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Role of pp-ips in rpd3 complex and the environmental stress response (ESR)

ABSTRACT: Cells respond to stress and starvation by adjusting their growth rate and enacting stress defense programs. In eukaryotes this involves inactivation of TORC1, which in turn triggers downregulation of ribosome and protein synthesis genes and upregulation of stress response genes. Here we report that the highly conserved inositol pyrophosphate second messengers (including 1-PP-IP5, 5-PP-IP4, and 5-PP-IP5) are also critical regulators of cell growth and the general stress response, acting in parallel to the TORC1 pathway to control the activity of the class I HDAC Rpd3L. In fact, yeast cells that cannot synthesize any of the PP-IPs mount little to no transcriptional response in osmotic, heat, or oxidative stress. Furthermore, PP-IP dependent regulation of Rpd3L occurs independently of the role individual PP-IPs (such as 5-PP-IP5) play in activating specialized stress/starvation response pathways. Thus, the PP-IP second messengers simultaneously activate and tune the global response to stress and starvation signals.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE45370 | GEO | 2013/03/22

SECONDARY ACCESSION(S): PRJNA193595

REPOSITORIES: GEO

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Role of pp-ips in rpd3 complex and the environmental stress response (ESR)

Project description:Cells respond to stress and starvation by adjusting their growth rate and enacting stress defense programs. In eukaryotes this involves inactivation of TORC1, which in turn triggers downregulation of ribosome and protein synthesis genes and upregulation of stress response genes. Here we report that the highly conserved inositol pyrophosphate second messengers (including 1-PP-IP5, 5-PP-IP4, and 5-PP-IP5) are also critical regulators of cell growth and the general stress response, acting in parallel to the TORC1 pathway to control the activity of the class I HDAC Rpd3L. In fact, yeast cells that cannot synthesize any of the PP-IPs mount little to no transcriptional response in osmotic, heat, or oxidative stress. Furthermore, PP-IP dependent regulation of Rpd3L occurs independently of the role individual PP-IPs (such as 5-PP-IP5) play in activating specialized stress/starvation response pathways. Thus, the PP-IP second messengers simultaneously activate and tune the global response to stress and starvation signals. 2-condition experiments. Includes the responses of wild-type (ACY 044) and mutant yeast strains (all are W303 background) to log growth and stress conditions. This series of microarrays were performed on null mutants of various genes in the inositol pyrophosphate synthesis pathway, including several members of the Rpd3L histone deacetylase complex. All mutants were made in W303 strain, MatA yeast, using standard techniques (homologous recombination). Several stress conditions were tested, including heat-shock, oxidative (H2O2), and osmotic stress (0.375M KCl). Cells in mid-log growth were subjected to stress for 20 minutes. In one instance the TOR inhibitor rapamycin was added to determine whether PP-IPs act above/at or below TORC1 in activating the ESR. Taken together, these microarrays show the role of the inositol pyrophosphate synthesis pathway in activating the ESR in stress.

2013-03-22 | E-GEOD-45370 | biostudies-arrayexpress

State Transitions in the TORC1 Signaling Pathway and Information Processing in S. cerevisiae

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

Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast

Project description:Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of- Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1’s response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.

2023-10-15 | GSE244380 | GEO

Sch9 Is a Major Target of TORC1 in Saccharomyces cerevisiae

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.

2007-04-28 | GSE7660 | GEO

Sch9 Is a Major Target of TORC1 in Saccharomyces cerevisiae

2010-09-15 | E-GEOD-7660 | biostudies-arrayexpress

Exonuclease Xrn1 regulates TORC1 signaling in response to SAM availability

Project description:Autophagy is a conserved process of cellular self-digestion that promotes survival during nutrient stress. In yeast, methionine starvation is sufficient to induce autophagy. One pathway of autophagy induction is governed by the SEACIT complex, which regulates TORC1 activity in response to amino acids through the Rag GTPases Gtr1 and Gtr2 This work identifies an unexpected yet critical role for Xrn1 in nutrient sensing and growth control that extends beyond its canonical housekeeping function in RNA degradation and indicates an avenue for RNA metabolism to function in amino acid signaling into TORC1.

2023-10-19 | GSE226779 | GEO

Saccharomyces cerevisiae

Project description:Role of pp-ips in rpd3 complex and the environmental stress response (ESR)

| PRJNA193595 | ENA

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (mRNA-Seq data)

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

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (ChIP-Seq data)

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

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (ChIP-Seq data)

2011-07-01 | GSE29124 | GEO

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