In planta determination of the mRNA-binding proteome of arabidopsis etiolated seedlings

Marlene Reichel, Yalin Liao, Mandy Rettel, Chikako Ragan, Maurits Evers, Anne Marie Alleaume, Rastislav Horos, Matthias W. Hentze, Thomas Preiss*, Anthony A. Millar

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    136 Citations (Scopus)

    Abstract

    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 adapted the mRNA-protein interactome capture method to investigate the RNA binding proteome in planta. From Arabidopsis thaliana 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 harboring 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 signaling proteins, cytoskeleton-associated proteins, membrane transporters, and enzymes, suggesting the scope and function of RNA-protein interactions within a plant cell is much broader than previously appreciated. Therefore, our foundation data set has provided an unbiased insight into the RNA binding proteome of plants, on which future investigations into plant RBPs can be based.

    Original languageEnglish
    Pages (from-to)2435-2452
    Number of pages18
    JournalPlant Cell
    Volume28
    Issue number10
    DOIs
    Publication statusPublished - Oct 2016

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