T3DB: an integrated database for bacterial type III secretion system

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Wang, Yejun ^a   Huang, He ^b   Sun, Ming'an ^a   Zhang, Qing ^a   Guo, Dianjing ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^b INSTITUTE OF PATHOGEN BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EFFECTIVE COMMUNICATION; FEATURE ANALYSIS; GRAM-NEGATIVE BACTERIA; HIGH QUALITY; INTEGRATED DATABASE; INTEGRATED PLATFORM; KNOWLEDGE BASE; ORTHOLOGS; PATHOGENECITY; PREDICTION TOOLS; REGULATORY GENES; RESEARCH DATA; RESEARCH GROUPS; TYPE III SECRETION SYSTEM;

BACTERIA; COMMUNICATION; DATA INTEGRATION; GENES; PROTEINS;

RESEARCH;

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

CHAPERONE;

ARTICLE; BACTERIAL GENE; BACTERIAL SECRETION SYSTEM; BACTERIUM; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; METABOLISM; MOLECULAR GENETICS;

BACTERIA; BACTERIAL SECRETION SYSTEMS; DATABASES, GENETIC; GENES, BACTERIAL; MOLECULAR CHAPERONES; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84862198161     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-66     Document Type: Article

References (27)

1. Hueck CJ. Type III protein secretion systems in bacterial pathogens of animals and pants. Microbiol Mol Biol Rev 1998, 62(2):379-433. 98920, 9618447.
2. Ghosp P. Process of protein transport by the type III secretion system. Microbiol Mol Biol Rev 2004, 68(4):771-795. 10.1128/MMBR.68.4.771-795.2004, 539011, 15590783.
3. Viprey V, Del Greco A, Golinowski W, Broughton WJ, Perret X. Symbiotic implications of type III protein secretion machinery in Rhizobium. Mol Microbiol 1998, 28(6):1381-1389. 10.1046/j.1365-2958.1998.00920.x, 9680225.
4. Marie C, Broughton WJ, Deakin WJ. Rhizobium type III secretion systems: legume charmers or alarmers?. Curr Opin Plant Biol 2001, 4(4):336-342. 10.1016/S1369-5266(00)00182-5, 11418344.
5. Kuhle V, Hensel M. Cellular microbiology of intracellular Salmonella enterica: functions of the type III secretion system encoded by Salmonella pathogenicity island 2. Cell Mol Life Sci 2004, 61(22):2812-2826. 10.1007/s00018-004-4248-z, 15558211.
6. Sun GW, Gan YH. Unraveling type III secretion systems in the highly versatile Burkholderia pseudomallei. Trends Microbiol 2010, 18(12):561-568. 10.1016/j.tim.2010.09.002, 20951592.
7. Lara-Tejero M, et al. A sorting platform determines the order of protein secretion in bacterial type III systems. Science 2011, 331:1188-1191. 10.1126/science.1201476, 21292939.
8. Tree JJ, et al. Controlling injection: regulation of type III secretion in enterohaemorrhagic Escherichia coli. Trends Microbiol 2009, 17:361-370. 10.1016/j.tim.2009.06.001, 19660954.
9. Ogawa M, et al. The versatility of Shigella effectors. Nat Rev Microbiol 2008, 6:11-16. 10.1038/nrmicro1814, 18059288.
10. Shao F. Biochemical functions of Yersinia type III effectors. Curr Opin Microbiol 2008, 11:21-29. 10.1016/j.mib.2008.01.005, 18299249.
11. Hauser AR. The type III secretion system of Pseudomonas aeruginosa: infection by injection. Nat Rev Microbiol 2009, 7:654-665. 10.1038/nrmicro2199, 2766515, 19680249.
12. Kay S, Bonas U. How Xanthomonas type III effectors manipulate the host plant. Curr Opin Microbiol 2009, 12:37-43. 10.1016/j.mib.2008.12.006, 19168386.
13. Pallen MJ, et al. Bioinformatics, genomics, and evolution of non-flagellar type-III secretion systems: a Darwinian perspective. FEMS Microbiol Rev 2005, 29:201-229. 10.1016/j.femsre.2005.01.001, 15808742.
14. Desvaux M, et al. Type III secretion: what's in a name?. Trends Microbiol 2006, 14:157-160. 10.1016/j.tim.2006.02.009, 16533600.
15. Tay DM, et al. T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. BMC Bioinformatics 2010, 11(Suppl 7):S4. 10.1186/1471-2105-11-S7-S4, 3040530, 21210983.
16. Jehl MA, et al. Effective-a database of predicted secreted bacterial proteins. Nucleic Acids Res 2011, 39:D591-D595. 10.1093/nar/gkq1154, 3013723, 21071416.
17. Wang Y, et al. High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 2011, 27:777-784. 10.1093/bioinformatics/btr021, 21233168.
18. Arnold R, et al. Sequence-based prediction of Type III Secreted proteins. PLoS Pathog 2009, 5:e1000376. 10.1371/journal.ppat.1000376, 2669295, 19390696.
19. Lower M, Schneider G. Prediction of Type III Secretion signals in genomes of Gram-negative bacteria. PLoS One 2009, 4:e5917. 10.1371/journal.pone.0005917, 2690842, 19526054.
20. Samudrala R, et al. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for Type III Secretion Systems. PLoS Pathog 2009, 5:e1000375. 10.1371/journal.ppat.1000375, 2668754, 19390620.
21. Garrity GM, et al. Bergey's Manual of Systematic Bacteriology 2005, Published by Springer, New York, 2.
22. He SY, et al. Type III protein secretion mechanism in mammalian and plant pathogens. Biochim Biophys Acta 2004, 1694:181-206. 10.1016/j.bbamcr.2004.03.011, 15546666.
23. Fu Y, Galan JE. The Salmonella Typhimurium phosphatase SptP is translocated into host cells and disrupts the actin cytoskeleton. Mol Microbiol 1998, 27(2):359-368. 10.1046/j.1365-2958.1998.00684.x, 9484891.
24. Black DS, Bliska JB. The RhoGAP activity of Yersinia pseudotuberculosis cytotoxin YopE is required for antiphagocytic function and virulence. Mol Microbiol 2000, 37(3):515-527.
25. Orchard RC, Alto NM. Mimicking GEFs: a common theme for bacterial pathogens. Cell Microbiol 2012, 14(1):10-18. 10.1111/j.1462-5822.2011.01703.x, 21951829.
26. Kaneko T, et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 2002, 9(6):189-197. 10.1093/dnares/9.6.189, 12597275.
27. Krause A, Doerfel A, Gottfert M. Mutational and transcriptional analysis of the type III secretion of Bradyrhizobium japonicum. MPMI 2002, 15(12):1228-1235. 10.1094/MPMI.2002.15.12.1228, 12481995.