SecReT6: A web-based resource for type VI secretion systems found in bacteria

Environmental Microbiology

Volumn 17, Issue 7, 2015, Pages 2196-2202

  Li, Jun ^a   Yao, Yufeng ^b   Xu, H Howard ^c   Hao, Limin ^d   Deng, Zixin ^a   Rajakumar, Kumar ^e   Ou, Hong Yu ^a  

^a Shanghai Jiao Tong University   (China)

^b SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^c CALIFORNIA STATE UNIVERSITY   (United States)

^d People's Liberation Army   (China)

^e UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); EUKARYOTA; NEGIBACTERIA; PROKARYOTA;

BACTERIAL PROTEIN; TYPE VI SECRETION SYSTEM;

FACTUAL DATABASE; GRAM NEGATIVE BACTERIUM; INTERNET; METABOLISM; MULTIGENE FAMILY; PHYSIOLOGY; TYPE VI SECRETION SYSTEM;

BACTERIAL PROTEINS; DATABASES, FACTUAL; GRAM-NEGATIVE BACTERIA; INTERNET; MULTIGENE FAMILY; TYPE VI SECRETION SYSTEMS;

EID: 84937020664     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12794     Document Type: Article

References (41)

1. Barret, M., Egan, F., Fargier, E., Morrissey, J.P., and O'Gara, F. (2011) Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology 157: 1726-1739.
2. Barret, M., Egan, F., and O'Gara, F. (2013) Distribution and diversity of bacterial secretion systems across metagenomic datasets. Environ Microbiol Rep 5: 117-126.
3. 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.
4. Bernard, C.S., Brunet, Y.R., Gueguen, E., and Cascales, E. (2010) Nooks and crannies in type VI secretion regulation. J Bacteriol 192: 3850-3860.
5. Bleves, S., Dunger, I., Walter, M.C., Frangoulidis, D., Kastenmuller, G., Voulhoux, R., and Ruepp, A. (2014) HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res 42: D671-D676.
6. Boyer, F., Fichant, G., Berthod, J., Vandenbrouck, Y., and Attree, I. (2009) Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? BMC Genomics 10: 104.
7. Broms, J.E., Sjostedt, A., and Lavander, M. (2010) The role of the Francisella tularensis pathogenicity island in type VI secretion, intracellular survival, and modulation of host cell signaling. Front Microbiol 1: 136.
8. de Bruin, O.M., Ludu, J.S., and Nano, F.E. (2007) The Francisella pathogenicity island protein IglA localizes to the bacterial cytoplasm and is needed for intracellular growth. BMC Microbiol 7: 1.
9. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
10. Chow, J., and Mazmanian, S.K. (2010) A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe 7: 265-276.
11. Coulthurst, S.J. (2013) The type VI secretion system - a widespread and versatile cell targeting system. Res Microbiol 164: 640-654.
12. Delcher, A.L., Bratke, K.A., Powers, E.C., and Salzberg, S.L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
13. Dong, T.G., Ho, B.T., Yoder-Himes, D.R., and Mekalanos, J.J. (2013) Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae. Proc Natl Acad Sci USA 110: 2623-2628.
14. Durand, E., Cambillau, C., Cascales, E., and Journet, L. (2014) VgrG, Tae, Tle, and beyond: the versatile arsenal of Type VI secretion effectors. Trends Microbiol 22: 498-507.
15. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
16. Finn, R.D., Clements, J., and Eddy, S.R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-W37.
17. Fritsch, M.J., Trunk, K., Diniz, J.A., Guo, M., Trost, M., and Coulthurst, S.J. (2013) Proteomic identification of novel secreted antibacterial toxins of the Serratia marcescens type VI secretion system. Mol Cell Proteomics 12: 2735-2749.
18. Hood, R.D., Singh, P., Hsu, F., Guvener, T., Carl, M.A., Trinidad, R.R., etal. (2010) A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe 7: 25-37.
19. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
20. Jiang, F., Waterfield, N.R., Yang, J., Yang, G., and Jin, Q. (2014) A Pseudomonas aeruginosa type VI secretion phospholipase D effector targets both prokaryotic and eukaryotic cells. Cell Host Microbe 15: 600-610.
21. Lery, L.M., Frangeul, L., Tomas, A., Passet, V., Almeida, A.S., Bialek-Davenet, S., etal. (2014) Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor. BMC Biol 12: 41.
22. Lesic, B., Starkey, M., He, J., Hazan, R., and Rahme, L.G. (2009) Quorum sensing differentially regulates Pseudomonas aeruginosa type VI secretion locus I and homologous loci II and III, which are required for pathogenesis. Microbiology 155: 2845-2855.
23. Lossi, N.S., Manoli, E., Forster, A., Dajani, R., Pape, T., Freemont, P., and Filloux, A. (2013) The HsiB1C1 (TssB-TssC) complex of the Pseudomonas aeruginosa type VI secretion system forms a bacteriophage tail sheathlike structure. J Biol Chem 288: 7536-7548.
24. Ma, L.S., Hachani, A., Lin, J.S., Filloux, A., and Lai, E.M. (2014) Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta. Cell Host Microbe 16: 94-104.
25. 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.
26. Miyata, S.T., Bachmann, V., and Pukatzki, S. (2013) Type VI secretion system regulation as a consequence of evolutionary pressure. J Med Microbiol 62: 663-676.
27. Mougous, J.D., Cuff, M.E., Raunser, S., Shen, A., Zhou, M., Gifford, C.A., etal. (2006) A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science 312: 1526-1530.
28. Russell, A.B., Hood, R.D., Bui, N.K., LeRoux, M., Vollmer, W., and Mougous, J.D. (2011) Type VI secretion delivers bacteriolytic effectors to target cells. Nature 475: 343-347.
29. Russell, A.B., Singh, P., Brittnacher, M., Bui, N.K., Hood, R.D., Carl, M.A., etal. (2012) A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe 11: 538-549.
30. Russell, A.B., LeRoux, M., Hathazi, K., Agnello, D.M., Ishikawa, T., Wiggins, P.A., etal. (2013) Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature 496: 508-512.
31. Russell, A.B., Peterson, S.B., and Mougous, J.D. (2014a) Type VI secretion system effectors: poisons with a purpose. Nat Rev Microbiol 12: 137-148.
32. Russell, A.B., Wexler, A.G., Harding, B.N., Whitney, J.C., Bohn, A.J., Goo, Y.A., etal. (2014b) A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe 16: 227-236.
33. Salomon, D., Kinch, L.N., Trudgian, D.C., Guo, X., Klimko, J.A., Grishin, N.V., etal. (2014) Marker for type VI secretion system effectors. Proc Natl Acad Sci USA 111: 9271-9276.
34. Sana, T.G., Hachani, A., Bucior, I., Soscia, C., Garvis, S., Termine, E., etal. (2012) The second type VI secretion system of Pseudomonas aeruginosa strain PAO1 is regulated by quorum sensing and Fur and modulates internalization in epithelial cells. J Biol Chem 287: 27095-27105.
35. Shneider, M.M., Buth, S.A., Ho, B.T., Basler, M., Mekalanos, J.J., and Leiman, P.G. (2013) PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature 500: 350-353.
36. Silverman, J.M., Brunet, Y.R., Cascales, E., and Mougous, J.D. (2012) Structure and regulation of the type VI secretion system. Annu Rev Microbiol 66: 453-472.
37. Silverman, J.M., Agnello, D.M., Zheng, H., Andrews, B.T., Li, M., Catalano, C.E., etal. (2013) Haemolysin coregulated protein is an exported receptor and chaperone of type VI secretion substrates. Mol Cell 51: 584-593.
38. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., and Barton, G.J. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
39. Whitney, J.C., Chou, S., Russell, A.B., Biboy, J., Gardiner, T.E., Ferrin, M.A., etal. (2013) Identification, structure, and function of a novel type VI secretion peptidoglycan glycoside hydrolase effector-immunity pair. J Biol Chem 288: 26616-26624.
40. Whitney, J.C., Beck, C.M., Goo, Y.A., Russell, A.B., Harding, B.N., De Leon, J.A., etal. (2014) Genetically distinct pathways guide effector export through the type VI secretion system. Mol Microbiol 92: 529-542.
41. Zhou, Y., Tao, J., Yu, H., Ni, J., Zeng, L., Teng, Q., etal. (2012) Hcp family proteins secreted via the type VI secretion system coordinately regulate Escherichia coli K1 interaction with human brain microvascular endothelial cells. Infect Immun 80: 1243-1251.