Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons

Summary Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studied, our understanding of C-degrons is still limited. Towards a comprehensive understanding of eukaryotic C-degron pathways, we performed an unbiased survey of C-degrons in budding yeast. We identified over 5000 potential C-degrons by stability profiling of random peptide libraries and of the yeast C-terminome. Combining machine learning, high-throughput mutagenesis and genetic screens revealed that the SCF ubiquitin ligase targets ∼40% of degrons using a single F-box substrate receptor Das1. Although sequence-specific, Das1 is highly promiscuous, recognizing a variety of C-degron motifs. By screening for endogenous substrates, we implicate SCF Das1 in degradation of orphan protein complex subunits. Altogether, this work provides a comprehensive view of a eukaryotic C-degronome and uncovers how an SCF/C-degron pathway of broad specificity contributes to proteostasis.