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Plant Cell. 2016 Oct;28(10):2435-2452. Epub 2016 Oct 11.

In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings.

Author information

1
Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia.
2
EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 2601, Australia.
3
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
4
EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 2601, Australia tony.millar@anu.edu.au thomas.preiss@anu.edu.au.
5
Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia.
6
Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia tony.millar@anu.edu.au thomas.preiss@anu.edu.au.

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.

PMID:
27729395
PMCID:
PMC5134986
DOI:
10.1105/tpc.16.00562
[Indexed for MEDLINE]
Free PMC Article

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