Discovering the RNA-binding proteome of plant leaves with an improved RNA interactome capture method
Author(s)
Type
Journal Article
Abstract
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.
Date Issued
2020-04-24
Date Acceptance
2020-04-20
Citation
Biomolecules, 2020, 10 (4)
ISSN
2218-273X
Publisher
MDPI AG
Journal / Book Title
Biomolecules
Volume
10
Issue
4
Copyright Statement
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/32344669
Subjects
Arabidopsis
Photosynthesis
Plant Leaves
Plant Proteins
Protein Domains
Protein Interaction Mapping
Proteome
Reproducibility of Results
RNA, Plant
RNA-Binding Proteins
Arabidopsis
plant
protein–RNA interaction
ptRIC
RBP
RBPome
RIC
RNA interactome capture
RNA-binding proteins
RNA-binding proteome
Publication Status
Published
Coverage Spatial
Switzerland
Article Number
661
Date Publish Online
2020-04-24