Microarray Identifies Transcription Factors Potentially Involved in Gravitropic Signal Transduction in Arabidopsis

C Adam Cook, Avery Tucker, Kaiyu Shen, Sarah E Wyatt


Gravity is a fundamental stimulus that affects plant growth and development. The gravity persistent signal (GPS) treatment uses a cold treatment to isolate the events of signal transduction. Plants are reoriented horizontally in the dark at 4°C for 1 hour and then returned to vertical at room temperature. A gene expression microarray was designed to identify genes that are regulated during the GPS treatment. Arabidopsis thaliana var. Columbia was grown to maturity with inflorescence stems of 8-10 cm. Total mRNA was collected from inflorescence stems at 2, 4, 10, and 30 min after reorientation in the cold. cDNA was synthesized from the mRNA and then probed against an Arabidopsis gene expression array with 4 replicates per time point. Analyses presented here focus on transcription factors because of their regulatory functions in response pathways. Five transcription factors (AtAIB, WRKY18, WRKY26, WRKY33, and BT2) were selected for further study based on their expression at 4 min. Quantitative real-time polymerase chain reaction ((PCR) RT-qPCR) was performed to confirm expression seen in the microarray data. Seeds of Arabidopsis lines containing T-DNA insertions in the genes were obtained, plants bred to homozygosity, and the mutants analyzed for GPS phenotype. Mutant analysis shows significant differences in curvature of inflorescence stems between mutants and wild type.


Chen, Han, Zhibing Lai, Junwei Shi, Yong Xiao, Zhixiang Chen, and Xinping Xu. 2010. “Roles of Arabidopsis WRKY18, WRKY40 and WRKY60 Transcription Factors in Plant Responses to Abscisic Acid and Abiotic Stress.” BMC Plant Biology10 (1): 281.

Guo, Anyuan, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, and Jingchu Luo. 2005. “DATF: A Database of Arabidopsis Transcription Factors.” Bioinformatics 21: 2568–69.

Hara, K., M. Yagi, T. Kusano, and H. Sano. 2000. “Rapid Systemic Accumulation of Transcripts Encoding a Tobacco WRKY Transcription Factor upon Wounding.” Molecular and General Genetics MGG 263 (1): 30–37.

Kiss, John Z., Rainer Hertel, and Fred D. Sack. 1989. “Amyloplasts Are Necessary for Full Gravitropic Sensitivity in Roots of Arabidopsis thaliana.” Planta 177 (2): 198–206.

Li, Hongmei, Jiaqiang Sun, Yingxiu Xu, Hongling Jiang, Xiaoyan Wu, and Chuanyou Li. 2007. “The bHLH-Type Transcription Factor AtAIB Positively Regulates ABA Response in Arabidopsis.” Plant Molecular Biology 65 (5): 655–65.

Liu, Zhi-Qiang, Lu Yan, Zhen Wu, Chao Mei, Kai Lu, Yong-Tao Yu, Shan Liang, Xiao-Feng Zhang, Xiao-Fang Wang, and Da-Peng Zhang. 2012. “Cooperation of Three WRKY-Domain Transcription Factors WRKY18, WRKY40, and WRKY60 in Repressing Two ABA-Responsive Genes ABI4 and ABI5 in Arabidopsis.” Journal of Experimental Botany 63 (18): 6371–92.

Pilet, P.-E., and P. W. Barlow. 1987. “The Role of Abscisic Acid in Root Growth and Gravireaction: A Critical Review.” Plant Growth Regulation 6 (3): 217–65.

Rushton, P J, J T Torres, M Parniske, P Wernert, K Hahlbrock, and I E Somssich. 1996. “Interaction of Elicitor-Induced DNA-Binding Proteins with Elicitor Response Elements in the Promoters of Parsley PR1 Genes.” The EMBO Journal15 (20): 5690–5700.

Sack, Fred D., M. Mitsu Suyemoto, and A. Carl Leopold. 1985. “Amyloplast Sedimentation Kinetics in Gravistimulated Maize Roots.” Planta 165 (3): 295–300.

Shang, Yi, Lu Yan, Zhi-Qiang Liu, Zheng Cao, Chao Mei, Qi Xin, Fu-Qing Wu, et al. 2010. “The Mg-Chelatase H Subunit of Arabidopsis Antagonizes a Group of WRKY Transcription Repressors to Relieve ABA-Responsive Genes of Inhibition.” The Plant Cell22 (6): 1909–35.

Shen, Kaiyu, Sarah E. Wyatt, and Vijayanand Nadella. 2012. “ArrayOU: A Web Application for Microarray Data Analysis and Visualization.” Journal of Biomolecular Techniques : JBT 23 (2): 37–39.

Wilkins, Henry, and R. L. Wain. 1975. “Abscisic Acid and the Response of the Roots of Zea mays L. Seedlings to Gravity.” Planta 126 (1): 19–23.

Wyatt, Sarah E., Aaron M. Rashotte, Matthew J. Shipp, Dominique Robertson, and Gloria K. Muday. 2002. “Mutations in the Gravity Persistence Signal Loci in Arabidopsis Disrupt the Perception And/or Signal Transduction of Gravitropic Stimuli.” Plant Physiology 130 (3): 1426–35.

Xu, Xinping, Chunhong Chen, Baofang Fan, and Zhixiang Chen. 2006. “Physical and Functional Interactions between Pathogen-Induced Arabidopsis WRKY18, WRKY40, and WRKY60 Transcription Factors.” The Plant Cell 18 (5): 1310–26.

Full Text: PG. 20-29 -- PDF