 22:498-507. [DOI: 10.1016/j.tim.2014.06.004] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 12/20/2022]
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15
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Hu H, Zhang H, Gao Z, Wang D, Liu G, Xu J, Lan K, Dong Y. Structure of the type VI secretion phospholipase effector Tle1 provides insight into its hydrolysis and membrane targeting. ACTA ACUST UNITED AC 2014; 70:2175-85. [DOI: 10.1107/s1399004714012899] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/03/2014] [Indexed: 08/30/2023]
Abstract
A diverse superfamily of phospholipases consisting of the type VI lipase effectors Tle1–Tle5 secreted by the bacterial type VI secretion system (T6SS) have recently been identified as antibacterial effectors that hydrolyze membrane phospholipids. These effectors show no significant homology to known lipases, and their mechanism of membrane targeting and hydrolysis of phospholipids remains unknown. Here, the crystal structure of Tle1 (∼96.5 kDa) fromPseudomonas aeruginosarefined to 2.0 Å resolution is reported, representing the first structure of this superfamily. Its overall structure can be divided into two distinct parts, the phospholipase catalytic module and the putative membrane-anchoring module; this arrangement has not previously been observed in known lipase structures. The phospholipase catalytic module has a canonical α/β-hydrolase fold and mutation of any residue in the Ser-Asp-His catalytic triad abolishes its toxicity. The putative membrane-anchoring module adopts an open conformation composed of three amphipathic domains, and its partial folds are similar to those of several periplasmic or membrane proteins. A cell-toxicity assay revealed that the putative membrane-anchoring module is critical to Tle1 antibacterial activity. A molecular-dynamics (MD) simulation system in which the putative membrane-anchoring module embedded into a bilayer was stable over 50 ns. These structure–function studies provide insight into the hydrolysis and membrane-targeting process of the unique phospholipase Tle1.
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16
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Ghequire MGK, De Mot R. Ribosomally encoded antibacterial proteins and peptides from Pseudomonas. FEMS Microbiol Rev 2014; 38:523-68. [PMID: 24923764 DOI: 10.1111/1574-6976.12079] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/26/2022] Open
Abstract
Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.
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Lu D, Shang G, Zhang H, Yu Q, Cong X, Yuan J, He F, Zhu C, Zhao Y, Yin K, Chen Y, Hu J, Zhang X, Yuan Z, Xu S, Hu W, Cang H, Gu L. Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex fromPseudomonas aeruginosareveal a calcium-dependent membrane-binding mechanism. Mol Microbiol 2014; 92:1092-112. [DOI: 10.1111/mmi.12616] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Defen Lu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
- The Liver Centre of Fujian Province; MengChao Hepatobiliary Hospital of Fujian Medical University; Fuzhou 350025 Fujian China
| | - Guijun Shang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Heqiao Zhang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
- School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Qian Yu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaoyan Cong
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Jupeng Yuan
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Fengjuan He
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Chunyuan Zhu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yanyu Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Kun Yin
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yuanyuan Chen
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Junqiang Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaodan Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Wei Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Huaixing Cang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
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18
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Zhang J, Zhang H, Gao Z, Hu H, Dong C, Dong YH. Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein. FEBS Lett 2014; 588:1891-8. [PMID: 24751834 DOI: 10.1016/j.febslet.2014.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/09/2014] [Accepted: 04/09/2014] [Indexed: 10/25/2022]
Abstract
The bacterial type VI secretion system (T6SS) is used by donor cells to inject toxic effectors into receptor cells. The donor cells produce the corresponding immunity proteins to protect themselves against the effector proteins, thereby preventing their self-intoxication. Recently, the C-terminal domain of VgrG3 was identified as a T6SS effector. Information on the molecular mechanism of VgrG3 and its immunity protein TsaB has been lacking. Here, we determined the crystal structures of native TsaB and the VgrG3C-TsaB complex. VgrG3C adopts a canonical phage-T4-lysozyme-like fold. TsaB interacts with VgrG3C through molecular mimicry, and inserts into the VgrG3C pocket.
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Affiliation(s)
- Jiulong Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China; School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People's Republic of China
| | - Heng Zhang
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, People's Republic of China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Haidai Hu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Cheng Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, People's Republic of China.
| | - Yu-Hui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
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19
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Whitney JC, Beck CM, Goo YA, Russell AB, Harding BN, De Leon JA, Cunningham DA, Tran BQ, Low DA, Goodlett DR, Hayes CS, Mougous JD. Genetically distinct pathways guide effector export through the type VI secretion system. Mol Microbiol 2014; 92:529-42. [PMID: 24589350 DOI: 10.1111/mmi.12571] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2014] [Indexed: 12/01/2022]
Abstract
Bacterial secretion systems often employ molecular chaperones to recognize and facilitate export of their substrates. Recent work demonstrated that a secreted component of the type VI secretion system (T6SS), haemolysin co-regulated protein (Hcp), binds directly to effectors, enhancing their stability in the bacterial cytoplasm. Herein, we describe a quantitative cellular proteomics screen for T6S substrates that exploits this chaperone-like quality of Hcp. Application of this approach to the Hcp secretion island I-encoded T6SS (H1-T6SS) of Pseudomonas aeruginosa led to the identification of a novel effector protein, termed Tse4 (type VI secretion exported 4), subsequently shown to act as a potent intra-specific H1-T6SS-delivered antibacterial toxin. Interestingly, our screen failed to identify two predicted H1-T6SS effectors, Tse5 and Tse6, which differ from Hcp-stabilized substrates by the presence of toxin-associated PAAR-repeat motifs and genetic linkage to members of the valine-glycine repeat protein G (vgrG) genes. Genetic studies further distinguished these two groups of effectors: Hcp-stabilized effectors were found to display redundancy in interbacterial competition with respect to the requirement for the two H1-T6SS-exported VgrG proteins, whereas Tse5 and Tse6 delivery strictly required a cognate VgrG. Together, we propose that interaction with either VgrG or Hcp defines distinct pathways for T6S effector export.
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Affiliation(s)
- John C Whitney
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
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20
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Yang X, Xu M, Wang Y, Xia P, Wang S, Ye B, Tong L, Jiang T, Fan Z. Molecular mechanism for self-protection against the type VI secretion system inVibrio cholerae. ACTA ACUST UNITED AC 2014; 70:1094-103. [DOI: 10.1107/s1399004714001242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/17/2014] [Indexed: 01/21/2023]
Abstract
VgrG proteins form the spike of the type VI secretion system (T6SS) syringe-like complex. VgrG3 ofVibrio choleraedegrades the peptidoglycan cell wall of rival bacteriaviaits C-terminal region (VgrG3C) through its muramidase activity. VgrG3C consists of a peptidoglycan-binding domain (VgrG3CPGB) and a putative catalytic domain (VgrG3CCD), and its activity can be inhibited by its immunity protein partner TsiV3. Here, the crystal structure ofV. choleraeVgrG3CCDin complex with TsiV3 is presented at 2.3 Å resolution. VgrG3CCDadopts a chitosanase fold. A dimer of TsiV3 is bound in the deep active-site groove of VgrG3CCD, occluding substrate binding and distorting the conformation of the catalytic dyad. Gln91 and Arg92 of TsiV3 are located in the centre of the interface and are important for recognition of VgrG3C. Mutation of these residues destabilized the complex and abolished the inhibitory activity of TsiV3 against VgrG3C toxicity in cells. Disruption of TsiV3 dimerization also weakened the complex and impaired the inhibitory activity. These structural, biochemical and functional data define the molecular mechanism underlying the self-protection ofV. choleraeand expand the understanding of the role of T6SS in bacterial competition.
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21
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Tümmler B, Wiehlmann L, Klockgether J, Cramer N. Advances in understanding Pseudomonas. F1000PRIME REPORTS 2014; 6:9. [PMID: 24592321 PMCID: PMC3913036 DOI: 10.12703/p6-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas aeruginosa, the type species of pseudomonads, is an opportunistic pathogen that colonizes a wide range of niches. Current genome sequencing projects are producing previously inconceivable detail about the population biology and evolution of P. aeruginosa. Its pan-genome has a larger genetic repertoire than the human genome, which explains the broad metabolic capabilities of P. aeruginosa and its ubiquitous distribution in aquatic habitats. P. aeruginosa may persist in the airways of individuals with cystic fibrosis for decades. The ongoing whole-genome analyses of serial isolates from cystic fibrosis patients provide the so far singular opportunity to monitor the microevolution of a bacterial pathogen during chronic infection over thousands of generations. Although the evolution in cystic fibrosis lungs is neutral overall, some pathoadaptive mutations are selected during the within-host evolutionary process. Even a single mutation may be sufficient to generate novel complex traits provided that predisposing mutational events have previously occurred in the clonal lineage.
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22
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Benz J, Meinhart A. Antibacterial effector/immunity systems: it's just the tip of the iceberg. Curr Opin Microbiol 2013; 17:1-10. [PMID: 24581686 DOI: 10.1016/j.mib.2013.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/31/2013] [Accepted: 11/09/2013] [Indexed: 01/22/2023]
Abstract
Bacteria do not live anchoretic; rather they are constantly in touch with their eukaryotic hosts and with other bacteria sharing their habitat. Therefore, bacteria have evolved sophisticated proteinaceous weapons. To harm other bacteria, they produce antibacterial effector proteins, which they either release into the environment or export via direct intercellular contact. Contact-dependent killing is mediated by two specialized secretion systems, the type V and VI secretion system, whereas contact-independent processes hijack other transport mechanisms. Regardless of the transport system, cells co-express immunity proteins to protect themselves from suicide and fratricide. In general, effector protein activities and secretion mechanisms differ between Gram-positive and Gram-negative bacteria and evidence is emerging that different effector/immunity systems act synergistically and thus extend the bacterial armory.
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Affiliation(s)
- Juliane Benz
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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