The RNA-binding protein repertoire of Arabidopsis thaliana

Claudius Marondedze, Ludivine Thomas, Natalia Lorena Gorron Serano, Kathryn S. Lilley, Christoph A Gehring

Research output: Contribution to journalArticlepeer-review

109 Scopus citations

Abstract

RNA-binding proteins (RBPs) have essential roles in determining the fate of RNA from synthesis to decay and have been studied on a protein-by-protein basis, or computationally based on a number of well-characterised RNA-binding domains. Recently, high-throughput methods enabled the capture of mammalian RNA-binding proteomes. To gain insight into the role of Arabidopsis thaliana RBPs at the systems level, we have employed interactome capture techniques using cells from different ecotypes grown in cultures and leaves. In vivo UV-crosslinking of RNA to RBPs, oligo(dT) capture and mass spectrometry yielded 1,145 different proteins including 550 RBPs that either belong to the functional category ‘RNA-binding’, have known RNA-binding domains or have orthologs identified in mammals, C. elegans, or S. cerevisiae in addition to 595 novel candidate RBPs. We noted specific subsets of RBPs in cultured cells and leaves and a comparison of Arabidopsis, mammalian, C. elegans, and S. cerevisiae RBPs reveals a common set of proteins with a role in intermediate metabolism, as well as distinct differences suggesting that RBPs are also species and tissue specific. This study provides a foundation for studies that will advance our understanding of the biological significance of RBPs in plant developmental and stimulus specific responses.
Original languageEnglish (US)
JournalScientific Reports
Volume6
Issue number1
DOIs
StatePublished - Jul 11 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): CRG3-62140383
Acknowledgements: The research was funded by the Office of Competitive Research Grant Program, grant number CRG3-62140383 from King Abdullah University of Science and Technology (KAUST). The authors would like to thank Dr. Harriet Parsons, Cambridge Centre for Proteomics (CCP), University of Cambridge for providing the Landsberg erecta cell suspension culture, Dr. Huoming Zhang, Bioscience Core laboratory at KAUST and Dr. Mike Deery at CCP, University of Cambridge for their assistance with Mass spectrometry.

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