The most pro-active repair process is likely BER, a pathway that corrects DNA modifications that arise either spontaneously or from attack by reactive chemicals. In fact, it has been estimated that well over 10,000 assaults will take place on our DNA each day, with the most prominent offender being reactive oxygen species (superoxide, hydroxyl radical, and hydrogen peroxide), a.k.a. free radicals. Moreover, BER is often responsible for correcting damages that arise spontenously, due to the inherent instability of DNA, or from alkylation of DNA. In all, BER copes with inappropriate bases (mismatched or damaged) that arise from replication errors or via chemical modification by oxidation or alkylation; sites of base loss that are formed by enzyme-catalyzed, spontaneous or mutagen-induced base release; and strand breaks that are products of free radical attack of DNA. Many of these same damages are generated by anti-cancer agents and environmental mutagens which generate free radicals (such as ionizing radiation and radiomimetic antibiotics). In essence, BER copes with those damages that are produced "every day".
BER involves the concerted effort of several repair proteins that recognize and excise specific DNA damages, eventually replacing the damaged moiety with a normal nucleotide and restoring the DNA back to its original state (Figure). Typically, the first step of BER involves the removal of an inappropriate base from DNA by a DNA glycosylase. DNA glycosylases bind specifically to a target base and hydrolyze the N-glycosylic bond, releasing the inappropriate base while keeping the DNA backbone intact. In humans, six DNA glycosylases have been identified, and each excises an overlapping subset of either spontaneously formed (e.g. hypoxanthine), oxidized (e.g. 8-oxo-7,8-dihydroguanine), alkylated (e.g. 3-methyladenine), or mismatched (e.g. T:G) bases. The abasic site (i.e. the site of base loss) that is formed by DNA glycosylase activity is subsequently recognized by Ape1 (the major AP endonuclease), which incises the phosphodiester backbone immediately 5' to the lesion leaving behind a strand break with a normal 3'-hydroxyl group and an abnormal 5'-abasic terminus. "Short-patch" BER proceeds with DNA Polb removing the 5'-abasic residue via its 5’-deoxyribose-phosphodiesterase activity and filling in the single nucleotide gap (Figure, pathway on left). To complete the process, the nick is then sealed by DNA Ligase I or a complex of XRCC1 and LigIII. Additionally, an alternative BER pathway (Figure, pathway on right) exists that involves the replacement of more than a single nucleotide and requires the Fen1 protein to excise the flap-like structure that is produced by DNA polymerase strand displacement. This "long-patch" process has been divided into two subpathways: a PCNA-stimulated, Polb-directed pathway and a PCNA-dependent, Pold/e
-directed pathway. The type of substrate encountered (i.e. the target damage or the form [circular or linear] of the DNA) likely dictates whether short-patch or either of the long-patch repair pathways is employed.
Strikingly, in most cases, mice that are engineered to lack a central BER component do not survive embryogenesis, suggesting an absolute requirement for this repair system in development. The likely interpretation is that BER is needed to cope with the every day accumulation of DNA damage, and that in its absence, the genome is damaged beyond compatibility with normal development. Alternatively, these proteins may serve yet unidentified roles in embryogenesis that are not repair related, but this seems unlikely given the similar results obtained with several different BER factors. In any case, BER is a vital process required for maintaining genetic integrity and for animal survival. It seems likely that mutations in BER that lead to a slightly reduced repair capacity, and not the absence of the repair system, will associate with cellular dysfunction.
by David M. Wilson III