1. Loyola Marymount University
Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis
Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. M. (2007) Molecular Biology of the Cell, 18,
Student Names
Department of Biology
Loyola Marymount University
BIOL 478
April 22, 2014

2. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

3. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

4. Chemostat cultures allow for fixed experimental conditions
Chemostat culture: chemical environment is static as medium is constantly being added and removed
Allows for fine control of variables
Specific growth rate
Some genes are context dependent
Adaptation: a rapid, highly dynamic stress-response phenomena
Acclimation: establishment of a physiological state in which regulatory mechanisms have resulted in full adaptation of genome expression to the environmental conditions

5. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

6. Viability of S. Cerevisiae grown in four conditions
Showing physiological traits of the yeast in all 4 different conditions
Yeast is viable at all temperatures in all conditions
Similar values show that growth not strictly affected by growth temperature

7. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

8. Environment Dependent Temperature-responsive Genes
Over 1000 genes were found to have a change in transcription level
Genes not consistently transcribed across the different conditions

9. Screening of Temperature-responsive Genes for Function
Wanted to find regulatory networks that linked genes
Grouped together to see if there were any similarities within their functional groups
Observed changes in
Transporters of limiting nutrient
Translational machinery
NCR genes and catabolite repression

10. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

11. Storage Carbohydrate Accumulation and Regulation
Trehalose and glycogen as markers of cold shock
Different levels in different conditions (12 vs. 30 C˚)
Accumulation and transcription of trehalose and glycogen not needed in steady state cold stress
More proteins at 12 C˚ than 30 C˚

12. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

13. Promoter Analysis Reveals Trends in Gene Regulation
STRE elements in promoters of downregulated genes in N-limited cultures
Upregulation in both conditions show PAC regulatory motifs in promoters
Common promoter sequences show possible regulation relationships

14. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

15. Comparison of Data Sets—Adaptation
Sahara et al. 2002, Schade et al. 2004, and Murata et al. 2006
Found 259 genes that all responded, but not consistent
Context dependent regulation

16. Adaptation and Acclimation
Chemostat study compared with Sahara et al. 2002, Schade et al. 2004, and Murata et al. 2006
29 genes total were in common, only 11 showed consistency

17. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

18. Effect of Growth Rate on Gene Expression
Genes consistently regulated in batch studies compared to genes that transcriptionally responded to growth rates (Castrillo and Regenberg)
Genes consistently regulated in chemostat study compared to Castrillo and Regenberg
Growth rate as affecting factor

19. Outline Importance of chemostat cultures Separation of variables
Adaptation vs. acclimation
Viability of S. cerevisiae in experimental conditions
Environment dependent temperature-responsive genes
Identification
Function
Accumulation and regulation of storage carbohydrates
Promoter analysis
Adaptation and acclimation
Growth rate and gene expression
Environmental stress response genes

20. Environmental Stress Response Gene Comparison
ESR: environmental stress response
General mechanism responds to multiple stimuli
Batch and chemostat genes compared with Gasch et al. 2000
Some genes showed opposite results

21. Summary
Chemostat cultures allow for separation of variables and can highlight condition-dependent transcription
S. cerevisiae able to grow under multiple conditions with different gene expression
Environment dependent temperature-responsive genes have similar functional groups
Accumulation and regulation of storage carbohydrates not present in long term exposure to cold stress
Promoter analysis reveals that functional groups of genes have similar promoters
Adaptation and acclimation have different gene sets associated with them
Growth rate can affect how genes are expressed
Environmental stress response genes different in batch vs. chemostat studies

22. Acknowledgments
Sammi Flores