environmental stress, chloroplast signaling,
transcription response, transcriptional network
Higher plants are exposed to various environmental stresses which affect their survival and growth. Organellar perturbation which is caused by environmental stresses results in modulation of nuclear gene expression as a feedback regulation to relieve these stresses. To understand mechanisms of environmental adaptation that is achieved in part through the chloroplast signaling, or retrograde signaling, we are analyzing the transcriptional network that orchestrates stress responses in higher plants. Determination of cis-regulatory elements in the promoter region is an old subject in plant science but still provides essential information on the transcriptional network, and, it is now much more easily and more comprehensively conducted with the aid of our recently developed methodologies of bioinformatics. Functional analysis of synthetic promoters that contain only one or two cis-regulatory elements provides precise information on the upstream signals driving the cis-elements, which is also necessary to understand the network. In addition, biochemical analysis of DNA-protein interaction that is scalable with the aid of oligo DNA and a cDNA resource of Arabidopsis transcription factors (TFs) enables empirical determination of a middle-scale transcriptional network, which is under trial in our laboratory.