Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress

Abstract

BackgroundExposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst of calcium that activates the Ser/Thr protein phosphatase calcineurin. Activated calcineurin dephosphorylates the transcription factor (TF) Crz1, which moves to the nucleus and binds to calcineurin/Crz1 responsive gene promoters. In this work we present a genome-wide study of the binding of Crz1 to gene promoters in response to high pH stress.ResultsEnvironmental alkalinization promoted a time-dependent recruitment of Crz1 to 152 intergenic regions, the vast majority between 1 and 5 min upon stress onset. Positional evaluation of the genomic coordinates combined with existing transcriptional studies allowed identifying 140 genes likely responsive to Crz1 regulation. Gene Ontology analysis confirmed the relevant impact of calcineurin/Crz1 on a set of genes involved in glucose utilization, and uncovered novel targets, such as genes responsible for trehalose metabolism. We also identified over a dozen of genes encoding TFs that are likely under the control of Crz1, suggesting a possible mechanism for amplification of the signal at the transcription level. Further analysis of the binding sites allowed refining the consensus sequence for Crz1 binding to gene promoters and the effect of chromatin accessibility in the timing of Crz1 recruitment to promoters.ConclusionsThe present work defines at the genomic-wide level the kinetics of binding of Crz1 to gene promoters in response to alkaline stress, confirms diverse previously known Crz1 targets and identifies many putative novel ones. Because of the relevance of calcineurin/Crz1 in signaling diverse stress conditions, our data will contribute to understand the transcriptional response in other circumstances that also involve calcium signaling, such as exposition to sexual pheromones or saline stress.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3006-6) contains supplementary material, which is available to authorized users.

Monovalent cation transporters at the plasma membrane in yeasts

“…Actually, the ENA1 promoter is one of the strongest Crz1 recruiters upon high pH stress (Petrezsélyová et al, ), reaching a peak between 2 and 5 min after shifting to pH 8.0. This fast kinetics is in accordance with the almost instantaneous cytosolic calcium peak (Viladevall et al, ), which is followed by a very quick Crz1 entry (1–2 min) into the nucleus (Petrezsélyová et al, ; Roque, Petrezsélyová, Serra‐Cardona, & Ariño, ).…”

Regulation of Rab5 isoforms by transcriptional and post‐transcriptional mechanisms in yeast

“…The promoter region of YPT53 contains a putative calcineurin‐dependent response element (CDRE; consensus sequence: AGCCNC) and a stress‐response element (STRE; AGGGG) 148 and 168 base pairs upstream of the orf. STREs are typically operated by the general stress‐responsive Msn2/4 TFs, but can also be engaged by Gis1 .…”

CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a

“…Ca 2+ /CRZ1-Calcineurin/Calmodulin is one of the best studied signaling pathways which provides protection and sensibility for fungal cells against stress conditions. This signaling pathway is already reported to confer Ca 2+ and cell wall stress tolerance in Aspergillus [56], pH responsiveness in S. cerevisiae [57] and it is either related to C. neoformans viability [29,33]. In addition, it is also reported that Ca 2+ supplementation may influence distinct regulatory mechanisms that control holocellulases expression in T. reesei [26].…”