Transcription profiling of S. cerevisiae Gcn4p-mediated transcriptional stress response
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Joel Moxley
PROVIDER: E-GEOD-4709 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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 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.
2010-03-07 | E-GEOD-15254 | biostudies-arrayexpress
Project description:Gcn4p-mediated transcriptional stress response
| PRJNA95591 | ENA
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
Project description:Deletion of several ribosomal proteins genes (RPKOs) has been shown to extend the lifespan of Saccharomyces cerevisiae in a Gcn4-dependent manner. To characterize the underlying mechanisms, we systematically analyzed the gene expression of both short- and long-lived RPKO strains at multiple levels. We found that up-regulation of amino acid biosynthesis and global down-regulation of protein synthesis are hallmarks of long-lived strains. We provide direct evidence that gene expression changes observed in long-lived strains result from translational up-regulation of GCN4 mRNA via skipping of upstream open reading frames (uORFs), in turn due to slow/defective ribosome assembly. We further demonstrate that Gcn4 acts as a transcriptional repressor on promoters of translation-related genes, thereby globally reducing protein synthesis. Our data suggest that the Gcn4-dependent increase in lifespan can be attributed partially to its ability to dampen the translation capacity of the cell, thereby engaging a well known mechanism of longevity.
2017-07-06 | PXD004760 | Pride
Project description:In response to stress, eukaryotes activate the integrated stress response (ISR) via phosphorylation of eIF2α to promote the translation of pro-survival effector genes, such as GCN4 in yeast. Complementing the ISR is the Target of Rapamycin (TOR) pathway, which regulates eIF4E function. Here we probe translational control in the absence of eIF4E in Saccharomyces cerevisiae. Intriguingly, we find that loss of eIF4E leads to de-repression of GCN4 translation. In addition, we find that de-repression of GCN4 translation is neither accompanied by eIF2α phosphorylation nor reduction in initiator ternary complex. Our data suggest that when eIF4E levels are depleted, GCN4 translation is de-repressed via a unique mechanism that may involve faster scanning by the small ribosome subunit due to increased local concentration of eIF4A. Overall, our findings suggest that relative levels of eIF4F components are key to ribosome dynamics and may play important roles in translational control of gene expression.
2023-01-25 | GSE223465 | GEO
Project description:In Saccharomyces cerevisiae, the Gcn2p kinase controls a gene expression program in response to nutrient deprivation. Upon amino acid deprivation Gcn2p phosphorylates the translation initiation factor 2a subunit (eIF2a). Phosphorylation of eIF2a transiently inhibits translation initiation, and favours selective translation of the GCN4 transcription factor mRNA. High levels of Gcn4p then activate the expression of genes encoding amino acid biosynthesis pathways. Besides nutrient deprivation, Gcn2p can also be activated by other stresses such as DNA damage. Previous studies in our lab suggested that Gcn2p regulated other cellular pathways apart from translation initiation. To gain insights into these new regulatory roles of Gcn2p, we generated a strain called (GCN2c) expressing a constitutively active Gcn2p kinase mutant. In the GCN2c strain, phosphorylation of eIF2a and translation of a GCN4-lacz reporter was constitutively high in the absence of amino acid starvation. We investigated the transcriptional profile of the GCN2c mutant strain by cDNA microarrays. As expected, numerous amino acid biosynthetic genes were upregulated, being dependent of Gcn4p. Most interestingly, expression of genes encoding proteins involved in DNA replication/repair was decreased, suggesting that Gcn2p could regulate cell cycle progression from G1 to S phase. Accordingly, the Gcn2c strain exhibited, i) slow growth, ii) a delayed entry into S phase, and iii) hypersensitivity to hydroxyurea. In addition, MMS treatment induced a G1 checkpoint and a growth defect which was dependent on Gcn2p and Gcn3p. Considering that MMS delays cell cycle progression by generating DNA lesions, the findings suggest that DNA damage induces a G1/S checkpoint by a novel pathway involving the protein kinase Gcn2p. Keywords: mutant analysis
2007-10-22 | GSE8111 | GEO
Project description:In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. Chromatin immunoprecipitation reveals Gcn4 binding not only at genes that are activated, but also at genes that are repressed upon Gcn4 overexpression. The promoters of repressed genes contain Rap1 binding motifs. Our data suggest that Gcn4 is a central regulator of protein synthesis under multiple perturbations - including ribosomal protein (RP) gene deletions, calorie restriction, rapamycin treatment - and provide an explanation for its role in longevity and stress response. This SuperSeries is composed of the SubSeries listed below.
2017-06-28 | GSE85591 | GEO
Project description:In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. Chromatin immunoprecipitation reveals Gcn4 binding not only at genes that are activated, but also at genes that are repressed upon Gcn4 overexpression. The promoters of repressed genes contain Rap1 binding motifs. Our data suggest that Gcn4 is a central regulator of protein synthesis under multiple perturbations - including ribosomal protein (RP) gene deletions, calorie restriction, rapamycin treatment - and provide an explanation for its role in longevity and stress response.
2017-06-28 | GSE85590 | GEO
Project description:In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. Chromatin immunoprecipitation reveals Gcn4 binding not only at genes that are activated, but also at genes that are repressed upon Gcn4 overexpression. The promoters of repressed genes contain Rap1 binding motifs. Our data suggest that Gcn4 is a central regulator of protein synthesis under multiple perturbations - including ribosomal protein (RP) gene deletions, calorie restriction, rapamycin treatment - and provide an explanation for its role in longevity and stress response.
2017-06-28 | GSE85588 | GEO
Project description:Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ~30% of all Gcn4 binding-motifs. Deviation from the consensus motif and nucleosome occupancy are key negative determinants of Gcn4 binding. Surprisingly, only ~40% of the bound sites are in promoter regions, and only ~50-67% of these activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ~300 Gcn4-bound sites are within coding sequences (CDS), with ~75 representing the only bound sites near Gcn4-induced genes. Many such unconventional sites map between divergent antisense and sub-genic sense transcripts induced within CDS, adjacent to induced TBP peaks—consistent with Gcn4 activation of cryptic, bidirectional internal promoters. Mutational analysis confirms that Gcn4 sites within CDS can activate sub-genic and full-length transcripts from the same or adjacent genes, showing that functional Gcn4 binding is not confined to promoters.
2018-02-26 | GSE110413 | GEO