Transcriptional regulation of carbon utilization in yeast

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The yeast Saccharomyces cerevisiae preferentially uses glucose as a carbon source. Upon glucose exhaustion, this yeast can use non-sugar carbons (non-fermentable carbons) such as ethanol, lactate and acetate. This results in massive reprogramming of gene expression to adapt to the new carbon source. This process is controlled by the master kinase Snf1 which phosphorylates various substrates including the transcription factors Cat8 and Sip4 that control expression of specific genes by binding to Carbon Source Response Elements found in the promoters of the target genes. For example, these factors upregulate the expression of PCK1 encoding a very important enzyme for gluconeogenesis. Cat8 and Sip4 belong to the Gal4 family of zinc cluster proteins that form an important class of transcriptional regulators in yeast. We have characterized the zinc cluster protein Rds2 by performing genome-wide localization (ChIP-chip) of this factor and found that it is a very important regulator of gluconeogenesis. However, Rds2 and Cat8 show a limited number of common target genes. Thus, they have specific and common functions. We are also characterizing another zinc cluster gene we named ERT1 (for Ethanol Regulator of Translation). ChIP-chip analysis shows that under ethanol conditions, this factor binds to some gluconeogenic genes (e.g. PCK1), ribosomal proteins genes as well as genes encoding mitochondrial components and two genes encoding two subunits of the TFIIIC complex involved in RNA polymerase III transcription. There is also evidence that another zinc cluster protein, Gsm1, is also involved in controlling gene expression for adaptation to a non-fermentable carbon source. Clearly, regulation of gene expression following glucose exhaustion is a more complex process than initially anticipated. This proposal is aimed at better characterizing the role of the transcription factors Rds2, Ert1, Cat8, Sip4, and Gsm1. More specifically we will: 1) Determine the role of Ert1 with glucose or ethanol as carbon sources 2) Study the function of Gsm1 3) Determine the relative contribution and the interplay of Rds2, Ert1, Cat8, Sip4 and Gsm1 in mediating utilization of ethanol, lactate, glycerol, and acetate as carbon sources.