Bacterial DNA repair genes and their aukaryotic homologues: 1. Mutations in genes involved in base excision repair [BER] and DNA-end processors and their implication in mutagenesis and human disease

• Autorzy: Krwawicz J. , Arczewska K.D. , Speina E. , Maciejewska A. , Grzesiuk E.
• Języki publikacji: EN

Abstrakty

EN

Base excision repair (BER) pathway executed by a complex network of proteins is the major system responsible for the removal of damaged DNA bases and repair of DNA single strand breaks (SSBs) generated by environmental agents, such as certain cancer therapies, or arising spontaneously during cellular metabolism. Both modified DNA bases and SSBs with ends other than 3'-OH and 5'-P are repaired either by replacement of a single or of more nucleotides in the processes called short-patch BER (SP-BER) or long-patch BER (LP-BER), respectively. In contrast to Escherichia coli cells, in human ones, the two BER sub-pathways are operated by different sets of proteins. In this review the selection between SP- and LP-BER and mutations in BER and end-processors genes and their contribution to bacterial mutagenesis and human diseases are considered.

Słowa kluczowe

EN

glycosylase; human disease; gene; DNA repair gene; base excision repair; DNA repair; cancer therapy; DNA damage; mutagenesis; mutation; protein interaction; endonuclease

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2007
• Tom: 54
• Numer: 3
• Opis fizyczny: p.413-434,fig.,ref.

Twórcy

autor

Krwawicz J.

• Polish Academy of Sciences, A.Pawinskiego 5a, 01-106 Warsaw, Poland

autor

Arczewska K.D.

autor

Speina E.

autor

Maciejewska A.

autor

Grzesiuk E.

Bibliografia

• Adachi H, Waza M, Katsuno M, Tanaka F, Doyu M, Sobue G (2007) Pathogenesis and molecular targeted therapyof spinal and bulbar muscular atrophy. Neuropathol Appl Neurobiol 33: 135–151.
• Ahel I, Rass U, El-Khamisy SF, Katyal S, Clements PM, McKinnon PJ, Caldecott KW, West SC (2006) The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443: 713–716.
• Akbari M, Otterlei M, Pena-Diaz J, Krokan HE (2007) Different organization of base excision repair of uracil in DNA in nuclei and mitochondria and selective upregulation of mitochondrial uracil-DNA glycosylase after oxidative stress. Neuroscience 145: 1201–1212.
• Akiyama M, Maki H, Sekiguchi M, Horiuchi T (1989) A specific role of MutT protein: to prevent dG.dA mispairing in DNA replication. Proc Natl Acad Sci USA 86:3949–3952.
• Albertella MR, Lau A, O’Connor MJ (2005) The overexpression of specialized DNA polymerases in cancer. DNA Repair (Amst) 4: 583–593.
• Allinson SL, Dianova, II, Dianov GL (2003) Poly(ADP-ribose) polymerase in base excision repair: always en gaged, but not essential for DNA damage processing. Acta Biochim Polon 50: 169–179.
• Arczewska KD, Kusmierek J (2007) Bacterial DNA repair genes and their eukaryotic homologues: 2. Role of bacterial mutator gene homologues in human disease. Overview of nucleotide pool sanitization and mismatch repair systems. Acta Biochim Polon 54: 435–457.
• Au KG, Cabrera M, Miller JH, Modrich P (1988) Escherichia coli mutY gene product is required for specific A–G----C.G mismatch correction. Proc Natl Acad Sci USA 85:9163–9166.
• Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M (2006) Crystal structure of SUMO-3–modified thymine-DNA glycosylase. J Mol Biol 359: 137–147.
• Babcock GT, Wikstrom M (1992) Oxygen activation and the conservation of energy in cell respiration. Nature 356: 301–309.
• Barbin A (2000) Etheno-adduct-forming chemicals: from mutagenicity testing to tumor mutation spectra. Mutat Res 462: 55–69.
• Bartsch H, Nair J (2006) Chronic inflammation and oxidative stress in the genesis and perpetuation of cancer: role of lipid peroxidation, DNA damage, and repair. Langenbecks Arch Surg 391: 499–510.
• Bebenek K, Kunkel TA (2004) Functions of DNA polymerases. Adv Protein Chem 69: 137–165.
• Bennett RA, Wilson DM, 3rd, Wong D, Demple B (1997) Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci USA 94: 7166–7169.
• Bentle MS, Bey EA, Dong Y, Reinicke KE, Boothman DA (2006) New tricks for old drugs: the anticarcinogenic potential of DNA repair inhibitors. J Mol Histol 37:203–218.
• Bhattacharyya N, Banerjee S (1997) A variant of DNA polymerase beta acts as a dominant negative mutant. Proc Natl Acad Sci USA 94: 10324–10329.
• Bhattacharyya N, Banerjee S (2003) Analysis of alterations in a base-excision repair gene in lung cancer. Methods Mol Med 74: 413–438.
• Bhattacharyya N, Chen HC, Comhair S, Erzurum SC, Banerjee S (1999) Variant forms of DNA polymerase beta in primary lung carcinomas. DNA Cell Biol 18: 549–554.
• Bhattacharyya N, Banerjee T, Patel U, Banerjee S (2001) Impaired repair activity of a truncated DNA polymerase beta protein. Life Sci 69: 271–280.
• Bjelland S, Seeberg E (1996) Different efficiencies of the Tag and AlkA DNA glycosylases from Escherichia coli in the removal of 3–methyladenine from single-stranded DNA. FEBS Lett 397: 127–129.
• Blaisdell JO, Hatahet Z, Wallace SS (1999) A novel role for Escherichia coli endonuclease VIII in prevention of spontaneous G→T transversions. J Bacteriol 181: 6396–6402.
• Boiteux S, Huisman O (1989) Isolation of a formamidopyrimidine-DNA glycosylase (fpg) mutant of Escherichia coli K12. Mol Gen Genet 215: 300–305.
• Borys-Brzywczy E, Arczewska KD, Saparbaev M, Hardeland U, Schar P, Kusmierek JT (2005) Mismatch dependent uracil/thymine-DNA glycosylases excise exocyclic hydroxyethano and hydroxypropano cytosine adducts. Acta Biochim Polon 52: 149–165.
• Burcham PC (1998) Genotoxic lipid peroxidation products: their DNA damaging properties and role in formation of endogenous DNA adducts Mutagenesis 13: 287–305.
• Burcham PC (1999) Internal hazards: baseline DNA damage by endogenous products of normal metabolism. Mutat Res 443: 11–36.
• Burkovics P, Szukacsov V, Unk I, Haracska L (2006) Human Ape2 protein has a 3’-5’ exonuclease activity that acts preferentially on mismatched base pairs. Nucleic Acids Res 34: 2508–2515.
• Cabelof DC, Guo Z, Raffoul JJ, Sobol RW, Wilson SH, Richardson A, Heydari AR (2003) Base excision repair deficiency caused by polymerase beta haploinsufficiency:
• accelerated DNA damage and increased mutational response to carcinogens. Cancer Res 63: 5799–5807.
• Cabrera M, Nghiem Y, Miller JH (1988) mutM, a second mutator locus in Escherichia coli that generates G.C----T.A transversions. J Bacteriol 170: 5405–5407.
• Caldecott KW (2007) Mammalian single-strand break repair: mechanisms and links with chromatin. DNA Repair (Amst) 6: 443–453.
• Caldecott KW, Tucker JD, Stanker LH, Thompson LH (1995) Characterization of the XRCC1–DNA ligase III complex in vitro and its absence from mutant hamster cells. Nucleic Acids Res 23: 4836–4843.
• Cao WH, Wang X, Frappart L, Rigal D, Wang ZQ, Shen Y, Tong WM (2007) Analysis of genetic variants of the poly(ADP-ribose) polymerase-1 gene in breast cancer in French patients. Mutat Res 632: 20–28.
• Chan KK, Zhang QM, Dianov GL (2006) Base excision repair fidelity in normal and cancer cells. Mutagenesis 21: 173–178.
• Cheadle JP, Sampson JR (2007) MUTYH-associated polyposis— from defect in base excision repair to clinical genetic testing. DNA Repair (Amst) 6: 274–279.
• Chen HC, Bhattacharyya N, Wang L, Recupero AJ, Klein EA, Harter ML, Banerjee S (2000) Defective DNA repair genes in a primary culture of human renal cell carcinoma. J Cancer Res Clin Oncol 126: 185–190.
• Clements PM, Breslin C, Deeks ED, Byrd PJ, Ju L, Bieganowski P, Brenner C, Moreira MC, Taylor AM, Caldecott KW (2004) The ataxia-oculomotor apraxia 1 gene product has a role distinct from ATM and interacts with the DNA strand break repair proteins XRCC1 and XRCC4. DNA Repair (Amst) 3: 1493–1502.
• Collins AR, Gaivao I (2007) DNA base excision repair as a biomarker in molecular epidemiology studies. Mol Aspects Med 28: 307–322.
• Connelly JC, Leach DR (2004) Repair of DNA covalently linked to protein. Mol Cell 13: 307–316.
• Cortazar D, Kunz C, Saito Y, Steinacher R, Schar P (2007) The enigmatic thymine DNA glycosylase. DNA Repair (Amst) 6: 489–504.
• De Ruyck K, Szaumkessel M, De Rudder I, Dehoorne A, Vral A, Claes K, Velghe A, Van Meerbeeck J, Thierens H (2007) Polymorphisms in base-excision repair and nucleotide-excision repair genes in relation to lung cancer risk. Mutat Res 631: 101–110.
• Dedon PC, Goldberg IH (1992) Free-radical mechanisms involved in the formation of sequence-dependent bistranded DNA lesions by the antitumor antibiotics bleomycin, neocarzinostatin, and calicheamicin. Chem Res Toxicol 5: 311–332.
• Dedon PC, Jiang ZW, Goldberg IH (1992) Neocarzinostatin-mediated DNA damage in a model AGT.ACT site: mechanistic studies of thiol-sensitive partitioning of C4’ DNA damage products. Biochemistry 31: 1917–1927.
• Deligezer U, Akisik EE, Dalay N (2007) Lack of association of XRCC1 codon 399Gln polymorphism with chronic myelogenous leukemia. Anticancer Res 27: 2453–2456.
• Demple B, DeMott MS (2002) Dynamics and diversions in base excision DNA repair of oxidized abasic lesions. Oncogene 21: 8926–8934.
• Dianov GL, Parsons JL (2007) Co-ordination of DNA single strand break repair. DNA Repair (Amst) 6: 454–460.
• Dianov GL, Sleeth KM, Dianova, II, Allinson SL (2003) Repair of abasic sites in DNA. Mutat Res 531: 157–163.
• Dianova, II, Sleeth KM, Allinson SL, Parsons JL, Breslin C, Caldecott KW, Dianov GL (2004) XRCC1–DNA polymerase beta interaction is required for efficient base excision repair. Nucleic Acids Res 32: 2550–2555.
• Dizdaroglu M (1992) Measurement of radiation-induced damage to DNA at the molecular level. Int J Radiat Biol 61: 175–183.
• Doetsch PW (2002) Translesion synthesis by RNA polymerases: occurrence and biological implications for transcriptional mutagenesis. Mutat Res 510: 131–140.
• Drablos F, Feyzi E, Aas PA, Vaagbo CB, Kavli B, Bratlie MS, Pena-Diaz J, Otterlei M, Slupphaug G, Krokan HE (2004) Alkylation damage in DNA and RNA-repair mechanisms and medical significance. DNA Repair (Amst) 3: 1389–1407.
• Duncan BK, Weiss B (1982) Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J Bacteriol 151: 750–755.
• El-Khamisy SF, Hartsuiker E, Caldecott KW (2007) TDP1 facilitates repair of ionizing radiation-induced DNA single-strand breaks. DNA Repair (Amst) Engelward BP, Allan JM, Dreslin AJ, Kelly JD, Wu MM, Gold B, Samson LD (1998) A chemical and genetic approach together define the biological consequences of 3-methyladenine lesions in the mammalian genome. J Biol Chem 273: 5412–5418.
• Fodde R, Kuipers J, Rosenberg C, Smits R, Kielman M, Gaspar C, van Es JH, Breukel C, Wiegant J, Giles RH, Clevers H (2001) Mutations in the APC tumour suppressor gene cause chromosomal instability. Nat Cell Biol 3: 433–438.
• Fortini P, Dogliotti E (2007) Base damage and single-strand break repair: mechanisms and functional significance of short- and long-patch repair subpathways. DNA Repair (Amst) 6: 398–409.
• Fowler RG, White SJ, Koyama C, Moore SC, Dunn RL, Schaaper RM (2003) Interactions among the Escherichia coli mutT, mutM, and mutY damage prevention pathways. DNA Repair (Amst) 2: 159–173.
• Friedberg EC, Meira LB (2004) Database of mouse strains carrying targeted mutations in genes affecting biological responses to DNA damage (Version 6). DNA Repair (Amst) 3: 1617–1638.
• Friedl W, Caspari R, Sengteller M, Uhlhaas S, Lamberti C, Jungck M, Kadmon M, Wolf M, Fahnenstich J, Gebert J, Moslein G, Mangold E, Propping P (2001) Can APC mutation analysis contribute to therapeutic decisions in familial adenomatous polyposis? Experience from 680 FAP families. Gut 48: 515–521.
• Fromme JC, Banerjee A, Verdine GL (2004) DNA glycosylase recognition and catalysis. Curr Opin Struct Biol 14:43–49.
• Gackowski D, Speina E, Zielinska M, Kowalewski J, Rozalski R, Siomek A, Paciorek T, Tudek B, Olinski R (2003) Products of oxidative DNA damage and repair as possible biomarkers of susceptibility to lung cancer. Cancer Res 63: 4899–4902.
• Gallinari P, Jiricny J (1996) A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 383: 735–738.
• Garg P, Burgers PM (2005) How the cell deals with DNA nicks Cell Cycle 4: 221–224.
• Goswami SC, Yoon JH, Abramczyk BM, Pfeifer GP, Postel EH (2006) Molecular and functional interactions between Escherichia coli nucleoside-diphosphate kinase and the uracil-DNA glycosylase Ung. J Biol Chem 281: 32131–32139.
• Guerreiro CS, Cravo ML, Brito M, Vidal PM, Fidalgo PO, Leitao CN (2007) The D1822V APC polymorphism interacts with fat, calcium, and fiber intakes in modulating the risk of colorectal cancer in Portuguese persons. Am J Clin Nutr 85: 1592–1597.
• Guillet M, Boiteux S (2003) Origin of endogenous DNA abasic sites in Saccharomyces cerevisiae. Mol Cell Biol 23:8386–8394.
• Hadi MZ, Coleman MA, Fidelis K, Mohrenweiser HW, Wilson DM, 3rd (2000) Functional characterization of Ape1 variants identified in the human population. Nucleic Acids Res 28: 3871–3879.
• Hadi MZ, Ginalski K, Nguyen LH, Wilson DM, 3rd (2002) Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III. J Mol Biol 316: 853–866.
• Halliwell B (1999) Oxygen and nitrogen are pro-carcinogens. Damage to DNA by reactive oxygen, chlorine and nitrogen species: measurement, mechanism and the effects of nutrition. Mutat Res 443: 37–52.
• Halliwell B, Aruoma OI (1991) DNA damage by oxygenderived species. Its mechanism and measurement in mammalian systems. FEBS Lett 281: 9–19.
• Hamm ML, Gill TJ, Nicolson SC, Summers MR (2007) Substrate specificity of Fpg (MutM) and hOGG1, two repair glycosylases. J Am Chem Soc 129: 7724–7725.
• Hardeland U, Bentele M, Lettieri T, Steinacher R, Jiricny J, Schar P (2001) Thymine DNA glycosylase. Prog Nucleic Acid Res Mol Biol 68: 235–253.
• Hardeland U, Kunz C, Focke F, Szadkowski M, Schar P (2007) Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2. Nucleic Acids Res 35: 3859–3867.
• Harrigan JA, Wilson DM, 3rd, Prasad R, Opresko PL, Beck G, May A, Wilson SH, Bohr VA (2006) The Werner syndrome protein operates in base excision repair and cooperates with DNA polymerase beta. Nucleic Acids Res 34: 745–754.
• Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A (1999) The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401: 301–304.
• Hill JW, Hazra TK, Izumi T, Mitra S (2001) Stimulation of human 8-oxoguanine-DNA glycosylase by AP-endonuclease: potential coordination of the initial steps in base excision repair. Nucleic Acids Res 29: 430–438.
• Jackson AL, Loeb LA (2001) The contribution of endogenous sources of DNA damage to the multiple mutations in cancer. Mutat Res 477: 7–21.
• Jaiswal AS, Balusu R, Armas ML, Kundu CN, Narayan S (2006) Mechanism of adenomatous polyposis coli (APC)-mediated blockage of long-patch base excision repair. Biochemistry 45: 15903–15914.
• Janion C, Sikora A, Nowosielska A, Grzesiuk E (2003) E. coli BW535, a triple mutant for the DNA repair genes xth, nth, and nfo, chronically induces the SOS response. Environ Mol Mutagen 41: 237–242.
• Jurado J, Maciejewska A, Krwawicz J, Laval J, Saparbaev MK (2004) Role of mismatch-specific uracil-DNA glycosylase in repair of 3,N4-ethenocytosine in vivo. DNA Repair (Amst) 3: 1579–1590.
• Katsara M, Tselios T, Deraos S, Deraos G, Matsoukas MT, Lazoura E, Matsoukas J, Apostolopoulos V (2006) Round and round we go: cyclic peptides in disease. Curr Med Chem 13: 2221–2232.
• Kavli B, Sundheim O, Akbari M, Otterlei M, Nilsen H, Skorpen F, Aas PA, Hagen L, Krokan HE, Slupphaug G (2002) hUNG2 is the major repair enzyme for removal of uracil from U : A matches, U:G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup. J Biol Chem 277: 39926–39936.
• Kavli B, Otterlei M, Slupphaug G, Krokan HE (2007) Uracil in DNA-general mutagen, but normal intermediate in acquired immunity. DNA Repair (Amst) 6: 505–516.
• Kim ST, Malhotra K, Smith CA, Taylor JS, Sancar A (1994) Characterization of (6–4) photoproduct DNA photolyase. J Biol Chem 269: 8535–8540.
• Klungland A, Lindahl T (1997) Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for Dnase IV (FEN1). Embo J 16: 3341–3348.
• Kondo E, Gu Z, Horii A, Fukushige S (2005) The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes. Mol Cell Biol 25: 4388–4396.
• Kopp HG, Kuczyk M, Classen J, Stenzl A, Kanz L, Mayer F, Bamberg M, Hartmann JT (2006) Advances in the treatment of testicular cancer. Drugs 66: 641–659.
• Kovtun IV, Liu Y, Bjoras M, Klungland A, Wilson SH, Mc- Murray CT (2007) OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells Nature 447: 447–452.
• Kowalczyk P, Ciesla JM, Saparbaev M, Laval J, Tudek B (2006) Sequence-specific p53 gene damage by chloroacetaldehyde and its repair kinetics in Escherichia coli. Acta Biochim Polon 53: 337–347.
• Kreutzer DA, Essigmann JM (1998) Oxidized, deaminated cytosines are a source of C→T transitions in vivo. Proc Natl Acad Sci USA 95: 3578–3582.
• Krokan HE, Standal R, Slupphaug G (1997) DNA glycosylases in the base excision repair of DNA. Biochem J 325 (Pt 1): 1–16.
• Krokan HE, Kavli B, Slupphaug G (2004) Novel aspects of macromolecular repair and relationship to human disease. J Mol Med 82: 280–297.
• Kruszewski M, Iwanenko T (2003) Labile iron pool correlates with iron content in the nucleus and the formation of oxidative DNA damage in mouse lymphoma L5178Y cell lines. Acta Biochim Polon 50: 211–215.
• Lang T, Maitra M, Starcevic D, Li SX, Sweasy JB (2004) A DNA polymerase beta mutant from colon cancer cells induces mutations. Proc Natl Acad Sci USA 101: 6074–6079.
• Lang T, Dalal S, Chikova A, DiMaio D, Sweasy JB (2007) The E295K DNA polymerase beta gastric cancer-associated variant interferes with base excision repair and induces cellular transformation. Mol Cell Biol 27: 5587–5596.
• Leppard JB, Champoux JJ (2005) Human DNA topoisomerase I: relaxation, roles, and damage control. Chromosoma 114: 75–85.
• Leppard JB, Dong Z, Mackey ZB, Tomkinson AE (2003) Physical and functional interaction between DNA ligase IIIalpha and poly(ADP-Ribose) polymerase 1 in DNA single-strand break repair. Mol Cell Biol 23: 5919–5927.
• Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915–926.
• Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362: 709–715.
• Lindahl T, Karran P, Wood RD (1997) DNA excision repair pathways. Curr Opin Genet Dev 7: 158–169.
• Liu Y, Beard WA, Shock DD, Prasad R, Hou EW, Wilson SH (2005) DNA polymerase beta and flap endonuclease 1 enzymatic specificities sustain DNA synthesis for long patch base excision repair. J Biol Chem 280: 3665–3674.
• Locker GY, Kaul K, Weinberg DS, Gatalica Z, Gong G, Peterman A, Lynch J, Klatzco L, Olopade OI, Bomzer CA, Newlin A, Keenan E, Tajuddin M, Knezetic J, Coronel S, Lynch HT (2006) The I1307K APC polymorphism in Ashkenazi Jews with colorectal cancer: clinical and pathologic features. Cancer Genet Cytogenet 169: 33–38.
• Loeb LA, Preston BD (1986) Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet 20: 201–230.
• Maddukuri L, Dudzińska D, Tudek B (2007) Bacterial DNA repair genes and their eukaryotic homologues: 4. The role of nucleotide excision DNA repair (NER) system in mammalian cells. Acta Biochim Polon 54: 469–482.
• Marenstein DR, Chan MK, Altamirano A, Basu AK, Boorstein RJ, Cunningham RP, Teebor GW (2003) Substrate specificity of human endonuclease III (hNTH1). Effect of human APE1 on hNTH1 activity. J Biol Chem 278: 9005–9012.
• Michaels ML, Pham L, Cruz C, Miller JH (1991) MutM, a protein that prevents G.C→T.A transversions, is formamidopyrimidine-DNA glycosylase. Nucleic Acids Res 19: 3629–3632.
• Michiels C, Raes M, Toussaint O, Remacle J (1994) Importance of Se-glutathione peroxidase, catalase, and Cu/Zn-SOD for cell survival against oxidative stress. Free Radic Biol Med 17: 235–248.
• Mosbaugh DW, Linn S (1982) Characterization of the action of Escherichia coli DNA polymerase I at incisions produced by repair endodeoxyribonucleases. J Biol Chem 257: 575–583.
• Narayan S, Jaiswal AS, Balusu R (2005) Tumor suppressor APC blocks DNA polymerase beta-dependent strand displacement synthesis during long patch but not short patch base excision repair and increases sensitivity to methylmethane sulfonate. J Biol Chem 280: 6942–6949.
• Neuberger MS, Harris RS, Di Noia J, Petersen-Mahrt SK (2003) Immunity through DNA deamination. Trends Biochem Sci 28: 305–312.
• Nieminuszczy J, Grzesiuk E (2007) Bacterial DNA repair genes and their eukaryotic homologues: 3. AlkB dioxygenase and Ada methyltransferase in the direct repair of alkylated DNA. Acta Biochim Polon 54: 459–468.
• Nilsen H, Krokan HE (2001) Base excision repair in a network of defence and tolerance. Carcinogenesis 22: 987–998.
• Nilsen H, Otterlei M, Haug T, Solum K, Nagelhus TA, Skorpen F, Krokan HE (1997) Nuclear and mitochondrial uracil-DNA glycosylases are generated by alternative splicing and transcription from different positions in the UNG gene. Nucleic Acids Res 25: 750–755.
• Nohmi T, Kim SR, Yamada M (2005) Modulation of oxidative mutagenesis and carcinogenesis by polymorphic forms of human DNA repair enzymes. Mutat Res 591: 60–73.
• Nowosielska A (2007) Bacterial DNA repair genes and their eukaryotic homologues: 5. The role of recombination in DNA repair and genome stability. Acta Biochim Polon 54: 484–494.
• Olinski R, Jaruga P, Zastawny TH (1998) Oxidative DNA base modifications as factors in carcinogenesis. Acta Biochim Polon 45: 561–572.
• Olinski R, Siomek A, Rozalski R, Gackowski D, Foksinski M, Guz J, Dziaman T, Szpila A, Tudek B (2007) Oxidative damage to DNA and antioxidant status in aging and age-related diseases. Acta Biochim Polon 54: 11–26.
• Parker A, Gu Y, Mahoney W, Lee SH, Singh KK, Lu AL (2001) Human homolog of the MutY repair protein (hMYH) physically interacts with proteins involved in long patch DNA base excision repair. J Biol Chem 276: 5547–5555.
• Parsons JL, Dianova, II, Allinson SL, Dianov GL (2005) Poly(ADP-ribose) polymerase-1 protects excessive DNA strand breaks from deterioration during repair in human cell extracts. FEBS J 272: 2012–2021.
• Pearl LH (2000) Structure and function in the uracil-DNA glycosylase superfamily. Mutat Res 460: 165–181.
• Pfeifer GP, You YH, Besaratinia A (2005) Mutations induced by ultraviolet light. Mutat Res 571: 19–31.
• Plo I, Liao ZY, Barcelo JM, Kohlhagen G, Caldecott KW, Weinfeld M, Pommier Y (2003) Association of XRCC1 and tyrosyl DNA phosphodiesterase (Tdp1) for the repair of topoisomerase I-mediated DNA lesions. DNA Repair (Amst) 2: 1087–1100.
• Postel EH, Abramczyk BM (2003) Escherichia coli nucleoside diphosphate kinase is a uracil-processing DNA repair nuclease. Proc Natl Acad Sci USA 100: 13247–13252.
• Postel EH, Abramczyk BA, Gursky SK, Xu Y (2002) Structure-based mutational and functional analysis identify human NM23–H2 as a multifunctional enzyme. Biochemistry 41: 6330–6337.
• Postel EH, Abramczyk BM, Levit MN, Kyin S (2000) Catalysis of DNA cleavage and nucleoside triphosphate synthesis by NM23–H2/NDP kinase share an active site that implies a DNA repair function. Proc Natl Acad Sci USA 97: 14194–14199.
• Prasad R, Liu Y, Deterding LJ, Poltoratsky VP, Kedar PS, Horton JK, Kanno S, Asagoshi K, Hou EW, Khodyreva SN, Lavrik OI, Tomer KB, Yasui A, Wilson SH (2007) HMGB1 Is a cofactor in mammalian base excision repair. Mol Cell 27: 829–841.
• Privezentzev CV, Saparbaev M, Laval J (2001) The HAP1 protein stimulates the turnover of human mismatchspecific thymine-DNA-glycosylase to process 3,N(4)-ethenocytosine residues. Mutat Res 480–481: 277–284.
• Proctor SJ, Wilkinson J (2006) Extreme Hodgkin’s lymphoma: current problem areas. Ann Oncol 17 (Suppl 4): iv15–17.
• Purmal AA, Lampman GW, Bond JP, Hatahet Z, Wallace SS (1998) Enzymatic processing of uracil glycol, a major oxidative product of DNA cytosine. J Biol Chem 273: 10026–10035.
• Rabbani G, Benzil D, Wallam MN, Chen B, Hoang A, Kancherla R, Ahmed T (2007) Combination therapy with thalidomide, temozolomide and tamoxifen improves quality of life in patients with malignant astrocytomas. Anticancer Res 27: 2729–2736.
• Radicella JP, Clark EA, Chen S, Fox MS (1993) Patch length of localized repair events: role of DNA polymerase I in mutY-dependent mismatch repair. J Bacteriol 175: 7732–7736.
• Rass U, Ahel I, West SC (2007) Actions of aprataxin in multiple DNA repair pathways. J Biol Chem 282: 9469–9474.
• Roos WP, Kaina B (2006) DNA damage-induced cell death by apoptosis. Trends Mol Med 12: 440–450.
• Rydberg B, Lindahl T (1982) Nonenzymatic methylation of DNA by the intracellular methyl group donor S-adenosyl-L-methionine is a potentially mutagenic reaction. Embo J 1: 211–216.
• Saito Y, Uraki F, Nakajima S, Asaeda A, Ono K, Kubo K, Yamamoto K (1997) Characterization of endonuclease III (nth) and endonuclease VIII (nei) mutants of Escherichia coli K-12. J Bacteriol 179: 3783–3785.
• Sakiyama T, Kohno T, Mimaki S, Ohta T, Yanagitani N, Sobue T, Kunitoh H, Saito R, Shimizu K, Hirama C, Kimura J, Maeno G, Hirose H, Eguchi T, Saito D, Ohki M, Yokota J (2005) Association of amino acid substitution polymorphisms in DNA repair genes TP53, POLI, REV1 and LIG4 with lung cancer risk. Int J Cancer 114: 730–737.
• Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS (2006) Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair. Chem Rev 106: 700–719.
• Sancar A (1994) Structure and function of DNA photolyase. Biochemistry 33: 2–9.
• Santella RM, Gammon M, Terry M, Senie R, Shen J, Kennedy D, Agrawal M, Faraglia B, Zhang F (2005) DNA adducts, DNA repair genotype/phenotype and cancer risk. Mutat Res 592: 29–35.
• Sattler U, Frit P, Salles B, Calsou P (2003) Long-patch DNA repair synthesis during base excision repair in mammalian cells. EMBO Rep 4: 363–367.
• Sedgwick B (2004) Repairing DNA-methylation damage Nat Rev Mol Cell Biol 5: 148–157.
• Shcherbakova PV, Fijalkowska IJ (2006) Translesion synthesis DNA polymerases and control of genome stability. Front Biosci 11: 2496–2517.
• Shen J, Gammon MD, Terry MB, Wang L, Wang Q, Zhang F, Teitelbaum SL, Eng SM, Sagiv SK, Gaudet MM, Neugut AI, Santella RM (2005) Polymorphisms in XRCC1 modify the association between polycyclic aromatic hydrocarbon-DNA adducts, cigarette smoking, dietary antioxidants, and breast cancer risk. Cancer Epidemiol Biomarkers Prev 14: 336–342.
• Simonelli V, Narciso L, Dogliotti E, Fortini P (2005) Base excision repair intermediates are mutagenic in mammalian cells. Nucleic Acids Res 33: 4404–4411.
• Sliwinski T, Ziemba P, Morawiec Z, Kowalski M, Zadrozny M, Blasiak J (2007) Polymorphisms of the DNA polymerase beta gene in breast cancer. Breast Cancer Res Treat 103: 161–166.
• Slupphaug G, Kavli B, Krokan HE (2003) The interacting pathways for prevention and repair of oxidative DNA damage. Mutat Res 531: 231–251.
• Speina E, Arczewska KD, Gackowski D, Zielinska M, Siomek A, Kowalewski J, Olinski R, Tudek B, Kusmierek JT (2005a) Contribution of hMTH1 to the maintenance of 8–oxoguanine levels in lung DNA of non-small-cell lung cancer patients. J Natl Cancer Inst 97: 384–395.
• Speina E, Ciesla JM, Graziewicz MA, Laval J, Kazimierczuk Z, Tudek B (2005b) Inhibition of DNA repair glycosylases by base analogs and tryptophan pyrolysate, Trp-P-1. Acta Biochim Polon 52: 167–178.
• Speina E, Zielinska M, Barbin A, Gackowski D, Kowalewski J, Graziewicz MA, Siedlecki JA, Olinski R, Tudek B (2003) Decreased repair activities of 1,N(6)-ethenoadenine and 3,N(4)-ethenocytosine in lung adenocarcinoma patients. Cancer Res 63: 4351–4357.
• Starcevic D, Dalal S, Sweasy JB (2004) Is there a link between DNA polymerase beta and cancer? Cell Cycle 3: 998–1001.
• Straussberg R, Basel-Vanagaite L, Kivity S, Dabby R, Cirak S, Nurnberg P, Voit T, Mahajnah M, Inbar D, Saifi GM, Lupski JR, Delague V, Megarbane A, Richter A, Leshinsky E, Berkovic SF (2005) An autosomal recessive cerebellar ataxia syndrome with upward gaze palsy, neuropathy, and seizures. Neurology 64: 142–144.
• Sung JS, Mosbaugh DW (2003) Escherichia coli uracil- and ethenocytosine-initiated base excision DNA repair: rate-limiting step and patch size distribution. Biochemistry 42: 4613–4625.
• Sung JS, Demple B (2006) Roles of base excision repair subpathways in correcting oxidized abasic sites in DNA. FEBS J 273: 1620–1629.
• Sweasy JB, Lang T, Starcevic D, Sun KW, Lai CC, Dimaio D, Dalal S (2005) Expression of DNA polymerase β cancer-associated variants in mouse cells results in cellular transformation. Proc Natl Acad Sci USA 102: 14350–14355.
• Takahashi T, Tada M, Igarashi S, Koyama A, Date H, Yokoseki A, Shiga A, Yoshida Y, Tsuji S, Nishizawa M, Onodera O (2007) Aprataxin, causative gene product for EAOH/AOA1, repairs DNA single-strand breaks with damaged 3’-phosphate and 3’-phosphoglycolate ends. Nucleic Acids Res 35: 3797–3809.
• Taylor AF, Weiss B (1982) Role of exonuclease III in the base excision repair of uracil-containing DNA. J Bacteriol 151: 351–357.
• Thorslund T, von Kobbe C, Harrigan JA, Indig FE, Christiansen M, Stevnsner T, Bohr VA (2005) Cooperation of the Cockayne syndrome group B protein and poly(ADP-ribose) polymerase 1 in the response to oxidative stress. Mol Cell Biol 25: 7625–7636.
• Tong WM, Yang YG, Cao WH, Galendo D, Frappart L, Shen Y, Wang ZQ (2007) Poly(ADP-ribose) polymerase-1 plays a role in suppressing mammary tumourigenesis in mice. Oncogene 26: 3857–3867.
• Tudek B (2007) Base excision repair modulation as a risk factor for human cancers. Mol Aspects Med 28: 258–275.
• Tudek B, Boiteux S, Laval J (1992) Biological properties of imidazole ring-opened N7-methylguanine in M13mp18 phage DNA. Nucleic Acids Res 20: 3079–3084.
• Tudek B, Swoboda M, Kowalczyk P, Olinski R (2006) Modulation of oxidative DNA damage repair by the diet, inflammation and neoplastic transformation. J Physiol Pharmacol 57 (Suppl 7): 33–49.
• Tuo J, Jaruga P, Rodriguez H, Dizdaroglu M, Bohr VA (2002) The cockayne syndrome group B gene product is involved in cellular repair of 8-hydroxyadenine in DNA. J Biol Chem 277: 30832–30837.
• Underwood BR, Rubinsztein DC (2007) Spinocerebellar ataxias caused by polyglutamine expansions: A review of therapeutic strategies. Cerebellum 1–7.
• Valko M, Rhodes CJ, Moncol J, Izakovic M, Mazur M (2006) Free radicals, metals and antioxidants in oxidative stress-induced cancer. Chem Biol Interact 160: 1–40.
• van Es JH, Giles RH, Clevers HC (2001) The many faces of the tumor suppressor gene APC. Exp Cell Res 264: 126–134.
• Vidal AE, Boiteux S, Hickson ID, Radicella JP (2001a) XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions. Embo J 20: 6530–6539.
• Vidal AE, Hickson ID, Boiteux S, Radicella JP (2001b) Mechanism of stimulation of the DNA glycosylase activity of hOGG1 by the major human AP endonuclease: bypass of the AP lyase activity step. Nucleic Acids Res 29: 1285–1292.
• von Kobbe C, Harrigan JA, May A, Opresko PL, Dawut L, Cheng WH, Bohr VA (2003) Central role for the Werner syndrome protein/poly(ADP-ribose) polymerase 1 complex in the poly(ADP-ribosyl)ation pathway after DNA damage. Mol Cell Biol 23: 8601–8613.
• von Kobbe C, Harrigan JA, Schreiber V, Stiegler P, Piotrowski J, Dawut L, Bohr VA (2004) Poly(ADP-ribose) polymerase 1 regulates both the exonuclease and helicase activities of the Werner syndrome protein. Nucleic Acids Res 32: 4003–4014.
• Walker FO (2007) Huntington’s disease. Lancet 369: 218–228.
• Wang YH (2007) Chromatin structure of repeating CTG/CAG and CGG/CCG sequences in human disease. Front Biosci 12: 4731–4741.
• Wang XG, Wang ZQ, Tong WM, Shen Y (2007) PARP1 Val762Ala polymorphism reduces enzymatic activity. Biochem Biophys Res Commun 354: 122–126.
• Whitehouse CJ, Taylor RM, Thistlethwaite A, Zhang H, Karimi-Busheri F, Lasko DD, Weinfeld M, Caldecott KW (2001) XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. Cell 104: 107–117.
• Wiederhold L, Leppard JB, Kedar P, Karimi-Busheri F, Rasouli-Nia A, Weinfeld M, Tomkinson AE, Izumi T, Prasad R, Wilson SH, Mitra S, Hazra TK (2004) AP endonuclease-independent DNA base excision repair in human cells. Mol Cell 15: 209–220.
• Wilson DM, 3rd, Bohr VA (2007) The mechanics of base excision repair, and its relationship to aging and disease. DNA Repair (Amst) 6: 544–559.
• Xia L, Zheng L, Lee HW, Bates SE, Federico L, Shen B, O’Connor TR (2005) Human 3-methyladenine-DNA glycosylase: effect of sequence context on excision, association with PCNA, and stimulation by AP endonuclease. J Mol Biol 346: 1259–1274.
• Xu Y, Derbyshire V, Ng K, Sun XC, Grindley ND, Joyce CM (1997) Biochemical and mutational studies of the 5’-3’ exonuclease of DNA polymerase I of Escherichia coli. J Mol Biol 268: 284–302.
• Xu Y, Potapova O, Leschziner AE, Grindley ND, Joyce CM (2001) Contacts between the 5’ nuclease of DNA polymerase I and its DNA substrate. J Biol Chem 276: 30167–30177.
• Yang H, Clendenin WM, Wong D, Demple B, Slupska MM, Chiang JH, Miller JH (2001) Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch. Nucleic Acids Res 29:743–752.
• Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335–340.
• Zauber NP, Sabbath-Solitare M, Marotta S, Zauber AG, Foulkes W, Chan M, Turner F, Bishop DT (2005) Clinical and genetic findings in an Ashkenazi Jewish population with colorectal neoplasms. Cancer 104: 719–729.
• Zhou T, Lee JW, Tatavarthi H, Lupski JR, Valerie K, Povirk LF (2005) Deficiency in 3’-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1). Nucleic Acids Res 33:289–297.