E-GEOD-8900 - Transcription profiling of S. cerevisiae to high carbon dioxide concentrations

Status
Submitted on 29 August 2007, released on 16 June 2008, last updated on 27 March 2012
Organism
Saccharomyces cerevisiae
Samples (18)
Array (1)
Protocols (29)
Description
Physiological effects of carbon dioxide and impact on genome-wide transcript profiles were analysed in chemostat cultures of Saccharomyces cerevisiae. In anaerobic, glucose-limited chemostat cultures grown at atmospheric pressure, cultivation under CO2-saturated conditions had only a marginal (<10%) impact on the biomass yield. Conversely, a 25% decrease of the biomass yield was found in aerobic, glucose-limited chemostat cultures aerated with a mixture of 79% CO2 and 21% O2. This observation indicated that respiratory metabolism is more sensitive to CO2 than fermentative metabolism. Consistent with the more pronounced physiological effects of CO2 in respiratory cultures, the number of CO2-responsive transcripts was higher in aerobic cultures than in anaerobic cultures. Many genes involved in mitochondrial functions showed a transcriptional response to elevated CO2 concentrations. This is consistent with an uncoupling effect of CO2 and/or intracellular bicarbonate on the mitochondrial inner membrane. Other transcripts that showed a significant transcriptional response to elevated CO2 included NCE103 (probably encoding carbonic anhydrase), PCK1 (encoding PEP carboxykinase) and members of the IMD gene family (encoding isozymes of inosine monophosphate dehydrogenase Experiment Overall Design: Knowledge on the genome-wide transcriptional response of S. cerevisiae to high CO2 concentrations may provide a deeper insight into the molecular mechanisms of CO2 stress. Such insight is essential to develop metabolic-engineering strategies for improving CO2 tolerance. Furthermore, identification of ‘signature transcripts’ that uniquely respond to CO2 stress may be applicable for diagnosing the CO2 status of industrial fermentations. It has recently been demonstrated that the combination of chemostat cultivation with DNA-microarray-based transcriptome analysis offers a powerful and reproducible approach to identify the transcriptional responses of yeasts to environmental parameters For this reason, in the present study we used chemostat cultures of S. cerevisiae to quantify the effect of CO2 on respiring and fermenting cells, and to determine the genome-wide transcriptional responses of this yeast to high CO2 concentrations.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to high carbon dioxide concentrations. Jaime Aguilera, Thomas Petit, Johannes H de Winde, Jack T Pronk. FEMS Yeast Res 5(6-7):579-93 (2005)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-8900.idf.txt
Sample and data relationshipE-GEOD-8900.sdrf.txt
Raw data (1)E-GEOD-8900.raw.1.zip
Processed data (1)E-GEOD-8900.processed.1.zip
Array designA-AFFY-27.adf.txt
R ExpressionSetE-GEOD-8900.eSet.r
Links