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

Abstract

Prions are infectious, self-perpetuating protein conformers. In mammals, pathological aggregation of the prion protein causes incurable neurodegenerative disorders, while in yeast <i>Saccharomyces cerevisiae</i>, prion formation may be neutral or even beneficial. According to the prevailing contemporary point of view, prion formation is considered to be a functional inactivation of the corresponding protein whose conformational state shifts from the functional monomeric one to the infectious aggregated one. The Swi1 protein forms the [<i>SWI</i>⁺] prion and belongs to the nucleosome remodeler complex SWI/SNF controlling the expression of a significant part of the yeast genome. In this work, we performed RNA sequencing of isogenic <i>S. cerevisiae</i> strains grown on the media containing galactose as the sole carbon source. These strains bore the [<i>SWI</i>⁺] prion or had its structural gene <i>SWI1</i> deleted. The comparative analysis showed that [<i>SWI</i>⁺] affects genome expression significantly weaker as compared to the <i>SWI1</i> deletion. Moreover, in contrast to [<i>SWI</i>⁺], the <i>SWI1</i> deletion causes the general inhibition of translation-related genes expression and chromosome I disomy. At the same time, the [<i>SWI</i>⁺] prion exhibits a specific pattern of modulation of the metabolic pathways and some biological processes and functions, as well as the expression of several genes. Thus, the [<i>SWI</i>⁺] prion only partially corresponds to the loss-of-function of <i>SWI1</i> and demonstrates several gain-of-function traits.