In Silico Prediction of Ligand-Binding Sites of Plant Receptor Kinases Using Conservation Mapping

Abstract

Plasma membrane-bound plant receptor-like kinases (RLKs) can be categorized based on their ligand-binding extracellular domain. The largest group encompasses RLKs having ectodomains with leucine-rich repeats (LRRs). The LRR-RLKs can further be assigned to classes mainly based on the number of LRRs. Many of the receptors of the classes X and XI with more than 20 LRRs are activated by small secreted peptide ligands. To understand how peptide signaling works, it is of interest to identify the amino acids of the receptor that are directly involved in ligand interaction. Such residues have most likely been conserved over evolutionary time and can therefore be predicted to be conserved in receptor orthologues of different plant species. Here we present an in silico method to identify such residues. This involves a simplified method for identification of orthologues and a web-based program for identifying the most conserved amino acids aside from the leucines that structure the ectodomain. The method has been validated for the LRR-RLKs HAESA (HAE) and PHYTOSULFOKINE RECEPTOR1 (PSKR1) for which conservation-mapping results closely matched recent structure-based identification of ligand and co-receptor-interacting residues.

The Sequenced Genomes of Non-Flowering Land Plants Reveal the (R)Evolutionary History of Peptide Signaling

“…The LRR units that are most importantly involved in peptide binding are often deviating somewhat from the strict consensus of the scaffold (Figure 4 and Supplemental Figure 3). Conserved non-scaffold amino acids are on the other hand likely to represent functional sites, including residues interacting with ligands or co-receptors (Helft et al, 2011;Orr and Aalen, 2017). (http://www.bentlab.russell.wisc.edu/main/main.php) reflecting the degree of amino acid identify and similarity in a given position (X-axis) and a given repeat (Y-axis) for the non-scaffold residues of PEPR and GSO orthologues, respectively.…”

“…The LRR units that are most importantly involved in peptide binding are often deviating somewhat from the strict consensus of the scaffold (Figure 4 and Supplemental Figure 3). Conserved non-scaffold amino acids are on the other hand likely to represent functional sites, including residues interacting with ligands or co-receptors (Helft et al, 2011; Orr and Aalen, 2017).…”

“…Repeat Conservation Mapping (RCM) (http://www.bentlab.russell.wisc.edu/main/main.php) is a computational method that removes the scaffold residues from the alignment of orthologous LRRs and thereafter calculates the conservation of the remaining residues, presented as a heat map reflecting the degree of amino acid identify and similarity in a given position in a given repeat (Helft et al, 2011; Orr and Aalen, 2017). RCM can be used to identify conserved residues in orthologous receptors, which opens for in vitro and in planta experimental testing of functional importance.…”

Sulfated plant peptide hormones

“…The conserved PSK protein family PF06404 (http://pfam.xfam.org/family/PF06404) consists of 352 homologous sequences found in 53 species from both mono- and dicotyledonous plant species, including Arabidopsis thaliana , Glycine soja , Brassica napus , Zea mays , and Oryza sativa . Sequence conservation and the presence of multiple genes encoding PSK in each species examined to date and an in silico conservation mapping for ligand-binding sites for PSKR1 orthologs suggest a conserved ligand–receptor interaction (Orr and Aalen, 2017). In Arabidopsis, seven loci have been annotated as putative PSK precursor genes.…”