Substrate-Specific Effects of Natural Genetic Variation on Proteasome Activity

Protein degradation controls the abundance of cellular proteins and serves an essential role in protein quality control by eliminating misfolded and damaged proteins. In eukaryotes, most protein degradation occurs in two steps. The ubiquitin system first targets proteins for degradation by attaching ubiquitin to them. The proteasome then selectively binds and degrades ubiquitinated proteins. Understanding how individual genetic differences affect the activity of the proteasome could improve our understanding of the many traits influenced by protein degradation. However, most assays that measure proteasomal protein degradation are not suitable for use in large samples or are affected by changes in the activity of the ubiquitin system. Using yeast, we built reporters that provide high-throughput measurements of proteasome activity independently of the ubiquitin system. We used measurements of proteasome activity from millions of live, single cells to identify regions of the genome with DNA variants that affect proteasomal protein degradation. We identified 15 such regions, showing that proteasome activity is a genetically complex trait. Using genome engineering, we found that one locus contained a variant in the promoter of a proteasome subunit gene that affected the activity of the proteasome towards multiple substrates. Our results demonstrate that individual genetic differences shape proteasome activity and suggest that these differences may contribute to variation in the many traits regulated by protein degradation.