Transcriptome Analysis of Plant Drought and Salt Stress Response

  • Motoaki Seki
  • Taishi Umezawa
  • Jong-Myong Kim
  • Akihiro Matsui
  • Taiko Kim To
  • Kazuo Shinozaki


Plants must adapt to drought and high-salinity stresses in order to survive. Molecular and genomic studies have shown that many genes with various functions are induced by drought and high-salinity stresses, and that the various signaling factors are involved in the stress responses. The development of microarray-based expression profiling methods, together with the availability of genomic and/or cDNA sequence data, and gene-knock-out mutants, has allowed significant progress in the characterization of the plant stress response. Recent studies also revealed that small RNAs, RNA processing and chromatin regulation are involved in the abiotic stress responses. In this review, we highlight recent progress in the research on the transcriptome for the response to plant drought and salt stress


drought stress high-salinity stress transcriptome transcription factors small RNAs RNA processing chromatin remodeling 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling, Plant Cell, 15: 63–78.PubMedGoogle Scholar
  2. Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C. et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana, Science 301: 653–657.PubMedGoogle Scholar
  3. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism and function, Cell 116: 281–297.PubMedGoogle Scholar
  4. Bartels and Sunkar (2005) Drought and salt tolerance in plants, Critical Reviews in Plant Sciences 24:23–58.Google Scholar
  5. Baulcombe, D. (2004) RNA silencing in plants, Nature 431: 356–363.Google Scholar
  6. Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R. and Zhum J.K. (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis, Cell 123: 1279–1291.PubMedGoogle Scholar
  7. Boudsocq, M. and Lauriere, C. (2005) Osmotic signaling in plants. Multiple pathways mediated by emerging kinase families, Plant Physiol. 138: 1185–1194.PubMedGoogle Scholar
  8. Bray, E.A. (2002) Classification of genes differentially expressed during water-deficit stress in Arabidopsis thaliana: an analysis using microarray and differential expression data, Ann. Bot. 89: 803–811.PubMedGoogle Scholar
  9. Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G.G., Oezcimen, A., Rocca-Serra, P. and Sansone, S.A. (2003) ArrayExpress-a public repository for microarray gene expression data at the EBI, Nucleic Acids Res. 31: 68–71.PubMedGoogle Scholar
  10. Brosche, M., Vinocur, B., Alatalo, E.R., Lamminmaki, A., Teichmann, T., Ottow, E.A., Djilianov, D., Afif, D., Bogeat-Triboulot, M.B., Altman, A., Polle, A., Dreyer, E., Rudd, S., Paulin, L., Auvinen, P. and Kangasjarvi, J. (2005) Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert, Genome Biol. 6: R101.PubMedGoogle Scholar
  11. Buchanan, C.D., Lim, S., Salzman, R.A., Kagiampakis, I., Morishige, D.T., Weers, B.D., Klein, R.R., Pratt, L.H., Cordonnier-Pratt, M.M., Klein, P.E. and Mullet, J.E. (2005) Sorghum bicolor’s transcriptome response to dehydration, high salinity and ABA, Plant Mol. Biol. 58:699–720.PubMedGoogle Scholar
  12. Carrington, J.C. and Ambros, V. (2003) Role of microRNAs in plant and animal development, Science 301: 336–338.PubMedGoogle Scholar
  13. Chen, W., Provart, N.J., Glazebrook, J., Katagiri, F., Chang, H.S., Eulgem, T., Mauch, F., Luan, S., Zou, G., Whitham, S.A., Budworth, P.R., Tao, Y., Xie, Z., Chen, X., Lam, S., Kreps, J.A., Harper, J.F., Si-Ammour, A., Mauch-Mani, B., Heinlein, M., Kobayashi, K., Hohn, T., Dangl, J.L., Wang, X. and Zhu, T. (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses, Plant Cell 14: 559–574.PubMedGoogle Scholar
  14. Cheong, Y.H., Chang, H.S., Gupta, R., Wang, X., Zhu, T. and Luan, S. (2002) Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis, Plant Physiol. 129: 661–677.PubMedGoogle Scholar
  15. Chini, A., Grant, J., Seki, M., Shinozaki, K. and Loake, G. (2004) Drought tolerance established by enhanced expression of the CC-NBS-LRR gene, ADR1, requires salicylic acid, EDS1 and ABI1. Plant J 38:810–822.Google Scholar
  16. Chinnusamy, V., Ohta, M., Kannar, S., Lee, B., Hong, Z., Agarwal, A. and Zhu, J.K. (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis, Genes Dev. 17: 1043–1054.PubMedGoogle Scholar
  17. Chinnusamy, V., Schumaker, K. and Zhu, J.K. (2004) Molecular genetic perspectives on cross-talk and specificity in abiotic stress signaling in plants, J. Exp. Bot. 55: 225–236.PubMedGoogle Scholar
  18. Cominelli, E., Galbiati, M., Vavasseur, A., Conti, L., Sala, T., Vuylsteke, M., Leonhardt, N., Dellaporta, S. and Tonelli, C. (2005) A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance, Curr. Biol. 15: 1196–1200.PubMedGoogle Scholar
  19. Craigon, D.J., James, N., Okyere, J., Higgins, J., Jotham, J. and May, S. (2004) NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service, Nucleic Acids Res. 32: D575–D577.PubMedGoogle Scholar
  20. Davletova, S., Schlauch, K., Coutu, J. and Mittler, R (2005) The Zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis, Plant Physiol. 139:847–856.PubMedGoogle Scholar
  21. Dharmasiri, N., Dharmasiri, S. and Estelle, M. (2005) The F-box protein TIR1 is an auxin receptor, Nature 435:441–445.PubMedGoogle Scholar
  22. Dubouzet, J.G., Sakuma, Y., Ito, Y., Kasuga, M., Dubouzet, E.G., Miura, S., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression, Plant J 33: 751–763.PubMedGoogle Scholar
  23. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository, Nucleic Acids Res. 30: 207–210.PubMedGoogle Scholar
  24. 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.Google Scholar
  25. Fujita, M., Fujita, Y., Maruyama, K., Seki, M., Hiratsu, K., Ohme-Takagi, M., Tran, L.S.P., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2004) A dehydration-induced NAC protein, RD26 is involved in ABA-dependent stress signaling pathway. Plant J. 39:863–876.PubMedGoogle Scholar
  26. Fujita, Y., Fujita, M., Sato, R., Maruyama, K., Parvez, M.M., Seki, M., Hiratsu, K., Ohme-Takagi, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2005) AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis, Plant Cell 17: 3470–3488.PubMedGoogle Scholar
  27. Furihata, T., Maruyama, K., Fujita, Y., Umezawa, T., Yoshida, R., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2006) Abscisic acid-dependent multisite phosphorylation regulates the activity of a transcription activator AREB1, Proc. Natl. Acad. Sci. USA 103: 1988–1993.PubMedGoogle Scholar
  28. Gong, Z., Lee, H., Xiong, L., Jagendorf, A., Stevenson, B. and Zhu, J.K. (2002) RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance, Proc. Natl. Acad. Sci. USA , 99:11507–11512.PubMedGoogle Scholar
  29. Gong, Q., Li, P., Ma, S., Rupassara, S.I. and Bohnert, H.J. (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana, Plant J. 44:826–839.PubMedGoogle Scholar
  30. Gu, R., Fonseca, S., Puskas, L.G., JR, L.H., Zvara, A., Dudits, D. and Pais, M. (2004) Transcript identifi- cation and profiling during salt stress and recovery of Populus euphratica, Tree Physiol. 24:265–276.PubMedGoogle Scholar
  31. Gulick, P.J., Drouin, S., Yu, Z., Danyluk, J., Poisson, G., Monroy, A.F. and Sarhan, F. (2005) Transcriptome comparison of winter and spring wheat responding to low temperature, Genome 48: 913–923.PubMedGoogle Scholar
  32. Han, M.H., Goud, S., Song, L. and Fedoroff, N. (2004) The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation, Proc. Natl. Acad. Sci. USA 101:1093–1098.PubMedGoogle Scholar
  33. 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.PubMedGoogle Scholar
  34. 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.PubMedGoogle Scholar
  35. Hiraguri, A., Itoh, R., Kondo, N., Nomura, Y., Aizawa, D., Murai, Y., Koiwa, H., Seki, M., Shinozaki, K. and Fukuhara, T. (2005) Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol. Biol. 57:173–188.PubMedGoogle Scholar
  36. Hugouvieux, V., Kwak, J.M. and Schroeder, J.I. (2001) An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis, Cell 106: 477–487.PubMedGoogle Scholar
  37. Hwang, E.W., Kim, K.A., Park, S.C., Jeong, M.J., Byun, M.O. and Kwon, H.B. (2005) Expression profiles of hot pepper (Capsicum annuum) genes under cold stress conditions, J. Biosci. 30: 657–667.PubMedGoogle Scholar
  38. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. and Shinozaki, K. (2004) Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences, Nucleic Acids Res. 32: 5096–5103.PubMedGoogle Scholar
  39. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. and Shinozaki, K. (2005) RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Res.12:247–256.PubMedGoogle Scholar
  40. Inan, G., Zhang, Q., Li, P., Wang, Z., Cao, Z., Zhang, H., Zhang, C., Quist, T.M., Goodwin, S.M., Zhu, J., Shi, H., Damsz, B., Charbaji, T., Gong, Q., Ma, S., Fredricksen, M., Galbraith, D.W., Jenks, M.A., Rhodes, D., Hasegawa, P.M., Bohnert, H.J., Joly, R.J., Bressan, R.A. and Zhu, J.K. (2004) Salt Cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles, Plant Physiol. 135: 1718–1737.PubMedGoogle Scholar
  41. Ito, Y., Katsura, K., Maruyama, K., Taji, T., Kobayashi, M., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol. 47:141–153.PubMedGoogle Scholar
  42. Kamei, A., Seki, M, Umezawa, T., Ishida, J., Satou, M., Akiyama, K., Zhu, J.K. and Shinozaki, K. (2005) Analysis of gene expression profiles in Arabidopsis salt overly sensitive mutants, sos2 and sos3 mutants. Plant Cell and Environ. 28:1267–1275.Google Scholar
  43. Kawasaki, S., Borchert, C., Deyholos, M., Wang, H., Brazille, S., Kawai, K., Galbraith, D. and Bohnert, H. (2001) Gene expression profiles during the initial phase of salt stress in rice, Plant Cell 13: 889–905.PubMedGoogle Scholar
  44. Kepinski, S. and Leyser, O. (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor, Nature 435: 446–451.PubMedGoogle Scholar
  45. Koiwa, H., Barb, A.W., Xiong, L., Li, F., McCully, M.G., Lee, B.H., Sokolchik, I., Zhu, J., Gong, Z., Reddy, M., Sharkhuu, A., Manabe, Y., Yokoi, S., Zhu, J.K., Bressan, R.A. and Hasegawa, P.M. (2002) C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development, Proc. Natl. Acad. Sci. USA 99:10893–10898.PubMedGoogle Scholar
  46. Koiwa, H., Hausmann, S., Bang, W.Y., Ueda, A., Kondo, N., Hiraguri, A., Fukuhara, T., Bahk, J.D., Yun, D.J., Bressan, R.A., Hasegawa, P.M. and Shuman, S. (2004) Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases, Proc. Natl. Acad. Sci. USA 101:14539–14544.PubMedGoogle Scholar
  47. 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.PubMedGoogle Scholar
  48. Kurihara, Y., Yuasa, T. and Watanabe, Y. (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis, RNA 12:206–212.PubMedGoogle Scholar
  49. Kuromori, T., Hirayama, T., Kiyosue, Y., Takabe, H., Mizukado, S., Sakurai, T., Akiyama, K., Kamiya, A., Ito, T. and Shinozaki, K. (2004) A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis. Plant J. 37: 897–905.PubMedGoogle Scholar
  50. Lan, L., Li, M., Lai, Y., Xu, W., Kong, Z., Ying, K., Han, B. and Xue, Y. (2005) Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.), Plant Mol. Biol.59: 151–164.PubMedGoogle Scholar
  51. Lee, B.H., Henderson, D.A. and Zhu, J.K. (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1, Plant Cell 17: 3155–3175.PubMedGoogle Scholar
  52. Li, J., Wang, X.Q., Watson, M.B. and Assmann, S.M. (2000) Regulation of abscisic acid-induced stomatal closure and anion channels by guard cell AAPK kinase, Science 287: 300–303.PubMedGoogle Scholar
  53. Li, J., Kinoshita, T., Pandey, S., Ng, C.K.Y., Gygi, S.P., Shimazaki, K. and Assmann, S.M. (2002) Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase, Nature 418: 793–797.PubMedGoogle Scholar
  54. Lu, C. and Fedoroff, N. (2000) A mutation in the Arabidopsis HYL1 gene encoding a dsRNA-binding protein affects responses to abscisic acid, auxin, and cytokinin, Plant Cell 12:2351–2366.PubMedGoogle Scholar
  55. Lu, C., Han, M.H., Guevara-Garcia, A. and Fedoroff, N.V. (2002) Mitogen-activated protein kinase signaling in postgermination arrest of development by abscisic acid, Proc. Natl. Acad. Sci. USA 99:15812–15817.PubMedGoogle Scholar
  56. Lu, C., Tej, S.S., Luo, S., Haudenschild, C.D., Meyers, B.C. and Green, P.J. (2005) Elucidation of the small RNA component of the transcriptome, Science 309: 1567–1569.PubMedGoogle Scholar
  57. Macknight, R., Duroux, M., Laurie, R., Dijkwel, P., Simpson, G. and Dean, C. (2002) Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA, Plant Cell 14: 877–888.PubMedGoogle Scholar
  58. Mahajan, S. and Tuteja, N. (2005) Cold, salinity and drought stresses: an overview, Archives of Biochemistry and Biophysics 444: 139–158.PubMedGoogle Scholar
  59. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors, Nature 437: 376–380.PubMedGoogle Scholar
  60. Maruyama, K., Sakuma, Y., Kasuga, M., Ito, Y., Seki, M., Goda, H., Shimada, Y., Yoshida, S., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2004) Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems, Plant J. 38:982–993.PubMedGoogle Scholar
  61. Narusaka, Y., Narusaka, M., Seki, M., Ishida, J., Nakashima, M., Kamiya, A., Enju, A., Sakurai, T., Satoh, M., Kobayashi, M., Tosa, Y., Park, P. and Shinozaki, K. (2003) The cDNA microarray analysis using an Arabidopsis pad3 mutant reveals the expression profiles and classification of genes induced by Alternaria brassicicola attack, Plant Cell Physiol 44: 377–387.PubMedGoogle Scholar
  62. Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., Voinnet, O. and Jones, J.D.G. (2006) A plant miRNA contributes to antibacterial resistance by repression by repressing auxin signaling, Science 312: 436–439.PubMedGoogle Scholar
  63. Nishimura, N., Kitahata, N., Seki, M., Narusaka, Y., Narusaka, M., Kuromori, T., Asami, T., Shinozaki, K. and Hirayama, T. (2005) Analysis of ABA Hypersensitive Germination 2 revealed the pivotal functions of PARN in stress response in Arabidopsis, Plant J. 44:972–984.PubMedGoogle Scholar
  64. Osakabe, Y., Maruyama, K., Seki, M., Satou, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2005) An LRR receptor kinase, RPK1, is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis, Plant Cell 17:1105–1119.PubMedGoogle Scholar
  65. Oztur, Z.N., Talame, V., Deyholos, M., Michalowski, C.B., Galbraith, D.W., Gozukirmizi, N., Tuberosa, R. and Bohnert, H.J. (2002) Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley, Plant Mol. Biol. 48: 551–573.PubMedGoogle Scholar
  66. Papp, I., Mur, L.A., Dalmadi, A., Dulai, S. and Koncz, C. (2004) A mutation in the Cap Binding Protein 20 gene confers drought tolerance to Arabidopsis, Plant Mol. Biol. 55:679–686.PubMedGoogle Scholar
  67. Quesada, V., Macknight, R., Dean, C. and Simpson, G.G. (2003) Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time, EMBO J. 22: 3142–3152.PubMedGoogle Scholar
  68. Rabbani, M.A., Maruyama, K., Abe, H., Khan, M.A., Katsura, K., Ito, Y., Yoshiwara, K., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2003) Monitoring expression profiles of rice (Oryza sativa L.) genes under cold, drought and high-salinity stresses, and ABA application using both cDNA microarray and RNA gel blot analyses, Plant Physiol. 133: 1755–1767.PubMedGoogle Scholar
  69. Ramanjulu, S. and Bartels, D. (2002) Drought- and desiccation-induced modulation of gene expression in plants, Plant Cell Environ. 25: 141–151.PubMedGoogle Scholar
  70. Razem, F.A., El-Kereamy, A., Abrams, S.R. and Hill, R.D. (2006) The RNA-binding protein FCA is an abscisic acid receptor, Nature 439: 290–294.PubMedGoogle Scholar
  71. Rensink, W.A., Lobst, S., Hart, A., Stegalkina, S., Liu, J. and Buell, C.R. (2005) Gene expression profiling of potato responses to cold, heat, and salt stress, Funct. Integr. Genomics, 5: 201–207.PubMedGoogle Scholar
  72. Richmond, T. and Somerville, S. (2000) Chasing the dream: plant EST microarrays, Curr. Opin. Plant Biol. 3: 108–116.PubMedGoogle Scholar
  73. Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C.Z., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J.Z., Ghandehari, D., Sherman, B.K. and Yu, G.L. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes, Science 290: 2105–2110.PubMedGoogle Scholar
  74. Sakuma, Y., Maruyama, K., Osakabe, Y., Feng, Q., Seki, M., Shinozaki K. and Yamaguchi-Shinozaki, K. (2006) Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18: 1292–1309.PubMedGoogle Scholar
  75. Savitch, L.V., Allard, G., Seki, M., Robert, L.S., Tinker, N.A., Huner, N.P.A., Shinozaki, K. and Singh, J. (2005) The effects of overexpression of two Brassica CBF/DREB1-like transcription factors on phytosynthetic capacity and freezing tolerance in Brassica napus, Plant Cell Physiol. 46: 1525–1539.PubMedGoogle Scholar
  76. 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 a full-length cDNA microarray, Plant Cell 13: 61–72.PubMedGoogle Scholar
  77. 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.Google Scholar
  78. 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.Google Scholar
  79. 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.Google Scholar
  80. Seki, M., Kamei, A., Satou, M., Sakurai, T., Fujita, M., Oono, Y., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2003) Transcriptome Analysis in Abiotic Stress Conditions in Higher Plants, Topics Curr. Genet. 4: 271–295.Google Scholar
  81. Seki, M., Satou, M., Sakurai, T., Akiyama, K., Iida, K., Ishida, J., Nakajima, M., Enju, A., Narusaka, M., Fujita, M., Oono, Y., Kamei, A/, Yamaguchi-Shinozaki. K. and Shinozaki, K. (2004) RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions, J. Exp. Bot. 55: 213–223.PubMedGoogle Scholar
  82. Seki, M., Ishida, J., Nakajima, M., Enju, A., Iida, K., Satou, M., Fujita, M., Narusaka, Y., Narusaka, M., Sakurai, T., Akiyama, K., Oono, Y., Kamei, A., Umezawa, T., Mizukado, S., Maruyama, K., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2005). Genomic analysis of stress response. In “Plant Abiotic Stress (Edited by Drs. M.A. Jenks and P.M. Hasegawa)”, pp. 248–265. Blackwell Publishing Ltd., Sheffield, UK.Google Scholar
  83. Shi, H., Xiong, L., Stevenson, B., Lu, T. and Zhu, J.K. (2002) The Arabidopsis salt overly sensitive 4 mutants uncover a critical role for vitamin B6 in plant salt tolerance, Plant Cell 14: 575–588.PubMedGoogle Scholar
  84. 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.PubMedGoogle Scholar
  85. 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.PubMedGoogle Scholar
  86. Simpson, G.G. (2004) The autonomous pathway: epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time, Curr. Opin. Plant Biol. 7: 570–574.PubMedGoogle Scholar
  87. Simpson, G.G., Dijkwel, P.P., Quesada, V., Henderson, I. and Dean, C. (2003) FY is an RNA 3’ end-processing factor that interacts with FCA to control the Arabidopsis floral transition, Cell 113: 777–787.PubMedGoogle Scholar
  88. Song, C.P., Agarwal, M., Ohta, M., Guo, Y., Halfter, U., Wang, P. and Zhu, J.K. (2005) Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses, Plant Cell 17: 2384–2396.PubMedGoogle Scholar
  89. Sridha, S. and Wu, K. (2006) Identification of AtHD2C as a novel regulator of abscisic responses in Arabidopsis, Plant J. 46: 124–133.PubMedGoogle Scholar
  90. Stolc, V., Samanta, M.P., Tongprasit, W., Sethi, H., Liang, S., Nelson, D.C., Hegeman, A., Nelson, C., Rancour, D., Bednarek, S., Ulrich, E.L., Zhao, Q., Wrobel, R.L., Newman, C.S., Fox, B.G., Phillips, G.N., Markley, J.L. and Sussman, M.R. (2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays, Proc. Natl. Acad. Sci. USA 102: 4453–4458.PubMedGoogle Scholar
  91. Sunkar, R. and Zhu, J.K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis, Plant Cell 16: 2001–2019.PubMedGoogle Scholar
  92. Taji, T., Seki, M., Satou, M., Sakurai, T., Kobayashi, M., Ishiyama, K., Narusaka, Y., Narusaka, M., Zhu, J.K. and Shinozaki, K. (2004) Comparative Genomics in Salt Tolerance between Arabidopsis and Arabidopsis-Related Halophyte Salt Cress Using Arabidopsis Microarray, Plant Physiol. 135: 1697–1709PubMedGoogle Scholar
  93. Teige, M., Scheikl, E., Eulgem, T., Doczi, R., Ichimura, K., Shinozaki, K., Dangl, J.L. and Hirt, H. (2004) The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis , Molecular Cell 15: 141–152.PubMedGoogle Scholar
  94. Thomashow, M.F. (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms, Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 571–599.PubMedGoogle Scholar
  95. Tian, L., Fong, M.P., Wang, J.J., Wei, N.E., Jiang, H., Doerge, R.W. and Chen, Z.J. (2005) Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development, Genetics 169: 337–345.PubMedGoogle Scholar
  96. Ulm, R., Ichimura, K., Mizoguchi, T., Peck, S.C., Zhu, T., Wang, X., Shinozaki, K. and Paszkowski, J. (2002) Distinct regulation of salinity and genotoxic stress responses by Arabidopsis MAP kinase phosphatase 1, EMBO J. 21: 6483–6493.PubMedGoogle Scholar
  97. Umezawa, T., Yoshida, R., Maruyama, K., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2004) SRK2C, a SNF1-related protein kinase 2, improves drought tolerance by controlling stress-responsive gene expression in Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA 101: 17306–17311.PubMedGoogle Scholar
  98. Umezawa, T., Fujita, M., Fujita, Y., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future, Curr. Opin. Biotechnol. 17:113–122.PubMedGoogle Scholar
  99. Vinocur, B. and Altman, A. (2005) Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations, Curr. Opin. Biotechnol. 16: 123–132.PubMedGoogle Scholar
  100. Vogel, J.T., Zarka, D.G., Van Buskirk, H.A., Fowler, S.G. and Thomashow, M.F. (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis, Plant J. 41: 195–211.PubMedGoogle Scholar
  101. Wang, H., Miyazaki, S., Kawai, K., Deyholos, M., Galbraith, D.W. and Bohnert, H.J. (2003) Temporal progression of gene expression responses to salt shock in maize roots, Plant Mol. Biol. 52: 873–891.PubMedGoogle Scholar
  102. Watkinson, J.I., Sioson, A.A., Vasquez-Robinet, C., Shukla, M., Kumar, D., Ellis, M., Heath, L.S., Ramakrishnan, N., Chevone, B., Watson, L.T., Zyl, L.V., Egertsdotter, U., Sederoff, R.R. and Grene, R. (2003) Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine, Plant Physiol. 133: 1702–1716.PubMedGoogle Scholar
  103. Wong, C.E., Li, Y., Labbe, A., Guevara, D., Nuin, P., Whitty, B., Diaz, C., Golding, G.B., Gray, G.R., Weretilnyk, E.A., Griffith, M. and Moffatt, B.A. (2006) Transcriptional profiling implicates novel interactions between abiotic stress and hormonal responses in Thellungiella, a close relative of Arabidopsis, Plant Physiol. 140: 1437–1450.PubMedGoogle Scholar
  104. Xiong, L., Gong, Z., Rock, C.D., Subramanian, S., Guo, Y., Xu, W., Galbraith, D. and Zhu, J.K. (2001) Modulation of abscisic acid signal transduction and biosynthesis by an Sm-like protein in Arabidopsis, Dev. Cell 1:771–781.PubMedGoogle Scholar
  105. Xiong, L. and Zhu, J.K. (2001) Abiotic stress signal transduction in plants: Molecular and genetic perspectives, Physiol. Plant. 112: 152–166.PubMedGoogle Scholar
  106. Xiong, L. and Zhu, J.K. (2002) Molecular and genetic aspects of plant responses to osmotic stress, Plant Cell Environment 25: 131–139.Google Scholar
  107. Xiong, L., Schumaker, K.S. and Zhu, J.K. (2002) Cell signaling during cold, drought, and salt stress, Plant Cell Suppl., S165–183.Google Scholar
  108. Xiong, L., Lee, H., Ishitani, M., Tanaka, Y., Stevenson, B., Koiwa, H., Bressan, R.A., Hasegawa, P.M. and Zhu, J.K. (2002) Repression of stress-responsive genes by FIERY2, a novel transcriptional regulator in Arabidopsis, Proc. Natl. Acad. Sci. USA 99: 10899–10904.PubMedGoogle Scholar
  109. Xu, Q., Belcastro, M.P., Villa, S.T., Dinkins, R.D., Clarke, S.G. and Downie, A.B. (2004) A second protein L-isoaspartyl methyltransferase gene in Arabidopsis produces two transcripts whose products are sequestered in the nucleus, Plant Physiol, 136: 2652–2664.PubMedGoogle Scholar
  110. Xue, G.P. and Loveridge, C.W. (2004) HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element, Plant J, 37: 326–339.PubMedGoogle Scholar
  111. 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-Neumann, 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.H., 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.PubMedGoogle Scholar
  112. Yamaguchi-Shinozaki, K. and Shinozaki, K. (2005) Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters, Trends Plant Sci. 10:88–94.PubMedGoogle Scholar
  113. Yamaguchi-Shinozaki, K. and Shinozaki, K. (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses, Annu. Rev. Plant Biol. 57:781–803.PubMedGoogle Scholar
  114. Yu, L.X. and Setter, T.L. (2003) Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water defecit, Plant Physiol. 131: 568–582.PubMedGoogle Scholar
  115. Zhang, J.Z. (2003) Overexpression analysis of plant transcription factors, Curr. Opin. Plant Biol. 6: 430–440.PubMedGoogle Scholar
  116. Zhu, J.K. (2002) Salt and drought stress signal transduction in plants, Annu. Rev. Plant Biol. 53: 247–273.PubMedGoogle Scholar
  117. Zhu, J., Shi, H., Lee, B.H., Damsz, B., Cheng, S., Stirm, V., Zhu, J.K., Hasegawa, P.M. and Bressan, R.A. (2004) An Arabidopsis homeodomain transcription factor gene, HOS9, mediates cold tolerance through a CBF-independent pathway, Proc. Natl. Acad. Sci. USA 101: 9873–9878.PubMedGoogle Scholar
  118. Zhu, J., Verslues, P.E., Zheng, X., Lee, B.H., Zhan, X., Manabe, Y., Sokolchik, I., Zhu, Y., Dong, C.H., Zhu, J.K., Hasegawa, P.M. and Bressan, R.A. (2005) HOS10 encodes an R2R3-type MYB transcription factor essential for cold acclimation in plants, Proc. Natl. Acad. Sci. USA 102: 9966–9971.PubMedGoogle Scholar
  119. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox, Plant Physiol.136: 2621–2632.PubMedGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Motoaki Seki
    • 1
  • Taishi Umezawa
    • 2
  • Jong-Myong Kim
    • 1
  • Akihiro Matsui
    • 1
  • Taiko Kim To
    • 1
  • Kazuo Shinozaki
    • 3
  1. 1.Plant Genomic Network Research Team, Plant Functional Genomics Research Group RIKEN Plant Science Center (PSC)RIKEN Yokohama InstituteTsurumi-kuJapan
  2. 2.Gene Discovery Research Team RIKEN Plant Science Center (PSC)RIKEN Tsukuba InstituteTsukubaJapan
  3. 3.CRESTJapan Science and Technology Corporation (JST)Japan

Personalised recommendations