The RNA-binding protein repertoire of Arabidopsis thaliana

Handle URI:
http://hdl.handle.net/10754/617258
Title:
The RNA-binding protein repertoire of Arabidopsis thaliana
Authors:
Marondedze, Claudius; Thomas, Ludivine; Serano, Natalia Lorena Gorron; Lilley, Kathryn S.; Gehring, Christoph A. ( 0000-0003-4355-4591 )
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.
KAUST Department:
Bioscience Core Laboratory; Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
The RNA-binding protein repertoire of Arabidopsis thaliana 2016, 6:29766 Scientific Reports
Publisher:
Springer Nature
Journal:
Scientific Reports
Issue Date:
11-Jul-2016
DOI:
10.1038/srep29766
Type:
Article
ISSN:
2045-2322
Sponsors:
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.
Additional Links:
http://www.nature.com/articles/srep29766
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorMarondedze, Claudiusen
dc.contributor.authorThomas, Ludivineen
dc.contributor.authorSerano, Natalia Lorena Gorronen
dc.contributor.authorLilley, Kathryn S.en
dc.contributor.authorGehring, Christoph A.en
dc.date.accessioned2016-07-20T12:35:07Z-
dc.date.available2016-07-20T12:35:07Z-
dc.date.issued2016-07-11-
dc.identifier.citationThe RNA-binding protein repertoire of Arabidopsis thaliana 2016, 6:29766 Scientific Reportsen
dc.identifier.issn2045-2322-
dc.identifier.doi10.1038/srep29766-
dc.identifier.urihttp://hdl.handle.net/10754/617258-
dc.description.abstractRNA-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.en
dc.description.sponsorshipThe 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.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/articles/srep29766en
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/en
dc.titleThe RNA-binding protein repertoire of Arabidopsis thalianaen
dc.typeArticleen
dc.contributor.departmentBioscience Core Laboratoryen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalScientific Reportsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCambridge Centre for Proteomics, Cambridge Systems Biology Centre, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UKen
dc.contributor.institutionHM.Clause, rue Louis Saillant, Z.I. La Motte, BP83, 26802 Portes-lès-Valence cédex, France.en
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorThomas, Ludivineen
kaust.authorSerano, Natalia Lorena Gorronen
kaust.authorGehring, Christoph A.en
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