Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE4158 | GEO | 2006/02/03
SECONDARY ACCESSION(S): PRJNA95005
REPOSITORIES: GEO
Similar Datasets
Project description:Two time courses after pulses of 0.2 g/l and 2 g/l glucose on cells growing in chemostat with galactose as the carbon source. The reference is sample from the chemostat at time 0.
2006-01-06 | E-SMDB-3593 | biostudies-arrayexpress
Project description:To understand the dynamics of transcriptional response to changing environments, well defined, easily controlled, and short-term perturbation experiments were undertaken. We subjected steady-state cultures of Saccharomyces cerevisiae in chemostats growing on limiting galactose to two different size pulses of glucose, well known to be a preferred carbon source. Although these pulses were not large enough to change growth rates or cell size, approximately 25% of the genes changed their expression at least 2-fold. Using DNA microarrays to estimate mRNA abundance, we found a number of distinguishable patterns of transcriptional response among the many genes whose expression changed. Many of these genes were already known to be regulated by particular transcription factors; we estimated five potentially relevant transcription factor activities from the observed changes in gene expression (i.e., Mig1p, Gal4p, Cat8p, Rgt1p, Adr1p, and Rcs1p). With these estimates, for two regulatory circuits involving interaction among multiple regulators we could generate dynamical models that quantitatively account for the observed transcriptional responses to the transient perturbations.
| S-EPMC1326188 | biostudies-literature
Project description:Cells must adjust their gene expression in order to compete in a constantly changing environment. Two alternative strategies could in principle ensure optimal coordination of gene expression with physiological requirement. First, the internal physiological state itself could feedback to regulated gene expression. Second, the expected physiological state could be inferred from the external environment, using evolutionary-tuned signaling pathways. Coordination of ribosomal biogenesis with the requirement for protein synthesis appears to be particularly important, since cells devote a large fraction of their biosynthetic capacity for ribosomal biogenesis. To define the relative importance of internal vs. external sensing to the regulation of ribosomal biogenesis gene expression, we subjected S. cerevisiae cells to conditions which decoupled the actual vs. environmentally-expected growth rate. Gene expression followed the environmental signal according to the expected, but not the actual, growth rate. Simultaneous monitoring of gene expression and growth rate in chemostat-grown cultures further confirmed that ribosome biogenesis genes responded rapidly to changes in the environments but were oblivious to longer-term changes in growth rate. Our results suggest that the capacity to anticipate and prepare for environmental changes presented a major selection force during yeast evolution. Keywords: Saccharomyces_Cerevisiae, Stress response, ADH1 deletion, time courses, chemostat
2007-02-28 | GSE6302 | GEO
Project description:This data file contains all the data used to produce Figure 4 of Saldanha, Brauer and Bostein. The limiting nutrient is indicated by the letter followed by the timecourse number. S= sulfate, P=phosphate, U=uracil, L=leucine. The chemostat comparisons are prefixed by CC. Channels are as noted in the individual arrays, and are consistent for a given timecouse, but may vary between time courses. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs
2005-07-16 | GSE2953 | GEO
Project description:Cells must adjust their gene expression in order to compete in a constantly changing environment. Two alternative strategies could in principle ensure optimal coordination of gene expression with physiological requirement. First, the internal physiological state itself could feedback to regulated gene expression. Second, the expected physiological state could be inferred from the external environment, using evolutionary-tuned signaling pathways. Coordination of ribosomal biogenesis with the requirement for protein synthesis appears to be particularly important, since cells devote a large fraction of their biosynthetic capacity for ribosomal biogenesis. To define the relative importance of internal vs. external sensing to the regulation of ribosomal biogenesis gene expression, we subjected S. cerevisiae cells to conditions which decoupled the actual vs. environmentally-expected growth rate. Gene expression followed the environmental signal according to the expected, but not the actual, growth rate. Simultaneous monitoring of gene expression and growth rate in chemostat-grown cultures further confirmed that ribosome biogenesis genes responded rapidly to changes in the environments but were oblivious to longer-term changes in growth rate. Our results suggest that the capacity to anticipate and prepare for environmental changes presented a major selection force during yeast evolution. Keywords: Saccharomyces_Cerevisiae, Stress response, ADH1 deletion, time courses, chemostat Experiment 1: ADH1 deletion cells, which grow faster on glycerol rather then glucose medium, were grown in both glucose and glycerol medium. The cells expression on glycerol is compared to their expression glucose (5 microarrays). Experiment 2: Time course of ADH1 deletion cells upon growth on glycerol and on glucose (7 microarrays). Experiment 3: Response of steady state grown cells to environmental perturbations. Cells were grown in glucose or histidine limited chemostats and reached steady state. The cells were then subjected to perturbations such as DTT, heat shock, NaCl, Clotrimazole, H2O2, and addition of limiting factors (histidine and glucose, respectively). Overall we have examined 10 timecourses with 83 microarrays.
2007-02-28 | E-GEOD-6302 | biostudies-arrayexpress
Project description:This data file contains all the data used to produce Figure 4 of Saldanha, Brauer and Bostein. The limiting nutrient is indicated by the letter followed by the timecourse number. S= sulfate, P=phosphate, U=uracil, L=leucine. The chemostat comparisons are prefixed by CC. Channels are as noted in the individual arrays, and are consistent for a given timecouse, but may vary between time courses. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Using regression correlation
2005-07-16 | E-GEOD-2953 | biostudies-arrayexpress
Project description:Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours. Groups of assays that are related as part of a time series. FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition Keywords: time_series_design
2005-08-26 | GSE3205 | GEO
Project description:Microarray time courses followed the response of 5 yeast strains to heat shock. Expression variation due to genetic, environmental, and genotype-by-environment interactions were identified. Keywords: Timecourse and single timepoint expression studies of stress response in yeast
2009-12-15 | GSE15147 | GEO
Project description:Wild type S. cerevisiae cells were grown under glucose or ammonium limitation in fully controlled aerobic chemostat cultures. At steady state, the limited nutrient was introduced into the growth medium in an impulse like manner to recover the medium to its non-limiting conditions. Samples were collected at steady state and following the impulse (20s, 40s, 60s, 8 min, 16 min, 24 min, 32 min, 1 hr, 2hr, 3hr, 4hr, 5hr, 7 hr) until the effect of the perturbation ceased to exist. The last sample was collected the second time the chemostat reached steady state.
2011-10-03 | E-MTAB-643 | biostudies-arrayexpress
Project description:The microarrays for the three time course experiments described in the publication titled "Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression". TC1 refers to the first time course investigating gene expression changes over the time course of growth while TC2 refers to the second time course. TC Motility_broth refers to the third time course described in the manuscript used to investigate the concurrent changes in motility and the expression of the genes in the flagellar regulon. Detailed description of the growth of H. pylori for these 3 time courses can be found in the Materials and Methods section of the manuscript along with the exact filtering criteria used to download the data from these arrays. Note that in all three time courses the data for each array were transformed after download such that the abundance of each gene's transcript represented by a given spot was relative to the level of that transcript at the 6 h time point. Also duplicate spots for each ORF on the microarray were averaged for analysis after transformation. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-11-22 | GSE3636 | GEO