Time of day shapes Arabidopsis drought transcriptomes

Plant Journal

Volumn 63, Issue 5, 2010, Pages 715-727

  Wilkins, Olivia ^a,b   Bräutigam, Katharina ^a,b   Campbell, Malcolm M ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Arabidopsis thaliana; diel; drought; microarray; stress; transcriptome

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; CHLOROPHYLL CONTENTS; COMPARATIVE ANALYSIS; CORE SET; DIEL; DIURNAL CHANGES; DIURNAL CYCLE; DROUGHT STRESS; GAIN INSIGHT; LEAF WATER; MITIGATING FACTOR; NATURAL CONDITIONS; ON DYNAMICS; RELATIVE WATER CONTENT; STRESS RESPONSE; TIME OF DAY; TIME POINTS; TRANSCRIPTOMES; WATER DEPRIVATION; WATER STRESS;

CHLOROPHYLL; GENES; PLANTS (BOTANY); PORPHYRINS; WATER CONTENT;

DROUGHT;

PHYTOHORMONE; WATER;

ARABIDOPSIS; ARTICLE; CIRCADIAN RHYTHM; CLUSTER ANALYSIS; DNA MICROARRAY; DROUGHT; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PLANT LEAF; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TIME;

ARABIDOPSIS; CIRCADIAN RHYTHM; CLUSTER ANALYSIS; DROUGHTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT GROWTH REGULATORS; PLANT LEAVES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TIME FACTORS; WATER;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 77956085371     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2010.04274.x     Document Type: Article

References (64)

1. Bates, B.C., Z.W, K., Wu, S. Palutikof, J.P., eds. 2008. Climate change and water. Technical paper of the intergovernmental panel on climate change. Geneva : IPCC. 210 pp.
2. Benjamini, Y. Hochberg, Y. (1995) Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57 (1 289 300.
3. Bieniawska, Z., Espinoza, C., Schlereth, A., Sulpice, R., Hincha, D.K. Hannah, M.A. (2008) Disruption of the arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol. 147 (1 263 279.
4. Blackman, S.A., Obendorf, R.L. Leopold, A.C. (1992) Maturation proteins and sugars in desiccation tolerance of developing soybean seeds. Plant Physiol. 100 (1 225 230.
5. Bläsing, O.E., Gibon, Y., Gunther, M., Hohne, M., Morcuende, R., Osuna, D., Thimm, O., Usadel, B., Scheible, W.R. Stitt, M. (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in arabidopsis. Plant Cell, 17 (12 3257 3281.
6. Bogeat-Triboulot, M.B., Brosche, M., Renaut, J. et al. (2007) Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in populus euphratica, a poplar growing in arid regions. Plant Physiol. 143 (2 876 892.
7. Bray, E.A. (2004) Genes commonly regulated by water-deficit stress in arabidopsis thaliana. J. Exp. Bot. 55 (407 2331 2341.
8. Brosche, M., Vinocur, B., Alatalo, E.R. et al. (2005) Gene expression and metabolite profiling of populus euphratica growing in the negev desert. Genome Biol. 6 (12 R101.
9. Chaves, M.M., Pereira, J.S., Maroco, J., Rodrigues, M.L., Ricardo, C.P.P., Osorio, M.L., Carvalho, I., Faria, T. Pinheiro, C. (2002) How plants cope with water stress in the field Photosynthesis and growth. Ann. Bot. 89, 907 916.
10. Christmann, A., Moes, D., Himmelbach, A., Yang, Y., Tang, Y. Grill, E. (2006) Integration of abscisic acid signalling into plant responses. Plant Biol. (Stuttg). 8 (3 314 325.
11. Correia, M.J., Pereira, J.S., Chaves, M.M., Rodrigues, M.L. Pacheco, C.A. (1995) Aba xylem concentrations determine maximum daily leaf conductance of field-grown vitis-vinifera l plants. Plant Cell Environ. 18 (5 511 521.
12. Covington, M.F. Harmer, S.L. (2007) The circadian clock regulates auxin signaling and responses in arabidopsis. PLoS Biol. 5 (8 e222.
13. Covington, M.F., Maloof, J.N., Straume, M., Kay, S.A. Harmer, S.L. (2008) Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol. 9 (8 R130.
14. Degenkolbe, T., Do, P.T., Zuther, E., Repsilber, D., Walther, D., Hincha, D.K. Kohl, K.I. (2008) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol. Biol. 69, 133 153.
15. Dodd, A.N., Salathia, N., Hall, A., Kevei, E., Toth, R., Nagy, F., Hibberd, J.M., Millar, A.J. Webb, A.A. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science, 309 (5734 630 633.
16. Gautier, L., Cope, L., Bolstad, B.M. Irizarry, R.A. (2004) Affy - analysis of affymetrix genechip data at the probe level. Bioinformatics, 20 (3 307 315.
17. Gentleman, R.C., Carey, V.J., Bates, D.M. et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5 (10 R80.
18. Gentleman, R.C., Carey, V.J., Huber, W. Hahne, F. 2009. Genefilter: Methods for filtering genes from microarray experiments. R Package : Version 1.24.2.
19. Goda, H., Sasaki, E., Akiyama, K. et al. (2008) The atgenexpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J. 55 (3 526 542.
20. Guo, P., Baum, M., Grando, S., Ceccarelli, S., Bai, G., Li, R., von Korff, M., Varshney, R.K., Graner, A. Valkoun, J. (2009) Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage. J. Exp. Bot. 60 (12 3531 3544.
21. Gutterson, N. Zhang, J.Z. (2004) Genomics applications to biotech traits: a revolution in progress? Curr. Opin. Plant Biol. 7 (2 226 230.
22. Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A. Kay, S.A. (2000) Orchestrated transcription of key pathways in arabidopsis by the circadian clock. Science, 290 (5499 2110 2113.
23. Hotta, C.T., Gardner, M.J., Hubbard, K.E., Baek, S.J., Dalchau, N., Suhita, D., Dodd, A.N. Webb, A.A.R. (2007) Modulation of environmental responses of plants by circadian clocks. Plant Cell Environ. 30 (3 333 349.
24. Huang, D., Wu, W., Abrams, S.R. Cutler, A.J. (2008) The relationship of drought-related gene expression in arabidopsis thaliana to hormonal and environmental factors. J. Exp. Bot. 59 (11 2991 3007.
25. Jang, I.C., Oh, S.J., Seo, J.S. et al. (2003) Expression of a bifunctional fusion of the escherichia coli genes for trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in transgenic rice plants increases trehalose accumulation and abiotic stress tolerance without stunting growth. Plant Physiol. 131 (2 516 524.
26. Karim, S., Aronsson, H., Ericson, H., Pirhonen, M., Leyman, B., Welin, B., Mantyla, E., Palva, E.T., Van Dijck, P. Holmstrom, K.O. (2007) Improved drought tolerance without undesired side effects in transgenic plants producing trehalose. Plant Mol. Biol. 64 (4 371 386.
27. Kawaguchi, R., Girke, T., Bray, E.A. Bailey-Serres, J. (2004) Differential mrna translation contributes to gene regulation under non-stress and dehydration stress conditions in arabidopsis thaliana. Plant J. 38 (5 823 839.
28. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J. Harter, K. (2007) The atgenexpress global stress expression data set: protocols, evaluation and model data analysis of uv-b light, drought and cold stress responses. Plant J. 50 (2 347 363.
29. Ko, J.H., Yang, S.H. Han, K.H. (2006) Upregulation of an arabidopsis ring-h2 gene, xerico, confers drought tolerance through increased abscisic acid biosynthesis. Plant J. 47 (3 343 355.
30. Kreps, J.A., Wu, Y., Chang, H.S., Zhu, T., Wang, X. Harper, J.F. (2002) Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 130 (4 2129 2141.
31. Legnaioli, T., Cuevas, J. Mas, P. (2009) Toc1 functions as a molecular switch connecting the circadian clock with plant responses to drought. EMBO J. 28 (23 3745 3757.
32. Leung, J., Merlot, S. Giraudat, J. (1997) The arabidopsis abscisic acid-insensitive2 (abi2) and abi1 genes encode homologous protein phosphatases 2c involved in abscisic acid signal transduction. Plant Cell, 9 (5 759 771.
33. Liu, J.J.J., Krenz, D.C., Galvez, A.F. de Lumen, B.O. (1998) Galactinol synthase (gs): increased enzyme activity and levels of mrna due to cold and desiccation. Plant Sci. 134 (1 11 20.
34. Matsui, A., Yokoyama, R., Seki, M., Ito, T., Shinozaki, K., Takahashi, T., Komeda, Y. Nishitani, K. (2005) Atxth27 plays an essential role in cell wall modification during the development of tracheary elements. Plant J. 42 (4 525 534.
35. McClung, C.R. (2006) Plant circadian rhythms. Plant Cell, 18 (4 792 803.
36. Mcgill, R., Tukey, J.W. Larsen, W.A. (1978) Variations of box plots. Am. Stat. 32 (1 12 16.
37. Michael, T.P., Breton, G., Hazen, S.P., Priest, H., Mockler, T.C., Kay, S.A. Chory, J. (2008a) A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol. 6 (9 1887 1898.
38. Michael, T.P., Mockler, T.C., Breton, G. et al. (2008b) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet. 4 (2 e14.
39. Miranda, J.A., Avonce, N., Suarez, R., Thevelein, J.M., Van Dijck, P. Iturriaga, G. (2007) A bifunctional tps-tpp enzyme from yeast confers tolerance to multiple and extreme abiotic-stress conditions in transgenic arabidopsis. Planta, 226 (6 1411 1421.
40. Mizuno, T. Yamashino, T. (2008) Comparative transcriptome of diurnally oscillating genes and hormone-responsive genes in arabidopsis thaliana: insight into circadian clock-controlled daily responses to common ambient stresses in plants. Plant Cell Physiol. 49 (3 481 487.
41. Mochida, K., Kawaura, K., Shimosaka, E., Kawakami, N., Shin, I.T., Kohara, Y., Yamazaki, Y. Ogihara, Y. (2006) Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat. Mol. Gen. Genomics. 276 (3 304 312.
42. Nishizawa, A., Yabuta, Y. Shigeoka, S. (2008) Galactinol and raffinose constitute a novel function to protect plants from oxidative damage. Plant Physiol. 147 (3 1251 1263.
43. Novakova, M., Motyka, V., Dobrev, P.I., Malbeck, J., Gaudinova, A. Vankova, R. (2005) Diurnal variation of cytokinin, auxin and abscisic acid levels in tobacco leaves. J. Exp. Bot. 56 (421 2877 2883.
44. Ozturk, Z.N., Talame, V., Deyholos, M., Michalowski, C.B., Galbraith, D.W., Gozukirmizi, N., Tuberosa, R. Bohnert, H.J. (2002) Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol. Biol. 48 (5 551 573.
45. Pfaffl, M.W. (2001) A new mathematical model for relative quantification in real-time rt-pcr. Nucleic Acids Res. 29 (9 e45.
46. Porra, R.J., Thompson, W.A. Kriedemann, P.E. (1989) Determination of accurate extinction coefficients and simultaneous-equations for assaying chlorophyll-a and chlorophyll-b extracted with 4 different solvents - verification of the concentration of chlorophyll standards by atomic-absorption spectroscopy. Biochim. Biophys. Acta, 975 (3 384 394.
47. Provart, N.J. Zhu, T. (2003) A browser-based functional classification superviewer for arabidopsis genomics. Currents Comput. Mol. Biol. 2003, 271 272.
48. R Development Core Team 2009. R: A language and environment for statistical computing. Vienna, Austria : R Foundation for Statistical Computing. http://www.R-project.Org.In.
49. Rabbani, M.A., Maruyama, K., Abe, H., Khan, M.A., Katsura, K., Ito, Y., Yoshiwara, K., Seki, M., Shinozaki, K. Yamaguchi-Shinozaki, K. (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cdna microarray and rna gel-blot analyses. Plant Physiol. 133 (4 1755 1767.
50. Roche, J., Hewezi, T., Bouniols, A. Gentzbittel, L. (2007) Transcriptional profiles of primary metabolism and signal transduction-related genes in response to water stress in field-grown sunflower genotypes using a thematic cdna microarray. Planta, 226 (3 601 617.
51. Sampedro, J. Cosgrove, D.J. (2005) The expansin superfamily. Genome Biol. 6 (12 242.
52. Sanchez, M., Gianzo, C., Sampedro, J., Revilla, G. Zarra, I. (2003) Changes in alpha-xylosidase during intact and auxin-induced growth of pine hypocotyls. Plant Cell Physiol. 44 (2 132 138.
53. Seki, M., Narusaka, M., Ishida, J. et al. (2002a) Monitoring the expression pattern of arabidopsis genes using full-length cdna microarray. Plant Cell Physiol. 43, S1 S1.
54. Seki, M., Narusaka, M., Ishida, J. et al. (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 (3 279 292.
55. Shi, L., Jones, W.D., Jensen, R.V. et al. (2008) The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics, 9 (Suppl 9 S10.
56. Smyth, G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 3, 26 pp.
57. Smyth, G.K. (2005) Limma: Linear models for microarray data. In : Bioinformatics and computational biology solutions using R and Bioconductor (Gentleman, R.C., Carey, V.J., Dudoit, S., Irizarry, R. Huber, W., eds). New York : Springer, pp. 397 420.
58. Street, N.R., Skogstrom, O., Sjodin, A., Tucker, J., Rodriguez-Acosta, M., Nilsson, P., Jansson, S. Taylor, G. (2006) The genetics and genomics of the drought response in populus. Plant J. 48 (3 321 341.
59. Taji, T., Ohsumi, C., Iuchi, S., Seki, M., Kasuga, M., Kobayashi, M., Yamaguchi-Shinozaki, K. Shinozaki, K. (2002) Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in arabidopsis thaliana. Plant J. 29 (4 417 426.
60. Talame, V., Ozturk, N.Z., Bohnert, H.J. Tuberosa, R. (2007) Barley transcript profiles under dehydration shock and drought stress treatments: a comparative analysis. J. Exp. Bot. 58 (2 229 240.
61. Wilkins, O., Waldron, L., Nahal, H., Provart, N.J. Campbell, M.M. (2009) Genotype and time of day shape the populus drought response. Plant J. 60 (4 703 715.
62. Wilkinson, S. Davies, W.J. (2002) Aba-based chemical signalling: the co-ordination of responses to stress in plants. Plant Cell Environ. 25 (2 195 210.
63. Wu, Z., Irizarry, R.A., Gentleman, R., Martinez-Murillo, F. Spencer, F. (2004) A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99, 909 917.
64. Xue, G.P., McIntyre, C.L., Glassop, D. Shorter, R. (2008) Use of expression analysis to dissect alterations in carbohydrate metabolism in wheat leaves during drought stress. Plant Mol. Biol. 67 (3 197 214.