In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant development and immunity. These plasma membrane receptors belong to large gene/protein families that are not easily classified computationally. This detailed analysis of these plasma membrane proteins brings a new source of information to the legume genetic, physiology and breeding research communities. A computational approach to identify and classify RLK and RLP proteins is presented. The strategy was evaluated using experimentally-validated RLK and RLP proteins and was determined to have a sensitivity of over 0.85, a specificity of 1.00, and a Matthews correlation coefficient of 0.91. The computational approach can be used to develop a detailed catalog of plasma membrane receptors (by type and domains) in several legume/crop species. The exclusive domains identified in legumes for RLKs are WaaY, APH Pkinase_C, LRR_2, and EGF, and for RLP are L-lectin LPRY and PAN_4. The RLK-nonRD and RLCK subclasses are also discovered by the methodology. In both classes, less than 20% of the total RLK predicted for each species belong to this class. Among the 10-species evaluated ~ 40% of the proteins in the kinome are RLKs. The exclusive legume domain combinations identified are B-Lectin/PR5K domains in G. max, M. truncatula, V. angularis, and V. unguiculata and a three-domain combination B-lectin/S-locus/WAK in C. cajan, M. truncatula, P. vulgaris, V. angularis. and V. unguiculata. The analysis suggests that about 2% of the proteins of each genome belong to the RLK family and less than 1% belong to RLP family. Domain diversity combinations are greater for RLKs compared with the RLP proteins and LRR domains, and the dual domain combination LRR/Malectin were the most frequent domain for both groups of plasma membrane receptors among legume and non-legume species. Legumes exclusively show Pkinase extracellular domains, and atypical domain combinations in RLK and RLP compared with the non-legumes evaluated. The computational logic approach is statistically well supported and can be used with the proteomes of other plant species.

中文翻译：

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豆类受体样激酶“ RLK”和受体样蛋白“ RLP”的计算鉴定。

在植物中，质膜被细胞壁包围，并锚定RLK和RLP蛋白，它们在感知发育和环境线索中起基本作用，对植物发育和免疫至关重要。这些质膜受体属于较大的基因/蛋白质家族，很难通过计算进行分类。对这些质膜蛋白的详细分析为豆类遗传，生理学和育种研究界提供了新的信息来源。提出了一种识别和分类RLK和RLP蛋白的计算方法。使用经过实验验证的RLK和RLP蛋白评估了该策略，并确定其敏感性超过0.85，特异性为1.00，马修斯相关系数为0.91。该计算方法可用于开发几种豆类/作物物种中质膜受体的详细目录（按类型和域划分）。在豆科植物中针对RLK识别的专有域是WaaY，APH Pkinase_C，LRR_2和EGF，对于RLP则是L-凝集素LPRY和PAN_4。该方法还发现了RLK-nonRD和RLCK子类。在这两个类别中，每个物种预测的RLK总数中不到20％属于该类别。在评估的10种物种中，约有40％的蛋白质是RLK。识别出的唯一的豆科植物结构域组合是马克斯海藻，截形衣藻，角果弧菌和无刺线虫中的B-凝集素/ PR5K结构域，以及在木麻黄虫中的三结构域B-凝集素/ S-基因座/ WAK， M. truncatula，寻常型P.V. angularis。和V. unguiculata。分析表明，每个基因组中约2％的蛋白质属于RLK家族，而少于1％的蛋白质属于RLP家族。与RLP蛋白和LRR结构域相比，RLK的结构域多样性组合更大，而双结构域组合LRR / Malectin是豆类和非豆类物种中两组质膜受体的最常见结构域。与未评估的豆类相比，豆类在RLK和RLP中仅显示Pkinase胞外域和非典型域组合。统计上很好地支持了计算逻辑方法，并且可以与其他植物物种的蛋白质组一起使用。在豆类和非豆类中，LRR / Malectin的双重结构域是两组质膜受体的最频繁结构域。与未评估的豆类相比，豆类在RLK和RLP中仅显示Pkinase胞外域和非典型域组合。统计上很好地支持了计算逻辑方法，并且可以与其他植物物种的蛋白质组一起使用。在豆类和非豆类中，LRR / Malectin的双重结构域是两组质膜受体的最频繁结构域。与未评估的豆类相比，豆类在RLK和RLP中仅显示Pkinase胞外域和非典型域组合。统计上很好地支持了计算逻辑方法，并且可以与其他植物物种的蛋白质组一起使用。