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Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis

Clavel, Marion, Pélissier, Thierry, Montavon, Thomas, Tschopp, Marie-Aude, Pouch-Pélissier, Marie-Noëlle, Descombin, Julie, Jean, Viviane, Dunoyer, Patrice, Bousquet-Antonelli, Cécile, Deragon, Jean-Marc
Plant molecular biology 2016 v.91 no.1-2 pp. 131-147
Arabidopsis thaliana, RNA-binding proteins, biogenesis, concerted evolution, double-stranded RNA, phylogeny, plant proteins, small interfering RNA, vascular plants
In this work, we retrace the evolutionary history of plant double-stranded RNA binding proteins (DRBs), a group of non-catalytic factors containing one or more double-stranded RNA binding motif (dsRBM) that play important roles in small RNA biogenesis and functions. Using a phylogenetic approach, we show that multiple dsRBM DRBs are systematically composed of two different types of dsRBMs evolving under different constraints and likely fulfilling complementary functions. In vascular plants, four distinct clades of multiple dsRBM DRBs are always present with the exception of Brassicaceae species, that do not possess member of the newly identified clade we named DRB6. We also identified a second new and highly conserved DRB family (we named DRB7) whose members possess a single dsRBM that shows concerted evolution with the most C-terminal dsRBM domain of the Dicer-like 4 (DCL4) proteins. Using a BiFC approach, we observed that Arabidopsis thaliana DRB7.2 (AtDRB7.2) can directly interact with AtDRB4 but not with AtDCL4 and we provide evidence that both AtDRB7.2 and AtDRB4 participate in the epigenetically activated siRNAs pathway.