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, 5492-5502 Sarah Carratt and Carmen Castaneda Department of Biology Loyola Marymount University BIOL 398/MATH 388 March 24, 2011

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)

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.

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

Important Definitions for Figures Division of time Early cold response (ECR) = up to 2 hours Late cold response (LCR) = 12-60 hours Regulation and color codes GREEN = down-regulated: repressed RED = up-regulated: induced

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 30-10 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.

Distribution of Functional Categories and Regulation Response in ECR & LCR 3 1 1 3 2 2

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

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

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

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

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, 5492-5502

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.