Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA106367 | ENA |
REPOSITORIES: ENA
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Project description:Background Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on transcriptional regulation. Steady-state chemostat cultures, which do enable accurate control, measurement and manipulation of individual cultivation parameters (e.g. specific growth rate, temperature, identity of the growth-limiting nutrient) appear to provide a promising experimental platform for such a combinatorial analysis. Results A microarray compendium of 170 steady-state chemostat cultures of the yeast Saccharomyces cerevisiae is presented and analyzed. The 170 microarrays encompass 55 unique conditions, which can be characterized by the combined settings of 10 different cultivation parameters. By applying a regression model to assess the impact of (combinations of) cultivation parameters on the transcriptome, most S. cerevisiae genes were shown to be influenced by multiple cultivation parameters, and in many cases by combinatorial effects of cultivation parameters. The inclusion of these combinatorial effects in the regression model led to higher explained variance of the gene expression patterns and resulted in higher function enrichment in subsequent analysis. We further demonstrate the usefulness of the compendium and regression analysis for interpretation of shake-flask-based transcriptome studies and for guiding functional analysis of (uncharacterized) genes and pathways. Conclusions Modeling the combinatorial effects of environmental parameters on the transcriptome is crucial for understanding transcriptional regulation. Chemostat cultivation offers a powerful tool for such an approach. Keywords: chemostat steady state samples
2009-02-05 | GSE11452 | GEO
Project description:Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and transcriptome has not been studied in detail. In this study, 24-h sinoidal temperature cycles, oscillating between 12 and 30M-BM-0C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose, and extracellular metabolites, as well as CO2-production rates showed regular, reproducible circadian rhytms. DTC also led to waves of transcriptional activation and repression, which involved one sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to primarily respond to changes in glucose concentration. Elimination of known glucose-responsive genes revealed overrepresentation of previously identified temperature-responsive genes as well as genes involved in cell cycle and de novo purine biosynthesis. Analyses of budding index and flow cytomery demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in the chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that DTC was sufficiently slow to allow S. cerevisiae chemostat cultures to almost completely acclimatize their transcriptome and physiology at the DTC temperature maximum, and to approach acclimation at the DTC temperature minimum. The aim of this study was to investigate the impact of diurnal temperature cycles on the physiology and transcriptome of S. cerevisiae and to assess the extent to which these responses can be predicted from steady-state analyses. To this end, we used a continuous cultivation set-up, in which the yeast was grown under controlled conditions and subjected to 24-h sinoidal temperature cycles. Since the sampling volume was kept within 5% of the reactor volume during 24 h, sampling from two independent duplicate cultures for microarray analysis was spread over the fifth and sixth temperature cycle. Sample points from the fifth and sixth temperature cycle were combined, resulting in six sample points covering one temperature cycle (at temperatures of 30; 21; 14.6; 12; 21 and 27.4M-BM-0C). For the last time point, one additional analytical duplicate sample was taken. Furthermore, steady-state chemostat cultures at constant temperatures of 12M-BM-0C and 30M-BM-0C (independent duplicate cultures at both temperatures) were sampled for microarray analysis. All this resulted in a total array set of 17 arrays.
2014-05-12 | E-GEOD-55372 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae IMS0002 which, after metabolic and evolutionary engineering, ferments the pentose sugar arabinose. Glucose and arabinose-limited anaerobic chemostat cultures of IMS0002 and its non-evolved ancestor IMS0001 were subjected to transcriptome analysis to identify key genetic changes contributing to efficient arabinose utilization by strain IMS0002.
2011-03-01 | GSE27539 | GEO
Project description:Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and transcriptome has not been studied in detail. In this study, 24-h sinoidal temperature cycles, oscillating between 12 and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose, and extracellular metabolites, as well as CO2-production rates showed regular, reproducible circadian rhytms. DTC also led to waves of transcriptional activation and repression, which involved one sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to primarily respond to changes in glucose concentration. Elimination of known glucose-responsive genes revealed overrepresentation of previously identified temperature-responsive genes as well as genes involved in cell cycle and de novo purine biosynthesis. Analyses of budding index and flow cytomery demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in the chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that DTC was sufficiently slow to allow S. cerevisiae chemostat cultures to almost completely acclimatize their transcriptome and physiology at the DTC temperature maximum, and to approach acclimation at the DTC temperature minimum.
2014-05-12 | GSE55372 | GEO
Project description:We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae. Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.
2011-11-01 | E-GEOD-33136 | biostudies-arrayexpress
Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors.
2012-10-18 | GSE41659 | GEO
Project description:Chemostat expression data of amylase producing yeast Saccharomyces cerevisiae
| PRJNA175391 | ENA
Project description:A three-factor design was applied to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures of Saccharomyces cerevisiae.
2009-01-15 | E-MTAB-78 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae is an excellent microorganism for industrial succinic acid production, but high succinic acid concentration will inhibit the growth of Saccharomyces cerevisiae then reduce the production of succinic acid. Through analysis the transcriptomic data of Saccharomyces cerevisiae with different genetic backgrounds under different succinic acid stress, we hope to find the response mechanism of Saccharomyces cerevisiae to succinic acid.
2022-01-09 | GSE193190 | GEO
Project description:The capacity of respiring cultures of Saccharomyces cerevisiae to instantaneously switch to fast alcoholic fermentation upon a transfer to anaerobic sugar-excess conditions is a key characteristic of Saccharomyces cerevisiae in many of its industrial applications. This transition was studied by exposing aerobic glucose-limited chemostat cultures grown at a low specific growth rate to two simultaneous perturbations: oxygen depletion and relief of glucose limitation. This shift towards fully fermentative conditions caused a massive transcriptional response, where one third of all genes within the genome were transcribed differentially. During the first 30 min, most of these changes were driven by relief from glucose limitation. An anaerobic induction response was only observed after the initial response to glucose excess. By comparing this study with public datasets representing dynamic and steady conditions, 14 up-regulated and 11 down-regulated genes were determined to be anaerobiosis specific and can therefore be use as “signature” transcripts for anaerobicity under dynamic as well as under steady state conditions Keywords: global transcriptional time-dependent profile
2008-06-16 | GSE8187 | GEO