T3_MM: A Markov Model Effectively Classifies Bacterial Type III Secretion Signals

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Wang, Yejun ^a,c   Sun, Ming'an ^b   Bao, Hongxia ^a   White, Aaron P ^c  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; CYSTEINE; LEUCINE; AMINO ACID; BACTERIAL PROTEIN;

ACCURACY; AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL STRAIN; CHLAMYDIA; COMPUTER PROGRAM; CONTROLLED STUDY; ESCHERICHIA; GENERALIZED LINEAR MODEL; HIDDEN MARKOV MODEL; MACHINE LEARNING; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROBABILITY; PROTEIN LOCALIZATION; PSEUDOMONAS; RALSTONIA; RANDOM FOREST; RECEIVER OPERATING CHARACTERISTIC; RHIZOBIACEAE; SALMONELLA; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; SUPPORT VECTOR MACHINE; TYPE III SECRETION SYSTEM; VALIDATION PROCESS; XANTHOMONAS; YERSINIA; ALGORITHM; BACTERIAL SECRETION SYSTEM; CHEMISTRY; CYTOPLASM; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; PROTEIN TRANSPORT; REPRODUCIBILITY; STATISTICAL MODEL;

ALGORITHMS; AMINO ACIDS; BACTERIAL PROTEINS; BACTERIAL SECRETION SYSTEMS; CYTOPLASM; GENE EXPRESSION REGULATION, BACTERIAL; MARKOV CHAINS; MODELS, STATISTICAL; PROBABILITY; PROTEIN TRANSPORT; RALSTONIA; REPRODUCIBILITY OF RESULTS; SALMONELLA; SOFTWARE;

EID: 84874637878     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058173     Document Type: Article

References (30)

1. Hueck CJ (1998) Type III protein secretion systems in bacterial pathogens of animals and plants. Mol. Biol. Rev., 62, 379-433.
2. Wang Y, Huang H, Sun M, Zhang Q, Guo D, (2012) T3DB: an integrated database for bacterial Type III Secretion System. BMC Bioinformatics 13: 66.
3. Enninga J, Rosenshine I (2009) Imaging the assembly, structure and activity of type III secretion systems.Cell Microbiol., 11, 1462-1470.
4. Izoré T, Job V, Dessen A (2011) Biogenesis, regulation, and targeting of the type III secretion system. Structure, 19, 603-12.
5. Lindeberg M, Collmer A (2009) Gene Ontology for type III effectors: capturing processes at the host-pathogen interface. Trends Microbiol., 17, 304-11.
6. Feng F, Zhou JM (2012) Plant-bacterial pathogen interactions mediated by type III effectors. Curr Opin Plant Biol., 15, 469-476.
7. Galán JE, Wolf-Watz H (2006) Protein delivery into eukaryotic cells by type III secretion machines. Nature, 444, 567-73.
8. Karavolos MH, Roe AJ, Wilson M, Henderson J, Lee JJ, et al. (2005) Type III secretion of the Salmonella effector protein SopE is mediated via an N-terminal amino acid signal and not an mRNA sequence. J. Bacteriol., 187, 1559-1567.
9. Lloyd SA, Norman M, Rosqvist R, Wolf-Watz H (2001) Yersinia YopE is targeted for type III secretion by N-terminal, not mRNA, signals. Mol. Microbiol., 39, 520-531.
10. Lloyd SA, Sjöström M, Andersson S, Wolf-Watz H (2002) Molecular characterization of type III secretion signals via analysis of synthetic N-terminal amino acid sequences. Mol. Microbiol., 43, 51-59.
11. Rüssmann H, Kubori T, Sauer J, Galán JE (2002) Molecular and functional analysis of the type III secretion signal of the Salmonella enterica InvJ protein. Mol. Microbiol., 46, 769-779.
12. Stebbins CE, Galán JE (2001) Maintenance of an unfolded polypeptide by a cognate chaperone in bacterial type III secretion. Nature, 414, 77-81.
13. Wang Y, Hou Y, Huang H, Liu GR, White AP, et al. (2008) Two oral HBx vaccines delivered by live attenuated Salmonella: both eliciting effective anti-tumor immunity. Cancer Lett, 263, 67-76.
14. Subtil A, Delevoye C, Balañá ME, Tastevin L, Perrinet S, et al. (2005) A directed screen for chlamydial proteins secreted by a type III mechanism identifies a translocated protein and numerous other new candidates. Mol. Microbiol., 56,1636-47.
15. Arnold R, Brandmaiers, Kleie F, Tischler P, Heinz E, et al. (2009) Sequence-based prediction of type III secreted proteins. PLoS pathogens, 5, e1000376.
16. Arnold R, Jehl A, Rattei T (2010) Targeting effectors: the molecular recognition of Type III secreted proteins. Microbes Infect., 12, 346-358.
17. Wang Y, Zhang Q, Sun MA, Guo D (2011) High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics, 2011, 27, 777-84.
18. Löwer M, Schneider G (2009) Prediction of type III secretion signals in genomes of gram-negative bacteria. PloS one, 4, e5917.
19. Samudrala R, Heffron F, McDermott JE (2009) Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS pathogens, 5, e1000375.
20. Yang Y, Zhao J, Morgan RL, Ma W, Jiang T (2010) Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinformatics, 11 Suppl 1, S47.
21. Mukaihara T, Tamura N, Iwabuchi M (2010) Genome-wide identification of a large repertoire of Ralstonia solanacearum type III effector proteins by a new functional screen. MPMI, 23, 251-262.
22. Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS, et al. (2011) Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates. PLoS Pathog 7(7): e1002132.
23. Spanò S, Liu X, Galán JE, (2011) Proteolytic targeting of Rab29 by an effector protein distinguishes the intracellular compartments of human-adapted and broad-host Salmonella. Proc Natl Acad Sci U S A. 108: 18418-18423.
24. Spanò S, Galán JE, (2012) A Rab32-dependent pathway contributes to Salmonella typhi host restriction. Science 338: 960-963.
25. Jarvik T, Smillie C, GroismanEA, Ochman H (2010) Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome. J. Bacteriol., 192 (2), 560-7.
26. Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, et al. (2012) The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc. Natl. Acad. Sci. U S A., 109 (20), E1277-86.
27. Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, et al. (2011) Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathog., 7(8), e1002191.
28. Burnal-Bayard J, Cardenal-Munoz E, Ramos-Morales F (2010) The Salmonella type III secretion effector, Salmonella leucine-rich repeat protein (SlrP), targets the human chaperone ERdj3. J Bio Chem., 285(21), 16360-16368.
29. Kim JH, Lee J, Oh B, Kimm K, Koh I (2004) Prediction of phosphorylation sites using SVMs. Bioinformatics, 20, 3179-3184.
30. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B 57: 289-300.