HIV-1 integration into the human genome is dependent on 3′-processing of the viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3′-processed DNA remained resistant. Here, we describe the mechanism by which the 3′-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage () of the 3′-processed DNA was significantly lower (approximately 2–2.5-fold) than the unprocessed HIV-1 DNA by TREX1. The values of human TREX1 for the processed U5 and U3 DNA substrates were 3.8 s and 4.5 s, respectively. In contrast, the unprocessed U5 and U3 substrates were cleaved at 10.2 s and 9.8 s, respectively. The efficiency of degradation (/K) of the 3′-processed DNA (U5-70.2 and U3-28.05 pMs) was also significantly lower than the unprocessed DNA (U5-103.1 and U3-65.3 pMs). Furthermore, the binding affinity (K) of TREX1 was markedly lower (∼2-fold) for the 3′-processed DNA than the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3′-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3′-processed DNA. These results pinpoint the mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3′-processed HIV-1 DNA.

中文翻译：

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三原修复核酸外切酶 1 通过有利的动力学、热力学、结构和构象特性优先降解无法整合的 HIV-1 DNA


HIV-1 整合到人类基因组中取决于病毒 DNA 的 3' 加工。最近，我们报道了细胞三素修复核酸外切酶 1 (TREX1) 通过降解未加工的病毒 DNA 来增强 HIV-1 整合，而具有整合能力的 3' 加工 DNA 仍保持抗性。在这里，我们描述了 3' 处理的 HIV-1 DNA 抵抗 TREX1 介导的降解的机制。我们的动力学研究表明，TREX1 对 3' 处理的 DNA 的切割率 () 显着低于未处理的 HIV-1 DNA（约 2-2.5 倍）。处理后的 U5 和 U3 DNA 底物的人 TREX1 值分别为 3.8 s 和 4.5 s。相比之下，未处理的 U5 和 U3 底物分别在 10.2 秒和 9.8 秒时裂解。 3'处理的DNA（U5-70.2和U3-28.05 pMs）的降解效率（/K）也显着低于未处理的DNA（U5-103.1和U3-65.3 pMs）。此外，TREX1 对 3' 加工 DNA 的结合亲和力 (K) 明显低于未加工 DNA（约 2 倍）。分子对接和动力学研究揭示了 TREX1 与 3' 加工和未加工的 HIV-1 DNA 的不同构象结合模式。特别是，未加工的 DNA 有利地定位在与 TREX1 催化残基发生极性相互作用的活性位点中。此外，与 3' 处理的 DNA 相比，TREX1 和未处理的 DNA 之间形成了稳定的复合物。这些结果查明了TREX1优先降解无整合能力的HIV-1 DNA的机制，并揭示了有整合能力的3'加工的HIV-1 DNA的独特结构和构象特性。