Skip to main content

Abstract

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

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism and function, Cell 116: 281–297.

    PubMed  CAS  Google Scholar 

  • Bartels and Sunkar (2005) Drought and salt tolerance in plants, Critical Reviews in Plant Sciences 24:23–58.

    CAS  Google Scholar 

  • Baulcombe, D. (2004) RNA silencing in plants, Nature 431: 356–363.

    Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Boudsocq, M. and Lauriere, C. (2005) Osmotic signaling in plants. Multiple pathways mediated by emerging kinase families, Plant Physiol. 138: 1185–1194.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Carrington, J.C. and Ambros, V. (2003) Role of microRNAs in plant and animal development, Science 301: 336–338.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Dharmasiri, N., Dharmasiri, S. and Estelle, M. (2005) The F-box protein TIR1 is an auxin receptor, Nature 435:441–445.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Kepinski, S. and Leyser, O. (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor, Nature 435: 446–451.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Mahajan, S. and Tuteja, N. (2005) Cold, salinity and drought stresses: an overview, Archives of Biochemistry and Biophysics 444: 139–158.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Ramanjulu, S. and Bartels, D. (2002) Drought- and desiccation-induced modulation of gene expression in plants, Plant Cell Environ. 25: 141–151.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Richmond, T. and Somerville, S. (2000) Chasing the dream: plant EST microarrays, Curr. Opin. Plant Biol. 3: 108–116.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Sridha, S. and Wu, K. (2006) Identification of AtHD2C as a novel regulator of abscisic responses in Arabidopsis, Plant J. 46: 124–133.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Sunkar, R. and Zhu, J.K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis, Plant Cell 16: 2001–2019.

    PubMed  CAS  Google Scholar 

  • 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: 1697–1709

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Thomashow, M.F. (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms, Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 571–599.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Vinocur, B. and Altman, A. (2005) Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations, Curr. Opin. Biotechnol. 16: 123–132.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Xiong, L. and Zhu, J.K. (2001) Abiotic stress signal transduction in plants: Molecular and genetic perspectives, Physiol. Plant. 112: 152–166.

    PubMed  CAS  Google Scholar 

  • Xiong, L. and Zhu, J.K. (2002) Molecular and genetic aspects of plant responses to osmotic stress, Plant Cell Environment 25: 131–139.

    CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Zhang, J.Z. (2003) Overexpression analysis of plant transcription factors, Curr. Opin. Plant Biol. 6: 430–440.

    PubMed  CAS  Google Scholar 

  • Zhu, J.K. (2002) Salt and drought stress signal transduction in plants, Annu. Rev. Plant Biol. 53: 247–273.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox, Plant Physiol.136: 2621–2632.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer

About this chapter

Cite this chapter

Seki, M., Umezawa, T., Kim, JM., Matsui, A., To, T.K., Shinozaki, K. (2007). Transcriptome Analysis of Plant Drought and Salt Stress Response. In: Jenks, M.A., Hasegawa, P.M., Jain, S.M. (eds) Advances in Molecular Breeding Toward Drought and Salt Tolerant Crops. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-5578-2_11

Download citation

Publish with us

Policies and ethics