Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array

Molecular Plant-Microbe Interactions

Volumn 17, Issue 9, 2004, Pages 999-1008

  Yang, Shihui ^a   Perna, Nicole T ^b   Cooksey, Donald A ^a   Okinaka, Yasushi ^c   Lindow, Steven E ^d   Ibekwe, A Mark ^e   Keen, Noel T ^a   Yang, Ching Hong ^f  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c HIROSHIMA UNIVERSITY   (Japan)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e U S SALINITY LABORATORY   (United States)

^f UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

Author keywords

Oxidative stress; Phosphotransferase system; Transport of oligogalacturonides; Type III secretion system

Indexed keywords

ERWINIA; ERWINIA CAROTOVORUM; ERWINIA CHRYSANTHEMI; ERWINIA CHRYSANTHEMI STR. 3937; ESCHERICHIA COLI; PECTOBACTERIUM; PROKARYOTA; SALMONELLA TYPHIMURIUM; VIOLA (ANGIOSPERM);

EID: 4143151686     PISSN: 08940282     EISSN: None     Source Type: Journal    
DOI: 10.1094/MPMI.2004.17.9.999     Document Type: Article

References (68)

1. Aguilar, I., Poza-Carrión, C., Guío, A., and Rodríguez-Palenzuela, P. 2002. Erwinia chrysanthemi genes specifically induced during infection in chicory leaves. Mol. Plant Pathol. 3:271-275.
2. Bauer, D. W., Bogdanove, A. J., Beer, S. V., and Collmer, A. 1994. Erwinia chrysanthemi hrp genes and their involvement in soft-rot pathogenesis and elicitation of the hypersensitive response. Mol. Plant-Microbe Interact. 7:573-581.
3. Bauer, D.W., Wei, Z. M., Beer, S. V., and Collmer, A. 1995. Erwinia chrysanthemi harpinEch: An elicitor of the hypersensitive response that contributes to soft-rot pathogenesis. Mol. Plant-Microbe Interact. 8:484-491.
4. Boch, J., Joardar, V., Gao, L., Robertson, T. L., Lim, M., and Kunkel, B. N. 2002. Identification of Pseudomonas syringae pv. tomato genes induced during infection of Arabidopsis thaliana. Mol. Microbiol. 44:73-88.
5. Bogdanove, A. J., Bauer. D. W., and Beer, S. V. 1998. Erwinia amylovora secretes dspE, a pathogenicity factor and functional avrE homolog, through the hrp (type III secretion) pathway. J. Bacteriol. 180:2244-2247.
6. 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. U.S.A. 100:10181-10186.
7. Chatterjee, A. K., Dumenyo, C. K., Liu, Y., and Chatterjee, A. 2000. Erwinia: Genetics of pathogenicity factors. Pages 236-259 in: Encyclopedia of Microbiology, Vol. 2, 2nd ed. J. Lederberg, ed. Academic Press, New York.
8. Chiang, S. L., and Mekalanos, J. J. 1998. Use of signature-tagged transposon mutagenesis to identify Vibrio cholerae genes critical for colonization. Mol. Microbiol. 27:797-805.
9. Collmer, A., and Keen, N. T. 1986. The role of pectic enzymes in plant pathogenesis. Annu. Rev. Phytopathol. 24:383-409.
10. Coulter, S. N., Schwan, W. R., Ng, E. Y., Langhorne, M. H., Ritchie, H. D., Westbrock-Wadman, S., Hufnagle, W. O., Folger, K. R., Bayer, A. S., and Stover, C. K. 1998. Staphylococcus aureus genetic loci impacting growth and survival in multiple infection environments. Mol. Microbiol. 30:393-404.
11. DeLisa, M. P., Wu, C. F., Wang, L., Valdes, J. J., and Bentley, W E. 2001. DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli. J. Bacteriol. 183:5239-5247.
12. Expert, D. 1999. Withholding and exchanging iron: Interactions between Erwinia spp. and their plant hosts. Annu. Rev. Phytopathol. 37:307-334.
13. Fouts, D. E., Abramovitch, R. B., Alfano, J. R., Baldo, A. M., Buell, C. R., Cartinhour, S., Chatterjee, A. K., D'Ascenzo, M., Gwinn, M. L., Lazarowitz, S. G., Lin, N. C., Martin, G. B., Rehm, A. H., Schneider, D. J., van Dijk, K., Tang, X. Y., and Collmer, A. 2002. Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl. Acad. Sci. U.S.A. 99:2275-2280.
14. Franza, T., and Expert, D. 1991. The virulence-associated chrysobactin iron uptake system of Erwinia chrysanthemi 3937 involves an operon encoding transport and biosynthetic functions. J. Bacteriol. 173:6874-6881.
15. Franza, T., Sauvage, C., and Expert, D. 1999. Iron regulation and pathogenicity in Erwinia chrysanthemi 3937: Role of the Fur repressor protein. Mol. Plant-Microbe Interact. 12:119-128.
16. Gaudriault, S., Malandrin, L., Paulin, J. P., and Barny, M. A. 1997. DspA, an essential pathogenicity factor of Erwinia amylovora showing homology with AvrE of Pseudomonas syringae, is secreted via the Hrp secretion pathway in a DspB-dependent way. Mol. Microbiol. 26:1057-1069.
17. Glasner, J. D., Liss, P., Plunkett, G., 3rd, Darling, A., Prasad, T., Rusch, M., Byrnes, A., Gilson, M., Biehl, B., Blattner, F. R., and Perna, N. T. 2003. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31:147-151.
18. Goodman, R. N., Kirly, Z., and Wood, K. R. 1986. The Biochemistry and Physiology of Plant Disease. University of Missouri Press, Columbia.
19. Gosink, K. K., Kobayashi, R., Kawagishi, I., and Hase, C. C. 2002. Analyses of the roles of the three cheA homologs in chemotaxis of Vibrio cholerae. J. Bacteriol. 184:1767-1771.
20. Hassouni, M. E., Chambost, J. P., Expert, D., Van Gijsegem, F., and Barras, F. 1999. The minimal gene set member msrA, encoding peptide methionine sulfoxide reductase, is a virulence determinant of the plant pathogen Erwinia chrysanthemi. Proc. Natl. Acad. Sci. U.S.A. 96:887-892.
21. Heithoff, D. M., Conner, C. P., Hanna, P. C., Julio, S. M., Hentschel, U., and Mahan, M. J. 1997. Bacterial infection as assessed by in vivo gene expression. Proc. Natl. Acad. Sci. U.S.A. 94:934-939.
22. Hugouvieux-Cotte-Pattat, N. 2004. The RhaS activator controls the Erwinia chrysanthemi 3937 genes rhiN, rhiT and rhiE involved in rhamnogalacturonan catabolism. Mol. Microbiol. 51:1961-1974.
23. Hugouvieux-Cotte-Pattat, N., and Reverchon, S. 2001. Two transporters, TogT and TogMNAB, are responsible for oligogalacturonide uptake in Erwinia chrysanthemi Mol. Microbiol. 41:1125-1132.
24. Hugouvieux-Cotte-Pattat, N., Condemine, G., Nasser, W., and Reverchon, S. 1996. Regulation of pectinolysis in Erwinia. Annu. Rev. Microbiol. 50:213-257.
25. Hugouvieux-Cotte-Pattat, N., Blot, N., and Reverchon, S. 2001. Identification of TogMNAB, an ABC transporter which mediates the uptake of pectic oligomers in Erwinia chrysanthemi 3937. Mol. Microbiol. 41:1113-1123.
26. s in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J. Bacteriol. 183:5445-5448.
27. Kilic, A. O., Herzberg, M. C., Meyer, M. W., Zhao, Z., and Tao, L. 1999. Streptococcal reporter gene-fusion vector for identification of in vivo expressed genes. Plasmid. 42:67-72.
28. Kim, K. S., Rao, N. N., Fraley, C. D., and Kornberg, A. 2002. Inorganic polyphosphate is essential for long-term survival and virulence factors in Shigella and Salmonella spp. Proc. Natl. Acad. Sci. U.S.A. 99:7675-7680.
29. Kornberg, A., Rao, N. N., and Ault-Riche, D. 1999. Inorganic polyphosphate: A molecule of many functions. Annu. Rev. Biochem. 68:89-125.
30. Laatu, M., and Condemine, G. 2003. Rhamnogalacturonate lyase RhiE is secreted by the Out system in Erwinia chrysanthemi. J. Bacteriol. 185:1642-1649.
31. Lai, Y. C., Peng, H. L., and Chang, H. Y. 2001. Identification of genes induced in vivo during Klebsiella pneumoniae CG4I infection. Infect. Immun. 69:7140-7145.
32. Larsen, M. H., and Boesen, H. T. 2001. Role of flagellum and chemotactic motility of Vibrio anguillarum for phagocytosis by and intracellular survival in fish macrophages. FEMS (Fed. Eur. Microbiol. Soc.) Microbiol Lett. 203:149-152.
33. Lehoux, D. E., Sanschagrin, F., and Levesque, R. C. 2002. Identification of in vivo essential genes from Pseudomonas aeruginosa by PCR-based signature-tagged mutagenesis. FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett. 210:73-80.
34. López-Solanilla, E., Llama-Palacios, A., Collmer, A., García-Olmedo, F., and Rodríguez-Palenzuela, P. 2001. Relative effects on virulence of mutations in the sap, pel, and hrp loci of Erwinia chrysanthemi. Mol. Plant-Microbe Interact. 14:386-393.
35. Mahan, M. J., Slauch, J. M., and Mekalanos, J. J. 1993. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259:686-688.
36. Mahan, M. J., Tobias, J. W., Slauch, J. M., Hanna, P. C., Collier, R. J., and Mekalanos, J. J. 1995. Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc. Natl. Acad. Sci. U.S.A. 92:669-673.
37. Marco, M. L., Legac, J., and Lindow, S. E. 2003. Conditional survival as a selection strategy to identify plant-inducible genes of Pseudomonas syringae. Appl. Environ. Microbiol. 69:5793-5801.
38. Merrell, D. S., Hava, D. L., and Camilli, A. 2002. Identification of novel factors involved in colonization and acid tolerance of Vibrio cholerae. Mol. Microbiol. 43:1471-1491.
39. Miller, W. G., and Lindow, S. E. 1997. An improved GFP cloning cassette designed for prokaryotic transcriptional fusions. Gene 191:149-153.
40. Nachin, L., and Barras, F. 2000. External pH: An environmental signal that helps to rationalize pel gene duplication in Erwinia chrysanthemi. Mol. Plant-Microbe Interact. 13:882-886.
41. Nachin L., El Hassouni M., Loiseau L., Expert D., and Barras F. 2001. SoxR-dependent response to oxidative stress and virulence of Erwinia chrysanthemi: The key role of SufC, an orphan ABC ATPase. Mol. Microbiol. 39:960-972.
42. Nasser, W., and Reverchon, S. 2002. H-NS-dependent activation of pectate lyases synthesis in the phytopathogenic bacterium Erwinia chrysanthemi is mediated by the PecT repressor. Mol. Microbiol. 43:733-748.
43. Nasser, W., Reverchon, S., Condemine, G., and Robert-Baudouy, J. 1994. Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis. J. Mol. Biol. 236:427-440.
44. Nasser, W., Bouillant, M. L., Salmond, G., and Reverchon, S. 1998. Characterization of the Erwinia chrysanthemi expI-expR locus directing the synthesis of two N-acyl-homoserine lactone signal molecules. Mol. Microbiol. 29:1391-1405.
45. Okinaka, Y., Yang, C.-H., Perna, N. T., and Keen, N. T. 2002. Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol. Plant-Microbe Interact. 15:619-629.
46. O'Toole, R., Milton, D. L., and Wolf-Watz, H. 1996. Chemotactic motility is required for invasion of the host by the fish pathogen Vibrio anguillarum. Mol. Microbiol. 19:625-637.
47. Perombelon, M. C. M., and Kelman, A. 1980. Ecology of the soft rot erwinias. Annu. Rev. Phytopathol. 18:361-387.
48. Polissi, A., Pontiggia, A., Feger, G., Altieri, M., Mottl, H., Ferrari, L., and Simon, D. 1998. Large scale identification of virulence genes from Streptococcus pneumoniae. Infect. Immun. 66:5620-5629.
49. Rainey, P. B. 1999. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1:243-257.
50. Rashid, M. H., and Kornberg, A. 2000. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U.S.A. 97:4885-4890.
51. Rashid, M. H., Rao, N. N., and Kornberg, A. 2000a. Inorganic polyphosphate is required for motility of bacterial pathogens. J. Bacteriol. 182:225-227.
52. Rashid, M. H., Rumbaugh, K., Passador, L., Davies, D. G., Hamood, A. N., Iglewski, B. H., and Kornberg, A. 2000b. Polyphosphate kinase is essential for biofilm development, quorum sensing, and virulence of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U.S.A. 97:9636-9641.
53. Reid, J. L., and Collmer, A. 1987. An nptI-SacB-SacR cartridge for constructing directed, unmarked mutation in gram-negative bacteria by marker exchange-eviction mutagenesis. Gene 57:239-246.
54. Reverchon, S., Rouanet, C., Expert, D., and Nasser, W. 2002. Characterization of indigoidine biosynthetic genes in Erwinia chrysanthemi and role of this blue pigment in pathogenicity. J Bacteriol. 184:654-665.
55. Reverchon, S., Expert, D., Robert-Baudouy, J., and Nasser, W. 1997. The cyclic AMP receptor protein is the main activator of pectinolysis genes in Erwinia chrysanthemi. J. Bacteriol. 179:3500-3508.
56. Saier, M. H., and Reizer, J. 1994. The bacterial phosphotransferase system: New frontiers 30 years later. Mol. Microbiol. 13:755-764.
57. Serres M. H., and Riley M. 2001. MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb. Comp. Genomics 5:205-222.
58. Shiba, T., Tsutsumi, K., Ishige, K., and Noguchi, T. 2000. Inorganic polyphosphate and polyphosphate kinase: Their novel biological functions and applications. Biochemistry (Moscow). 65:315-323.
59. Tardy, F., Nasser, W., Robert-Baudouy, J., and Hugouvieux-Cotte-Pattat, N. 1997. Comparative analysis of the five major Erwinia chrysanthemi pectate lyases: Enzyme characteristics and potential inhibitors. J. Bacteriol. 179:2503-2511.
60. Toth, I. K., Bell, K. S., Holeva, M. C., and Birch, P. R. 2003. Pathogen profile, Soft rot erwiniae: From genes to genomes. Mol. Plant Pathol. 4:17-30.
61. Valdivia, R. H., and Falkow, S. 1996. Bacterial genetics by flow cytometry: Rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction. Mol. Microbiol. 22:367-378.
62. Valdivia, R. H., and Falkow, S. 1997. Fluorescence-based isolation of bacterial genes expressed within host cells. Science 277:2007-2011.
63. Von Kruger, W. M. A., Humphreysa, S., and Ketley, J. M. 1999. A role for the PhoBR regulatory system homologue in the Vibrio cholerae phosphate limitation response and intestinal colonization. Microbiology 145:2463-2475.
64. Wang, J., Mushegian, A., Lory, S., and Jin, S. 1996. Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection. Proc. Natl. Acad. Sci. U.S.A. 93:10434-10439.
65. Wassenaar, T. M., and Gaastra, W. 2001. Bacterial virulence: Can we draw the line? FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett. 201:1-7.
66. Wei, Y., Lee, J. M., Richmond, C., Blattner, F. R., Rafalski, J. A., and LaRossa, R. A. 2001. High-density microarray-mediated gene expression profiling of Escherichia coli. J. Bacteriol. 183:545-556.
67. Wu, Y., Lee, S. W., Hillman, J. D., and Progulske-Fox, A. 2002. Identification and testing of Porphyromonas gingivalis virulence genes with a pPGIVET system. Infect. Immun. 70:928-937.
68. Yang, C.-H., Gavilanes-Ruiz, M., Okinaka, Y., Vedel, R., Berthuy, I., Boccara, M., Chen, J. W., Perna, N. T., and Keen, N. T. 2002. hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol. Plant-Microbe Interact. 15:472-480.