DNA protein crosslink proteolysis repair: From yeast to premature ageing and cancer in humans

Abstract

DNA-protein crosslinks (DPCs) are a specific type of DNA lesion consisting of a protein covalently and irreversibly bound to DNA, which arise after exposure to physical and chemical crosslinking agents. DPCs can be bulky and thereby pose a barrier to DNA replication and transcription. The persistence of DPCs during S phase causes DNA replication stress and genome instability. The toxicity of DPCs is exploited in cancer therapy: many common chemotherapeutics kill cancer cells by inducing DPC formation. Recent work from several laboratories discovered a specialized repair pathway for DPCs, namely DPC proteolysis (DPCP) repair. DPCP repair is carried out by replication-coupled DNA-dependent metalloproteases: Wss1 in yeast and SPRTN in metazoans. Mutations in SPRTN cause premature ageing and liver cancer in humans and mice; thus, defective DPC repair has great clinical ramifications. In the present review, we will revise the current knowledge on the mechanisms of DPCP repair and on the regulation of DPC protease activity, while highlighting the most significant unresolved questions in the field. Finally, we will discuss the impact of faulty DPC repair on disease and cancer therapy.

Keywords: Ageing; Cancer; DNA-protein crosslinks; Genome stability; Post-translational modification; SPRTN protease.

Fig. 1

Schematic of DPC repair pathways. A. Non-enzymatic DPCs are cleaved by proteases and the DNA-bound peptide remnant is bypassed by translesion synthesis (TLS) polymerases. B. Following cleavage of the bulk of the protein component of the enzymatic DPCs, Top1- and Top2-ccs, peptide remnants can be excised by phosophodiesterases. Alternatively, nucleases can also remove DPCs by cleaving the DNA to which DPCs are attached.

Fig. 2

A. Phylogenetic tree of SPRT and WLM families. The newly identified SPRT-like protein group, ACRC, is evolutionary close to the SPRT family. ACRC orthologs are found in archea and eukarya, while absent in prokaryotes. Alanyl aminopeptidase family of gluzincins were used as an outgroup. Protein sequences of SprT and WLM domains were aligned using MAFFT and the phylogenetic tree was constructed in PhyML. B. Comparison of SPRTN and ACRC SprT domains. The protease core of ACRC is similar to that of SPRTN. The SprT domain of ACRC (in black) was modelled according to the yeast Wss1b structure (5JIG) and overlapped with the model of the SprT domain of SPRTN protein (abylysin template, 4JIU) (in multiple colours). Protease core consists of two α-helices (in green), catalytic glutamate (in yellow) and three zinc binding histidines (in red). Homology models were created in SWISS-MODEL workspace and visualized in UCSF Chimera.

Fig. 3

Summary of regulation layers of DPC proteases. A. SPRTN is degraded in G1 phase after ubiquitylation by APC/Cdh1. This ensures the levels of the protease are low when its activity is less needed. B. Wss1 or SPRTN (in red) are recruited to DNA for cleavage of the substrate (DPC; in brown): this ensures that their protease activity is restricted to the chromatin environment. C. DNA also stimulates Wss1 or SPRTN self-cleavage: this helps to prevent unscheduled proteolysis of DNA-associated proteins. D. Left, SPRTN is modified by ubiquitin and de-ubiquitylated upon DPC formation induced by formaldehyde (FA). Right, DPCs might be modified by ubiquitin (or ubiquitin-like proteins) to recruit DPC proteases to the site of damage. Colour Code: Red: Wss1 or SPRTN protease; Brown: DPC; Green: Ubiquitin or Ubiquitin-like protein.