Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of yeast S. cerevisiae over three successive metabolic cycles

ABSTRACT: Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity. Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time. This data set contains the raw affymetrix gene expression data over three successive metabolic cycles. 12 time intervals per cycle, ~25 min per time interval.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Benjamin Tu

PROVIDER: E-GEOD-3431 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes.

Tu Benjamin P BP Kudlicki Andrzej A Rowicka Maga M McKnight Steven L SL

Science (New York, N.Y.) 20051027 5751

Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity. Essential cellular ...[more]

PMID: 16254148

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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.

Dataset Information

Transcription profiling of yeast S. cerevisiae over three successive metabolic cycles

Publications

Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes.

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