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Analyzing Acclimation Response of Saccharomyces Cerevisiae to Low Temperature BIO 398-01: Bioinformatics Lab April 27, 2010 Alex George Bobak Seddighzadeh Outline • Background of Yeast • Tai et al. Paper – Experimental Design – Data significance • Data Analysis – – – – Hypothesis Materials / Methods Results Discussion QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Saccharomyces cerevisiae • Unicellular eukaryotic organism • Model organism – Response to cold-shock has been comprehensively studied • Optimal temperature for growth between 25-35°C – Below 10°C cell growth stops • Ideally, transcriptional response of yeast can be applied to human biology QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Chemostat culture of Tai et al. allowed for new analysis of cold temperature response • Controlled specific growth rate by using a chemostat culture because of its previous implications on genome-wide transcription • Used two nutrient-limiting batches grown aerobically to limit variables – Reduced content dependency of transcriptional responses Results identify a ‘core’ set of regulated genes in response to prolonged exposure to cold temperature • Analyzing common group of regulated genes between nutrient-limited cultures establishes a ‘core’ set of context-independent, regulated genes • This ‘core’ set of genes was analyzed and compared to previous studies to provide further data for cold temperature response of S. cerevisiae Down-regulation of metabolism was most significant in Nitrogen-limited cultures • Out of the top 15 down-regulated GO terms, over half were associated with metabolism • Down-regulation of sugar metabolism indicates acclimation of yeast to cold temperature • In addition, the metabolism of amino acids and allantois were down-regulated showing the importance of keeping proteins in the cell • Finally, the down-regulation of iron (Fe) transporters is probably a result of anaerobic growth conditions because of its function in aerobic respiration Table ##: Fourteen most significant up-regulated GO terms of Nitrogen-limited cultures Table ##: Fifteen most significant downregulated GO terms of Nitrogen-limited cultures Protein production is main result of cold temperature transcriptional regulation in Nitrogen-limited cultures • GMP and IMP (key players in nucleic acid synthesis) indicates mRNA production • Up-regulation of both ribosomal subunits shows the necessity for protein production – Also, cold temperatures slow down initiation of translation • One-third of the top 15 GO terms are related to methylation, indicating the presence of newly transcribed mRNA and tRNA needed for protein synthesis • Biotin production and subsequent metabolism is a result of anaerobic growth due to its function in oxidation