Transcriptional profiling of the yeast forkhead transcription factor Hcm1

In S. cerevisiae, the forkhead transcription factor Hcm1 has been involved in chromosome segregation, spindle pole dynamics and budding. We found that, in response to oxidative stress stimuli, Hcm1 shifts from cytoplasm to the nucleus, interacting with the histone deacetylase Sir2, which regulates Hcm1 localization. Hcm1-overexpressing cells showed increased resistance to oxidative stress which can be attributed to increased catalase and Sod2 activities. Microarray analysis revealed that genes corresponding to mitochondrial function and transition from exponential to stationary phase are clearly induced in these cells which consistently showed higher rates of oxygen consumption due to an increase in mitochondria – possibly triggered by higher amounts of Abf2, a protein involved in mitochondrial biogenesis. In wild-type cells, when glucose levels decreased by 50%, we observed Hcm1 translocation to the nucleus and increased Hcm1 levels. We conclude that Hcm1 may act as an early regulator to respond to nutrient limitation, increasing stress resistance and mitochondrial function and thereby allowing the cells to adapt to nutrient limitations by shifting from fermentative to respiratory metabolism. Four strains were used: WT (strain CML128), Δhcm1 (a deleted strain derived from CML128), HCM1HA (an HA tagged strain derived from CML128), and tetHCM1HA (an overexpressor of Hcm1 with a tet promoter regulatable with doxycycline derived from HCM1HA. Addition of doxy repressed Hcm1 expression). We compared the expression profile of Δhcm1 vs WT; tetHCM1HA vs HCM1HA, tetHCM1HA vs tetHCM1HA + 10h doxycycline. As controls we also compared HCM1HA vs WT; HCM1HA + 4h doxycycline vs HCM1; HCM1HA + 10h doxycycline vs HCM1. A Dye-swap was carried out for each RNA sample. Total number of chips analyzed: 12