Antiviral Role of Plant-Encoded RNA-Dependent RNA Polymerases Revisited with Deep Sequencing of Small Interfering RNAs of Virus Origin

Several recent studies profiled virus-specific small interfering RNAs (vsRNAs) using next generation sequencing platforms and compellingly implicated plant-encoded RNA-dependent RNA polymerases (RDR) in vsRNA biogenesis and vsRNA-mediated antiviral defense. Specifically, both RDR1 and RDR6 were found to contribute to the accumulation of vsRNAs in virus-infected cells. While RDR1 was responsible for the majority of vsRNAs in plants infected with three different viruses, RDR6 acted as a surrogate when RDR1 function was disrupted. Mechanistically, vsRNAs associated with RDR1 mostly mapped to viral RNA regions close to the 5' ends, whereas those associated with RDR6 mapped to more 3' regions and appeared to be dependent on higher viral RNA concentrations. Knocking out both RDR I and RDR6 led to drastically diminished vsRNA levels concomitant with enhanced viral RNA accumulation. In conclusion, these studies established that RDR1 and RDR6 function synergistically to contain RNA virus infections through the RNA silencing-based antiviral defense.