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.
