Prediction and characterization of protein-protein interaction network in Xanthomonas oryzae pv. oryzae PXO99A

Research in Microbiology

Volumn 164, Issue 10, 2013, Pages 1035-1044

  Guo, Jing ^a   Li, Huan ^a   Chang, Ji Wei ^a   Lei, Yang ^a   Li, Sen ^a   Chen, Ling Ling ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Domain combination method; Flagellar and chemotaxis system; Interolog method; K nearest neighbors classification method; Signal transduction system

Indexed keywords

CYCLIC AMP; RNA POLYMERASE BETA SUBUNIT;

ARTICLE; BACTERIAL STRAIN; CHEMOTAXIS; METABOLIC REGULATION; NONHUMAN; PATHOGENICITY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; XANTHOMONAS ORYZAE;

BACTERIA (MICROORGANISMS); XANTHOMONAS ORYZAE PV. ORYZAE;

DOMAIN COMBINATION METHOD; FLAGELLAR AND CHEMOTAXIS SYSTEM; INTEROLOG METHOD; K-NEAREST NEIGHBORS CLASSIFICATION METHOD; SIGNAL TRANSDUCTION SYSTEM;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, BACTERIAL; ORYZA SATIVA; PLANT DISEASES; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL; XANTHOMONAS;

EID: 84889097051     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2013.09.001     Document Type: Article

References (64)

1. Albert R. Scale-free networks in cell biology. J. Cell Sci. 2004, 118:4947-4957.
2. Aldridge P., Hughes K.T. Regulation of flagellar assembly. Curr. Opin. Microbiol. 2002, 5:160-165.
3. Aldridge P., Paul R., Goymer P., Rainey P., Jenal U. Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus. Mol. Microbiol. 2003, 47:1695-1708.
4. Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., et al. UniProt the Universal protein knowledgebase. Nucleic Acids Res. 2004, 32:115-119.
5. Ausmees N., Mayer R., Weinhouse H., Volman G., Amikam D., Benzimanc M., et al. Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity. FEMS Microbiol. Lett. 2001, 204:163-167.
6. Barthelemy M. Betweenness centrality in large complex networks. Eur. Phys. J. B. 2004, 38:163-168.
7. Brown K.R., Jurisica I. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol. 2007, 8:R95.
8. Butland G., Peregrín-Alvarez J.M., Li J., Yang W., Yang X., Canadien V., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005, 433:531-537.
9. Chang A.L., Tuckerman J.R., Gonzalez G., Mayer R., Weinhouse H., Volman G., et al. Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 2001, 40:3420-3426.
10. Dasgupta N., Wolfgang M.C., Goodman A.L., Arora S.K., Jyot J., Lory S., et al. A four-tiered transcriptional regulatory circuit controls flagellar biogenesis in Pseudomonas aeruginosa. Mol. Microbiol. 2003, 50:809-824.
11. De Bodt S., Proost S., Vandepoele K., Rouzé P., Van de Peer Y. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 2009, 10:288.
12. Deng M., Mehta S., Sun F., Chen T. Inferring domain-domain interactions from protein-protein interactions. Genome Res. 2002, 12:1540-1548.
13. Eisenbach M., Caplan S.R. Bacterial chemotaxis unsolved mystery of the flagellar switch. Curr. Biol. 1998, 8:444-446.
14. Finn R.D., Mistry J., Schuster-Böckler B., Griffiths-Jones S., Hollich V., Lassmann T., et al. Pfam clans, web tools and services. Nucleic Acids Res. 2006, 34:247-251.
15. Galperin M.Y., Natale D.A., Aravind L., Koonin E.V. A specialized version of the HD hydrolase domain implicated in signal transduction. J. Mol. Microbiol. Biotechnol. 1999, 1:303-305.
16. Galperin M.Y., Nikolskaya A.N., Koonin E.V. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol. Lett. 2001, 203:11-21.
17. Galperin M.Y. Bacterial signal transduction network in a genomic perspective. Environ. Microbiol. 2004, 6:552-567.
18. Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., et al. A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
19. Guarracino M.R., Nebbia A. Predicting protein-protein interactions with k-nearest neighbors classification algorithm. Proceedings of the 6th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics 15-17 October 2009; Genoa 2010, 139-150. Springer-Verlag, Berlin Heidelberg. F. Masulli, L.E. Peterson, R. Tagliaferri (Eds.).
20. Han D., Kim H.S., Seo J., Jang W. A domain combination based probabilistic framework for protein-protein interaction prediction. Genome Informa. 2003, 14:250-259.
21. Harris M.A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32:258-261.
22. He F., Zhang Y., Chen H., Zhang Z., Peng Y.L. The prediction of protein-protein interaction networks in rice blast fungus. BMC Genomics 2008, 9:519.
23. He X., Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genet. 2006, 2:e88.
24. He Y.W., Xu M., Lin K., Ng Y.J., Wen C.M., Wang L.H., et al. Genome scale analysis of diffusible signal factor regulon in Xanthomonas campestris pv. campestris identification of novel cell-cell communication-dependent genes and functions. Mol. Microbiol. 2006, 59:610-622.
25. Helmann J.D. Alternative sigma factors and the regulation of flagellar gene expression. Mol. Microbiol. 1991, 5:2875-2882.
26. Hermjakob H., Montecchi-Palazzi L., Lewington C., Mudali S., Kerrien S., Orchard S., et al. IntAct an open source molecular interaction database. Nucleic Acids Res. 2004, 32:452-455.
27. Hur A.B., Noble W. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinform. 2006, 7:2.
28. Jenal U., Malone J. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu. Rev. Genet. 2006, 40:385-407.
29. Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature 2001, 411:41-42.
30. Josenhans C., Niehus E., Amersbach S., Hörster A., Betz C., Drescher B., et al. Functional characterization of the antagonistic flagellar late regulators FliA and FlgM of Helicobacter pylori and their effects on the H. pylori transcriptome. Mol. Microbiol. 2002, 43:307-322.
31. Kazmierczak M.J., Wiedmann M., Boor K.J. Alternative sigma factors and their roles in bacterial virulence. Microbiol. Mol. Biol. Rev. 2005, 69:527-543.
32. Kim J.G., Park D., Kim B.C., Cho S.W., Kim Y.T., Park Y.J., et al. Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. BMC Bioinforma. 2008, 9:41.
33. LaCount D.J., Vignali M., Chettier R., Phansalkar A., Bell R., Hesselberth J.R., et al. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 2005, 438:103-107.
34. Lee B.M., Park Y.J., Park D.S., Kang H.W., Kim J.G., Song E.S., et al. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res. 2005, 33:577-586.
35. Lehner B., Fraser A.G. A first-draft human protein-interaction map. Genome Biol. 2004, 5:R63.
36. Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., et al. A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543.
37. Mew T.W. Current status and future prospects of research on bacterial blight of rice. Annu. Rev. Phytopathol. 2007, 25:359-382.
38. Mirel D.B., Lustre V.M., Chamberlin M.J. An operon of Bacillus subtilis motility genes transcribed by the sigma D form of RNA polymerase. J. Bacteriol. 1992, 174:4197-4204.
39. Missiakas D., Raina S. The extracytoplasmic function sigma factors role and regulation. Mol. Microbiol. 1998, 28:1059-1066.
40. Ng S.K., Zhang Z., Tan S.H., Lin K. InterDom a database of putative interacting protein domains for validating predicated protein interactions and complexes. Nucleic Acids Res. 2003, 31:251-254.
41. O'Brien K.P., Remm M., Sonnhammer E.L. Inparanoid a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 2005, 33:476-480.
42. Ochiai H., Inoue Y., Takeya M., Sasaki A., Kaku H. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Jpn. Agric. Res. Q. 2005, 39:275-287.
43. Parrish J.R., Yu J., Liu G., Hines J.A., Chan J.E., Mangiola B.A., et al. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 2007, 8:R130.
44. Phizicky E.M., Fields S. Protein-protein interactions methods for detection and analysis. Microbiol. Rev. 1995, 59:94-123.
45. Prouty M.G., Correa N.E., Klose K.E. The novel sigma54- and sigma28-dependent flagellar gene transcription hierarchy of Vibrio cholerae. Mol. Microbiol. 2001, 39:1595-1609.
46. Pruitt K.D., Tatusova T., Maglott D.R. NCBI Reference Sequence, RefSeq. a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, 33:501-504.
47. Rai R., Ranjan M., Pradhan B.B., Chatterjee S. Atypical regulation of virulence-associated functions by a diffusible signal factor in Xanthomonas oryzae pv. oryzae. Mol. Plant Microbe. Interact 2012, 25:789-801.
48. Rain J.C., Selig L., De Reuse H., Battaglia V., Reverdy C., Simon S., et al. The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409:211-215.
49. Raman K. Construction and analysis of protein-protein interaction networks. Automot. Exp. 2010, 2:2.
50. Rodrigue S., Provvedi R., Jacques P.E., Gaudreau L., Manganelli R. The sigma factors of Mycobacterium tuberculosis. FEMS Microbiol. Rev. 2006, 30:926-941.
51. Salzberg S.L., Sommer D.D., Schatz M.C., Phillippy A.M., Rabinowicz P.D., Tsuge S., et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 2008, 9:204.
52. Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 2000, 18:1257-1261.
53. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
54. Shen J., Zhang J., Luo X., Zhu W., Yu K., Chen K., et al. Predicting protein-protein interactions based only on sequences information. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:4337-4341.
55. Shi M.G., Xia J.F., Li X.L., Huang D.S. Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset. Amino Acids 2010, 38:891-899.
56. Sun J.C., Xu J.L., Cao J.P., Liu Q., Guo X.K., Shi T.L., et al. Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans. Chin. Sci. Bull. 2006, 51:1296-1305.
57. Tal R., Wong H.C., Calhoon R., Gelfand D., Fear A.L., Volman G., et al. Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacter xylinum genetic organization and occurrence of conserved domains in isoenzymes. J. Bacteriol. 1998, 180:4416-4425.
58. Tischler A.D., Camilli A. Cyclic diguanylate (c-di-GMP) regulates Vibrio cholerae biofilm formation. Mol. Microbiol. 2004, 53:857-869.
59. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
60. Wojcik J., Schächter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 2001, 17:296-305.
61. Wolfgang M.C., Lee V.T., Gilmore M.E., Lory S. Coordinate regulation of bacterial virulence genes by a novel adenylatecyclase-dependent signaling pathway. Dev. Cell. 2003, 4:253-263.
62. Wösten M.M., Wagenaar J.A., van Putten J.P. The FlgS/FlgR two-component signal transduction system regulates the flaregulon in Campylobacter jejuni. J. Biol. Chem. 2004, 279:16214-16222.
63. Yang T.C., Leu Y.W., Chang-Chien H.C., Hu R.M. Flagellar biogenesis of Xanthomonas campestris requires the alternative sigma factors RpoN2 and FliA and is temporally regulated by FlhA, FlhB, and FlgM. J. Bacteriol. 2009, 191:2266-2275.
64. Zhang J., Gao S.Q., Wu M.S., He C.Y. Regulation of flagellar gene expression by the transcriptional regulator FleQxoo and the alternative sigma factor σ54 RpoNxoo in Xanthomonas oryzae pv. oryzae. Acta Phytophysiol. Sin. 2008, 38:449-455.