Abstract
In human cells, oxidative pyrimidine lesions are restored by the base excision repair pathway initiated by homologues of Endo III (hNTH1) and Endo VIII (hNEIL1 and hNEIL2). In this study we have quantitatively analyzed and compared their activity toward nine oxidative base lesions and an apurinic/apyrimidinic (AP) site using defined oligonucleotide substrates. hNTH1 and hNEIL1 but not hNEIL2 excised the two stereoisomers of thymine glycol (5R-Tg and 5S-Tg), but their isomer specificity was markedly different: the relative activity for 5R-Tg:5S-Tg was 13:1 for hNTH1 and 1.5:1 for hNEIL1. This was also the case for their Escherichia coli homologues: the relative activity for 5R-Tg:5S-Tg was 1:2.5 for Endo III and 3.2:1 for Endo VIII. Among other tested lesions for hNTH1, an AP site was a significantly better substrate than urea, 5-hydroxyuracil (hoU), and guanine-derived formamidopyrimidine (mFapyG), whereas for hNEIL1 these base lesions and an AP site were comparable substrates. In contrast, hNEIL2 recognized an AP site exclusively, and the activity for hoU and mFapyG was marginal. hNEIL1, hNEIL2, and Endo VIII but not hNTH1 and Endo III formed cross-links to oxanine, suggesting conservation of the -fold of the active site of the Endo VIII homologues. The profiles of the excision of the Tg isomers with HeLa and E. coli cell extracts closely resembled those of hNTH1 and Endo III, confirming their major contribution to the repair of Tg isomers in cells. However, detailed analysis of the cellular activity suggests that hNEIL1 has a significant role in the repair of 5S-Tg in human cells.
Highlights
DNA carrying vital genetic information of cells constantly suffers from spontaneous deamination and depurination, alkylation, and oxidation [1,2,3]
No bands were evident that indicated the contamination of Endo III or Endo VIII from the E. coli host. hNEIL1 and hNEIL2 were incubated with 19AP/A containing an AP site in the presence of NaBH4, and the trapped reaction intermediate was analyzed by SDSPAGE (Fig. 1B). hNEIL1 and hNEIL2 gave rise to a single trapped species, which migrated slower than that formed with Endo VIII (29.6 kDa)
This result further confirmed that the hNEIL1 and hNEIL2 preparations were free from Endo VIII and Endo III (23.4 kDa)
Summary
CATCGATAGCATCCTXCCTTCTCTC a G, A, and C indicate the base opposite the damage (X) in double-stranded substrates. Studies into the repair function of the mammalian Endo VIII homologues reveal that like Endo III and Endo VIII, NTH1 and NEIL1/NEIL2 exhibit, albeit not fully, redundant damage specificity and primarily recognize oxidative pyrimidine lesions [14, 31,32,33,34,35,36,37] Their activities toward oxidized base lesions have been assessed using different substrates (oligonucleotides with different sequence contexts or calf thymus DNA) and assay methods (nicking assays of DNA and release assays of damaged bases), making the quantitative comparison of activity data rather difficult. These results, together with those obtained from cell extracts, indicate that base lesions generated by reactive oxygen species are removed from DNA at distinct rates in cells, and that their genotoxic effects can be differentially attenuated in keeping with their repair kinetics
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