Bobak Seddighzadeh Week 11

Terms:

acclimation: adaptation to prolongued exposure
trehalose: disaccharide that is involved in the ability of plants/animals to withstand desiccation due to its hight water retention
batch culture: a large-scale closed culture in which cells are grown in a fixed volume of nutrient medium under specific environmental conditions
cis-regulatory motif: a motif is a nucleotide/ amino acid sequence that is widespread and is believed to have biological significance
specific growth rate: increase in cell mass per unit cell mass per unit time-- unites = reciprocal time
desaturase: an enzyme that removes two hydrogens from a fatty acid, resulting in a carbon-carbon double bond
Mannoproteins: yeast cell wall components that contain large numbers of mannose groups
chemostat : a bioreactor to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant
catabolite repression: repression of certain sugar metabolizing operons in favor of glucose utilization when glucose is predominant carbon source
Sphingolipids: a class of lipids derived from the aliphatic amino alcohol sphingosine.

Introduction

optimum growth range fro S Cerevisiae is 25-35 degrees Celsius
Suboptimal temperaturs affect varous cellular process such as growth phase, respiration, lipid composition
time scale of exposure important in interpretation
- cold shock versus prolonged exposure produce different responses
Other studies found two distinct phases during cold shock: early and late
- Trehalose consistently observed in studies as a increased response
Problems with other studies:
- Transcriptome data reveals major discrepancies
- Trehalose accumulation only essential below ten degrees Celsius
- Differences between adaptation and acclimation haven’t been thoroughly investigated
Main results presented in study:
- S cerevisiae was grown at 12 to 30 degrees Celsius in anaerobic chemostat cultures
- Fixed growth rate
- Transcription analyzed in both glucose and ammonium limited conditions for both temperatures
The signifigance of their study is that they found better insight on S Cerevisiae adaptations to cold exposure by creating a more accurate and reliable data set by growing the cultures in a chemostat

Methods

The prototrophic haploid reference S. cerevisiae strain were grown at 12 or 30 degrees Celsius
Concetrations of metabolites were analyzed using high performaance liquid chromatography
Results from each growth condition were collected from three independent culture replicates and were hybridized to the chip for the microarray
They hypridized four microarray chips. One for each growth condition
Three individually cultured biological replicates were used
They do not list the steps found in Overview of Microarray Data Analysis section

Results:

Table 1: Shows that biomass yields were similar at both temperatures indicated growth rates were not affected severely by growth temperature
Figure 1: Shows the transcriptome responses glocuse and ammonium limited chemostat cultures.
- Glucose limited cultures yielded 494 different genes compared to 806 nitrogen limited cultures
- 235 genes showed up or down regulations in both conditions
- 16% of genome included in temperature response genes
Figure 2: Analyzed temperature-responsive genes (1065) for specific functional categories and cis-regulatory motifs
- Growth limiting nutrient kinetics were alerted.
- High affinity ammonia permeases were expressed less in 12C sample and the low affinity was expressed more in 12C sample
- Protein synthesis genes were more expressed at 12C than 30C, especially for N-limiting cultures
- Increased concentration of limiting nutrients resulted in catabolite repression
Table 2: Trehalose and glycogen levels were significantly lower at 12C (except for glycogen in glucose-limited culture)
Table 3: The small number of genes that showed a consistent transcriptional response to low temperature during acclimation and adaptation
- 91 were consistently up regulated at low temperature, and only 48 were consistently down-regulated

Figure 4: Twenty-nine genes were transcriptionally regulated during both adaptation and acclimation to low temperature
- only 11 genes showed a consistent pattern of regulation in all four situations

Figure 5: Negligible Overlap with Growth-rate–responsive Genes was Observed
- 25% of down-regulated genes and 10% of up-regulated are likely to be only related to specific growth rate.
Figure 6: A Significant Overlap Between Regulated Genes in Batch Cultures Exist

Discussion

the transcriptional response to a stimulus has been shown to be dependent on other environmental parameters

There is a growing body of evidence that specific growth rate itself has a strong effect on genome-wide transcription

less than 1% of the temperature-responsive genes identified in the present chemostat

study showed a growth-rate–dependent transcript level

In batch cultures of S. cerevisiae, exposure to low temperatures causes an increased synthesis of storage carbohydrates (in particular trehalose) and transcriptional up-regulation of genes involved in storage carbohydrate metabolism
- These effects weren’t observed in their studies

yielded a set of 235 genes that showed a consistent transcriptional response to low temperature

The only clearly defined group of genes that was regulated in chemostats and batchculture studies on low-temperature adaptation had to do with lipid metabolism

chaperone-encoding genes were transcriptionally down-regulated at low temperature in the chemostat cultures in contrast to being upregulated in other batch culture studies

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