Prediction of bacterial type IV secreted effectors by C-terminal features

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Wang, Yejun ^a   Wei, Xiaowei ^a   Bao, Hongxia ^a   Liu, Shu Lin ^a,b  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

Effector; Helicobacter pylori; Machine learning; Secretion signal prediction; Sequence analysis; Type IV secretion system

Indexed keywords

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; BACTERIAL PROTEINS; BACTERIAL SECRETION SYSTEMS; GENOME, BACTERIAL; HELICOBACTER PYLORI; PROTEIN STRUCTURE, TERTIARY; SALMONELLA TYPHIMURIUM; SOFTWARE;

EID: 84892603339     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-50     Document Type: Article

References (39)

1. Alvarez-Martinez CE, Christie PJ. Biological diversity of prokaryotic type IV secretion system. Microbiol Mol Biol 2009, 73(4):775-808.
2. Backert S, Meyer TF. Type IV secretion systems and their effectors in bacterial pathogenesis. Curr Opion Microbiol 2006, 9:207-217.
3. Censini S, Lange C, Xiang Z, Crabtree JE, Ghiara P, Borodovsky M, Rappuoli R, Covacci A. Cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci USA 1996, 93:14648-14653.
4. Tegtmeyer N, Wessler S, Backert S. Role of the cag-parhogenicity island encoded type IV secretion system in Helicobacter pylori pathogenesis. FEBS J 2011, 278:1190-1202.
5. Segal G, Purcell M, Shuman HA. Host cell killing and bacterial conjugation require overlapping sets of genes within a 22-kb region of the Legionella pneumophila genome. Proc Natl Acad Sci USA 1998, 95:1669-1674.
6. Vogel JP, Andrews HL, Wong SK, Isberg RR. Conjugative transfer by the virulence system of Legionella pneumophila. Science 1998, 279:873-876.
7. Saenz HL, Engel P, Stoeckli MC, Lanz C, Raddatz G, Vayssier-Taussat M, Birtles R, Schuster SC, Dehio C. Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors. Nat Genet 2007, 39:1469-1476.
8. Rhomberg TA, Truttmann MC, Guye P, Ellner Y, Dehio C. A translocated protein of Bartonella hensela: interferes with endocytic uptake of individual bacteria and triggers uptake of large bacterial aggregates via the invasome. Cell Microbiol 2009, 11:927-945.
9. Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EP. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 2011, 7:e1002222.
10. Ding Z, Atmakuri K, Christie PJ. The outs and ins of bacterial type IV secretion substrates. Trends Microbiol 2003, 11:527-535.
11. Cambronne ED, Roy CR. Recognition and delivery of effector proteins into eukaryotic cells by bacterial secretion systems. Traffic 2006, 7:929-939.
12. Ward DV, Zambryski PC. The six functions of Agrobacterium VirE2. Proc Natl Acad Sci USA 2001, 98:385-386.
13. Schrammeijer B, den Dulk-Ras A, Vergunst AC, Jurado Jácome E, Hooykaas PJ. Analysis of Vir protein translocation from Agrobacterium tumefaciens using saccharomyces cerevisiae as a model: evidence for transport of a novel effector protein VirE3. Nucleic Acids Res 2003, 31:860-868.
14. Schröder G, Krause S, Zechner EL, Traxler B, Yeo HJ, Lurz R, Waksman G, Lanka E. TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system: inner membrane gate for exported substrates?. J Bacteriol 2002, 184:2767-2779.
15. Coers J, Kagan JC, Matthews M, Nagai H, Zuckman DM, Roy CR. Dentification of Icm protein complexes that play distinct roles in the biogenesis of an organelle permissive for Legionella pneumophila intracellular growth. Mol Microbiol 2000, 38:719-736.
16. Hofreuter D, Odenbreit S, Püls J, Schwan D, Haas R. Genetic competence in Helicobacter pylori: mechanisms and biological implications. Res Microbiol 2000, 151(6):487-491.
17. 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:e1000508.
18. Chen C, Banga S, Mertens K, Weber MM, Gorbaslieva I, Tan Y, Luo ZQ, Samuel JE. Large-scale identification and translocation of type IV secretion substrates by Coxiella burnetii. Proc Natl Acad Sci USA 2010, 107(50):21755-21760.
19. Ramarao N, Gray-Owen SD, Backert S, Meyer TF. Helicobacter pylori inhibits phagocytosis by professional phagocytes involving type IV secretion components. Mol Microbiol 2000, 37:1389-1404.
20. Fehri LF, Rechner C, Janssen S, Mak TN, Holland C, Bartfeld S, Brüggemann H, Meyer TF. Helicobacter pylori-induced modification of the histone H3 phosphorylation status in gastric epithelial cells reflects its impact on cell cycle regulation. Epigenetics 2009, 4:577-586.
21. Vergunst AC, Schrammeijer B, den Dulk-Ras A, de Vlaam CM, Regensburg-Tuïnk TJ, Hooykaas PJ. VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science 2000, 290:979-982.
22. Simone M, McCullen CA, Stahl LE, Binns AN. The carboxy-terminus of VirE2 from Agrobacterium tumefaciens is required for its transport to host cells by the virB-encoded type IV transport system. Mol Microbio 2001, 41:1283-1293.
23. Vergunst AC, van Lier MC, den Dulk-Ras A, Stüve TA, Ouwehand A, Hooykaas PJ. Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium. Proc Natl Acad Sci USA 2005, 102:832-837.
24. Schulein R, Guye P, Rhomberg TA, Schmid MC, Schröder G, Vergunst AC, Carena I, Dehio C. A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells. Proc Natl Acad Sci USA 2005, 102:856-861.
25. Hohlfeld S, Pattis I, Püls J, Plano GV, Haas R, Fischer W. A C-terminal translocation signal is necessary, but not sufficient for type IV secretion of the Helicobacter pylori CagA protein. Mol Microbiol 2006, 59:1624-1637.
26. Wang Y, Zhang Q, Sun M, Guo D. High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 2011, 27:777-84.
27. Wang Y, Sun M, Bao H, Zhang Q, Guo D. Effective identification of bacterial type III secretion signals using joint elemental features. PLos One 2013, 8(4):e59754.
28. Yang Y, Zhao J, Morgan RL, Ma W, Jiang T. Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinf 2010, 11(S1):S47.
29. Löwer M, Schneider G. Prediction of type III secretion signals in genomes of gram-negative bacteria. PLoS One 2009, 4(6):e5917.
30. 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.
31. 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.
32. Wang Y, Sun M, Bao H, White AP. T3_MM: a markov model effectively classifies bacterial type III secretion signals. PLoS One 2013, 8(3):e58173.
33. Hueck CJ. Type III protein secretion systems in bacterial pathogens of animals and plants. Micorbiol Mol Biol Rev 1998, 62(2):379-433.
34. Wang Y, Huang H, Sun M, Zhang Q, Guo D. T3DB: an integrated database for bacterial type III secretion system. BMC Bioinf 2012, 13:66.
35. Dunn OJ. Multiple comparisons among means. J Am Stat Assoc 1961, 56:52-64.
36. Bailey TL, Elkan C. Fitting A Mixture Model By Expectation Maximization To Discover Motifs In Biopolymers. Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology 1994, 28-36. Menlo Park, California: AAAI Press.
37. Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nuceic Acids Res 2005, 33:W72-W76.
38. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinf 2008, 9:40.
39. Shatsky M, Nussinov R, Wolfson HJ. A method for simultaneous alignment of multiple protein structures. Proteins Struct Funct Bioinf 2004, 56(1):143-156.