1. Cold Adaption in Budding Yeast
Babette Schade, Gregor Jansen, Malcolm Whiteway, Karl D. Entian, and David Y. Thomas (2004) Molecular Biology of the Cell, Vol. 15,
Sarah Carratt and Carmen Castaneda
Department of Biology
Loyola Marymount University
BIOL 398/MATH 388
March 24, 2011

2. Stress Affects Transcriptional Response
QUESTION:
How do cold temperatures and other stress stimuli affect transcriptional response in S. cerevisiae?
FIGURES 1 & 2:
Identify the programmed responses to stress at 10°C
Contrast early and late cold response for functional categories
Compare cold shock as defined by Schade et al. (10°C) to Gasch (25°C)
Outline (GAAAASH)

3. Cells Respond to Stress
Unicellular organisms are affected by a variety of extreme changes in their environments
Developed programmed responses to stress into the genetic code, not random
The transcription of genes is changed
~10% of the genome responds
Genes involved are defined as ESR
Little known about mechanisms responsible for growth and survival at low temperatures
Cold causes different changes in the physical and biochemical properties
Ability to adapt is determined by different regulatory mechanisms
Background
Changes in their environment like nutrients, acidity, osmolarity temperature, toxins and radiation
Extensively done with S. cerevisiae, previous study rsponses to heat shock
Yeast cells undergoing heat shock rapidly induce a large group of heat shock proteins mediated by the transcription factor Hsf1p. ESR- environmental stress response. Induced ESR genes tend to be those involved in a variety of cell functions like protein folding &degradation, transport, & carbohydrate metabolism. Repressed deal with cell growth
The transcription of genes is changed which is general stress response.
Physical & biochemical properties such as decrease in membrane fluidity results in slower lateral diffusion of membrane proteins, dec activity of membrane associated enzymes, and membrane transport.

4. Regulatory Mechanisms of S. cerevisiae
Small set of genes up-regulated in response to reduced temperatures
NSR1: encodes nucleolin-like protein involved in pre-RNA processing and ribosome biogenesis
TIP1, TIR1 and TIR2: encode proteins for maintaining cell wall integrity under stress
This study looks at mechanisms responsible for growth and survival at low temperatures

5. Important Definitions for Figures
Division of time
Early cold response (ECR) = up to 2 hours
Late cold response (LCR) = hours
Regulation and color codes
GREEN = down-regulated: repressed
RED = up-regulated: induced

6. Hierarchical cluster analysis shows
Along the horizontal we have genes clustered.
On the vertical axis the individual chips are clustered.
Temperature change in yeast from degrees. As the temperature begins to drop we have more genes activated and responding to the change in temperature. We see a peak in activity at the 12 hr mark were 2/3 of the genes are either down regulated, green, or up, red. D-F are considered the ECR genes while, LCR are A-C.
Decrease in temperature meant that more genes were active.
LCR genes are more active.

7. Distribution of Functional Categories and Regulation Response in ECR & LCR3 1 1 3 2 2

8. Increased LCR Down-Regulated Genes
Transcription:
Increased LCR Down-Regulated Genes 1 1
mRNA is synthesized from DNA
833 genes for transcription
down-regulated: cell is attempting to conserve energy
up-regulated: innate attempt to maintain homeostasis

9. Large Increase in LCR Down-Regulated Genes
Protein Synthesis:
Large Increase in LCR Down-Regulated Genes 2 2
proteins synthesized from mRNA
380 genes for protein synthesis
down-regulated: cell does NOT inefficient energy use
up-regulated: stays low, indicates no deficiencies 9

10. Increased LCR Up-Regulated Genes (Reversal)
Stress Response:
Increased LCR Up-Regulated Genes (Reversal) 3 3
respond to environment (cold), emergencies, ect.
294 genes for stress response
ECR: more down-regulated than up-regulated
LCR: more up-regulated genes than down-regulated
significance related to function 10

11. Defining Cold Shock in ECR
Gasch vs Schade:
Defining Cold Shock in ECR
Gasch: 37 to 25
Schade: 30 to 10
key differences in regulation of lower region
indicates that there may be different genes
a/b: Gasch genes with transcriptional response
Transcriptional profiles of early cold response during temperature downshifts. The ECR genes, represented by the 2-h time point, were compared with a temperature downshift from 37 to 25°C at the indicated time points (Gasch et al., 2000). Labels a and b represent genes showing a correlation in transcriptional response after shift from 37 to 25°C

12. References
In this presentation, images and data were used from the following source:
Schade et. al. “Cold Adaption in Budding Yeast” (2004) Molecular Biology of the Cell, Vol. 15,

13. Acknowledgements
We would like to thank the following people for their help with this presentation:
Dr. Kam D. Dahlquist, Ph.D.
Dr. Ben G. Fitzpatrick, Ph.D.