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

Julian Stingele,Roberto Bellelli,Ferdinand Alte,Graeme Hewitt,Grzegorz Sarek,Sarah L Maslen,Susan E Tsutakawa,Annabel Borg,Svend Kjær,John A Tainer,J Mark Skehel,Michael Groll,Simon J Boulton

doi:10.1016/j.molcel.2016.09.031

Abstract

SummaryCovalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription. Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast. The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive. Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans. Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents. SPRTN accomplishes DPC processing through a unique DNA-induced protease activity, which is controlled by several sophisticated regulatory mechanisms. Cellular, biochemical, and structural studies define a DNA switch triggering its protease activity, a ubiquitin switch controlling SPRTN chromatin accessibility, and regulatory autocatalytic cleavage. Our data also provide a molecular explanation on how SPRTN deficiency causes the premature aging and cancer predisposition disorder Ruijs-Aalfs syndrome.

Highlights

The integrity of DNA is constantly challenged by structural and chemical alterations (Lindahl, 1993)
DNA lesions range from abasic sites, small and bulky adducts, to single- and double-strand breaks, which are repaired by lesion-specific and generally well-understood mechanisms (Friedberg et al, 2014)
Biochemical, and structural data, we establish the mechanism of SPRTN’s DNA-dependent proteolytic activity, and we identify several safeguarding mechanisms that act to constrain SPRTN’s potentially toxic activity, including a ubiquitin switch regulating its chromatin accessibility and a negative feedback loop based on autocatalytic cleavage

Summary

Introduction

The integrity of DNA is constantly challenged by structural and chemical alterations (Lindahl, 1993). Restoration of the native DNA sequence and structure by damage-specific repair mechanisms is essential to ensuring genome stability. DNA lesions range from abasic sites, small and bulky adducts, to single- and double-strand breaks, which are repaired by lesion-specific and generally well-understood mechanisms (Friedberg et al, 2014). Specific repair mechanisms for one particular type of lesion, covalent DNA-protein crosslinks (DPCs), have remained elusive. This is despite DPCs being extremely toxic as they directly block essential chromatin transactions, such as replication and transcription (Fu et al, 2011; Nakano et al, 2012, 2013)

Results

Discussion

Conclusion