Abstract
As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson–Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures – either global or local – determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.
Highlights
Since their discovery some 50 years ago (Diener and Raymer, 1967; Diener, 1972, 2003) viroids have exerted a particular fascination because they are the lowest step of the biological scale: simple RNA genomes of just ∼250–400 nucleotides
Data from three independent lines support that this elongated conformation is biologically significant: (i) a lessthan-unit (341 nt) infectious Potato spindle tuber viroid (PSTVd) variant, identified in plants agrotransformed with the dimeric form of an in vitro-deleted 350bp PSTVd-cDNA unit, results from an additional 9-nt deletion in vivo that restores the rod-like secondary structure (Wassenegger et al, 1994), (ii) the longer-than-unit natural variants of Coconut cadang–cadang viroid (CCCVd; Haseloff et al, 1982) and Citrus exocortis viroid (CEVd) (Semancik et al, 1994; Fadda et al, 2003b) accumulating in infected tissues result from repetitions of the right terminal domain that preserve the rod-like secondary structure, and (iii) replication and directional PSTVd trafficking across specific cellular boundaries is mediated or influenced by RNA motifs, loops, of the rod-like secondary structure
CONCLUDING REFLECTIONS AND PROSPECTS The hypothesis that single-stranded RNA chains fold into a series of hairpin-like helices in which base-pairing by hydrogen bonds takes place, being extruded as loops the bases with no partner available, was proposed more than 50 years ago (Fresco et al, 1960). This first RNA secondary structure model has been fully validated and is at the core of all studies on RNA structure including predictions with algorithms that search for secondary structures of minimal free energy
Summary
Since their discovery some 50 years ago (Diener and Raymer, 1967; Diener, 1972, 2003) viroids have exerted a particular fascination because they are the lowest step of the biological scale: simple RNA genomes of just ∼250–400 nucleotides (nt).
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