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Open AccessArticle

Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method

1
Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
2
Fakultät für Biologie, Universität Duisburg-Essen, North Rhine-Westphalia, 45117 Essen, Germany
3
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
*
Authors to whom correspondence should be addressed.
Biomolecules 2020, 10(4), 661; https://doi.org/10.3390/biom10040661
Received: 1 April 2020 / Revised: 16 April 2020 / Accepted: 20 April 2020 / Published: 24 April 2020
(This article belongs to the Special Issue Ribonucleoprotein Particles (RNPs): From Structure to Function)
RNA-binding proteins (RBPs) play a crucial role in regulating RNA function and fate. However, the full complement of RBPs has only recently begun to be uncovered through proteome-wide approaches such as RNA interactome capture (RIC). RIC has been applied to various cell lines and organisms, including plants, greatly expanding the repertoire of RBPs. However, several technical challenges have limited the efficacy of RIC when applied to plant tissues. Here, we report an improved version of RIC that overcomes the difficulties imposed by leaf tissue. Using this improved RIC method in Arabidopsis leaves, we identified 717 RBPs, generating a deep RNA-binding proteome for leaf tissues. While 75% of these RBPs can be linked to RNA biology, the remaining 25% were previously not known to interact with RNA. Interestingly, we observed that a large number of proteins related to photosynthesis associate with RNA in vivo, including proteins from the four major photosynthetic supercomplexes. As has previously been reported for mammals, a large proportion of leaf RBPs lack known RNA-binding domains, suggesting unconventional modes of RNA binding. We anticipate that this improved RIC method will provide critical insights into RNA metabolism in plants, including how cellular RBPs respond to environmental, physiological and pathological cues. View Full-Text
Keywords: RNA-binding proteins; RBP; protein–RNA interaction; RNA-binding proteome; RBPome; RNA interactome capture; RIC; ptRIC; Arabidopsis; plant RNA-binding proteins; RBP; protein–RNA interaction; RNA-binding proteome; RBPome; RNA interactome capture; RIC; ptRIC; Arabidopsis; plant
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Bach-Pages, M.; Homma, F.; Kourelis, J.; Kaschani, F.; Mohammed, S.; Kaiser, M.; van der Hoorn, R.A.L.; Castello, A.; Preston, G.M. Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method. Biomolecules 2020, 10, 661.

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