title: The RNA-binding protein repertoire of Arabidopsis thaliana.
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.
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
authors.forename: Claudius
authors.initials: C
authors.lastname: Marondedze
authors.affiliation: Bioscience Core Laboratory, 4700 King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.
authors.forename: Ludivine
authors.initials: L
authors.lastname: Thomas
authors.affiliation: Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.
authors.forename: Natalia L
authors.initials: NL
authors.lastname: Serrano
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
authors.affiliation: Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.
authors.forename: Chris
authors.initials: C
authors.lastname: Gehring
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D016601:RNA-Binding Proteins