Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the Ca2+/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca2+ and Na+, and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca2+ (200 mM) or Na+ (0.8 M) to yeast. 163 genes exhibited increased expression that was reduced 50% or more by calcineurin inhibition. These calcineurin dependent genes function in signaling pathways, ion/small molecule transport, cell wall maintenance, vesicular transport, and include many open reading frames of heretofore-unknown function. Three distinct gene classes were defined: 28 genes displayed calcineurin-dependent induction in response to Ca2+ and Na+, 125 showed calcineurin-dependent expression following Ca2+ but not Na+ addition, and 10 were regulated by calcineurin in response to Na+ but not Ca2+. Analysis of crz1D cells established Crz1p as the major effecter of calcineurin-regulated gene expression in yeast. We identified the Crz1p binding site as 5-GNGGC(G/T)CA-3 by in vitro site selection. A similar sequence, 5-GAGGCTG-3, was identified as a common sequence motif in the upstream regions of calcineurin/Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set Computed