Abstract
Viroids, due to their small size and lack of protein-coding capacity, must rely essentially on their hosts for replication. Intriguingly, viroids have evolved the ability to replicate in two cellular organella, the nucleus (family Pospiviroidae) and the chloroplast (family Avsunviroidae). Viroid replication proceeds through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in both polarity strands: i) synthesis of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase, in both instances redirected to transcribe RNA templates, ii) cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae the oligomeric RNAs provide the proper conformation but not the catalytic activity, and iii) circularization. The host RNA polymerases, most likely assisted by additional host proteins, start transcription from specific sites, thus implying the existence of viroid promoters. Cleavage and ligation in the family Pospiviroidae is probably catalyzed by an RNase III-like enzyme and an RNA ligase able to circularize the resulting 5′ and 3′ termini. Whether a chloroplastic RNA ligase mediates circularization in the family Avsunviroidae, or this reaction is autocatalytic, remains an open issue.
Highlights
Perhaps the most striking aspect of viroids from a functional perspective is that, in contrast to viruses, they lack protein-coding ability [1,2]
Viroids replicate through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in the strands of both polarities: i) synthesis of longer-than-unit strands catalyzed by a host nuclear or chloroplastic RNA polymerase that reiteratively transcribes the initial circular template, ii) processing to unit-length, which remarkably is mediated by hammerhead ribozymes in the family Avsunviroidae, and iii) circularization resulting from the action of an RNA
The first argument supporting this view is that whereas the cleavage sites of Hop stunt viroid (HSVd) and Apple scar skin viroid (ASSVd) (+) strands map at equivalent positions in a similar hairpin I/double-stranded structure, these viroids cannot form the GAAA-capped hairpin
Summary
Perhaps the most striking aspect of viroids from a functional perspective is that, in contrast to viruses, they lack protein-coding ability [1,2]. Studies on how viroids replicate have revealed aspects of RNA metabolism that were totally unanticipated, some of which might play a role in their hosts. Illustrating this point, naturally-encoded hammerhead ribozymes have been discovered in the genome of Arabidopsis thaliana [10] and mouse [11]; the latter, embedded in a messenger RNA, is able to reduce protein expression in vivo
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