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Transcriptomic Analysis Reveals Calcium Regulation of Specific Promoter Motifs in Arabidopsis[W]

Many stimuli cause brief elevations in the concentration of calcium in plant cells, and these changes trigger appropriate responses from the cell. This work shows that specific short DNA sequences in some plant genes recognize such changes in calcium levels and allow these genes to be activated; this information aids our understanding of how plants respond to specific environmental stresses. Increases in intracellular calcium concentration ([Ca2+]c) mediate plant responses to stress by regulating the expression of genes encoding proteins that confer tolerance. Several plant stress genes have previously been shown to be calcium-regulated, and in one case, a specific promoter motif Abscisic Acid Responsive–Element (ABRE) has been found to be regulated by calcium. A comprehensive survey of the Arabidopsis thaliana transcriptome for calcium-regulated promoter motifs was performed by measuring the expression of genes in Arabidopsis seedlings responding to three calcium elevations of different characteristics, using full genome microarray analysis. This work revealed a total of 269 genes upregulated by [Ca2+]c in Arabidopsis. Bioinformatic analysis strongly indicated that at least four promoter motifs were [Ca2+]c-regulated in planta. We confirmed this finding by expressing in plants chimeric gene constructs controlled exclusively by these cis-elements and by testing the necessity and sufficiency of calcium for their expression. Our data reveal that the C-Repeat/Drought-Responsive Element, Site II, and CAM box (along with the previously identified ABRE) promoter motifs are calcium-regulated. The identification of these promoter elements targeted by the second messenger intracellular calcium has implications for plant signaling in response to a variety of stimuli, including cold, drought, and biotic stress.