1. Tai LT, Daran-Lapujade P, Walsh MC, Pronk JT, Daran JM
Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis
Tai LT, Daran-Lapujade P, Walsh MC, Pronk JT, Daran JM
(2007) American Society for Cell Biology 18:
Alex George
Bobek Seddighzadeh
Journal Club Presentation
BIOL /S10: Bioinformatics Lab
April 13, 2010

2. Outline DNA microarrays determine gene expression
Chemostat cultures foster constant growth rates
Suboptimal temperatures influence cellular processes
Investigate steady state acclimatized growth of suboptimal temperature growth of S. cerevisiae.
In-depth analysis of the tables and result presented in the study
Discussion on temperature and growth rate changes that illicit a transcriptional response

3. DNA microarrays are used to determine gene expression levels
Each spot contains a probe that correlates to a gene
Labeled sample is washed over chip to form complementary bonds
Strength of fluorescent signal indicates more binding
Our experiment: Only one sample hybridized at a time- relative abundance
Benefits of single chip: Poor sample can’t affect the raw data;
data is more easily comparable
Drawback: Twice as many chips needed

4. Chemostat cultures maintain a constant specific growth rate
Batch culture- limited supply of nutrients provided
Chemostat culture- nutrients are continuously provided in order to control specific growth rate
Specific growth rate has been shown to impact transcript profiles

5. Suboptimal Temperatures Affect Various Cellular Processes/Characteristics
Optimum growth range for S Cerevisiae:
25-35 C⁰
Below this temperature Enzyme Kinetics slow
Cellular processes/characteristics affected:
Growth Phase
Respiration
Membrane lipid composition
Trehalose content

6. Time Exposure is Important to Low-Temp Parameters on Microbial Physiology
Cold shock: sudden exposure to environmental changes
The response to cold shock triggers adaptation
Prolonged exposures leads to acclimation
Acclimation: a permanently adapted physiological state in response to environment

7. Limitations From Previous Studies Led to Further Investigations by Tai et al.
Major discrepancies exist amongst low-temperature transcriptome data published
Batch cultures do not allow for control of specific growth rate and culture variables
The differences between adaptation and acclimation have not been thoroughly investigated
The goal of this study:
Investigate Steady state acclimatized growth of suboptimal temperature growth of S. cerevisiae.
Grow S. cerevisiae in anaerobic chemostat cultures at fixed specific growth grate of 0.03 h ⁻1

8. Growth efficiency and fermentation rates were not severely affected by growth temperature

9. The number of significantly different and similar genes between 12º and 30ºC cultures for both N and C limitations

10. C-Limiting: Down (136 genes)
Heat Map representing the level of expression of a total of 1065 genes in Nitrogen- and Carbon-Limiting Cultures
C & N-Limiting:Up
(96 genes)
N-limiting: Up
(202 genes)
C-Limiting: Up
(123 genes)
C-lim. 30ºC
C-lim 12ºC
N-lim 30ºC
N-lim 12ºC
Different genes along the gradient represent various genes such as “Ribosome biogenesis” or “Amino acid Transport”
C & N-Limiting: Down
(139 genes)
N-Limiting: Down
(369 genes)
C-Limiting: Down (136 genes)

11. Trehalose and glycogen levels were not affected by increased gene expression
No change in carbohydrates contradicts results from batch culture studies
Greater change in Nitrogen content than protein content indicates increase of rRNA in Nitrogen limiting cultures

12. Few Genes Showed Consistent Responses in Acclimation and Adaption
Only 91 genes were consistently up regulated

13. More Stress Response Elements are Upstream of genes that Were Reduced
Once cells become adapted to cold temp, the stress response and up-regulation of carbohydrate storage recedes

14. Of 29 Genes, only 11 Genes Showed Consistent Patterns of Regulation
The only genes that were defined as commonly regulated on low temperature adaptations were involved in lipid metabolism

15. 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.

16. A Significant Overlap Between Regulated Genes in Batch Cultures Exist

17. Environmental factors make isolating one variable difficult
In study, changing the temperature resulted in a higher residual glucose concentration in 12° C cultures
By combining two variables, such as nutrients and temperature, a core set of genes can be identified because the responses are content-independent

18. Change in specific growth rate may illicit response, not temperature
Previous studies indicated increase in synthesis of storage carbohydrates and regulation of carbohydrate storage genes as temperature decreases
Chemostat study shows no correlation indicating role of specific growth rate

19. Slow temperature change elicits different transcriptional response than cold-shock
235 genes responded to low temperature regardless of limiting nutrient
Only one gene was in common with batch culture studies
Indicates transcription regulation for acclimation is different than that for acclimitization