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Daptomycin is an antibiotic used to treat infections caused by multidrug-resistant gram-positive pathogens. With increasing resistance to other antibiotics, an increase in daptomycin consumption is expected, which poses a potential threat of emergence of antibiotic resistance. These facts explain the need to study possible mechanisms for resistance emergence. In vitro selection of resistance to daptomycin in methicillin-resistant Staphylococcus aureus SA0420 of the ST239 genetic line was carried out. After 40 passages, the derivative strain was characterized by an increase in daptomycin minimum inhibitory concentration (MIC) from 1 to 64 µg/mL and a decrease in the doubling time and growth rate, while the induced autolytic activity did not change. During the selection and assessment of population diversity by the whole genome sequencing, both homo-mutations (nucleotide substitutions in 96–100% of reads after the alignment with the control genome at the particular position) and hetero-mutations (5‒95% of alternative reads) were revealed. After the fifth passage, the mutation in the S295L codon of the mprF gene was identified. The 40th passage revealed an additional mutation in the R50C codon; this mutation was not previously described. A new variant of the A214T mutation was detected in the Cls2 protein. The hetero-mutation in the Q493K codon of the walK regulatory gene associated with the cell wall was identified during the fifth passage and was not detected during further passaging. Hetero-mutations were also found in the ktrA and ntpA genes encoding the potassium uptake protein and phosphate transport protein, respectively. By the 40th passage of the selection, stop codons in the hypothetical gene yhfP (SACOL1927) were identified. Therefore, daptomycin resistance arises through the development of hetero-populations. After the 5th, 20th, and 40th passages, homo- and hetero-mutations in the genes with the proved role in the emergence of daptomycin resistance (mprF, cls2, and walK), as well as in the potential candidates (ktrA, ntpA, and yhfP), were revealed.

Amyloids are highly ordered aggregates of protein fibrils exhibiting cross-β structure formed by intermolecular hydrogen bonds. Pathological amyloid deposition is associated with the development of several socially significant incurable human diseases. Of particular interest are infectious amyloids, or prions, that cause several lethal neurodegenerative diseases in humans and can be transmitted from one organism to another. Because of almost complete absence of criteria for infectious and non-infectious amyloids, there is a lack of consensus, especially, in the definition of similarities and differences between prions and non-infectious amyloids. In this review, we formulated contemporary molecular-biological criteria for identification of prions and non-infectious amyloids and focused on explaining the differences between these two types of molecules.

The SUP35 gene of the yeast Saccharomyces cerevisiae encodes the translation termination factor eRF3. Mutations in this gene lead to the suppression of nonsense mutations and a number of other pleiotropic phenotypes, one of which is impaired chromosome segregation during cell division. Similar effects result from replacing the S. cerevisiae SUP35 gene with its orthologues. A number of genetic and epigenetic changes that occur in the sup35 background result in partial compensation for this suppressor effect. In this study we showed that in S. cerevisiae strains in which the SUP35 orthologue from the yeast Pichia methanolica replaces the S. cerevisiae SUP35 gene, chromosome VIII disomy results in decreased efficiency of nonsense suppression. This antisuppressor effect is not associated with decreased stop codon read-through. We identified SBP1, a gene that localizes to chromosome VIII, as a dosage-dependent antisuppressor that strongly contributes to the overall antisuppressor effect of chromosome VIII disomy. Disomy of chromosome VIII also leads to a change in the yeast strains' tolerance of a number of transition metal salts.

Mutations in genes of omnipotent nonsense suppressors SUP35 and SUP45 in yeast Saccharomyces cerevisiae encoding translation termination factors eRF3 and eRF1, respectively, and prionization of the eRF3 protein may lead to the suppression of some frameshift mutations (CPC mutations). Partial inactivation of the translation termination factor eRF3 was studied in strains with unstable genetically modified prions and also in transgenic yeast S. cerevisiae strains with the substitution of the indigenous SUP35 gene for its homolog from Pichia methanolica or for a recombinant S. cerevisiae SUP35gene. It was shown that this partial inactivation leads not only to nonsense suppression, but also to suppression of the frameshift lys2-90 mutation. Possible reasons for the correlation between nonsense suppression and suppression of the CPC lys2-90 mutation and mechanisms responsible for the suppression of CPC mutations during inactivation of translation termination factors are discussed.

Site-directed mutagenesis and nucleotide sequence analysis were used to study the roles of the global and local contexts in suppression of the lys2-90 frameshift (FS) mutation inSaccharomyces cerevisiae. Global context features established for the LYS2 mRNA region containing the extra T (lys2-90) were similar to those characteristic of regions involved in translational frameshifting. These were a potential ability of the region to form a pseudoknot and the presence of heptanucleotide CUU UGA C with the “hungry” UGA nonsense codon in the pseudoknot. Some local context features proved to be essential for the phenotypic expression of FS suppression as a result of translational frameshifting. Two amino acid substitutions determined by the nucleotide sequence between the extra U and the UGA nonsense codon lacked expression. A dependence was observed between the efficiency of FS suppression and the type of the nonsense codon located at a particular position downstream of the extra nucleotide (UGA > UAG > UAA). When translation termination was inactivated, nonsense suppression and FS suppression correlated with each other. These results suggest that translational frameshifting, which underlies suppression in the case of inactivation of translation termination, most likely takes place on the nonsense codon arising as a result of insertion of an extra nucleotide.