Exogenous dsRNA made accessible to Dicer by two eukaryotic RNA-dependent RNA polymerases

Discrimination of self from non-self RNA is a critical requirement for any cell to respond to infections and to maintain cellular integrity. We report novel functions for two RNA-dependent RNA polymerases (RDRs) in Paramecium in the detection of exogenous RNA. In the RNA interference (RNAi) mechanism, RDRs are normally involved in the production of large amounts of secondary siRNAs in response to an initial primary siRNA. To characterize the function of RDRs in context of exogenous RNA recognition, we developed a novel dsRNA delivery system using dextran nanoparticles to deliver heteroduplex dsRNA to cells as food particles, mimicking the natural phagosomal entry pathway. Subsequent small RNA sequencing allows us to dissect siRNAs produced from exogenous RNA or RDR transcripts. Contrary to expectations of how dsRNA-induced silencing is triggered, our data show that Dicer is unable to directly cleave exogenous dsRNA while two RDRs are required for the initial steps of dsRNA-induced RNAi. Paradoxically, these two RDRs must replicate dsRNA to make it available for Dicer cleavage and primary siRNA accumulation. Our data also show that this system works efficiently also with exogenous ssRNA, although RDR2 is dispensable for ssRNA conversion. The function of RDRs in this protist is in contrast to that in animals, plants and fungi and extends the functional diversity of these polymerases. RDR-associated complexes appear to control the entry of food and symbiont-derived RNA into the RNAi machinery, enabling complex RNA interactions with the environment.