Discovering the RNA-binding proteome of plant leaves with an improved RNA interactome capture method

Bach-Pages, M., Homma, F., Kourelis, J., Kaschani, F., Mohammed, S., Kaiser, M., van der Hoorn, R. A.L., Castello, A. and Preston, G. M. (2020) Discovering the RNA-binding proteome of plant leaves with an improved RNA interactome capture method. Biomolecules, 10(4), 661. (doi: 10.3390/biom10040661) (PMID:32344669) (PMCID:PMC7226388)

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.

• Item Type: Articles
• Additional Information: Funding: Marcel Bach-Pages is supported by Biotechnology and Biological Sciences Research Council (BBSRC, grant BB/M011224/1), the Lorna Casselton Memorial Scholarship at St. Cross College (University of Oxford) and a John Fell Fund (University of Oxford) award to Gail Preston and Alfredo Castello. Renier van der Hoorn is supported by ERC grant 616449 ‘GreenProteases’. Alfredo Castello is supported by an MRC Career Development Award MR/L019434/1 and MRC grant MR/R021562/1.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Castello, Professor Alfredo

Creator Roles

Castello, A.: Conceptualization, Formal analysis, Funding acquisition, Project administration, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing

• Authors: Bach-Pages, M., Homma, F., Kourelis, J., Kaschani, F., Mohammed, S., Kaiser, M., van der Hoorn, R. A.L., Castello, A., and Preston, G. M.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Biomolecules
• Publisher: MDPI
• ISSN: 2218-273X
• ISSN (Online): 2218-273X
• Copyright Holders: Copyright © 2020 by the authors
• First Published: First published Biomolecules 10(4):661
• Publisher Policy: Reproduced under a Creative Commons license