Functional lability of RNA-dependent RNA polymerases in animals.

Natalia Pinzón,Hector Escrivá,Hervé Seitz,Stéphanie Bertrand,Lucie Subirana,Isabelle Busseau,Gregory S Barsh

doi:10.1371/journal.pgen.1007915

Abstract

RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways.

Highlights

Small interfering RNAs play a central role in the RNA interference (RNAi) response
We find that RNAdependent RNA polymerase (RdRP) are much more common in animals than previously thought, but their genes were independently lost in many lineages
Focusing on a species with RdRP genes, we found that it does not use them for RNAi

Summary

Introduction

Small interfering RNAs (siRNAs) play a central role in the RNA interference (RNAi) response. The template RNA and the RdRP product are believed to hybridize, forming a long double-stranded RNA which is subsequently cleaved by Dicer nucleases into double-stranded siRNAs (reviewed in [5]). RdRPs have been implicated in RNAi and in RNA-directed heterochromatinization [6,7,8,9], but the exact nature of their products remains elusive: fungal RdRPs are frequently proposed to polymerize long RNAs which can form Dicer substrates after annealing to the RdRP template [10,11,12]. It is usually believed that their products are long RNAs that anneal with the template to generate a Dicer substrate, and that model has gained experimental support in one organism, Tetrahymena [17]

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Results

Discussion

Conclusion