Structure, function, and dynamics of viral RNAs and RNA-containing complexes

项目总结 真核细胞使用不同的机制来调节翻译，其中许多依赖于 与蛋白质合成机制直接相互作用的结构化RNA元件。这 病毒RNA也采用普遍而强大的基因表达调控策略， 它必须使用与细胞RNA相同的生物机制。尽管它们很重要，但 细胞和病毒RNA结构依赖的翻译的详细机制 人们对控制权知之甚少。为了解决这一差距，我们建议在以前的基础上 通过研究两种不同的BUT发现内部核糖体进入位点(IRES)RNA功能 与细胞翻译机制直接对接的相关类别的病毒RNA。这个 首先包括一类不同的病毒RNA，称为tRNA样结构(TLSS)，它模仿tRNAs 以一种神秘的方式结合各种细胞蛋白质；在这样做时，它们增强了 以未知的方式进行翻译。随着新的假定的tRNA模拟物被发现，这项工作 具有广泛适用性的洞察力。第二个是终止上游核糖体结合 位点(Turb)RNA，存在于两个开放阅读框之间的界面上，在那里它们 使用未知的RNA结构驱动核糖体重新启动。有证据表明，RNA序列 而结构可以在核糖体重新启动中发挥重要作用，因此对这些病毒Turb的研究 承诺揭示这一过程的基本原则。对于这些研究，我们提出了一个 利用我们在三维RNA方面的大量专业知识的“结构向前”战略 结构测定，与生物化学相结合，将结构与功能联系起来，发展 详细的新机械模型。此外，我们将使用我们的结构发现来指导小说 生物信息学搜索旨在找到这些结构元素的新版本 细胞和病毒RNA。我们预计，我们的工作将引发关于自然的新问题， RNA结构依赖的翻译控制的多样性、分布和力量，提出了新的 需要研究的系统，并帮助进一步理解广泛的基本原则。

PROJECT SUMMARY Eukaryotic cells use diverse mechanisms to regulate translation, many of which depend on structured RNA elements that interact directly with the protein synthesis machinery. This ubiquitous and powerful strategy for regulating gene expression is also adopted by viral RNAs, which must use the same biological machinery as cellular RNAs. Despite their importance, the detailed mechanisms that underlie both cellular and viral RNA structure-dependent translational control are poorly understood. To address this gap, we propose to build on our previous discoveries of internal ribosome entry site (IRES) RNA function by studying two different but related classes of viral RNAs that interface directly with the cellular translation machinery. The first comprises a diverse class of viral RNAs called tRNA-like structures (TLSs) that mimic tRNAs in mysterious ways and use this to bind a variety of cellular proteins; in so doing they enhance translation by unknown means. As new putative tRNA mimics are being discovered, this work promises insight of broad applicability. The second are termination upstream ribosome binding sites (TURBS) RNAs, which exist at the interface between two open reading frames where they drive ribosome reinitiation using unknown RNA structure. Evidence suggests that RNA sequence and structure can play an important role in ribosome reinitiation, thus studies of these viral TURBS promise to reveal foundational principles of this process. For these studies, we propose a ‘structure-forward’ strategy that exploits our substantial expertise in three-dimensional RNA structure determination, coupled with biochemistry to link structure with function and develop detailed new mechanistic models. In addition, we will use our structural discoveries to guide novel bioinformatics searches aimed at finding new versions of these structured elements in both cellular and viral RNAs. We anticipate that our work will inspire new questions about the nature, diversity, distribution, and power of RNA structure-dependent control of translation, suggest new systems to study, and help further understand broad underlying principles.