E-GEOD-15254 - Transcription profiling by array of yeast gcn2, gcn4 and gln3 deletion mutants treated with rapamycin or 3-amino-1,2,4-triazole (3-AT)

Status
Released on 7 March 2010, last updated on 18 August 2014
Organism
Saccharomyces cerevisiae
Samples (72)
Array (1)
Protocols (8)
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 In this study, we carried out microarray analyses in a collection of yeast strains deleted for GCN2, GCN4, and GLN3, individually or in combinations, to explore the importance of the TOR and GAAC pathways in directing the transcriptome in response to amino acid starvation and rapamycin treatment.
Experiment type
transcription profiling by array 
Contacts
Ron Wek <rwek@iupui.edu>, Howard J Edenberg, Jeanette N McClintick, Kirk A Staschke, Ronald C Wek, Souvik Day
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-15254.idf.txt
Sample and data relationshipE-GEOD-15254.sdrf.txt
Raw data (1)E-GEOD-15254.raw.1.zip
Processed data (1)E-GEOD-15254.processed.1.zip
Array designA-AFFY-27.adf.txt
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