Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

Ubiquitin-proteasome system (UPS) protein degradation regulates protein abundance and eliminates misfolded and damaged proteins from eukaryotic cells. Variation in UPS activity influences numerous cellular and organismal phenotypes. However, to what extent such variation results from individual genetic differences is almost entirely unknown. Here, we developed a statistically powerful mapping approach to characterize the genetic basis of variation in UPS activity. Using the yeast Saccharomyces cerevisiae, we systematically mapped genetic influences on the N-end rule, a UPS pathway that recognizes N-degrons, degradation-promoting signals in protein N-termini. We identified 149 genomic loci that influence UPS activity across the complete set of N-degrons. Resolving four loci to individual causal nucleotides identified regulatory and missense variants in ubiquitin system genes whose products process (NTA1), recognize (UBR1 and DOA10), and ubiquitinate (UBC6) cellular proteins. Each of these genes contained multiple causal variants and several individual variants had substrate-specific effects on UPS activity. A cis-acting promoter variant that modulates UPS activity by altering UBR1 expression also alters the abundance of 36 proteins without affecting levels of the corresponding mRNAs. Our results demonstrate that natural genetic variation shapes the full sequence of molecular events in protein ubiquitination and implicate genetic influences on the UPS as a prominent source of post-translational variation in gene expression.泛素-蛋白酶体系统（Ubiquitin-proteasome system, UPS）介导的蛋白质降解，可调控真核细胞内的蛋白质丰度，并清除错误折叠与受损的蛋白质。UPS活性的变异会影响众多细胞及机体表型。然而，这类变异在多大程度上源于个体遗传差异，目前几乎完全未知。本研究开发了一种统计学效力强劲的定位方法，用以解析UPS活性变异的遗传基础。本研究以酿酒酵母（Saccharomyces cerevisiae）为模型，系统定位了遗传因素对N端规则（N-end rule）的调控作用——N端规则是一类识别蛋白质N端降解信号（N-degrons）的UPS通路。我们在全部N端降解信号组中，共鉴定出149个影响UPS活性的基因组位点。通过将四个基因组位点解析至单个致因核苷酸，我们在泛素系统相关基因中鉴定到了调控变异与错义变异：这些基因的编码产物分别负责细胞蛋白质的加工（NTA1）、识别（UBR1与DOA10）以及泛素化修饰（UBC6）。上述每个基因均包含多个致病变异，且部分单个变异对UPS活性具有底物特异性调控效应。一个通过改变UBR1表达来调控UPS活性的顺式作用启动子变异，可在不影响对应mRNA水平的前提下，改变36种蛋白质的丰度。本研究结果表明，自然遗传变异可塑造蛋白质泛素化过程的完整分子事件链，并证实UPS所受的遗传调控是基因表达翻译后变异的重要来源。