Genomic survey of RNA recognition motif (RRM) containing RNA binding proteins from barley (Hordeum vulgare ssp. vulgare)

Authors: Mahalingam, Ramamurthy; Walling, Jason

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2019
Publication Date: 2/15/2020
Citation: Mahalingam, R., Walling, J.G. 2019. Genomic survey of RNA recognition motif (RRM) containing RNA binding proteins from barley (Hordeum vulgare ssp. vulgare). Genomics. 112(2):1829-1839. https://doi.org/10.1016/j.ygeno.2019.10.016.
DOI: https://doi.org/10.1016/j.ygeno.2019.10.016

Interpretive Summary: Post-transcriptional gene regulation has been shown to play a key role during plant development and in response to changes in the external environment. A well-studied post-transcriptional gene regulation mechanism in plants is mediated by microRNAs. Another mechanism of post-transcriptional gene regulation mediated by RNA binding proteins (RBPs) is less well studied. In this study we took a bioinformatic approach to identify all the ‘RNA binding proteins’ in the barley genome. We identified 363 proteins. A systematic analysis integrating information from Interpro, Pfam and Prosite databases was undertaken to identify the various protein domains present in the barley RBPs. More than half of the RBPs in barley contained the classical RNA recognition Motif (RRM). We analyzed some of the well characterized gene families containing the RRMs such as PolyA binding proteins, Serine/Arginine Rich proteins, and Glycine-rich RBPs in barley. Furthermore, we reanalyzed a recently published proteome study of various barley malting stages and identified 37 RBPs. This survey provides a frame work for further functional characterization of barley RBPs with unique domain composition. Novel RBPs associated with barley malting process such as the musashi-like proteins will be subjects for further investigation.

Technical Abstract: One of the major mechanisms of post-transcriptional gene regulation is achieved by proteins bearing well-defined sequence motifs involved in ‘RNA binding'. In eukaryotes, RNA binding proteins (RBPs) are key players of RNA metabolism that includes synthesis, processing, editing, modifying, transport, storage and stability of RNA. In plants, the family of RBPs is vastly expanded compared to other eukaryotes including humans. In this study we identified 363 RBPs in the barley genome. Gene ontology enrichment analysis of barley RBPs indicated these proteins were in all the major cellular compartments and associated with key biological processes including translation, splicing, seed development and stress signaling. Members with the classical RNA binding motifs such as the RNA recognition motif (RRM), KH domain, Helicase, CRM, dsRNA and Pumilio were identified in the repertoire of barley RBPs. Similar to Arabidopsis, the RRM containing RBPs were the most abundant in barley genome. In-depth analysis of the RRM containing proteins - polyA binding proteins, Ser/Arg rich proteins and Glycine-rich RBPs were undertaken. Reanalysis of the proteome dataset of various stages during barley malting identified 38 RBPs suggesting an important role for these proteins during the malting process. This survey provides a systematic analysis of barley RBPs and serves as the basis for the further functional characterization of this important family of proteins.