A ubiquitin switch controls autocatalytic inactivation of the DNA–protein crosslink repair protease SPRTN

Abstract

Repair of covalent DNA–protein crosslinks (DPCs) by the metalloprotease SPRTN prevents genome instability, premature aging and carcinogenesis. SPRTN is specifically activated by DNA structures containing single- and double-stranded features, but degrades the protein components of DPCs promiscuously and independent of amino acid sequence. This lack of specificity is useful to target diverse protein adducts, however, it requires tight control in return, in order to prohibit uncontrolled proteolysis of chromatin proteins. Here, we discover the components and principles of a ubiquitin switch, which negatively regulates SPRTN. We demonstrate that monoubiquitylation is induced in an E3 ligase-independent manner and, in contrast to previous assumptions, does not control chromatin access of the enzyme. Data obtained in cells and in vitro reveal that monoubiquitylation induces inactivation of the enzyme by triggering autocatalytic cleavage in trans while also priming SPRTN for proteasomal degradation in cis. Finally, we show that the deubiquitylating enzyme USP7 antagonizes this negative control of SPRTN in the presence of DPCs.

The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability

“…As expected, here we could not detect p97 and PCNA, two known SPRTN interactors ( Centore et al., 2012 ; Davis et al., 2012 ; Ghosal et al., 2012 ; Juhasz et al., 2012 ; Machida et al., 2012 ; Mosbech et al., 2012 ), which instead were readily detected in SPRTN’s native immunoprecipitates ( Figure S4 A). SPRTN appeared to be modified by both SUMO and ubiquitin, but after FA treatment these modifications decreased, in line with previously published data ( Zhao et al., 2021 ). Thus, the large majority of the SUMO and ubiquitin signals in SPRTN immunoprecipitates come from substrates and binding proteins, especially after FA treatment when SPRTN engages in DPC proteolysis.…”

Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma

“…The normal cell cycle is the basic condition to ensure the correct sequence, integrity and fidelity of life activities and study suggests metabolic dysfunction linking to DNA damage causes dysregulated cell cycle, which will lead to genomic instability [ 45 , 46 ]. In addition, research shows that metalloproteinase SPRTN involved in biosynthesis of amino acids and metabolism regulates covalent DNA-protein crosslinks to prevent genome instability and carcinogenesis [ 47 ]. HIF, a major participant in sensing and adapting to hypoxia, is closely related to genome instability and cancer progression [ 48 ].…”

Enzymatic bypass of an N6-deoxyadenosine DNA–ethylene dibromide–peptide cross-link by translesion DNA polymerases

“…Ubiquitination is a key step for proteolysis by the nuclear DNA-dependent metalloprotease SPRTN (18). SPRTN uses an accessory process (i.e., ubiquitination) to repair cross-links because the ubiquitin controls its activity (34). SPRTN-mediated proteolysis also depends on the location of protein cross-links on the DNA strands (30).…”