## 4 Discussion
### Regulatory Network Responsible for the Cellular Switch from a Variable to a Stable Environment  
More information was extracted by searching for regulatory proteins that may affect the expression of genes in our gene set. This analysis was performed using the Yeastract+ online tool [20]. As demonstrated in Table 1 and Table S2, there is a very high correlation between the functions of genes in our gene set and the regulatory responsibilities of TFs on the Yeastract+ output list. Within the group of TFs for upregulated genes, we observed those involved in the regulation of catabolism of various nonfermentable carbon sources (Adr1p, Cat8p) and nitrogen sources (Gzf3p, Dal80p, Dal81p). Within the group ascribed to downregulated genes, we observed numerous TFs related to the stress response (Com2p, Crz1p, Hot1p, Rpi1p, Sdd4p, Sfl1p, Sko1p, Wtm2p). We also observed TFs responsible for the induction of filamentous growth (Mig1p, Nrg1p, Nrg2p, Sfl1p), cell wall integrity (Gat4p, Rlm1p, Rpi1p), and membrane rigidity (Mga2p). The association of downregulated genes with the cell periphery, especially with lipid membrane composition, is consistent with the observed upregulation of a subset of genes encoding peroxisomal proteins (see above). TFs responsible for the regulation of amino acid biosynthesis and assimilation (Met4p, Stp1p, Stp2p) were also present. In accordance with the downregulation of ribosomal protein genes, Ifh1p, a TF regulating the transcription of these genes, was present. Superficially, no clear evidence of the existence of master regulators emerged from this analysis; however, there was a clear tendency toward diminished stress alertness and reduced nutrient reserves and protein biosynthetic capacity. The involvement of TFs, such as Sfl1p and Rpi1p, in more than one of these processes, suggests their coordinated action during adaptation to a less challenging environment. Notably, certain TFs, e.g., Mga2p and Rlm1p, have quite specific regulatory roles in y yeast cells according to SGD, yet in the Yeastract+ database, they influence the expression of numerous genes. These or other TFs of still poorly defined regulatory roles may function as switches functioning in the transition from turbulent to tranquil environments. It is also possible that such a switch is of a different nature. How Could a Constant Cell Environment Induce a Drift in Gene Expression Patterns, and Why Would It Make Biological Sense for the Drift to Be Slow? The observed changes, downregulation of genes involved in ribosome biogenesis, a shift in balance towards catabolism, and downregulation of stress response and protection genes, suggests that prolonged continuous culture under stable, nonstressful conditions requires fewer resources. This in turn lowers the demand for transactions on the cell periphery, which is exactly what we see. _S. cerevisiae_ cells can occupy various niches differing in nutrient availability and the overall variability of environmental conditions. It is conceivable that survival in unpredictable environments requires a surplus of resources to allow for quick responses to rapid changes. The existence of such overcapacity has been previously reported in microorganisms [33; 34], and it has been considered a trait beneficial for fitness under varying growth conditions [35]. It appears that overcapacity is a more general strategy of yeast cell survival in dynamic environments, affecting various cellular functions, such as environmental stress protection, protein biosynthesis, or the ability to acquire and assimilate diverse nutrients [36]. Conversely, in stable conditions, withdrawing overcapacity would be advantageous. Indeed, as a part of adaptive changes occurring in stable chemostat culture conditions, a reduction in this overcapacity was observed for metabolism [14; 15; 31] and for the signaling networks that regulate it [10]. Therefore, our results are consistent with these observations with one important distinction.