BAG6 and RNF126 are broadly involved in protein quality control of non-native missense protein variants

Protein quality control (PQC) degradation is a vigorous and selective system that limits the accumulation of harmful, non-native and aggregation-prone proteins. Specific PQC pathways have been described for misfolded ER proteins, aberrant translational products and mislocalized proteins. However, many components involved in PQC of structurally unstable cytosolic proteins are unknown despite such proteins being a common consequence of pathogenic coding variants. Here, we present results from a genome-wide CRISPR knockout screen to identify components involved in PQC of the Parkin R42P variant. We find that HSP90 and STIP1 stabilize Parkin, while the BAG6 chaperone and E3 ubiquitin ligase RNF126 are critical for PQC degradation. Variant abundance by massively parallel sequencing (VAMP-seq) reveal >1000 Parkin variants, including several variants linked to autosomal recessive juvenile Parkinsonism, are BAG6 targets. Pathogenic missense variants in phenylalanine hydroxylase (PAH) and the tumor suppressor FLCN are also stabilized in BAG6 and RNF126 knockout cells. We propose that BAG6 and RNF126 are broadly involved in PQC and may represent targets for the development of therapeutics for protein misfolding diseases.