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

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Abstract

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.

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Acknowledgments

This work was supported by l’Agence Nationale de la Recherche (ANR-06-BLAN-0203-02), by the CNRS, by the Université de Perpignan (UPVD). It was also published under the framework of the LABEX: ANR-10-LABX-0036_NETRNA and benefits from a funding from the state managed by the French National Research Agency as part of the Investments for the future program. M.C. and T.M. were supported by a grant from the French Ministry of Research and M-A.T. by a core grant from ETH-Z.

Author contributuion

MC and TP carried out the molecular biology studies and JMD the molecular evolution studies. VJ and JD provided general technical help. TM, PD and MAT made the BIFC work. CBA and MNPP helped with the immunoprecipitation experiments. MC, TP, PD and JMD conceived the study, and participated in its design. JMD coordinated the writing of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Jean-Marc Deragon.

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Clavel, M., Pélissier, T., Montavon, T. et al. Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis. Plant Mol Biol 91, 131–147 (2016). https://doi.org/10.1007/s11103-016-0448-9

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  • DOI: https://doi.org/10.1007/s11103-016-0448-9

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