RNA 3D Structural Motifs As A New Constraint of Viral and Subviral RNA Evolution

该项目解决了一个具有基本和实际重要性的基本生物学问题：传染性RNA病毒的基因组如何进化以感染宿主？拟议的活动将为回答这一问题提供新的知识。从长远来看，这样的知识库可能有助于开发新的方法，用于预测新的感染因子的出现和开发新的抗病毒治疗方法。病毒和亚病毒RNA的一个普遍结构特征是存在许多环和突起，两侧是茎。这些通常被描述为没有特定结构和功能定义的未配对区域。该项目旨在证明这些区域实际上显示结构特征并介导关键功能。这些包括病毒复制和在整个宿主中的系统运动。该项目为本科生/研究生和博士后提供跨学科培训。该项目还将通过与市中心一所高中的合作，让非裔美国人、非洲人、西班牙裔/拉丁美洲人和妇女等代表性不足群体的高中生参与，大大加强中等教育。最近对rRNA和一些其他RNA的晶体结构研究表明，绝大多数环/凸起是高度结构化的三维（3D）基序，具有由非Watson-Crick碱基对形成的明确几何形状，并且这些基序通常介导RNA-RNA、RNA-蛋白质和RNA-小配体相互作用。该项目将测试感染性RNA中的3D基序作为RNA序列变体进化的关键约束的假设。为此，目标1将测试马铃薯纺锤块茎类病毒RNA 3D基序是否介导复制和系统运输，并限制RNA序列进化。目的2将测试是否特定的RNA基序蛋白质相互作用是一个主要的机制，为3D模体约束。从该项目开发的新原理和研究工具可能会显着推进在不同生物体中基于RNA的基因调控的许多新兴前沿领域的研究，从细菌到植物再到人类。这些包括（i）最近发现的非编码RNA模板转录的DNA依赖性RNA聚合酶调控基因表达的机制和进化，（ii）最近发现的细胞非编码环状RNA基因调控的结构基础，和（iii）RNA结构介导的细胞RNA细胞间运输机制，以调节基因表达在生物体水平。

This project addresses a fundamental biological question of basic and practical importance: How does the genome of an infectious RNA virus evolve to infect a host? The proposed activities will contribute new knowledge to answer this question. In the long-term, such a knowledge base may enable development of new methods for predicting the emergence of new infectious agents and for developing new anti-viral therapeutics. A universal structural feature of viral and subviral RNAs is the presence of many loops and bulges flanked by stems. These are often described as unpaired regions without specific structural and functional definitions. This project seeks to demonstrate that these regions in fact display structural features and mediate key functions. These include viral replication and systemic movement throughout the host. The project provides interdisciplinary training for undergraduate/graduate students and postdocs. Through collaboration with an inner-city high school, the project will also greatly enhance secondary education by involving participation of high school students from underrepresented groups including African American, African, Hispanic/Latino and women. Recent crystal structure studies on rRNAs and some other RNAs demonstrate that the vast majority of loops/bulges are highly structured three-dimensional (3D) motifs with well-defined geometry formed by non-Watson-Crick base pairs, and that these motifs often mediate RNA-RNA, RNA-protein and RNA-small ligand interactions. This project will test the hypothesis that 3D motifs in an infectious RNA function as a critical constraint on the evolution of RNA sequence variants. Towards this end Aim 1 will test whether Potato spindle tuber viroid RNA 3D motifs mediate replication and systemic trafficking and constrain the RNA sequence evolution. Aim 2 will test whether specific RNA motif-protein interaction is a major mechanism for the 3D motif constraint. The new principles and research tools developed from this project may significantly advance research in a number of emerging frontiers of RNA-based gene regulation in different organisms ranging from bacteria, to plants to humans. These include (i) mechanism and evolution of recently discovered noncoding RNA-templated transcription by DNA-dependent RNA polymerases to regulate gene expression, (ii) structural basis of gene regulation by recently discovered cellular noncoding circular RNAs, and (iii) mechanisms of RNA structure-mediated intercellular trafficking of cellular RNAs to regulate gene expression at the organismal level.