BIO 398-01: Bioinformatics Lab 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 Data Analysis Experimental Design Data significance Data Analysis Hypothesis Materials / Methods Results Discussion

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

Chemostat culture of Tai et al 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 down-regulated 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