Transcript Analyzing Acclimation Response of

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
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Hypothesis
Materials / Methods
Results
Discussion
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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
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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