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Response of gcr1 null mutant to glucose

ABSTRACT: This experiment was done to detect the transcriptomic defects in the gcr1 null mutant, relative to an isogenic wild type, in the immediate response to glucose. Keywords: time course

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE5575 | GEO | 2006/11/27

SECONDARY ACCESSION(S): PRJNA95433

REPOSITORIES: GEO

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Response of gcr1 null mutant to glucose

Project description:This experiment was done to detect the transcriptomic defects in the gcr1 null mutant, relative to an isogenic wild type, in the immediate response to glucose. Keywords: time course Both gcr1 mutant and wild type cells were grown in YEP containing 3% pyruvate to early/mid log phase. The 0min sample was taken just prior to glucose addition. After addition of glucose, samples were taken at 20min and 60min. Total RNA was extracted for both strains and expression was measured by competitive hybridization of the mutant and wild type labeled cRNA for each time point.

2010-06-30 | E-GEOD-5575 | biostudies-arrayexpress

Transcriptome response to gcr1 deletion in raffinose, galactose, and glucose

Project description:This experiment compares transcriptomic response of yeast cells to the deletion of Gcr1 to isogenic wild type strains, grown in YEP(3%)R at 23C. The goal was to identify misregulated target genes and analyze the functional classifications of those targets. Keywords: cell type comparison

2006-11-27 | GSE5027 | GEO

Transcriptome response to the deletion of Gcr1, Nup84 or Nup84 & Gcr1 (double deletion)

Project description:This experiment compares the transcriptional response of yeast cells to the deletion of Gcr1, Nup84, or both, to isogenic wild type strains grown in YPD at 23C. The goal was to identify misregulated target genes and analyze the functional classifications of those targets. Keywords: cell type comparison (knock-outs)

2007-08-22 | GSE3853 | GEO

ChIP-seq for two forms of Gcr1, during exponential phase and diauxic shift

Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and added a TAP tag protein to the Gcr1(U) and Gcr1(S), using HIS3MX6 marker system. We conducted ChIP-seq for both strains during the glycolytic phase or after the diauxic shift.

2020-07-07 | GSE153841 | GEO

RNA-seq for two forms of Gcr1, during exponential phase and diauxic shift

Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and performed RNA-seq for the two strains. Since Gcr1 works as a glycolytic gene transcription factor, we extracted whole RNA at the exponential phase (6 hrs after incubation) and the diauxic shift (12 hrs after incubation).

2020-07-07 | GSE153842 | GEO

Saccharomyces cerevisiae

Project description:Response of gcr1 null mutant to glucose

| PRJNA95433 | ENA

Transcription profiling of S. cerevisiae S. cerevisiae strain CEN.PK113.7D and the isogenic sfp1 null mutant were grown in chemostat cultures under ethanol(aerobic)- and glucose(anaerobic)- limitation to determine SFP1 dependent transcription

Project description:In Saccharomyces cerevisiae growth, size control and cell cycle progression are strictly coordinated and regulated according to the nutritional conditions. In particular, ribosome biogenesis appears a key event in this regulatory network. SFP1 encodes a zinc-finger protein promoting the transcription of a large cluster of genes involved in ribosome biogenesis. It has been suggested that Sfp1 is a cell size modulator acting at Start. To better study the regulatory role of Sfp1 and its putative involvement in cell size and cycle control, we analysed the behaviour of an sfp1 null mutant strain and of an isogenic reference strain growing in chemostat cultures. This approach allowed us to analyze both strains at the same specific growth rate, thus eliminating the secondary effects due to the slow growing phenotype that the sfp1 null mutant shows in shake flask. We studied glucose(anaerobic)- and ethanol(aerobic)-limited cultures, as paradigms of two different metabolic states. Major alterations of the transcriptional profile were observed during growth on glucose, while no significant differences were observed when comparing ethanol growing cultures. In particular, in the former growth condition, Sfp1 appears involved in the control of ribosome biogenesis but not of ribosomal protein gene expression. Experiment Overall Design: The reference S. cerevisiae strain CEN.PK113.7D and the isogenic sfp1 null mutant were grown in chemostat cultures under ethanol(aerobic)- and glucose(anaerobic)- limitation. The dilution rate was set at 0.10 h-1 and 0.05 h-1 for ethanol- and glucose-limited cultures, respectively. A genome-wide transcriptional analysis was performed for the reference and the sfp1 null mutant strains for each growth condition. All data presented in this work were derived from three independent chemostat cultures (12 samples in total were analysed).

2008-06-13 | E-GEOD-5238 | biostudies-arrayexpress

Glucose uptake is required for glucose-stimulated transcriptional response in Saccharomyces cerevisiae

Project description:Saccharomyces cerevisiae developed elegant mechanisms to monitor nutrient availability and trigger adaptative responses to nutrient deficiency. Nutrient sensing requires close coordination of cell surface sensors with intracellular mechanisms. This yeast senses the presence of glucose by two modified hexose transporters, Rgt2 and Snf3 (regulating expression of genes encoding hexose transporters) and the G-protein coupled receptor Gpr1 (modulating Protein Kinase A (PKA) activity).. It has been difficult to differentiate between cellular responses mediated by cell surface and intracellular sensors, respectively. Using a strain that is devoid of glucose uptake, we show that the mere presence of glucose does not elicit any glucose-dependent transcriptional responses. This indicates that signals generated by surface sensors are not sufficient to mediate glucose-dependent transcriptional responses. Instead, intracellular glucose or metabolites derived from it are required for transcriptional changes associated with glucose exposure. We used microarrays from biological triplicate samples to measure the global transcriptional response to sudden addition of glucose to yeast cells growing at steady state on ethanol. The experiment was conducted using a strain that is devoid of glucose uptake and compared with an isogenic strain. The CEN.PK strain was used in this research. A strain with all known hexose transporters deleted (Null strain) was compared with an isogenic reference. The two strains were grown in a chemostat (D = 0.1 h-1) using ethanol as the carbon source. Transcriptional responses between the strains were measured in biological triplicates at steady state and then pulsed with glucose at time t = 0. Transcriptional response was measured again after t = 20 min to determine changes in gene expression changes only in response to the presence of glucose.

2010-03-06 | E-GEOD-20566 | biostudies-arrayexpress

Transcription profiling of Saccharomyces cerevisiae reveals Stb3 deletion affects gene expression within 10 minutes of glucose addition

Project description:Microarrays were conducted to asses the effect of Stb3 deletion in immediate transcriptional induction in response to glucose Experiment Overall Design: Response of Stb3 delete cells was compared to that of wild type (BY4742) in cells grown for 3 days in YPD and cells that received 2% glucose for 10 minutes after the 3 day growth period. Two repetitive samples were done for each timepoint.

2009-04-30 | E-GEOD-8379 | biostudies-arrayexpress

Stb3 deletion affects gene expression within 10 minutes of glucose addition

Project description:Microarrays were conducted to asses the effect of Stb3 deletion in immediate transcriptional induction in response to glucose Keywords: Stb3, immediate glucose induction, growth genes.

2007-07-06 | GSE8379 | GEO

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