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

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

PROVIDER: PRJNA308574 | ENA |

REPOSITORIES: ENA

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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.

2017-01-12 | GSE76715 | GEO

Saccharomyces cerevisiae S288C

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

| PRJNA308443 | ENA

Saccharomyces cerevisiae S288C

Project description:Global transcriptome changes after nitrogen replenishment in S288c yeast strain

| PRJNA308444 | ENA

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-01-10 | GSE76778 | GEO

Dynamic mRNA gene expression following a rapamycin treatment

2015-04-07 | GSE54851 | GEO

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

Comparing effects of rapamycin and caffeine on gene expression in YPD media

Project description:To identify genes influenced by rapamycin and caffeine in strains W303a, S288c, and Sigma 2000 Keywords: Drug dose response

2006-04-04 | GSE4584 | GEO

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. A sample was taken at steady-state 10 minutes before , and then 3, 7, 10, 14, 24, 56 and 120 minutes after rapamycin treatment. Biological triplicate gene expression was measured for samples -10, 7 and 24 minutes after shift, for a total of 14 chips. Changes were generally evaluated relative to the steady-state point (-10 minutes). Biological variability can be assessed from the replicates time points. Other dynamic omics data are associated with this dataset. Consult the publication for more details.

2015-04-07 | E-GEOD-54851 | biostudies-arrayexpress

Integration of the general amino acid control and nitrogen regulatory pathways in yeast nitrogen assimilation

Project description:Two nutrient sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), control yeast growth and metabolism in response to changes in nutrient availability. Starvation for amino acids activates the GAAC pathway, involving Gcn2p phosphorylation of eIF2 and preferential translation of GCN4, a transcription activator of genes involved in amino acid metabolism. TOR senses nitrogen availability and regulates gene expression through transcription factors, such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome in response to amino acid starvation and rapamycin treatment. Of the ~2500 genes whose expression was changed by 2-fold or greater, Gcn4p and Gln3p were required for 542 and 657 genes, respectively. While Gcn4p activates a common core of 57 genes in response to amino acid starvation or rapamycin treatment, the different stress arrangements allow for variations in Gcn4p-directed transcription. With few exceptions, genes requiring Gcn2p eIF2 kinase for induced expression also required Gcn4p, emphasizing the role of Gcn2p as an upstream activator of Gcn4p-directed transcription. There is also significant coordination between the GAAC and TOR pathways, with Gcn4p being required for activation of more genes during rapamycin treatment than Gln3p. Importantly, TOR regulates the GAAC-directed transcription of genes required for assimilation of nitrogen sources, such as γ-amino-butyric acid. Therefore, yeast has integrated gene expression responses to amino acid abundance and nitrogen source quality through the control of Gcn2p phosphorylation of eIF2 and GCN4 translation. Keywords: gene expression

2010-03-01 | GSE15254 | GEO

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