Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Abstract

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG geneERCC5lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair

“…During final stages of revision of this work, a related study was published ( 51 ). This integrated structural study includes the structure of a DNA-free XPG construct, where the XPG helical arch had been replaced by that of Pyrococcus furiosus FEN1.…”

Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin

“…Notably, this same NEIL1 C-terminal acetylated region is reported to bind Poly(ADP-Ribose) Polymerase 1 (PARP1) ( 105 ), suggesting future NEIL1 localization studies might test the role of PARylation using PARP1 and poly(ADP-ribose) glycohydrolase (PARG) inhibitors ( 106 , 107 ). Because mouse models support shared substrate specificity for BER enzymes ( 108 , 109 ), despite distinct physical genomic targets ( 110 ), it will also be useful to determine the relative contribution of other BER and DNA repair enzymes, such as those associated with mismatch repair ( 111 ) or with the multi-repair pathway nuclease XPG associated with both nucleotide and base excision repair ( 112 ), to genome stability. More generally and illustrating how DG’s may overcome the pervasive nature of oxidative DNA base damage by over-lapping specificities that allow them to back each other up, the intersection of base and nucleotide excision repair has been seen for oxidative alkylations such as cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine ( 67 ).…”

XPG is Modulated by miR-4715-3p and rs873601 Genotypes in Lung Cancer

“…The correction by XPG is regulated by sequences and motifs that scaffold and sculpture damaged DNA by binding both NER bubble junctions and replication forks. 4,16 Genetic variants and posttranscriptional regulation alter functional motifs, and alterations in functional motifs may reduce DNA repair capacity and lead to increased cancer risks. 17,18 Our results revealed that miR-4715-3p modulated XPG expression and may have altered its repair ability, resulting in lung cancer [Supplementary Figure 2].…”

“…A recent study detected downregulation of miR-4715-3p in upper gastrointestinal adenocarcinoma (UCG), miR-4715-3p has putative binding sites in the 3UTR of AURKA, and miR-4715-3p mediated a reduction in AURKA levels, which in turn resulted in GPX4 inhibition and cell ferroptosis. 4 Bioinformatics analysis using TargetScan indicated that miR-4715-3p targeted the 7mer-m8 site in the 3UTR of XPG [Supplementary Figure 2], and the target site covered the rs873601 region, partially contributing to interaction between rs873601 and miR-4715-3p.…”

“…XPG (accession number: DI095823), an endonuclease bound to the 3ʹ-ends of the NER system, specifically functions to recognize and remove damaged DNA strands. 4 The DNA repair capacity of XPG is related to inherited factors, 5 thus, polymorphisms in the NER pathway modify DNA repair capacity. 6 XPG has been proposed as a candidate marker for cancer susceptibility, prognosis, and treatment response, including susceptibility to colorectal cancer 7 and gastric cancer, 8 sensitivity to anticancer treatment of non-smallcell lung cancer (NSCLC), 9 and prognosis of advanced NSCLC.…”