Robust Incision of Benoz[<i>a</i>]pyrene-7,8-dihyrodiol-9,10-epoxide−DNA Adducts by a Recombinant Thermoresistant Interspecies Combination UvrABC Endonuclease System

Jiang, Guo Hui; Skorvaga, Milan; Croteau, Deborah L.; Houten, Bennett Van; States, J. Christopher

doi:10.1021/bi052515e

Cited by 11 publications

(19 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…BcaUvrC and UvrC from T. maritima showed comparable DNA binding in the presence of BcaUvrB (data not shown). However, TmaUvrC has been shown previously to form a productive complex with BcaUvrB (57,59) and is more active in DNA incisions than BcaUvrC. BcaUvrC was used in the AUC and MST studies, and TmaUvrC was used in the DNA incision, AFM, MST, and BLI analyses.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Wirth

Gross

Roth

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

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...

show abstract

Section: Methodsmentioning

confidence: 99%

“…Because B. caldotenax UvrC has been described to carry out only the 5Ј incision (59), for the incision assays we used UvrC from T. maritima, which has been previously shown to interact with UvrB from B. caldotenax (57). Experiments were carried out using at least three different protein batches.…”

Section: Methodsmentioning

confidence: 99%

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Wirth

Gross

Roth

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…In a few experiments, all three UvrABC proteins were from E. coli . The UvrA Bca and UvrB Bca , as well as all of the UvrC proteins, were overexpressed in E. coli cells and purified as described by Jiang et al [51]. …”

Section: Methodsmentioning

confidence: 99%

Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

et al. 2011

Self Cite

View full text Add to dashboard Cite

Nucleotide excision repair (NER) is an important prokaryotic and eukaryotic defense mechanism that removes a large variety of structurally distinct lesions in cellular DNA. While the proteins involved are completely different, the mode of action of these two repair systems is similar, involving a cut-and-patch mechanism in which an oligonucleotide sequence containing the lesion is excised. The prokaryotic and eukaryotic NER damage-recognition factors have common structural features of β-hairpin intrusion between the two DNA strands at the site of the lesion. In the present study, we explored the hypothesis that this common β-hairpin intrusion motif is mirrored in parallel NER incision efficiencies in the two systems. We have utilized human HeLa cell extracts and the prokaryotic UvrABC proteins to determine their relative NER incision efficiencies. We report here comparisons of relative NER efficiencies with a set of stereoisomeric DNA lesions derived from metabolites of benzo[a]pyrene and equine estrogens in different sequence contexts, utilizing 21 samples. We found a general qualitative trend towards similar relative NER incision efficiencies for ~ 65% of these substrates; the other cases deviate mostly by ~ 30% or less from a perfect correlation, although several more distant outliers are also evident. This resemblance is consistent with the hypothesis that lesion recognition through β-hairpin insertion, a common feature of the two systems, is facilitated by local thermodynamic destabilization induced by the lesions in both cases. In the case of the UvrABC system, varying the nature of the UvrC endonuclease, while maintaining the same UvrA/B proteins, can markedly affect the relative incision efficiencies. These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER.

show abstract

“…Since BD conformers are highly susceptible to excision in prokaryotic 24,36 and human 16 NER assays, we investigated the population balance between MG and BD conformations in the two sequence contexts. For the thermodynamic analyses, we employed the ensembles of structures derived from the last 7.0 ns of the MD simulations, using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology 38 in the AMBER 8.0 simulation package.…”

Section: Minor Groove Conformers Are Favored In Both Duplex Sequence mentioning

confidence: 99%

“…The 10S (+)-trans-anti-[BP]-N 2 -dG adducts are known to be more susceptible to NER by prokaryotic 36 and eukaryotic 16 DNA repair factors when they are in BD rather than in MG conformations in CG*C sequence contexts. Furthermore, in the case of a 2-aminofluorene-C8-guanine adduct, BD conformations have recently been shown to manifest greater susceptibility to prokaryotic NER, as compared to orientations of the adduct in a groove of B-DNA.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair

Cai

Patel

Geacintov

et al. 2007

Journal of Molecular Biology

View full text Add to dashboard Cite

The nucleotide excision repair (NER) machinery excises a variety of bulky DNA lesions, but with varying efficiencies. The structural features of the DNA lesions that govern these differences are not well understood. An intriguing model system for studying structure-function relationships in NER is the major adduct derived from the reaction of the highly tumorigenic metabolite of benzo [a]pyrene, (+)-anti-benzo[a]pyrene diol epoxide, with the exocyclic amino group of guanine ((+)-trans-anti-[BP]-N 2 -dG, or G*). The rates of incision of the stereochemically identical lesions catalyzed by the prokaryotic UvrABC system was shown to be greater by a factor of 2.3±0.3 in the TG*T than in the CG*C sequence context [Biochemistry 46 (2007) 7006-7015]. Here we employ molecular dynamics simulations to elucidate the origin of the greater excision efficiency in the TG*T case and, more broadly, to delineate structural parameters that enhance NER. Our results show that the BP aromatic ring system is 5′-directed along the modified strand in the B-DNA minor groove in both sequence contexts. However, the TG*T modified duplex is much more dynamically flexible, featuring more perturbed and mobile Watson-Crick hydrogen bonding adjacent to the lesion, a greater impairment in stacking interactions, more dynamic local roll/ bending, and more minor groove flexibility. These characteristics explain a number of experimental observations concerning the (+)-trans-anti-[BP]-N 2 -dG adduct in double-stranded DNA with the TG*T sequence context: its conformational heterogeneity in NMR solution studies, its highly flexible bend, and its lower thermal stability. By contrast, the CG*C modified duplex is characterized by a single BP conformation and a rigid bend. While current recognition models of bulky lesions by NER factors have stressed the importance of impaired Watson-Crick pairing/ stacking and bending, our results highlight the likelihood of an important role for the local dynamics in the vicinity of the lesion.

show abstract

Robust Incision of Benoz[a]pyrene-7,8-dihyrodiol-9,10-epoxide−DNA Adducts by a Recombinant Thermoresistant Interspecies Combination UvrABC Endonuclease System

Cited by 11 publications

References 37 publications

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair

Contact Info

Product

Resources

About