Viroids may elicit down-regulation of host gene expression via RNA-silencing

Distinct molecular mechanisms have been proposed for explaining how viroids, small non-protein-coding RNAs that infect plants, interfere with their host gene expression and elicit disease symptoms. On the one hand, by mimicking structural features of cellular RNAs, viroids may impair the host transcriptional and RNA trafficking machineries, which are usurped and redirected to facilitate their own replication and movement. On the other hand, the identification in viroid-infected plants of viroid-derived small RNAs (vd-sRNAs) of 21-24 nt, structurally similar to the small interfering RNAs that mediate RNA silencing, suggests that this RNA-based regulatory network largely conserved in eukaryotes is used by viroids for modifying host gene expression. By deep sequencing and rapid amplification of cDNA ends (RACE) we have recently shown that a host mRNA, coding for a gene involved in chloroplast development, is actually targeted for cleavage (in a sequence specific manner as predicted by RNA silencing), by two vd-RNAs accumulating in peach tissues infected by a chloroplast replicating viroid (Peach latent mosaic viroid). These results thus support a direct involvement of RNA silencing in viroid pathogenesis, particularly considering that the two vd-sRNAs map at the viroid pathogenicity determinant. Several other potential targets of vd-sRNAs have been identified in the same experimental system by bioinformatics and degradome-based analyses, suggesting a wider role of RNA silencing in plant-viroid interactions. These results highlight the power of genome-wide approaches for further dissecting the host pathways targeted