Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

Abstract

In the model eukaryote Saccharomyces cerevisiae, the transcription factor Cst6p has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol but hardly binds to the promoter at any gene when cells are grown on glucose. The retarded growth of the CST6 deletion mutant on ethanol is attributed to the markedly decreased expression of NCE103, encoding a carbonic anhydrase, which is a direct target of Cst6p. The target genes of Cst6p have a large overlap with those of stress-responsive transcription factors, such as Sko1p and Skn7p. In addition, a CST6 deletion mutant growing on ethanol shows hypersensitivity to oxidative stress and ethanol stress, assigning Cst6p as a new member of the stress-responsive transcriptional regulatory network. These results show that mapping of genome-wide binding sites can provide new insights into the function of transcription factors and highlight the highly connected and condition-dependent nature of the transcriptional regulatory network in S. cerevisiae.

Ethanol stress stimulates sumoylation of transcription factor Cst6 which restricts expression of its target genes

“…(Enserink 2015;Niskanen et al 2015)). Cst6 is part of the stress-responsive transcriptional regulatory network and it was previously shown to be involved in regulating transcription during ethanol, oxidative and heat shock stress (Suzuki et al 2011;Wu and Li 2008;Liu et al 2016;Garcia-Gimeno and Struhl 2000). To explore the effect of stress on Cst6 sumoylation, we examined its sumoylation levels by IP-immunoblot in lysates derived from cells grown under different stress conditions (Figures 2A and B).…”

“…Our data demonstrates that sumoylation of Cst6 increases during ethanol and oxidative stress, and further experiments were performed to investigate the role that sumoylation plays in regulating Cst6 function in these conditions. Previous studies on Cst6 highlighted its importance for cell growth in the presence of alternative carbon sources (Garcia-Gimeno and Struhl 2000;Liu et al 2016). Typically, lab yeast strains are grown in media containing glucose, but other carbon sources, such as glycerol, ethanol, and raffinose, can be used as alternatives.…”

“…In the absence of Cst6, cells grow poorly in alternative carbon sources, including ethanol (Garcia-Gimeno and Struhl 2000;Liu et al 2016). We wished to investigate whether the level of Cst6 sumoylation changes with different types of media and carbon sources used for growth.…”

“…It contains a bZIP DNA binding domain, binds to DNA as a homodimer or a heterodimer with Aca1, another yeast bZIP transcription factor, and it recognises cAMP response element (CRE)-like promoter sequences (Garcia-Gimeno and Struhl 2000). A recent study showed that the Cst6 binding site (5ʹ-GTGACGT-3ʹ) has an additional guanine nucleotide at the 5ʹ end of the consensus CRE motif (5ʹ-TGACGT-3ʹ), implying that it has a somewhat different binding site preference than other bZIP transcription factors (Liu et al 2016). Through genome-wide binding site analysis, the study also identified 59 protein-coding genes as putative targets for Cst6 regulation.…”

“…Through genome-wide binding site analysis, the study also identified 59 protein-coding genes as putative targets for Cst6 regulation. Gene ontology (GO) analysis of these genes revealed that Cst6 controls different cellular processes including transcription, cellular respiration, gluconeogenesis, stress response, and pseudohyphal growth, signifying the importance of its function in budding yeast (Liu et al 2016).…”