Price David H
Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA 52240, USA.
Viruses. 2025 May 29;17(6):779. doi: 10.3390/v17060779.
All beta- and gamma-herpesviruses utilize a set of six viral proteins to facilitate transcription from specific promoters that become active late in the viral life cycle. These proteins form a complex that interacts with a TA-rich sequence upstream of the late transcription start sites and recruits RNA polymerase II (Pol II). The structure of any of the late transcription factors (LTFs) alone or in complexes has not been solved by standard means yet, but a fair amount is known about how the proteins interact and where the complex is positioned over the late promoters. Here, AlphaFold3 was used to predict and analyze the LTF complex using proteins from the beta-herpesviruses HCMV, MCMV, HHV6, and HHV7, and from the gamma-herpesviruses EBV and KSHV. The predicted structures had high levels of confidence and were remarkably similar even though there is little sequence conservation in the LTFs across the viruses. The results are consistent with most of the previously determined information concerning the interaction of the factors with each other and with DNA. A conserved threonine phosphorylation in one of the subunits that is critical to the function of the LTFs is predicted to be at the junction of five subunits. AlphaFold 3 predicts seven metal ion binding sites in each of the four beta-herpesviruses and either five or six in the gamma-herpesviruses created by conserved residues in three of the subunits. The structures also provide insights into the function of the subunits and which host general transcription factors (GTFs) may or may not be utilized during initiation.
所有的β-和γ-疱疹病毒都利用一组六种病毒蛋白来促进特定启动子的转录，这些启动子在病毒生命周期后期变得活跃。这些蛋白形成一个复合物，与晚期转录起始位点上游富含TA的序列相互作用，并募集RNA聚合酶II（Pol II）。单独或处于复合物中的任何晚期转录因子（LTF）的结构尚未通过标准方法解析出来，但对于这些蛋白如何相互作用以及复合物在晚期启动子上的定位，人们已经了解了不少。在这里，使用AlphaFold3对来自β-疱疹病毒HCMV、MCMV、HHV6和HHV7以及γ-疱疹病毒EBV和KSHV的蛋白组成的LTF复合物进行预测和分析。预测的结构具有很高的可信度，并且尽管不同病毒的LTF之间几乎没有序列保守性，但它们却非常相似。结果与先前确定的关于这些因子彼此之间以及与DNA相互作用的大部分信息一致。预测在一个对LTF功能至关重要的亚基中，一个保守的苏氨酸磷酸化位点位于五个亚基的交界处。AlphaFold 3预测在四种β-疱疹病毒中的每一种中都有七个金属离子结合位点，在γ-疱疹病毒中有五个或六个，这些位点由三个亚基中的保守残基形成。这些结构还为亚基的功能以及在起始过程中可能或不可能利用哪些宿主通用转录因子（GTF）提供了见解。
