In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings — ASN Events

In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings (#119)

Yalin Liao 1 , Marlene Reichel 2 , Mandy Rettel 3 , Chikako Ragan 1 , Maurits Evers 1 , Anne-Marie Alleaume 3 , Rastislav Horos 3 , Matthias W Hentze 3 , Anthony A Millar 2 , Thomas Preiss 1 4
  1. Department of Genome Sciences, The Australian National University, Canberra, ACT, Australia
  2. Division of Plant Science, Research School of Biology, The Australian National University, Acton (Canberra), ACT, Australia
  3. European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
  4. Victor Chang Cardiac Research Institute, Sydney, NSW, Australia

RNA-binding proteins (RBPs) control the fate and expression of a transcriptome. Despite this fundamental importance, our understanding of plant RBPs is rudimentary, being mainly derived via bioinformatic extrapolation from other kingdoms. Here, we have adapted the methodology of ‘mRNA-protein interactome capture’ to investigate the RNA-binding proteome in planta. From Arabidopsis thaliana (At) etiolated seedlings, we captured more than 700 proteins, including 300 with high confidence that we have defined as the At-RBP set. Approximately 75% of these At-RBPs are bioinformatically linked with RNA biology, containing a diversity of canonical RNA-binding domains (RBDs). As no prior experimental RNA-binding evidence exists for the majority of these proteins, their capture now authenticates them as RBPs. Moreover, we identified protein families harbouring emerging and potentially novel RBDs, including WHIRLY, LIM, ALBA, DUF1296 and YTH domain-containing proteins, the latter being homologous to animal RNA methylation readers. Other At-RBP set proteins include major signalling proteins, cytoskeleton-associated proteins, membrane transporters and enzymes, suggesting the potential scope and function of RNA-protein interactions within a plant cell is much broader than previously appreciated. Therefore, our foundation dataset has provided an unbiased insight into the RNA-binding proteome of plants, on which future investigations into plant RBPs can be based.

  1. Reichel M, Liao Y*, Rettel M, Ragan C, Evers M, Alleaume AM, Horos R, Hentze MW, Preiss T*, Millar AA. In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings. Plant Cell. 2016 Oct 11. *Co-first/correspondence.
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