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

项目摘要 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也采用了普遍存在的和强有力的调控基因表达的策略， 它必须使用与细胞RNA相同的生物机制。尽管其重要性， 细胞和病毒RNA结构依赖性翻译的详细机制 控制知之甚少。为了弥补这一差距，我们建议在以前的基础上， 通过研究两种不同的，但 直接与细胞翻译机制相互作用的病毒RNA的相关类别。的 首先包括一种称为tRNA样结构（TLSs）的病毒RNA， 以神秘的方式结合各种细胞蛋白质;这样做， 用未知的方法翻译随着新的假定的tRNA模拟物被发现，这项工作 具有广泛的适用性。第二种是终止上游核糖体结合 位点（TURBS）RNA，其存在于两个开放阅读框之间的界面处， 使用未知的RNA结构驱动核糖体重新起始。证据表明RNA序列 结构在核糖体再起始中起重要作用，因此， 承诺揭示这一过程的基本原则。对于这些研究，我们建议 利用我们在三维RNA方面的丰富专业知识的“结构向前”策略 结构测定，与生物化学相结合，将结构与功能联系起来， 详细的新机械模型。此外，我们将利用我们的结构发现来指导小说 生物信息学搜索旨在发现这些结构元件的新版本， 细胞和病毒RNA。我们期望我们的工作能激发出关于自然的新问题， 多样性，分布，和权力的RNA结构依赖的翻译控制，建议新的 系统进行研究，并帮助进一步了解广泛的基本原则。

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.