背景:在植物中,质膜被细胞壁包围,锚定RLK和RLP蛋白,在发育和环境线索的感知中起着至关重要的作用,并且在植物发育和免疫中起着至关重要的作用。这些质膜受体属于大的基因/蛋白质家族,其在计算上不容易分类。对这些质膜蛋白质的详细分析为豆类遗传带来了新的信息来源,生理和育种研究社区。
结果:提出了一种鉴定和分类RLK和RLP蛋白的计算方法。使用实验验证的RLK和RLP蛋白评估该策略,并确定其灵敏度超过0.85,特异性为1.00,马修斯相关系数为0.91。计算方法可用于开发几种豆科植物/作物物种中质膜受体的详细目录(按类型和结构域)。在豆类中为RLK确定的专属域名是WaaY,APHP激酶_C,LRR_2和EGF,RLP是L-凝集素LPRY和PAN_4。该方法还发现了RLK-nonRD和RLCK子类。在这两个类中,每个物种预测的RLK总数中,只有不到20%属于此类。在评估的10个物种中,kinome中的〜40%的蛋白质是RLK。鉴定的独家豆类结构域组合是G.max中的B-Lectin/PR5K结构域,特伦卡特拉先生,五、角,和V.unguiculata和C.cajan的三结构域组合B-凝集素/S-基因座/WAK,特伦卡特拉先生,P.vulgaris,五、角。和V.unguiculata。
结论:分析表明,每个基因组中约有2%的蛋白质属于RLK家族,不到1%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,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。豆类仅显示P激酶胞外域,RLK和RLP中的非典型结构域组合与非豆科植物相比。计算逻辑方法在统计上得到了很好的支持,可以与其他植物物种的蛋白质组一起使用。
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.