Haploid yeast cells undergo a reversible phenotypic switch associated with chromosome II copy number

Abstract

Background SUP35 and SUP45 are essential genes encoding polypeptide chain release factors. However, mutants for these genes may be viable but display pleiotropic phenotypes which include, but are not limited to, nonsense suppressor phenotype due to translation termination defect. [PSI +] prion formation is another Sup35p-associated mechanism leading to nonsense suppression through decreased availability of functional Sup35p. [PSI +] differs from genuine sup35 mutations by the possibility of its elimination and subsequent re-induction. Some suppressor sup35 mutants had also been shown to undergo a reversible phenotypic switch in the opposite direction. This reversible switching had been attributed to a prion termed [ISP +]. However, even though many phenotypic and molecular level features of [ISP +] were revealed, the mechanism behind this phenomenon has not been clearly explained and might be more complex than suggested initially.ResultsHere we took a genomic approach to look into the molecular basis of the difference between the suppressor (Isp−) and non-suppressor (Isp+) phenotypes. We report that the reason for the difference between the Isp+ and the Isp− phenotypes is chromosome II copy number changes and support our finding with showing that these changes are indeed reversible by reproducing the phenotypic switch and tracking karyotypic changes. Finally, we suggest mechanisms that mediate elevation in nonsense suppression efficiency upon amplification of chromosome II and facilitate switching between these states.Conclusions(i) In our experimental system, amplification of chromosome II confers nonsense suppressor phenotype and guanidine hydrochloride resistance at the cost of overall decreased viability in rich medium. (ii) SFP1 might represent a novel regulator of chromosome stability, as SFP1 overexpression elevates frequency of the additional chromosome loss in our system. (iii) Prolonged treatment with guanidine hydrochloride leads to selection of resistant isolates, some of which are disomic for chromosome II.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0464-4) contains supplementary material, which is available to authorized users.

Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes

“…Recent years have seen a huge amount of published S. cerevisiae genome sequences, which have revealed a high level of genetic diversity, phenotypic variation and copy number variation in this species [ 24 , 37 , 38 , 39 , 40 ]. In some of the works, it has been shown that structural changes in the genome (such as CNVs) may have an adaptive role (e.g., [ 38 ]), however, it remains unclear if selective pressure may actively facilitate the accumulation of genetic changes.…”

“…Previously, several similar observations of aneuploidies associated with nonsense suppression and release factor genes have been reported. These include a phenomenon of reversible nonsense suppressor phenotype switching due to chromosome II copy number observed in the presence of missense mutations in the SUP35 and SUP45 genes [ 40 ]. This case is reminiscent of the chromosome II disomy, which we observed in this work in the sup35-203 mutant.…”

RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae

“…Thus, the chromosome I disomy may potentially alleviate this process by increasing ade1-14 levels, which was previously found to compensate for the growth defects of the strains with the same genotype on a media without adenine [43]. Notably, the aneuploidy was demonstrated to be associated with the formation of different non-chromosomal determinants affecting the translation termination efficiency, like [ ISP + ] (initially described as a prion form of the transcriptional regulator Sfp1 [11] and later connected with the chromosome II copy number [69]), as well as the [ ASP + ] (chromosome VIII disomy [70]). Probably, the prion formation by several proteins regulating key biological processes could induce genome instability in a few fractions of cells that are inherited by progeny under selective pressure and determine adaptive phenotypic traits like resistance to poisonous compounds.…”

Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage

“…Custom 8x15k design (AMID 028943) Agilent arrays were used. CGH analysis was carried out as described previously ( Drozdova et al 2016a ). The data were processed with the CGH-Miner Excel add-in ( Wang et al, 2005 ) and a custom R function based on the clac package.…”