Alternative excision repair pathways

Abstract

Alternative excision repair (AER) is a category of excision repair initiated by a single nick, made by an endonuclease, near the site of DNA damage, and followed by excision of the damaged DNA, repair synthesis, and ligation. The ultraviolet (UV) damage endonuclease in fungi and bacteria introduces a nick immediately 5' to various types of UV damage and initiates its excision repair that is independent of nucleotide excision repair (NER). Endo IV-type apurinic/apyrimidinic (AP) endonucleases from Escherichia coli and yeast and human Exo III-type AP endonuclease APEX1 introduce a nick directly and immediately 5' to various types of oxidative base damage besides the AP site, initiating excision repair. Another endonuclease, endonuclease V from bacteria to humans, binds deaminated bases and cleaves the phosphodiester bond located 1 nucleotide 3' of the base, leading to excision repair. A single-strand break in DNA is one of the most frequent types of DNA damage within cells and is repaired efficiently. AER makes use of such repair capability of single-strand breaks, removes DNA damage, and has an important role in complementing BER and NER.

Figure 1.

CPD glycosylase, UVDE, and AP endonuclease in action. The first steps of base excision repair initiated by DNA glycosylase for base damage (A), and by CPD glycosylase for CPD (B), are compared with those of alternative excision repair initiated by UVDE (C), and AP endonuclease (D).

Figure 2.

Comparison of AER with NER for repair of UV damage in S. pombe. (A) Strand bias of CPD removal on the myo2 locus in the nuclear genome in WT (wild-type) (a), uvdeΔ (b), rad13Δ (c), and rad13Δ uvdeΔ (d). Cells with or without functional NER (rad13Δ) or AER (uvdeΔ) were irradiated with 100 J/m² of 254-nm UV and allowed to repair damage for 0–120 min at 30°C. Each point represents a mean value calculated from four hybridizations with two independent UV irradiations and DNA isolations. (Open circles) Transcribed strand, (closed circles) nontranscribed strand. (B) Contribution of NER and UVER to UV resistance of S. pombe in growth phase (a), or in stationary phase (b). uvde disruption causes a larger increase of UV sensitivity in growth phase. In addition, note that wild-type cells in exponential phase are more UV sensitive than those in stationary phase. (Open circles) Wild-type, (triangles) uvdeΔ, (plus signs), rad13Δ, (closed circles) rad13Δ uvdeΔ. (From Yasuhira et al. 1999 and Yasuhira and Yasui 2000; adapted, with permission, © American Society for Biochemistry and Molecular Biology.)

Figure 3.

Accumulation of poly(ADP-ribose) and XRCC1 at UVDE-induced SSB in the nucleus of human NER-deficient XPA cell line expressing N. crassa UVDE. The cell was irradiated with UVC light of 20 J/m² through pores of 3 µm in diameter in a filter covered over the cell. (Upper panels, green) Poly(ADP-ribose) accumulates immediately at the irradiated site and dissociates rapidly, whereas XRCC1 (red) accumulates and retains at the irradiated site. In cells treated with PARP inhibitor (DIQ) or cells transfected with vector plasmid, neither poly(ADP-ribose) nor XRCC1 accumulation was observed. (Adapted from Lan et al. 2004.)

Figure 4.

Repair pathways of BER, AER, and SSBR.