XPG: a multitasking genome caretaker

Abstract

The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1-XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.

Keywords: DNA damage response; NER; Structure; XPG/ERCC5; Xeroderma pigmentosum–Cockayne syndrome.

Fig. 1

Nucleotide excision repair mechanism. A Transcription-coupled NER. Pol II stalling at UV lesions recruits CSB, whose prolonged binding to Pol II triggers CSA recruitment, which is part of the larger CRL4^CSA complex that also comprises DDB1, CUL4A and RBX1. CRL4^CSA interacts with ELOF1 and ubiquitylates CSB and Pol II to target these for proteasomal degradation. Next, UVSSA and USP7 are recruited, which, respectively, recruit TFIIH and de-ubiquitylate and stabilize CSB. B Global genome NER. DDB2, as part of the CRL4^DDB2 complex, binds to UV lesions and facilitates their efficient recognition and stable binding by XPC, by means of auto-ubiquitylation and XPC ubiquitylation. Stable binding of XPC leads to TFIIH recruitment, followed by RNF111-mediated ubiquitylation and dissociation of XPC. C Core NER reaction. Stable association of XPC or UVSSA to lesions recruits TFIIH, which unwinds the DNA with its helicase activity to verify the damage. XPA displaces the TFIIH CAK subcomplex and stimulates its helicase activity. RPA binds the undamaged strand and together with XPA positions the ERCC1–XPF and XPG endonucleases 5ʹ and 3ʹ to the lesion, respectively. XPF 5ʹ incision is followed by XPG 3ʹ incision after which PCNA and DNA polymerases, together with other re-synthesis factors, are recruited to fill the gap

Fig. 2

XPG structure and DNA substrate binding. A DNA substrates of XPG. XPG binds to and incises 5ʹ flap structures, 5ʹ single-stranded tails of splayed arms, and the 3ʹ junction of DNA bubbles. B XPG schematic structure. XPG contains two nuclease domains N and I, separated by a unique spacer region, a PCNA-interacting Protein (PIP) box and three Nuclear Localization Signal (NLS) regions. The D1 and D2 boxes are highly conserved among eukaryotes. C XPG interactions with DNA. Crystal structure of the catalytic core of XPG in complex with a splayed-arm DNA substrate. XPG interacts with dsDNA via a helix-2-turn-helix (H2TH) module (shown in purple) and an adjacent α-helix (shown in orange). Furthermore, a hydrophobic wedge and β-pin interact with the ss/dsDNA junction. Image depicts structure PDB 6TUW (complex 1) from [76] and was generated using PyMol

Fig. 3

XPG functions in genome maintenance pathways other than NER. A Repair of oxidative damage. Initial binding of XPG to an oxidized base stimulates Nth1 DNA-binding activity, followed by removal of the oxidized base and repair by BER. B R-loop processing. R-loops arise when during Pol II transcription the nascent mRNA hybridizes with one of the DNA strands. One of the 3ʹ prime junctions of the resulting bubble structure is recognized and processed by XPG endonuclease activity. C Homologous Recombination. HR of DSBs generated by endogenous DNA damage is initiated by DNA end resection followed by RPA coating of the resulting ssDNA. XPG interacts with and facilitates the loading of the BRCA2–PALB2–RAD51 complex to DSB sites. RAD51 replaces RPA and promotes the presynaptic filament to initiate HR. Of note, closed XPG circles represent putative non-catalytic activity and open XPG circles represent catalytic activity of XPG