Rates of mRNA synthesis and decay can be measured on a genome-wide scale in yeast by dynamic transcriptome analysis (DTA), which combines non-perturbing metabolic RNA labeling with dynamic kinetic modeling.DTA reveals that most mRNA synthesis rates are around several transcripts per cell and cell cycle, and most mRNA half-lives range around a median of 11 min.DTA realistically monitors the cellular response to osmotic stress with higher sensitivity and temporal resolution than transcriptomics, and can be used to follow changes in RNA metabolism in gene regulatory systems.

The regulation of ribosome biogenesis in response to environmental conditions is a key aspect of cell growth control. Ribosomal protein (RP) genes are regulated by the nutrient-sensitive, conserved target of rapamycin (TOR) signaling pathway. TOR controls the subcellular localization of protein kinase A (PKA) and the PKA-regulated kinase YAK1. However, the target transcription factor(s) of the TOR-PKA pathway are unknown. We show that regulation of RP gene transcription via TOR and PKA in yeast involves the Forkhead-like transcription factor FHL1 and the two cofactors IFH1 (a coactivator) and CRF1 (a corepressor). TOR, via PKA, negatively regulates YAK1 and maintains CRF1 in the cytoplasm. Upon TOR inactivation, activated YAK1 phosphorylates and activates CRF1. Phosphorylated CRF1 accumulates in the nucleus and competes with IFH1 for binding to FHL1 at RP gene promoters, and thereby inhibits transcription of RP genes. Thus, we describe a signaling mechanism linking an environmental sensor to ribosome biogenesis.

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The TOR (target of rapamycin) and RAS/cyclic AMP (cAMP) signaling pathways are the two major pathways controlling cell growth in response to nutrients in yeast. In this study we examine the functional interaction between TOR and the RAS/cAMP pathway. First, activation of the RAS/cAMP signaling pathway confers pronounced resistance to rapamycin. Second, constitutive activation of the RAS/cAMP pathway prevents several rapamycin-induced responses, such as the nuclear translocation of the transcription factor MSN2 and induction of stress genes, the accumulation of glycogen, the induction of autophagy, the down-regulation of ribosome biogenesis (ribosomal protein gene transcription and RNA polymerase I and III activity), and the down-regulation of the glucose transporter HXT1. Third, many of these TOR-mediated responses are independent of the previously described TOR effectors TAP42 and the type 2A-related protein phosphatase SIT4. Conversely, TOR-controlled TAP42/SIT4-dependent events are not affected by the RAS/cAMP pathway. Finally, and importantly, TOR controls the subcellular localization of both the protein kinase A catalytic subunit TPK1 and the RAS/cAMP signaling-related kinase YAK1. Our findings suggest that TOR signals through the RAS/cAMP pathway, independently of TAP42/SIT4. Therefore, the RAS/cAMP pathway may be a novel TOR effector branch.The Saccharomyces cerevisiae targets of rapamycin, TOR1 and TOR2, are functionally and structurally conserved protein kinases that control a large and diverse set of growth-related readouts in response to nutrient availability (53). In yeast, rapamycin treatment or TOR depletion results in several physiological changes characteristic of starved cells, including inhibition of translation initiation, inhibition of ribosome biogenesis, specific changes in transcription, sorting and turnover of nutrient permeases, accumulation of storage carbohydrates (such as glycogen), and induction of autophagy (reviewed in references 12 and 52). Nitrogen (in particular glutamine) and possibly carbon are important nutrients in the context of yeast TOR signaling (13,56). Mammalian TOR (mTOR) controls translation and other growth-related processes in response to amino acids and a growth factor signal (e.g., insulin). The growth factor input into the mTOR pathway is via phosphatidylinositol 3-kinase (PI3K), PDK1, and protein kinase B (PKB; also known as Akt). The precise nature of the link between mTOR and PI3K signaling remains to be determined but may involve the PKB-mediated phosphorylation and inhibition of the tuberous sclerosis protein complex (TSC1-TSC2) upstream of mTOR. Control of translation by mTOR is via activation of S6 kinase (S6K) and inhibition of the eIF4E inhibitor 4E-BP1 (reviewed in reference 30).The yeast TORs control several readouts via a phosphatase switch composed of the type 2A-related phosphatase SIT4, the PP2A/SIT4-associated protein TAP42, and the TAP42-interacting protein TIP41 (16,29,31). Under good nutrient conditions, TOR promotes the binding of SIT4 to TAP...