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.
Highlights
We noted specific subsets of RNA-binding proteins (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 species and tissue specific
We show the diversity of RNA-binding domains and infer that RBPs have a role in cellular metabolic processes and abiotic stress responses
We applied the interactome capture technique according to established protocols[30,31]
Summary
Previous studies in yeast (S. cerevisiae) have shown, that the total amount of transcribed RNA that will eventually be translated is only about 0.5%1,2 This percentage implies the presence of a tightly regulated post-transcriptional control, that is in parts achieved by RNA-binding proteins (RBPs)[3,4]. RBPs together with noncoding (nc)RNAs such as microRNAs have been reported to direct and regulate the post-transcriptional fate of mRNA in the nucleus and cytoplasm, affecting many processes that include splicing, 3′-end formation, editing, localization and translation (reviewed elswhere[5]). In Arabidopsis thaliana alone there are >200 different annotated RBPs of which www.nature.com/scientificreports/
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