A quantitative model of human DNA base excision repair. I. mechanistic insights

Abstract

Base excision repair (BER) is a multistep process involving the sequential activity of several proteins that cope with spontaneous and environmentally induced mutagenic and cytotoxic DNA damage. Quantitative kinetic data on single proteins of BER have been used here to develop a mathematical model of the BER pathway. This model was then employed to evaluate mechanistic issues and to determine the sensitivity of pathway throughput to altered enzyme kinetics. Notably, the model predicts considerably less pathway throughput than observed in experimental in vitro assays. This finding, in combination with the effects of pathway cooperativity on model throughput, supports the hypothesis of cooperation during abasic site repair and between the apurinic/apyrimidinic (AP) endonuclease, Ape1, and the 8-oxoguanine DNA glycosylase, Ogg1. The quantitative model also predicts that for 8-oxoguanine and hydrolytic AP site damage, short-patch Polbeta-mediated BER dominates, with minimal switching to the long-patch subpathway. Sensitivity analysis of the model indicates that the Polbeta-catalyzed reactions have the most control over pathway throughput, although other BER reactions contribute to pathway efficiency as well. The studies within represent a first step in a developing effort to create a predictive model for BER cellular capacity.

Apurinic/Apyrimidinic Endonuclease (APE/REF-1) Haploinsufficient Mice Display Tissue-specific Differences in DNA Polymerase β-Dependent Base Excision Repair

“…Similar results have also been obtained with other bifunctional DNA glycosylases such as endonuclease III (hNTH1), responsible for recognition and removal of ring-saturated pyrimidines (36). These studies, in addition to a recent mathematical model of BER throughput (37), suggest a preference for ␤-pol-mediated MFG-BER in vivo.…”

“…Our laboratory has also demonstrated that ␤-pol expression and activity strongly correlate with MFG-BER under a variety of environmental stimuli (52,53,58,59). A recent study (37) examining kinetic data of various BER enzymes has also suggested that ␤-polmediated MFG-BER may be the predominant BER pathway in vivo. As such, the finding that decreased levels of APE in livers of APE-haploinsufficient mice resulted in decreased MFG-BER was surprising.…”

Estimating the Effect of Human Base Excision Repair Protein Variants on the Repair of Oxidative DNA Base Damage

“…This implicitly assumes homogeneity and deterministic, continuous reaction kinetics, which are justified by the high concentration of repair proteins as discussed in ref. 28. If Michaelis-Menten assumptions hold for a biochemical system, then k cat is interpreted as the catalytic turnover rate of the enzyme (its ''activity'') and K M is a function of the affinity of the enzyme for the substrate.…”

“…Consequently, we apply a mathematical model of human BER that integrates biological knowledge of enzyme mechanisms and biochemical data on enzyme kinetics and protein concentration obtained from the literature. This model has been used to interpret published data from in vitro pathway reconstitution and cell extracts to evaluate mechanistic hypotheses of enzyme cooperativity and coordination and predict the relative significance of the BER subpathways (28). Notably, the model recently predicted that under normal conditions, background oxidative DNA base damage level is at the low end of the widely varying published measurements (i.e., up to hundreds of lesions per cell) and that the background level is relatively stable to small changes in enzyme kinetics (29).…”

Measurement and Meaning of Oxidatively Modified DNA Lesions in Urine

“…A recent report failed to show 8-oxoGua -containing oligomers in urine (71), implying that further processing occurs, perhaps ultimately yielding 8-oxodG, or that they do not exist. However, under normal circumstances, the role of nucleotide excision repair in the removal of 8-oxoGua and perhaps other small oxidatively generated DNA lesions would seem to be negligible (102)(103)(104)(105)(106), although results from xeroderma pigmentosum cell lines have not entirely excluded the possibility (72,103,107,108). …”