Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants

Abstract

BackgroundLeucine-rich repeat receptor-like protein kinases (LRR-RLKs) are the largest group of receptor-like kinases in plants and play crucial roles in development and stress responses. The evolutionary relationships among LRR-RLK genes have been investigated in flowering plants; however, no comprehensive studies have been performed for these genes in more ancestral groups. The subfamily classification of LRR-RLK genes in plants, the evolutionary history and driving force for the evolution of each LRR-RLK subfamily remain to be understood.ResultsWe identified 119 LRR-RLK genes in the Physcomitrella patens moss genome, 67 LRR-RLK genes in the Selaginella moellendorffii lycophyte genome, and no LRR-RLK genes in five green algae genomes. Furthermore, these LRR-RLK sequences, along with previously reported LRR-RLK sequences from Arabidopsis thaliana and Oryza sativa, were subjected to evolutionary analyses. Phylogenetic analyses revealed that plant LRR-RLKs belong to 19 subfamilies, eighteen of which were established in early land plants, and one of which evolved in flowering plants. More importantly, we found that the basic structures of LRR-RLK genes for most subfamilies are established in early land plants and conserved within subfamilies and across different plant lineages, but divergent among subfamilies. In addition, most members of the same subfamily had common protein motif compositions, whereas members of different subfamilies showed variations in protein motif compositions. The unique gene structure and protein motif compositions of each subfamily differentiate the subfamily classifications and, more importantly, provide evidence for functional divergence among LRR-RLK subfamilies. Maximum likelihood analyses showed that some sites within four subfamilies were under positive selection.ConclusionsMuch of the diversity of plant LRR-RLK genes was established in early land plants. Positive selection contributed to the evolution of a few LRR-RLK subfamilies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0891-5) contains supplementary material, which is available to authorized users.

Broad substrate-specific phosphorylation events are associated with the initial stage of plant cell wall recognition inNeurospora crassa

“…As the structure of LRR motifs can lead to a conformational flexibility necessary to the protein interaction (Kobe and Deisenhofer, 1995), the phosphorylation in between these regions might also affect the binding properties by influencing the conformational structure of the binding sites. The phosphorylation of Ser/Thr residues between subdomains of LRR-RLK (leucine-rich repeat receptor-like protein kinase) was also previously described as being essential for catalytic activation of some protein kinases (Bojar et al, 2014; Liu et al, 2017).…”

“…Interestingly, a major “hot spot” of phosphorylation appears to lie between two LRR (leucine-rich repeat) regions (Figure 3A). This motif is present in proteins with diverse functions and provides a versatile structural framework for the formation of protein-protein (Kobe and Deisenhofer, 1995; Kobe and Kajava, 2001) and ligand binding sites (Liu et al, 2017). As the structure of LRR motifs can lead to a conformational flexibility necessary to the protein interaction (Kobe and Deisenhofer, 1995), the phosphorylation in between these regions might also affect the binding properties by influencing the conformational structure of the binding sites.…”

The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis

“…Symbiont‐expressed microRNAs (miRNAs), have also been identified as a potential epigenetic mechanism between the microbiome and the host genomes (Liu, Du, Huang, Gao, & Yu, ; Williams, Stedtfeld, Tiedje, & Hashsham, ; Xue et al, ). Small noncoding RNAs of symbionts can regulate gene expression by repressing the translation of target messenger RNAs from the host genome (Cannell, Kong, & Bushell, ).…”

“…This is thought to promote homeostasis and prevent an immune response to commensal gut bacteria (Xue et al, ). Recent evidence also indicates that the miRNA‐coordinated epigenetic communication between the host and microbiome is reciprocal, with host genetics able to shape the gut microbiome (Liu et al, ; Williams et al, ). For example, host extracellular miRNAs secreted by epithelial intestinal cells of mice may be regulating bacterial gene expression and ultimately bacterial growth within the intestine (Liu et al, ; Williams et al, ), serving as a potential mechanism for molecular communication within the hologenome.…”

“…Symbiont-expressed microRNAs (miRNAs), have also been identified as a potential epigenetic mechanism between the microbiome and the host genomes (Liu, Du, Huang, Gao, & Yu, 2017;Williams, Stedtfeld, Tiedje, & Hashsham, 2017;Xue et al, 2011).…”