Exploring RNA Silencing As A Pathogenicity Factor In Plant - Virus Interactions

RNA silencing (RS) is a conserved eukaryotic mechanism acting as anti-viral immune system in plants. Small interfering RNAs (siRNAs) are RS effectors accumulating in virus-infected tissues as immune system components, providing target specificity for post-transcriptional degradation of invading RNAs. Virus-derived siRNAs (vsiRNAs, 21-24 nt) are abundant in infected plants, with certain regions ("hot spots") more represented than others. Two isolates of Potato virus Y (PVY), PVYC-to and PVY-SON41, yield very different disease phenotypes on tomato (Solanum lycopersicum), the former inducing leaf distortions, the latter mild symptoms. We applied in silico and molecular approaches to identify PVY vsiRNAs suppressing host mRNAs by sequence complementarity and RS-based suppression, inducing dysfunctional processes upon infection. Aim was to explore differential expression of host-targeting vsiRNA, as responsible of isolates differences. A computational pipeline retrieved 21nt vsiRNAs from PVY isolates, complementary to predicted mRNAs (Solgenomics, ITAG2.3). Two PVYC-to genome regions showed specific secondary structures absent in PVY-SON41, accounting for vsiRNAs accumulation. Two tomato transcript lists were obtained, perfectly or imperfectly (one or two mismatches) complementary to vsiRNA computed for either PVY isolates, putative targets of vsiRNA-driven RS suppression. Targets common to both isolates were discarded, leaving a gene list representing only PVYC-to targets. Quantitative RT-PCR of transcription factors (e.g. NAC, MYB, TCP, HD-ZIP, MADS-box families) active in leaf development and morphogenesis showed differential expression upon PVYC-to and PVY-SON41 infections. Lower isolate-specific mRNA accumulation suggested RSdriven post-transcriptional regulation, confirming a link between symptoms and vsiRNAs-mediated RS. Results from vsiRNAs deep sequencing from infected leaves are also discussed.