RNA interactome capture in Brachypodium reveals a flowering plant core RBPome
Abstract BackgroundRNA binding proteins regulate gene expression at the post-transcriptional level by controlling the fate of RNA, in processes such as mRNA localization, translation, splicing and stability. The annotation of RNA binding proteins is mainly based on the well-known RNA binding domains and motifs. However, novel RNA binding proteins without such conventional domains have been identified in different species using in vivo RNA interactome capture. To find support for novel conserved RNA binding proteins in plants, we applied an optimized RNA interactome capture to the monocot model Brachypodium distachyon.ResultsWe provide experimental evidence for 203 RNA binding proteins isolated from Brachypodium shoot tissue and leaf mesophyll protoplasts, and grouped these into classic RNA binding proteins with recognizable RNA binding domains and motifs, and candidate RNA binding proteins without such domains. Compared to RNA binding proteins captured in Arabidopsis thaliana, candidate RNA binding proteins involved in carbon fixation and carbon metabolic pathways are highly conserved. We tried to validate the RNA binding proteins captured in this research through a silica-based method, but this method appears not efficient for plants. This may indicate that optimized methods to validate high throughout RNA binding proteome are required for plants.ConclusionsOur results provide classic and candidate RNA binding proteins in Brachypodium distachyon and conserved RNA binding proteins in flowering plants. Future functional characterization should point out what the significance of RNA binding is for the function of these proteins.