ArticleBMC genomics2020
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 31 citations in OpenAlex.
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- Genetic Diversity, Predictive Protein Structures, and Interaction Networks of Cysteine-Rich Receptor-Like Kinases inComputational and structural biotechnology journal · 2026Article
- Exploring associations between metabolites and gene transcripts of common bean (Phaseolus vulgaris L.) in response to rust (Uromyces appendiculatus) infection.BMC plant biology · 2025Article
- PRGminer: harnessing deep learning for the prediction of resistance genes involved in plant defense mechanisms.Frontiers in plant science · 2025Article
- A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members inPlants (Basel, Switzerland) · 2024Article
- Leveraging coevolutionary insights and AI-based structural modeling to unravel receptor-peptide ligand-binding mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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- GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel.Frontiers in plant science · 2024Article
- Genome-wide analysis and characterization of the LRR-RLK gene family provides insights into anthracnose resistance in common bean.Scientific reports · 2023Article
- Virus induced gene silencing confirms oligogenic inheritance of brown stem rot resistance in soybean.Frontiers in plant science · 2023Article
- Evolutionary gain and loss of a plant pattern-recognition receptor for HAMP recognition.eLife · 2022Article
- PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication.Plant biotechnology journal · 2022Article
- Genome-Wide Analysis of theGenes · 2022Article
- Prediction of Plant Resistance Proteins Based on Pairwise Energy Content and Stacking Framework.Frontiers in plant science · 2022Article
- The Common BeanFrontiers in plant science · 2022Article
- Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth inPlants (Basel, Switzerland) · 2021Article
- Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.BMC genomics · 2021Article
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4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundIn 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.
resultsA 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.
conclusionsThe 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.
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