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Turgut Genç T., Günay M.

International Journal of Natural and Engineering Sciences (IJNES) , vol.16, no.1, pp.1-10, 2022 (Peer-Reviewed Journal)


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.