Abstract
Plant Glycine-rich proteins (GRP), a superfamily with a glycine-rich domain, play an important role in various stresses such as high or low temperature stress and drought stress. GRP genes have been studied in many plants, but seldom in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a total of 64 GRP genes were identified in Chinese cabbage by homology comparative analysis. The physical and chemical characteristics predicted by ProtParam tool revealed that 62.5% of BrGRPs were alkaline, 53.1% were stable, and 79.7% were hydrophilic. Conserved domain analysis by MEME and TBtools showed that 64 BrGRPs contained 20 of the same conserved motifs, based on which BrGRPs were classified into five main classes and four subclasses in class IV to clarify their evolutionary relationship. Our results demonstrated that The BrGRP genes were located on ten chromosomes and in three different subgenomes of Chinese cabbage, and 43 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the transcriptome data, 64 BrGRP genes showed abnormal expression under high temperature stress, 52 under low temperature stress, 39 under drought stress, and 23 responses to soft rot. A large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE were found in their promoter regions by PlantCare, which corresponded with differential expressions. Two BrGRP genes-w546 (Bra030284) and w1409 (Bra014000), both belonging to the subfamily Subclass IVa RBP-GRP (RNA binding protein-glycine rich protein), were up-regulated under 150 mmol⋅L–1 NaCl stress in Chinese cabbage. However, the overexpressed w546 gene could significantly inhibit seed germination, while w1409 significantly accelerated seed germination under 100 mmol⋅L–1 NaCl or 300 mmol⋅L−1 mannitol stresses. In short, most BrGRP genes showed abnormal expression under adversity stress, and some were involved in multiple stress responses, suggesting a potential capacity to resist multiple biotic and abiotic stresses, which is worthy of further study. Our study provides a systematic investigation of the molecular characteristics and expression patterns of BrGRP genes and promotes for further work on improving stress resistance of Chinese cabbage.
Highlights
Plant glycine-rich protein (GRP) is a class of proteins consisting of glycine-rich repeat sequences
64 BrGRP genes were identified in the Chinese cabbage genome based on the 41 AtGRP genes in Arabidopsis
The BrGRP genes in Chinese cabbage were mainly composed of alkaline hydrophilic stable proteins and are secreted outside the cell membrane and nucleus, with only a few found in organelles such as mitochondria and chloroplast
Summary
Plant glycine-rich protein (GRP) is a class of proteins consisting of glycine-rich repeat sequences. Class IV GRPs, named RNA-binding proteins (RBPs), have no signal peptide at their N-terminus These proteins have other structures besides the glycine-rich sequences, such as the RNArecognition motif (RRM), cold-shock domain (CSD), and CCHC (CCHC = C-X2-C-X4-H-X4-C; C = Cys, H = His, X = variable amino acid) zinc finger structure. Class IV can be divided into four subgroups based on its domains: Subclass IVa (single RRM), Subclass IVb (single RRM and CCHC zinc-finger motif), Subclass IVc (cold shock domain and two or even more zinc-fingers), and Subclass IVd (two RRM motifs) (Mangeon et al, 2010) These RNA recognition domains can usually recognize each other or interact with proteins without any RNA recognition domain to bind to their target (Dreyfuss et al, 2002; Lorkovic and Barta, 2002). Class V GRPs are similar to the members of class III as the glycine repeats are arranged differently and presented with the mixed mode of (GGX)n and (GXGX)n (Bocca et al, 2005)
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