XPA: A key scaffold for human nucleotide excision repair

Sugitani, Norie; Sivley, R. Michael; Perry, Kelly E.; Capra, John A.; Chazin, Walter J.

doi:10.1016/j.dnarep.2016.05.018

Cited by 96 publications

(105 citation statements)

References 128 publications

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“…This is notable, as XPA is absolutely required for NER. It is a scaffold protein that contacts many of the other NER protein components, and also binds to DNA [9–11] (Fig. 1A).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional consequences of XPA disruption in human cell lines

et al. 2017

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Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage. We then analyzed four genetically matched human cell line pairs deficient or proficient in XPA. Of the ∼14,000 genes transcribed in each cell line, 325 genes (2%) had a significant XPA-dependent directional change in gene expression that was common to all four pairs (with a false discovery rate of 0.05). These genes were enriched in pathways for the maintenance of mitochondria. Only 27 common genes were different by more than 1.5-fold. The most significant hits were AKR1C1 and AKR1C2, involved in steroid hormone metabolism. AKR1C2 protein was lower in all of the immortalized XPA-deficient cells. Retinoic acid treatment led to modest XPA-dependent activation of some genes with transcription-related functions. We conclude that XPA status does not globally influence human gene transcription. However, XPA significantly influences expression of a small subset of genes important for mitochondrial functions and steroid hormone metabolism. The results may help explain defects in neurological function and sterility in individuals with xeroderma pigmentosum.

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“…This is notable, as XPA is absolutely required for NER. It is a scaffold protein that contacts many of the other NER protein components, and also binds to DNA [9–11] (Fig. 1A).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional consequences of XPA disruption in human cell lines

et al. 2017

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“…The structure informs on XPA, which is essential for NER 16 . XPA contains an Nterminal zinc finger and a DNA-binding domain with an extended helix and an intercalating ß-hairpin ( Fig.…”

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confidence: 99%

“…3i). Several sites of mutations that cause severe Xeroderma pigmentosum 16 map to XPA residues that interact with DNA ( Fig. 3c).…”

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confidence: 99%

“…XPA and XPG also stimulate XPB and XPD, and this may facilitate DNA opening 4,14,18,19 and XPD migration in the 3' direction to scan the DNA strand for the lesion 13 . XPA chaperons TFIIH-DNA interactions and anchors the NER machinery to the 5' edge of the repair bubble, where it is ideally positioned to recruit XPF-ERCC1 and complete the repair assembly when the lesion is encountered 16 . The two endonucleases XPF and XPG can now incise the lesion-containing DNA strand near the 5'-and the 3'-edge of the repair bubble, respectively, to remove the lesion-containing DNA fragment 1 .…”

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confidence: 99%

“…Patches of positively charged residues in proximity to the DNA backbone are indicated. Residues that are mutated in Xeroderma pigmentosum16 are highlighted in yellow. Mutation of encircled residues decreases DNA affinity36 .…”

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confidence: 99%

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Structural basis of TFIIH activation for nucleotide excision repair

Kokić

Chernev

Tegunov

et al. 2019

Preprint

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Genomes are constantly threatened by DNA damage, but cells can remove a large variety of DNA lesions by nucleotide excision repair (NER) 1 . Mutations in NER factors compromise cellular fitness and cause human diseases such as Xeroderma pigmentosum (XP), Cockayne syndrome and trichothiodystrophy 2,3 . The NER machinery is built around the multisubunit transcription factor IIH (TFIIH), which opens the DNA repair bubble, scans for the lesion, and coordinates excision of the damaged DNA single strand fragment 1,4 . TFIIH consists of a kinase module and a core module that contains the ATPases XPB and XPD 5 . Here we prepare recombinant human TFIIH and show that XPB and XPD are stimulated by the additional NER factors XPA and XPG, respectively. We then determine the cryo-electron microscopy structure of the human core TFIIH-XPA-DNA complex at 3.6 Å resolution. The structure represents the lesion-scanning intermediate on the NER pathway and rationalizes the distinct phenotypes of disease mutations. It reveals that XPB and XPD bind double-and single-stranded DNA, respectively, consistent with their translocase and helicase activities. XPA forms a bridge between XPB and XPD, and retains the DNA at the 5'-edge of the repair bubble. Biochemical data and comparisons with prior structures 6,7 explain how XPA and XPG can switch TFIIH from a transcription factor to a DNA repair factor. During transcription, the kinase module inhibits the repair helicase XPD 8 . For DNA repair, XPA dramatically rearranges the core TFIIH structure, which reorients the ATPases, releases the kinase module and displaces a 'plug' element from the DNA-binding pore in XPD.This enables XPD to move by ~80 Å, engage with DNA, and scan for the lesion in a XPGstimulated manner. Our results provide the basis for a detailed mechanistic analysis of the NER mechanism.

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Xeroderma Pigmentosum and Related Diseases

Schubert

Emmert

2019

Harper's Textbook of Pediatric Dermatology

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XPA: A key scaffold for human nucleotide excision repair

Cited by 96 publications

References 128 publications

Transcriptional consequences of XPA disruption in human cell lines

Transcriptional consequences of XPA disruption in human cell lines

Structural basis of TFIIH activation for nucleotide excision repair

Xeroderma Pigmentosum and Related Diseases

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