Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Sato, Yoshiharu ^a   Takaya, Akiko ^a   Yamamoto, Tomoko ^a  

^a CHIBA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; DOMAIN DISTRIBUTION; EXPERIMENTAL VERIFICATION; GRAM-NEGATIVE BACTERIA; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SUBSTRATE SPECIFICITY; TYPE III SECRETION SYSTEM; VIRULENCE PROTEINS;

DISCRIMINANT ANALYSIS; GENES; OPTIMIZATION; SALMONELLA; SUPPORT VECTOR MACHINES; TOOLS;

FORECASTING;

NEGIBACTERIA; PSEUDOMONAS SYRINGAE; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM;

BACTERIAL PROTEIN; VIRULENCE FACTOR;

ARTICLE; BACTERIAL SECRETION SYSTEM; CHEMISTRY; COMPUTER PROGRAM; DNA MICROARRAY; GRAM NEGATIVE BACTERIUM; META ANALYSIS (TOPIC); METABOLISM; PATHOGENICITY; PROTEIN TRANSPORT; SECRETION; SUPPORT VECTOR MACHINE; VIRULENCE;

BACTERIAL PROTEINS; BACTERIAL SECRETION SYSTEMS; GRAM-NEGATIVE BACTERIA; META-ANALYSIS AS TOPIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN TRANSPORT; SOFTWARE; SUPPORT VECTOR MACHINES; VIRULENCE; VIRULENCE FACTORS;

EID: 81055131616     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-442     Document Type: Article

References (44)

1. Durand E, Verger D, Rego AT, Chandran V, Meng G, Fronzes R, Waksman G. Structural biology of bacterial secretion systems in gram-negative pathogens--potential for new drug targets. Infect Disord Drug Targets 2009, 9(5):518-547. 10.2174/187152609789105722, 19594425.
2. Saier MH. Protein secretion and membrane insertion systems in gram-negative bacteria. J Membr Biol 2006, 214(2):75-90. 10.1007/s00232-006-0049-7, 17546510.
3. Filloux A, Hachani A, Bleves S. The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology 2008, 154(Pt 6):1570-1583.
4. Petnicki-Ocwieja T, Schneider DJ, Tam VC, Chancey ST, Shan L, Jamir Y, Schechter LM, Janes MD, Buell CR, Tang X, Collmer A, Alfano JR. Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 2002, 99(11):7652-7657. 10.1073/pnas.112183899, 124312, 12032338.
5. Cunnac S, Lindeberg M, Collmer A. Pseudomonas syringae type III secretion system effectors: repertoires in search of functions. Curr Opin Microbiol 2009, 12(1):53-60. 10.1016/j.mib.2008.12.003, 19168384.
6. Schechter LM, Vencato M, Jordan KL, Schneider SE, Schneider DJ, Collmer A. Multiple approaches to a complete inventory of Pseudomonas syringae pv. tomato DC3000 type III secretion system effector proteins. Mol Plant Microbe Interact 2006, 19(11):1180-1192. 10.1094/MPMI-19-1180, 17073301.
7. Tobe T, Beatson SA, Taniguchi H, Abe H, Bailey CM, Fivian A, Younis R, Matthews S, Marches O, Frankel G, Hayashi T, Pallen MJ. An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci USA 2006, 103(40):14941-14946. 10.1073/pnas.0604891103, 1595455, 16990433.
8. Deng W, de Hoog CL, Yu HB, Li Y, Croxen MA, Thomas NA, Puente JL, Foster LJ, Finlay BB. A comprehensive proteomic analysis of the type III secretome of Citrobacter rodentium. J Biol Chem 2010, 285(9):6790-6800. 10.1074/jbc.M109.086603, 2825473, 20034934.
9. Geddes K, Worley M, Niemann G, Heffron F. Identification of new secreted effectors in Salmonella enterica serovar Typhimurium. Infect Immun 2005, 73(10):6260-6271. 10.1128/IAI.73.10.6260-6271.2005, 1230965, 16177297.
10. Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD, Adkins JN, Heffron F. Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants. Infect Immun 2011, 79(1):33-43. 10.1128/IAI.00771-10, 3019877, 20974834.
11. Yoon H, Ansong C, Adkins JN, Heffron F. Discovery of Salmonella Virulence Factors Translocated via Outer Membrane Vesicles to Murine Macrophages. Infect Immun 2011, 79(6):2182-2192. 10.1128/IAI.01277-10, 3125828, 21464085.
12. Vinatzer BA, Jelenska J, Greenberg JT. Bioinformatics correctly identifies many type III secretion substrates in the plant pathogen Pseudomonas syringae and the biocontrol isolate P. fluorescens SBW25. Mol Plant Microbe Interact 2005, 18(8):877-888. 10.1094/MPMI-18-0877, 16134900.
13. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
14. Eswarappa SM, Janice J, Balasundaram SV, Dixit NM, Chakravortty D. Host-specificity of Salmonella enterica serovar Gallinarum: insights from comparative genomics. Infect Genet Evol 2009, 9(4):468-473. 10.1016/j.meegid.2009.01.004, 19454277.
15. Wang Y, Zhang Q, Sun MA, Guo D. High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 2011, 27(6):777-784. 10.1093/bioinformatics/btr021, 21233168.
16. Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T. Sequence-based prediction of type III secreted proteins. PLoS Pathog 2009, 5(4):e1000376. 10.1371/journal.ppat.1000376, 2669295, 19390696.
17. Samudrala R, Heffron F, McDermott JE. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog 2009, 5(4):e1000375. 10.1371/journal.ppat.1000375, 2668754, 19390620.
18. Yang Y, Zhao J, Morgan RL, Ma W, Jiang T. Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinformatics 2010, 11(Suppl 1):S47. 10.1186/1471-2105-11-S1-S47, 3009519, 20122221.
19. Lower M, Schneider G. Prediction of type III secretion signals in genomes of gram-negative bacteria. PLoS One 2009, 4(6):e5917. 10.1371/journal.pone.0005917, 2690842, 19526054.
20. Kim JG, Park BK, Yoo CH, Jeon E, Oh J, Hwang I. Characterization of the Xanthomonas axonopodis pv. glycines Hrp pathogenicity island. J Bacteriol 2003, 185(10):3155-3166. 10.1128/JB.185.10.3155-3166.2003, 154065, 12730176.
21. Burstein D, Zusman T, Degtyar E, Viner R, Segal G, Pupko T. Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog 2009, 5(7):e1000508. 10.1371/journal.ppat.1000508, 2701608, 19593377.
22. Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15(3):1281-1295. 10.1093/nar/15.3.1281, 340524, 3547335.
23. Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 1982, 10(22):7055-7074. 10.1093/nar/10.22.7055, 326988, 6760125.
24. Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 1986, 24(1-2):28-38. 10.1007/BF02099948, 3104616.
25. Power PM, Jones RA, Beacham IR, Bucholtz C, Jennings MP. Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli. Biochem Biophys Res Commun 2004, 322(3):1038-1044. 10.1016/j.bbrc.2004.08.022, 15336569.
26. Li YD, Li YQ, Chen JS, Dong HJ, Guan WJ, Zhou H. Whole genome analysis of non-optimal codon usage in secretory signal sequences of Streptomyces coelicolor. Biosystems 2006, 85(3):225-230. 10.1016/j.biosystems.2006.02.006, 16644095.
27. Shimizu K, Hirose S, Noguchi T. POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics 2007, 23(17):2337-2338. 10.1093/bioinformatics/btm330, 17599940.
28. Joly DL, Feau N, Tanguay P, Hamelin RC. Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.). BMC Genomics 2010, 11:422. 10.1186/1471-2164-11-422, 2996950, 20615251.
29. Ma W, Dong FF, Stavrinides J, Guttman DS. Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race. PLoS Genet 2006, 2(12):e209. 10.1371/journal.pgen.0020209, 1713259, 17194219.
30. Buchan DW, Ward SM, Lobley AE, Nugent TC, Bryson K, Jones DT. Protein annotation and modelling servers at University College London. Nucleic Acids Res 38(Web Server):W563-568.
31. Ouali M, King RD. Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000, 9(6):1162-1176. 10.1110/ps.9.6.1162, 2144653, 10892809.
32. McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16(4):404-405. 10.1093/bioinformatics/16.4.404, 10869041.
33. Buchko GW, Niemann G, Baker ES, Belov ME, Smith RD, Heffron F, Adkins JN, McDermott JE. A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins. Mol Biosyst 2010, 6(12):2448-2458. 10.1039/c0mb00097c, 20877914.
34. Kampenusa I, Zikmanis P. Distinguishable codon usage and amino acid composition patterns among substrates of leaderless secretory pathways from proteobacteria. Appl Microbiol Biotechnol 2010, 86(1):285-293. 10.1007/s00253-009-2423-8, 20107986.
35. Subtil A, Delevoye C, Balana ME, Tastevin L, Perrinet S, Dautry-Varsat A. A directed screen for chlamydial proteins secreted by a type III mechanism identifies a translocated protein and numerous other new candidates. Mol Microbiol 2005, 56(6):1636-1647. 10.1111/j.1365-2958.2005.04647.x, 15916612.
36. Takaya A, Suzuki M, Matsui H, Tomoyasu T, Sashinami H, Nakane A, Yamamoto T. Lon, a stress-induced ATP-dependent protease, is critically important for systemic Salmonella enterica serovar typhimurium infection of mice. Infect Immun 2003, 71(2):690-696. 10.1128/IAI.71.2.690-696.2003, 145356, 12540547.
37. Takaya A, Tomoyasu T, Tokumitsu A, Morioka M, Yamamoto T. The ATP-dependent lon protease of Salmonella enterica serovar Typhimurium regulates invasion and expression of genes carried on Salmonella pathogenicity island 1. J Bacteriol 2002, 184(1):224-232. 10.1128/JB.184.1.224-232.2002, 134781, 11741864.
38. Cirillo DM, Valdivia RH, Monack DM, Falkow S. Macrophage-dependent induction of the Salmonella pathogenicity island 2 type III secretion system and its role in intracellular survival. Mol Microbiol 1998, 30(1):175-188. 10.1046/j.1365-2958.1998.01048.x, 9786194.
39. McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F. Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infect Immun 2011, 79(1):23-32. 10.1128/IAI.00537-10, 3019878, 20974833.
40. Kanehisa M. The KEGG database. Novartis Found Symp 2002, 247:91-101. discussion 101-103, 119-128, 244-152.
41. Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, Hochstrasser DF. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 1999, 112:531-552.
42. Olson SA. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 2002, 3(1):87-91. 10.1093/bib/3.1.87, 12002227.
43. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555-556.
44. Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics 2004, 20(4):586-587. 10.1093/bioinformatics/btg461, 14990457.