Endonucleases excision-repair

Chemistry of glycosylases and endonucleases involved in base-excision repair 98CRV1221. 

Figure 36-23. Base excision-repair of DNA. The enzyme uracil DNA glycosylase removes the uracil created by spontaneous deamination of cytosine in the DNA. An endonuclease cuts the backbone near the defect then, after an endonuclease removes a few bases, the defect is filled in by the action of a repair polymerase and the strand is rejoined by a ligase. (Courtesy of B Alberts.)...

Lindahl, T. (1979). DNA glycoslylases, endonucleases for apurinic/apyrimidinic sites and base excision repair. Proc. Nuc. Acid Res. Mol. Biol. 22 109-118. 

Comparison between DNA repair and phospholipid repair The processes that can lead to DNA damage and the type of damage are described in Chapter 9 and Appendix 9.6. The repair processes involve removal of the specific nucleotide(s) by an exonuclease and replacement of the nucleotide by a DNA polymerase. Since the strand must be broken to remove the damage (by an endonuclease) these parts of the strand must be repaired by a ligase. The process is known as excision-repair. Of interest, there is a degree of similarity between the removal of damaged polyunsaturated fatty acids from phospholipids in membranes and replacement with a new fatty acid by two enzymes, a deacylase and an acyltransferase (see above and Chapter 11), and excision-repair of DNA. 

Bennett, R.A., Wilson, D.M., 3rd, Wong, D., and 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. 

Utilising a reversion assay in Salmonella enterica, Prieto et al reported an increased frequency of point mutations following bile-salt exposure. Mutations were predominantly nucleotide substitutions (GC to AT transitions) and -1 frameshift mutations.The frameshifts were dependent on SOS induction and linked to the activity of DinB polymerase (Pol IV). The authors proposed that the GC to AT transitions stimulated by bile, could have arisen from oxidative processes giving rise to oxidised cytosine residues. Consistent with this hypothesis, the authors demonstrated that strains of S. enterica-lacking enzymes required for base-excision repair (endonuclease III and exonuclease IV) and the removal of oxidised bases, demonstrated increased bile-acid sensitivity compared with competent strains. In another study using E. coli, resistance to the DNA-damaging effects of bile was associated with Dam-directed mismatch repair, a pathway also involved with the repair of oxidative DNA lesions. ... 

Pyrimidine dimers and other forms of DNA damage can be removed by a general excision repair mechanism. The first reaction in this form of repair involves forming nicks about the damaged region of the DNA. In (a) we see the mode of incision of UV-irradiated DNA by the pyrimidine-dimer-specific glycosylase and AP endonuclease... 

S.S. David and S.D. Williams, Chemistry of glycosylases and endonucleases involved in base-excision repair, Chem. Rev., 98 (1998) 1221-1261. 

Nucleotide excision and base removal followed by the action of apurinic-apyrimidine endonucleases (AP endonucleases) are the two types of excision repair that currently are thought to occur. A number of nucleotides are excised from the damaged DNA strand. After excision, the correct complementary bases are replaced by polymerase action, with the intact strand as template. Finally, the new strand is attached covalently to the adjacent undamaged old strand by the enzyme DNA ligase. 

Finally, in addition to nucleotide excision repair and base excision repair, an alternative repair pathway exists to remove PyroPyr and (6 ) photoproducts in some organisms, including Schizosaccharomyces pombe. In this alternative pathway, an enzyme called UV dimer endonuclease cleaves DNA immediately 5 to the damaged lesion. The damage is then removed by a 5 to 3 exonuclease (26, 27). Additionally, AP endonucleases, like Nfo in E. coli and APEl in humans, have the ability to incise immediately 5 to nonbulky lesions caused by oxidative damage and initiate excision of the lesion by a 5 to 3 exonuclease (28). 

Figure 5 Base excision repair in mammalian cells. In base excision repair, the damaged nucleotide is removed in a two-step process. A glycosylase cleaves the glycosidic bond of the damaged base, releasing it, and then AP lyase and AP endonuclease cleave the phosphodlester bonds on either side of the abasic site, which releases the deoxyribose.

Lindahl T. DNA glycosylases, endonucleases for apurinic/apyrim-idinic sites and base excision repair. Prog. Nucleic Acids. Mol. Biol. Res. 1979 22 135-192. 

D. The damage to DNA caused by ultraviolet light (pyrimidine dimers) can be repaired by the excision repair pathway. In some cases, the missing enzyme is a repair endonuclease. 

R461 K. Morikawa and M. Shirikawa, Three-Dimensional Structural View of Damaged-DMA Recognition T4 Endonuclease V, E. coli Vsr, Protein, and Human Nucleotide Excision Repair Factor XPA , Mutat. Res., 2000,460, 257... 

Antioxidant compounds include the well-known vitamins C and E, ubiquinone, uric acid, and many others. Antioxidant compounds are sacrificed to oxidation in order to directly protect more important cellular components [1-4, 6]. Antioxidant enzymes, such as superoxide dismutases, glutathione peroxidases, and quinone reductases, act catalytically to convert oxidants to less reactive species [5,6]. The essential cytoplasmic and nuclear proteolytic enzyme, proteasome recognizes and selectively degrades oxidized proteins [6, 8, 9]. Oxidized membrane lipids are recognized and selectively removed by lipases, particularly phospholipase A2 [6, 8,10]. Oxidatively modified DNA is subject to removal or excision repair by a wide series of DNA repair enzymes including endonucleases, glycosylases, polymerases, and ligases [6,8,11 ]. 

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