An integrated approach to investigate tor signaling mechanism in Saccharomyces cerevisiae

Target of rapamycin (TOR) signaling, a conserved mechanism from yeast to human, is the major regulator of cell metabolism and growth. Rapamycin, an immunosuppressive and anti-proliferative drug, and caffeine, a widely used psychoactive drug, target and inhibit TOR function. In this study the long-term administration effects of 2 nM rapamycin and 5 mM caffeine, together with oxygen availability and acidity as well as the rapamycin dosage (2 nM or 200 nM) on yeast transcriptional and metabolic responses were comparatively investigated. For this purpose batch cultivations of yeast cells were carried out in the absence and presence of rapamycin and caffeine with different levels of oxygen availability and pH. Batch cultivations were conducted under micro-aerated conditions where pH was maintained at 5.5 to investigate the effects of the rapamycin dosage. The analysis of the transcriptional responses of yeast cells to the long term presence of rapamycin revealed that long term administration of low dose of rapamycin resulted in more subtle changes in transcriptional responses of yeast causing a partial TOR inhibition than the administration of high dose. However both low and high doses of rapamycin resulted in a set of transcriptional changes mimicking nutrient starvation responses of yeast cells and they both induced autophagy and altered membrane trafficking. Low dose of rapamycin was still effective at the transcriptome level by leading metabolism to autophagy but this dose may not be enough to block the proliferation of aggressive tumors. The effects of caffeine in the long term administration resulted in a wider set of transcriptional changes resembling the high dose of rapamycin treatment; high dose of rapamycin or caffeine suppressed the growth-related processes and increased the energy requirement of the cells. pH was observed to be more decisive parameter on the transcriptional responses of the cells than the oxygen level and both oxygen availability and pH should be carefully evaluated during rapamycin or caffeine treatment