Abstract
Being nonprotein-coding RNAs, viroids depend almost entirely on host-encoded proteins for replication in the nuclei (members of the family Pospiviroidae) or in the chloroplasts (members of the family Avsunviroidae). Viroids replicate through an RNA-based rolling-circle mechanism with three stages: (1) production of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase; (2) cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae only the oligomeric (+) RNAs provide the proper conformation to be cleaved by an RNase of class III; and (3) circularization catalyzed by DNA ligase I (family Pospiviroidae) or by a chloroplastic isoform of tRNA ligase (family Avsunviroidae). These enzymes (and ribozymes) are most likely assisted by other host proteins. It is therefore remarkable that viroids have acquired for their replication the ability to manipulate the template specificity of DNA-dependent RNA polymerases, redirecting them to transcribe RNA, and the substrate specificity of a DNA ligase to act on RNA.
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