biostudies-literatureWeickert PEuropean Research CouncilDeutsche Forschungsgemeinschaft (German Research Foundation)European Molecular Biology Organization (EMBO)Alfried Krupp von Bohlen und Halbach-Stiftung (Alfried Krupp von Bohlen und Halbach Foundation)352https://www.ebi.ac.uk/biostudies/studies/S-EPMC9867749biostudies-literatureUnknown14(1)DNA-protein crosslinks (DPCs) are pervasive DNA lesions that are induced by reactive metabolites and various chemotherapeutic agents. Here, we develop a technique for the Purification of x-linked Proteins (PxP), which allows identification and tracking of diverse DPCs in mammalian cells. Using PxP, we investigate DPC repair in cells genetically-engineered to express variants of the SPRTN protease that cause premature ageing and early-onset liver cancer in Ruijs-Aalfs syndrome patients. We find an unexpected role for SPRTN in global-genome DPC repair, that does not rely on replication-coupled detection of the lesion. Mechanistically, we demonstrate that replication-independent DPC cleavage by SPRTN requires SUMO-targeted ubiquitylation of the protein adduct and occurs in addition to proteasomal DPC degradation. Defective ubiquitin binding of SPRTN patient variants compromises global-genome DPC repair and causes synthetic lethality in combination with a reduction in proteasomal DPC repair capacity.Nature communicationsSPRTN patient variants cause global-genome DNA-protein crosslink repair defects.PMC9867749801750Alfried Krupp PrizeYIP4644Project ID 213249687 - SFB 1064Weickert PGotz MJForne IZhao SDurauer SImhof AStingele JLi HYAcampora ACCordes JYaneva DfalseSPRTN patient variants cause global-genome DNA-protein crosslink repair defects.DNA-protein crosslinks (DPCs) are pervasive DNA lesions that are induced by reactive metabolites and various chemotherapeutic agents. Here, we develop a technique for the Purification of x-linked Proteins (PxP), which allows identification and tracking of diverse DPCs in mammalian cells. Using PxP, we investigate DPC repair in cells genetically-engineered to express variants of the SPRTN protease that cause premature ageing and early-onset liver cancer in Ruijs-Aalfs syndrome patients. We find an unexpected role for SPRTN in global-genome DPC repair, that does not rely on replication-coupled detection of the lesion. Mechanistically, we demonstrate that replication-independent DPC cleavage by SPRTN requires SUMO-targeted ubiquitylation of the protein adduct and occurs in addition to proteasomal DPC degradation. Defective ubiquitin binding of SPRTN patient variants compromises global-genome DPC repair and causes synthetic lethality in combination with a reduction in proteasomal DPC repair capacity.2023-01-01T00:00:00Z2023 Jan2025-04-27T01:41:01.812Z2025-02-19T03:00:22.929ZS-EPMC98677493668166210.1038/s41467-023-35988-1