Viroids: an Ariadne's thread into the RNA labyrinth

Abstract

Viroids are structurally, functionally and evolutionarily different from viruses. Despite their small, non-protein-encoding, single-stranded circular RNA genome, viroids can infect higher plants and cause certain diseases. Members of the two viroid families, Pospiviroidae and Avsunviroidae, have evolved to usurp the transcriptional machinery of their host nuclei and chloroplasts, respectively, in which replication proceeds through a rolling-circle mechanism involving RNA polymerization, cleavage and ligation. Remarkably, viroids subvert certain DNA-dependent RNA polymerases to transcribe RNA templates, and, in the family Avsunviroidae, post-transcriptional cleavage is catalysed by hammerhead ribozymes. Viroids are models for studying RNA evolution and for analysing RNA transport in plants, because they can move intracellularly, intercellularly through plasmodesmata and to distal parts of the plant through the vascular system. Viroids elicit RNA-silencing phenomena, which might mediate some of their biological properties, including pathogenesis. As some viroids behave as catalytic RNAs, they are regarded as remnants of the RNA world.

Figure 1

Genome structure and replication mechanism of viroids. (A) Scheme of the rod-like genomic RNA that is characteristic of the family Pospiviroidae with the central (C), pathogenic (P), variable (V), and terminal left and right (TL and TR, respectively) domains. The central conserved region (CCR; genus Pospiviroid), the terminal conserved region (TCR; genera Pospiviroid, Apscaviroid and part of Coleviroid) and the terminal conserved hairpin (TCH; genera Hostuviroid and Cocadviroid) are shown. Blue arrows indicate the flanking sequences that, together with the upper strand of the CCR, form hairpin I, as depicted in the inset box for the type species of the five genera of the family Pospiviroidae: Potato spindle tuber viroid (PSTVd), Hop stunt viroid (HSVd), Coconut cadang-cadang viroid (CCCVd), Apple scar skin viroid (ASSVd) and Coleus blumei viroid 1 (CbVd-1). The red double-headed arrow connects two residues of PSTVd linked after ultraviolet irradiation as a consequence of forming part of loop E. (B) Scheme of the branched genomic RNA of Peach latent mosaic viroid (PLMVd; family Avsunviroidae), in which the sequences conserved in most natural hammerhead ribozymes are shown on a red and blue background for (+) and (−) polarities, respectively, and the self-cleavage sites are indicated by arrowheads. The red circle denotes a kissing-loop interaction. The structure of the (+) hammerhead ribozyme is shown in the inset box, with Roman and Arabic numerals depicting helices I, II and III, and loops 1 and 2, respectively, and the arrowhead indicating the self-cleavage site. The green oval indicates a tertiary interaction between loops 1 and 2 that enhances catalytic activity. (C) Asymmetric and symmetric pathways of the rolling-circle replication mechanism that is used by members of the families Pospiviroidae and Avsunviroidae, respectively. Red and blue lines refer to (+) and (−) strands, respectively. Arrowheads point to cleavage sites of a host factor (HF) or ribozymes (Rz), and the resulting 5′ and 3′ groups are indicated.