DNA Polymerase Beta Research Articles

Association of Two Polymorphisms of DNA Polymerase Beta in Exon-9 and Exon-11 with Ovarian Carcinoma in India

DNA polymerase beta (polβ ) is a key enzyme in the base excision repair pathway. It is 39 kDa protein, with two subunits, one large subunit of 31 kDa having catalytic activity between exon V to exon XIV, and an 8 kDa smaller subunit having single strand DNA binding activity. Exons V to VII have double strand DNA binding activity, whereas exons VIII to XI account for the nucleotidyl transferase activity and exons XII to XIV the dNTP selection activity. To examine the association between polβ polymorphisms and the risk of ovarian cancer, the present case control study was performed using 152 cancer samples and non-metastatic normal samples from the same patients. In this study, mutational analysis of polβ genomic DNA was undertaken using primers from exons IX to XIV - the portion having catalytic activity. We detected alteration in DNA polymerase beta by SSCP. Two specific heterozygous point mutations of polβ were identified in Exon 9:486, A->C (polymorphism 1; 11.18%) and in Exon 11:676, A->C (polymorphism 2; 9.86%). The correlation study involving polymorphism 1 and 4 types of tissue showed a significant correlation between mucinous type with a Pearson correlation value of 4.03 (p=0.04). The association among polymorphism 2 with serous type and stage IV together have shown Pearson χ2 value of 3.28 with likelihood ratio of 4.4 (p=0.07) with OR =2.08 (0.3- 14.55). This indicates that there is a tendency of correlation among polymorphism 2, serous type and stage IV, indicating a risk factor for ovarian cancer. Hence, the results indicate that there is a tendency for polβ polymorphisms being a risk factor for ovarian carcinogenesis in India.

Abstract 3121: Systematic analysis of the DNA synthesis fidelity of somatic mutations of polymerase beta found in prostate cancer

Abstract Human DNA polymerase beta (polβ) is a monomeric protein of 335 amino acids and functions in base excision repair and meiotic recombination. Human polα is over-expressed in many cancer cells like ovarian, prostate, breast, colon and chronic myelogenous leukemia. To obtain clues of possible functions in vivo, we have determined the fidelity of DNA synthesis of polα with forward mutation assay which scored the sequence errors caused in the lacZ-α gene in M13mp2 during DNA synthesis to fill a 407-nucleotide gap. Three of seven of the somatic polα mutants, p.E232K, p.E123K and pE216K, which we identified previously in prostate tumors, were tested. The results indicated that the somatic mutants of human DNA polymerase beta display altered fidelity. The fidelity for large deletions and complex changes of the pE232K and pE123K muatants are three and 31 times lower respectively, compared to wild type polα. The T>G transversion at position 103, which is the most common feature of polB base substitution error spectrum, is observed six times and two times lower for the pE123K and p.E216K mutants than wild polymerase beta. Our data show that somatic mutations in prostate cancer change both the synthesis fidelity and/or mutation type compared with wild type polymerase beta. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3121. doi:1538-7445.AM2012-3121

Abstract 3108: Exploring base excision repair variants as potential defining events in cancer patient populations and characterization of models for pre-clinical studies

Abstract Background Deficiencies in base excision repair (BER) may increase the cell's dependence on alternative repair pathways and so define a patient population for novel inhibitors of DNA damage repair. Notably, cancer associated molecular events in DNA polymerase beta (POLα) have been described in various disease backgrounds including colorectal cancer (CRC), gastric, breast and prostate (1-5). Although functional consequence has been linked to certain POLα mutations and splice variants, their prevalence in defined disease segments remains largely undefined. Aim We set out to ascertain the prevalence of POLα deficiencies in CRC, and subsequently investigated protein and gene expression profiling as alternative methods for defining BER defects in cancer. Methods/Results A comprehensive study of clinical (CRC; N=64), tumour explant (CRC; N=36) and cell line (mixed origin; N=280) samples revealed that cancer-associated mutations in the polymerase encoding domain of POLα (1-3) are not common events in CRC. Additionally, a previously described splice variant of POLα lacking part of the polymerase domain (3-4), was assayed and found to be expressed at similar levels in CRC and normal tissue. This would suggest that expression of the POLα splice variant is not a defining element of CRC in western populations. Expression profiling using Fluidigm Taqman revealed a subset of BER genes more highly expressed in CRC clinical samples and mixed cell lines compared with normal tissue. While protein expression profiles did not reflect relative gene expression in selected cell line models, we observed an additional low molecular weight band in a subset of cells profiled for POLB expression. Furthermore, we report variations in the expression of the scaffold protein XRCC1 in colorectal and breast cell lines and propose that this could also provide a mechanism for variation in DNA repair capacity. Summary Although from our studies sequencing and transcript analysis of POLα do not provide suitable markers of BER deficiency in CRC, we report aberrant banding patterns in POLα by Western blotting and variation in XRCC1 protein expression in a subset of cell lines analyzed. We hypothesize that these variants may confer a BER deficient phenotype. 1. Lang, T. et al. (2004Proc. Natl Acad. Sci. USA, 101, 6074-6079. 2. Tan, Xiao-Hui, et al Cancer Letters: 2005: 220: 101-114 3. Wang, L et al Cancer Research, 1992; 52:4824-4827 4. Bhattacharyya, N. et al. (1997) Proc. Natl Acad. Sci. USA, 94, 10324-10329 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3108. doi:1538-7445.AM2012-3108

Y265C DNA polymerase beta knockin mice survive past birth and accumulate base excision repair intermediate substrates

DNA is susceptible to damage by a wide variety of chemical agents that are generated either as byproducts of cellular metabolism or exposure to man-made and harmful environments. Therefore, to maintain genomic integrity, having reliable DNA repair systems is important. DNA polymerase β is known to be a key player in the base excision repair pathway, and mice devoid of DNA polymerase beta do not live beyond a few hours after birth. In this study, we characterized mice harboring an impaired pol β variant. This Y265C pol β variant exhibits slow DNA polymerase activity but WT lyase activity and has been shown to be a mutator polymerase. Mice expressing Y265C pol β are born at normal Mendelian ratios. However, they are small, and 60% die within a few hours after birth. Slow proliferation and significantly increased levels of cell death are observed in many organs of the E14 homozygous embryos compared with WT littermates. Mouse embryo fibroblasts prepared from the Y265C pol β embryos proliferate at a rate slower than WT cells and exhibit a gap-filling deficiency during base excision repair. As a result of this, chromosomal aberrations and single- and double-strand breaks are present at significantly higher levels in the homozygous mutant versus WT mouse embryo fibroblasts. This is study in mice is unique in that two enzymatic activities of pol β have been separated; the data clearly demonstrate that the DNA polymerase activity of pol β is essential for survival and genome stability.

DNA polymerase beta from Trypanosoma cruzi is involved in kinetoplast DNA replication and repair of oxidative lesions

Specific DNA repair pathways from Trypanosoma cruzi are believed to protect genomic DNA and kinetoplast DNA (kDNA) from mutations. Particular pathways are supposed to operate in order to repair nucleotides oxidized by reactive oxygen species (ROS) during parasite infection, being 7,8-dihydro-8-oxoguanine (8oxoG) a frequent and highly mutagenic base alteration. If unrepaired, 8oxoG can lead to cytotoxic base transversions during DNA replication. In mammals, DNA polymerase beta (Polβ) is mainly involved in base excision repair (BER) of oxidative damage. However its biological role in T. cruzi is still unknown. We show, by immunofluorescence localization, that T. cruzi DNA polymerase beta (Tcpolβ) is restricted to the antipodal sites of kDNA in replicative epimastigote and amastigote developmental stages, being strictly localized to kDNA antipodal sites between G1/S and early G2 phase in replicative epimastigotes. Nevertheless, this polymerase was detected inside the mitochondrial matrix of trypomastigote forms, which are not able to replicate in culture. Parasites over expressing Tcpolβ showed reduced levels of 8oxoG in kDNA and an increased survival after treatment with hydrogen peroxide when compared to control cells. However, this resistance was lost after treating Tcpolβ overexpressors with methoxiamine, a potent BER inhibitor. Curiously, a presumed DNA repair focus containing Tcpolβ was identified in the vicinity of kDNA of cultured wild type epimastigotes after treatment with hydrogen peroxide. Taken together our data suggest participation of Tcpolβ during kDNA replication and repair of oxidative DNA damage induced by genotoxic stress in this organelle.

Isolation and Characterization of High Affinity Aptamers Against DNA Polymerase Iota

Human DNA-polymerase iota (Pol ι) is an extremely error-prone enzyme and the fidelity depends on the sequence context of the template. Using the in vitro systematic evolution of ligands by exponential enrichment (SELEX) procedure, we obtained an oligoribonucleotide with a high affinity to human Pol ι, named aptamer IKL5. We determined its dissociation constant with homogenous preparation of Pol ι and predicted its putative secondary structure. The aptamer IKL5 specifically inhibits DNA-polymerase activity of the purified enzyme Pol ι, but did not inhibit the DNA-polymerase activities of human DNA polymerases beta and kappa. IKL5 suppressed the error-prone DNA-polymerase activity of Pol ι also in cellular extracts of the tumor cell line SKOV-3. The aptamer IKL5 is useful for studies of the biological role of Pol ι and as a potential drug to suppress the increase of the activity of this enzyme in malignant cells.

Biological Relevance of DNA Polymerase Beta and Translesion Synthesis Polymerases to Cancer and its Treatment

The cellular genome is constantly subject to DNA damage caused by endogenous factors or exogenously by damaging agents such as ionizing radiation or various anticancer agents. The base excision repair (BER) enzyme, DNA polymerase β, and the polymerases involved in translesion synthesis (TLS) have been shown to contribute to cellular tolerance and repair of DNA lesions by anticancer treatments, particularly the platinum cytotoxic drugs. Moreover, there is robust preclinical evidence linking alterations in DNA pol β and TLS polymerase levels to cancer. DNA polymerases may therefore be potential targets to increase the sensitivity of cancer cells to chemotherapy drugs. In this article, the physical and chemical properties of DNA polymerase β and the translesion synthesis polymerases are reviewed with a view to identifying how they may act as targets for anticancer treatment. The potential clinical role of new DNA polymerase inhibitors is discussed and how they may be combined with conventional cytotoxic agents.

Liverworts-Potential Source of Medicinal Compounds

The bryophytes contain the Marchantiophyta (liverworts), Bryophyta (mosses) and Anthocerotophyta (hornworts) among which the Marchantiophyta contain cellular oil body and they produce a number of terpenoids, aromatic compounds and acetogenins, several of which show interesting biological activity such as allergenic contact dermatitis, insecticide, insect antifeedant, cytotoxic, piscicidal, muscle relaxing, plant growth regulatory, anti-HIV, DNA polymerase beta inhibitory, anti-obesity, neurotrophic, NO production inhibitory, antimicrobial and antifungal activities. The isolation and chemical structures of biologically active compounds and their total synthesis are reviewed.

Biological Relevance of DNA Polymerase Beta and Translesion Synthesis Polymerases to Cancer and its Treatment

The cellular genome is constantly subject to DNA damage caused by endogenous factors or exogenously by damaging agents such as ionizing radiation or various anticancer agents. The base excision repair (BER) enzyme, DNA polymerase β, and the polymerases involved in translesion synthesis (TLS) have been shown to contribute to cellular tolerance and repair of DNA lesions by anticancer treatments, particularly the platinum cytotoxic drugs. Moreover, there is robust preclinical evidence linking alterations in DNA pol β and TLS polymerase levels to cancer. DNA polymerases may therefore be potential targets to increase the sensitivity of cancer cells to chemotherapy drugs. In this article, the physical and chemical properties of DNA polymerase β and the translesion synthesis polymerases are reviewed with a view to identifying how they may act as targets for anticancer treatment. The potential clinical role of new DNA polymerase inhibitors is discussed and how they may be combined with conventional cytotoxic agents. Keywords: Base excision repair, cisplatin, DNA damage repair, DNA polymerase, oxaliplatin, radiotherapy, translesion synthesis

A new member of the dna polymerase beta superfamily in human myeloblast leukemia hl-60 cells

A new member of the dna polymerase beta superfamily in human myeloblast leukemia hl-60 cells

Effect of DNA polymerase beta on apoptosis and mitochondrial membrane potential induced by hydroquinone, a metabolite of benzene

To explore the effect and mechanism of DNA polymerase β expression level on cell apoptosis and mitochondrial membrane potential induced by hydroquinone. Polβ wild-type cells (polβ+/+), polβ overexpressed cells (polβ oe) and polβ null cells (polβ-/-) were applied as a model cell system, The effect of cell apoptosis and mitochondrial membrane potential induced by different doses of hydroquinone were analyzed by flow cytometry. The ROS and ·OH assay kit were used to examine the cellular ROS and ·OH level. The activity of cellular SOD and GSH-Px were tested by Chemiluminescence method after exposed to different concentrations of hydroquinone. With the dose of hydroquinone increased, the rate of apoptosis and falling of mitochondrial membrane potential (ΔΨm) in cells were increased compared with the control. When compared with polβ+/+ cells, the rate of apoptosis in polβ-/- cells exposed to 20.00, 40.00, 80.00 µmol/L hydroquinone increased and the rate of apoptosis in polβ oe cells exposed to 10.00, 20.00, 40.00, 80.00 µmol/L hydroquinone decreased (P < 0.05). Compared with polβ+/+ cells (20.60% ± 0.57%, 37.95% ± 0.64%, 44.50% ± 1.27%, 57.55% ± 1.06%), the rate of cell which undergone mitochondrial depolarization in polβ-/- cells treated with 10.00, 20.00, 40.00, 80.00 µmol/L hydroquinone (33.60% ± 1.55%, 46.05% ± 1.77%, 52.75% ± 2.05%, 75.20% ± 0.56%) increased. The rate of cell which undergone mitochondrial depolarization in polβ oe cells exposed to 10.00, 20.00, 40.00, 80.00 µmol/L hydroquinone (16.05% ± 1.20%, 29.80% ± 1.21%, 35.15% ± 1.06%, 53.80% ± 0.85%) decreased (P < 0.05). When compared with polβ+/+ cells, fluorescent intensity of polβ-/- cells treated with different dosages of hydroquinone increased, while which of polβ oe cells decreased (P < 0.05). Compared with polβ+/+ cells, ·OH level of polβ-/- cells treated with 20.00, 40.00 µmol/L hydroquinone significantly enhanced, while which of polβ oe cells decreased sharply (P < 0.05). Under the same concentrations of hydroquinone, the activity of SOD and GSH-Px were decreased most rapidly in polβ-/- cells. The activity of SOD and GSH-Px in polβ oe cells decreased slower than in the polβ-/- cells. Hydroquinone could induced apoptosis by the generation of ROS and decrease of ΔΨm; polβ could protect cells from apoptosis induced by hydroquinone through decrease of ROS level and depolarization of mitochondria.

The Structural Basis for Substrate Recognition by Mammalian Polynucleotide Kinase 3′ Phosphatase

Mammalian polynucleotide kinase 3' phosphatase (PNK) plays a key role in the repair of DNA damage, functioning as part of both the nonhomologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. We have now determined crystal structures of murine PNK with DNA molecules bound to both of its active sites. The structure of ssDNA engaged with the 3'-phosphatase domain suggests a mechanism of substrate interaction that assists DNA end seeking. The structure of dsDNA bound to the 5'-kinase domain reveals a mechanism of DNA bending that facilitates recognition of DNA ends in the context of single-strand and double-strand breaks and suggests a close functional cooperation in substrate recognition between the kinase and phosphatase active sites.

Effects of DNA polymerase beta on the genotoxicity and genetic instability induced by benzo(a)pyrene

To explore the effects of DNA polymerase β expression level on the genotoxicity and genetic instability induced by benzo(a)pyrene (BaP),and provide experimental the basis for further study on the carcinogenic molecular mechanism of BaP. Three kinds of cell lines with the identical genetic background, polβ wild-type cells (polβ+/+), polβ null cells (polβ-/-) and polβ overexpression cells (polβ oe) were applied as cellular models. The oxidative damage, genotoxicity and genetic instability induced by BaP were analyzed by using different methods respectively. Cell viability and colony forming ability of 3 kinds of cell lines exposed to BaP decreased with BaP. After treated with 5 and 20 µmol/L concentration of BaP, fluorescence intensity of polβ-/- cell line was significantly higher than that of other two cell lines (P < 0.05). When treated with 5.00 µmol/L and 20.00 µmol/L concentration of BaP, the SOD activities (76.56 ± 2.84 and 62.78 ± 4.28 U/mg pro) of polβ-/- cell line were significantly lower than that (84.85 ± 3.59) of control group and those (85.21 ± 3.20 and 76.90 ± 3.38 U/mg pro) of polβ+/+ cell line. In 20.00 µmol/L BaP group. SOD activity (82.59 ± 4.64 U/mg pro) of polβ oe cell line was lower than that (88.58 ± 6.77 U/mg pro) of control but higher than that of polβ+/+ cell line (P < 0.05). In 1.25, 5.00 and 20.00 µmol/L concentration BaP groups, the micronucleus rates of polβ-/- cell line were much higher than those of polβ+/+ cell line (P < 0.05). In 5.00 and 20.00 µmol/L concentration BaP groups, the micronucleus rates of polβ oe cell line were significantly lower than those of polβ+/+ line (P < 0.05). In 5.00 and 20.00 µmol/L concentration BaP groups, HPRT gene mutation frequencies (26.16 × 10(-6) and 37.51 × 10(-6); 27.68 × 10(-6) and 38.63 × 10(-6)) in polβ-/- cells and polβ oe cells were significantly higher than those (19.76 × 10(-6) and 24.78 × 10(-6)) of polβ+/+ cells (P < 0.05). Polβ could play a role in protecting the cells from the genotoxicity and genetic instability induced by BaP, and the normal expression level of polβ was indispensable for maintaining genome stability.

Down syndrome as a model of DNA polymerase beta haploinsufficiency and accelerated aging

Down syndrome is a condition of intellectual disability characterized by accelerated aging. As with other aging syndromes, evidence accumulated over the past several decades points to a DNA repair defect inherent in Down syndrome. This evidence has led us to suggest that Down syndrome results in reduced DNA base excision repair (BER) capacity, and that this contributes to the genomic instability and the aging phenotype of Down syndrome. We propose important roles for microRNA and/or folate metabolism and oxidative stress in the dysregulation of BER in Down syndrome. Further, we suggest these pathways are involved in the leukemogenesis of Down syndrome. We have reviewed the role of BER in the processing of oxidative stress, and the impact of folate depletion on BER capacity. Further, we have reviewed the role that loss of BER, specifically DNA polymerase beta, plays in accelerating the rate of aging. Like that seen in the DNA polymerase beta heterozygous mouse, the aging phenotype of Down syndrome is subtle, unlike the aging phenotypes seen in the classical progeroid syndromes and mouse models of aging. As such, Down syndrome may provide a model for elucidating some of the basic mechanisms of aging.

Abstract B37: A DNA polymerase beta gene harboring the colon cancer-associated G231D variant increases the sensitivity of cells to chemotherapeutic agents and induces cellular transformation

Abstract Rapidly advancing technology has resulted in the generation of the genomic sequences of several human tumors. These studies have revealed that tumors are heterogeneous and contain many mutations, supporting the mutator phenotype hypothesis of human cancer. Drivers of carcinogenesis are thought to be mutated genes that occur at high frequencies in large numbers of human tumors. However, functional characterization of many of the somatic mutations is lacking. We have identified several mutations of the DNA polymerase beta (POLB) gene in human colorectal cancer. Pol beta is the main polymerase involved in the base excision repair (BER) pathway and aberrant expression of Pol beta has been linked to a cancerous phenotype. In this study, we characterized the homozygous G231D mutation that was identified in a Stage 3 colorectal tumor. We have demonstrated that its expression in epithelial cells induced cellular transformation and increased the rate of proliferation. The transformed phenotype persisted in the cells even once the expression of G231D was extinguished. These data indicated that the expression of G231D caused an inheritable change; this change is most likely due to an increase in genomic instability caused by unfilled gaps proceeding through replication. Expression of G231D was insufficient to rescue Pol beta-deficient cells treated with chemotherapeutic agents suggesting that these agents may be effectively used to treat tumors harboring this mutation. Biochemical analysis of G231D revealed that it was 100-fold slower than WT Pol beta as determined by pre-steady state kinetics. The slow rate was a result of the decreased binding affinity of nucleotides by G231D. Residue 231 of Pol beta lies in close proximity to the template strand of the DNA. Molecular modeling showed that the change from a glycine to a negatively charged amino acid caused a repulsion between the template and residue 231 leading to the disruption of the dNTP binding pocket. Together, these data indicate that a person harboring the G231D Pol beta mutation may have an increased risk of cancer. Moreover, the altered sensitivity to chemotherapeutic drugs in cells carrying the G231D variant may have further implications in how to better improve the therapeutic outcome in patients with this mutation and supports the need for personalized cancer therapies. 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 B37.

A review of recent experiments on step-to-step “hand-off” of the DNA intermediates in mammalian base excision repair pathways

The current "working model" for mammalian base excision repair involves two sub-pathways termed single-nucleotide base excision repair and long patch base excision repair that are distinguished by their repair patch sizes and the enzymes/co-factors involved. These base excision repair sub-pathways are designed to sequester the various DNA intermediates, passing them along from one step to the next without allowing these toxic molecules to trigger cell cycle arrest, necrotic cell death, or apoptosis. Although a variety of DNA-protein and protein-protein interactions are known for the base excision repair intermediates and enzymes/co-factors, the molecular mechanisms accounting for step-to-step coordination are not well understood. In this review, we explore the question of whether there is an actual step-to-step "hand-off" of the DNA intermediates during base excision repair in vitro. The results show that when base excision repair enzymes are pre-bound to the initial single-nucleotide base excision repair intermediate, the DNA is channeled from apurinic/apyrimidinic endonuclease 1 to DNA polymerase beta and then to DNA ligase. In the long patch base excision repair sub-pathway, where the 5'-end of the incised strand is blocked, the intermediate after polymerase beta gap filling is not channeled from polymerase beta to the subsequent enzyme, flap endonuclease 1. Instead, flap endonuclease 1 must recognize and bind to the intermediate in competition with other molecules.

An Abridged Transition State Model To Derive Structure, Dynamics, and Energy Components of DNA Polymerase β Fidelity

We show how a restricted reaction surface can be used to facilitate the calculation of biologically important contributions of active site geometries and dynamics to DNA polymerase fidelity. Our analysis, using human DNA polymerase beta (pol β), is performed within the framework of an electrostatic linear free energy response (EFER) model. The structure, dynamics, and energetics of pol β-DNA-dNTP interactions are computed between two points on the multidimensional reaction free energy surface. "Point 1" represents a ground state activation intermediate (GSA), which is obtained by deprotonating the terminal 3'OH group of the primer DNA strand. "Point 2" is the transition state (PTS) for the attack of the 3'O(-) (O(nuc)) on the P(α) atom of dNTP substrate, having the electron density of a dianionic phosphorane intermediate. Classical molecular dynamics simulations are used to compute the geometric and dynamic contributions to the formation of right and wrong O(nuc)-P chemical bonds. Matched dCTP·G and mismatched dATP·G base pairs are used to illustrate the analysis. Compared to the dCTP·G base pair, the dATP·G mismatch has fewer GSA configurations with short distances between O(nuc) and P(α) atoms and between the oxygen in the scissile P-O bond (O(lg)) and the nearest structural water. The thumb subdomain conformation of the GSA complex is more open for the mismatch, and the H-bonds in the mispair become more extended during the nucleophilic attack than in the correct pair. The electrostatic contributions of pol β and DNA residues to catalysis of the right and wrong P-O(nuc) bond formation are 5.3 and 3.1 kcal/mol, respectively, resulting in an 80-fold contribution to fidelity. The EFER calculations illustrate the considerable importance of Arg183 and an O(lg)-proximal water molecule to pol β fidelity.

A Triad Interaction in the Fingers Subdomain of DNA Polymerase Beta Controls Polymerase Activity

DNA polymerase beta (pol beta) is the main polymerase involved in the base excision repair pathway responsible for repairing damaged bases in the DNA. Previous studies on the H285D mutant of pol beta suggested that the C-terminal region of the polymerase is important for polymerase function. In this study, the C-terminal region of pol beta was mutated to assess its role in polymerization. Kinetic experiments showed that the C-terminal region is required for wild-type polymerase activity. Additionally, an interaction between the fingers and palm subdomain revealed itself to be required for polymerase activity. The E316R mutant of pol beta was shown to have a 29,000-fold reduction in polymerization rate with no reduction in nucleotide binding, suggesting that there exists a noncovalent mechanistic step between nucleotide binding and nucleophilic attack of the primer 3'-hydroxyl group on the α-PO(4) of the nucleotide. Molecular modeling studies of the E316R mutant demonstrate that disrupting the interaction between Arg182 and Glu316 disrupts the packing of side chains in the hydrophobic hinge region and may be hampering the conformational change during polymerization. Taken together, these data demonstrate that the triad interaction of Arg182, Glu316, and Arg333 is crucial for polymerase function.

Role of DNA polymerase beta in the genotoxicity of arsenic

Arsenic, an important hazard in the environment, is associated with human cancer and other degenerative diseases. However, the mechanisms underlying arsenic hazardous effects remain unclear. It has been reported arsenic exposure can result in increased cellular reactive oxygen species and oxidative DNA damage. This suggests DNA base excision repair (BER), the major pathway for repairing oxidative DNA damage, may be involved in combating arsenic hazardous effects. As a critical repair enzyme in BER, DNA polymerase beta (Pol β) might play an essential role in reducing arsenic toxicity. To test this hypothesis, we evaluated arsenic-induced cytotoxic and genotoxic effects under Pol β deficiency. Our results demonstrated that the viability of Pol β-deficient mouse embryonic fibroblasts was much lower than that of Pol β wild-type cells after treatment with arsenite (As(3+) ). An increased level of DNA damage and significantly delayed arsenite-induced DNA damage repair in Pol β-deficient cells indicated reduced repair of DNA lesions under Pol β deficiency. This was consistent with the increase in the frequency of micronuclei (MN), an indicator of chromosomal breakage, which was also observed in Pol β-deficient cells treated with arsenite. In contrast, cells harboring overexpressed Pol β resulted in a lower level of DNA damage and MN than Pol β wild-type cells, indicating overexpression of the enzyme can combat arsenic-induced genotoxic effects. In conclusion, our results indicate an important role for Pol β in repairing arsenite-induced DNA damage and maintaining chromosomal integrity and further suggest deficiency of BER may be involved in arsenic genotoxicity and carcinogenicity.

DNA polymerase beta is critical for genomic stability of sperm cells

Maintaining genome integrity in germ cells is important, given that the germ cells produce the next generation of offspring. Base excision repair is a DNA repair pathway that is responsible for the repair of most endogenous DNA damage. A key enzyme that functions in this repair pathway is DNA polymerase beta (Pol β). We previously used conditional gene targeting to engineer mice with sperm deleted of the Pol B gene, which encodes Pol β. We characterized mutagenesis in the sperm of these mice and compared it to wild-type and mice heterozygous for the Pol B gene. We found that sperm obtained that were heterozygously or homozygously deleted of the Pol B gene exhibited increased mutation frequencies compared to wild-type sperm. We identified an increase in transition mutations in both heterozygously and homozygously deleted sperm, and the types of mutations induced suggest that a polymerase other than Pol β functions in its absence. Interestingly, most of the transversions we observed were induced only in heterozygous, compared with wild-type sperm. Our results suggest that haploinsufficiency of Pol β leads to increased frequencies and varieties of mutations. Our study also shows that Pol β is critical for genome stability in the germline.