Molecular insights into the recruitment of TFIIH to sites of DNA damage

Oksenych, Valentyn; Jesus, Bruno Bernardes de; Zhovmer, Alexander; Egly, Jean‐Marc; Coin, Frédéric

doi:10.1038/emboj.2009.230

Cited by 108 publications

(116 citation statements)

References 46 publications

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“…at a photoproduct site where base pairing is locally disturbed). The action of XPB in initiating the repair bubble may allow the XPD helicase to bind and extend the nascent bubble, a situation analogous to that suggested for eukaryal NER (12). Patch repair in the archaea may require the action of the 3Ј-flap nuclease XPF to complete the excision step (23,26).…”

Section: Discussionmentioning

confidence: 92%

“…The most likely motif implicated in strand separation is therefore the Thm domain, with single-stranded DNA dragged across of the tops of the two motor domains, bringing it close to the position of the RED motif. Both the Thm domain and the RED motif have recently been implicated as important for binding of TFIIH to DNA damage sites (12).…”

Section: Cloning Expression and Purification Of The Xpb-bax1mentioning

confidence: 99%

“…Mutations that target the helicase motifs of XPB do not disrupt the function of TFIIH in NER, leading to the suggestion that XPB should be considered as an ATP-dependent molecular switch, perhaps opening DNA structure locally (11). Recent studies confirm the essential requirement for XPB ATPase activity in the recruitment of TFIIH to DNA damage sites (12). In contrast, the ATPase activity of XPD is not required.…”

mentioning

confidence: 99%

“…A crystal structure of the core of XPB from Archaeoglobus fulgidus revealed the presence of two canonical motor domains and two accessory domains named the thumb (Thm) domain and damage recognition domain (DRD) with putative roles in DNA damage detection (17). The relevance of the archaeal XPB structure to an understanding of the eukaryal protein was emphasized by the finding that the Thm domain and a conserved RED motif identified in the archaeal enzyme are essential for the function of eukaryal XPB in NER (12).…”

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confidence: 99%

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The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

Rouillon

White

2010

Journal of Biological Chemistry

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XPB helicase is an integral part of transcription factor TFIIH, required for both transcription initiation and nucleotide excision repair (NER). Along with the XPD helicase, XPB plays a crucial but only partly understood role in defining and extending the DNA repair bubble around lesions in NER. Archaea encode clear homologues of XPB and XPD, and structural studies of these proteins have yielded key insights relevant to the eukaryal system. Here we show that archaeal XPB functions with a structure-specific nuclease, Bax1, as a helicase-nuclease machine that unwinds and cleaves model NER substrates. DNA bubbles are extended by XPB and cleaved by Bax1 at a position equivalent to that cut by the XPG nuclease in eukaryal NER. The helicase activity of archaeal XPB is dependent on the conserved Thumb domain, which may act as the helix breaker. The N-terminal damage recognition domain of XPB is shown to be crucial for XPB-Bax1 activity and may be unique to the archaea. These findings have implications for the role of XPB in both archaeal and eukaryal NER and for the evolution of the NER pathway. XPB is shown to be a very limited helicase that can act on small DNA bubbles and open a defined region of the DNA duplex. The specialized functions of the accessory domains of XPB are now more clearly delineated. This is also the first direct demonstration of a repair function for archaeal XPB and suggests strongly that the role of XPB in transcription occurred later in evolution than that in repair.The superfamily 2 helicase XPB (Rad25 in Saccharomyces cerevisiae) is an essential component of transcription factor TFIIH. The ATPase activity of XPB is required for both nucleotide excision repair (NER) 2 and transcription initiation from RNA polymerase II promoters (1, 2). The NER pathway is a highly flexible system that is required for the detection and removal of a wide variety of bulky and helix-distorting lesions, including photoproducts. Mutations in the xpb or xpd genes in humans can cause the serious genetic diseases xeroderma pigmentosum, trichothiodystrophy, and Cockayne's syndrome, due to defects in both transcription and repair (reviewed in Ref.3). Examples of xpb mutations in humans are much more rare than those seen in the xpd gene, probably due to the crucial role of the XPB protein in basal transcription (4).Although the ATPase activities of both proteins are required for NER (5), the respective roles of the XPB and XPD helicase components of TFIIH are still a matter of debate. XPD is the more robust helicase (6), and it has been suggested to bind 5Ј of the DNA lesion and translocate in a 5Ј to 3Ј direction toward the damage site, potentially acting as a sensor or proofreader of DNA damage for the NER pathway either by jamming directly on DNA lesions (7) or perhaps through damage sensing by its iron-sulfur cluster binding domain (8, 9). However, little direct evidence exists in support of these possibilities at present, and indeed it is not yet clear whether XPD or XPB binds first at repair sites or whether they bi...

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Section: Discussionmentioning

confidence: 92%

Section: Cloning Expression and Purification Of The Xpb-bax1mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

Rouillon

White

2010

Journal of Biological Chemistry

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“…The mode of action of XPB is supposed to be similar in both the opening of DNA at the promoter and at the site of the lesion -large conformational change upon ATP hydrolysis allowing for local, but essential destabilization of DNA helix. It was shown that DNA opening in NER depends on the ATPase, but not on the helicase activity of XPB in combination with the processive helicase activity of XPD [26]. Expansion of the DNA bubble around the damage is facilitated by replication protein A (RPA).…”

mentioning

confidence: 99%

Transcription factor IIH – the protein complex with multiple functions

Mydlikova¹,

Gurský²,

Piršel³

2010

neo

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Transcription factor IIH (TFIIH) is eukaryotic multi protein complex identified in early 90's. Subsequent years have shown exceptional conservation of its structure from yeast to human. Although initially considered to be exclusively a basal transcription factor responsible for initiation of transcription and transition from initiation to elongation, TFIIH is also important in nucleotide excision repair for opening DNA at the site of a lesion and for recruitment of additional repair factors. Recently it was suggested that intact holocomplex of TFIIH is required for cell cycle regulation. Moreover, mutations in TFIIH subunits lead to three distinct genetic disorders: xeroderma pigmentosum (DNA repair disorder/cancer syndrome), Cockayne syndrome (DNA repair disorder/transcription syndrome/segmental progeria) and trichothiodystrophy (DNA repair disorder/transcription syndrome). This review is focused on the TFIIH structure, its role in transcription, DNA repair and cell cycle regulation and association with some human hereditary disorders.

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Robust DNA repair in PAXX‐deficient mammalian cells

et al. 2018

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To ensure genome stability, mammalian cells employ several DNA repair pathways. Nonhomologous DNA end joining ( NHEJ ) is the DNA repair process that fixes double‐strand breaks throughout the cell cycle. NHEJ is involved in the development of B and T lymphocytes through its function in V(D)J recombination and class switch recombination ( CSR ). NHEJ consists of several core and accessory factors, including Ku70, Ku80, XRCC 4, DNA ligase 4, DNA ‐ PK cs, Artemis, and XLF . Paralog of XRCC 4 and XLF ( PAXX ) is the recently described accessory NHEJ factor that structurally resembles XRCC 4 and XLF and interacts with Ku70/Ku80. To determine the physiological role of PAXX in mammalian cells, we purchased and characterized a set of custom‐generated and commercially available NHEJ ‐deficient human haploid HAP 1 cells, PAXX Δ , XRCC 4 Δ , and XLF Δ . In our studies, HAP 1 PAXX Δ cells demonstrated modest sensitivity to DNA damage, which was comparable to wild‐type controls. By contrast, XRCC 4 Δ and XLF Δ HAP 1 cells possessed significant DNA repair defects measured as sensitivity to double‐strand break inducing agents and chromosomal breaks. To investigate the role of PAXX in CSR , we generated and characterized Paxx −/− and Aid −/− murine lymphoid CH 12F3 cells. CSR to IgA was nearly at wild‐type levels in the Paxx −/− cells and completely ablated in the absence of activation‐induced cytidine deaminase ( AID ). In addition, Paxx −/− CH 12F3 cells were hypersensitive to zeocin when compared to wild‐type controls. We concluded that Paxx ‐deficient mammalian cells maintain robust NHEJ and CSR .

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Molecular insights into the recruitment of TFIIH to sites of DNA damage

Cited by 108 publications

References 46 publications

The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

Transcription factor IIH – the protein complex with multiple functions

Robust DNA repair in PAXX‐deficient mammalian cells

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