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Analyzing Acclimation Response of Saccharomyces cerevisiae to Low Temperature

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

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Analyzing Acclimation Response of Saccharomyces cerevisiae to Low Temperature

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  1. Analyzing Acclimation Response of Saccharomyces cerevisiae to Low Temperature BIO 398-01: Bioinformatics Lab April 27, 2010 Alex George Bobak Seddighzadeh

  2. Outline • Background of Yeast • Tai et al. Paper • Experimental Design • Data significance • Data Analysis • Hypothesis • Materials / Methods • Results • Discussion

  3. 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

  4. 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

  5. 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

  6. Cold Temperatures Affect Enzyme Kinetics, Membrane Composition, and Cytosolic Solute Concentrations • General predictions • Up-regulation of protein synthesis • Up-regulation of ribosomal proteins • Up-regulation of trehalose and cholesterol accumulation/production • Down regulation of carbohydrate anabolism • Nitrogen-Limited • Down-regulation of protein anabolism • Up-regulation of protein catabolism • Carbon-Limited • Up-regulation of B-oxidation • Down-regulation of glycolytic pathways

  7. Materials & Methods: GenMAPP • Upload S. cerevisiae data onto GenMAPP • Launch Expression Dataset Manger • Select the appropriate dataset • Data Type Specification • Convert Data • 70 Errors while converting • Customize the new Expresison Dataset • Orange correlated to increase; Blue correlated to decreased • Establish the criterion

  8. Materials & Methods: MAPPFinder • Upload the correct gene database • Calculate new results on the dataset • Choose the Color Set and Criteria • Run the analysis • List the top 10 gene ontology terms • Go to ranked list

  9. Materials & Methods: Excel • We opened our data with excel in order to filter our results to find significant changes and GO terms • The following is the criteria we used to cut the number of terms to about 20 per condition: • Permute p-value <0.05 • Z score > 2 • Number changed >3 and < 100 • Percent Changed • Carbon-limited Increased: > 40% • Carbon-limited Decreased: > 60% • Nitrogen-Limited Increased: > 50% • Nitrogen-Limited Decreased: > 63%

  10. Fourteen most significant up-regulated GO terms of Nitrogen-limited cultures

  11. Fifteen most significant down-regulated GO terms of Nitrogen-limited cultures

  12. Fifteen most significant down-regulated GO terms of Carbon-limited cultures

  13. Seventeen most significant up-regulated GO terms of Carbon-limited cultures

  14. Protein production is main result of cold temperature transcriptional regulation in Nitrogen-limited cultures • GMP and IMPD (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

  15. 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 allantoin 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

  16. C-limited Environments Up-regulate Protein Processing and Down-regulate Respiration • Need more ribosomes to make up for slowed enzyme kinetics • Altered gene expression need more processing and packaging • Want to increases chances of survival in Carbon stress through symbiotic relationships • Reduction in proteins involved in respiratory pathways due to lack of glucose • Cellular respiration involves many redox reactions

  17. References • Tai, L.S., Daran-Lapujade, P., Walsh, M.C., Pronk, J.T., Daran, J.M. Acclimation of Saccharomyces Cervisiae to Low Temperature. Molecular Biology of the Cell 18, 5100-5112

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