Comparative Analysis of Interaction of Human and Yeast DNA Damage Recognition Complexes with Damaged DNA in Nucleotide Excision Repair

Krasikova, Y. S.; Rechkunova, N. I.; Maltseva, Ekaterina A.; Pestryakov, P. E.; Petruseva, I. O.; Sugasawa, Kaoru; Chen, Xuejing; Min, Jo Young; Lavrik, Olga I.

doi:10.1074/jbc.m112.444026

Cited by 31 publications

(22 citation statements)

References 36 publications

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“…The lower band is attributed to a single XPC molecule-DNA complex and the higher one is attributed to complexes with two XPC molecules bound per DNA molecule. Similar double-molecule XPC-RAD23B -DNA complexes have been reported by other workers [10, 40–42]. However, when an adduct is present, the two bands are no longer distinguishable.…”

Section: Resultssupporting

confidence: 86%

The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

Lee

Cai

et al. 2014

DNA Repair

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The first eukaryotic NER factor that recognizes NER substrates is the heterodimeric XPC-RAD23B protein. The currently accepted hypothesis is that this protein recognizes the distortions/destabilization caused by DNA lesions rather than the lesions themselves. The resulting XPC-RAD23B -DNA complexes serve as scaffolds for the recruitment of subsequent NER factors that lead to the excision of the oligonucleotide sequences containing the lesions. Based on several well-known examples of DNA lesions like the UV radiation-induced CPD and 6-4 photodimers, as well as cisplatin-derived intrastrand cross-linked lesions, it is generally believed that the differences in excision activities in human cell extracts is correlated with the binding affinities of XPC-RAD23B to these DNA lesions. However, using electrophoretic mobility shift assays, we have found that XPC-RAD23B binding affinities of certain bulky lesions derived from metabolically activated polycyclic aromatic hydrocarbon compounds such as benzo[a]pyrene and dibenzo[a,l]pyrene, are not directly, or necessarily correlated with NER excision activities observed in cell-free extracts. These findings point to features of XPC-RAD23B-bulky DNA adduct complexes that may involve the formation of NER-productive or unproductive forms of binding that depend on the structural and stereochemical properties of the DNA adducts studied. The pronounced differences in NER cleavage efficiencies observed in cell-free extracts may be due to differences in the successful recruitment of subsequent NER factors by the XPC-RAD23B-DNA adduct complexes, and/or in the verification step. These phenomena appear to depend on the structural and conformational properties of the class of bulky DNA adducts studied.

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Section: Resultssupporting

confidence: 86%

The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

Lee

Cai

et al. 2014

DNA Repair

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“…To this end, we made long DNA-damage arrays by tandemly ligating multiple linearized plasmids, each contained either one CPD or one fluorescein-modified deoxythymidine (Fl-dT) per 2,030 bp, as previously described (Ghodke et al, 2014). Rad4 binds tightly to Fl-dT (Krasikova et al, 2013), making it a model substrate with high specificity (Figure S2A). As expected, SAQD-labeled Rad4-Rad23 formed arrays of nonmotile complexes when introduced into flow cells in the presence of Fl-dT DNA tightropes (Figure 3A–B and Movie S4), with inter-particle spacing being integer-multiples of 2 kbp (Figure S3).…”

Section: Resultsmentioning

confidence: 99%

Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process

et al. 2016

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SUMMARY Nucleotide excision repair (NER) is an evolutionarily conserved mechanism that processes helix-destabilizing and/or -distorting DNA lesions, such as UV-induced photoproducts. Here, we investigate the dynamic protein-DNA interactions during the damage recognition step using single-molecule fluorescence microscopy. Quantum dot-labeled Rad4-Rad23 (yeast XPC-RAD23B ortholog) forms nonmotile complexes or conducts a one-dimensional search via either random diffusion or constrained motion. Atomic force microcopy analysis of Rad4 with the β-hairpin domain 3 (BHD3) deleted reveals that this motif is non-essential for damage-specific binding and DNA bending. Furthermore, we find that deletion of seven residues in the tip of β-hairpin in BHD3 increases Rad4-Rad23 constrained motion at the expense of stable binding at sites of DNA lesions, without diminishing cellular UV resistance or photoproduct repair in vivo. These results suggest a distinct intermediate in the damage recognition process during NER, allowing dynamic DNA damage detection at a distance.

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“…For this study FITC-dU containing duplexes of different lengths (15mer ODN11 and 30mer ODN10, see Table S1) were used, in which the fluorescein, needed for the detection, functions as the lesion. It is well known that Rad14 binds the fluorescein-containing base with significant affinity (see below) (45). Formation of the lesion recognition complex with FITC-dU and the full length proteins Rad14fl and XPAfl was demonstrated by a gel shift experiment (Fig.…”

Section: Analysis Of the (Rad14) 2 -Dna Complex In Solutionmentioning

confidence: 99%

Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

Koch

Kuper

Gasteiger

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Nucleotide excision repair (NER) is responsible for the removal of a large variety of structurally diverse DNA lesions. Mutations of the involved proteins cause the xeroderma pigmentosum (XP) cancer predisposition syndrome. Although the general mechanism of the NER process is well studied, the function of the XPA protein, which is of central importance for successful NER, has remained enigmatic. It is known, that XPA binds kinked DNA structures and that it interacts also with DNA duplexes containing certain lesions, but the mechanism of interactions is unknown. Here we present two crystal structures of the DNA binding domain (DBD) of the yeast XPA homolog Rad14 bound to DNA with either a cisplatin lesion (1,2-GG) or an acetylaminofluorene adduct (AAF-dG). In the structures, we see that two Rad14 molecules bind to the duplex, which induces DNA melting of the duplex remote from the lesion. Each monomer interrogates the duplex with a β-hairpin, which creates a 13mer duplex recognition motif additionally characterized by a sharp 70°DNA kink at the position of the lesion. Although the 1,2-GG lesion stabilizes the kink due to the covalent fixation of the crosslinked dG bases at a 90°angle, the AAF-dG fully intercalates into the duplex to stabilize the kinked structure.

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Comparative Analysis of Interaction of Human and Yeast DNA Damage Recognition Complexes with Damaged DNA in Nucleotide Excision Repair

Cited by 31 publications

References 36 publications

The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process

Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

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