Orchestral maneuvers at the damaged sites in nucleotide excision repair

Abstract

To safeguard the genome from the accumulation of deleterious effects arising from DNA lesions, cells developed several DNA repair mechanisms that remove specific types of damage from the genome. Among them, Nucleotide Excision Repair (NER) is unique in its ability to remove a very broad spectrum of lesions, the most important of which include UV-induced damage, bulky chemical adducts and some forms of oxidative damage. Two sub-pathways exist in NER; Transcription-Coupled Repair (TC-NER) removes lesion localized exclusively in transcribed genes while Global Genome Repair (GG-NER) removes lesions elsewhere. In TC- or GG-NER, more than 30 proteins detect, open, incise and resynthesize DNA. Intriguingly, half of them are involved in the detection of DNA damage, implying that this is a crucial repair step requiring a high level of regulation. We review here the complex damage recognition step of GG-NER with a focus on post-translational modifications that help the comings and goings of several protein complexes on the same short damaged DNA locus.

Fig. 1

Structure of NER substrates. Structures of the main NER substrate cyclobutane pyrimidine dimer and the more peculiar dG-acetylaminofluorene, (1,2)dGG-cisplatin and dG-benzopyrene adducts are shown

Fig. 2

The global genome nucleotide excision repair sub-pathway. In global genome nucleotide excision repair the damage sensor XPC-HR23B-CEN2 scans the DNA for helix-distorting lesions (Step I). UV-DDB may be involved in damage recognition depending on the nature of the lesion. Upon binding of the XPC complex to the damage, HR23B dissociates from the complex. XPC attracts the TFIIH transcription/repair complex that anchors to the damaged DNA though its XPB ATPase activity (Step II), followed by the last recognition complex XPA-RPA. Upon recruitment of XPA, the CAK (CDK-activating kinase) subcomplex of TFIIH dissociates from the core complex (Step III) and liberates the 5′–3′ XPD helicase activity that further opens the double helix around the lesion until the encounter of a DNA lesion and release XPC-CEN2 for DNA (Step IV). The single-stranded DNA-binding protein replication protein A (RPA) coats the undamaged strand as TFIIH opens DNA. XPA further verifies the presence of a lesion and recruits the structure specific endonuclease ERCC1-XPF heterodimer. Further, XPG cuts the damaged strand 3′ to the lesion, and triggers the incision in 5′ to the lesion by ERCC1-XPF (Step V). A 22–30 nucleotide-long single-strand damaged oligonucleotide is then excised and the trimeric proliferating cell nuclear antigen (PCNA) ring recruits DNA Polymerases for gap-filling DNA synthesis (Step VI). The NER reaction is completed through sealing the final nick by DNA ligase 1 (or ligase III depending of the cell cycle stage) (Step VII). A red line delineates the four steps of damage recognition in NER

Fig. 3

Structural features of DNA damage recognition by XPC. Upper panel, schematic representation of Rad4/XPC. Lower panel, simplified diagram of the Rad4/XPC complex bound to damaged DNA: the transglutaminase domain (TGD) is indicated in gold while the beta hairpin domains BHD1, 2 and 3 are indicated in purple, blue and red. The two disordered linked thymidines are indicated schematically, and the two flipped-out adenines bound to Rad4/XPC are colored orange

Fig. 4

Post-translational modifications of damage recognition proteins. Functional domains of XPC and XPA are indicated. In red, the NER factors that interact with XPC and XPA are indicated together with their binding sites. The SUMOylation of XPC triggers the recruitment of RNF111 that ubiquitylates K655. For XPC, the transglutaminase domain (TGD) is indicated in gold while the beta hairpin domains BHD1, 2 and 3 are indicated in purple, blue and red. For XPA, the Zinc finger is indicated in light blue, the PAR-binding motif (PBM) is indicated in gold, the DNA-binding site is indicated in gray. PARP1 interacts with XPA through the PBM