The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens

Molecular Plant-Microbe Interactions

Volumn 19, Issue 6, 2006, Pages 665-681

  Ditt, Renata F ^a   Kerr, Kathleen F ^a   De Figueiredo, Paul ^a   Delrow, Jeff ^b   Comai, Luca ^a   Nester, Eugene W ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN;

ARABIDOPSIS; ARTICLE; CELL CULTURE; CLASSIFICATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; PLANT DISEASE; PROTEIN MOTIF; REGULATORY SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RHIZOBIUM RADIOBACTER;

AMINO ACID MOTIFS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELLS, CULTURED; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT DISEASES; REGULATORY ELEMENTS, TRANSCRIPTIONAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RHIZOBIUM RADIOBACTER;

AGROBACTERIUM; AGROBACTERIUM TUMEFACIENS; ARABIDOPSIS; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); RHIZOBIUM;

EID: 33646863227     PISSN: 08940282     EISSN: None     Source Type: Journal    
DOI: 10.1094/MPMI-19-0665     Document Type: Article

References (75)

1. Alfano, J. R., and Collmer, A. 2004. Type III secretion system effector proteins: Double agents in bacterial disease and plant defense. Annu. Rev. Phytopathol. 42:385-414.
2. Axelos, M., Bardet, C., Liboz, T., Le Van Thai, A., Curie, C., and Lescure, B. 1989. The gene family encoding the Arabidopsis thaliana translation elongation factor EF-1 alpha: Molecular cloning, characterization and expression. Mol. Gen. Genet. 219:106-112.
3. Bailey, T. L., and Elkan, C. 1995. The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3:21-29.
4. Bako, L., Umeda, M., Tiburcio, A. F., Schell, J., and Koncz, C. 2003. The VirD2 pilot protein of Agrobacterium-transferred DNA interacts with the TATA box-binding protein and a nuclear protein kinase in plants. Proc. Natl. Acad. Sci. U.S.A. 100:10108-10113.
5. Ballas, N., and Citovsky, V. 1997. Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Agrobacterium VirD2 protein. Proc. Natl. Acad. Sci. U.S.A. 94:10723-10728.
6. Bevort, M., and Leffers, H. 2000. Down regulation of ribosomal protein mRNAs during neuronal differentiation of human NTERA2 cells. Differentiation 66:81-92.
7. Brencic, A., and Winans, S. C. 2005. Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria. Microbiol. Mol. Biol. Rev. 69:155-194.
8. Brown, R. L., Kazan, K., McGrath, K. C., Maclean, D. J., and Manners, J. M. 2003. A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis. Plant Physiol. 132:1020-1032.
9. Casati, P., and Walbot, V. 2003. Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content. Plant Physiol. 132:1739-1754.
10. Casey, T. M., Pakay, J. L., Guppy, M., and Arthur, P. G. 2002. Hypoxia causes downregulation of protein and RNA synthesis in noncontracting mammalian cardiomyocytes. Circ. Res. 90:777-783.
11. Chen, J. Q., Dong, Y., Wang, Y. J., Liu, Q., Zhang, J. S., and Chen, S. Y. 2003. An AP2/EREBP-type transcription-factor gene from rice is cold-inducible and encodes a nuclear-localized protein. Theor. Appl. Genet. 107:972-979.
12. Christie, P. J., and Vogel, J. P. 2000. Bacterial type IV secretion: Conjugation systems adapted to deliver effector molecules to host cells. Trends Microbiol. 8:354-360.
13. Cui, X., Kerr, M. K., and Churchill, G. A. 2003. Transformations for cDNA microarray data. Stat. Appl. Genet. Mol. Biol. Vol. 2, No. 1, Article 4. Online publication
14. Denekamp, M., and Smeekens, S. C. 2003. Integration of wounding and osmotic stress signals determines the expression of the AtMYB102 transcription factor gene. Plant Physiol. 132:1415-1423.
15. Deng, W., Chen, L., Wood, D. W., Metcalfe, T., Liang, X., Gordon, M. P., Comai, L., and Nester, E. W. 1998. Agrobacterium VirD2 protein interacts with plant host cyclophilins. Proc. Natl. Acad. Sci. U.S.A. 95:7040-7045.
16. Ditt, R. F., Nester, E. W., and Comai, L. 2001. Plant gene expression response to Agrobacterium tumefaciens. Proc. Natl. Acad. Sci. U.S.A. 98:10954-10959.
17. Ditt, R. F., Nester, E., and Comai, L. 2005. The plant cell defense and Agrobacterium tumefaciens. FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett. 247:207-213.
18. Escobar, M. A., and Dandekar, A. M. 2003. Agrobacterium tumefaciens as an agent of disease. Trends Plant Sci. 8:380-386.
19. Fazzio, T. G., Kooperberg, C., Goldmark, J. P., Neal, C., Basom, R., Delrow, J., and Tsukiyama, T. 2001. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell Biol. 21:6450-6460.
20. Gelvin, S. B. 2000. Agrobacterium and plant genes involved in T-DNA transfer and integration. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51:223-256.
21. Gelvin, S. B. 2003. Agrobacterium-mediated plant transformation: The biology behind the "gene-jockeying" tool. Microbiol. Mol. Biol. Rev. 67:16-37.
22. Guan, Y., and Nothnagel, E. A. 2004. Binding of arabinogalactan proteins by Yariv phenylglycoside triggers wound-like responses in Arabidopsis cell cultures. Plant Physiol. 135:1346-1366.
23. Hammond-Kosack, K. E., and Jones, J. D. 1996. Resistance gene-dependent plant defense responses. Plant Cell 8:1773-1791.
24. Huang, L., McCluskey, M. P., Ni, H., and LaRossa, R. A. 2002. Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light. J. Bacteriol. 184:6845-6858.
25. Hughes, J. D., Estep, P. W., Tavazoie, S., and Church, G. M. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296:1205-1214.
26. Jeffrey, I. W., Bushell, M., Tilleray, V. J., Morley, S., and Clemens, M. J. 2002. Inhibition of protein synthesis in apoptosis: Differential requirements by the tumor necrosis factor alpha family and a DNA-damaging agent for caspases and the double-stranded RNA-dependent protein kinase. Cancer Res. 62:2272-2280.
27. Kalde, M., Barth, M., Somssich, I. E., and Lippok, B. 2003. Members of the Arabidopsis WRKY group III transcription factors are part of different plant defense signaling pathways. Mol. Plant-Microbe Interact. 16:295-305.
28. Kerr, M. K. 2003. Design considerations for efficient and effective microarray studies. Biometrics 59:822-828.
29. Kim, H. J., Hyun, Y., Park, J. Y., Park, M. J., Park, M. K., Kim, M. D., Lee, M. H., Moon, J., Lee, I., and Kim, J. 2004. A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nat. Genet. 36:167-171.
30. Kosugi, S., and Ohashi, Y. 1997. PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell 9:1607-1619.
31. Kosugi, S., Suzuka, I., Ohashi, Y., Murakami, T., and Arai, Y. 1991. Upstream sequences of rice proliferating cell nuclear antigen (PCNA) gene mediate expression of PCNA-GUS chimeric gene in meristems of transgenic tobacco plants. Nucleic Acids Res. 19:1571-1576.
32. Kosugi, S., Suzuka, I., and Ohashi, Y. 1995. Two of three promoter elements identified in a rice gene for proliferating cell nuclear antigen are essential for meristematic tissue-specific expression. Plant J. 7:877-886.
33. Lacroix, B., Vaidya, M., Tzfira, T., and Citovsky, V. 2005. The VirE3 protein of Agrobacterium mimics a host cell function required for plant genetic transformation. EMBO (Eur. Mol. Biol. Organ.) J. 24:428-437.
34. Lin, J. F., and Wu, S. H. 2004. Molecular events in senescing Arabidopsis leaves. Plant J. 39:612-628.
35. Ludwig, A., and Tenhaken, R. 2001. Suppression of the ribosomal L2 gene reveals a novel mechanism for stress adaptation in soybean. Planta 212:792-798.
36. Lui, W. O., Foukakis, T., Liden, J., Thoppe, S. R., Dwight, T., Hoog, A., Zedenius, J., Wallin, G., Reimers, M., and Larsson, C. 2005. Expression profiling reveals a distinct transcription signature in follicular thyroid carcinomas with a PAX8-PPAR(gamma) fusion oncogene. Oncogene 24:1467-1476.
37. Maleck, K., Levine, A., Eulgem, T., Morgan, A., Schmid, J., Lawton, K. A., Dangl, J. L., and Dietrich, R. A. 2000. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat. Genet. 26:403-410.
38. Manevski, A., Bertoni, G., Bardet, C., Tremousaygue, D., and Lescure, B. 2000. In synergy with various cis-acting elements, plant insterstitial telomere motifs regulate gene expression in Arabidopsis root meristems. FEBS (Fed. Eur. Biol. Soc.) Lett. 483:43-46.
39. Marathe, R., Guan, Z., Anandalakshmi, R., Zhao, H., and Dinesh-Kumar, S. P. 2004. Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Mol. Biol. 55:501-520.
40. May, M. J., and Leaver, C. J. 1993. Oxidative stimulation of glutathione synthesis in Arabidopsis thaliana suspension cultures. Plant Physiol. 103:621-627.
41. Nam, J., Mysore, K. S., Zheng, C., Knue, M. K., Matthysse, A. G., and Gelvin, S. B. 1999. Identification of T-DNA tagged Arabidopsis mutants that are resistant to transformation by Agrobacterium. Mol. Gen. Genet. 261:429-438.
42. Narasimhulu, S. B., Deng, X. B., Sarria, R., and Gelvin, S. B. 1996. Early transcription of Agrobacterium T-DNA genes in tobacco and maize. Plant Cell 8:873-886.
43. Nester, E. W. 2000. DNA and protein transfer from bacteria to eukaryotes-the Agrobacterium story. Mol. Plant Pathol. 1:87-90.
44. Nimchuk, Z., Eulgem, T., Holt, B. F., 3rd, and Dangl, J. L. 2003. Recognition and response in the plant immune system. Annu. Rev. Genet. 37:579-609.
45. Pu, X. A., and Goodman, R. N. 1992. Induction of necrogenesis by Agrobacterium tumefaciens on grape explants. Physiol. Mol. Plant Pathol. 41:241-254.
46. Raghavan, C., Ong, E. K., Dalling, M. J., and Stevenson, T. W. 2005. Effect of herbicidal application of 2,4-dichlorophenoxyacetic acid in Arabidopsis. Funct. Integr. Genomics 5:4-17.
47. Redman, J. C., Haas, B. J., Tanimoto, G., and Town, C. D. 2004. Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J. 38:545-561.
48. Regad, F., Lebas, M., and Lescure, B. 1994. Interstitial telomeric repeats within the Arabidopsis thaliana genome. J. Mol. Biol. 239:163-169.
49. Roberts, R. L., Metz, M., Monks, D. E., Mullaney, M. L., Hall, T., and Nester, E. W. 2003. Purine synthesis and increased Agrobacterium tumefaciens transformation of yeast and plants. Proc. Natl. Acad. Sci. U.S.A. 100:6634-6639.
50. Schenk, P. M., Kazan, K., Wilson, I., Anderson, J. P., Richmond, T., Somerville, S. C., and Manners, J. M. 2000. Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc. Natl. Acad. Sci. U.S.A. 97:11655-11660.
51. Schenk, P. M., Kazan, K., Manners, J. M., Anderson, J. P., Simpson, R. S., Wilson, I. W., Somerville, S. C., and Maclean, D. J. 2003. Systemic gene expression in Arabidopsis during an incompatible interaction with Alternaria brassicicola. Plant Physiol. 132:999-1010.
52. Schoof, H., Lenhard, M., Haecker, A., Mayer, K. F., Jurgens, G., and Laux, T. 2000. The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100:635-644.
53. Schrammeijer, B., Risseeuw, E., Pansegrau, W., Regensburg-Tuink, T. J., Crosby, W. L., and Hooykaas, P. J. 2001. Interaction of the virulence protein VirF of Agrobacterium tumefaciens with plant homologs of the yeast Skp1 protein. Curr. Biol. 11:258-262.
54. Schrammeijer, B., den Dulk-Ras, A., Vergunst, A. C., Jurado Jacome, E., and Hooykaas, P. J. 2003. 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. 31:860-868.
55. Singh, K. B., Foley, R. C., and Onate-Sanchez, L. 2002. Transcription factors in plant defense and stress responses. Curr. Opin. Plant Biol. 5:430-436.
56. Smolen, G. A., Pawlowski, L., Wilensky, S. E., and Bender, J. 2002. Dominant alleles of the basic helix-loop-helix transcription factor ATR2 activate stress-responsive genes in Arabidopsis. Genetics 161:1235-1246.
57. Sturm, A., and Chrispeels, M. J. 1990. cDNA cloning of carrot extracellular beta-fructosidase and its expression in response to wounding and bacterial infection. Plant Cell 2:1107-1119.
58. Tao, Y., Xie, Z., Chen, W., Glazebrook, J., Chang, H.-S., Han, B., Zhu, T., Zou, G., and Katagiri, F. 2003. Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Plant Cell 15:317-330.
59. Tao, Y., Rao, P. K., Bhattacharjee, S., and Gelvin, S. B. 2004. Expression of plant protein phosphatase 2C interferes with nuclear import of the Agrobacterium T-complex protein VirD2. Proc. Natl. Acad. Sci. U.S.A. 101:5164-5169.
60. Tremousaygue, D., Manevski, A., Bardet, C., Lescure, N., and Lescure, B. 1999. Plant interstitial telomere motifs participate in the control of gene expression in root meristems. Plant J. 20:5535-61.
61. Tremousaygue, D., Garnier, L., Bardet, C., Dabos, P., Herve, C., and Lescure, B. 2003. Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J. 33:957-966.
62. Tusher, V. G., Tibshirani, R., and Chu, G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A. 98:5116-5121.
63. Tzfira, T., Vaidya, M., and Citovsky, V. 2001. VIP1, an Arabidopsis protein that interacts with Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. EMBO (Eur. Mol. Biol. Organ.) J. 20:3596-3607.
64. Tzfira, T., Vaidya, M., and Citovsky, V. 2002. Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. Proc. Natl. Acad. Sci. U.S.A. 99:10435-10440.
65. Tzfira, T., Li, J., Lacroix, B., and Citovsky, V. 2004. Agrobacterium T-DNA integration: Molecules and models. Trends Genet. 20:375-383.
66. van Wees, S. C. M., Chang, H.-S., Zhu, T., and Glazebrook, J. 2003. Characterization of the early response of Arabidopsis to Alternaria brassicicola infection using expression profiling. Plant Physiol. 132:606-617.
67. Veena, Jiang, H., Doerge, R. W., and Gelvin, S. B. 2003. Transfer of T-DNA and Vir proteins to plant cells by Agrobacterium tumefaciens induces expression of host genes involved in mediating transformation and suppresses host defense gene expression. Plant J. 35:219-236.
68. Vergunst, A. C., Schrammeijer, B., den Dulk-Ras, A., de Vlaam, C. M., Regensburg-Tuink, T. J., and Hooykaas, P. J. 2000. VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science 290:979-982.
69. Wan, J., Dunning, F. M., and Bent, A. F. 2002. Probing plant-pathogen interactions and downstream defense signaling using DNA microarrays. Funct. Integr. Genomics 2:259-273.
70. Wang, Y. J., Zhang, Z. G., He, X. J., Zhou, H. L., Wen, Y. X., Dai, J. X., Zhang, J. S., and Chen, S. Y. 2003. A rice transcription factor OsbHLH1 is involved in cold stress response. Theor. Appl. Genet. 107:1402-1409.
71. Wood, D. W., Setubal, J. C., Kaul, R., Monks, D. E., Kitajima, J. P., Okura, V. K., Zhou, Y., Chen, L., Wood, G. E., Almeida, N. F., Jr., Woo, L., Chen, Y., Paulsen, I. T., Eisen, J. A., Karp, P. D., Bovee, D., Sr., Chapman, P., Clendenning, J., Deatherage, G., Gillet, W., Grant, C., Kutyavin, T., Levy, R., Li, M. J., McClelland, E., Palmieri, A., Raymond, C., Rouse, G., Saenphimmachak, C., Wu, Z., Romero, P., Gordon, D., Zhang, S., Yoo, H., Tao, Y., Biddle, P., Jung, M., Krespan, W., Perry, M., Gordon-Kamm, B., Liao, L., Kim, S., Hendrick, C., Zhao, Z. Y., Dolan, M., Chumley, F., Tingey, S. V., Tomb, J. F., Gordon, M. P., Olson, M. V., and Nester, E. W. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317-2323.
72. Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:1362-4962.
73. Yokoyama, R., and Nishitani, K. 2001. A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant Cell Physiol. 42:1025-1033.
74. Zhu, J., Oger, P. M., Schrammeijer, B., Hooykaas, P. J., Farrand, S. K., and Winans, S. C. 2000. The bases of crown gall tumorigenesis. J. Bacteriol. 182:3885-3895.
75. Zhu, Y., Nam, J., Humara, J. M., Mysore, K. S., Lee, L. Y., Cao, H., Valentine, L., Li, J., Kaiser, A. D., Kopecky, A. L., Hwang, H. H., Bhattacharjee, S., Rao, P. K., Tzfira, T., Rajagopal, J., Yi, H., Veena, Yadav, B. S., Crane, Y. M., Lin, K., Larcher, Y., Gelvin, M. J., Knue, M., Ramos, C., Zhao, X., Davis, S. J., Kim, S. I., Ranjith-Kumar, C. T., Choi, Y. J., Hallan, V. K., Chattopadhyay, S., Sui, X., Ziemienowicz, A., Matthysse, A. G., Citovsky, V., Hohn, B., and Gelvin, S. B. 2003. Identification of Arabidopsis rat mutants. Plant Physiol. 132:494-505.