Gene expression analysis of yeast strains with a nonsense mutation in the eRF3-coding gene highlights possible mechanisms of adaptation

In yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 (SUP45) and eRF3 (SUP35), which are essential for viability. Previous studies have revealed that presence of nonsense mutations in these genes leads to amplification of mutant alleles (sup35-n and sup45-n) which appears to be necessary for viability of such cells. However, the mechanism of this phenomenon remained unclear. In this study, we used RNA-Seq to reveal the complete set of gene expression changes that occur during cellular adaptation to the introduction of the sup35-218 nonsense allele. Our analysis demonstrated significant changes in the transcription of genes that control the cell cycle: decrease in the expression of genes of the anaphase promoting complex APC/C (APC9, CDC23), their activator CDC20 and an increase in the expression of FKH1 transcription factor, main cell cycle kinase CDC28 and cyclins that induce DNA biosynthesis. We propose a model according to which yeast adaptation to nonsense mutations in the translation termination factor genes occurs as a result of a delayed cell cycle progression beyond the G2-M stage, which leads to an extension of the S and G2 phases and an increase in the number of copies of the mutant sup35-n allele. Gene expression profiles (from RNA-seq) of cells of the U-14-D1690 and L-14-D1690 strains with a deletion of a normal chromosomal copy of SUP35 and bearing a wild-type allele of the corresponding gene on plasmids with either URA3 or LEU2 marker genes (3 and 4 replicates, respectively) were compared to those of the 218-L-D1690 strain bearing a mutant sup35-218 allele of the same gene (3 replicates).