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

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 RNAinterference (RNAi), RDRs are normally involved in the production of large amounts of secondary small interfering RNAs (siRNAs). To characterize the function of RDRs in context of exogenous RNA recognition, we developed a novel double-stranded RNA (dsRNA) application system using dextran nanoparticles to deliver heteroduplex dsRNA to cells as food particles, mimicking the natural phagosomal entry. Small RNA sequencing allows to dissect siRNAs produced from exogenous RNA or RDR transcripts. Contrary to expectations, our data show that Dicer is unable to directly cleave exogenous dsRNA while two RDRs, RDR1 and RDR2, are required for the initial steps of dsRNA-induced RNAi. Paradoxically, these two RDRs must replicate dsRNA before Dicer cleavage. This system works efficiently also with exogenous single-stranded RNA (ssRNA), although RDR2 is dispensable for ssRNA conversion. The function of RDRs is in contrast to that in animals, plants and fungi and extends the functional diversity of these polymerases as RDR-associated complexes appear to control the entry of food RNA into the RNAi machinery.