Journal Article

Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction

Di Serio, Francesco, Navarro, Beatriz, Bisztray, György, Pantaleo, Vitantonio, Dalmay, Tamas, Gisel, Andreas, Burgyán, József, Moxon, Simon

2009

Overview

Background: Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21–24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms. Methodology/Principal Findings: To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1) were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots) of the genomic (+) and (−) viroid RNAs, with a prevalence of those from the (−) strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots. Conclusions/Significance: These findings show that different Dicer-like enzymes (DCLs) target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Analysis / Arabidopsis thaliana / Biochemistry/RNA Structure / Biosynthesis / Blotting, Northern / Cellular structure / defense mechanisms / Deoxyribonucleic acid / DNA / DNA methylation / DNA Primers - genetics / Enzymes / Fines & penalties / Flowers & plants / Gene expression / Genes / Genomes / Grapevine yellow speckle viroid 1 / Health aspects / high-throughput nucleotide sequencing / Hop stunt viroid / Host plants / Infection / Methylation / MicroRNAs / MicroRNAs - genetics / Models, Genetic / Molecular Biology/RNA-Protein Interactions / non-coding RNA / Nucleic acids / Nucleotide sequence / Oligonucleotides - chemistry / Plant Diseases - genetics / Plant Diseases - virology / Plant viruses / Plants - genetics / Ribonucleic acid / RNA / RNA Interference / RNA polymerase / RNA, Plant - genetics / RNA-mediated interference / Sequence Alignment / Sequence Analysis, DNA - methods / Stunt / Viral infections / Viroids / Viroids - genetics / Virology/Effects of Virus Infection on Host Gene Expression / Virology/Host Antiviral Responses / Virology/Viral and Gene Regulation / Viruses / Vitis - genetics / Vitis vinifera