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

Evgeniia M Maksiutenko; Yury A Barbitoff; Andrew G Matveenko; Svetlana E Moskalenko; Galina A Zhouravleva

doi:10.3390/genes12122019

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

Genes (Basel). 2021 Dec 19;12(12):2019. doi: 10.3390/genes12122019.

Authors

Evgeniia M Maksiutenko^{1

2}, Yury A Barbitoff^{1

3}, Andrew G Matveenko¹, Svetlana E Moskalenko^{1

2}, Galina A Zhouravleva^{1

4}

Affiliations

¹ Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia.
² St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 199034 St. Petersburg, Russia.
³ Bioinformatics Institute, 197342 St. Petersburg, Russia.
⁴ Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.

Abstract

Protein synthesis (translation) is one of the fundamental processes occurring in the cells of living organisms. Translation can be divided into three key steps: initiation, elongation, and termination. In the yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 and eRF3. These factors are encoded by the SUP45 and SUP35 genes, which are essential; deletion of any of them leads to the death of yeast cells. However, viable strains with nonsense mutations in both the SUP35 and SUP45 genes were previously obtained in several groups. The survival of such mutants clearly involves feedback control of premature stop codon readthrough; however, the exact molecular basis of such feedback control remain unclear. To investigate the genetic factors supporting the viability of these SUP35 and SUP45 nonsense mutants, we performed whole-genome sequencing of strains carrying mutant sup35-n and sup45-n alleles; while no common SNPs or indels were found in these genomes, we discovered a systematic increase in the copy number of the plasmids carrying mutant sup35-n and sup45-n alleles. We used the qPCR method which confirmed the differences in the relative number of SUP35 and SUP45 gene copies between strains carrying wild-type or mutant alleles of SUP35 and SUP45 genes. Moreover, we compare the number of copies of the SUP35 and SUP45 genes in strains carrying different nonsense mutant variants of these genes as a single chromosomal copy. qPCR results indicate that the number of mutant gene copies is increased compared to the wild-type control. In case of several sup45-n alleles, this was due to a disomy of the entire chromosome II, while for the sup35-218 mutation we observed a local duplication of a segment of chromosome IV containing the SUP35 gene. Taken together, our results indicate that gene amplification is a common mechanism of adaptation to nonsense mutations in release factor genes in yeast.

Keywords: WGS; amplification; chromosome instability; eRF1; eRF3; nonsense suppression; plasmid copy number; release factors; translation termination; yeast.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Physiological
Chromosomes, Fungal / genetics
Codon, Nonsense
Gene Amplification*
Peptide Termination Factors / genetics*
Saccharomyces cerevisiae / genetics
Saccharomyces cerevisiae / growth & development*
Saccharomyces cerevisiae Proteins / genetics*
Whole Genome Sequencing

Substances

Codon, Nonsense
Peptide Termination Factors
SUP35 protein, S cerevisiae
SUP45 protein, S cerevisiae
Saccharomyces cerevisiae Proteins