Arabidopsis transcriptome reveals control circuits regulating redox homeostasis and the role of an AP2 transcription factor

Abha Khandelwal , Thanura Elvitigala , Bijoy Ghosh , and Ralph Quatrano ^*

Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130l; Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX 79409

^* Corresponding author; email: rsq{at}wustl.edu.

Sensors and regulatory circuits that maintain redox homeostasisplay a central role in adjusting plant metabolism and developmentto changing environmental conditions. We report here controlnetworks in Arabidopsis that respond to photosynthetic (PS)stress. We independently subjected Arabidopsis leaves to twocommonly used PSII inhibitors; high light (HL) and 3-(3,4-dichlorophenyl)-1,1-dimethylurea(DCMU). Microarray analysis of expression patterns during theperiod of redox adjustment to these inhibitors reveals that20% and 8% of the transcriptome are under HL and DCMU regulation,respectively. Approximately 6% comprise a subset of genes commonto both perturbations, the redox responsive genes (RRGs). Aredox network was generated in an attempt to identify geneswhose expression is tightly coordinated during adjustment tohomeostasis, using expression of these RRGs under HL conditions.Ten sub-networks were identified from the network. Hierarchalsub-clustering of sub-networks responding to the DCMU stressidentified novel groups of genes that were tightly controlledwhile adjusting to homeostasis. Upstream analysis of the promotersof the genes in these clusters revealed different motifs foreach sub-network, including motifs that were previously identifiedwith responses to other stresses such as light, dehydrationor ABA. Functional categorization of RRGs demonstrated involvementof genes in many metabolic pathways, including several familiesof transcription factors, especially those in the AP2 family.Using a T-DNA insertion in one AP2 transcription factor (RRTF1)from the RRGs, we showed that the genes predicted to be withinthe sub-network containing RRTF1 were changed in this insertionline ( ${Delta}$ rrtf1). Furthermore, ${Delta}$ rrtf1 showed greater sensitivityto photosynthetic stress compared to the wild type.