Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur without Genome Modifications

Abstract

Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. These adaptive changes can skew the results of large-scale studies. It is commonly assumed that these adaptations reflect changes in the genome, and this assumption has been confirmed experimentally in rare cases. Here we show that in a population of budding yeast cells grown for over 200 generations in continuous culture in non-limiting minimal medium and therefore not subject to selection pressure, remodeling of transcriptome occurs, but not as a result of the accumulation of adaptive mutations. The observed changes indicate a shift in the metabolic balance towards catabolism, a decrease in ribosome biogenesis, a decrease in general stress alertness, reorganization of the cell wall, and transactions occurring at the cell periphery. These adaptive changes signify the acquisition of a new lifestyle in a stable nonstressful environment. The absence of underlying adaptive mutations suggests these changes may be regulated by another mechanism.

Keywords: Saccharomyces cerevisiae; adaptation; epigenetic; stress alertness; transcription factor; transcriptome.

Figure 1

Overrepresentation of Gene Ontology (GO) terms in the group of upregulated (A) and downregulated (B) genes selected in the course of transcriptome analysis. The analysis was performed using Cytoscape (v3.8.0) [18] with the BiNGO (v3.0.3) plugin [19] and GO Slim Term Mapper (https://www.yeastgenome.org/goSlimMapper). GO terms belonging to Biological process and Cellular Component categories are shown.

Figure 2

All upregulated (A) and downregulated (B) genes selected in the course of transcriptome analysis sorted according to the functional category assigned to them. For clarity, the number of GO terms, shown in Figure 1, was reduced by merging the lists of genes of similar functions. Sorting was performed manually based on GO annotations assigned to genes and the descriptions of their functions in the Saccharomyces Genome Database (SGD). Below the gray bar are genes whose functions were not overrepresented within the gene sets. Genes with LogRatio above 2.33 or below −2.33, i.e., whose expression changed at least 5-fold, are marked in bold face. See Figure S3 for the expanded version of this figure listing genes together with the short descriptions of their functions taken from SGD.