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Results for “Excision Repair”

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PubMed1995

Mechanisms of DNA damage recognition in mammalian nucleotide excision repair.

The ability of nucleotide excision repair (NER) to process multiple forms of DNA damage is highly dependent on the precision by which DNA modifications are located in the genome. Studies of mammalian NER have shown that this system eliminates a wide range of chemically and structurally distinct DNA lesions whereby some types of damage are repaired at higher rates than others. Although the biochemical basis for this broad but heterogeneous response to DNA damage is poorly understood, recent discoveries in closely related areas of DNA metabolism indicate that selectivity for specific sites is achieved through the assembly of nucleoprotein complexes, in which DNA is frequently bent and unwound. In many cases, selectivity may be further enhanced by the action of specialized DNA helicases. These principles in protein-DNA recognition suggest a hypothetical mechanism of damage recognition that accounts for the wide substrate range of mammalian NER and also accommodates its preference for specific DNA lesions.

Animals↗

PubMed2003

Lack of involvement of nucleotide excision repair gene polymorphisms in colorectal cancer.

DNA repair has an essential role in protecting the genome from damage by endogenous and environmental agents. Polymorphisms in DNA repair genes and differences in repair capacity between individuals have been widely documented. For colorectal cancer, the loss of mismatch repair gene activity is a key genetic determinant. Nucleotide excision repair (NER), recombination repair (RR) and base excision repair (BER) pathways have critical roles in protection against other cancers, and we wished to investigate their role in colorectal cancer. We have compared the frequency of polymorphisms in the NER genes, XPD, XPF, XPG, ERCC1; in the BER gene, XRCC1; and in the RR gene, XRCC3; in colorectal cancer patients and in a control group. No significant associations were found for any of the NER gene polymorphisms or for the XRCC1 polymorphism. The C allele (position 18067) of the XRCC3 gene was weakly but significantly associated with colorectal cancer (odds ratio 1.52, 95% confidence interval 1.04-2.22, P=0.03). For all patients who were heterozygous for any of the repair genes studied, tumour tissue was investigated for loss of heterozygosity (LOH). Only one example of LOH was found for all the genes examined. From the association and LOH data, we conclude that these genes do not have an important role in protection against colorectal carcinogenesis.

Cell Transformation, Neoplastic↗

PubMed1993

DNA excision repair as a component of adaptation to low doses of ionizing radiation in Escherichia coli.

In this study we examined whether or not DNA excision repair is a component of adaptation induced by very low-dose ionizing radiation in Escherichia coli, a well-characterized prokaryote, and investigated the relationship between enhanced excision repair and the SOS response. Competent E. coli cells were irradiated using low doses (0.1-10 Gy) of 137Cs gamma-rays, allowed to recover for 2 h and were then transformed using pUC18 DNA containing approximately 22 oxidized thymine residues (thymine glycols) per molecule. Successful transformants were identified by recovery of plasmid-borne ampicillin resistance and the resulting data (colony counts) were used to calculate ratios of plasmid recovery in irradiated to control cells. Results showed that cells irradiated with very low doses (0.1-0.5 Gy) were up to 30-40% more efficient at utilizing thymine glycol-containing pUC18 DNA. The enhanced excision repair by very low doses (< 0.5 Gy) of gamma-rays was shown to be independent of the recA-controlled SOS response in experiments using recA cells or cells carrying recA-lacZ gene fusions. The stimulating effect in AB1157 prototype cells were subsequently confirmed using a DNA precipitation assay in which DNA incision events were accumulated by inhibiting DNA ligation with ethidium bromide. Our data suggest that there seems to be narrow 'windows' of dose-effect for the induction of SOS-independent DNA excision repair. Being similar to mammalian cell studies, the dose range for this effect was about 200-fold less than D37 for radiation survival.

Adaptation, Physiological↗

PubMed1997

DNA excision repair profiles of normal and leukemic human lymphocytes: functional analysis at the single-cell level.

Recent evidence has linked cellular DNA repair capacity to the chemosensitivity of cancer cells to alkylating agents. Using single-cell gel electrophoresis ("comet assay"), we have analyzed the induction and differential processing of DNA damage in human lymphocytes derived from healthy donors and from patients with chronic lymphatic leukemia (CLL) after exposure to N-ethyl-N-nitrosourea in vitro. The extent of comet formation in lymphocytes after N-ethyl-N-nitrosourea exposure appears to depend predominantly on the processing of DNA repair intermediates, because strand breaks in plasmid DNA were not induced by ethylation before the addition of nuclear proteins. Although the initial level of a specific alkylation product (O6-ethylguanine) in nuclear DNA was uniform, different dose-response curves were obtained for the comet size in individual cell samples immediately after exposure, with small intercellular variation. The individual kinetics of DNA repair varied significantly between specimens derived from both healthy individuals and CLL patients; for the DNA repair half-time (t1/2), large difference was found. Pretreatment of cells with methoxyamine as a DNA repair modifier blocking the base excision repair pathway revealed a quite similar extent of base excision repair-independent DNA incision in almost all normal lymphocyte samples. In contrast, this portion varied relatively and absolutely to a great extent among individual samples of CLL lymphocytes, suggesting a loss of stringent control of DNA repair processes in these cells. The comet assay can thus be used to gain information about interindividual variation in the efficiency of different DNA repair processes in small samples of normal cells and their malignant counterparts.

Carcinogens↗

PubMed2000

Alternative excision repair pathway of UV-damaged DNA in Schizosaccharomyces pombe operates both in nucleus and in mitochondria.

The fission yeast, Schizosaccharomyces pombe, possesses a UV-damaged DNA endonuclease-dependent excision repair (UVER) pathway in addition to nucleotide excision repair pathway for UV-induced DNA damage. We examined cyclobutane pyrimidine dimer removal from the myo2 locus on the nuclear genome and the coI locus on the mitochondrial genome by the two repair pathways. While nucleotide excision repair repairs damage only on the nuclear genome, UVER efficiently removes cyclobutane pyrimidine dimers on both nuclear and mitochondrial genomes. The ectopically expressed wild type UV-damaged DNA endonuclease was localized to both nucleus and mitochondria, while modifications of N-terminal methionine codons restricted its localization to either of two organelles, suggesting an alternative usage of multiple translation initiation sites for targeting the protein to different organelles. By introducing the same mutations into the chromosomal copy of the uvde(+) gene, we selectively inactivated UVER in either the nucleus or the mitochondria. The results of UV survival experiments indicate that although UVER efficiently removes damage on the mitochondrial genome, UVER in the mitochondria hardly contributes to UV resistance of S. pombe cells. We suggest a possible UVER function in mitochondria as a backup system for other UV damage tolerance mechanisms.

Cell Nucleus↗

PubMed1997

Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway.

Mutagenic abasic (AP) sites are generated directly by DNA-damaging agents or by DNA glycosylases acting in base excision repair. AP sites are corrected via incision by AP endonucleases, removal of deoxyribose 5-phosphate, repair synthesis, and ligation. Mammalian DNA polymerase beta (Polbeta) carries out most base excision repair synthesis and also can excise deoxyribose 5-phosphate after AP endonuclease incision. Yeast two-hybrid analysis now indicates protein-protein contact between Polbeta and human AP endonuclease (Ape protein). In vitro, binding of Ape protein to uncleaved AP sites loads Polbeta into a ternary complex with Ape and the AP-DNA. After incision by Ape, only Polbeta exhibits stable DNA binding. Kinetic experiments indicated that Ape accelerates the excision of 5'-terminal deoxyribose 5-phosphate by Polbeta. Thus, the two central players of the base excision repair pathway are coordinated in sequential reactions.

DNA Polymerase I↗

PubMed2006

The role of XRCC1 polymorphisms in base excision repair of etheno-DNA adducts in French vinyl chloride workers.

OBJECTIVES: The purpose of this study was to examine whether polymorphisms in the XRCC1 DNA-repair protein can affect the base excision repair capacity to remove etheno-DNA adducts induced by vinyl chloride exposure that account for the occurrence of mutant biomarkers of effect seen in exposed workers. MATERIALS AND METHODS: Using polymerase chain reaction-restriction fragment length polymorphism and fluorescence polarization techniques, we examined the effect of three x-ray cross complementing-1 protein polymorphisms, at codons 194, 280 and 399, on the occurrence of mutant biomarkers in ras-p21 and p53 induced by vinyl chloride exposure in a cohort of 211 French vinyl chloride workers to correlate differences in genotype with differences in the presence of these biomarkers. Also, cell cultures of lymphoblast lines from a pair of individuals, one homozygous wild-type and one homozygous variant for the codon 399 polymorphism, were exposed to the reactive intermediate of vinyl chloride, and, using an enzyme-linked immunosorbent assay, levels of etheno-DNA adducts generated and repaired were measured and compared. RESULTS: After adjusting for age, smoking, alcohol drinking and cumulative vinyl chloride exposure, compared to workers who were homozygous wild-type for all alleles, the odds ratio for the presence of either biomarker increased to 2.0 (95% CI: 1.0-3.9) for workers with any one variant allele and to 2.4 (95% CI: 1.1-5.2) for workers with more than one variant allele. Data from the cell culture experiments indicating that repair of etheno-DNA adducts is considerably better in wild-type cells compared to polymorphic cells were supportive of the epidemiologic results. CONCLUSIONS: This study provides further evidence that polymorphisms in XRCC1 can be an important biomarker of susceptibility in populations exposed to agents that produce damage removed by base excision repair.

Adult↗

PubMed2001

Repair of triplex-directed DNA alkylation by nucleotide excision repair.

Triplex-forming oligonucleotides (TFOs) are being investigated as highly specific DNA binding agents to inhibit the expression of clinically relevant genes. So far, they have been shown to inhibit transcription from the HER-2/neu gene in vitro, whereas their use in vivo has been studied to a limited extent. This study uses a TFO-chlorambucil (chl) conjugate capable of forming site-specific covalent guanine adducts within the HER-2/neu promoter. We demonstrate that nucleotide excision repair (NER) represents a mechanism of cellular resistance to TFO-directed DNA alkylation. In vitro repair assays demonstrate that triplex-directed chl-guanine adducts are substrates for repair by NER competent cell extracts but not XP12BE cell extracts deficient in NER. The degree of repair is estimated by a ligation-mediated polymerase chain reaction with a pre-formed triplex in a plasmid transfected into repair competent cells, indicating that approximately 25% of the guanine adducts are removed after 24 h. These data indicate that guanine adducts from TFO-directed alkylation are a substrate for NER and that DNA repair is a significant barrier to the intracellular persistence of target gene binding by TFOs.

Alkylation↗

PubMed1995

Detection of nucleotide excision repair incisions in human fibroblasts by immunostaining for PCNA.

During nucleotide excision repair, damaged DNA is incised on both sides of a lesion and an oligomer containing the damage is excised and replaced by repair DNA synthesis. The latter step is accomplished in vitro by proteins that include the DNA polymerase accessory factor PCNA, which binds to DNA ends to initiate repair synthesis. An increased association of PCNA with nuclei occurs after UV irradiation of nonreplicating DNA in normal human fibroblasts, probably following incision of damaged DNA. This property was used to detect the catalysis of nucleotide excision repair incisions in damaged DNA in vivo, by immunostaining of quiescent human fibroblasts with the widely available PC10 antibody. We summarize here a comprehensive survey of PCNA immunostaining in repair-defective xeroderma pigmentosum (XP) cells in comparison to normal cells. XP-A and XP-G cells were completely defective in staining for PCNA 30 min after UV irradiation. This strongly suggests that XPA and XPG proteins are absolutely required in cells before any incisions can be formed in damaged DNA. XP-B, XP-C, XP-D, and XP-F cells showed an intermediate level of staining for PCNA after UV irradiation, indicative of partial incision capacity in those cells. UV-irradiated XP-E and XP-V cells showed normal PCNA immunostaining levels, consistent with evidence that the corresponding factors are not essential for the incision step of repair. The results provide further evidence for the involvement of PCNA in the repair process in vivo and give an alternative to traditional approaches for measurement of nucleotide excision repair capability.

Antibodies, Monoclonal↗

PubMed1996

The HMG-domain protein Ixr1 blocks excision repair of cisplatin-DNA adducts in yeast.

Ixr1 is a yeast HMG-domain protein which binds the major DNA adducts of the antitumor drug cisplatin. Previous work demonstrated that Saccharomyces cerevisiae cells lacking the IXR1 gene were two-fold less sensitive to cisplatin treatment than wild-type cells, and the present investigation reveals a six-fold difference in yeast having a different background. The possibility that the lower cytotoxicity of cisplatin in the ixr1 strain is the result of enhanced repair was investigated in rad1, rad2, rad4, rad6, rad9, rad10, rad14 and rad52 backgrounds. In three of the excision repair mutants, rad2, rad4 and rad14, the differential sensitivity caused by removing the Ixr1 protein was nearly abolished. This result demonstrates that the greater cisplatin resistance in the ixr1 strain is most likely a consequence of excision repair, supporting the theory that Ixr1 and other HMG-domain proteins can block repair of the major cisplatin-DNA adducts in vivo. The differential sensitivity of wild-type cells and those lacking Ixr1 persisted in the rad1 and rad10 strains, however, indicating that these two proteins act at a stage in the excision repair pathway where damage recognition is less critical. A model is proposed to account for these results, which is strongly supported recently identified functional roles for the rad excision repair gene products. A rad52 mutant was more sensitive to cisplatin than the RAD52 parental strain, which reveals that Rad52, a double-strand break repair protein, repairs cisplatin-DNA adducts, probably interstrand cross-links. A rad52 ixr1 strain was less sensitive to cisplatin than the rad52 IXR1 strain, consistent with Ixr1 not blocking repair of cisplatin adducts removed by Rad52 rad6 strains behaved similarly, except they were both substantially more sensitive to cisplatin. Interruption of the RAD9 gene, which is involved in DNA-damage-induced cell cycle arrest, had no affect on cisplatin cytotoxicity.

Antineoplastic Agents↗

PubMed1999

Detection of chromatin-bound PCNA in mammalian cells and its use to study DNA excision repair.

Compelling evidence indicates that proliferating cell nuclear antigen (PCNA) is an indispensable factor not only in DNA replication but in nucleotide excision repair (NER), alternative pathway of base excision repair (BER), and mismatch repair. The common function of PCNA in each of these is to assist in the initiation of DNA synthesis by providing a scaffolding clamp as a trimer catalyzed by RF-C at the 3'-OH terminus of a nascent DNA strand, to which DNA polymerase delta or epsilon can bind. Interestingly, DNA synthesis is reported to be ingeniously inhibited in replication, but not in NER owing to the interaction with CDKN1A (formerly known as p21/WAF1/CIP1). Furthermore, several proteins, XPG, FEN1, and DNA ligase I, recently were shown to competitively bind to the same region of PCNA, the interdomain connector loop, to which DNA polymerase delta or epsilon also binds. PCNA therefore seems to have a regulatory role in these DNA transactions. The in vitro reconstituted experimental system has been a powerful tool to obtain these lines of evidence, but another approach, immunofluorescence studies, also has been a contributor. In fact, the involvement of PCNA in DNA replication, NER, and BER has for the first time been indicated by a unique method that makes visible only in vivo chromatin-bound PCNA. The usefulness of this method and the importance of cooperative studies done with in vitro and in vivo experimental systems is discussed in terms of DNA excision repair.

Animals↗

PubMed2026

Biochemical, structural and mutational landscapes of base excision repair enzymes and cancer: from atomic resolution to tumor signatures.

PURPOSE: Base excision repair (BER) is the predominant pathway for repairing non‑bulky oxidized and alkylated DNA base lesions, and its fidelity depends on the coordinated action of lesion‑specific DNA glycosylases and downstream repair enzymes. This review aims to summarize recent structural, biochemical, and genomic insights into three base excision repair enzymes, MUTYH DNA glycosylase, NTHL1 DNA glycosylase, and DNA polymerase β. CONCLUSION: This review outlines how MUTYH, NTHL1 and DNA polymerase β protect the genome from mutagenesis, highlights major germline variants associated with disease, and synthesizes the current knowledge on the characteristic single base substitution (SBS) mutational signatures that occur when these repair enzymes are dysfunctional.

Base excision repair↗

PubMed2001

Highly efficient base excision repair (BER) in human and rat male germ cells.

The quality of germ cell DNA is critical for the fate of the offspring, yet there is limited knowledge of the DNA repair capabilities of such cells. One of the main DNA repair pathways is base excision repair (BER) which is initiated by DNA glycosylases that excise damaged bases, followed by incision of the generated abasic (AP) sites. We have studied human and rat methylpurine-DNA glycosylase (MPG), uracil-DNA glycosylase (UNG), and the major AP endonuclease (HAP1/APEX) in male germ cells. Enzymatic activities and western analyses indicate that these enzymes are present in human and rat male germ cells in amounts that are at least as high as in somatic cells. Minor differences were observed between different cellular stages of rat spermatogenesis and spermiogenesis. Repair of methylated DNA was also studied at the cellular level using the Comet assay. The repair was highly efficient in both human and rat male germ cells, in primary spermatocytes as well as round spermatids, compared to rat mononuclear blood cells or hepatocytes. This efficient BER removes frequently occurring DNA lesions that arise spontaneously or via environmental agents, thereby minimising the number of potential mutations transferred to the next generation.

Animals↗

PubMed1989

Human nucleotide excision repair in vitro: repair of pyrimidine dimers, psoralen and cisplatin adducts by HeLa cell-free extract.

We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiated DNA and the nicking is only slightly reduced when pyrimidine dimers are eliminated from the substrate by DNA photolyase. In contrast to the nicking assay, the extract gives a strong signal with UV irradiated substrate in the repair synthesis assay. The repair synthesis activity is ATP dependent and is reduced by about 50% by prior treatment of the substrate with DNA photolyase indicating that this fraction of repair synthesis is due to removal of pyrimidine dimers by nucleotide excision. Psoralen and cisplatin adducts which are known to be removed by nucleotide excision repair also elicited repair synthesis activity 5-10 fold above the background synthesis. When M13RF DNA containing a uniquely placed psoralen adduct was used in the reaction, complete repair was achieved in a fraction of molecules as evidenced by the restoration of psoralen inactivated KpnI restriction site. This activity is absent in xeroderma pigmentosum group A cells. We conclude that our cell-free extract contains the human nucleotide excision repair enzyme activity.

Cell-Free System↗

PubMed2000

Removal of oxygen free-radical-induced 5',8-purine cyclodeoxynucleosides from DNA by the nucleotide excision-repair pathway in human cells.

Exposure of cellular DNA to reactive oxygen species generates several classes of base lesions, many of which are removed by the base excision-repair pathway. However, the lesions include purine cyclodeoxynucleoside formation by intramolecular crosslinking between the C-8 position of adenine or guanine and the 5' position of 2-deoxyribose. This distorting form of DNA damage, in which the purine is attached by two covalent bonds to the sugar-phosphate backbone, occurs as distinct diastereoisomers. It was observed here that both diastereoisomers block primer extension by mammalian and microbial replicative DNA polymerases, using DNA with a site-specific purine cyclodeoxynucleoside residue as template, and consequently appear to be cytotoxic lesions. Plasmid DNA containing either the 5'R or 5'S form of 5',8-cyclo-2-deoxyadenosine was a substrate for the human nucleotide excision-repair enzyme complex. The R diastereoisomer was more efficiently repaired than the S isomer. No correction of the lesion by direct damage reversal or base excision repair was detected. Dual incision around the lesion depended on the core nucleotide excision-repair protein XPA. In contrast to several other types of oxidative DNA damage, purine cyclodeoxynucleosides are chemically stable and would be expected to accumulate at a slow rate over many years in the DNA of nonregenerating cells from xeroderma pigmentosum patients. High levels of this form of DNA damage might explain the progressive neurodegeneration seen in XPA individuals.

Base Sequence↗

PubMed1985

Deficiency of UV-induced excision repair in human thymocytes.

The capacity of human thymocytes and of differentiated lymphocytes circulating in peripheral blood to perform unscheduled DNA synthesis (a measure of nucleotide excision repair) after UV irradiation was measured by radioautographic analysis. Only 4% of immature T lymphocytes, but 68% of circulating lymphocytes exhibited unscheduled DNA synthesis. When UV sensitivity of peripheral blood lymphocytes and thymocytes from the same donor were compared, the thymocytes, in each case, were significantly more UV sensitive than were the circulating lymphocytes. Peripheral blood lymphocytes from subjects undergoing halothane and morphine anesthesia during surgery showed 56% less excision repair capacity than those from unanesthetized donors. The difference occurred in the number of cells capable of repair rather than in the extent of repair synthesis per cell. Ultraviolet-induced unscheduled DNA synthesis occurred in only 3% of the thymocytes removed from rats killed by cervical dislocation. Therefore, the deficiency of excision repair was observed in rat thymocytes which had not been affected by anesthesia or surgical trauma. Since the thymus contains more than 90% immature T-cells, our results indicate that immature T-cells are deficient in nucleotide excision repair whereas the majority of mature peripheral blood lymphocytes exhibit such repair.

Animals↗

PubMed2002

Trapping of DNA nucleotide excision repair factors by nonrepairable carcinogen adducts.

Nucleotide excision repair is part of a cellular defense system that protects genome integrity.Here, this versatile repair system was challenged with mixtures of DNA adducts that were generated to mimic the wide spectrum of bulky lesions produced by complex genotoxic insults. Probing human excision activity with substrate combinations instead of single lesions resulted in a strong bias for particular base adducts, such that the repair factors were immobilized on a small fraction of damaged DNA, whereas the simultaneous excision of other sites was suppressed. Immobilization of excision factors was also induced by nonrepairable decoy adducts, thereby revealing a mechanism of repair inhibition because of hijacking of critical subunits. Thus, the efficiency of excision repair in response to bulky carcinogen-DNA damage is dependent on an antagonistic interaction with both substrate and decoy adducts.

2-Acetylaminofluorene↗

PubMed1999

Base excision repair of oxidative DNA damage activated by XPG protein.

Oxidized pyrimidines in DNA are removed by a distinct base excision repair pathway initiated by the DNA glycosylase--AP lyase hNth1 in human cells. We have reconstituted this single-residue replacement pathway with recombinant proteins, including the AP endonuclease HAP1/APE, DNA polymerase beta, and DNA ligase III-XRCC1 heterodimer. With these proteins, the nucleotide excision repair enzyme XPG serves as a cofactor for the efficient function of hNth1. XPG protein promotes binding of hNth1 to damaged DNA. The stimulation of hNth1 activity is retained in XPG catalytic site mutants inactive in nucleotide excision repair. The data support the model that development of Cockayne syndrome in XP-G patients is related to inefficient excision of endogenous oxidative DNA damage.

Base Sequence↗