PathoPlant®: A database on plant-pathogen interactions

In Silico Biology

Volumn 4, Issue 4, 2004, Pages 529-536

  Bülow, Lorenz ^a   Schindler, Martin ^a   Choi, Claudia ^b   Hehl, Reinhard ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^b BIOBASE GMBH   (Germany)

Author keywords

Avirulence factor; Database; Interaction; Pathogen; Pathway; Phytopathogen; Plant; Plant defense; Resistance; Signal perception; Signal transduction; Susceptibility; Virulence

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; COMPARATIVE STUDY; COMPUTER MODEL; GENBANK; GENETIC ASSOCIATION; GENETIC DATABASE; INTERNET; LINKAGE ANALYSIS; MEDLINE; NONHUMAN; PATHOPLANT DATABASE; PLANT DEFENSE; PLANT PATHOGEN INTERACTION; SIGNAL DETECTION; SIGNAL TRANSDUCTION; SWISS-PROT; BIOLOGY; COMPUTER PROGRAM; FACTUAL DATABASE; HOST PARASITE INTERACTION; MICROBIOLOGY; PLANT DISEASE; PLANT PHYSIOLOGY; VIRULENCE;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HOST-PARASITE RELATIONS; PLANT DISEASES; PLANT PHYSIOLOGY; SIGNAL TRANSDUCTION; SOFTWARE; VIRULENCE;

EID: 15044347563     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (40)

1. Abeles, F. B., Morgan, P. W. and Saltveit, M. E. Jr. (1992). Ethylene in plant biology. 2nd ed. Academic Press, San Diego.
2. Alonso, J. M., Hirayama, T., Roman, G., Nourizadeh, S. and Ecker, J. R. (1999). EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science 284, 2148-2152.
3. Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
4. Ausubel, F. M., Katagiri, F., Mindrinos, M. and Glazebrook, J. (1995). Use of Arabidopsis thaliana defense-related mutants to dissect the plant response to pathogens. Proc. Natl. Acad. Sci. USA 92, 4189-4196.
5. Buell, C. R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I. T., Gwinn, M. L., Dodson, R. J., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Daugherty, S., Brinkac, L., Beanan, M. J., Haft, D. H., Nelson, W. C., Davidsen, T., Zafar, N., Zhou, L., Liu, J., Yuan, Q., Khouri, H., Fedorova, N., Tran, B., Russell, D., Berry, K., Utterback, T., Van Aken, S. E., Feldblyum, T. V., D'Ascenzo, M., Deng, W. L., Ramos, A. R., Alfano, J. R., Cartinhour, S., Chatterjee, A. K., Delaney, T. P., Lazarowitz, S. G., Martin, G. B., Schneider, D. J., Tang, X., Bender, C. L., White, O., Fraser, C. M. and Collmer, A. (2003). The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100, 10181-10186.
6. Chang, C., Kwok, S. F., Bleecker, A. B. and Meyerowitz, E. M. (1993). Arabidopsis ethylene-response gene ETR1: Similarity of product to two-component regulators. Science 262, 539-544.
7. Chao, Q., Rothenberg, M., Solano, R., Roman, G., Terzaghi, W. and Ecker, J. R. (1997). Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell 89, 1133-1144.
8. Choi, C., Krull, M., Kel, A., Kel-Margoulis, O., Pistor, S., Potapov, A., Voss, N. and Wingender, E. (2004). TRANSPATH®- a high quality database focused on signal transduction. Comp. Funct. Genom. 5, 163-168.
9. Clark, K. L., Larsen, P. B., Wang, X. and Chang, C. (1998). Association of the Arabidopsis CTR1 Raf-like kinase with the ETR1 and ERS ethylene receptors. Proc. Natl. Acad. Sci. USA 95, 5401-5406.
10. Devadas, S. K., Enyedi, A. and Raina, R. (2002). The Arabidopsis hrl1 mutation reveals novel overlapping roles for salicylic acid, jasmonic acid and ethylene signalling in cell death and defence against pathogens. Plant J. 30, 467-480.
11. Dong, X., Mindrinos, M., Davis, K. R. and Ausubel, F. M. (1991). Induction of Arabidopsis defense genes by virulent and avirulent Pseudomonas syringae strains and by a cloned avirulence gene. Plant Cell 3, 61-72.
12. Greenberg, J. T. (1997). Programmed cell death in plant-pathogen interactions. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48, 525-545.
13. Greenberg, J. T. and Vinatzer, B. A. (2003). Identifying type III effectors of plant pathogens and analyzing their interaction with plant cells. Curr. Opin. Microbiol. 6, 20-28.
14. Guttman, D. S., Vinatzer, B. A., Sarkar, S. F., Ranall, M. V., Kettler, G. and Greenberg, J. T. (2002). A functional screen for the type III (Hrp) secretome of the plant pathogen Pseudomonas syringae. Science 295, 1722-1726.
15. Hammond-Kosack, K. E. and Jones, J. D. (1997). Plant disease resistance genes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48, 575-607.
16. Hua, J., Chang, C., Sun, Q. and Meyerowitz, E. M. (1995). Ethylene insensitivity conferred by Arabidopsis ERS gene. Science 269, 1712-1714.
17. Hua, J., Sakai, H., Nourizadeh, S., Chen, Q. G., Bleecker, A. B., Ecker, J. R. and Meyerowitz, E. M. (1998). EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis. Plant Cell 10 1321-1332.
18. Kieber, J. J., Rothenberg, M., Roman, G., Feldmann, K. A. and Ecker, J. R. (1993). CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72, 427-441.
19. Knoester, M., van Loon, L. C., van den Heuvel, J., Hennig, J., Bol, J. F. and Linthorst, H. J. M. (1998). Ethylene-insensitive tobacco lacks nonhost resistance against soil-borne fungi. Proc. Natl. Acad. Sci. USA 95, 1933-1937.
20. Kolchanov, N. A., Anan'ko, E. A., Kolpakov, F. A., Podkolodnaia, O. A., Ignat'eva, E. V., Goriachkovskaia, T. N. and Stepanenko, E. L. (2000). Gene networks. Mol. Biol. (Mosk.) 34, 533-544.
21. Kolchanov, N. A., Nedosekina, E. A., Ananko, E. A., Likhoshvai, V. A., Podkolodny, N. L., Ratushny, A. V., Stepanenko, I. L., Podkolodnaya, O. A., Ignatieva, E. V. and Matushkin, Y. G. (2002). GeneNet database: description and modeling of gene networks. In Silico Biol. 2, 0009.
22. Krull, M., Voss, N., Choi, C., Pistor, S., Potapov, A. and Wingender, E. (2003). TRANSPATH®: An integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res. 31, 97-100.
23. Lund, S. T., Stall, R. E. and Klee, H. J. (1998). Ethylene regulates the susceptible response to pathogen infection in tomato. Plant Cell 10 371-382.
24. Matys, V., Fricke, E., Geffers, R., Gössling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A. E., Kel-Margoulis, O. V., Kloos, D. U., Land, S., Lewicki-Potapov, B., Michael, H., Münch, R., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S. and Wingender, E. (2003). TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378.
25. Münch, R., Hiller, K., Barg, H., Heldt, D., Linz, S., Wingender, E. and Jahn, D. (2003). PRODORIC: Prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266-269.
26. Nürnberger, T. and Scheel, D. (2001). Signal transmission in the plant immune response. Trends Plant Sci. 6, 372-379.
27. Ouaked, F., Rozhon, W., Lecourieux, D. and Hirt, H. (2003). A MAPK pathway mediates ethylene signaling in plants. EMBO J. 22, 1282-1288.
28. Penninckx, I. A., Thomma, B. P., Buchala, A., Metraux, J. P. and Broekaert, W. F. (1998). Concomitant activation of jasmonate and ethylene response pathways is required for induction of a plant defensin gene in Arabidopsis. Plant Cell 10, 2103-2113.
29. Pontier, D., Balague, C. and Roby, D. (1998). The hypersensitive response. C. R. Acad. Sci. III, Sci. Vie 321, 721-734.
30. Ryals, J., Uknes, S. and Ward, E. (1994). Systemic acquired resistance. Plant Physiol. 104, 1109-1112.
31. Sakai, H., Hua, J., Chen, Q. G., Chang, C., Medrano, L. J., Bleecker, A. B. and Meyerowitz, E. M. (1998). ETR2 is an ETR1-like gene involved in ethylene signaling in Arabidopsis. Proc. Natl. Acad. Sci. USA 95, 5812-5817.
32. Schacherer, F., Choi, C., Götze, U., Krull, M., Pistor, S. and Wingender, E. (2001). The TRANSPATH signal transduction database: A knowledge base on signal transduction networks. Bioinformatics 17, 1053-1057.
33. Scofield, S. R., Tobias, C. M., Rathjen, J. P., Chang, J. H., Lavelle, D. T., Michelmore, R. W. and Staskawicz, B. J. (1996). Molecular basis of gene-for-gene specificity in bacterial speck disease of tomato. Science 274, 2063-2065.
34. Solano, R., Stepanova, A., Chao, Q. and Ecker, J. R. (1998). Nuclear events in ethylene signaling: A transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 12 3703-3714.
35. Steffens, N. O., Galuschka, C., Schindler, M., Bülow, L. and Hehl R. (2004). AthaMap: An online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res. 32 Database issue, D368-372.
36. Stepanova, A. N. and Ecker, J. R. (2000). Ethylene signaling: From mutants to molecules. Curr. Opin. Plant Biol. 3, 353-360.
37. Tang, X., Frederick, R. D., Zhou, J., Halterman, D. A., Jia, Y. and Martin, G. B. (1996). Initiation of plant disease resistance by physical interaction of AvrPto and Pto kinase. Science 274, 2060-2063.
38. Thomma, B. P., Penninckx, I. A., Broekaert, W. F. and Cammue, B. P. (2001). The complexity of disease signaling in Arabidopsis. Curr. Opin. Immunol. 13, 63-68.
39. Wang, K. L., Li, H. and Ecker, J. R. (2002). Ethylene biosynthesis and signaling networks. Plant Cell 14 Suppl., S131-S151.
40. Whalen, M. C., Innes, R. W., Bent, A. F. and Staskawicz, B. J. (1991). Identification of Pseudomonas syringae pathogens of Arabidopsis and a bacterial locus determining avirulence on both Arabidopsis and soybean. Plant Cell 3, 49-59.