Genomic and Post-Translational Modification Analysis of Leucine-Rich-Repeat Receptor-Like Kinases in Brassica rapa

Abstract

Among several receptor-like kinases (RLKs), leucine-rich-repeat receptor-like kinases (LRR-RLKs) are a major group of genes that play crucial roles in growth, development and stress responses in plant systems. Given that they have several functional roles, it is important to investigate their roles in Brassica rapa. In the present study, 303 LRR-RLKs were identified in the genome of B. rapa and comparative phylogenetic analysis of 1213 combined LRR-RLKs of B. rapa, Arabidopsis thaliana, Oryza sativa and Populus trichocarpa helped us to categorize the gene family into 15 subfamilies based on their sequence and structural similarities. The chromosome localizations of 293 genes allowed the prediction of duplicates, and motif conservation and intron/exon patterns showed differences among the B. rapa LRR-RLK (BrLRR-RLK) genes. Additionally, computational function annotation and expression analysis was used to predict their possible functional roles in the plant system. Biochemical results for 11 selected genes showed variations in phosphorylation activity. Interestingly, BrBAK1 showed strong auto-phosphorylation and trans-phosphorylation on its tyrosine and threonine residues compared with AtBAK1 in previous studies. The AtBAK1 receptor kinase is involved in plant growth and development, plant innate immunity, and programmed cell death, and our results suggest that BrBAK1 might also be involved in the same functions. Another interesting result was that BrBAK1, BrBRI1, BrPEPR1 and BrPEPR2 showed activity with both anti-phosphotyrosine and anti-phosphothreonine antibodies, indicating that they might have dual-specificity kinase activity. This study provides comprehensive results for the BrLRR-RLKs, revealing expansion of the gene family through gene duplications, structural similarities and variations among the genes, and potential functional roles according to gene ontology, transcriptome profiling and biochemical analysis.

Duplication and Divergence of Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Genes in Basal Angiosperm Amborella trichopoda

“…Hence, the results suggested LRR-RLK genes from different subfamilies and even genes from the same subfamilies exhibited expressional divergence. Similar results have also been obtained from the expression analyses of LRR-RLK genes from other plants (Zan et al, 2013; Rameneni et al, 2015; Wei et al, 2015; Shumayla et al, 2016; Zhou et al, 2016). …”

“…In this study, we focused on the number of LRR repeats in the LRR domain and motifs in the KD domain. Previous studies in eudicots and monocots reported that members within the same LRR-RLK subfamily tend to have a similar number of LRR repeats, whereas members of different subfamilies exhibit a different number of LRR repeats (Shiu and Bleecker, 2001; Sun and Wang, 2011; Zan et al, 2013; Rameneni et al, 2015; Wei et al, 2015; Magalhães et al, 2016; Shumayla et al, 2016). The protein structure analyses of LRR-RLK proteins in A. trichopoda reinforced the conclusion that the same subfamily members tend to have broadly the same number of LRR repeats in the LRR domain (Figures 3A,B and Table 1), while members of different subfamilies have different numbers of LRR repeats in the LRR domain.…”

“…For example, in genomes of A. thaliana, B. rapa, Citrus clementina and Citrus sinensis, S. lycopersicum and P. trichocarpa , 213, 303, 300, 297, 234, and 379 LRR-RLK genes, respectively, have been identified (Shiu and Bleecker, 2001; Zan et al, 2013; Rameneni et al, 2015; Wei et al, 2015; Magalhães et al, 2016). In G. max genome, as many as 467 genes were identified (Zhou et al, 2016).…”

“…Gene duplication is very prominent in the evolution of the LRR-RLK gene family in plants (Lehti-Shiu et al, 2009; Lehti-Shiu and Shiu, 2012). In eudicots, such as A. thaliana, Brassica rapa, Solanum lycopersicum and Populus trichocarpa , 213, 303, 234, and 379 LRR-RLK genes, respectively, have been identified from the analysis of genome sequences (Shiu and Bleecker, 2001; Zan et al, 2013; Rameneni et al, 2015; Wei et al, 2015). Based on the sequence similarity and domain conservation, as many as 467 genes were identified in the Glycine max genome (Zhou et al, 2016).…”

Identification of candidate genes for blackleg resistance in the new Brassica juncea canola

“…In Brassica plants, genome-wide studies of LRR-RLKs and LRR-RLPs are limited. To date, only one study of LRR-RLK genes has been reported; in B. rapa (Rameneni et al, 2015). By contrast, genome-wide studies of nucleotide binding site-leucine-rich repeat (NBS-LRR) genes have been widely performed on several Brassica species, such as B.…”