Sch9 Is a Major Target of TORC1 in Saccharomyces cerevisiae
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE7660 | GEO | 2007/04/28
SECONDARY ACCESSION(S): PRJNA99759
REPOSITORIES: GEO
Similar Datasets
Project description:The Target Of Rapamycin (TOR) protein is a Ser/Thr kinase that functions in two distinct multiprotein complexes: TORC1 and TORC2. These conserved complexes regulate many different aspects of cell growth in response to intra- and extracellular cues. Here we report the first bona fide substrate of yeast TORC1: the AGC-kinase Sch9. Six amino acids in the c-terminus of Sch9 are directly phosphorylated by TORC1. Phosphorylation of these residues is lost upon rapamycin-treatment as well as carbon- or nitrogen-starvation and transiently reduced following application of osmotic, oxidative or thermal stress. TORC1-dependent phosphorylation is required for Sch9 activity and replacement of residues phosphorylated by TORC1 with Asp/Glu renders Sch9 activity TORC1-independent. Sch9 is required for TORC1 to properly regulate ribosome biogenesis, translation initiation and entry into G0 phase, but not expression of Gln3-dependent genes. Our results suggest that Sch9 functions analogously to the mammalian TORC1 substrate S6K1 rather than the mTORC2 substrate PKB/Akt. Keywords: time course, cell type. Global transcriptional analysis of rapamycin response was conducted on cells expressing either a wild-type, Sch9(WT), or TOR-independent allele of Sch9, Sch9(2D3E). Reference samples used were cells collected immediately prior to rapamycin treatment for the respective cell genotypes. Test samples were collected 20, 30, 60, 90, 120, and 180min post rapamycin treatment.
2010-09-15 | E-GEOD-7660 | biostudies-arrayexpress
Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis. mRNA-Seq of 8 S. cerevisiae strains treated with either DMSO alone or 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.
2011-07-01 | E-GEOD-29122 | biostudies-arrayexpress
Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis. ChIP-Seq of 8 S. cerevisiae strains treated with 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.
2011-07-01 | E-GEOD-29124 | biostudies-arrayexpress
Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis.
2011-07-01 | GSE29124 | GEO
Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis.
2011-07-01 | GSE29122 | GEO
Project description:We show that the sensitivity of tsc mutant cells to rapamycin is mediated by TORC1 and can be suppressed by overexpression of the 2-oxoglutarate-Fe(II) dependent oxygenase, Isp7. We show that Isp7 is a novel regulator of amino acids uptake that acts via regulation of gene expression, both upstream and downstream of TOR signaling. suppressed by overexpression of the putative 2-oxoglutarate-Fe(II) dependent oxygenase, Isp7. We show that Isp7 is a novel master regulator of amino acids uptake that acts via regulation of gene expression, both upstream and downstream of TOR signaling. TOR proteins reside in two distinct complexes, TOR complex 1 and 2 (TORC1 and TORC2) that are central for the regulation of cellular growth, proliferation and survival. TOR is also the target for the immunosuppressive and anti-cancer drug rapamycin. In Schizosaccharaomyces pombe, disruption of the TSC complex, mutations in which can lead to the Tuberous Sclerosis syndrome in humans, results in a rapamycin sensitive phenotype under poor nitrogen conditions. We show here that the sensitivity to rapamycin is mediated via inhibition of TORC1 and suppressed by overexpression of isp7+, a member of the family of 2-oxoglutarate-Fe(II) dependent oxygenases. The transcript level of isp7+ is negatively regulated by TORC1 but positively regulated by TORC2. Yet, we find extensive similarity between the transcriptome of cells disrupted for isp7+ and cells mutated in the catalytic subunit of TORC1. Moreover, Isp7 regulates amino acid permease expression similarly to TORC1 and in contrast to TORC2. Overexpression of isp7+ induces TORC1-dependent phosphorylation of ribosomal protein Rps6, while inhibiting TORC2-dependent phosphorylation and activation of the AGC-like kinase Gad8. Taken together, our findings suggest a central role for Isp7 in amino acid homeostasis and the presence of isp7+-dependent regulatory loops that affect both TORC1 and TORC2. 6 Samples (arrays) were performed. We generated pairwise comparison between DISP7 and WT, using Partek Genomics Suite. Genes with pâ¤5%[FDR] and a fold-change difference of â¥2\1.5 or <-2\-1.5 were selected.
2014-02-05 | E-GEOD-52759 | biostudies-arrayexpress
Project description:We show that the sensitivity of tsc mutant cells to rapamycin is mediated by TORC1 and can be suppressed by overexpression of the 2-oxoglutarate-Fe(II) dependent oxygenase, Isp7. We show that Isp7 is a novel regulator of amino acids uptake that acts via regulation of gene expression, both upstream and downstream of TOR signaling. suppressed by overexpression of the putative 2-oxoglutarate-Fe(II) dependent oxygenase, Isp7. We show that Isp7 is a novel master regulator of amino acids uptake that acts via regulation of gene expression, both upstream and downstream of TOR signaling. TOR proteins reside in two distinct complexes, TOR complex 1 and 2 (TORC1 and TORC2) that are central for the regulation of cellular growth, proliferation and survival. TOR is also the target for the immunosuppressive and anti-cancer drug rapamycin. In Schizosaccharaomyces pombe, disruption of the TSC complex, mutations in which can lead to the Tuberous Sclerosis syndrome in humans, results in a rapamycin sensitive phenotype under poor nitrogen conditions. We show here that the sensitivity to rapamycin is mediated via inhibition of TORC1 and suppressed by overexpression of isp7+, a member of the family of 2-oxoglutarate-Fe(II) dependent oxygenases. The transcript level of isp7+ is negatively regulated by TORC1 but positively regulated by TORC2. Yet, we find extensive similarity between the transcriptome of cells disrupted for isp7+ and cells mutated in the catalytic subunit of TORC1. Moreover, Isp7 regulates amino acid permease expression similarly to TORC1 and in contrast to TORC2. Overexpression of isp7+ induces TORC1-dependent phosphorylation of ribosomal protein Rps6, while inhibiting TORC2-dependent phosphorylation and activation of the AGC-like kinase Gad8. Taken together, our findings suggest a central role for Isp7 in amino acid homeostasis and the presence of isp7+-dependent regulatory loops that affect both TORC1 and TORC2.
2014-02-05 | GSE52759 | GEO
Project description:TOR kinase complex I (TORC1) is a key regulator of cell growth and metabolism in all eukaryotes. Previous studies in yeast have shown that three GTPases, Gtr1, Gtr2 and Rho1, bind TORC1 in nitrogen and amino acid starvation conditions to block phosphorylation of the S6 kinase Sch9 and activate protein phosphatase 2A (PP2A). This leads to down-regulation of 450 Sch9-dependent protein and ribosome synthesis genes, and up-regulation of 100 PP2A-dependent nitrogen assimilation and amino acid synthesis genes. Here, using bandshift assays and microarray measurements, we show that the TORC1 pathway also populates three other stress/starvation states. First, in glucose starvation conditions, the AMP activated protein kinase (AMPK/Snf1) and at least one other factor, push the TORC1 pathway into an off state where Sch9- branch signaling and PP2A-branch signaling are both inhibited. Remarkably, the TORC1 pathway remains in the glucose starvation (PP2A off) state even when cells are simultaneously starved for nitrogen and glucose. Second, in osmotic stress, the MAPK Hog1/p38 drives the TORC1 pathway into a different Sch9 off, PP2A off state, where PP2A-branch signaling can still be activated by nitrogen starvation. Third, in oxidative stress and heat stress, TORC1-Sch9 signaling is blocked while weak PP2A-branch signaling occurs. Together, our data show that the TORC1 pathway acts an information-processing hub, activating different genes in different conditions to ensure that available energy is allocated to drive growth, amino acid synthesis or a stress response, depending on the needs of the cell.
2014-07-29 | GSE58992 | GEO
Project description:To resolve the temporal sequence of phosphorylation events responding to nutritional and chemically induced up and downshifts of TORC1 signaling in S. cerevisiae wildtype, we performed quantitative MS phosphoproteomics upon nitrogen-quality up and downshifts and rapamycin treatment. We generated a high quality dataset byapplying a high resolution sampling, parallel sample processing and a dedicated data analysis pipeline that allowed us to select significant transient dynamics. By exploiting the temporal resolution of our data and the complementary of the shift experiments, we identified early phosphorylation changes regulated directly by TORC1 or by its proximal substrate kinases, and found both established and novel candidate TORC1 targets. Among the candidateTORC1 targets were the metabolic enzymes Amd1, Hom3, Nth1 and Tsl1, involved in nucleotide, amino acid and storage carbohydrate metabolism. Functional assessment of the role of phosphorylation for these and other enzymes was achieved by correlating phosphopeptide with the corresponding enzyme-associated metabolite dynamics. Candidate kinases regulating these enzymes were identified by establishing TORC1-proximity and differential kinase activity criteria. Our work provides first evidence of TORC1-dependent regulation of the metabolic enzymes Amd1and Hom3 by the kinases Sch9 and Atg1, respectively, providing mechanistic insights into on how TORC1 controls nucleotide and amino acid metabolism in response to the quality of the nitrogen source.
2022-02-22 | PXD000940 | Pride
Project description:To resolve the temporal sequence of phosphorylation events responding to nutritional and chemically induced up and downshifts of TORC1 signaling in S. cerevisiae wildtype, we performed quantitative MS phosphoproteomics upon nitrogen-quality up and downshifts and rapamycin treatment. We generated a high quality dataset byapplying a high resolution sampling, parallel sample processing and a dedicated data analysis pipeline that allowed us to select significant transient dynamics. By exploiting the temporal resolution of our data and the complementary of the shift experiments, we identified early phosphorylation changes regulated directly by TORC1 or by its proximal substrate kinases, and found both established and novel candidate TORC1 targets. Among the candidateTORC1 targets were the metabolic enzymes Amd1, Hom3, Nth1 and Tsl1, involved in nucleotide, amino acid and storage carbohydrate metabolism. Functional assessment of the role of phosphorylation for these and other enzymes was achieved by correlating phosphopeptide with the corresponding enzyme-associated metabolite dynamics. Candidate kinases regulating these enzymes were identified by establishing TORC1-proximity and differential kinase activity criteria. Our work provides first evidence of TORC1-dependent regulation of the metabolic enzymes Amd1and Hom3 by the kinases Sch9 and Atg1, respectively, providing mechanistic insights into on how TORC1 controls nucleotide and amino acid metabolism in response to the quality of the nitrogen source.
2022-02-22 | PXD000939 | Pride