Genetic Basis of Variation in Ubiquitin-Proteasome System Activity

Abstract

AbstractThe ubiquitin-proteasome system (UPS) is the cell’s primary pathway for targeted protein degradation. Although the molecular mechanisms controlling UPS activity are well-characterized, we have almost no knowledge of how these mechanisms are shaped by heritable genetic variation. To address this limitation, we developed an approach that combines fluorescent UPS activity reporters with a statistically powerful genetic mapping framework to comprehensively characterize genetic influences on UPS activity in the yeast Saccharomyces cerevisiae. We applied this approach to substrates of the UPS N-end rule, which relates a protein’s degradation rate to the identity of its N-terminal amino acid (“N-degron”) through the Arg/N-end and Ac/N-end pathways. Genetic influences on UPS activity were numerous and complex, comprising 149 loci influencing UPS activity across the 20 N-degrons. Many loci specifically affected individual pathways or degrons and multiple loci exerted divergent effects on distinct UPS pathways. One Arg/N-end pathway-specific locus resulted from multiple causal variants in the promoter, open reading frame, and terminator of the UBR1 E3 ubiquitin ligase gene. These variants differentially affected substrates bound by the Type 1 and Type 2 recognition sites of Ubr1p. Collectively, our results provide the first systematic characterization of genetic influences on UPS activity and a generalizable approach for mapping genetic effects on protein degradation with high statistical power and quantitative precision.