The concept of "protein-based inheritance" defines prions as epigenetic determinants that cause several heritable traits in eukaryotic microorganisms, such as Saccharomyces cerevisiae and Podospora anserina. Previously, we discovered a non-chromosomal factor, [NSI⁺], which possesses the main features of yeast prions, including cytoplasmic infectivity, reversible curability, dominance, and non-Mendelian inheritance in meiosis. This factor causes omnipotent suppression of nonsense mutations in strains of S. cerevisiae bearing a deleted or modified Sup35 N-terminal domain. In this work, we identified protein determinants of [NSI⁺] using an original method of proteomic screening for prions. The suppression of nonsense mutations in [NSI⁺] strains is determined by the interaction between [SWI⁺] and [PIN⁺] prions. Using genetic and biochemical methods, we showed that [SWI⁺] is the key determinant of this nonsense suppression, whereas [PIN⁺] does not cause nonsense suppression by itself but strongly enhances the effect of [SWI⁺]. We demonstrated that interaction of [SWI⁺] and [PIN⁺] causes inactivation of SUP45 gene that leads to nonsense suppression. Our data show that prion interactions may cause heritable traits in Saccharomyces cerevisiae. The data presented in the paper deepens and enriches the concept of protein-based inheritance. According to this concept, prion conformational switches change protein functional activity, and such changes are inherited. Here, for the first time, we demonstrate that heritable traits may appear not only due to a conformational switch of one protein but also can be caused by interactions between different prions. To identify the novel epigenetic factor that causes suppression of nonsense mutations in yeast, we applied our original method of proteomic screening of prions. We have shown that two yeast proteins, which normally do not interact, in prion form demonstrate genetic interaction: one is the key determinant of the suppression of nonsense mutation, while the second enhances this effect. Thus, by analogy with monogenic and polygenic inheritance, in the framework of the prion concept, we can distinguish “monoprionic” and “polyprionic” inheritance. We assume that new examples of polyprionic inheritance will be revealed using modern proteomic methods for identification of prions.

The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification.

Amyloids are non-branching fibrils that are composed of stacked monomers stabilized by intermolecular β-sheets. Some amyloids are associated with incurable diseases, whereas others, functional amyloids, regulate different vital processes. The prevalence and significance of functional amyloids in wildlife are still poorly understood. In recent years, by applying new approach of large-scale proteome screening, a number of novel candidate amyloids were identified in the yeast Saccharomyces cerevisiae, many of which are localized in the yeast cell wall. In this work, we showed that one of these proteins, Toh1, possess amyloid properties. The Toh1-YFP hybrid protein forms detergent-resistant aggregates in the yeast cells while being expressed under its own P_TOH1 or inducible P_CUP1 promoter. Using bacterial system for generation of extracellular amyloid aggregates C-DAG, we demonstrated that the N-terminal Toh1 fragment, containing amyloidogenic regions predicted in silico, binds Congo Red dye, manifests ‘apple-green’ birefringence when examined between crossed polarizers, and forms amyloid-like fibrillar aggregates visualized by TEM. We have established that the Toh1(20–365)-YFP hybrid protein fluorescent aggregates are co-localized with a high frequency with Rnq1C-CFP and Sup35NM-CFP aggregates in the yeast cells containing [PIN⁺] and [PSI⁺] prions, and physical interaction of these aggregated proteins was confirmed by FRET. This is one of a few known cases of physical interaction of non-Q/N-rich amyloid-like protein and Q/N-rich amyloids, suggesting that interaction of different amyloid proteins may be determined not only by similarity of their primary structures but also by similarity of their secondary structures and of conformational folds.

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. Copyright © 2015 John Wiley & Sons, Ltd.

Amyloids are the fibrillar protein aggregates with cross-β structure. Traditionally amyloids were associated with pathology, however, nowadays more data is emerging about functional amyloids playing essential roles in cellular processes. We conducted screening for functional amyloids in rat brain. One of the identified proteins was STXBP1 taking part in vesicular transport and neurotransmitter secretion. Using SDD-AGE and protein fractionation we found out that STXBP1 forms small detergent-insoluble aggregates in rat brain. With immunoprecipitation analysis and C-DAG system, we showed that STXBP1 forms amyloid-like fibrils. Thus, STXBP1 demonstrates amyloid properties in rat brain and in bacterial expression system.

Bioresource collections represent a unique source of biological diversity for research in genetics and related disciplines. The Department of Genetics and Biotechnology of St. Petersburg State University is the oldest department of genetics in Russia, founded in 1919. Throughout the entire period of development, the geneticists of St. Petersburg University have collected unique forms of plants, animals and microorganisms, on which their research was based. Many of these studies including regulation of translation termination in yeast, amyloids and prions of different organisms, genetic mapping of valuable morphological and biochemical traits to create first rye chromosome maps, and several aspects of transcription regulation in plants, had a significant novelty. The most active accumulation of collections of genetic resources at St. Petersburg State University started in the 1950-1970s when important scientific directions in the genetics of microorganisms, plants and animals, many of which continue today, were established at the department. Genetic collections are actively used in educational work for teaching dozens of educational courses. Currently, the interdisciplinary genetic collections of St. Petersburg State University consist of seven sections including genetic collections of rye, radish, garden pea, Chlamydomonas algae, Saccharomyces yeast and plasmids, Komagataella yeast, Drosophila fly. This review describes in detail the collections of the Department of Genetics and Biotechnology of St. Petersburg State University and discusses their current state, application and development prospects. bioresource collections, genetic collections, yeast, rye, plasmid, Saccharomyces cerevisiae, Drosophila melanogaster, Komagataella phaffii, Secale cereale, Chlamydomonas reinhardtii, Raphanus sativus, Pisum sativum