TRANSCRIPTOMIC ANALYSIS OF GLYCOGEN METABOLISM AFTER CAFFEINE TREATMENT IN Saccharomyces cerevisiae

Abstract

Saccharomyces cerevisiae is used as a model organism for investigating the metabolic and
genetic regulations in higher organisms. Glycogen is a storage carbohydrate in yeast cells and is used as
an energy source. Glycogen is accumulated at the onset of the stationary phase and the logarithmic phase
during different environmental and intracellular stress conditions. Glycogen level in the cell is regulated
by different sensory and signaling pathways. TOR signaling pathway is activated when the environmental
conditions are suitable, but it is repressed after rapamycin/caffeine treatment or nutrient starvation. In this
study, the effect of the TOR signaling pathway on glycogen metabolism was determined with the Next
Generation Sequencing method in S. cerevisiae. The total RNA isolated from yeast cells grown in a
medium containing caffeine was used for the Next Generation Sequencing analysis. The differentially
expressed genes after caffeine treatment were determined by comparing the caffeine-treated cells to
untreated cells. It was determined that the transcription of 44% of the genes was expressed differentially
after caffeine treatment, and 20% of differentially expressed genes were found to be up-regulated. The
transcription of genes involved in glycogen metabolism, except PGM1, was up-regulated after caffeine
treatment. The inactivation of Tor1p caused to increase in PGM2, UGP1, GLG1, GSY1, GSY2, GLC3,
GPH1, and GDB1 transcription at least 2 fold. In silico analysis revealed that these genes include at least
one STRE sequence in their promoter regions for binding of Msn2/4 transcription factors. It was observed
that after caffeine treatment MSN2 transcription was down-regulated while MSN4 transcription was
upregulated. This indicates that the Msn4 transcription factor was more effective than Msn2p in upregulating genes in glycogen metabolism. In conclusion, repression of the TOR signaling pathway by
caffeine causes Msn4p-dependent transcriptional activation of genes involved in glycogen metabolism.