Bobak Seddighzadeh Week 11

[[Media:Yeast_paper_journal_club2.ppt]]

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

Introduction Methods
 * 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
 * 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


 * Using combinatorial approaches, core sets of genes can be defined


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

study showed a growth-rate–dependent transcript level
 * less than 1% of the temperature-responsive genes identified in the present chemostat


 * 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
 * Chemostat-based transcriptome analysis at 12 and 30°C


 * 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