Transcriptomic Analysis Reveals Calcium Regulation of Specific Promoter Motifs inArabidopsis 

Abstract

Increases in intracellular calcium concentration ([Ca 2+ ] 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 calciumregulated, 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 [Ca 2+ ] c in Arabidopsis. Bioinformatic analysis strongly indicated that at least four promoter motifs were [Ca 2+ ] 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.

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

“…However, three upregulated clusters are also enriched for TCP binding motifs, and TCPs also play a role in the circadian clock (Pruneda-Paz et al, 2009;Giraud et al, 2010) and control of JA biosynthesis (Schommer et al, 2008). Recently, TCP binding sites were shown to be enriched in calcium-responsive gene promoters (Whalley et al, 2011), which may explain the large number of defenserelated gene promoters containing TCP binding motifs.…”

The EF-Hand Ca2+ Binding Protein MICU Choreographs Mitochondrial Ca2+ Dynamics in Arabidopsis

“…Rapid adjustment is particularly important for the endosymbiotic organelles, i.e., the mitochondria and the chloroplasts, since perturbation of the finely tuned metabolic, redox, and chemiosmotic processes can severely affect cellular homeostasis or even trigger programmed cell death (Kim et al, 2006;Logan, 2007). Dynamic changes in free Ca 2+ concentrations have been recognized to act in the transduction within the cell of both endogenous and external signals in order to regulate biotic and abiotic stress responses (Knight et al, 1991;Kiegle et al, 2000;Whalley et al, 2011), developmental programs (Foreman et al, 2003;Monshausen et al, 2008), stomatal dynamics (Gilroy et al, 1991;Allen et al, 2000;Pei et al, 2000;Kim et al, 2010), protein import into cell compartments (Chigri et al, 2006), and symbiotic plant-microbe interactions (Wais et al, 2000;Miller et al, 2013).…”

Plastidial metabolite MEcPP induces a transcriptionally centered stress-response hub via the transcription factor CAMTA3

“…A reporter line containing luciferase (LUC) driven by a synthetic promoter with four copies of the RSRE (4×RSRE:LUC) has confirmed the multistress responsive nature of RSRE induction and established the line as suitable for readout of stress-induced rapid transcriptional responses (4). Indeed, exploiting the 4×RSRE:LUC line unraveled roles for [Ca 2+ ] cyt , reactive oxygen species (ROS), MAPK signaling, and hormone signaling in modulating this stress-responsive transcriptional hub (4,(8)(9)(10) and further identified a member of the calmodulin-binding transcriptional activator (CAMTA) family, CAMTA3, as the predominant transcription factor that activates RSRE and, by extension, induces the GSR (10, 11).Forward genetic studies directed at unraveling the components of stress-signaling networks in plants led to the discovery of the small stress-specific plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP), which functions both as an intermediate of the methylerythritol phosphate (MEP) pathway for isoprenoids biosynthesis and as a communicator of environmental perturbations from the plastid to the nucleus (12, 13). The ceh1 (constitutively expressing hydroperoxide lyase1) mutant accumulates large quantities of MEcPP and displays various stress-associated phenotypes such as compromised growth, high salicylic acid (SA) content, and constitutive activation of the unfolded protein response (UPR) required for restoration of protein-folding homeostasis in the endoplasmic reticulum (ER) (13-15).…”

“…A reporter line containing luciferase (LUC) driven by a synthetic promoter with four copies of the RSRE (4×RSRE:LUC) has confirmed the multistress responsive nature of RSRE induction and established the line as suitable for readout of stress-induced rapid transcriptional responses (4). Indeed, exploiting the 4×RSRE:LUC line unraveled roles for [Ca 2+ ] cyt , reactive oxygen species (ROS), MAPK signaling, and hormone signaling in modulating this stress-responsive transcriptional hub (4,(8)(9)(10) and further identified a member of the calmodulin-binding transcriptional activator (CAMTA) family, CAMTA3, as the predominant transcription factor that activates RSRE and, by extension, induces the GSR (10, 11).…”