Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray

Plant Molecular Biology

Volumn 56, Issue 1, 2004, Pages 29-55

  Takahashi, Seiji ^a,d   Seki, Motoaki ^a,b   Ishida, Junko ^b   Satou, Masakazu ^b   Sakurai, Tetsuya ^b   Narusaka, Mari ^b   Kamiya, Asako ^b   Nakajima, Maiko ^b   Enju, Akiko ^b   Akiyama, Kenji ^b   Yamaguchi Shinozaki, Kazuko ^c   Shinozaki, Kazuo ^a,b  

^a RIKEN TSUKUBA INSTITUTE   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c JAPAN INTERNATIONAL RESEARCH CENTER FOR AGRICULTURAL SCIENCES   (Japan)

^d TOHOKU UNIVERSITY   (Japan)

Author keywords

Abiotic stress; Arabidopsis thaliana; cDNA microarray; Full length cDNA; T87 cell culture

Indexed keywords

ACIDS; CELLS; CROSSTALK; DNA; SODIUM CHLORIDE;

ABSCISIC ACID (ABA); MICROARRAYS; SIGNALING PATHWAYS; VENN DIAGRAM ANALYSIS;

GENES;

ABSCISIC ACID; COMPLEMENTARY DNA; HYDROGEN PEROXIDE; HYPERTONIC SOLUTION; MANNITOL; MESSENGER RNA; SODIUM CHLORIDE;

ARABIDOPSIS; ARTICLE; CELL CULTURE; CHEMISTRY; COMPARATIVE STUDY; CYTOLOGY; DNA MICROARRAY; DNA SEQUENCE; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; NORTHERN BLOTTING; OSMOTIC PRESSURE; OXIDATIVE STRESS; PROMOTER REGION; SEEDLING; TIME;

ABSCISIC ACID; ARABIDOPSIS; BLOTTING, NORTHERN; CELLS, CULTURED; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; HYDROGEN PEROXIDE; HYPERTONIC SOLUTIONS; MANNITOL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OSMOTIC PRESSURE; OXIDATIVE STRESS; PROMOTER REGIONS (GENETICS); RNA, MESSENGER; SEEDLING; SEQUENCE ANALYSIS, DNA; SODIUM CHLORIDE; TIME FACTORS; TRANSCRIPTION, GENETIC;

ACIDS; CELLS; GENES; NUCLEIC ACIDS; SODIUM COMPOUNDS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA; EUKARYOTA;

EID: 19944434202     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-004-2200-0     Document Type: Article

References (73)

1. Abe, H., Yamaguchi-Shinozaki, K., Urao, T., Iwasaki, T., Hosokawa, D. and Shinozaki, K. 1997. Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9: 1859-1868.
2. Abe, H., Urao, T., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. 2003. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcription activators in abscisic acid signaling. Plant Cell 15: 63-78.
3. Aharoni, A. and Vorst, O. 2002. DNA microarrays for functional plant genomics. Plant Mol. Biol. 48: 99-118.
4. 2+-regulated kinases. EMBO J. 20: 1051-1063.
5. Axelos, M., Curie, C., Mazzolini, L., Bardet, C. and Lescure, B. 1992. A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures. Plant Physiol. Biochem. 30: 123-128.
6. Banzet, N., Richaud, C., Deveaux, Y., Kazmaier, M., Gagnon, J. and Triantaphylides, C. 1998. Accumulation of small heat shock proteins, including mitochondrial HSP22, induced by oxidative stress and adaptive response in tomato cells. Plant J. 13: 519-527.
7. Bohnert, H.J., Nelson, D.E. and Jensen, R.G. 1995. Adaptations to environmental stresses. Plant Cell 7: 1099-1111.
8. Bonetta, D. and McCourt, P. 1998. Genetic analysis of ABA signal transduction pathways. Trends Plant Sci. 3: 231-235.
9. Bray, E.A. 1997. Plant responses to water deficit. Trends Plant Sci. 2: 48-54.
10. 2-inducible, Arabidopsis glutathione S-transferase gene contains closely linked OBF- and OBP1-binding sites. Plant J. 10: 955-966.
11. Choi, H., Hong, J., Ha, J., Kang, J. and Kim, S.Y. 2000. ABFs, a family of ABA-responsive element binding factors J. Biol. Chem. 275: 1723-1730.
12. Cutler, A.J. and Krochko, J.E. 1999. Formation and breakdown of ABA. Trends Plant Sci. 4: 472-478.
13. Desikan, R., A-H-Mackerness, S., Hancock, J.T. and Neill, S.J. 2001. Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiol. 127: 159-172.
14. Eulgem, T., Rushton, P.J., Robatzek, S. and Somssich, I.E. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5: 199-206.
15. Eulgem, T., Rushton, P.J., Schmelzer, E., Hahlbrock, K. and Somssich, I.E. 1999. Early nuclear events in plant defence signaling: rapid gene activation by WRKY transcription factors. EMBO J. 18: 4689-4699.
16. Finkelstei, D., Ewing, R., Gollub, J., Sterky, F., Cherry, J.M. and Somerville, S. 2002. Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium. Plant Mol. Biol. 48: 119-131.
17. Fowler, S. and Thomashow, M.F. 2002. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14: 1675-1690.
18. Grill, E. and Himmelbach, A. 1998. ABA signal transduction. Curr. Opin. Plant Biol. 1: 412-418.
19. Guan, L. and Scandalios, J.G. 1993. Characterization of the catalase antioxidant defense gene Cat1 of maize, and its developmentally regulated expression in transgenic tobacco. Plant J. 3: 527-536.
20. 2 is the likely intermediary signaling molecule for the response. Plant J. 22: 87-95.
21. Harper, J.F., Manney, L., DeWitt, N.D., Yoo, M.H. and Sussman, M.R. 1990. The Arabidopsis thaliana plasma membrane H(+)-ATPase multigene family. Genomic sequence and expression of a third isoform. J. Biol. Cliem. 265: 13601-13608.
22. Hasegawa, P.M., Bressan, R.A., Zhu, J.K. and Bohnert, H.J. 2000. Plant cellular and molecular responses to high salinity. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51: 463-499.
23. Hazen, S.P., Wu, Y. and Kreps, J.A. 2003. Gene expression profiling of plant responses to abiotic stress. Funct. Integr. Genomics 3: 105-111.
24. Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. 1999. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27: 297-300.
25. Himmelbach, A., Item, M. and Grill, E. 1998. Signaling of abscisic acid to regulate plant growth. Philos. Trans. R. Soc. Lond. R. Biol. Sci. 353: 1439-1444.
26. Ingram, J. and Bartels, D. 1996. The molecular basis of dehydration tolerance in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 377-403.
27. Jouanneau, J.-P. and Péaud-Lenoël, C. 1967. Croissance et synthèse des protéines de suspensions cellulaires de tabac sensibles à la kinétine. Physiol. Plant. 20: 834-850.
28. Kawasaki, S., Borchert, C., Deyholos, M., Wang, H., Brazille, S., Kawai, K., Galbraith, D. and Bohnert, H.J. 2001. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13: 889-905.
29. Kiyosue, T., Yamaguchi-Shinozaki, K. and Shinozaki, K. 1994. Cloning of cDNAs for genes that are early-responsive to dehydration stress (ERDs) in Arabidopsis thaliana L.: identification of three ERDs as HSP cognate genes. Plant Mol. Biol. 25: 791-798.
30. Kreps, J.A., Wu, Y., Chang, H.S., Zhu, T., Wang, X. and Harper, J.F. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 130: 2129-2141.
31. Kurkela, S. and Borg-Franck, M. 1990. Cloning and characterization of a cold- and ABA-inducible Arabidopsis gene. Plant Mol. Biol. 15: 137-144.
32. Kurkela, S. and Borg-Franck, M. 1992. Structure and expression of kin2, one of two cold- and ABA-induced genes of Arabidopsis thaliana. Plant Mol. Biol. 19: 689-692.
33. Kwak, J.M., Mori, I.C., Pei, Z.M., Leonhardt, N., Torres, M.A., Dangl, J.L., Bloom, R.E., Bodde, S., Jones, J.D. and Schroeder, J.I. 2003. NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis. EMBO J. 22: 2623-2633.
34. Lebel, E., Heifetz, P., Thorne, L., Uknes, S., Ryals, J. and Ward, E. 1998. Functional analysis of regulatory sequences controlling PR-1 gene expression in Arabidopsis. Plant J. 16: 223-323.
35. Lee, Y.H. and Chun, J.Y. 1998. A new homeodomain-leucine zipper gene from Arabidopsis thaliana induced by water stress and abscisic acid treatment. Plant Mol. Biol. 37: 377-384.
36. Leung, J., Bouvier-Durand, M., Morris, P.C., Guerrier, D., Chefdor, F. and Giraudat, J. 1994. Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase. Science 264: 1448-1452.
37. Lippuner, V., Cyert, M.S. and Gasser, C.S. 1996. Two class of plant cDNA clones differentially complement yeast calcineurin mutants and increase salt tolerance of wild-type yeast. J. Biol. Chem. 271: 12859-12866.
38. Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K. and Shinozaki, K. 1998. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10: 1391-1406.
39. Medford, J.I., Elmer, J.S. and Klee, H.J. 1991. Molecular cloning and characterization of genes expressed in shoot apical meristems. Plant Cell 3: 359-370.
40. Meyer, K., Leube, M.P. and Grill, E. 1994. A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana. Science 264: 1452-1455.
41. 2+ channels in guard cells requires cytosolic NAD(P)H and is differentially disrupted upstream and downstream of reactive oxygen species production in abi1-1 and abi2-1 protein phosphatase 2C mutants. Plant Cell 13: 2513-2523.
42. Neill, S.J., Desikan, R., Clarke and Hancock, J.T. 2002b. Hydrogen peroxide signaling. Curr. Opin. Plant Biol. 5: 388-395.
43. Neill, S.J., Desikan, R., Clarke, A., Hurst, R.D. and Hancock, J.T. 2002a. Hydrogen peroxide and nitric oxide as signaling molecules in plants. J. Exp. Bot. 53: 1237-1247.
44. Okamuro, J.K., Caster, B., Villarroel, V., VanMontagu, M. and Jofuku, K.D. 1997. The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc. Natl. Acad. Sci. USA 94: 7076-7081.
45. Pei, Z.M., Murata, Y., Benning, G., Thomine, S., Klusener, B., Allen, G.J., Grill, E. and Schroeder, J.I. 2000. Calcium channels activated by hydrogen peroxide mediate abscisic acid signaling in guard cells. Nature 406: 731-734.
46. Price, A.H. and Hendry, G.A.F. 1991. Iron-catalyzed oxygen radical formation and its possible contribution to drought damage in nine native grasses and three cereals. Plant Cell Environ. 14: 477-484.
47. Reymond, P., Weber, H., Damond, M. and Farmer, E.E. 2000. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12: 707-720.
48. Rushmore, T.H., Morton, M.R. and Pickett, C.B. 1991. The antioxidant responsive element. Activation by oxidative stress and identification of the DNA consensus sequence required for functional activity. J. Biol. Chem. 266: 11632-11639.
49. Sakuma, Y., Liu, Q., Dubouzet, J.G., Abe, H., Shinozaki, K. and Yamaguchi-Shinozaki, K. 2002. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and col-inducible gene expression. Biochem. Biophys. Res. Commun. 290: 998-1009.
50. Sambrook, J., Fritsch, E.F. and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
51. Sarafian, V., Kim, Y., Poole, R.J. and Rea, P.A. 1992. Molecular cloning and sequence of cDNA encoding the pyrophosphate-energized vacuolar membrane proton pump of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 89: 1775-1779.
52. Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y. and Shinozaki, K. 1998. High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J. 15: 707-720.
53. Seki, M., Ishida, J., Narusaka, M., Fujita, M., Nanjo, T., Umezawa, T., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., Satou, M., Akiyama, K., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y. and Shinozaki, K. 2002c. Monitoring the expression pattern of ca. 7000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct. Integr. Genomics 2: 282-291.
54. Seki, M., Kamei, A., Yamaguchi-Shinozaki, K. and Shinozaki, K. 2003. Molecular responses to drought, salinity and frost: common and different paths for plant protection. Curr. Opin. Biotechnol. 14: 194-199.
55. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y. and Shinozaki, K. 2001. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses using full-length cDNA microarray. Plant Cell 13: 61-72.
56. Seki, M., Narusaka, M., Ishida, J., Nanjo, T., Fujita, M., Oono, Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., Satou, M., Akiyama, K., Taji, T., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y. and Shinozaki, K. 2002b. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold, and high-salinity stresses using a full-length cDNA microarray. Plant J. 31: 279-292.
57. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., Muramatsu, M., Hayashizaki, Y., Kawai, J., Carninci, P., Itoh, M., Ishii, Y., Arakawa, T., Shibata, K., Shinagawa, A. and Shinozaki, K. 2002a. Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141-145.
58. Shinozaki, K. and Yamaguchi-Shinozaki, K. 1997. Gene expression and signal transduction in water-stress response. Plant Physiol. 115: 327-334.
59. Shinozaki, K. and Yamaguchi-Shinozaki, K. 2000. Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr. Opin. Plant Biol. 3: 217-223.
60. Shinozaki, K., Yamaguchi-Shinozaki, K. and Seki, M. 2003. Regulatory network of gene expression in the drought and cold stress responses. Curr. Opin. Plant Biol. 6: 410-417.
61. Taji T., Ohsumi C., Iuchi S., Seki M., Kasuga M., Kobayashi, M., Yamaguchi-Shinozaki, K. and Shinozaki, K. 2002. Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in Arabidopsis thaliana. Plant J. 29: 417-426.
62. Takahashi, S., Katagiri, T., Hirayama, T., Yamaguchi-Shinozaki, K. and Shinozaki, K. 2001. Hyperosmotic stress induces a rapid and transient increase in inositol 1,4,5-trisphosphate independent of abscisic acid in Arabidopsis cell culture. Plant Cell Physiol. 42: 214-222.
63. 2+-binding protein is induced by abscisic acid during dehydration. Plant Cell Physiol. 41: 898-903.
64. Thimm, O., Essigmann, B., Kloska, S., Altmann, T. and Buckhout, T.J. 2001. Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis. Plant Physiol. 127: 1030-1043.
65. Thomashow, M.F. 1999. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 571-599.
66. Uno, Y., Furihata, T., Abe, H., Yoshida, R., Shinozaki, K. and Yamaguchi-Shinozaki, K. 2000. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc. Natl. Acad. Sci. USA 97: 11632-11637.
67. Urao, T., Yamaguchi-Shinozaki, K., Urao, S. and Shinozaki, K. 1993. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell 5: 1529-1539.
68. Xu, W., Chambbell, P., Vargheese, A.K. and Braam, J. 1996. The Arabidopsis XET-related gene family: environmental and hormonal regulation of expression. Plant J. 9: 879-889.
69. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Newmann, G., Liu, S.X., Lam, B., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H.L., Tripp, M., Chang, C.H., Lee, J.M., Toriumi, M., Chan, M.M., Tang, C.C., Onodera, C.S., Deng, J.M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A.D., Gurjal, M., Hansen, N.F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V.W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P.X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E.K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R.W., Theologis, A. and Ecker, J.R. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846.
70. Yamaguchi-Shinozaki, K., Koizumi, M., Urao, S. and Shinozaki, K. 1992. Molecular cloning and characterization of 9 cDNAs for genes that are responsive to desiccation in Arabidopsis thaliana: sequence analysis of one cDNA clone that encodes a putative transmembrane channel protein. Plant Cell Physiol. 33: 217-224.
71. Yamaguchi-Shinozaki, K. and Shinozaki, K. 1994. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6: 251-264.
72. Yuasa, T., Ichimura, K., Mizoguchi, T. and Shinozaki, K. 2001. Oxidative stress activates ATMPK6, an Arabidopsis homologue of MAP kinase. Plant Cell Physiol. 42: 1012-1016.
73. Zhu, J.-K. 2002. Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 53: 247-273.