SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
Biology Department, Tomsk State University, 634050 Tomsk, Russia.
Int J Mol Sci. 2023 May 23;24(11):9113. doi: 10.3390/ijms24119113.
The protein encoded by the vaccinia virus gene has base excision repair uracil-DNA -glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG along DNA between two uracil residues. The salt dependence of the correlated cleavage, together with the similar affinity of vvUNG for damaged and undamaged DNA, support the one-dimensional diffusion mechanism of lesion search. Unlike short gaps, covalent adducts partly block vvUNG translocation. Kinetic experiments show that once a lesion is found it is excised with a probability ~0.76. Varying the distance between two uracils, we use a random walk model to estimate the mean number of steps per association with DNA at ~4200, which is consistent with vvUNG playing a role as a processivity factor. Finally, we show that inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.
痘苗病毒基因编码的蛋白质具有碱基切除修复尿嘧啶-DNA -糖苷酶(vvUNG)活性,并且在病毒复制复合物中充当持续性因子。使用不同于 PolN/PCNA 滑动夹子的蛋白质是正痘病毒复制的独特特征,为药物设计提供了有吸引力的目标。然而,vvUNG 的内在持续性从未被估计过,这使得病毒聚合酶是否具有足够的持续性成为一个悬而未决的问题。在这里,我们使用相关切割测定法来表征 vvUNG 在两个尿嘧啶残基之间沿 DNA 的易位。相关切割的盐依赖性,以及 vvUNG 对受损和未受损 DNA 的相似亲和力,支持损伤搜索的一维扩散机制。与短间隙不同,共价加合物部分阻止 vvUNG 易位。动力学实验表明,一旦发现病变,其被切除的概率约为 0.76。改变两个尿嘧啶之间的距离,我们使用随机游走模型来估计与 DNA 结合的平均关联步数约为 4200,这与 vvUNG 作为持续性因子发挥作用一致。最后,我们表明携带四氢-2,4,6-三氧嘧啶基的抑制剂可以抑制 vvUNG 的持续性。