The transcription factors Swi4 and Hap4 contribute to the regulation of the transcriptional response to cold shock in Saccharomyces cerevisiae
Authors: Wyllie Kevin W. , McGee Kevin P. , Hong Monica V. , Dahlquist Kam D. 
Published: November 2023

Cold shock treatment of budding yeast, Saccharomyces cerevisiae, causes changes in gene expression, but which transcription factors regulate this response is still unknown. We have observed that strains individually deleted for the Swi4 and Hap4 transcription factors are impaired for growth at cold temperatures. Thus, the purpose of this study was to determine how the transcription factors Swi4 and Hap4 regulate the transcriptional response to cold shock in yeast. BY4741 yeast cells deleted for each transcription factor were subjected to cold shock at 13°C, followed by recovery at 30°C. Samples were collected before cold shock (t0), after 30 and 60 minutes of cold shock (t30, t60), and after 30 and 60 minutes (t90, t120) of recovery at 30°C. Then, total RNA from these cell samples was isolated and aRNA was synthesized and indirectly labeled with the Cy3 and Cy5 dyes, followed by hybridization to DNA microarrays. Four independent replicates of this experiment were performed for each deletion strain, swapping the dye orientation for two of the replicates. An ANOVA test was used to determine which genes had a log2 fold change significantly different than zero at any of the timepoints studied. The results showed that the Δswi4 strain had 2233 out of 6189 (36%) genes with a Benjamini and Hochberg adjusted p value < 0.05. The expression profiles of this set of genes was clustered using the Short Time Series Expression Miner (stem) software. The two most significant expression profiles were up‐regulation during cold shock followed by down‐regulation during recovery, and vice versa. Gene Ontology categories enriched in these profiles included ribosome biogenesis and glycogen metabolic processing, respectively. The ANOVA test performed on the data from the Δhap4 strain showed that 1749 out of 6189 genes (28%) had a Benjamini and Hochberg adjusted p value < 0.05. When this set of genes was subjected to clustering with the stem software, the two most significant expression profiles were up‐regulation followed by a steeper, over‐compensatory down‐regulation which then went back to baseline expression, and a brief period of down‐regulation which also returned to baseline expression. Examples of Gene Ontology categories enriched in these two profiles are carbohydrate transport, and apoptotic processes, respectively. We are in the process of comparing these data to the wild type strain. We have also screened additional transcription factor deletion strains for impaired growth at different temperatures (15°C, 20°C, 30°C, and 37°C). We observed that the Δphd1 strain was impaired for growth at all temperatures, while the Δnrg1 strain was impaired for growth at 30°C and 37°C, but grew more quickly than the wild type strain at 15°C and 20°C, which suggests that these strains may be worthy of future investigation as to cold shock and recovery.

Support or Funding Information

This work was partially supported by NSF award 0921038 (K.D.D.), a Kadner‐Pitts Research Grant (K.D.D., M.V.H.), the Loyola Marymount University Summer Undergraduate Research Program 2015 (K.P.M., K.W.W.), and a Loyola Marymount University Honors Summer Research Fellowship (M.V.H.).