Orr Russell J S, Aalen Reidunn Birgitta
Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
Methods Mol Biol. 2017;1621:93-105. doi: 10.1007/978-1-4939-7063-6_9.
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.
质膜结合的植物类受体激酶（RLKs）可根据其配体结合胞外结构域进行分类。最大的一类包括具有富含亮氨酸重复序列（LRRs）胞外结构域的RLKs。LRR-RLKs可主要根据LRRs的数量进一步分为不同类别。X类和XI类中许多具有超过20个LRR的受体被小分泌肽配体激活。为了解肽信号传导如何起作用，确定受体中直接参与配体相互作用的氨基酸很有意义。这些残基很可能在进化过程中得以保留，因此可以预测在不同植物物种的受体直系同源物中是保守的。在此，我们提出一种计算机模拟方法来识别这些残基。这涉及一种简化的直系同源物鉴定方法以及一个基于网络的程序，用于识别构成胞外结构域的除亮氨酸之外最保守的氨基酸。该方法已针对LRR-RLKs类的HAESA（HAE）和植物磺肽素受体1（PSKR1）进行了验证，其保守性映射结果与最近基于结构鉴定的配体和共受体相互作用残基密切匹配。
