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Global transcriptome changes after nitrogen replenishment following or not a rapamycin treatment in S288c yeast strain

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae S288C

PROVIDER: GSE76778 | GEO | 2017/01/10

SECONDARY ACCESSION(S): PRJNA308574

REPOSITORIES: GEO

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Global transcriptome changes after nitrogen replenishment following a rapamycin treatment in S288c yeast strain

Project description:The study on the effect of nitrogen replenishment on the gene expression following a rapamycin treatment showed that the down-regulation of the glycolytic transcripts was generally suppressed after this treatment. This indicated that the TOR signaling pathway likely controls the expression of the glycolytic gene under these conditions.

2017-01-12 | GSE76716 | GEO

Global transcriptome changes after nitrogen replenishment in S288c yeast strain

Project description:The study on the effect of nitrogen replenishment on the gene expression showed that 390 genes were significantly upregulated (with a logFC ranging from 4.5 to 0.8), among which those related to RNA binding, ribosome binding, structural constituent of ribosome, transferase activity and transcription. 833 genes were significantly down-regulated (with a logFC ranging from -0.8 to -5.2) including those related to stress response, amino-acid catabolism process, protein catabolic process (ubiquitin-dependent and vacuolar protein degradation). But the most interesting and unexpected changes were those related to the down-regulation of the glycolytic transcripts. In fact, we observed a rapid down-regulation of many glycolytic mRNA (25/34) 30 min after nitrogen repletion. These data were surprising as expression of the glycolytic genes are generally considered as stable and sometimes they are even used as housekeeping control genes. In addition, the decoupling of the glycolytic gene expression from the expression of RP genes, ribosomal genes or those related to protein synthesis is unique to the present dataset as in most other data expression of these groups are tightly correlated when nutrients are available. This prompts us to examine in some details the factors which led to the control of the glycolytic mRNA instability in conditions of nitrogen replenishment.

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Global transcriptome changes after nitrogen replenishment following or not a rapamycin treatment in S288c yeast strain

Project description:Global transcriptome changes after nitrogen replenishment following or not a rapamycin treatment in S288c yeast strain

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Target of rapamycin complex 1 and Tap42-associated phosphatases are required for sensing changes in nitrogen conditions in the yeast Saccharomyces cerevisiae.

Project description:In yeast target of rapamycin complex 1 (TORC1) and Tap42-associated phosphatases regulate expression of genes involved in nitrogen limitation response and the nitrogen discrimination pathway. However, it remains unclear whether TORC1 and the phosphatases are required for sensing nitrogen conditions. Utilizing temperature sensitive mutants of tor2 and tap42, we examined the role of TORC1 and Tap42 in nuclear entry of Gln3, a key transcription factor in yeast nitrogen metabolism, in response to changes in nitrogen conditions. Our data show that TORC1 is essential for Gln3 nuclear entry upon nitrogen limitation and downshift in nitrogen quality. However, Tap42-associated phosphatases are required only under nitrogen limitation condition. In cells grown in poor nitrogen medium, the nitrogen permease reactivator kinase (Npr1) inhibits TORC1 activity and alters its association with Tap42, rendering Tap42-associated phosphatases unresponsive to nitrogen limitation. These findings demonstrate a direct role for TORC1 and Tap42-associated phosphatases in sensing nitrogen conditions and unveil an Npr1-dependent mechanism that controls TORC1 and the phosphatases in response to changes in nitrogen quality.

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Carbon: nitrogen stoichiometry following afforestation: a global synthesis.

Project description:Though carbon (C): nitrogen (N) stoichiometry has been widely studied in terrestrial ecosystems, little is known about its variation following afforestation. By synthesizing the results of 53 studies, we examined temporal and spatial variation in C: N ratios and in N-C scaling relationships of both the organic and the mineral soil horizons. Results showed that C: N ratios remained constant in the mineral horizon but significantly decreased in the organic horizon over the age sequence following afforestation. Among different climate zones, C: N ratios of the organic and the mineral horizons increased and decreased, respectively, with increasing mean annual temperature (MAT) (decreasing latitude). Pasture exhibited higher C: N ratios than cropland in the organic horizon while C: N of the mineral horizon did not change much among different land use types. For both the organic and the mineral horizons, hardwoods exhibited lower C: N ratios than pine and softwoods. Additionally, N and C in general scaled isometrically in both the organic and the mineral horizons over the age sequence and among different climate zones, land use types, and plantation species following afforestation. Our results suggest that C and N may remain coupled following afforestation.

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LC-MS analysis of yeast metabolome extracts under rapamycin treatment and nitrogen source downshift

Project description:Yeast of different genotypes were exposed to nutrient downshifts either through treatment of the cells with the drug rapamycin, or by shifting the cells to media containing a poor nitrogen source.

2022-07-21 | MSV000089934 | MassIVE

Dynamic mRNA gene expression following a rapamycin treatment

Project description:Dynamic mRNA gene expression from the wildtype YSBN6 during a rapamycin treatment (rapamycin-induced downshift). Rapamycin was added to yeast cells growing exponentially on glutamine as sole nitrogen source.

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Brain Protein Synthesis Rates in the UM-HET3 Mouse Following Treatment With Rapamycin or Rapamycin With Metformin.

Project description:Treatment with the mechanistic target of rapamycin (mTOR) inhibitor, rapamycin (RAP), alone and in combination with the antidiabetic drug, metformin (RAP+MET), extends lifespan in mice. The mechanisms underlying lifespan extension are unclear. One possibility is improved capacity for proteostatic maintenance. We have previously characterized peripheral protein synthesis rates following treatment with RAP. However, it is unknown if RAP+MET elicits similar changes, or if either treatment affects protein synthesis in the brain. We hypothesized that 8 weeks of treatment with RAP and RAP+MET would alter brain protein synthesis rates to reflect proteostatic processes. Using the stable isotopic tracer, deuterium oxide (D2O), we demonstrate in UM-HET3 mice that protein synthesis rates measured in whole brain were unaffected by treatment in young male mice, whereas RAP+MET decreased mitochondrial protein synthesis in young females. Conversely, RAP increased mitochondrial protein synthesis rates in older females. Activity through the AMPK/mTOR pathway was affected in a sex-specific manner in young mice, and minimal changes were observed in the older cohort. Thus, we establish D2O for measurements of biogenesis in the brain. These results provide initial insights into the effects of RAP and RAP+MET on brain protein synthesis. Additionally, these data emphasize that responses to slowed aging treatments vary with sex and age.

| S-EPMC7175973 | biostudies-literature

GNPS - LC-MS analysis of yeast metabolome extracts under rapamycin treatment and nitrogen source downshift

2022-07-21 | MSV000089934 | GNPS

Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast.

Project description:Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.

| S-EPMC2878067 | biostudies-literature

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