The capture and characterization of root mRNA interactomes from canola and rice

Abstract

The advent of RNA interactome capture (RIC) has helped facilitate the comprehensive identification of RNA-binding proteins (RBPs) in various eukaryotic systems. To date, published plant RIC studies have been restricted to Arabidopsis and used several cell types and tissues, including seedlings, suspension cell cultures, mesophyll protoplasts and leaves. The focus of this study was to expand RIC to root tissue using two plant species, the oilseed crop Brassica napus (canola) and the cereal crop Oryza sativa (rice). The optimization and application of root RIC resulted in the identification of 499 proteins and 334 proteins comprising the root mRNA-binding proteomes (RBPomes) of canola and rice, respectively. In both RBPomes, approximately 80% of captured proteins were linked to RNA biology, with RRM-containing proteins and ribosomal proteins being among the most overrepresented protein groups. Consistent with trends observed in other RIC studies, novel RNA-binding proteins that lacked known RNA-binding domains included metabolic enzymes, proteins associated with the cytoskeleton, and membrane transporters, among others were captured. In addition to both RBPomes sharing a high degree of similarity at the compositional level, comparative analysis of orthologs predicted for captured proteins to the collective Arabidopsis RBPome revealed that 46 proteins in the canola and rice root RBPomes were unique to root tissue. The results from this research expands the plant RBPome and provides foundational information regarding the RBPs involved in post-transcriptional control in plants.