Biochemistry and molecular biology of a model viroid.

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Biochemistry and Molecular Biology of a Model Viroid Viroids infect higher plants worldwide causing diseases which result in significant losses for agriculture affecting not only food, but ornamental and industrial plants. Viroids are small (250-400 nt), single-stranded, circular RNAs that replicate through a DNA-independent rolling circle mechanism. Although they do not code for any known protein and are not protected by a protein capsid, viroids can obviate a plant's cellular defense mechanism and act as parasites, making them the smallest self-replicating genetic elements identified to date. In essence, these species constitute an ideal biological system for detailed RNA structure/function analyses. Our model species is the Peach latent mosaic viroid (PLMVd). Our long term goal is to learn how viroids elicit pathogenesis in infected trees. To do so, we will address three questions, from distinct disciplines, illustrating the integrative approach of this research program: 1. By deep-sequencing, we will investigate the dynamics of population within PLMVd, and put forth a practical definition of quasispecies (Genetic); 2. We will further our analysis of viroid small interfering RNAs and identify peach endogenous miRNA with altered expression in infected trees in order to understand how this mechanism relates to pathogenesis (Molecular Biology); and; 3. Considering that structure elucidation is paramount to understanding viroid life cycle, we will determine the structure of at least one variant of every viroid species and related circular satellite RNAs (Structural Biochemistry). In brief, we will use viroids to advance boundaries of life sciences.