© Borgis - New Medicine 1/2013, s. 14-20
*Paweł Kowalczyk1, Jolanta Krzyczkowska2, Urszula Jankiewicz3
Mechanisms of the dna repair in bacterial and yeast cells
1Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
2Department of Chemistry, Faculty of Food Sciences, Warsaw University of Life Sciences, Warsaw, Poland
3Department of Biochemistry, Warsaw University of Life Sciences, Warsaw, Poland
Malfunctioning of some DNA repair pathways predisposes to certain types of cancer. Impaired base excision repair, nucleotide excision repair, mismatch repair and recombination are implied in human tissues. These repair pathways are engaged very quickly in the cell when the external (chemical carcinogens) and internal (lipid peroxidation products) compounds react directly with DNA. This reaction may either lead to different modifications (damages) in DNA and genes. This damages may lead finally to mutation and cancer progression and induce different DNA repair mechanisms such as. BER, NER, HR and MMR. In the BER mechanisms repair is initiated by the action of a damage-specific DNA N-glycosylase that is responsible for the recognition and removal of an altered base through cleavage of the N-glycosylic bond and action of AP-endonuclease. Nucleotide excision repair (NER) is the most versatile and flexible DNA repair pathway of living cells as it deals with a wide range of structurally unrelated DNA lesions. NER corrects a wide array of DNA lesions that distort the DNA double helix, interfere in base pairing and block DNA duplication and transcription. The most common examples of these lesions are the cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs) induced by ultraviolet radiation (UV) and bases with large substitutes derived from chemicals such as polycyclic aromatic hydrocarbons or exocyclic adducts. Homologous recombination, utilize large regions of DNA homology, usually the homological chromosome, to exchange damaged DNA for the intact one. DNA mismatch-repair system (MMR) is involved in the repair of mispaired bases formed during replication, genetic recombination and as a result of DNA damage.
Different mechanisms of the DNA repair
To counteract deleterious consequences of DNA damage, the cells developed several repair mechanisms which eliminate from genomes mis-instructive or non-instructive elements, as well as seal DNA breaks. Various repair systems can be classified into the following groups, according to repair mechanism:
1. Sanitisation of nucleotide pool from modified nucleoside triphosphates, which prevents their incorporation into DNA by DNA polymerases.
2. Direct reversal of DNA damage, which occurs without breaking of the double helix.
3. Excision repair, in which a fragment of DNA strand containing the lesion is excised, followed by DNA resynthesis on the template of the opposite intact strand. Three different systems utilize the excision mode for DNA repair:
– Mismatch repair, which eliminates replication errors, some damaged DNA bases, as well as small loops.
– Base excision repair, initiated by DNA glycosylases which cleave out the damaged base and initiate the synthesis step.
– Nucleotide excision repair, in which a larger fragment of damaged DNA strand is removed (12-13 nucleotides in E. coli, 24-32 in eucaryota).
4. Recombination, which is working in the situation of gross damage and unavailability of intact opposite DNA strand or for double-strand break (DSB) repair.
5. SOS repair, based on translesion synthesis past DNA damages by specified class of low fidelity DNA polymerases tolerant of template structure abnormality, but introducing errors into DNA. Repair of exocyclic, unsubstituted etheno-DNA adducts is realized mainly by base excision repair pathway (1). 1,N2-propanoguanosine with a hexyl side chain derived from hydroxynonenal interaction with DNA was shown to be eliminated by nucleotide excision repair in mammalian cells (2, 3).
Base excision repair
Base excision repair constitutes the primary defense against lesions that do not heavily distort the DNA structure. BER is responsible for the removal of a variety of lesions. These include spontaneous hydrolytic depurination of DNA, deamination of bases, products of reaction with hydroxyl radicals, and covalent DNA adducts formed by intracellular LPO and small reactive metabolites, such as methylating agents. Repair is initiated by the action of a damage-specific DNA N-glycosylase that is responsible for the recognition and removal of an altered base through cleavage of the N-glycosylic bond (4, 5). Base removal generates an apurinic/apyrimidinic (AP) site, a noncoding DNA lesion that is both cytotoxic and mutagenic. The abasic site is the substrate for an AP endonuclease that hydrolyzes the phosphodiester bond 5” to an abasic site (6-9). Cleavage by AP-endonuclease generates a 3”-OH terminus suitable for extension by a DNA polymerase. The resulting 5” terminus contains a deoxyribose phosphate residue (dRP), which must be removed and replaced in order to complete repair. BER can proceed via two pathways, designated short patch (10) or long patch repair (11, 12). In the short patch repair pathway DNA polymerase β adds a single nucleotide and also cleaves the 5”-deoxyribose phosphate residue using an intrinsic deoxyribosephosphate lyase (dRP lyase) activity (13, 14). A DNA ligase then seals the nick to complete repair. This generates a repair product where only the damaged nucleotide is replaced. In the long patch DNA polymerase δ/ε or β and PCNA extend DNA chain at the 3”-OH terminus generated by an AP-endonuclease, displacing the strand at the 5” end. The antibodies directed against PCNA totally suppress repair patches longer than one nucleotide. This creates a baseless sugar-containing flap, removed by a human flap-endonuclease (FEN1) which is also engaged in excision of primers during replication. DNA ligase I in long patch or ligase III in the short patch seal phosphodiester bonds.
DNA glycosylases are often able to act upon a variety of DNA adducts that result from the action of a number of DNA damaging agents, although with different efficiencies and sometimes overlapping specificities. The lesions recognized by DNA glycosylases include noncanonical Watson-Crick base pairs and bases altered by deamination, oxidation and alkylation. On the basis of their primary substrate specificity all identified DNA glycosylases have been classified into several types, namely, DNA glycosylases of deaminated, mismatched, alkylated, and oxidized bases as well as of pyrimidine-dimers. DNA glycosylases are generally globular, monomeric, small proteins, ranging in molecular mass from 16 to 60 kDa. They often contain a conserved motif of helix-harpin-helix (HhH) which enables them to bind DNA. DNA glycosylases act on damaged bases by flipping damaged nucleotides out of the DNA into an enzyme active site pocket, where the excision takes place (15-17). DNA glycosylases can be separated into two groups: 1) enzymes that possess only N-glycosylase activity to generate an AP site (monofunctional DNA glycosylases), and 2) proteins that possess DNA glycosylase activity and an activity to incise the phosphodiester backbone immediately 3” of the resulting AP site via b-elimination, or 3” and 5” via b-δ-elimination, resulting in a single nucleotide gap flanked by phosphate termini (3”/5”) (bifunctional glycosylases/AP lyases) (18). Due to an associated lyase activity, bifunctional glycosylases are sometimes termed endonucleases. Cloning of the OGG1 gene from Saccharomyces cerevisiae has revealed that DNA glycosylases are not necessarily conserved throughout phylogeny, yet there is a DNA-repair protein superfamily with a wide substrate specificity found from bacteria to man.
Nucleotide excision repair (NER)
Nucleotide excision repair (NER) is the most versatile and flexible DNA repair pathway of living cells as it deals with a wide range of structurally unrelated DNA lesions. NER corrects a wide array of DNA lesions that distort the DNA double helix, interfere in base pairing and block DNA duplication and transcription. The most common examples of these lesions are the cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs), induced by ultraviolet radiation (UV), and bases with large substitutes derived from chemicals such as polycyclic aromatic hydrocarbons (19). However, NER can also correct smaller modified bases. This is the major pathway responsible for removing from DNA such exocyclic adducts as M1G and 1,N2-propanoguanine (20, 21). The overall processes of NER in eukaryotic and prokaryotic cells are similar, but there are many differences in detail. NER can be separated into two subpathways, slow, global genome repair (GGR) and fast, transcription-coupled repair (TCR). Global repair is the process by which most lesions are repaired regardless of their location in the genome. Transcription-coupled repair is characterized by the more rapid repair of lesions in the transcribed strand of an expressed gene than in the nontranscribed strand or in the rest of the genome (22). The mechanism of these two pathways is mainly similar except for recognition of the damage and, therefore, for initiation of the process. In E. coli, both subpathways require the full set of NER proteins, but transcription-coupled repair additionally requires an actively transcribing RNA polymerase (RNAP) and at least one additional factor, the transcription repair coupling factor, encoded by the mfd gene (23). The latter factor is thought to recruit Uvr proteins to RNAP arrested at a lesion on the transcribed strand (24), resulting in rapid repair of the transcription-blocking lesion.
NER in E. coli requires six proteins: UvrA, UvrB, UvrC, UvrD, DNA polymerase I, and ligase (25). In vivo, UvrA is present both as a monomer and a dimer, the latter complexing with UvrB for initial DNA damage recognition. This UvrA2B heterotrimer may carry out limited, ATP-dependent, processive scanning of the damaged region until the actual damage site is encountered (26). At this point, a conformational change occurs in the protein-DNA complex, leading to release of the UvrA dimer, stable UvrB-DNA binding, and a local bending and unwinding of the damaged region of DNA. UvrC then binds to the UvrB-DNA complex, unmasking the cryptic endonuclease activity of UvrB. In the case of UV photoproducts, this activity causes an incision to be made four bases 3” from the lesion. A second incision is made by the UvrBC complex seven bases 5” from the lesion. UvrD, also known as DNA helicase II, releases UvrC and the oligonucleotide between the dual incisions, leaving UvrB at a 12-base gap on one strand. DNA polymerase I fills the gap and dissociates the UvrB protein from the DNA. The repair process is completed by DNA ligase, which seals the nick.
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1. Gros L, Ishchenko AA, Saparbaev M: Enzymology of repair of etheno-adducts. Mutat Res 2003; 531(1-2): 219-229. 2. Chung FL, Zhang L, Ocando JE et al.: Role of 1,N2-propanodeoxyguanosine adducts as endogenous DNA lesions in rodens and humans, IARC Scientific Publication 1999; 150, IARC, Lyon, 45-54. 3. Chung FL, Nath RG, Ocando J et al.: Deoxyguanosine adducts of t-4-hydroxy-2-nonenal are endogenous DNA lesions in rodents and humans: detection and potential sources. Cancer Res 2000; 60: 1507-1511. 4. Krokan HE, Standal R, Slupphaug G: DNA glycosylases in the base excision repair of DNA. Biochem J 1997; 325: 1-16. 5. Krokan HE, Nilsen H, Skorpen F et al.: Base excision repair of DNA in mammalian cells. FEBS Lett 2000; 476(1-2): 73-77. 6. Kane CM, Linn S: Purification and characterization of an apurinic/apyrimidinic endonuclease from HeLa cells. J Biol Chem 1981; 256: 3405-3414. 7. Demple B, Herman T, Chen DS: Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Proc Natl Acad Sci USA 1991; 88: 11450-11454. 8. Robson CN, Hickson ID: Isolation of cDNA clones encoding a human apurinic/ /apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in E. coli xth (exonuclease III) mutants. Nucleic Acids Res 1991; 19(20): 5519-5523. 9. Seki S, Hatsushika M, Watanabe S et al.: cDNA cloning, sequencing, expression and possible domain structure of human APEX nuclease homologous to Escherichia coli exonuclease III. Biochim. Biophys Acta 1992; 1131: 287-299. 10. Kubota Y, Nash RA, Klungland A et al.: Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase β and the XRCC1 protein. EMBO J 1996; 15: 6662-6670. 11. Fortini P, Pascucci B, Parlanti E et al.: Different DNA polymerases are involved in the short- and long-patch base excision repair in mammalian cells. Biochemistry 1998; 37(11): 3575-3580. 12. Frossina G, Fortini P, Rossi O et al.: Two pathways for base excision repair in mammalian cells. J Biol Chem 1996; 271: 9573-9578. 13. Bennett RA, Wilson DM, Wong D et al.: Interaction of human apurinic endonuclease and DNA polymerase in the base excision repair pathway. Proc Natl Acad Sci USA 1997; 94: 7166-7169. 14. Podlutsky AJ, Dianova II, Wilson SH et al.: DNA synthesis and dRPase activities of polymerase are both essential for single-nucleotide patch base excision repair in mammalian cell extracts. Biochemistry 2001; 40: 809-813. 15. Lau AY, Scharer, Samson L et al.: Crystal structure of a human alkylbase- DNA repair enzyme complexed to DNA: Mechanisms for Nucleotide flipping and base excision. Cell 1998; 95: 249-258. 16. Stivers JT, Pankiewicz KW, Watanabe KA: Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry 1999; 38: 952-963. 17. Hollis T, Ichikawa Y, Ellenberger T: DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J 2000; 19: 758-766. 18. Dodson ML, Michaels ML, Lloyd RS: Unified catalytic mechanism for DNA glycosylases. J Biol Chem 1994; 269: 32709-32712. 19. de Laat WL, Jaspers NG, Hoeijmakers JH: Molecular mechanism of nucleotide excision repair. Genes Dev 1999; 13: 768-785. 20. Fink SP, Reddy GR, Marnett LJ: Mutagenicity in Escherichia coli of the major DNA adduct derived from the endogenous mutagen malondialdehyde. Proc Natl Acad Sci USA 1997; 94: 8652-8657. 21. Johnson KA, Fink SP, Marnett LJ: Repair of propanodeoxyguanosine by nucleotide excision repair in vivo and in vitro. J Biol Chem 1997; 272: 11434-11438. 22. Mellon I, Hanawald PC: Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature 1989; 342: 95-98. 23. Selby CP, Witkin EM, Sancar A: Escherichia coli mdf mutant deficient in “mutation frequency decline” lacks strand-specific repair: in vivo complementation with purified coupling factor. Proc Natl Acad Sci. USA 1991; 88: 11574-11578. 24. Selby CP, Sancar A: Molecular mechanism of transcription repair coupling. Science 1993; 260: 53-58. 25. Friedberg EC, Walker GC, Siede W: DNA Repair and Mutagenesis. American Society of Microbiology Press 1995; Washington, DC. 26. Grossman L, Thiagalingam S: Nucleotide excision repair, a tracking mechanism in search of damage. J Mol Biol 1993; 268: 16871-16874. 27. Lehmann AR: DNA repair-deficient diseases, Xeroderma pigmentosum, Cockayne”s syndrome and trichothiodistrophy. Biochimie 2003; 85(11); 1101-1111. 28. Aboussekhra A, Biggerstaff M, Shivji MK et al.: Mammalian DNA nucleotide excision repair reconstituted with purified protein components. Cell 1995; 80(6): 859-868. 29. Mu D, Hsu DS, Sancar A: Reaction mechanism of human DNA repair excision nuclease. J Biol Chem 1996; 271(14): 8285-8294. 30. Constantinou A, Gunz D, Evans E et al.: Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair. J Biol Chem 1999; 274(9): 5637-5648. 31. O”Donovan A, Davies AA, Moggs JG et al.: XPG endonuclease makes the 3” incision in human DNA nucleotide excision repair. Nature 1994; 371(6496): 432-435. 32. Moggs JG, Yarema KJ, Essigmann JM et al.: Analysis of incision sites produced by human cell extracts and purified proteins during nucleotide excision repair of a 1,3-intrastrand d(GpTpG)-cisplatin adduct. J Biol Chem 1996; 271(12): 7177-7186. 33. Wood RD, Shivji MK: Which DNA polymerase are used for DNA repair in eucaryotes? Carcinogenesis 1997; 18; 605-610. 34. Kowalczykowski SC, Dixon DA, Eggleston AK et al.: Biochemistry of homologous recombination in Escherichia coll. Microbiol Rev 1994; 58(3): 401-465. 35. Kowalczykowski SC, Eggleston AK: Homologous pairing and DNA strand-exchange proteins. Annu Rev Biochem 1994; 63: 991-1043. 36. Kuzminov A: Unraveling the late stages of recombinational repair: metabolism of DNA junctions in Escherichia coli. Bioessays 1996; 18(9): 757-765. 37. Roca AI, Cox MM: RecA protein: structure, function, and role in recombinational DNA repair. Prog Nucleic Acid Res Mol Biol 1997; 56: 129-223. 38. Dixon DA, Kowalczykowski SC: The recombination hotspot chi is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme. Cell 1993; 73(1): 87-96. 39. Anderson DG, Kowalczykowski SC: The recombination hot spot chi is a regulatory element that switches. Genes Dev 1997; 11(5): 571-581. 40. Stahl FW, Stahl MM: Recombination pathway specificity of Chi. Genetics 1977; 86(4): 715-725. 41. Smith KC, Wang TV, Sharma RC: RecA-dependent DNA repair in UV-irradiated Escherichia coli. J Photochem Photobiol B 1987; 1(1): 1-11. 42. Umezu K, Kolodner RD: Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein. J Biol Chem 1994; 269(47): 30005-30013. 43. West SC: Processing of recombination intermediates by the RuvABC proteins. Annu Rev Genet 1997; 31: 213-244. 44. Grilley M, Griffith J, Modrich P: Bidirectional excision in methyl-directed mismatch repair. J Biol Chem 1993; 268 (16): 11830-11837. 45. Allen DJ, Makhov A, Grilley M et al.: MutS mediates heteroduplex loop formation by a translocation mechanism. EMBO J 1997; 16: 4467-4476. 46. Mechanic LE, Frankel BL, Matson SW: Escherichia coli MutL loads DNA helicase II onto DNA. J Biol Chem 2000; 275: 38337-38346. 47. Ni TT, Marsischky GT, Kolodner RD: MSH2 and MSH6 are required for removal of adenine misincorporated opposite 8-oxo-guanine in S. cerevisiae. Mol Cell 1999: 4: 439-444. 48. Acharya S, Wilson T, Gradia S et al.: hMSH2 forms specific mispair-binding complexes with hMSH3 and hMSH6. Proc. Natl. Acad. Sci. USA 1996; 93: 13629-13634. 49. Kolodner RD, Marsischky GT: Eukaryotic DNA mismatch repair. Curr Opin Genet Dev 1999; 9: 89-96. 50. Johnson KA, Mierzwa ML, Fink SP et al.: MutS recognition of exocyclic DNA adducts that are endogenous products of lipid oxidation J Biol Chem 1999; 38: 27112-27118. 51. Kowalczyk P: The influence of exocyclic DNA adducts in bacterial and mammalian genome instability. New Medicine 2012; 3: 68-73. 52. Kowalczyk P: M13mp18 phage model as a tools of research mutagenie and cytotoxic biological and environmental compounds. New Medicine 2012; 4: 116-121.