Base excision repair (BER)

The principal repair pathway for the removal of oxidative damage is BER. Enzymes in this pathway recognise relatively few but frequent DNA lesions such as abasic sites, deaminated C and A, and individual bases damaged by oxidative intermediates or alkylating agents. Most of these lesions do not greatly distort the DNA helix structure. In both prokaryotes and eukaryotes, BER is initiated by DNA glycosylases, a class of enzymes that each recognise a specific set of modified bases (reviewed in [1]). DNA glycosylases cleave the N-glycosylic bond between the target base and the deoxyribose, releasing a free base and leaving an apurinic/apyrimidinic (AP) site. In mammalian cells two pathways for the processing of AP sites have been described: a single nucleotide insertion (or "short patch") pathway, catalysed by DNA polymerase b [2, 3], which is almost identical to the bacterial model; and a proliferating cell nuclear antigen (PCNA) dependent ("long patch") pathway, involving a resynthesis patch of 2 to <13 nucleotides [4, 5] (see Figure). Additional variations on each of these BER pathways have also been reported (reviewed in [6, 7]).

Short patch BER

In the "short patch" model an AP endonuclease cleaves the phosphodiester bond immediately 5' to the AP site, generating 5'-sugar-phosphate and 3'-OH ends as it nicks the DNA [8]. Removal of the 5'-sugar-phosphate moeity by a deoxyribophosphodiesterase (dRpase) results in a single nucleotide gap that is then filled by a DNA polymerase and sealed by DNA ligase [3, 9-11]. In mammalian cells DNA polymerase b (DNA pol b) is the major polymerase for this pathway [3, 9-11]. Interestingly, DNA pol b also contains intrinsic dRPase activity, and can remove the 5'-sugar-phosphate residue itself before filling in the single nucleotide gap [12, 13]. Ligation of the resynthesised nucleotide is mediated by either DNA ligase I or an XRCC1/DNA ligase III complex, which have each been shown to interact with DNA pol b [3, 14, 15].

Long patch BER

Although the "short-patch" pathway appears to be the most active for the repair of AP sites, an alternative "long patch" BER pathway has been reported [4, 16]. As in "short patch" BER repair, the AP sites are processed by an AP endonuclease which cleaves immediately 5' to the AP site, generating 5'-sugar-phosphate and 3'-OH ends. However, in this process, the 5'-sugar phosphate residue is not removed by a dRpase, rather DNA pol d or e adds several nucleotides to the 3' end of the nick displacing the 5'-sugar-phosphate as part of a single stranded flap structure. This flap structure is recognised and excised by flap endonuclease (FEN1) and DNA is finally ligated by DNA ligase I. This pathway is dependent on PCNA, which presumably plays a role in loading DNA pol d or e onto the DNA as well as stimulating the activity of FEN1 [17].

Consequences of defective BER

Oxidative DNA damage has been implicated in the etiology of ageing, as well as that of cancer [18-20]. Defects in key activities of the BER process, such as AP endonuclease, DNA pol b and the XRCC1-DNA ligase III heterodimer, lead to embryonic lethal phenotypes in mice, indicating that repair of endogenous DNA lesions is essential during embryonic development [11, 21, 22]. However, Cockayne syndrome may serve as a human model for defective BER. CS cells exhibit an impaired ability to remove oxidative damage from active genes, but not from inactive DNA [23, 24]. This suggests the existence of a mechanism coupling BER to transcription, and allowing for the preferential removal of damage in active genes, as has been demonstrated for NER [25, 26]. Indeed, CS cells appear to be defective in the transcription-coupled repair (TCR) components of both NER and BER. Furthermore there it has been demonstrated that the breast cancer gene BRCA1 plays a role in the transcription-coupled repair of oxidative damage [27, 28]. This suggests a possible link between BER capacity and the predisposition towards breast cancer.

For additional information on the role of the CS proteins in BER see: CS news release.

Functional overlap of NER and BER pathways

Further indications of an overlap between these two excision pathways, arise from the recent demonstration that the NER protein, XPG, plays a direct role role in activating a glycosylase involved in BER [29, 30], and the defects in XPG which are associated with the presentation of CS symptoms are also associated with deficiencies in BER (in addition to the NER defect associated with all XP-G individuals) [24]. Additionally, NER processes have been implicated in the repair of AP sites and a variety of single base modifications [31-36]. This has led to suggestions that, at least for some types of damage, NER may act as a backup for the BER pathway.

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