SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems.

Type VI Secretion Systems / genetics Acinetobacter baumannii / genetics Bacterial Proteins / genetics Genome, Bacterial
Acinetobacter baumannii T6SS-related protein Type VI Secretion System database prediction

Journal

Science China. Life sciences
ISSN: 1869-1889
Titre abrégé: Sci China Life Sci
Pays: China
ID NLM: 101529880

Informations de publication

Date de publication:
03 2023
Historique:
received: 07 04 2022
accepted: 27 07 2022
pubmed: 9 11 2022
medline: 28 3 2023
entrez: 8 11 2022
Statut: ppublish

Résumé

Type VI Secretion System (T6SS) plays significant roles in microbial activities via injecting effectors into adjacent cells or environments. T6SS increasingly gained attention due to its important influence on pathogenesis, microbial competition, etc. T6SS-associated research is explosively expanding on numerous grounds that call for an efficient resource. The SecReT6 version 3 provides comprehensive information on T6SS and the interactions between T6SS and T6SS-related proteins such as T6SS regulators and T6SS effectors. To assist T6SS researches like microbial competition and regulatory mechanisms, SecReT6 v3 developed online tools for detection and analysis of T6SS and T6SS-related proteins and estimation of T6SS-dependent killing risk. We have identified a novel T6SS regulator and T6SS-dependent killing capacity in Acinetobacter baumannii clinical isolates with the aid of SecReT6 v3. 17,212 T6SSs and plentiful T6SS-related proteins in 26,573 bacterial complete genomes were also detected, analyzed and incorporated into the database. The database is freely available at https://bioinfo-mml.sjtu.edu.cn/SecReT6/ .

Identifiants

DOI: 10.1007/s11427-022-2172-x PMID: 36346548
pubmed: 36346548
doi: 10.1007/s11427-022-2172-x
pii: 10.1007/s11427-022-2172-x
doi:

Substances chimiques

Type VI Secretion Systems 0
Bacterial Proteins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

626-634

Informations de copyright

© 2022. Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.

Références

Allsopp, L.P., Wood, T.E., Howard, S.A., Maggiorelli, F., Nolan, L.M., Wettstadt, S., and Filloux, A. (2017). RsmA and AmrZ orchestrate the assembly of all three type VI secretion systems in Pseudomonas aeruginosa. Proc Natl Acad Sci USA 114, 7707–7712.
pubmed: 28673999 pmcid: 5530658 doi: 10.1073/pnas.1700286114
Almagro Armenteros, J.J., Tsirigos, K.D., Sønderby, C.K., Petersen, T.N., Winther, O., Brunak, S., von Heijne, G., and Nielsen, H. (2019). SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 37, 420–423.
pubmed: 30778233 doi: 10.1038/s41587-019-0036-z
An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G.I., Lithgow, T., et al. (2017). SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. Sci Rep 7, 41031.
pubmed: 28112271 pmcid: 5253721 doi: 10.1038/srep41031
Basler, M., Ho, B.T., and Mekalanos, J.J. (2013). Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell 152, 884–894.
pubmed: 23415234 pmcid: 3616380 doi: 10.1016/j.cell.2013.01.042
Bernal, P., Furniss, R.C.D., Fecht, S., Leung, R.C.Y., Spiga, L., Mavridou, D.A.I., and Filloux, A. (2021). A novel stabilization mechanism for the type VI secretion system sheath. Proc Natl Acad Sci USA 118, e2008500118.
pubmed: 33558227 pmcid: 7896307 doi: 10.1073/pnas.2008500118
Böck, D., Medeiros, J.M., Tsao, H.F., Penz, T., Weiss, G.L., Aistleitner, K., Horn, M., and Pilhofer, M. (2017). In situ architecture, function, and evolution of a contractile injection system. Science 357, 713–717.
pubmed: 28818949 pmcid: 6485382 doi: 10.1126/science.aan7904
Bodenhofer, U., Bonatesta, E., Horejš-Kainrath, C., and Hochreiter, S. (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31, btv494.
doi: 10.1093/bioinformatics/btv494
Bondage, D.D., Lin, J.S., Ma, L.S., Kuo, C.H., and Lai, E.M. (2016). VgrG C terminus confers the type VI effector transport specificity and is required for binding with PAAR and adaptor-effector complex. Proc Natl Acad Sci USA 113, E3931–E3940.
pubmed: 27313214 pmcid: 4941472 doi: 10.1073/pnas.1600428113
Borgeaud, S., Metzger, L.C., Scrignari, T., and Blokesch, M. (2015). The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science 347, 63–67.
pubmed: 25554784 doi: 10.1126/science.1260064
Burkinshaw, B.J., Liang, X., Wong, M., Le, A.N.H., Lam, L., and Dong, T. G. (2018). A type VI secretion system effector delivery mechanism dependent on PAAR and a chaperone-co-chaperone complex. Nat Microbiol 3, 632–640.
pubmed: 29632369 doi: 10.1038/s41564-018-0144-4
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: architecture and applications. BMC BioInf 10, 421.
doi: 10.1186/1471-2105-10-421
Chen, L., Zou, Y., She, P., and Wu, Y. (2015). Composition, function, and regulation of T6SS in Pseudomonas aeruginosa. Microbiol Res 172, 19–25.
pubmed: 25721475 doi: 10.1016/j.micres.2015.01.004
Coyne, M.J., and Comstock, L.E. (2019). Type VI secretion systems and the gut microbiota. Microbiol Spectr 7, PSIB-0009-2018.
doi: 10.1128/microbiolspec.PSIB-0009-2018
Eichinger, V., Nussbaumer, T., Platzer, A., Jehl, M.A., Arnold, R., and Rattei, T. (2016). EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Nucleic Acids Res 44, D669–D674.
pubmed: 26590402 doi: 10.1093/nar/gkv1269
Finn, R.D., Clements, J., and Eddy, S.R. (2011). HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39, W29–W37.
pubmed: 21593126 pmcid: 3125773 doi: 10.1093/nar/gkr367
Fridman, C.M., Keppel, K., Gerlic, M., Bosis, E., and Salomon, D. (2020). A comparative genomics methodology reveals a widespread family of membrane-disrupting T6SS effectors. Nat Commun 11, 1085.
pubmed: 32109231 pmcid: 7046647 doi: 10.1038/s41467-020-14951-4
Fu, Y., Ho, B.T., and Mekalanos, J.J. (2018). Tracking Vibrio cholerae cell-cell interactions during infection reveals bacterial population dynamics within intestinal microenvironments. Cell Host Microbe 23, 274–281.e2.
pubmed: 29398650 pmcid: 6031135 doi: 10.1016/j.chom.2017.12.006
Hersch, S.J., Watanabe, N., Stietz, M.S., Manera, K., Kamal, F., Burkinshaw, B., Lam, L., Pun, A., Li, M., Savchenko, A., et al. (2020). Envelope stress responses defend against type six secretion system attacks independently of immunity proteins. Nat Microbiol 5, 706–714.
pubmed: 32094588 pmcid: 7190449 doi: 10.1038/s41564-020-0672-6
Ho, B.T., Basler, M., and Mekalanos, J.J. (2013). Type 6 secretion systemmediated immunity to type 4 secretion system-mediated gene transfer. Science 342, 250–253.
pubmed: 24115441 pmcid: 4034461 doi: 10.1126/science.1243745
Joshi, A., Kostiuk, B., Rogers, A., Teschler, J., Pukatzki, S., and Yildiz, F. H. (2017). Rules of engagement: the type VI secretion system in Vibrio cholerae. Trends Microbiol 25, 267–279.
pubmed: 28027803 doi: 10.1016/j.tim.2016.12.003
Jurėnas, D., and Journet, L. (2021). Activity, delivery, and diversity of Type VI secretion effectors. Mol Microbiol 115, 383–394.
pubmed: 33217073 doi: 10.1111/mmi.14648
Katoh, K., and Standley, D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30, 772–780.
pubmed: 23329690 pmcid: 3603318 doi: 10.1093/molbev/mst010
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.L. (2001). Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305, 567–580.
pubmed: 11152613 doi: 10.1006/jmbi.2000.4315
Le, N.H., Pinedo, V., Lopez, J., Cava, F., and Feldman, M.F. (2021). Killing of Gram-negative and Gram-positive bacteria by a bifunctional cell wall-targeting T6SS effector. Proc Natl Acad Sci USA 118, e2106555118.
pubmed: 34588306 pmcid: 8501793 doi: 10.1073/pnas.2106555118
Li, J., Yao, Y., Xu, H.H., Hao, L., Deng, Z., Rajakumar, K., and Ou, H.Y. (2015). SecReT6: a web-based resource for type VI secretion systems found in bacteria. Environ Microbiol 17, 2196–2202.
pubmed: 25640659 doi: 10.1111/1462-2920.12794
Liang, X., Moore, R., Wilton, M., Wong, M.J.Q., Lam, L., and Dong, T.G. (2015). Identification of divergent type VI secretion effectors using a conserved chaperone domain. Proc Natl Acad Sci USA 112, 9106–9111.
pubmed: 26150500 pmcid: 4517263 doi: 10.1073/pnas.1505317112
Lin, H.H., Filloux, A., and Lai, E.M. (2020). Role of recipient susceptibility factors during contact-dependent interbacterial competition. Front Microbiol 11, 603652.
pubmed: 33281802 pmcid: 7690452 doi: 10.3389/fmicb.2020.603652
Medema, M.H., Takano, E., and Breitling, R. (2013). Detecting sequence homology at the gene cluster level with MultiGeneBlast. Mol Biol Evol 30, 1218–1223.
pubmed: 23412913 pmcid: 3670737 doi: 10.1093/molbev/mst025
Mok, B.Y., de Moraes, M.H., Zeng, J., Bosch, D.E., Kotrys, A.V., Raguram, A., Hsu, F.S., Radey, M.C., Peterson, S.B., Mootha, V.K., et al. (2020). A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637.
pubmed: 32641830 pmcid: 7381381 doi: 10.1038/s41586-020-2477-4
Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490.
pubmed: 20224823 pmcid: 2835736 doi: 10.1371/journal.pone.0009490
Quentin, D., Ahmad, S., Shanthamoorthy, P., Mougous, J.D., Whitney, J.C., and Raunser, S. (2018). Mechanism of loading and translocation of type VI secretion system effector Tse6. Nat Microbiol 3, 1142–1152.
pubmed: 30177742 pmcid: 6488228 doi: 10.1038/s41564-018-0238-z
Russell, A.B., Wexler, A.G., Harding, B.N., Whitney, J.C., Bohn, A.J., Goo, Y.A., Tran, B.Q., Barry, N.A., Zheng, H., Peterson, S.B., et al. (2014). A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe 16, 227–236.
pubmed: 25070807 pmcid: 4136423 doi: 10.1016/j.chom.2014.07.007
Si, M., Zhao, C., Burkinshaw, B., Zhang, B., Wei, D., Wang, Y., Dong, T. G., and Shen, X. (2017). Manganese scavenging and oxidative stress response mediated by type VI secretion system in Burkholderia thailandensis. Proc Natl Acad Sci USA 114, E2233–E2242.
pubmed: 28242693 pmcid: 5358365 doi: 10.1073/pnas.1614902114
Sievers, F., and Higgins, D.G. (2018). Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 27, 135–145.
pubmed: 28884485 doi: 10.1002/pro.3290
Storey, D., McNally, A., Åstrand, M., Sa-Pessoa Graca Santos, J., Rodriguez-Escudero, I., Elmore, B., Palacios, L., Marshall, H., Hobley, L., Molina, M., et al. (2020). Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent. PLoS Pathog 16, e1007969.
pubmed: 32191774 pmcid: 7108748 doi: 10.1371/journal.ppat.1007969
Sullivan, M.J., Petty, N.K., and Beatson, S.A. (2011). Easyfig: a genome comparison visualizer. Bioinformatics 27, 1009–1010.
pubmed: 21278367 pmcid: 3065679 doi: 10.1093/bioinformatics/btr039
Vettiger, A., Winter, J., Lin, L., and Basler, M. (2017). The type VI secretion system sheath assembles at the end distal from the membrane anchor. Nat Commun 8, 16088.
pubmed: 28703218 pmcid: 5511345 doi: 10.1038/ncomms16088
Wang, J., Brodmann, M., and Basler, M. (2019a). Assembly and subcellular localization of bacterial type VI secretion systems. Annu Rev Microbiol 73, 621–638.
pubmed: 31226022 doi: 10.1146/annurev-micro-020518-115420
Wang, J., Li, J., Hou, Y., Dai, W., Xie, R., Marquez-Lago, T.T., Leier, A., Zhou, T., Torres, V., Hay, I., et al. (2021). BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. Nucleic Acids Res 49, D651–D659.
pubmed: 33084862 doi: 10.1093/nar/gkaa899
Wang, J., Yang, B., Leier, A., Marquez-Lago, T.T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K.C., Strugnell, R.A., et al. (2018). Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinformatics 34, 2546–2555.
pubmed: 29547915 pmcid: 6061801 doi: 10.1093/bioinformatics/bty155
Wang, Y., Wang, Z., Chen, Y., Hua, X., Yu, Y., and Ji, Q. (2019b). A highly efficient CRISPR-Cas9-based genome engineering platform in Acinetobacter baumannii to understand the H
pubmed: 31548010 doi: 10.1016/j.chembiol.2019.09.003
Weber, B.S., Hennon, S.W., Wright, M.S., Scott, N.E., de Berardinis, V., Foster, L.J., Ayala, J.A., Adams, M.D., and Feldman, M.F. (2016). Genetic dissection of the type VI secretion system in Acinetobacter and identification of a novel peptidoglycan hydrolase, TagX, required for its biogenesis. mBio 7, e01253–16.
pubmed: 27729508 pmcid: 5061870 doi: 10.1128/mBio.01253-16
Yadav, S.K., Magotra, A., Ghosh, S., Krishnan, A., Pradhan, A., Kumar, R., Das, J., Sharma, M., and Jha, G. (2021). Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors. EMBO Rep 22, e53112.
pubmed: 34060187 pmcid: 8183404 doi: 10.15252/embr.202153112
Yu, G., Lam, T.T.Y., Zhu, H., and Guan, Y. (2018). Two methods for mapping and visualizing associated data on phylogeny using Ggtree. Mol Biol Evol 35, 3041–3043.
pubmed: 30351396 pmcid: 6278858 doi: 10.1093/molbev/msy194
Zhao, W., Caro, F., Robins, W., and Mekalanos, J.J. (2018). Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. Science 359, 210–213.
pubmed: 29326272 pmcid: 8010019 doi: 10.1126/science.aap8775
Zhu, L., Xu, L., Wang, C., Li, C., Li, M., Liu, Q., Wang, X., Yang, W., Pan, D., Hu, L., et al. (2021). T6SS translocates a micropeptide to suppress STING-mediated innate immunity by sequestering manganese. Proc Natl Acad Sci USA 118, e2103526118.
pubmed: 34625471 pmcid: 8545469 doi: 10.1073/pnas.2103526118

Auteurs

Jianfeng Zhang (J)

State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Intensive Care Unit, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.

Jiahao Guan (J)

State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Meng Wang (M)

State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Gang Li (G)

Department of Laboratory Medicine, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 201500, China.

Marko Djordjevic (M)

Quantitative Biology Group, Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia.

Cui Tai (C)

State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Hui Wang (H)

State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.

Zixin Deng (Z)

State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Zhaoyan Chen (Z)

Intensive Care Unit, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China. 24707542@qq.com.

Hong-Yu Ou (HY)

State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. hyou@sjtu.edu.cn.
Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. hyou@sjtu.edu.cn.

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Classifications MeSH

questionsmedicales.fr › Structures macromoléculaires › Complexes multiprotéiques › Systèmes de translocation des protéines › Systèmes bactériens de sécrétion › Systèmes de sécrétion de type VI › SecReT6 update: a comprehensive resource of...
questionsmedicales.fr › Bactéries › Proteobacteria › Gammaproteobacteria › Moraxellaceae › Acinetobacter › Acinetobacter baumannii › SecReT6 update: a comprehensive resource of...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › SecReT6 update: a comprehensive resource of...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › SecReT6 update: a comprehensive resource of...