DNA-protein crosslink proteases in genome stability

Abstract

Proteins covalently attached to DNA, also known as DNA-protein crosslinks (DPCs), are common and bulky DNA lesions that interfere with DNA replication, repair, transcription and recombination. Research in the past several years indicates that cells possess dedicated enzymes, known as DPC proteases, which digest the protein component of a DPC. Interestingly, DPC proteases also play a role in proteolysis beside DPC repair, such as in degrading excess histones during DNA replication or controlling DNA replication checkpoints. Here, we discuss the importance of DPC proteases in DNA replication, genome stability and their direct link to human diseases and cancer therapy.

Fig. 1. Proteolysis protects cells from DPC toxicity during various DNA metabolic processes.

a DPCs on the leading or lagging strand can pose impediments for helicase and/or polymerase progression. b Proteolysis removes the bulk of this obstacle (DPC), and reduces the crosslinked protein to a peptide (remnant) that can be bypassed by TLS polymerase, thus resuming DNA replication. c DPCs can block transcription, but the mechanisms of transcription-dependent DPC proteolysis have not been explored.

Fig. 2. The structural features of the known DPC proteases.

Domains/motifs for interactions are color-coded. Red: protease domains. Orange: Cdc48/p97 interaction. Green: PCNA interaction. Ochre: DNA binding. Blue: SUMO/ubiquitin/proteasome binding. The catalytic residues in the protease domains are underlined. The sites of disease-associated mutations in SPRTN (RJALS), FAM111A (KCS2)^,, and FAM111B (POIKTMP) are marked in red. The asterisk in SPRTN indicates the site of nonsense mutations in RJALS patients that generate the protein SPRTN-ΔC. RVP, retroviral protease. U1 and U2, potential UBLs in FAM111A.

Fig. 3. Overlapping and non-overlapping functions of DPC proteases.

a Wss1 and Ddi1 are both required for the repair of non-enzymatic DPCs and Topo-1ccs during replication. b FAM111A and SPRTN have both been implicated in Topo-1cc resolution, based on CPT resistance. c Sensitivity to PARP-1 inhibitors and DNA combing assays suggest that FAM111A, but not SPRTN, is involved in the resolution of trapped PARP-1. d Human GCNA resolves DNMT1 crosslinks at 5-azadC incorporation sites (red arrowhead), behind the replication fork. e GCNA resolves Topo-2ccs in flies, worms and zebrafish.

Fig. 4. Proteolysis of non-DPC substrates during DNA replication.

a Wss1 cleaves excess histones binding to ssDNA after fork stalling. ssDNA is formed after HU. b PARP-1 is recruited to DNA to repair different types of damage, including base adducts generated by alkylating agents. In the presence of PARP inhibitors, self-PARylation and chromatin dissociation are blocked. Trapped PARP-1 represents a barrier for replication. FAM111A confers resistance to PARP inhibitors, but whether it acts proteolytically on PARP-1 awaits formal verification. c During DNA replication SPRTN cleaves the C-terminus of Chk1 and releases the active kinase domain (K) from chromatin.