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The Plant Cell, Vol. 14, 559-574, March 2002, Copyright © 2002,
American Society of Plant Biologists

Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses

Wenqiong Chena, Nicholas J. Provarta, Jane Glazebrooka, Fumiaki Katagiria, Hur-Song Changa, Thomas Eulgemb, Felix Mauchc, Sheng Luand, Guangzhou Zoua, Steve A. Whitham1,a, Paul R. Budwortha, Yi Taoa, Zhiyi Xie2,a, Xi Chene, Steve Lame, Joel A. Krepsa, Jeffery F. Harperf, Azzedine Si-Ammourc, Brigitte Mauch-Manic, Manfred Heinleing, Kappei Kobayashig, Thomas Hohng, Jeffery L. Danglb, Xun Wanga and Tong Zhu3,a

a Torrey Mesa Research Institute, Syngenta Research and Technology, 3115 Merryfield Row, San Diego, California 92121
b Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
c Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland
d Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
e Syngenta Biotechnology, Inc., 3054 Cornwallis Road, Research Triangle Park, North Carolina 27709
f Scripps Research Institute, 3528 General Atomics Court, San Diego, California 92121
g Friedrich Miescher Institute, Maulbeerstrasse 66, CH-4058 Basel, Switzerland

3 To whom correspondence should be addressed. E-mail tong.zhu{at}syngenta.com; fax 858-812-1097

Numerous studies have shown that transcription factors are important in regulating plant responses to environmental stress. However, specific functions for most of the genes encoding transcription factors are unclear. In this study, we used mRNA profiles generated from microarray experiments to deduce the functions of genes encoding known and putative Arabidopsis transcription factors. The mRNA levels of 402 distinct transcription factor genes were examined at different developmental stages and under various stress conditions. Transcription factors potentially controlling downstream gene expression in stress signal transduction pathways were identified by observed activation and repression of the genes after certain stress treatments. The mRNA levels of a number of previously characterized transcription factor genes were changed significantly in connection with other regulatory pathways, suggesting their multifunctional nature. The expression of 74 transcription factor genes responsive to bacterial pathogen infection was reduced or abolished in mutants that have defects in salicylic acid, jasmonic acid, or ethylene signaling. This observation indicates that the regulation of these genes is mediated at least partly by these plant hormones and suggests that the transcription factor genes are involved in the regulation of additional downstream responses mediated by these hormones. Among the 43 transcription factor genes that are induced during senescence, 28 of them also are induced by stress treatment, suggesting extensive overlap responses to these stresses. Statistical analysis of the promoter regions of the genes responsive to cold stress indicated unambiguous enrichment of known conserved transcription factor binding sites for the responses. A highly conserved novel promoter motif was identified in genes responding to a broad set of pathogen infection treatments. This observation strongly suggests that the corresponding transcription factors play general and crucial roles in the coordinated regulation of these specific regulons. Although further validation is needed, these correlative results provide a vast amount of information that can guide hypothesis-driven research to elucidate the molecular mechanisms involved in transcriptional regulation and signaling networks in plants.




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Photosynthetic Acclimation Is Reflected in Specific Patterns of Gene Expression in Drought-Stressed Loblolly Pine
Plant Physiology, December 1, 2003; 133(4): 1702 - 1716.
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S. Perelman, M. A. Mazzella, J. Muschietti, T. Zhu, and J. J. Casal
Finding Unexpected Patterns in Microarray Data
Plant Physiology, December 1, 2003; 133(4): 1717 - 1725.
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 Plant CellHome page
S. Chakravarthy, R. P. Tuori, M. D. D'Ascenzo, P. R. Fobert, C. Despres, and G. B. Martin
The Tomato Transcription Factor Pti4 Regulates Defense-Related Gene Expression via GCC Box and Non-GCC Box cis Elements
PLANT CELL, December 1, 2003; 15(12): 3033 - 3050.
[Abstract] [Full Text] [PDF]

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Y. Jiao, H. Yang, L. Ma, N. Sun, H. Yu, T. Liu, Y. Gao, H. Gu, Z. Chen, M. Wada, et al.
A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development
Plant Physiology, December 1, 2003; 133(4): 1480 - 1493.
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H. Wintz, T. Fox, Y.-Y. Wu, V. Feng, W. Chen, H.-S. Chang, T. Zhu, and C. Vulpe
Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis
J. Biol. Chem., November 28, 2003; 278(48): 47644 - 47653.
[Abstract] [Full Text] [PDF]

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T. Mengiste, X. Chen, J. Salmeron, and R. Dietrich
The BOTRYTIS SUSCEPTIBLE1 Gene Encodes an R2R3MYB Transcription Factor Protein That Is Required for Biotic and Abiotic Stress Responses in Arabidopsis
PLANT CELL, November 1, 2003; 15(11): 2551 - 2565.
[Abstract] [Full Text] [PDF]

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D. Thirkettle-Watts, T. C. McCabe, R. Clifton, C. Moore, P. M. Finnegan, D. A. Day, and J. Whelan
Analysis of the Alternative Oxidase Promoters from Soybean
Plant Physiology, November 1, 2003; 133(3): 1158 - 1169.
[Abstract] [Full Text] [PDF]

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T. M. Korves and J. Bergelson
A Developmental Response to Pathogen Infection in Arabidopsis
Plant Physiology, September 1, 2003; 133(1): 339 - 347.
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 Plant CellHome page
C. Johnson, E. Boden, and J. Arias
Salicylic Acid and NPR1 Induce the Recruitment of trans-Activating TGA Factors to a Defense Gene Promoter in Arabidopsis
PLANT CELL, August 1, 2003; 15(8): 1846 - 1858.
[Abstract] [Full Text] [PDF]

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J. P. Hammond, M. J. Bennett, H. C. Bowen, M. R. Broadley, D. C. Eastwood, S. T. May, C. Rahn, R. Swarup, K. E. Woolaway, and P. J. White
Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants
Plant Physiology, June 1, 2003; 132(2): 578 - 596.
[Abstract] [Full Text] [PDF]

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N. J. Provart, P. Gil, W. Chen, B. Han, H.-S. Chang, X. Wang, and T. Zhu
Gene Expression Phenotypes of Arabidopsis Associated with Sensitivity to Low Temperatures
Plant Physiology, June 1, 2003; 132(2): 893 - 906.
[Abstract] [Full Text] [PDF]

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P. M. Schenk, K. Kazan, J. M. Manners, J. P. Anderson, R. S. Simpson, I. W. Wilson, S. C. Somerville, and D. J. Maclean
Systemic Gene Expression in Arabidopsis during an Incompatible Interaction with Alternaria brassicicola
Plant Physiology, June 1, 2003; 132(2): 999 - 1010.
[Abstract] [Full Text] [PDF]

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Y. Narusaka, M. Narusaka, M. Seki, J. Ishida, M. Nakashima, A. Kamiya, A. Enju, T. Sakurai, M. Satoh, M. Kobayashi, et al.
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., April 15, 2003; 44(4): 377 - 387.
[Abstract] [Full Text] [PDF]

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B. Cooper, J. D. Clarke, P. Budworth, J. Kreps, D. Hutchison, S. Park, S. Guimil, M. Dunn, P. Luginbuhl, C. Ellero, et al.
A network of rice genes associated with stress response and seed development
PNAS, April 15, 2003; 100(8): 4945 - 4950.
[Abstract] [Full Text] [PDF]

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M. TESTER and R. DAVENPORT
Na+ Tolerance and Na+ Transport in Higher Plants
Ann. Bot., April 1, 2003; 91(5): 503 - 527.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
D. Hui, J. Iqbal, K. Lehmann, K. Gase, H. P. Saluz, and I. T. Baldwin
Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphingidae) and Its Natural Host Nicotiana attenuata: V. Microarray Analysis and Further Characterization of Large-Scale Changes in Herbivore-Induced mRNAs
Plant Physiology, April 1, 2003; 131(4): 1877 - 1893.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
O. Lorenzo, R. Piqueras, J. J. Sanchez-Serrano, and R. Solano
ETHYLENE RESPONSE FACTOR1 Integrates Signals from Ethylene and Jasmonate Pathways in Plant Defense
PLANT CELL, January 1, 2003; 15(1): 165 - 178.
[Abstract] [Full Text] [PDF]

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M. Zik and V. F. Irish
Global Identification of Target Genes Regulated by APETALA3 and PISTILLATA Floral Homeotic Gene Action
PLANT CELL, January 1, 2003; 15(1): 207 - 222.
[Abstract] [Full Text] [PDF]

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M. D. Mikkelsen, B. L. Petersen, E. Glawischnig, A. B. Jensen, E. Andreasson, and B. A. Halkier
Modulation of CYP79 Genes and Glucosinolate Profiles in Arabidopsis by Defense Signaling Pathways
Plant Physiology, January 1, 2003; 131(1): 298 - 308.
[Abstract] [Full Text] [PDF]

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J. A. Kreps, Y. Wu, H.-S. Chang, T. Zhu, X. Wang, and J. F. Harper
Transcriptome Changes for Arabidopsis in Response to Salt, Osmotic, and Cold Stress
Plant Physiology, December 1, 2002; 130(4): 2129 - 2141.
[Abstract] [Full Text] [PDF]

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L. Rizhsky, H. Liang, and R. Mittler
The Combined Effect of Drought Stress and Heat Shock on Gene Expression in Tobacco
Plant Physiology, November 1, 2002; 130(3): 1143 - 1151.
[Abstract] [Full Text] [PDF]

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M. Menges, L. Hennig, W. Gruissem, and J. A. H. Murray
Cell Cycle-regulated Gene Expression in Arabidopsis
J. Biol. Chem., October 25, 2002; 277(44): 41987 - 42002.
[Abstract] [Full Text] [PDF]

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E. J. Klok, I. W. Wilson, D. Wilson, S. C. Chapman, R. M. Ewing, S. C. Somerville, W. J. Peacock, R. Dolferus, and E. S. Dennis
Expression Profile Analysis of the Low-Oxygen Response in Arabidopsis Root Cultures
PLANT CELL, October 1, 2002; 14(10): 2481 - 2494.
[Abstract] [Full Text] [PDF]

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Y. H. Cheong, H.-S. Chang, R. Gupta, X. Wang, T. Zhu, and S. Luan
Transcriptional Profiling Reveals Novel Interactions between Wounding, Pathogen, Abiotic Stress, and Hormonal Responses in Arabidopsis
Plant Physiology, June 1, 2002; 129(2): 661 - 677.
[Abstract] [Full Text] [PDF]


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