Urrutia Kathleen, Chen Yu Hsuan, Tang Jin, Hung Ta I, Zhang Guodong, Xu Wenyan, Zhao Wenxin, Tonthat Dylan, Chang Chia-En A, Zhao Linlin
Department of Chemistry, University of California, Riverside, CA 92521, USA.
Peking University Cancer Hospital Yunnan, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China.
Nucleic Acids Res. 2024 Dec 11;52(22):14093-14111. doi: 10.1093/nar/gkae1144.
Mitochondrial DNA (mtDNA) is indispensable for mitochondrial function and is maintained by DNA repair, turnover, mitochondrial dynamics and mitophagy, along with the inherent redundancy of mtDNA. Base excision repair (BER) is a major DNA repair mechanism in mammalian mitochondria. Mitochondrial BER enzymes are implicated in mtDNA-mediated immune response and inflammation. mtDNA is organized into mitochondrial nucleoids by mitochondrial transcription factor A (TFAM). The regulation of DNA repair activities by TFAM-DNA interactions remains understudied. Here, we demonstrate the modulation of DNA repair enzymes by TFAM concentrations, DNA sequences and DNA modifications. Unlike previously reported inhibitory effects, we observed that human uracil-DNA glycosylase 1 (UNG1) and AP endonuclease I (APE1) have optimal activities at specific TFAM/DNA molar ratios. High TFAM/DNA ratios inhibited other enzymes, OGG1 and AAG. In addition, TFAM reduces the accumulation of certain repair intermediates. Molecular dynamics simulations and DNA-binding experiments demonstrate that the presence of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in certain sequence motifs enhances TFAM-DNA binding, partially explaining the inhibition of OGG1 activity. Bioinformatic analysis of published 8-oxodG, dU, and TFAM-footprint maps reveals a correlation between 8-oxodG and TFAM locations in mtDNA. Collectively, these results highlight the complex regulation of mtDNA repair by DNA sequence, TFAM concentrations, lesions and repair enzymes.
线粒体DNA（mtDNA）对于线粒体功能不可或缺，并通过DNA修复、周转、线粒体动力学和线粒体自噬以及mtDNA固有的冗余性来维持。碱基切除修复（BER）是哺乳动物线粒体中的一种主要DNA修复机制。线粒体BER酶参与mtDNA介导的免疫反应和炎症。mtDNA由线粒体转录因子A（TFAM）组织成线粒体核仁。TFAM与DNA相互作用对DNA修复活性的调节仍未得到充分研究。在这里，我们证明了TFAM浓度、DNA序列和DNA修饰对DNA修复酶的调节作用。与先前报道的抑制作用不同，我们观察到人类尿嘧啶-DNA糖基化酶1（UNG1）和AP核酸内切酶I（APE1）在特定的TFAM/DNA摩尔比下具有最佳活性。高TFAM/DNA比率会抑制其他酶，如OGG1和AAG。此外，TFAM会减少某些修复中间体的积累。分子动力学模拟和DNA结合实验表明，特定序列基序中8-氧代-7,8-二氢-2'-脱氧鸟苷（8-oxodG）的存在增强了TFAM与DNA的结合，部分解释了对OGG1活性的抑制作用。对已发表的8-oxodG、dU和TFAM足迹图谱进行生物信息学分析，揭示了mtDNA中8-oxodG与TFAM位置之间的相关性。总的来说，这些结果突出了DNA序列、TFAM浓度、损伤和修复酶对mtDNA修复的复杂调节作用。
