In TFIIH, XPD Helicase Is Exclusively Devoted to DNA Repair

Kuper, Jochen; Braun, Cathy; Elias, Agnes; Michels, G.; Sauer, Florian; Schmitt, Dominik; Poterszman, Arnaud; Egly, Jean‐Marc; Kisker, Caroline

doi:10.1371/journal.pbio.1001954

Cited by 82 publications

(102 citation statements)

References 50 publications

(151 reference statements)

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“…However, interactions of eukaryotic XPD with the TFIIH component p44 are required to activate XPD's helicase activity (supplemental Fig. S5) (18). XPD in the absence of p44 would hence not translocate to a lesion from a separate loading site, would subsequently not be able to form the lesion-specific stable complex, and would likely dissociate from the DNA (consistent with our data).…”

Section: Uvrb and Xpd Helicase Activities Are Activated By Proteinsupporting

confidence: 86%

“…However, no protein interactions are required for DNA binding by XPD. DNA binding affinity with a K D of ϳ100 nM has been reported for XPD Ϯ p44 (18). Our EMSA studies show comparable binding of XPD to lesion-containing and nondamaged DNA in the absence or presence of p44 (Fig.…”

Section: Dna Substrates For Studying Uvrb(c) and Xpd(/p44) In The Abssupporting

confidence: 79%

“…XPD and p44 (residues 1-285) from C. thermophilum were expressed and purified via affinity and size exclusion followed by anion exchange chromatography, as described (18). All proteins were purified to at least 95% homogeneity as judged from Coomassie-stained SDS gels (supplemental Fig.…”

Section: Methodsmentioning

confidence: 99%

“…In contrast, DNA binding affinity of XPD is independent of protein interactions (18). However, interactions of eukaryotic XPD with the TFIIH component p44 are required to activate XPD's helicase activity (supplemental Fig.…”

Section: Uvrb and Xpd Helicase Activities Are Activated By Proteinmentioning

confidence: 99%

“…Specifically, we focus on UvrB(C) from thermophilic bacteria (Bacillus caldotenax and Thermotoga maritima) and XPD/p44 from the thermostable fungus Chaetomium thermophilum (with comparable enzymatic properties as the human enzyme and 74% sequence homology (18)), in isolation from other NER factors. Potential reasons for the evolvement of differences in NER lesion recognition between the different kingdoms of life are discussed.…”

mentioning

confidence: 99%

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Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Wirth

Gross

Roth

et al. 2016

Journal of Biological Chemistry

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Nucleotide excision repair is an important and highly conserved DNA repair mechanism with an exceptionally large range of chemically and structurally unrelated targets. Lesion verification is believed to be achieved by the helicases UvrB and XPD in the prokaryotic and eukaryotic processes, respectively. Using single molecule atomic force microscopy analyses, we demonstrate that UvrB and XPD are able to load onto DNA and pursue lesion verification in the absence of the initial lesion detection proteins. Interestingly, our studies show different lesion recognition strategies for the two functionally homologous helicases, as apparent from their distinct DNA strand preferences, which can be rationalized from the different structural features and interactions with other nucleotide excision repair protein factors of the two enzymes. Nucleotide excision repair (NER)4 is an important DNA repair mechanism with a large range of chemically and structurally unrelated targets. Examples range from bulky DNA adducts to interstrand DNA cross-links caused by antitumor drugs (1-3). In humans, NER is the only repair system for the removal of UV irradiation-induced photoproducts such as the intrastrand cross-linking cyclobutane-pyrimidine dimers (CPDs), and dysfunctional NER is responsible for severe diseases, including xeroderma pigmentosum (XP) (1-3).The mechanism of NER is highly conserved between organisms. In bacteria, NER involves the proteins UvrA, UvrB, and UvrC. In the current model of prokaryotic NER, a hetero-tetrameric complex of UvrA and UvrB (UvrA 2 B 2 ) scans the DNA for lesions. When a lesion is encountered, initial lesion sensing by a dimer of UvrA is based on detection of DNA distortion. Conformational changes in the UvrA 2 B 2 complex result in an unwinding and opening of dsDNA around the lesion, providing an unpaired (bubble) region likely required by UvrB to thread onto one of the ssDNA strands. The helicase UvrB is believed to verify the presence of a lesion by insertion of a ␤-hairpin via interactions with residues at the base of the hairpin (2). Upon lesion verification by UvrB, UvrA dissociates from the complex, and ATP re-binding by UvrB results in the formation of the lesion-specific UvrB-DNA complex, which recruits the NER endonuclease UvrC (UvrBC complex). UvrC carries out two incisions on either side of the lesion. The 12-13-nucleotide (nt)-long ssDNA stretch (2) containing the lesion can then be removed together with the endonuclease by the helicase UvrD, and the resulting gap is filled and sealed by DNA polymerase I and ligase.Eukaryotic NER encompasses a total of ϳ30 proteins, including the xeroderma pigmentosum group proteins (XPA-XPG). Repair can either be initiated by a stalled RNA polymerase in transcription-coupled NER or via global genome NER. In global genome NER, upon initial detection of short destabilized DNA structures by the CEN2-XPC-HR23B complex, the ATPase/ helicase XPB, which is part of the 10-subunit transcription factor IIH (TFIIH) complex, then directly interacts with XPC (4) and...

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Section: Uvrb and Xpd Helicase Activities Are Activated By Proteinsupporting

confidence: 86%

Section: Dna Substrates For Studying Uvrb(c) and Xpd(/p44) In The Abssupporting

confidence: 79%

Section: Methodsmentioning

confidence: 99%

Section: Uvrb and Xpd Helicase Activities Are Activated By Proteinmentioning

confidence: 99%

mentioning

confidence: 99%

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Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Wirth

Gross

Roth

et al. 2016

Journal of Biological Chemistry

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Xeroderma Pigmentosum and Related Diseases

Schubert

Emmert

2019

Harper's Textbook of Pediatric Dermatology

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Nucleotide Excision Repair and Transcription‐Associated Genome Instability

et al. 2019

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Transcription is a potential threat to genome integrity, and transcription‐associated DNA damage must be repaired for proper messenger RNA (mRNA) synthesis and for cells to transmit their genome intact into progeny. For a wide range of structurally diverse DNA lesions, cells employ the highly conserved nucleotide excision repair (NER) pathway to restore their genome back to its native form. Recent evidence suggests that NER factors function, in addition to the canonical DNA repair mechanism, in processes that facilitate mRNA synthesis or shape the 3D chromatin architecture. Here, these findings are critically discussed and a working model that explains the puzzling clinical heterogeneity of NER syndromes highlighting the relevance of physiological, transcription‐associated DNA damage to mammalian development and disease is proposed.

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In TFIIH, XPD Helicase Is Exclusively Devoted to DNA Repair

Abstract: The DNA helicase activity of the xeroderma pigmentosum D protein, a crucial subunit of TFIID, is only needed for its role in DNA repair, not for transcription.

Cited by 82 publications

References 50 publications

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Xeroderma Pigmentosum and Related Diseases

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

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