DNA Base Excision Repair Protein Research Articles

Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation.

The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates the completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus-specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.

Photon versus proton neurotoxicity: Impact on mitochondrial function and 8-OHdG base-excision repair mechanism in human astrocytes

This study assesses and compares the neurotoxic effects of proton and photon radiation on mitochondrial function and DNA repair capabilities of human astrocytes. Human astrocytes received either proton (0.5 Gy and 3 Gy), photon (0.5 Gy and 3 Gy), or sham-radiation treatment. The mRNA expression level of the DNA repair protein OGG1 was determined via RT-qPCR. The levels of 8-OHdG in the cell media were measured via ELISA. Real-time kinetic analysis of extracellular oxygen consumption rates was performed to assess mitochondrial function. Radiation-induced changes in mitochondrial mass and oxidative activity were assessed using fluorescent imaging with MitoTracker™ Green FM and MitoTracker™ Orange CM-H2TMRos dyes respectively. PCR was used to quantify the alteration in the mitochondrial DNA content, measured as the mitochondrial to nuclear DNA ratio. A significant increase in mitochondrial mass and levels of reactive oxygen species was observed after radiation treatment. Additionally, real-time PCR analysis indicated a significant depletion of mitochondrial DNA content in the irradiated cells when compared to the control. This was accompanied by a decreased gene expression of the DNA base-excision repair protein OGG1 and reduced clearance of 8-OHdG adducts from the genome. Photon radiation treatment was associated with a more detrimental cellular impact when compared to the same dose of proton radiation. These results are indicative of a radiation-induced dose-dependent decrease in mitochondrial function, an increase in senescence and astrogliosis, and impairment of the DNA repair capabilities in healthy glial cells. Photon irradiation was associated with a more significant disruption in mitochondrial function and base-excision repair mechanisms in vitro in comparison to proton treatment.

Functional Role of N-Terminal Extension of Human AP Endonuclease 1 In Coordination of Base Excision DNA Repair via Protein-Protein Interactions.

Human apurinic/apyrimidinic endonuclease 1 (APE1) has multiple functions in base excision DNA repair (BER) and other cellular processes. Its eukaryote-specific N-terminal extension plays diverse regulatory roles in interaction with different partners. Here, we explored its involvement in interaction with canonical BER proteins. Using fluorescence based-techniques, we compared binding affinities of the full-length and N-terminally truncated forms of APE1 (APE1NΔ35 and APE1NΔ61) for functionally and structurally different DNA polymerase β (Polβ), X-ray repair cross-complementing protein 1 (XRCC1), and poly(adenosine diphosphate (ADP)-ribose) polymerase 1 (PARP1), in the absence and presence of model DNA intermediates. Influence of the N-terminal truncation on binding the AP site-containing DNA was additionally explored. These data suggest that the interaction domain for proteins is basically formed by the conserved catalytic core of APE1. The N-terminal extension being capable of dynamically interacting with the protein and DNA partners is mostly responsible for DNA-dependent modulation of protein–protein interactions. Polβ, XRCC1, and PARP1 were shown to more efficiently regulate the endonuclease activity of the full-length protein than that of APE1NΔ61, further suggesting contribution of the N-terminal extension to BER coordination. Our results advance the understanding of functional roles of eukaryote-specific protein extensions in highly coordinated BER processes.

Abstract P-21: The Oligomeric State of Base Excision DNA Repair Proteins and Their Complexes Explored by Dynamic Light Scattering

Abstract P-21: The Oligomeric State of Base Excision DNA Repair Proteins and Their Complexes Explored by Dynamic Light Scattering

Dynamic light scattering study of base excision DNA repair proteins and their complexes

Base excision repair (BER) involves many enzymes acting in a coordinated fashion at the most common types of DNA damage. The coordination is facilitated by interactions between the enzymes and accessory proteins, X-ray repair cross-complementing protein 1 (XRCC1) and poly(ADP-ribose) polymerase 1 (PARP1). Here we use dynamic light scattering (DLS) technique to determine the hydrodynamic sizes of several BER enzymes and proteins, DNA polymerase β (Polβ), apurinic/apyrimidinic endonuclease 1 (APE1), tyrosyl-DNA phosphodiesterase 1 (TDP1), XRCC1 and PARP1, present alone or in the equimolar mixtures with each other. From the DLS data combined with glutaraldehyde cross-linking experiments and previous quantitative binding data the oligomeric states of BER proteins and their complexes are estimated. All the proteins have been proposed to form homodimers upon their self-association. The most probable oligomerization state of the binary complexes formed by PARP1 with various proteins is a heterotetramer. The oligomerization state of the binary complexes formed by XRCC1 varies from heterodimer to heterotetramer, depending on the partner. The DLS technique is applied for the first time to measure the hydrodynamic sizes of PARP1 molecules covalently bound with poly(ADP-ribose) (PAR) synthesized upon the automodification reaction. PARP1 has been detected to form huge conglomerates stabilized by Mg2+ coordinated bonds with PAR polymers.

Interplay between base excision repair protein XRCC1 and ALDH2 predicts overall survival in lung and liver cancer patients

BackgroundTo deliver efficacious personalised cancer treatment, it is essential to characterise the cellular metabolism as well as the genetic stability of individual tumours. In this study, we describe a new axis between DNA repair and detoxification of aldehyde derivatives with important implications for patient prognosis and treatment.MethodsWestern blot and qPCR analyses were performed in relevant non-transformed and cancer cell lines from lung and liver tissue origin in combination with bioinformatics data mining of The Cancer Genome Atlas database from lung and hepatocellular cancer patients.ResultsUsing both biochemical and bioinformatics approaches, we revealed an association between the levels of expression of the aldehyde detoxifying enzyme aldehyde dehydrogenase 2 (ALDH2) and the key DNA base excision repair protein XRCC1. Across cancer types, we found that if one of the corresponding genes exhibits a low expression level, the level of the other gene is increased. Surprisingly, we found that low ALDH2 expression levels associated with high XRCC1 expression levels are indicative for a poor overall survival, particularly in lung and liver cancer patients. In addition, we found that Mithramycin A, a XRCC1 expression inhibitor, efficiently kills cancer cells expressing low levels of ALDH2.ConclusionsOur data suggest that lung and liver cancers require efficient single-strand break repair for their growth in order to benefit from a low aldehyde detoxification metabolism. We also propose that the ratio of XRCC1 and ALDH2 levels may serve as a useful prognostic tool in these cancer types.

DNA base excision repair proteins APE-1 and XRCC-1 are overexpressed in oral tongue squamous cell carcinoma.

DNA repair systems play a critical role in protecting the human genome from damage caused by carcinogens. Modifications in DNA repair genes may be responsible for tumor development and resistance of malignant cells to chemotherapeutic agents. The major pathway for oxidative DNA damage repair is the base excision repair pathway. This study aimed to assess the immunoexpression of DNA repair proteins APE-1 and XRCC-1 and its association with clinical, histologic, and survival parameters in oral tongue squamous cell carcinoma, to investigate a possible role for those proteins in tumor behavior. The expression of APE-1 and XRCC-1 was evaluated by immunohistochemistry in 82 cases of oral tongue squamous cell carcinoma. Histopathological grading was performed for each case. Pearson's chi-square and Fisher's exact tests were used to determine the association between protein expressions and clinicopathological features of tumors, whereas Kaplan-Meier curves and Cox regression were used to analyze disease-specific and disease-free survival. Statistical significance was set at P ≤ 0.05. APE-1 was highly expressed in the nucleus and cytoplasm in 64.6% of cases, and XRCC-1 showed overexpression only in the nucleus in 61% of cases. High expression of XRCC-1 was significantly associated with tumors at early clinical stages (I and II, P < 0.01) and nodal status (P = 0.03). Both proteins were not associated with other clinical parameters, histopathological grading, or survival. DNA base excision repair proteins APE-1 and XRCC-1 are upregulated in oral tongue squamous cell carcinoma, and XRCC-1 expression is associated with better clinical staging and nodal status.

Abstract P5-08-17: A study of c-Jun N-terminal kinase (JNK) and c-Jun as biomarkers in early breast cancer

Abstract Background The AP-1 transcription factor c-Jun is a key downstream target of c-Jun N-terminal kinase (JNK) which mediates intracellular signalling associated with a variety of cellular functions. The JNK pathway in breast cancer (BC) can be attenuated via loss of function mutations in MAPK kinases as well as via PIK3CA mutations; however, there is contradictory information about the role of JNK pathway and its clinical implications in BC. Methods In the current study, the clinicopathological implications of JNK and JUN mRNA expressions were evaluated in multiple independent BC datasets: a) Training-set (Uppsala cohort; n=249), b) Test-set (human genome atlas database; n=540), c) External validation-set (METABRIC cohort; n=1952) and d) Multicentre pooled databases (n=5530). The clinicopathological associations of their phosphorylated proteins (p-Jnk and p-c-Jun) were assessed in the Nottingham Tenovus Primary BC Series (n= 1650) and in an ER negative cohort (n=450). Results Both JNK and c-JUN mRNA high expressions were significantly associated with PAM50-Luminal A and ER+/HER2-/low proliferation molecular BC subtypes, tubular/lobular types, and integrative molecular clusters 4 (IntClust.4), ps&amp;lt;0.001. Whereas BC that had both low JNK and c-JUN mRNA, were significantly associated with large tumour size, high grade, absence of hormonal receptors (HR), HER2 overexpression, PAM50 HER2 and PAM50 Basal molecular subtypes, and IntClust.1, 9 and 10 BCs; ps&amp;lt;0.001. There was a significant positive correlations between p-Jnk and p-c-Jun protein levels (p&amp;lt;0.0001), however; our data suggested that differential p-Jnk/p-c-Jun expression may influence BC phenotypes. BC with p-Jnk-ve/p-c-Jun-ve were associated with the most aggressive phenotypes including largest tumour size, highest grade, lympho-vascular invasion, absence of HR, basal-like-phenotype, HER2 overexpression, and loss of double strand , single stand and base excision DNA repair proteins (ps&amp;lt;0.0001). In addition p-Jnk-ve/ pc-Jun-ve phenotype was associated with the lowest levels of p-38, ATF2, and p-ATF2; ps&amp;lt;0.001. Interestingly, low levels of either c-JUN-mRNA or pc-Jun protein, was associated with, PAM50-luminal B, epithelial mesenchymal transition and TP53 mutation and loss of its downstream proteins such as MDM2, MDM4, Bcle2 and p21; ps&amp;lt;0.05. JNK+ (mRNA and p-Jnk) and c-JUN+ (mRNA and p-c-Jun) individually were associated with prolonged BC specific survival (ps&amp;lt;0.001). Multivariate cox regression models that included other validated prognostic factors and therapies revealed that c-JUN-mRNA (Uppsala: p=0.005 and METABIRIC: p=0.036) and p-c-Jun (HR: 0.69; 95% CI = 0.55-0.88; p=0.002) were independently associated with clinical outcome. Furthermore, in ER+ high risk BC, exposure to tamoxifen was associated with decreased risk of death from BC in those patients with p-c-Jun-ve BC (HR: 0.65; 95% CI: 0.45-0.95; p=0.025). Conclusion JNK and c-JUN mRNA as well as p-Jnk and p-c-Jun protein levels are associated with luminal BC, with p-c-Jun being found to be an independent prognostic factor. The interaction between p-Jnk, p-c-Jun and TP53 mutation could predict response to endocrine therapy in ER+ BC. The role of the transcriptionally active form of c-JUN warrants further investigation with regard to its role in BC. Citation Format: Palmieri C, Rudraraju B, Giannoudis A, Moore D, Shaw J, Chan S, Ellis IO, Caldas C, Coombes RC, Carroll JS, Ali S, Abdel-Fatah TMA. A study of c-Jun N-terminal kinase (JNK) and c-Jun as biomarkers in early breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-08-17.

APE1, the DNA base excision repair protein, regulates the removal of platinum adducts in sensory neuronal cultures by NER

Peripheral neuropathy is one of the major side effects of treatment with the anticancer drug, cisplatin. One proposed mechanism for this neurotoxicity is the formation of platinum adducts in sensory neurons that could contribute to DNA damage. Although this damage is largely repaired by nuclear excision repair (NER), our previous findings suggest that augmenting the base excision repair pathway (BER) by overexpressing the repair protein APE1 protects sensory neurons from cisplatin-induced neurotoxicity. The question remains whether APE1 contributes to the ability of the NER pathway to repair platinum-damage in neuronal cells. To examine this, we manipulated APE1 expression in sensory neuronal cultures and measured Pt-removal after exposure to cisplatin. When neuronal cultures were treated with increasing concentrations of cisplatin for two or three hours, there was a concentration-dependent increase in Pt-damage that peaked at four hours and returned to near baseline levels after 24h. In cultures where APE1 expression was reduced by ∼80% using siRNA directed at APE1, there was a significant inhibition of Pt-removal over eight hours which was reversed by overexpressing APE1 using a lentiviral construct for human wtAPE1. Overexpressing a mutant APE1 (C65 APE1), which only has DNA repair activity, but not its other significant redox-signaling function, mimicked the effects of wtAPE1. Overexpressing DNA repair activity mutant APE1 (226+177APE1), with only redox activity was ineffective suggesting it is the DNA repair function of APE1 and not its redox-signaling, that restores the Pt-damage removal. Together, these data provide the first evidence that a critical BER enzyme, APE1, helps regulate the NER pathway in the repair of cisplatin damage in sensory neurons.

DNA polymerase β deficiency is linked to aggressive breast cancer: A comprehensive analysis of gene copy number, mRNA and protein expression in multiple cohorts

Short arm of chromosome 8 is a hot spot for chromosomal breaks, losses and amplifications in breast cancer. Although such genetic changes may have phenotypic consequences, the identity of candidate gene(s) remains to be clearly defined. Pol β gene is localized to chromosome 8p12-p11 and encodes a key DNA base excision repair protein. Pol β may be a tumour suppressor and involved in breast cancer pathogenesis. We conducted the first and the largest study to comprehensively evaluate pol β in breast cancer. We investigated pol β gene copy number changes in two cohorts (n = 128 &n = 1952), pol β mRNA expression in two cohorts (n = 249 &n = 1952) and pol β protein expression in two cohorts (n = 1406 &n = 252). Artificial neural network analysis for pol β interacting genes was performed in 249 tumours. For mechanistic insights, pol β gene copy number changes, mRNA and protein levels were investigated together in 128 tumours and validated in 1952 tumours. Low pol β mRNA expression as well as low pol β protein expression was associated high grade, lymph node positivity, pleomorphism, triple negative, basal-like phenotypes and poor survival (ps < 0.001). In oestrogen receptor (ER) positive sub-group that received tamoxifen, low pol β protein remains associated with aggressive phenotype and poor survival (ps < 0.001). Artificial neural network analysis revealed ER as a top pol β interacting gene. Mechanistically, there was strong positive correlation between pol β gene copy number changes and pol β mRNA expression (p < 0.0000001) and between pol β mRNA and pol β protein expression (p < 0.0000001). This is the first study to provide evidence that pol β deficiency is linked to aggressive breast cancer and may have prognostic and predictive significance in patients.

275 Targeting XRCC1 (X-ray Repair Cross-complementing Gene 1), a Key DNA Base Excision Repair Protein for Personalized Therapy in Breast and Ovarian Cancer

275 Targeting XRCC1 (X-ray Repair Cross-complementing Gene 1), a Key DNA Base Excision Repair Protein for Personalized Therapy in Breast and Ovarian Cancer

Impact of DNA polymorphisms in key DNA base excision repair proteins on cancer risk

Genetic variation in DNA repair genes can modulate DNA repair capacity and may be related to cancer risk. However, study findings have been inconsistent. Inheritance of variant DNA repair genes is believed to influence individual susceptibility to the development of environmental cancer. Reliable knowledge on which the base excision repair (BER) sequence variants are associated with cancer risk would help elucidate the mechanism of cancer. Given that most of the previous studies had inadequate statistical power, we have conducted a systematic review on sequence variants in three important BER proteins. Here, we review published studies on the association between polymorphism in candidate BER genes and cancer risk. We focused on three key BER genes: 8-oxoguanine DNA glycosylase (OGG1), apurinic/apyrimidinic endonuclease (APE1/APEX1) and x-ray repair cross-complementing group 1 (XRCC1). These specific DNA repair genes were selected because of their critical role in maintaining genome integrity and, based on previous studies, suggesting that single-nucleotide polymorphisms (SNPs) in these genes have protective or deleterious effects on cancer risk. A total of 136 articles in the December 13, 2010 MEDLINE database (National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/pubmed/) reporting polymorphism in OGG1, XRCC1 or APE1 genes were analyzed. Many of the reported SNPs had diverse association with specific human cancers. For example, there was a positive association between the OGG1 Ser326Cys variant and gastric and lung cancer, while the XRCC1 Arg399Gln variant was associated with reduced cancer risk. Gene-environment interactions have been noted and may be important for colorectal and lung cancer risk and possibly other human cancers.

HMGN1 Protein Regulates Poly(ADP-ribose) Polymerase-1 (PARP-1) Self-PARylation in Mouse Fibroblasts

In mammalian cells, the nucleosome-binding protein HMGN1 (high mobility group N1) affects the structure and function of chromatin and plays a role in repair of damaged DNA. HMGN1 affects the interaction of DNA repair factors with chromatin and their access to damaged DNA; however, not all of the repair factors affected have been identified. Here, we report that HMGN1 affects the self-poly(ADP-ribosyl)ation (i.e., PARylation) of poly(ADP-ribose) polymerase-1 (PARP-1), a multifunctional and abundant nuclear enzyme known to recognize DNA lesions and promote chromatin remodeling, DNA repair, and other nucleic acid transactions. The catalytic activity of PARP-1 is activated by DNA with a strand break, and this results in self-PARylation and PARylation of other chromatin proteins. Using cells obtained from Hmgn1(-/-) and Hmgn1(+/+) littermate mice, we find that in untreated cells, loss of HMGN1 protein reduces PARP-1 self-PARylation. A similar result was obtained after MMS treatment of these cells. In imaging experiments after low energy laser-induced DNA damage, less PARylation at lesion sites was observed in Hmgn1(-/-) than in Hmgn1(+/+) cells. The HMGN1 regulation of PARP-1 activity could be mediated by direct protein-protein interaction as HMGN1 and PARP-1 were found to interact in binding assays. Purified HMGN1 was able to stimulate self-PARylation of purified PARP-1, and in experiments with cell extracts, self-PARylation was greater in Hmgn1(+/+) than in Hmgn1(-/-) extract. The results suggest a regulatory role for HMGN1 in PARP-1 activation.

Abstract B55: Glioblastoma xenografts obtained from patient derived cancer stem cells preserve the heterogeneous response to targeted therapy

Abstract Molecular and signaling pathway heterogeneity contributes to the poor prognosis and high recurrence rate after therapy prevalent for glioblastoma (GBM) patients. Our goal was to test response to pharmacological agents targeting signaling pathways deregulated in glioblastomas: mTOR, RAF/MEK/ERK, VEGFR-2/PDGFRbeta, in preclinical models that use cancer stem cells to preserve the molecular signatures and heterogeneity characteristic of GBMs. Response to the DNA alkylating agent temozolomide (TMZ), used in the standard of care of GBMs, was assessed and correlated with the 06-methylguanine-DNA methyltransferase (MGMT) promoter methylation status, a known predictive biomarker. The efficacy of targeting the base-excision DNA repair protein poly (ADP-ribose) polymerase (PARP) in potentiating TMZ therapy was tested. Neurosphere cultures enriched in cancer stem cells were obtained from four GBM tumors resected at our institution, three from first surgery and one from a post-treatment recurrence. Neurosphere cells were orthotopically implanted in nude mice. TMZ (Schering-Plough), the PI3K/mT0R dual inhibitor BEZ-235 (Novartis), the PARP inhibitor ABT-888 (Abbott Laboratories), and the multi-kinase inhibitor Sorafenib Tosylate (BAY43-9006, Nexavar), which blocks RAF kinase and the VEGFR-2/PDGFRbeta signaling cascade, were tested as part of the Ivy Genomics-Based Medicine Consortium. For the chemoprofiling studies, mice were implanted with each GBM neurosphere line, and divided into treatment cohorts. Drugs were administered 5 days/week intragastrically, for 4 weeks (BEZ-235, Sorafenib and control), or 2 cycles of 1 week each (TMZ and TMZ/ABT-888). Animals were sacrificed when moribund and brain tissue was harvested for molecular profiling and immunohistochemistry. Kaplan-Meier survival curves were compared by log-rank test to evaluate response to treatment. TMZ monotherapy significantly increased survival of xenografts derived from treatment naïve tumors with methylated MGMT promoter. The PARP inhibitor in combination to TMZ did not further improve survival for this cohort. TMZ treatment had no significant effect in survival for the xenografts obtained from the glioblastoma with unmethylated MGMT promoter, but the PARP inhibitor significantly potentiated TMZ for this line. As monotherapy, both the multi-kinase inhibitor Sorafenib and the pan-PI3K/mTOR inhibitor BEZ-235 were effective for one of the four lines. Xenografts derived from the recurrent, previously treated tumor, did not exhibited a significant response to the regimens tested. Improved design of pre-clinical studies using patient derived cancer stem cells will accelerate the pace of translational research, allowing for biomarker identification and testing of targeted agents currently under clinical investigation in animal models that preserve the molecular signatures and heterogeneity of GBMs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B55.

Intestinal Inflammation and Cancer

Patients with ulcerative colitis and Crohn's disease are at increased risk for developing colorectal cancer (CRC). Chronic inflammation is believed to promote carcinogenesis. The risk for colon cancer increases with the duration and anatomic extent of colitis and presence of other inflammatory disorders (such as primary sclerosing cholangitis), whereas it decreases when patients take drugs to reduce inflammation (such as mesalamine and steroids). The genetic features that lead to sporadic CRC-chromosome instability, microsatellite instability, and DNA hypermethylation-also occur in colitis-associated CRC. Unlike the normal colonic mucosa, cells of the inflamed colonic mucosa have these genetic alterations before there is any histologic evidence of dysplasia or cancer. The reasons for these differences are not known, but oxidative stress is likely to be involved. Reactive oxygen and nitrogen species produced by inflammatory cells can affect regulation of genes that encode factors that prevent carcinogenesis (such as p53, DNA mismatch repair proteins, and DNA base excision-repair proteins), transcription factors (such as nuclear factor-κB), or signaling proteins (such as cyclooxygenases). Administration of agents that cause colitis in healthy rodents or genetically engineered, cancer-prone mice accelerates development of colorectal tumors. Mice genetically prone to inflammatory bowel disease also develop CRC, especially in the presence of bacterial colonization. Individual components of the innate and adaptive immune response have also been implicated in carcinogenesis. These observations offer compelling support for the role of inflammation in colon carcinogenesis.

Methylation-independent DNA Binding Modulates Specificity of Repressor of Silencing 1 (ROS1) and Facilitates Demethylation in Long Substrates

DNA cytosine methylation is an epigenetic mark that promotes gene silencing and performs critical roles during reproduction and development in both plants and animals. The genomic distribution of DNA methylation is the dynamic outcome of opposing methylation and demethylation processes. In plants, active demethylation occurs through a base excision repair pathway initiated by 5-methycytosine (5-meC) DNA glycosylases of the REPRESSOR OF SILENCING 1 (ROS1)/DEMETER (DME) family. To gain insight into the mechanism by which Arabidopsis ROS1 recognizes and excises 5-meC, we have identified those protein regions that are required for efficient DNA binding and catalysis. We have found that a short N-terminal lysine-rich domain conserved in members of the ROS1/DME family mediates strong methylation-independent binding of ROS1 to DNA and is required for efficient activity on 5-meC.G, but not for T.G processing. Removal of this domain does not significantly affect 5-meC excision from short molecules, but strongly decreases ROS1 activity on long DNA substrates. This region is not required for product binding and is not involved in the distributive behavior of the enzyme on substrates containing multiple 5-meC residues. Altogether, our results suggest that methylation-independent DNA binding allows ROS1 to perform a highly redundant search for efficient excision of a nondamaged, correctly paired base such as 5-meC in long stretches of DNA. These findings may have implications for understanding the evolution of structure and target specificity in DNA glycosylases.

Post-ischemic administration of peptide with apurinic/apyrimidinic endonuclease activity inhibits induction of cell death after focal cerebral ischemia/reperfusion in mice

Previous scientific research has elucidated the correlation between changes in levels of the DNA base excision repair protein, apurinic/apyrimidinic endonuclease/redox factor-1 (APE/Ref-1), and ischemic neuronal DNA damage. However, to date, no studies have addressed the question of whether treatment involving this protein's repair function may prevent ischemic neuron death in vivo. Therefore, we aimed to investigate whether treatment with APE peptide is sufficient to prevent neuron death after ischemia/reperfusion (I/R) in mice. Mice were subjected to intraluminal suture occlusion of the middle cerebral artery for 1 h followed by reperfusion. Post-ischemic treatment with the peptide containing only the APE repair functional domain was introduced intracerebroventricularly. Endonuclease activity assay and immunohistochemistry were performed. Assays of apurinic/apyrimidinic (AP) sites, single-strand DNA breaks, caspase-3 activity, and cell death were examined and quantified. We found that post-ischemic administration of the APE peptide up to 4 h after reperfusion significantly inhibited the induction of cell death and subsequent infarct volume, measured 24 h after I/R.

Dual actions involved in arsenite-induced oxidative DNA damage.

Arsenic is a recognized human carcinogen, but the mechanism of carcinogenesis is not well understood. Oxidative stress and inhibition of DNA damage repair have been postulated as potential carcinogenic actions of arsenic. The present study tests the hypothesis that arsenite not only induces oxidative stress but also inhibits the activity of the DNA base excision repair protein, poly(ADP-ribose) polymerase-1 (PARP-1), leading to exacerbation of the oxidative DNA damage induced by arsenic. HaCat cells were treated with arsenite for 24 h before measuring 8-hydroxyl-2'-deoxyguanosine (8-OHdG), PARP-1 activity, and reactive oxygen species (ROS). Zinc supplementation and PARP-1 siRNA were used to increase or decrease, respectively, the PARP-1 protein's physiological function. At high concentrations (10 microM or higher), arsenite greatly induced oxidative DNA damage, as indicated by 8-OHdG formation. At lower concentrations (1 microM), arsenite did not produce detectable 8-OHdG, but was still able to effectively inhibit PARP-1 activity. Zinc supplementation reduced the formation of 8-OHdG, restored the PARP-1 activity inhibited by arsenite, but did not decrease ROS production. SiRNA knockdown of PARP-1 did not affect the 8-OHdG level induced by arsenic, while it greatly increased the 8-OHdG level produced by hydrogen peroxide indicating that PARP-1 is a molecular target of arsenite. Our findings demonstrate that in addition to inducing oxidative stress at higher concentrations, arsenite can also inhibit the function of a key DNA repair protein, PARP-1, even at very low concentrations, thus exacerbating the overall oxidative DNA damage produced by arsenite, and potentially, by other oxidants as well.

Inhibition of the Redox Function of Ape-1/ref-1 in Myeloid Leukemia Cells Results in Enhanced Sensitivity to Retinoic Acid Induced Differentiation and Apoptosis.

Ape-1/ref-1 is a multifunctional base excision DNA repair protein that is involved in the repair of abasic sites in DNA. However, it also has a distinct role in the redox regulation of a variety of cellular proteins, such as Fos, Jun, p53, NFκB, PAX, HIF-1α, HLF, and others. Ape-1/ref-1 maintains these proteins in a reduced state thereby facilitating their DNA binding and transcriptional activation capability. HL-60 cells are known to respond to retinoic acid (RA) with terminal granulocytic differentiation and apoptosis, which is mediated through the RA receptors. Previous experiments suggested that elevated Ape-1/ref-1 expression is related to differentiation and apoptosis. To further define the role of the redox function of Ape-1/ref-1 in this relationship, redox function was blocked using two techniques. First, we used retroviral gene transduction to over-express a redox-inactive C-65 mutant of Ape1/ref-1 in HL-60 myeloid leukemia cells and examined the response to retinoic acid. In a second set of experiments we used an Ape-1/ref-1 specific small molecule inhibitor to pharmacologically block the redox function and again examined the response to retinoic acid. Differentiation was evaluated by morphologic change in differential cell counts and expression of CD11b by flow cytometry. Apoptosis was assayed by annexin-PI staining on flow cytometry and cell cycle analysis was examined with propidium iodide flow cytometry.Results:1.HL-60 cells expressing high levels of C-65 Ape-1/ref-1 responded to retinoic acid with a significantly higher level of differentiation and a moderate increase in apoptosis.2.Pharmacologic blockade of Ape-1/ref-1 redox function resulted in a profound increase in differentiation and a moderate increase in apoptosis compared to controls.3.dose dependent studies with retinoic acid demonstrated a similar degree of differentiation (CD11b expression) in cells treated with 10 μmolar retinoic acid and those treated with the redox inhibitor + 0.1 μmolar retinoic acid; alllowing HL-60 cells in the presence of the redox inhibitor to give a similar response to a 100 fold lower dose of retinoic acid.The redox inhibitor alone did not induce differentiation and induced only a minimal amount of apoptosis but did increase the number of cells in S phase significantly. In conclusion, our data supports the contention that redox function of Ape-1/ref-1 may be important for controlling RA-induced myeloid differentiation and programmed cell death. The implication of these findings is that myeloid leukemia cells may be sensitized to retinoids by manipulation of the redox status of Ape-1/ref-1.

Dynamic Basis for One-Dimensional DNA Scanning by the Mismatch Repair Complex Msh2-Msh6

The ability of proteins to locate specific sites or structures among a vast excess of nonspecific DNA is a fundamental theme in biology. Yet the basic principles that govern these mechanisms remain poorly understood. For example, mismatch repair proteins must scan millions of base pairs to find rare biosynthetic errors, and they then must probe the surrounding region to identify the strand discrimination signals necessary to distinguish the parental and daughter strands. To determine how these proteins might function we used single-molecule optical microscopy to answer the following question: how does the mismatch repair complex Msh2-Msh6 interrogate undamaged DNA? Here we show that Msh2-Msh6 slides along DNA via one-dimensional diffusion. These findings indicate that interactions between Msh2-Msh6 and DNA are dominated by lateral movement of the protein along the helical axis and have implications for how MutS family members travel along DNA at different stages of the repair reaction.