201
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Tomanicek SJ, Hughes RC, Ng JD, Coates L. Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1003-12. [PMID: 20823514 PMCID: PMC2935215 DOI: 10.1107/s1744309110028575] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 07/16/2010] [Indexed: 01/28/2023]
Abstract
The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5'-phosphodiester bond at an AP site to generate a free 3'-hydroxyl group and a 5'-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.
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Affiliation(s)
- Stephen J. Tomanicek
- Oak Ridge National Laboratory, Neutron Scattering Science Division, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ronny C. Hughes
- Oak Ridge National Laboratory, Neutron Scattering Science Division, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Laboratory for Structural Biology, Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Joseph D. Ng
- Laboratory for Structural Biology, Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Leighton Coates
- Oak Ridge National Laboratory, Neutron Scattering Science Division, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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202
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Nishizawa S, Sato Y, Xu Z, Morita K, Li M, Teramae N. Abasic site-based DNA aptamers for analytical applications. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.484865] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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203
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Hebert SL, Lanza IR, Nair KS. Mitochondrial DNA alterations and reduced mitochondrial function in aging. Mech Ageing Dev 2010; 131:451-62. [PMID: 20307565 PMCID: PMC2910809 DOI: 10.1016/j.mad.2010.03.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Revised: 03/03/2010] [Accepted: 03/14/2010] [Indexed: 12/23/2022]
Abstract
Oxidative damage to mitochondrial DNA increases with aging. This damage has the potential to affect mitochondrial DNA replication and transcription which could alter the abundance or functionality of mitochondrial proteins. This review describes mitochondrial DNA alterations and changes in mitochondrial function that occur with aging. Age-related alterations in mitochondrial DNA as a possible contributor to the reduction in mitochondrial function are discussed.
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Affiliation(s)
| | | | - K. Sreekumaran Nair
- Corresponding author: K. Sreekumaran Nair, Endocrine Research Unit, Mayo Clinic, 200 First St. SW, Joseph 5-194, Rochester, MN 55905, Telephone: 507-255-2415, Fax: 507-255-4828,
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204
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Kinde-Carson MN, Ferguson C, Oyler NA, Harbison GS, Meints GA. Solid state 2H NMR analysis of furanose ring dynamics in DNA containing uracil. J Phys Chem B 2010; 114:3285-93. [PMID: 20151717 DOI: 10.1021/jp9091656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions, such as uracil, in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Increased dynamic properties in lesion-containing DNAs have been suggested to assist recognition and specificity. Deuterium solid-state nuclear magnetic resonance (SSNMR) has been used to directly observe local dynamics of the furanose ring within a uracil:adenine (U:A) base pair and compared to a normal thymine:adenine (T:A) base pair. Quadrupole echo lineshapes, <T(1Z)>, and <T(2e)> relaxation data were collected, and computer modeling was performed. The results indicate that the relaxation times are identical within the experimental error, the solid lineshapes are essentially indistinguishable above the noise level, and our lineshapes are best fit with a model that does not have significant local motions. Therefore, U:A base pair furanose rings appear to have essentially identical dynamic properties as a normal T:A base pair, and the local dynamics of the furanose ring are unlikely to be the sole arbiter for uracil recognition and specificity in U:A base pairs.
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205
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DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection. Clin Sci (Lond) 2010; 119:187-202. [PMID: 20522025 DOI: 10.1042/cs20100041] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mycobacteria, including most of all MTB (Mycobacterium tuberculosis), cause pathogenic infections in humans and, during the infectious process, are exposed to a range of environmental insults, including the host's immune response. From the moment MTB is exhaled by infected individuals, through an active and latent phase in the body of the new host, until the time they reach the reactivation stage, MTB is exposed to many types of DNA-damaging agents. Like all cellular organisms, MTB has efficient DNA repair systems, and these are believed to play essential roles in mycobacterial pathogenesis. As different stages of infection have great variation in the conditions in which mycobacteria reside, it is possible that different repair systems are essential for progression to specific phases of infection. MTB possesses homologues of DNA repair systems that are found widely in other species of bacteria, such as nucleotide excision repair, base excision repair and repair by homologous recombination. MTB also possesses a system for non-homologous end-joining of DNA breaks, which appears to be widespread in prokaryotes, although its presence is sporadic within different species within a genus. However, MTB does not possess homologues of the typical mismatch repair system that is found in most bacteria. Recent studies have demonstrated that DNA repair genes are expressed differentially at each stage of infection. In the present review, we focus on different DNA repair systems from mycobacteria and identify questions that remain in our understanding of how these systems have an impact upon the infection processes of these important pathogens.
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206
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Schomacher L, Smolorz S, Ciirdaeva E, Ber S, Kramer W, Fritz HJ. Helix-hairpin-helix protein MJ1434 from Methanocaldococcus jannaschii and EndoIV homologue TTC0482 from Thermus thermophilus HB27 do not process DNA uracil residues. Nucleic Acids Res 2010; 38:5119-29. [PMID: 20410075 PMCID: PMC2926615 DOI: 10.1093/nar/gkq270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The mutagenic threat of hydrolytic DNA cytosine deamination is met mostly by uracil DNA glycosylases (UDG) initiating base excision repair. However, several sequenced genomes of archaeal organisms are devoid of genes coding for homologues of the otherwise ubiquitous UDG superfamily of proteins. Previously, two possible solutions to this problem were offered by (i) a report of a newly discovered family of uracil DNA glycosylases exemplified by MJ1434, a protein found in the hyperthermophilic archaeon Methanocaldococcus jannaschii, and (ii) the description of TTC0482, an EndoIV homologue from the hyperthermophilic bacterium Thermus thermophilus HB27, as being able to excise uracil from DNA. Sequence homologues of both proteins can be found throughout the archaeal domain of life. Three proteins orthologous to MJ1434 and the family founder itself were tested for but failed to exhibit DNA uracil glycosylase activity when produced in an Ung-deficient Escherichia coli host. Likewise, no DNA uracil processing activity could be detected to be associated with TTC0482, while the protein was fully active as an AP endonuclease. We propose that the uracil processing activities formerly found were due to contaminations with Ung enzyme. Use of Δung-strains as hosts for production of putatively DNA-U processing enzymes provides a simple safeguard.
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Affiliation(s)
- Lars Schomacher
- Abteilung Molekulare Genetik und Präparative Molekularbiologe, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
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207
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Wang YF, Yu ZY, Wu J, Liu CB. Electron delocalization and charge transfer in polypeptide chains. J Phys Chem A 2010; 113:10521-6. [PMID: 19731905 DOI: 10.1021/jp9020036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, the electron structure and charge-transfer mechanism in polypeptide chains are investigated according to natural bond orbitals (NBO) analysis at the level of B3LYP/6-311++G**. The results indicate that the delocalization of electrons between neighboring peptide subgroups can occur in two opposite directions, and the delocalization effect in the direction from the carboxyl end to the amino end has an obvious advantage. As a result of a strong hyperconjugative interaction, the lowest unoccupied NBO of the peptide subgroup, pi*C-O, has significant delocalization to neighboring subgroups, and the energies of these NBOs decrease from the carboxyl end to the amino end. The formation of intramolecular O...H-N type hydrogen bonds also helps to delocalize the electron from the carboxyl end to the amino end. Thus, the electron will flow to the amino end. The superexchange mechanism is suggested in the electron-transfer process.
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Affiliation(s)
- Ye-Fei Wang
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100 Shandong, China
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208
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Koval VV, Kuznetsov NA, Ishchenko AA, Saparbaev MK, Fedorova OS. Real-time studies of conformational dynamics of the repair enzyme E. coli formamidopyrimidine-DNA glycosylase and its DNA complexes during catalytic cycle. Mutat Res 2010; 685:3-10. [PMID: 19751748 DOI: 10.1016/j.mrfmmm.2009.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 08/20/2009] [Indexed: 05/28/2023]
Abstract
Fpg protein from Escherichia coli belongs to the class of DNA glycosylases/abasic site lyases excising several oxidatively damaged purines in the base excision repair pathway. In this review, we summarize the results of our studies of Fpg protein from E. coli, elucidating the intrinsic mechanism of recognition and excision of damaged bases in DNA.
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Affiliation(s)
- Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave. 8, Novosibirsk 630090, Russia
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209
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Pal S, Polyak SJ, Bano N, Qiu WC, Carithers RL, Shuhart M, Gretch DR, Das A. Hepatitis C virus induces oxidative stress, DNA damage and modulates the DNA repair enzyme NEIL1. J Gastroenterol Hepatol 2010; 25:627-34. [PMID: 20074151 PMCID: PMC3565844 DOI: 10.1111/j.1440-1746.2009.06128.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Hepatitis C virus (HCV)-induced chronic inflammation may induce oxidative stress which could compromise the repair of damaged DNA, rendering cells more susceptible to spontaneous or mutagen-induced alterations, the underlying cause of liver cirrhosis and hepatocellular carcinoma. In the current study we examined the induction of reactive oxygen species (ROS) resulting from HCV infection and evaluated its effect on the host DNA damage and repair machinery. METHODS HCV infected human hepatoma cells were analyzed to determine (i) ROS, (ii) 8-oxoG and (iii) DNA glycosylases NEIL1, NEIL2, OGG1. Liver biopsies were analyzed for NEIL1. RESULTS Human hepatoma cells infected with HCV JFH-1 showed 30-60-fold increases in ROS levels compared to uninfected cells. Levels of the oxidatively modified guanosine base 8-oxoguanine (8-oxoG) were significantly increased sixfold in the HCV-infected cells. Because DNA glycosylases are the enzymes that remove oxidized nucleotides, their expression in HCV-infected cells was analyzed. NEIL1 but not OGG1 or NEIL2 gene expression was impaired in HCV-infected cells. In accordance, we found reduced glycosylase (NEIL1-specific) activity in HCV-infected cells. The antioxidant N-acetyl cystein (NAC) efficiently reversed the NEIL1 repression by inhibiting ROS induction by HCV. NEIL1 expression was also partly restored when virus-infected cells were treated with interferon (IFN). HCV core and to a lesser extent NS3-4a and NS5A induced ROS, and downregulated NEIL1 expression. Liver biopsy specimens showed significant impairment of NEIL1 levels in HCV-infected patients with advanced liver disease compared to patients with no disease. CONCLUSION Collectively, the data indicate that HCV induction of ROS and perturbation of NEIL1 expression may be mechanistically involved in progression of liver disease and suggest that antioxidant and antiviral therapies can reverse these deleterious effects of HCV in part by restoring function of the DNA repair enzyme/s.
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Affiliation(s)
- Sampa Pal
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195-7110 USA.
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210
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Liu XP, Li CP, Hou JL, Liu YF, Liang RB, Liu JH. Expression and characterization of thymine-DNA glycosylase from Aeropyrum pernix. Protein Expr Purif 2010; 70:1-6. [DOI: 10.1016/j.pep.2009.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2009] [Revised: 10/04/2009] [Accepted: 10/06/2009] [Indexed: 10/20/2022]
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211
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Malshetty VS, Jain R, Srinath T, Kurthkoti K, Varshney U. Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis. Microbiology (Reading) 2010; 156:940-949. [DOI: 10.1099/mic.0.034363-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The incorporation of dUMP during replication or the deamination of cytosine in DNA results in the occurrence of uracils in genomes. To maintain genomic integrity, uracil DNA glycosylases (UDGs) excise uracil from DNA and initiate the base-excision repair pathway. Here, we cloned, purified and biochemically characterized a family 5 UDG, UdgB, from Mycobacterium smegmatis to allow us to use it as a model organism to investigate the physiological significance of the novel enzyme. Studies with knockout strains showed that compared with the wild-type parent, the mutation rate of the udgB
− strain was approximately twofold higher, whereas the mutation rate of a strain deficient in the family 1 UDG (ung
−) was found to be ∼8.4-fold higher. Interestingly, the mutation rate of the double-knockout (ung
−/udgB
−) strain was remarkably high, at ∼19.6-fold. While CG to TA mutations predominated in the ung
− and ung
−/udgB
− strains, AT to GC mutations were enhanced in the udgB
− strain. The ung
−/udgB
− strain was notably more sensitive to acidified nitrite and hydrogen peroxide stresses compared with the single knockouts (ung
− or udgB
−). These observations reveal a synergistic effect of UdgB and Ung in DNA repair, and could have implications for the generation of attenuated strains of Mycobacterium tuberculosis.
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Affiliation(s)
- Vidyasagar S. Malshetty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Ruchi Jain
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Thiruneelakantan Srinath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Krishna Kurthkoti
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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212
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Abdel-Malek ZA, Kadekaro AL, Swope VB. Stepping up melanocytes to the challenge of UV exposure. Pigment Cell Melanoma Res 2010; 23:171-86. [PMID: 20128873 DOI: 10.1111/j.1755-148x.2010.00679.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Exposure to solar ultraviolet radiation (UV) is the main etiological factor for skin cancer, including melanoma. Cutaneous pigmentation, particularly eumelanin, afforded by melanocytes is the main photoprotective mechanism, as it prevents UV-induced DNA damage in the epidermis. Therefore, maintaining genomic stability of melanocytes is crucial for prevention of melanoma, as well as keratinocyte-derived basal and squamous cell carcinoma. A critical independent factor for preventing melanoma is DNA repair capacity. The response of melanocytes to UV is mediated mainly by a network of paracrine factors that not only activate melanogenesis, but also DNA repair, anti-oxidant, and survival pathways that are pivotal for maintenance of genomic stability and prevention of malignant transformation or apoptosis. However, little is known about the stress response of melanocytes to UV and the regulation of DNA repair pathways in melanocytes. Unraveling these mechanisms might lead to strategies to prevent melanoma, as well as non-melanoma skin cancer.
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Affiliation(s)
- Zalfa A Abdel-Malek
- Department of Dermatology, University of Cincinnati Collage of Medicine, Cincinnati, OH, USA.
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213
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Raeder ILU, Moe E, Willassen NP, Smalås AO, Leiros I. Structure of uracil-DNA N-glycosylase (UNG) from Vibrio cholerae: mapping temperature adaptation through structural and mutational analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:130-6. [PMID: 20124707 PMCID: PMC2815677 DOI: 10.1107/s1744309109052063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/03/2009] [Indexed: 11/10/2022]
Abstract
The crystal structure of Vibrio cholerae uracil-DNA N-glycosylase (vcUNG) has been determined to 1.5 A resolution. Based on this structure, a homology model of Aliivibrio salmonicida uracil-DNA N-glycosylase (asUNG) was built. A previous study demonstrated that asUNG possesses typical cold-adapted features compared with vcUNG, such as a higher catalytic efficiency owing to increased substrate affinity. Specific amino-acid substitutions in asUNG were suggested to be responsible for the increased substrate affinity and the elevated catalytic efficiency by increasing the positive surface charge in the DNA-binding region. The temperature adaptation of these enzymes has been investigated using structural and mutational analyses, in which mutations of vcUNG demonstrated an increased substrate affinity that more resembled that of asUNG. Visualization of surface potentials revealed a more positive potential for asUNG compared with vcUNG; a modelled double mutant of vcUNG had a potential around the substrate-binding region that was more like that of asUNG, thus rationalizing the results obtained from the kinetic studies.
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Affiliation(s)
- Inger Lin Uttakleiv Raeder
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Elin Moe
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Nils Peder Willassen
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Arne O. Smalås
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Ingar Leiros
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
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214
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Pukáncsik M, Békési A, Klement É, Hunyadi-Gulyás É, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG. Physiological truncation and domain organization of a novel uracil-DNA-degrading factor. FEBS J 2010; 277:1245-59. [DOI: 10.1111/j.1742-4658.2009.07556.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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215
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Gredilla R, Bohr VA, Stevnsner T. Mitochondrial DNA repair and association with aging--an update. Exp Gerontol 2010; 45:478-88. [PMID: 20096766 DOI: 10.1016/j.exger.2010.01.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/10/2010] [Accepted: 01/14/2010] [Indexed: 01/07/2023]
Abstract
Mitochondrial DNA is constantly exposed to oxidative injury. Due to its location close to the main site of reactive oxygen species, the inner mitochondrial membrane, mtDNA is more susceptible than nuclear DNA to oxidative damage. The accumulation of DNA damage is thought to play a critical role in the aging process and to be particularly deleterious in post-mitotic cells. Thus, DNA repair is an important mechanism for maintenance of genomic integrity. Despite the importance of mitochondria in the aging process, it was thought for many years that mitochondria lacked an enzymatic DNA repair system comparable to that in the nuclear compartment. However, it is now well established that DNA repair actively takes place in mitochondria. Oxidative DNA damage processing, base excision repair mechanisms were the first to be described in these organelles, and consequently the best understood. However, new proteins and novel DNA repair pathways, thought to be exclusively present in the nucleus, have recently been described also to be present in mitochondria. Here we review the main mitochondrial DNA repair pathways and their association with the aging process.
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Affiliation(s)
- Ricardo Gredilla
- Danish Center for Molecular Gerontology, Department of Molecular Biology, Aarhus University, C.F. Moellers allé 3, Aarhus C, Denmark
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216
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Howell WM, Grundberg I, Faryna M, Landegren U, Nilsson M. Glycosylases and AP-cleaving enzymes as a general tool for probe-directed cleavage of ssDNA targets. Nucleic Acids Res 2010; 38:e99. [PMID: 20081204 PMCID: PMC2853139 DOI: 10.1093/nar/gkp1238] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The current arsenal of molecular tools for site-directed cleavage of single-stranded DNA (ssDNA) is limited. Here, we describe a method for targeted DNA cleavage that requires only the presence of an A nucleotide at the target position. The procedure involves hybridization of a complementary oligonucleotide probe to the target sequence. The probe is designed to create a deliberate G:A mismatch at the desired position of cleavage. The DNA repair enzyme MutY glycosylase recognizes the mismatch structure and selectively removes the mispaired A from the duplex to create an abasic site in the target strand. Addition of an AP-endonuclease, such as Endonuclease IV, subsequently cleaves the backbone dividing the DNA strand into two fragments. With an appropriate choice of an AP-cleaving enzyme, the 3′- and 5′-ends of the cleaved DNA are suitable to take part in subsequent enzymatic reactions such as priming for polymerization or joining by DNA ligation. We define suitable standard reaction conditions for glycosylase/AP-cleaving enzyme (G/AP) cleavage, and demonstrate the use of the method in an improved scheme for in situ detection using target-primed rolling-circle amplification of padlock probes.
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Affiliation(s)
- W Mathias Howell
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Se-751 85 Uppsala, Sweden.
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217
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Bharti SK, Varshney U. Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli. Nucleic Acids Res 2010; 38:2291-301. [PMID: 20056657 PMCID: PMC2853124 DOI: 10.1093/nar/gkp1210] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Uracil DNA glycosylase (Ung) initiates the uracil excision repair pathway. We have earlier characterized the Y66W and Y66H mutants of Ung and shown that they are compromised by ∼7- and ∼170-fold, respectively in their uracil excision activities. In this study, fluorescence anisotropy measurements show that compared with the wild-type, the Y66W protein is moderately compromised and attenuated in binding to AP-DNA. Allelic exchange of ung in Escherichia coli with ung::kan, ungY66H:amp or ungY66W:amp alleles showed ∼5-, ∼3.0- and ∼2.0-fold, respectively increase in mutation frequencies. Analysis of mutations in the rifampicin resistance determining region of rpoB revealed that the Y66W allele resulted in an increase in A to G (or T to C) mutations. However, the increase in A to G mutations was mitigated upon expression of wild-type Ung from a plasmid borne gene. Biochemical and computational analyses showed that the Y66W mutant maintains strict specificity for uracil excision from DNA. Interestingly, a strain deficient in AP-endonucleases also showed an increase in A to G mutations. We discuss these findings in the context of a proposal that the residency of DNA glycosylase(s) onto the AP-sites they generate shields them until recruitment of AP-endonucleases for further repair.
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Affiliation(s)
- Sanjay Kumar Bharti
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012 and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012 and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- *To whom correspondence should be addressed. Tel: +91 80 2293 2686; Fax: +91 80 2360 2697; ;
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218
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Steininger S, Ahne F, Winkler K, Kleinschmidt A, Eckardt-Schupp F, Moertl S. A novel function for the Mre11-Rad50-Xrs2 complex in base excision repair. Nucleic Acids Res 2009; 38:1853-65. [PMID: 20040573 PMCID: PMC2847237 DOI: 10.1093/nar/gkp1175] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Mre11/Rad50/Xrs2 (MRX) complex in Saccharomyces cerevisiae has well-characterized functions in DNA double-strand break processing, checkpoint activation, telomere length maintenance and meiosis. In this study, we demonstrate an involvement of the complex in the base excision repair (BER) pathway. We studied the repair of methyl-methanesulfonate-induced heat-labile sites in chromosomal DNA in vivo and the in vitro BER capacity for the repair of uracil- and 8-oxoG-containing oligonucleotides in MRX-deficient cells. Both approaches show a clear BER deficiency for the xrs2 mutant as compared to wildtype cells. The in vitro analyses revealed that both subpathways, long-patch and short-patch BER, are affected and that all components of the MRX complex are similarly important for the new function in BER. The investigation of the epistatic relationship of XRS2 to other BER genes suggests a role of the MRX complex downstream of the AP-lyases Ntg1 and Ntg2. Analysis of individual steps in BER showed that base recognition and strand incision are not affected by the MRX complex. Reduced gap-filling activity and the missing effect of aphidicoline treatment, an inhibitor for polymerases, on the BER efficiency indicate an involvement of the MRX complex in providing efficient polymerase activity.
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Affiliation(s)
- Sylvia Steininger
- Institute of Radiation Biology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
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219
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Poplawski T, Loba K, Pawlowska E, Szczepanska J, Blasiak J. Genotoxicity of urethane dimethacrylate, a tooth restoration component. Toxicol In Vitro 2009; 24:854-62. [PMID: 20005290 DOI: 10.1016/j.tiv.2009.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 11/26/2009] [Accepted: 12/03/2009] [Indexed: 01/15/2023]
Abstract
Urethane dimethacrylate (UDMA) is used in dental restorative materials in its polymeric form. However, the process of polymerization is usually incomplete and the monomers of UDMA can diffuse into the oral cavity and the pulp, reaching millimolar concentrations. In the present work we showed that UDMA at 0.1 and 1.0 mM decreased the viability of and induced DNA damage in lymphocytes in a concentration dependent manner, but it did not affect a plasmid DNA in vitro. UDMA at 1mM induced apoptosis in lymphocytes. The lymphocytes exposed to UDMA were able to repair their DNA within 60 min. Analysis with DNA repair enzymes Endo III and Fpg showed that UDMA induced mainly oxidative DNA lesions. Vitamin C and chitosan decreased genotoxic effect of UDMA. Our results show that monomers of UDMA may exert pronounced cyto- and genotoxic effects in human lymphocytes and chitosan can be considered as a protection against such effects.
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Affiliation(s)
- Tomasz Poplawski
- Department of Molecular Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
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220
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Hughes RC, Tomanicek SJ, Ng JD, Coates L. Purification, crystallization and preliminary crystallographic analysis of a thermostable endonuclease IV from Thermotoga maritima. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1317-9. [PMID: 20054139 DOI: 10.1107/s1744309109047393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Accepted: 11/09/2009] [Indexed: 11/10/2022]
Abstract
The DNA-repair enzyme endonuclease IV from the thermophilic bacterium Thermotoga maritima MSB8 (reference sequence NC_000853) has been expressed in Escherichia coli and crystallized for X-ray analysis. T. maritima endonuclease IV is a 287-amino-acid protein with 32% sequence identity to E. coli endonuclease IV. The protein was purified to homogeneity and was crystallized using the sitting-drop vapor-diffusion method. The protein crystallized in space group P6(1), with one biological molecule in the asymmetric unit, corresponding to a Matthews coefficient of 2.39 A(3) Da(-1) and 47% solvent content. The unit-cell parameters of the crystals were a = b = 123.2, c = 35.6 A. Microseeding and further optimization yielded crystals with an X-ray diffraction limit of 2.36 A. A single 70 degrees data set was collected and processed, resulting in an overall R(merge) and a completeness of 9.5% and 99.3%, respectively.
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Affiliation(s)
- Ronny C Hughes
- Oak Ridge National Laboratory, Neutron Scattering Science Division, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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221
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Cole HA, Tabor-Godwin JM, Hayes JJ. Uracil DNA glycosylase activity on nucleosomal DNA depends on rotational orientation of targets. J Biol Chem 2009; 285:2876-85. [PMID: 19933279 DOI: 10.1074/jbc.m109.073544] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The activity of uracil DNA glycosylases (UDGs), which recognize and excise uracil bases from DNA, has been well characterized on naked DNA substrates but less is known about activity in chromatin. We therefore prepared a set of model nucleosome substrates in which single thymidine residues were replaced with uracil at specific locations and a second set of nucleosomes in which uracils were randomly substituted for all thymidines. We found that UDG efficiently removes uracil from internal locations in the nucleosome where the DNA backbone is oriented away from the surface of the histone octamer, without significant disruption of histone-DNA interactions. However, uracils at sites oriented toward the histone octamer surface were excised at much slower rates, consistent with a mechanism requiring spontaneous DNA unwrapping from the nucleosome. In contrast to the nucleosome core, UDG activity on DNA outside the core DNA region was similar to that of naked DNA. Association of linker histone reduced activity of UDG at selected sites near where the globular domain of H1 is proposed to bind to the nucleosome as well as within the extra-core DNA. Our results indicate that some sites within the nucleosome core and the extra-core (linker) DNA regions represent hot spots for repair that could influence critical biological processes.
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Affiliation(s)
- Hope A Cole
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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222
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Sikora A, Mielecki D, Chojnacka A, Nieminuszczy J, Wrzesinski M, Grzesiuk E. Lethal and mutagenic properties of MMS-generated DNA lesions in Escherichia coli cells deficient in BER and AlkB-directed DNA repair. Mutagenesis 2009; 25:139-47. [PMID: 19892776 DOI: 10.1093/mutage/gep052] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methylmethane sulphonate (MMS), an S(N)2-type alkylating agent, generates DNA methylated bases exhibiting cytotoxic and mutagenic properties. Such damaged bases can be removed by a system of base excision repair (BER) and by oxidative DNA demethylation catalysed by AlkB protein. Here, we have shown that the lack of the BER system and functional AlkB dioxygenase results in (i) increased sensitivity to MMS, (ii) elevated level of spontaneous and MMS-induced mutations (measured by argE3 --> Arg(+) reversion) and (iii) induction of the SOS response shown by visualization of filamentous growth of bacteria. In the xth nth nfo strain additionally mutated in alkB gene, all these effects were extreme and led to 'error catastrophe', resulting from the presence of unrepaired apurinic/apyrimidinic (AP) sites and 1-methyladenine (1meA)/3-methylcytosine (3meC) lesions caused by deficiency in, respectively, BER and AlkB dioxygenase. The decreased level of MMS-induced Arg(+) revertants in the strains deficient in polymerase V (PolV) (bearing the deletion of the umuDC operon), and the increased frequency of these revertants in bacteria overproducing PolV (harbouring the pRW134 plasmid) indicate the involvement of PolV in the error-prone repair of 1meA/3meC and AP sites. Comparison of the sensitivity to MMS and the induction of Arg(+) revertants in the double nfo alkB and xth alkB, and the quadruple xth nth nfo alkB mutants showed that the more AP sites there are in DNA, the stronger the effect of the lack of AlkB protein. Since the sum of MMS-induced Arg(+) revertants in xth, nfo and nth xth nfo and alkB mutants is smaller than the frequency of these revertants in the BER(-) alkB(-) strain, we consider two possibilities: (i) the presence of AP sites in DNA results in relaxation of its structure that facilitates methylation and (ii) additional AP sites are formed in the BER(-) alkB(-) mutants.
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Affiliation(s)
- Anna Sikora
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
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223
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DNA damage/repair and polymorphism of the hOGG1 gene in lymphocytes of AMD patients. J Biomed Biotechnol 2009; 2009:827562. [PMID: 19885394 PMCID: PMC2766933 DOI: 10.1155/2009/827562] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 06/25/2009] [Accepted: 08/24/2009] [Indexed: 11/17/2022] Open
Abstract
Oxidative stress is thought to play a role in the pathogenesis of age-related macular degeneration (AMD). We determined the extent of oxidative DNA damage and the kinetics of its removal as well as the genotypes of the Ser326Cys polymorphism of the hOGG1 gene in lymphocytes of 30 wet AMD patients and 30 controls. Oxidative DNA damage induced by hydrogen peroxide and its repair were evaluated by the comet assay and DNA repair enzymes. We observed a higher extent of endogenous oxidative DNA damage and a lower efficacy of its repair in AMD patients as compared with the controls. We did not find any correlation between the extent of DNA damage and efficacy of DNA repair with genotypes of the Ser326Cys polymorphism. The results obtained suggest that oxidative DNA damage and inefficient DNA repair can be associated with AMD and the variability of the hOOG1 gene may not contribute to this association.
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224
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Fujimoto Y, Morinaga K, Abe M, Kitamura T, Sakuma S. Selenite induces oxidative DNA damage in primary rat hepatocyte cultures. Toxicol Lett 2009; 191:341-6. [PMID: 19822199 DOI: 10.1016/j.toxlet.2009.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/02/2009] [Accepted: 10/02/2009] [Indexed: 11/28/2022]
Abstract
The effects of selenite ions on oxidative DNA damage in primary rat hepatocyte cultures were examined. Selenite ions dose-dependently stimulated 8-hydroxydeoxyguanosine formation in DNA from the hepatocyte cultures at concentrations of 1, 5 and 10 micromol/L (1.6-, 2.5- and 3.6-fold). Selenite ions also induced DNA fragmentation in nucleus from the hepatocyte cultures at concentrations of 5 and 10 micromol/L. Selenite ions could not affect protein expression levels of 8-oxoguanine DNA glycosylase 1 which is responsible for excision of 8-hydroxydeoxyguanosine from DNA, but could increase 2',7'-dichlorofluorescein-fluorescence intensity from 2',7'-dichlorodihydrofluorescein, an indicator of reactive oxygen species generation, at concentrations of 5 and 10 micromol/L. Furthermore, an increase in 8-hydroxydeoxyguanosine induced by selenite ions (10 micromol/L) was inhibited by free radical scavengers (alpha-tocopherol, N-acetyl-L-cysteine, and melatonin) at concentrations more than 50 micromol/L. These observations imply that selenite ions have the potential to induce oxidative DNA damage in the liver through an increase in reactive oxygen species formation, but not a decrease in 8-oxoguanine DNA glycosylase 1 protein expression levels.
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Affiliation(s)
- Yohko Fujimoto
- Laboratory of Physiological Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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225
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Abstract
Heterochromatin protein 1 (HP1) family members are versatile proteins involved in transcription, chromatin organization, and replication. Recent findings now have implicated HP1 proteins in the DNA damage response as well. Cell-biological approaches showed that reducing the levels of all three HP1 isoforms enhances DNA repair, possibly due to heterochromatin relaxation. Additionally, HP1 is phosphorylated in response to DNA damage, which was suggested to initiate the DNA damage response. These findings have led to the conclusion that heterochromatic proteins are inhibitory to repair and that their dissociation from heterochromatin may facilitate repair. In contrast with an inhibitory role, a more active role for HP1 in DNA repair also was proposed based on the finding that all HP1 isoforms are recruited to UV-induced lesions, oxidative lesions, and DNA breaks. The loss of HP1 renders nematodes highly sensitive to DNA damage, and mice lacking HP1beta suffer from genomic instability, suggesting that the loss of HP1 is not necessarily beneficial for repair. These findings raise the possibility that HP1 facilitates DNA repair by reorganizing chromatin, which may involve interactions between phosphorylated HP1 and other DNA damage response proteins. Taken together, these studies illustrate an emerging role of HP1 proteins in the response to genotoxic stress.
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226
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Todorov IN, Todorov GI. Multifactorial nature of high frequency of mitochondrial DNA mutations in somatic mammalian cells. BIOCHEMISTRY (MOSCOW) 2009; 74:962-70. [DOI: 10.1134/s000629790909003x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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227
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Nakatani K. Recognition of Mismatched Base Pairs in DNA. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1055] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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228
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Wang YF, Yang G, Liu CB. Electron transfers in proteins: investigations with a modified through-bond coupling model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:021927. [PMID: 19792171 DOI: 10.1103/physreve.80.021927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 07/15/2009] [Indexed: 05/28/2023]
Abstract
By integrating the merits of previous models, a modified through-bond coupling (MTBC) model is proposed in this work and shows obvious improvement compared with previous models. With the MTBC model, the dominant electron coupling pathways in the polypeptide chains were identified, where the N-H bonds were found to be essential to the electron couplings. The local structures of peptides and proteins were finely characterized by the electron couplings and decay factors since they are structure sensitive. The neighboring carbonyl O-O distances are qualitatively correlated with the decay factors, and the deviations from the transconfigurations will weaken the coupling interactions. When the two amino acids being studied are not close in sequence, the couplings through hydrogen bonds are probably the main pathway because the electron transfers in this way save many steps, albeit the decay factor is less than that of per bond, consistent with the classical electron-tunneling model developed by Beratan [Science 252, 1285 (1991)]. It was found that the MTBC model can be effectively extended to study the electron transfers in complex biological systems with the combination of the fragment approach, which takes into account the contributions of key hydrogen bonds.
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Affiliation(s)
- Ye-Fei Wang
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100 Shandong, People's Republic of China
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229
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Shalaby NA, Parks AL, Morreale EJ, Osswalt MC, Pfau KM, Pierce EL, Muskavitch MAT. A screen for modifiers of notch signaling uncovers Amun, a protein with a critical role in sensory organ development. Genetics 2009; 182:1061-76. [PMID: 19448274 PMCID: PMC2728848 DOI: 10.1534/genetics.108.099986] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Accepted: 05/11/2009] [Indexed: 12/14/2022] Open
Abstract
Notch signaling is an evolutionarily conserved pathway essential for many cell fate specification events during metazoan development. We conducted a large-scale transposon-based screen in the developing Drosophila eye to identify genes involved in Notch signaling. We screened 10,447 transposon lines from the Exelixis collection for modifiers of cell fate alterations caused by overexpression of the Notch ligand Delta and identified 170 distinct modifier lines that may affect up to 274 genes. These include genes known to function in Notch signaling, as well as a large group of characterized and uncharacterized genes that have not been implicated in Notch pathway function. We further analyze a gene that we have named Amun and show that it encodes a protein that localizes to the nucleus and contains a putative DNA glycosylase domain. Genetic and molecular analyses of Amun show that altered levels of Amun function interfere with cell fate specification during eye and sensory organ development. Overexpression of Amun decreases expression of the proneural transcription factor Achaete, and sensory organ loss caused by Amun overexpression can be rescued by coexpression of Achaete. Taken together, our data suggest that Amun acts as a transcriptional regulator that can affect cell fate specification by controlling Achaete levels.
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Affiliation(s)
- Nevine A Shalaby
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467, USA
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230
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Imamura K, Wallace SS, Doublié S. Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA. J Biol Chem 2009; 284:26174-83. [PMID: 19625256 DOI: 10.1074/jbc.m109.021907] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Endonuclease VIII (Nei) is a DNA glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. We determined the crystal structures of a NEIL1 ortholog from the giant Mimivirus (MvNei1) unliganded and bound to DNA containing tetrahydrofuran (THF), which is the first structure of any Nei with an abasic site analog. The MvNei1 structures exhibit the same overall architecture as other enzymes of the Fpg/Nei family, which consists of two globular domains joined by a linker region. MvNei1 harbors a zincless finger, first described in human NEIL1, rather than the signature zinc finger generally found in the Fpg/Nei family. In contrast to Escherichia coli Nei, where a dramatic conformational change was observed upon binding DNA, the structure of MvNei1 bound to DNA does not reveal any substantial movement compared with the unliganded enzyme. A protein segment encompassing residues 217-245 in MvNei1 corresponds to the "missing loop" in E. coli Nei and the "alphaF-beta10 loop" in E. coli Fpg, which has been reported to be involved in lesion recognition. Interestingly, the corresponding loop in MvNei1 is ordered in both the unliganded and furan-bound structures, unlike other Fpg/Nei enzymes where the loop is generally ordered in the unliganded enzyme or in complexes with a lesion, and disordered otherwise. In the MvNei1.tetrahydrofuran complex a tyrosine located at the tip of the putative lesion recognition loop stacks against the furan ring; the tyrosine is predicted to adopt a different conformation to accommodate a modified base.
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Affiliation(s)
- Kayo Imamura
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405-0068, USA
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231
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Boesch P, Ibrahim N, Paulus F, Cosset A, Tarasenko V, Dietrich A. Plant mitochondria possess a short-patch base excision DNA repair pathway. Nucleic Acids Res 2009; 37:5690-700. [PMID: 19625491 PMCID: PMC2761273 DOI: 10.1093/nar/gkp606] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Despite constant threat of oxidative damage, sequence drift in mitochondrial and chloroplast DNA usually remains very low in plant species, indicating efficient defense and repair. Whereas the antioxidative defense in the different subcellular compartments is known, the information on DNA repair in plant organelles is still scarce. Focusing on the occurrence of uracil in the DNA, the present work demonstrates that plant mitochondria possess a base excision repair (BER) pathway. In vitro and in organello incision assays of double-stranded oligodeoxyribonucleotides showed that mitochondria isolated from plant cells contain DNA glycosylase activity specific for uracil cleavage. A major proportion of the uracil–DNA glycosylase (UDG) was associated with the membranes, in agreement with the current hypothesis that the DNA is replicated, proofread and repaired in inner membrane-bound nucleoids. Full repair, from uracil excision to thymidine insertion and religation, was obtained in organello following import of a uracil-containing DNA fragment into isolated plant mitochondria. Repair occurred through single nucleotide insertion, which points to short-patch BER. In vivo targeting and in vitro import of GFP fusions showed that the putative UDG encoded by the At3g18 630 locus might be the first enzyme of this mitochondrial pathway in Arabidopsis thaliana.
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Affiliation(s)
- Pierre Boesch
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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232
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Baldwin MR, O'Brien PJ. Human AP endonuclease 1 stimulates multiple-turnover base excision by alkyladenine DNA glycosylase. Biochemistry 2009; 48:6022-33. [PMID: 19449863 DOI: 10.1021/bi900517y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human alkyladenine DNA glycosylase (AAG) locates and excises a wide variety of damaged purine bases from DNA, including hypoxanthine that is formed by the oxidative deamination of adenine. We used steady state, pre-steady state, and single-turnover kinetic assays to show that the multiple-turnover excision of hypoxanthine in vitro is limited by release of the abasic DNA product. This suggests the possibility that the product release step is regulated in vivo by interactions with other base excision repair (BER) proteins. Such coordination of BER activities would protect the abasic DNA repair intermediate and ensure its correct processing. AP endonuclease 1 (APE1) is the predominant enzyme for processing abasic DNA sites in human cells. Therefore, we have investigated the functional effects of added APE1 on the base excision activity of AAG. We find that APE1 stimulates the multiple-turnover excision of hypoxanthine by AAG but has no effect on single-turnover excision. Since the amino terminus of AAG has been implicated in other protein-protein interactions, we also characterize the deletion mutant lacking the first 79 amino acids. We find that APE1 fully stimulates the multiple-turnover glycosylase activity of this mutant, demonstrating that the amino terminus of AAG is not strictly required for this functional interaction. These results are consistent with a model in which APE1 displaces AAG from the abasic site, thereby coordinating the first two steps of the base excision repair pathway.
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Affiliation(s)
- Michael R Baldwin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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233
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López-Camarillo C, Lopez-Casamichana M, Weber C, Guillen N, Orozco E, Marchat LA. DNA repair mechanisms in eukaryotes: Special focus in Entamoeba histolytica and related protozoan parasites. INFECTION GENETICS AND EVOLUTION 2009; 9:1051-6. [PMID: 19591963 DOI: 10.1016/j.meegid.2009.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 06/22/2009] [Accepted: 06/29/2009] [Indexed: 01/11/2023]
Abstract
Eukaryotic cell viability highly relies on genome stability and DNA integrity maintenance. The cellular response to DNA damage mainly consists of six biological conserved pathways known as homologous recombination repair (HRR), non-homologous end-joining (NHEJ), base excision repair (BER), mismatch repair (MMR), nucleotide excision repair (NER), and methyltransferase repair that operate in a concerted way to minimize genetic information loss due to a DNA lesion. Particularly, protozoan parasites survival depends on DNA repair mechanisms that constantly supervise chromosomes to correct damaged nucleotides generated by cytotoxic agents, host immune pressure or cellular processes. Here we reviewed the current knowledge about DNA repair mechanisms in the most relevant human protozoan pathogens. Additionally, we described the recent advances to understand DNA repair mechanisms in Entamoeba histolytica with special emphasis in the use of genomic approaches based on bioinformatic analysis of parasite genome sequence and microarrays technology.
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Affiliation(s)
- César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México DF, Mexico.
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234
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Dherin C, Gasparutto D, O'Connor TR, Cadet J, Boiteux S. Excision by the human methylpurine DNAN‐glycosylase of cyanuric acid, a stable and mutagenic oxidation product of 8‐oxo‐7,8‐dihydroguanine. Int J Radiat Biol 2009; 80:21-7. [PMID: 14761847 DOI: 10.1080/09553000310001632976] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
PURPOSE 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-cyanuric acid (cyanuric acid nucleoside or dCa) has been shown to be formed upon exposure of 8-oxo-7,8-dihydroguanine- (8-oxoG) containing oligodeoxyribonucleotides (ODN) to oxidizing agents. When present in DNA, cyanuric acid (Ca) is readily bypassed by Escherichia coli DNA polymerases, which preferentially incorporate 2'-deoxyadenosine-5'-monophosphate (dAMP) opposite to the lesion. Therefore, Ca could be a mutagenic DNA lesion yielding G.C to T.A transversions like 8-oxoG. These results call attention to the potential importance of secondary oxidation products of 8-oxoG. The present study investigates the capability of several DNA N-glycosylases to remove the Ca lesion in DNA. MATERIALS AND METHODS A site-specifically modified 22-mer ODN containing a single Ca residue was hybridized with complementary sequences yielding four DNA duplexes harbouring Ca opposite each of the regular DNA bases. The four Ca.N duplexes were used as substrates for nine DNA N-glycosylases from bacterial, yeast or human origin. RESULTS The results show that the human methylpurine DNA N-glycosylase (Mpg) can remove Ca from DNA duplexes. Interestingly, oxidized base-specific DNA N-glycosylases, Fpg, Nth, Ntg1, Ntg2, Ogg1, hNth1 and hOgg1, cannot repair Ca in DNA. Furthermore, the removal of Ca by Mpg varied markedly depending on the opposite DNA base, the rank being Ca.C=Ca.T>Ca.G=Ca.A. CONCLUSIONS 8-OxoG-derived lesions in DNA such as spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), oxaluric acid (Oa), oxazolone (Oz) and Ca are substrates of base excision repair DNA N-glycosylases. Most of them, Sp, Gh, Oa and Oz, are substrates of the oxidized bases-specific enzymes such as Nth or Fpg. In contrast, Ca is substrate of the human methylpurine DNA N-glycosylase (Mpg).
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Affiliation(s)
- C Dherin
- CEA, Département de Radiobiologie et Radiopathologie, UMR217 CNRS/CEA Radiobiologie Moléculaire et Cellulaire, BP6, F92265 Fontenay aux Roses, France
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235
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Dalhus B, Laerdahl JK, Backe PH, Bjørås M. DNA base repair--recognition and initiation of catalysis. FEMS Microbiol Rev 2009; 33:1044-78. [PMID: 19659577 DOI: 10.1111/j.1574-6976.2009.00188.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Endogenous DNA damage induced by hydrolysis, reactive oxygen species and alkylation modifies DNA bases and the structure of the DNA duplex. Numerous mechanisms have evolved to protect cells from these deleterious effects. Base excision repair is the major pathway for removing base lesions. However, several mechanisms of direct base damage reversal, involving enzymes such as transferases, photolyases and oxidative demethylases, are specialized to remove certain types of photoproducts and alkylated bases. Mismatch excision repair corrects for misincorporation of bases by replicative DNA polymerases. The determination of the 3D structure and visualization of DNA repair proteins and their interactions with damaged DNA have considerably aided our understanding of the molecular basis for DNA base lesion repair and genome stability. Here, we review the structural biochemistry of base lesion recognition and initiation of one-step direct reversal (DR) of damage as well as the multistep pathways of base excision repair (BER), nucleotide incision repair (NIR) and mismatch repair (MMR).
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Affiliation(s)
- Bjørn Dalhus
- Centre for Molecular Biology and Neuroscience (CMBN), Rikshospitalet University Hospital, Oslo, Norway
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236
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Schurman SH, Hedayati M, Wang Z, Singh DK, Speina E, Zhang Y, Becker K, Macris M, Sung P, Wilson DM, Croteau DL, Bohr VA. Direct and indirect roles of RECQL4 in modulating base excision repair capacity. Hum Mol Genet 2009; 18:3470-83. [PMID: 19567405 DOI: 10.1093/hmg/ddp291] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
RECQL4 is a human RecQ helicase which is mutated in approximately two-thirds of individuals with Rothmund-Thomson syndrome (RTS), a disease characterized at the cellular level by chromosomal instability. BLM and WRN are also human RecQ helicases, which are mutated in Bloom and Werner's syndrome, respectively, and associated with chromosomal instability as well as premature aging. Here we show that primary RTS and RECQL4 siRNA knockdown human fibroblasts accumulate more H(2)O(2)-induced DNA strand breaks than control cells, suggesting that RECQL4 may stimulate repair of H(2)O(2)-induced DNA damage. RTS primary fibroblasts also accumulate more XRCC1 foci than control cells in response to endogenous or induced oxidative stress and have a high basal level of endogenous formamidopyrimidines. In cells treated with H(2)O(2), RECQL4 co-localizes with APE1, and FEN1, key participants in base excision repair. Biochemical experiments indicate that RECQL4 specifically stimulates the apurinic endonuclease activity of APE1, the DNA strand displacement activity of DNA polymerase beta, and incision of a 1- or 10-nucleotide flap DNA substrate by Flap Endonuclease I. Additionally, RTS cells display an upregulation of BER pathway genes and fail to respond like normal cells to oxidative stress. The data herein support a model in which RECQL4 regulates both directly and indirectly base excision repair capacity.
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Affiliation(s)
- Shepherd H Schurman
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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237
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Gutman BL, Niyogi KK. Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana. J Biol Chem 2009; 284:17006-17012. [PMID: 19372224 PMCID: PMC2719338 DOI: 10.1074/jbc.m109.008342] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 04/15/2009] [Indexed: 11/06/2022] Open
Abstract
Chloroplasts are the sites of photosynthesis in plants, and they contain their own multicopy, requisite genome. Chloroplasts are also major sites for production of reactive oxygen species, which can damage essential components of the chloroplast, including the chloroplast genome. Compared with mitochondria in animals, relatively little is known about the potential to repair oxidative DNA damage in chloroplasts. Here we provide evidence of DNA glycosylase-lyase/endonuclease activity involved in base excision repair of oxidized pyrimidines in chloroplast protein extracts of Arabidopsis thaliana. Three base excision repair components (two endonuclease III homologs and an apurinic/apyrimidinic endonuclease) that might account for this activity were identified by bioinformatics. Transient expression of protein-green fluorescent protein fusions showed that all three are targeted to the chloroplast and co-localized with chloroplast DNA in nucleoids. The glycosylase-lyase/endonuclease activity of one of the endonuclease III homologs, AtNTH2, which had not previously been characterized, was confirmed in vitro. T-DNA insertions in each of these genes were identified, and the physiological and biochemical phenotypes of the single, double, and triple mutants were analyzed. This mutant analysis revealed the presence of a third glycosylase activity and potentially another pathway for repair of oxidative DNA damage in chloroplasts.
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Affiliation(s)
- Benjamin L Gutman
- From the Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Krishna K Niyogi
- From the Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102.
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238
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Jozwiakowski SK, Connolly BA. Plasmid-based lacZalpha assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase. Nucleic Acids Res 2009; 37:e102. [PMID: 19515939 PMCID: PMC2731893 DOI: 10.1093/nar/gkp494] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The preparation of a gapped pUC18 derivative, containing the lacZα reporter gene in the single-stranded region, is described. Gapping is achieved by flanking the lacZα gene with sites for two related nicking endonucleases, enabling the excision of either the coding or non-coding strand. However, the excised strand remains annealed to the plasmid through non-covalent Watson–Crick base-pairing; its removal, therefore, requires a heat–cool cycle in the presence of an exactly complementary competitor DNA. The gapped plasmids can be used to assess DNA polymerase fidelity using in vitro replication, followed by transformation into Escherichia coli and scoring the blue/white colony ratio. Results found with plasmids are similar to the well established method based on gapped M13, in terms of background (∼0.08% in both cases) and the mutation frequencies observed with a number of DNA polymerases, providing validation for this straightforward and technically uncomplicated approach. Several error prone variants of the archaeal family-B DNA polymerase from Pyrococcus furiosus have been investigated, illuminating the potential of the method.
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Affiliation(s)
- Stanislaw K Jozwiakowski
- Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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239
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Du Y, Wooten MC, Wooten MW. Oxidative damage to the promoter region of SQSTM1/p62 is common to neurodegenerative disease. Neurobiol Dis 2009; 35:302-10. [PMID: 19481605 DOI: 10.1016/j.nbd.2009.05.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 05/11/2009] [Accepted: 05/17/2009] [Indexed: 01/21/2023] Open
Abstract
Recently we reported that declined SQSTM1/p62 expression in Alzheimer disease brain was age-correlated with oxidative damage to the p62 promoter. The objective of this study was to examine whether oxidative damage to the p62 promoter is common to DNA recovered from brain of individuals with neurodegenerative disease. Increased 8-OHdG staining was observed in brain sections from Alzheimer's disease (AD), Parkinson disease (PD), Huntington disease (HD), Frontotemporal dementia (FTD), and Pick's disease compared to control subjects. In parallel, the p62 promoter exhibited elevated oxidative damage in samples from various diseases compared to normal brain, and damage was negatively correlated with p62 expression in FTD samples. Oxidative damage to the p62 promoter induced by H2O2 treatment decreased its transcriptional activity. In keeping with this observation, the transcriptional activity of a Sp-1 element deletion mutant displayed reduced stimulus-induced activity. These findings reveal that oxidative damage to the p62 promoter decreased its transcriptional activity and might therefore account for decreased expression of p62. Altogether these results suggest that pharmacological means to increase p62 expression may be beneficial in delaying the onset of neurodegeneration.
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Affiliation(s)
- Yifeng Du
- Department of Biological Sciences, Cellular and Molecular Biosciences Program, 331 Funchess Hall, Auburn University, AL 38849, USA
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240
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Li M, Sato Y, Nishizawa S, Seino T, Nakamura K, Teramae N. 2-Aminopurine-modified abasic-site-containing duplex DNA for highly selective detection of theophylline. J Am Chem Soc 2009; 131:2448-9. [PMID: 19191489 DOI: 10.1021/ja8095625] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Aminopurine-modified abasic-site-containing duplex [DNA 5'-TCTGC GTCCT PXT TAACG CACAC-3'/3'-AGACG CAGGA TCA ATTGC GTGTG-5'; P = 2-aminopurine, X = abasic site (Spacer-C3), C = receptor base] is capable of selectively binding to the bronchodilator theophylline with a dissociation constant of 10 microM (5 degrees C, pH 7.0, I = 0.11 M) and is applicable to monitoring serum theophylline concentrations.
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Affiliation(s)
- Minjie Li
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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241
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Akbari M, Peña-Diaz J, Andersen S, Liabakk NB, Otterlei M, Krokan HE. Extracts of proliferating and non-proliferating human cells display different base excision pathways and repair fidelity. DNA Repair (Amst) 2009; 8:834-43. [PMID: 19442590 DOI: 10.1016/j.dnarep.2009.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/03/2009] [Accepted: 04/13/2009] [Indexed: 10/20/2022]
Abstract
Base excision repair (BER) of damaged or inappropriate bases in DNA has been reported to take place by single nucleotide insertion or through incorporation of several nucleotides, termed short-patch and long-patch repair, respectively. We found that extracts from proliferating and non-proliferating cells both had capacity for single- and two-nucleotide insertion BER activity. However, patch size longer than two nucleotides was only detected in extracts from proliferating cells. Relative to extracts from proliferating cells, extracts from non-proliferating cells had approximately two-fold higher concentration of POLbeta, which contributed to most of two-nucleotide insertion BER. In contrast, two-nucleotide insertion in extracts from proliferating cells was not dependent on POLbeta. BER fidelity was two- to three-fold lower in extracts from the non-proliferating compared with extracts of proliferating cells. Furthermore, although one-nucleotide deletion was the predominant type of repair error in both extracts, the pattern of repair errors was somewhat different. These results establish two-nucleotide patch BER as a distinct POLbeta-dependent mechanism in non-proliferating cells and demonstrate that BER fidelity is lower in extracts from non-proliferating as compared with proliferating cells.
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Affiliation(s)
- Mansour Akbari
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, NTNU, N-7489 Trondheim, Norway.
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242
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Micronucleus Occurrence Related to Base Excision Repair Gene Polymorphisms in Chinese Workers Occupationally Exposed to Vinyl Chloride Monomer. J Occup Environ Med 2009; 51:578-85. [DOI: 10.1097/jom.0b013e3181990d19] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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243
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Przybylski JL, Wetmore SD. Designing an Appropriate Computational Model for DNA Nucleoside Hydrolysis: A Case Study of 2′-Deoxyuridine. J Phys Chem B 2009; 113:6533-42. [DOI: 10.1021/jp810472q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer L. Przybylski
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge Alberta T1K 3M4 Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge Alberta T1K 3M4 Canada
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244
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Buzzeo MC, Barton JK. Redmond Red as a redox probe for the DNA-mediated detection of abasic sites. Bioconjug Chem 2009; 19:2110-2. [PMID: 18831574 DOI: 10.1021/bc800339y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redmond Red, a fluoropore containing a redox-active phenoxazine core, has been explored as a new electrochemical probe for the detection of abasic sites in double-stranded DNA. The electrochemical behavior of Redmond Red-modified DNA at gold surfaces exhibits stable, quasi-reversible voltammetry with a midpoint potential centered around -50 mV versus NHE. Importantly, with Redmond Red positioned opposite an abasic site within the DNA duplex, the electrochemical response is significantly enhanced compared to Redmond Red positioned across from a base. Redmond Red, reporting only if well-stacked in the duplex, represents a sensitive probe to detect abasic sites electrochemically in a DNA-mediated reaction.
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Affiliation(s)
- Marisa C Buzzeo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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245
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Visnes T, Doseth B, Pettersen HS, Hagen L, Sousa MML, Akbari M, Otterlei M, Kavli B, Slupphaug G, Krokan HE. Uracil in DNA and its processing by different DNA glycosylases. Philos Trans R Soc Lond B Biol Sci 2009; 364:563-8. [PMID: 19008197 DOI: 10.1098/rstb.2008.0186] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Uracil in DNA may result from incorporation of dUMP during replication and from spontaneous or enzymatic deamination of cytosine, resulting in U:A pairs or U:G mismatches, respectively. Uracil generated by activation-induced cytosine deaminase (AID) in B cells is a normal intermediate in adaptive immunity. Five mammalian uracil-DNA glycosylases have been identified; these are mitochondrial UNG1 and nuclear UNG2, both encoded by the UNG gene, and the nuclear proteins SMUG1, TDG and MBD4. Nuclear UNG2 is apparently the sole contributor to the post-replicative repair of U:A lesions and to the removal of uracil from U:G contexts in immunoglobulin genes as part of somatic hypermutation and class-switch recombination processes in adaptive immunity. All uracil-DNA glycosylases apparently contribute to U:G repair in other cells, but they are likely to have different relative significance in proliferating and non-proliferating cells, and in different phases of the cell cycle. There are also some indications that there may be species differences in the function of the uracil-DNA glycosylases.
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Affiliation(s)
- Torkild Visnes
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway
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246
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Darbary H, Stoler DL, Anderson GR. Family cancer syndromes: inherited deficiencies in systems for the maintenance of genomic integrity. Surg Oncol Clin N Am 2009; 18:1-17, vii. [PMID: 19056039 DOI: 10.1016/j.soc.2008.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Familial cancer syndromes have revealed important fundamental features regarding how all cancers arise through destabilization of the genome, such that somatic evolution can select for the disruption of critical cellular coordinating and regulatory features. The authors examine those cellular genes and systems whose normal role is to preserve genomic integrity and relate them to the genetic foundations of heritable cancers. By examining how these cellular systems normally function, how family cancer genes are able to affect the process of tumor progression can be learned. In so doing, a clearer picture of how sporadic cancers arise is additionally gained.
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Affiliation(s)
- Huferesh Darbary
- Department of Cancer Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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247
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Bhakat KK, Mantha AK, Mitra S. Transcriptional regulatory functions of mammalian AP-endonuclease (APE1/Ref-1), an essential multifunctional protein. Antioxid Redox Signal 2009; 11:621-38. [PMID: 18715144 PMCID: PMC2933571 DOI: 10.1089/ars.2008.2198] [Citation(s) in RCA: 197] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The mammalian AP-endonuclease (APE1/Ref-1) plays a central role in the repair of oxidized and alkylated bases in mammalian genomes via the base excision repair (BER) pathway. However, APE1, unlike its E. coli prototype Xth, has two unique and apparently distinct transcriptional regulatory activities. APE1 functions as a redox effector factor (Ref-1) for several transcription factors including AP-1, HIF1-alpha, and p53. APE1 was also identified as a direct trans-acting factor for repressing human parathyroid hormone (PTH) and renin genes by binding to the negative calcium-response element (nCaRE) in their promoters. We have characterized APE1's post-translational modification, namely, acetylation which modulates its transcriptional regulatory function. Furthermore, stable interaction of APE1 with several other trans-acting factors including HIF-1alpha, STAT3, YB-1, HDAC1, and CBP/p300 and formation of distinct trans-acting complexes support APE1's direct regulatory function for diverse genes. Multiple functions of mammalian APE1, both in DNA repair and gene regulation, warrant extensive analysis of its own regulation and dissection of the mechanisms. In this review, we have discussed APE1's own regulation and its role as a transcriptional coactivator or corepressor by both redox-dependent and redox-independent (acetylation-mediated) mechanisms, and explore the potential utility of targeting these functions for enhancing drug sensitivity of cancer cells.
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Affiliation(s)
- Kishor K Bhakat
- Department of Biochemistry and Molecular Biology, and Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA.
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248
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Repair and tolerance of oxidative DNA damage in plants. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2009; 681:169-179. [DOI: 10.1016/j.mrrev.2008.07.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/11/2008] [Accepted: 07/17/2008] [Indexed: 11/19/2022]
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249
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Poplawski T, Pawlowska E, Wisniewska-Jarosinska M, Ksiazek D, Wozniak K, Szczepanska J, Blasiak J. Cytotoxicity and genotoxicity of glycidyl methacrylate. Chem Biol Interact 2009; 180:69-78. [PMID: 19428346 DOI: 10.1016/j.cbi.2009.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 02/02/2009] [Accepted: 02/04/2009] [Indexed: 12/11/2022]
Abstract
Methacrylates are used in the polymer form as composite restorative materials in dentistry. However, the polymers can release monomers and co-monomers into the oral cavity and pulp, from where they can migrate into the bloodstream reaching virtually all organs. The local concentration of the released monomers can be in the millimolar range, high enough to induce adverse biological effects. Genotoxicity of methacrylate monomers is of a special significance due to potential serious phenotypic consequences, including cancer, and long latency period. In the present work, we investigated cytotoxicity and genotoxicity of glycidyl methacrylate (GMA) in the human peripheral blood lymphocytes and the CCR-CM human cancer cells. GMA at concentrations up to 5mM evoked a concentration-dependent decrease in the viability of the lymphocytes up to about 80%, as assessed by flow cytometry. This agent did not induce strand breaks in the isolated plasmid DNA, but evoked concentration-dependent DNA damage in the human lymphocytes evaluated by the alkaline and neutral comet assay. This damage included oxidative modifications to the DNA bases, as checked by DNA repair enzymes Endo III and Fpg as well as single and double DNA strand breaks. The lymphocytes exposed to GMA at 2.5 microM were able to remove about 90% of damage to their DNA in 120 min. The ability of GMA to induce DNA double-strand breaks was confirmed by pulsed field gel electrophoresis. The drug evoked apoptosis and induced an increase in the G2/M cell population, accompanied by a decrease in the S cell population and an increase in G0/G1 cell population. Due to broad spectrum of GMA genotoxicity, including DNA double-strand breaks, and a potential long-lasting exposure to this compound, its use should be accompanied by precautions, reducing the chance of its release into blood stream and the possibility to induce adverse biological effects.
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Affiliation(s)
- Tomasz Poplawski
- Department of Molecular Genetics, University of Lodz, Lodz, Poland
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250
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Vértessy BG, Tóth J. Keeping uracil out of DNA: physiological role, structure and catalytic mechanism of dUTPases. Acc Chem Res 2009; 42:97-106. [PMID: 18837522 DOI: 10.1021/ar800114w] [Citation(s) in RCA: 183] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The thymine-uracil exchange constitutes one of the major chemical differences between DNA and RNA. Although these two bases form the same Watson-Crick base pairs with adenine and are equivalent for both information storage and transmission, uracil incorporation in DNA is usually a mistake that needs to be excised. There are two ways for uracil to appear in DNA: thymine replacement and cytosine deamination. Most DNA polymerases readily incorporate dUMP as well as dTMP depending solely on the availability of the d(U/T)TP building block nucleotides. Cytosine deamination results in mutagenic U:G mismatches that must be excised. The repair system, however, also excises U from U:A "normal" pairs. It is therefore crucial to limit thymine-replacing uracils.dUTP is constantly produced in the pyrimidine biosynthesis network. To prevent uracil incorporation into DNA, representatives of the dUTP nucleotidohydrolase (dUTPase) enzyme family eliminate excess dUTP. This Account describes recent studies that have provided important detailed insights into the structure and function of these essential enzymes.dUTPases typically possess exquisite specificity and display an intriguing homotrimer active site architecture. Conserved residues from all three monomers contribute to each of the three active sites within the dUTPase. Although even dUTPases from evolutionarily distant species possess similar structural and functional traits, in a few cases, a monomer dUTPase mimics the trimer structure through an unusual folding pattern. Catalysis proceeds by way of an SN2 mechanism; a water molecule initiates in-line nucleophilic attack. The dUTPase binding pocket is highly specific for uracil. Phosphate chain coordination involves Mg2+ and is analogous to that of DNA polymerases. Because of conformational changes in the enzyme during catalysis, most crystal structures have not resolved the residues in the C-terminus. However, recent high-resolution structures are beginning to provide in-depth structural information about this region of the protein.The dUTPase family of enzymes also shows promise as novel targets for anticancer and antimicrobial therapies. dUTPase is upregulated in human tumor cells. In addition, dUTPase inhibitors could also fight infectious diseases such as malaria and tuberculosis. In these respective pathogens, Plasmodium falciparum and Mycobacterium tuberculosis, the biosynthesis of dTMP relies exclusively on dUTPase activity.
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Affiliation(s)
- Beáta G Vértessy
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
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