Abstract
Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here.
Highlights
In the diverse field of plant pathogens, viroids are extremely interesting because of both their small size (246–401 nucleotides; nt) and their single-stranded, non-coding RNA genome
Probing viroids of the family Pospiviroidae The goal of this study is to provide an overview of the secondary structures, in solution, of the viroids from the family Pospiviroidae by elucidating, at a one nucleotide resolution, the structures of many representative species by selective 29-hydroxyl acylation analyzed by primer extension (SHAPE)
A previous study using traditional SHAPE coupled with computer assisted secondary structure prediction permitted the resolution of the structures of five distinct viroid species from three different genera of the family Pospiviroidae
Summary
In the diverse field of plant pathogens, viroids are extremely interesting because of both their small size (246–401 nucleotides; nt) and their single-stranded, non-coding RNA genome. Using only these characteristics, they are able to replicate autonomously and to move systemically in their host plants in which they induce visible symptoms of the viroid infection [1]. They are able to replicate autonomously and to move systemically in their host plants in which they induce visible symptoms of the viroid infection [1] Since their discovery in 1971 [2], more than 30 species have been described and classified into two families: the Avsunviroidae and the Pospiviroidae. The Pospiviroidae are divided into three subfamilies, namely, Pospiviroinae, Apscaviroinae, and Coleviroinae. The subfamily Pospiviroinae includes three genera, the Pospiviroid, the Hostuviroid and the Cocadviroid, whereas the subfamilies Apscaviroinae and Coleviroinae consists of one genus each, the Apscaviroid and the Coleviroid, respectively
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