GSE169677
Reprogramming of RNA silencing triggered by Cucumber Mosaic Virus infection in Arabidopsis
RNA silencing has an important role mediating sequence-specific virus resistance. Here, we analyzed in detail the interference of Cucumber Mosaic Virus (CMV) with the RNA silencing machinery of Arabidopsis thaliana. We detected that CMV infection induced the production of viral small interfering RNAs (vsiRNAs) that account for a significant part of the sRNome affecting the levels of other sRNA classes. Furthermore, we analyzed the incorporation of vsiRNAs into the main ARGONAUTE (AGO) proteins with a described antiviral role and the viral RNA silencing suppressor (VRS) 2b, by combining protein immunoprecipitation with sRNA high-throughput sequencing. vsiRNAs accumulated to high levels in AGO2, followed by AGO1, AGO5 and AGO7. Interestingly, vsiRNAs represented a significant percentage of AGO-loaded sRNAs and displaced other endogenous sRNAs. As a countermeasure, the VSR 2b loaded vsiRNAs and mRNA-derived siRNAs, which affected the expression of the genes they derived from. Additionally, we analyzed how vsiRNAs incorporated into the endogenous RNA silencing pathways by exploring their target mRNAs using parallel analysis of RNA end (PARE) sequencing. This strategy allowed us to identify 61 genes with degradome data supporting their vsiRNA-mediated cleavage. This work exemplifies the complex relationship of RNA viruses with the endogenous RNA silencing machinery and the multiple aspects of virus resistance and virulence that this interaction induces. Overall design: Analysis of sRNA (infected and mock tissues including AGO and 2b-IPed) and PARE sequencing during CMV infection in Arabidopsis thaliana rosette leaves