Matthew E. Jurek Week 11

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(Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analyis: outlined materials and methods)
(Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analyis: outlined results)
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#*Microarray data was analyzed using Fisher's exact test with a Bonferroni correction in order to acheive a p value threshold of .01.
#*Microarray data was analyzed using Fisher's exact test with a Bonferroni correction in order to acheive a p value threshold of .01.
#*This data was then compared to previously published low-temperature transcriptome datasets.
#*This data was then compared to previously published low-temperature transcriptome datasets.
 +
#Results
 +
#*Biomass and fermentation rates did not differ significantly between cultures grown at 12 and 30 degrees C in carbon and nitrogen limited environments.
 +
#*Glucose-limited cultures: 494 genes yielded a significant difference amongst transcript levels at the two temps
 +
#*Nitrogen-limited cultures: 806 genes exhibited this type of behavior
 +
#*235 genes showed a change in regulation when both were limited
 +
#*Hextose transporter genes HXT2, HXT3, and HXT4 exhibited increased transcript levels at 12 degrees C
 +
#*HXT5 and HXT16 showed reduced transcription at this temp
 +
#*There are 3 genes that encode ammonia permeases. In the ammonium-limited cultures at 12 degrees C, 2 were reduced and one showed increased transcription.
 +
#*Important to note the specific growth rate of .03/h in this experiment is close to the maximum specific growth rate at 12 degrees versus 30 degrees
 +
#*Trehalose accumulation is a sign of low-temp adaptation
 +
#*However, there was not an increase in transcription of genes that metabolize trehalose and glycogen in this experiment
 +
#*Thus, the accumulation of trehalose and glycogen is not necessary for acclimation at low temps in yeast
 +
#*To date, the exact relevance of storage carbohydrate metabolism during adaptation remains a mystery.
 +
#*There was a noted up-regulation of translational machinery at low temps, especially 12 degrees C.
 +
#*Increased protein content could be a compensation mechanism for reduced enzyme kinetics at low temps.
 +
#*Three pre-existing datasets show 259 genes that responded to temp downshifts.
 +
#*Genes within these datasets were observed for up-regulation or down-regulation in the given conditions.
 +
#*Three genes consistently up-regulated at low temps were involved in lipid metabolism while three genes consistently down-regulated were involved in encoding transporters.
 +
#*Multiple stimuli are often responsible for changes in gene regulation.
 +
#*Batch culture results are unreliable as specific growth rate fluctuates with temperature and oxygen solubility is impacted by temperature.
 +
#*Genes that appear to signal cold shock in batch cultures may exhibit different behaviors in chemostat cultures.
 +
#*An ESR mechanism has been proposed in the regulation of yeast genes that exhibit transcriptional changes in response to multiple environmental stresses.
 +
#*In this study, it was found that ESR is NOT a response to growth at low temperature. ESR occurs following sudden exposure to suboptimal temps.

Revision as of 01:09, 4 April 2013

Matthew E. Jurek BIOL398-03/S13

Contents

Assignment Page

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Biological Terms

  1. trehalose- also known as mycose or tremalose, is a natural alpha-linked disaccharide formed by an α,α-1,1-glucoside bond between two α-glucose units.
  2. mannoprotein- component of yeast cell walls; protein covalently linked to polymers of mannose.
  3. chromatography- the separation of mixtures into their constituents by preferential adsorption by a solid, as a column of silica (column chromatography) or a strip of filter paper (paper chromatography) or by a gel.
  4. immunoprecipitation- the separation of an antigen from a solution by the formation of a large complex with its specific antibody.
  5. catabolite- a product of catabolic action.
  6. kinetics- the branch of mechanics that deals with the actions of forces in producing or changing the motion of masses.
  7. ceramides- ceramides are a family of lipid molecules. A ceramide is composed of sphingosine and a fatty acid.
  8. orthologue- one of two or more homologous gene sequences found in different species.
  9. ergosterol- a compound present in ergot and many other fungi. A steroid alcohol, it is converted to vitamin D2 when irradiated with ultraviolet light.
  10. transcriptome- the transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNA produced in one or a population of cells.

via Biology Online Dictionary

Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analyis

Tai et al. (2007) Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis. Molecular Biology of the Cell 18: 5100–5112.

  1. Introduction
    • On the cellular level, yeast responds in a number of ways to temperature changes (temps outside the 25-30 degree C optimum).
    • Temperatures below the optimum range slow cellular processes.
    • Effects of low temperature depend on exposure time
    • Sudden exposure results in adaptaion
    • Prolonged exposure results in acclimation
    • Previous studies have focused on cold shock (sudden exposure) and found 2 phases of cold-shock response
    • Current low-temp transcriptome databases contain major discrepancies
    • Previous studies have focused on batch culutures: hard to distinguish temp effects on transcription from effects of specific growth rate
    • Chemostat cultures allow for control of specific growth rate independent of culture conditions such as metabolites, pH, and oxygen availability.
    • Overall Goal: Focus on genome-wide transcriptional regulation by exploring steady-state acclimatized growth of yeast at low temps
  2. Materials and Methods
    • Haploid strain CEN.PK113-7D was grown at both 12 and 30 degrees C, anaerobically, in a chemostat
    • The chemstat contained a dilution rate of .03/h, pH of 5.0 and stirrer speed of 600rpm.
    • The cultures were contained in a synthetic medium that limited either carbon or nitrogen. Every other requirement was in excess.
    • Each growth condition consisted of 3 independent replicates.
    • Microarray data was analyzed using Fisher's exact test with a Bonferroni correction in order to acheive a p value threshold of .01.
    • This data was then compared to previously published low-temperature transcriptome datasets.
  3. Results
    • Biomass and fermentation rates did not differ significantly between cultures grown at 12 and 30 degrees C in carbon and nitrogen limited environments.
    • Glucose-limited cultures: 494 genes yielded a significant difference amongst transcript levels at the two temps
    • Nitrogen-limited cultures: 806 genes exhibited this type of behavior
    • 235 genes showed a change in regulation when both were limited
    • Hextose transporter genes HXT2, HXT3, and HXT4 exhibited increased transcript levels at 12 degrees C
    • HXT5 and HXT16 showed reduced transcription at this temp
    • There are 3 genes that encode ammonia permeases. In the ammonium-limited cultures at 12 degrees C, 2 were reduced and one showed increased transcription.
    • Important to note the specific growth rate of .03/h in this experiment is close to the maximum specific growth rate at 12 degrees versus 30 degrees
    • Trehalose accumulation is a sign of low-temp adaptation
    • However, there was not an increase in transcription of genes that metabolize trehalose and glycogen in this experiment
    • Thus, the accumulation of trehalose and glycogen is not necessary for acclimation at low temps in yeast
    • To date, the exact relevance of storage carbohydrate metabolism during adaptation remains a mystery.
    • There was a noted up-regulation of translational machinery at low temps, especially 12 degrees C.
    • Increased protein content could be a compensation mechanism for reduced enzyme kinetics at low temps.
    • Three pre-existing datasets show 259 genes that responded to temp downshifts.
    • Genes within these datasets were observed for up-regulation or down-regulation in the given conditions.
    • Three genes consistently up-regulated at low temps were involved in lipid metabolism while three genes consistently down-regulated were involved in encoding transporters.
    • Multiple stimuli are often responsible for changes in gene regulation.
    • Batch culture results are unreliable as specific growth rate fluctuates with temperature and oxygen solubility is impacted by temperature.
    • Genes that appear to signal cold shock in batch cultures may exhibit different behaviors in chemostat cultures.
    • An ESR mechanism has been proposed in the regulation of yeast genes that exhibit transcriptional changes in response to multiple environmental stresses.
    • In this study, it was found that ESR is NOT a response to growth at low temperature. ESR occurs following sudden exposure to suboptimal temps.
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