Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae

Transfer of quiescent Saccharomyces cerevisiae cells to fresh medium rapidly induces hundreds of genes needed for growth. A large subset of these genes is regulated via a DNA sequence motif known as the ribosomal RNA processing element (RRPE). However, no RRPE-binding proteins have been identified. We screened a panel of 6144 glutathione S-transferase-open reading frame fusions for RRPE-binding proteins and identified Stb3 as a specific RRPE-binding protein, both in vitro and in vivo. Chromatin immunoprecipitation experiments showed that glucose increases Stb3 binding to RRPE-containing promoters. Microarray experiments demonstrated that the loss of Stb3 inhibits the transcriptional response to fresh glucose, especially for genes with RRPE motifs. However, these experiments also showed that not all genes containing RRPEs were dependent on Stb3 for expression. Overall our data support a model in which Stb3 plays an important but not exclusive role in the transcriptional response to growth conditions.