Stb3 Plays a Role in the Glucose-Induced Transition from Quiescence to Growth inSaccharomyces cerevisiae

Abstract

Addition of glucose to quiescent Saccharomyces cerevisiae cells causes the immediate induction of $1000 genes. These genes include ribosomal proteins (RP) and non-RP genes needed for ribosome production and other growth processes. RRPE sequence elements are commonly found 59 of non-RP growth gene ORFs, and Stb3 has recently been identified as an RRPE binding protein. Stb3 overexpression (Stb3OE) produces a slow growth phenotype that is associated with reduced expression of non-RP genes and a drop in the rate of amino acid incorporation. Genes affected by Stb3 are associated with a TGAAAAA motif. Stb3 is restricted to the nucleus in quiescent cells and is immediately released into the cytoplasm after glucose repletion. The Stb3OE slow growth phenotype is reversed by loss of Hos2 histone deactylase activity, consistent with the idea that repression involves histone deacetylation. SCH9 overexpression or PPH22 deletion, mutations that activate target of rapamycin (Tor) nutrient sensing pathways, also reverse the Stb3OE phenotype. Inhibition of Tor signaling makes the phenotype more severe and restricts Stb3 to the nucleus. The results support a model in which Stb3 is one of the components that repress a large set of growth genes as nutrients are depleted. This repression is ended by glucose.

Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae

“…Our results are consistent with the independent finding that the binding of Stb3 to the RRPE-containing NSR1 and DBP10 promoters is increased in response to glucose replenishment and that an stb3⌬ strain fails to increase the expression of RRB genes during this environmental change (23). However, a more recent investigation by the same group indicated that Stb3 may also be acting as a repressor, as overexpression of STB3 results in decreased expression of growthrelated genes, and this is alleviated by deletion of the HOS2 histone deacetylase (22). In fact, these seemingly contradictory roles are both consistent with our observations that the RRPE sequence is involved in both transcriptional activation and repression of the same genes under different circumstances.…”

Integration of Multiple Nutrient Cues and Regulation of Lifespan by Ribosomal Transcription Factor Ifh1

“…Furthermore, TORC1 and PKA inactivate repressors of ribi genes such as Dot6p and Tod6p (Huber et al, 2011; Lippman and Broach, 2009). Stb3p, a repressor of rRNA processing genes, is also inactivated by TORC1 and glucose (Huber et al, 2011; Liko et al, 2010). We show that Ifh1p is yet another ribosomal transcription factor that is exposed to phosphorylation by TORC1 and PKA signaling.…”

Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

“…First, we identified classes of nucleosomes that were found in the same promoters as a given cis-regulatory element more often than would have been expected by chance. Several classes of nucleosome gain were associated with PAC elements and ribosomal RNA-processing elements (RRPEs), which repress protein syn- thesis genes upon stress (6,41,46,48,82), and Rap1p sites that regulate RP genes (44). Nucleosomes depleted with different dynamics were found in association with several stress-activated transcription factors: all classes of nucleosome depletion were found within promoters containing the related Msn2p and Mig1p binding sites ([CCCCT] and [GCCCCV], respectively), while specific classes were found associated with Pdr3p, Yap1p, and Rpn4p binding sites at genes involved in redox response, oxidative stress, and proteasome expression, respectively.…”