Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN

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Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN Lawrence Berkeley National Laboratory Recent Work Title Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Permalink https://escholarship.org/uc/item/01s2z6gk Journal Molecular cell, 64(4) ISSN 1097-2765 Authors Stingele, Julian Bellelli, Roberto Alte, Ferdinand et al. Publication Date 2016-11-01 DOI 10.1016/j.molcel.2016.09.031 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Article Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN Graphical Abstract Authors Julian Stingele, Roberto Bellelli, Ferdinand Alte, ..., J. Mark Skehel, Michael Groll, Simon J. Boulton Correspondence [email protected] In Brief Stingele et al. discover the SPRTN metalloprotease to be crucial for DNA- protein crosslink repair in higher eukaryotes. In addition, several regulatory principles constraining SPRTN’s potentially toxic activity are described: a ubiquitin switch controlling chromatin access, a DNA switch triggering protease activity, and a negative feedback loop based on autocatalytic cleavage. Highlights Accession Numbers d The SPRTN metalloprotease repairs DNA-protein crosslinks 5JIG 5LN5 d A DNA switch controls SPRTN’s protease activity d A ubiquitin switch controls chromatin access of SPRTN d Structural insights reveal unique features of the SPRTN/Wss1 protease family Stingele et al., 2016, Molecular Cell 64, 688–703 November 17, 2016 ª 2016 The Author(s). Published by Elsevier Inc. http://dx.doi.org/10.1016/j.molcel.2016.09.031 Molecular Cell Article Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN Julian Stingele,1 Roberto Bellelli,1 Ferdinand Alte,2 Graeme Hewitt,1 Grzegorz Sarek,1 Sarah L. Maslen,3 Susan E. Tsutakawa,4 Annabel Borg,1 Svend Kjær,1 John A. Tainer,4,5 J. Mark Skehel,3 Michael Groll,2 and Simon J. Boulton1,6,* 1The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK 2Center for Integrated Protein Science at the Department Chemie, Lehrstuhl fur€ Biochemie, Technische Universitat€ Munchen,€ Lichtenbergstrasse 4, 85747 Garching, Germany 3MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK 4Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA 6Lead Contact *Correspondence: [email protected] http://dx.doi.org/10.1016/j.molcel.2016.09.031 SUMMARY and Bartek, 2009). DNA lesions range from abasic sites, small and bulky adducts, to single- and double-strand breaks, which Covalent DNA-protein crosslinks (DPCs) are toxic are repaired by lesion-specific and generally well-understood DNA lesions that interfere with essential chromatin mechanisms (Friedberg et al., 2014). However, specific repair transactions, such as replication and transcription. mechanisms for one particular type of lesion, covalent DNA-pro- Little was known about DPC-specific repair mecha- tein crosslinks (DPCs), have remained elusive. This is despite nisms until the recent identification of a DPC-pro- DPCs being extremely toxic as they directly block essential chro- cessing protease in yeast. The existence of a DPC matin transactions, such as replication and transcription (Fu et al., 2011; Nakano et al., 2012, 2013). protease in higher eukaryotes is inferred from data Xenopus laevis Covalent crosslinking of proteins to DNA can be caused by in egg extracts, but its identity re- various exogenous agents, such as ionizing radiation (IR), UV mains elusive. Here we identify the metalloprotease light, certain metal ions, and, importantly, platinum-based che- SPRTN as the DPC protease acting in metazoans. motherapeutics such as cisplatin and derivatives (Barker et al., Loss of SPRTN results in failure to repair DPCs and 2005; Stingele and Jentsch, 2015). Moreover, DPCs are induced hypersensitivity to DPC-inducing agents. SPRTN by endogenously produced reactive metabolites, such as form- accomplishes DPC processing through a unique aldehyde or acetaldehyde. Notably, formaldehyde is directly DNA-induced protease activity, which is controlled produced within chromatin as a by-product of the histone deme- by several sophisticated regulatory mechanisms. thylation reaction (Shi et al., 2004; Swenberg et al., 2011). Cellular, biochemical, and structural studies define Furthermore, abasic sites bear an aldehyde group that efficiently a DNA switch triggering its protease activity, a reacts with nucleosome proteins, thereby forming DPCs (Scze- panski et al., 2010). DPCs also are produced enzymatically by ubiquitin switch controlling SPRTN chromatin the entrapment of normally transient covalent DNA-protein reac- accessibility, and regulatory autocatalytic cleavage. tion intermediates of enzymes, such as topoisomerases 1 and 2 Our data also provide a molecular explanation (TOP1 and TOP2). Distortions within the DNA (e.g., caused by on how SPRTN deficiency causes the premature nearby DNA damage) or small molecules such as camptothecin aging and cancer predisposition disorder Ruijs-Aalfs (CPT) or etoposide inhibit religation and result in stable DPC syndrome. formation (Pommier, 2006). These enzymatic DPCs can be reversed by specific tyrosil-DNA phosphodiesterases (TDP1 and TDP2 acting on TOP1- and TOP2- adducts, respectively), INTRODUCTION which hydrolyze the covalent bond between the topoiso- merase’s active site residue and the DNA (Pommier et al., The integrity of DNA is constantly challenged by structural and 2014). Apart from these unique cases of enzymatic DPCs, it chemical alterations (Lindahl, 1993). Hence, restoration of the has been suggested that DPCs are generally repaired by canon- native DNA sequence and structure by damage-specific repair ical DNA repair pathways, such as nucleotide excision repair and mechanisms is essential to ensuring genome stability. Germline homologous recombination (Baker et al., 2007; de Graaf et al., mutations in crucial DNA repair enzymes result in several prema- 2009; Nakano et al., 2007, 2009). ture aging and cancer predisposition syndromes, highlighting Very recently a protease-based DPC repair mechanism was the fundamental importance of DNA repair in mammals (Jackson discovered in budding yeast (Stingele et al., 2014) and in 688 Molecular Cell 64, 688–703, November 17, 2016 ª 2016 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). A Dvc-1 - C. elegans C PROTEASE PIP SHP SIM UBZ SPRTN - H. sapiens 100 224- 255- 270- 344- N2 PROTEASE SHP PIP 231 263 276 367 UBZ fcd-2 75 252- 325- 453- 261 332 475 50 % Viability% 25 dvc-1 PROTEASE fcd-2; dvc-1 SHP VIM SIM SIM 0 Wss1 - S. cerevisiae 02468 152- 208- 247- 265- Formaldehyde [mM] 160 218 252 269 B D 100 100 N2 100 N2 75 75 75 N2 50 50 50 fcd-2 % Viability % Viability % dvc-1 25 25 Viability % 25 dvc-1 dvc-1 0 0 0 fcd-2; dvc-1 02468 0 200 400 ctrl 24 48 72 Formaldehyde [mM] Cisplatin [μM] 200 μM Cisplatin [h] E 100 100 100 N2 xpa-1(RNAi) 75 75 75 N2 50 50 dvc-1 50 N2 % Viability % Viability % 25 dvc-1 25 Viability% 25 dvc-1 xpa-1(RNAi); dvc-1 0 0 0 0 70 140 070140 02468 IR [Gy] UVC [J/m2] Formaldehyde [mM] FG**** H 300 100 100 N2 100 him-6 N2 75 75 200 50 50 50 dvc-1 100 Brood sizeBrood % Viability % 25 Viability % 25 him-6 % Viable% progeny dvc-1 him-6; dvc-1 0 0 0 0 02468 0 100 200 300 400 N2 N2 Formaldehyde [mM] Cisplatin [μM] dvc-1him-6 dvc-1him-6 him-6; dvc-1 him-6; dvc-1 Figure 1. SPRTN/Dvc-1 Provides Resistance toward DPC-Inducing Agents in Worms and Operates Independently of FANCD2/Fcd-2 and Parallel to BLM/Him-6 (A) Domain structures and evolutionary distances of the protease domain of SPRTN/Wss1 protease family members of humans, worms, and budding yeast. SPRTN/Wss1 proteases bear interaction domains for p97/Cdc48 (SHP-box, VIM), recognition modules for ubiquitin (UBZ) or SUMO (SIM), and in metazoansa PCNA-interaction motif (PIP-box). (B) C. elegans mutant strains lacking functional SPRTN (dvc-1) are specifically sensitive to the DPC-inducing agents. Formaldehyde sensitivity was determined in synchronized L1 larvae. Cisplatin, UVC light, and IR sensitivities were assessed by measuring embryonic survival of progeny after exposure of adult animals. Error bars indicate SEM of –two to four independent experiments. (C) FANCD2 is not involved in providing formaldehyde resistance in synchronized L1 larvae. Error bars indicate SEM of two independent experiments. (D) FANCD2 provides resistance to chronic cisplatin exposure by a mechanism distinct to DPC repair by SPRTN. Viability was assessed by determination of embryonic survival of progeny of young adult animals kept on cisplatin-containing plates (200 mM) for the indicated amount of time. Error bars indicate SEM of two independent experiments. (E) Loss of XPA does not result in increased formaldehyde sensitivity in synchronized L1 worms. Error bars indicate SEM of two independent experiments. (legend continued on next page) Molecular Cell 64, 688–703, November 17, 2016 689 Xenopus laevis egg extracts (Duxin et al., 2014). In yeast, DPC assessing sensitivity to DPC-inducing agents. DNA damage proteolysis is catalyzed by the metalloprotease Wss1, which sensitivity is typically measured in worms by treating young adult permits replication in the presence of DPCs and provides resis- animals, followed by determining viability of their progeny as a tance toward DPC-inducing agents. Intriguingly, Wss1 is a DNA- proxy for repair defects in the germline, which is the only prolif- dependent protease that degrades DNA-bound substrates erating tissue in adult animals (Figure S1A). However, this treat- in vitro irrespective of identity. Importantly, in Xenopus egg ex- ment regimen is not suitable for testing formaldehyde sensitivity, tracts, a DPC-containing plasmid is repaired by a similar mech- because treated adult worms succumb to death at doses that anism, indicating that protease-based DPC repair is conserved.
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