Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues

Abstract

This study focused on the identification and phylogenetic analysis of glycine-rich RNA binding proteins that contain an RNA recognition motif (RRM)-type RNA binding domain in addition to a region with contiguous glycine residues in representative plant species. In higher plants, glycine-rich proteins with an RRM have met considerable interest as they are responsive to environmental cues and play a role in cold tolerance, pathogen defense, flowering time control, and circadian timekeeping. To identify such RRM containing proteins in plant genomes we developed an RRM profile based on the known glycine-rich RRM containing proteins in the reference plant Arabidopsis thaliana. The application of this remodeled RRM profile that omitted sequences from non-plant species reduced the noise when searching plant genomes for RRM proteins compared to a search performed with the known RRM_1 profile. Furthermore, we developed an island scoring function to identify regions with contiguous glycine residues, using a sliding window approach. This approach tags regions in a protein sequence with a high content of the same amino acid, and repetitive structures score higher. This definition of repetitive structures in a fixed sequence length provided a new glance for characterizing patterns which cannot be easily described as regular expressions. By combining the profile-based domain search for well-conserved regions (the RRM) with a scoring technique for regions with repetitive residues we identified groups of proteins related to the A. thaliana glycine-rich RNA binding proteins in eight plant species.

A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate

“…In addition to RBP45A (AT4G54900), we found multiple members of the family of GLYCINE-RICH PROTEINs, GRP2 (AT14G13850), GRP7 (AT2G21660), and GRP8 (AT4G39260) interacted with this sequence motif (Figures 5A and S4 and Table S4). GRPs are nuclear localized hnRNP-like proteins (Streitner et al, 2012) that are required for numerous processes in plants, including responses to various biotic and abiotic stresses via their function in regulating both alternative splicing and microRNA biogenesis (Lewinski et al, 2016). Therefore, we were unsurprised when we observed that similar levels of GRP7 and GPR8 were present in the nuclei of both root hair and nonhair cells (Figure S6F).…”

Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea

“…An increasing number of RBG genes have been isolated and identified in diverse species, including Arabidopsis thaliana (Arabidopsis) [13][14][15], Oryza sativa [13,14,16], Zea mays [14,17], Brassica rapa [14,18], Ipomoea trifida [19], Gossypium arboreum and Gossypium raimondii [20], Vitis vinifera [21]. In addition to being the first to reveal the Class IVd GRP genes in Arabidopsis and rice, Krishnamurthy screened the whole genomes of Arabidopsis and rice and uncovered more RBG genes (IVa = 7; IVb = 3; IVc = 4; and IVd = 5 in Arabidopsis and IVa = 6; IVb = 2; IVc = 2; and IVd = 4 in rice) than an earlier study (IVa = 8; IVb = 3; and IVc = 2 in Arabidopsis and IVa = 6; IVb = 3; and IVc = 2 in rice) [13,14].…”