Figure 1.

Structural characteristics of the viroids in the families Pospiviroidae and Avsunviroidae. (A) Members of the family Pospiviroidae adopt a rod-shaped secondary structure that has been functionally separated into five domains (TL, P, C, V and TR; differentially shaded). They contain conserved motifs: the features of the CCR (blue box) and the presence of TCR or TCH (orange and pink boxes, respectively) define the characteristics of each genus, as indicated. Together with the conserved sequence of the upper strand of the CCR, the flanking variable nucleotides (indicated by arrows) form an imperfect hairpin (hairpin I). Both the characteristic CCR sequence of PSTVd and the hairpin that forms are shown in the upper and lower inserts, respectively. (B) Avsunviroidae viroids adopt rod-shaped, branched or semibranched secondary structures (genus Avsunviroid, Pelamoviroid and Elaviroid, respectively). They contain conserved sequences of hammerhead ribozymes (HHR) that are functional in positive and negative strands (light and dark gray boxes, respectively, with the self-cleavage sites indicated by solid or empty arrowheads, respectively). In PLMVd, ‘kissing-loops’ tertiary interactions are indicated by lines. The insert includes the sequence of the HHR of ELVd with the classic representation that gives name to these ribozymes (left) next to the same HHR in both polarities according to the data of X-ray crystallography and NMR. Tertiary interactions between loops 1 and 2 are shown with lines. HO- and >P, 5′-hydroxyl and 2′,3′-phosphodiester groups, respectively; CCR, central conserved region; HHR, hammerhead ribozyme; N, any nucleotide; TCR, terminal conserved region; and TCH, terminal conserved hairpin.