Search Results (32)

This study identifies and classifies resistance gene analogues (RGAs) in the genomes of Brassica nigra, Sinapis arvensis and Sinapis alba using the RGAugury pipeline. RGAs were categorised into four main classes: receptor-like kinases (RLKs), receptor-like proteins (RLPs), nucleotide-binding leucine-rich repeat (NLR) proteins and transmembrane-coiled-coil (TM-CC) genes. A total of 4499 candidate RGAs were detected, with species-specific proportions. RLKs were the most abundant across all genomes, followed by TM-CCs and RLPs. The sub-classification of RLKs and RLPs identified LRR-RLKs, LRR-RLPs, LysM-RLKs, and LysM-RLPs. Atypical NLRs were more frequent than typical ones in all species. Atypical NLRs were more frequent than typical ones in all species. We explored the relationship between chromosome size and RGA count using regression analysis. In B. nigra and S. arvensis, larger chromosomes generally harboured more RGAs, while S. alba displayed the opposite trend. Exceptions were observed in all species, where some larger chromosomes contained fewer RGAs in B. nigra and S. arvensis, or more RGAs in S. alba. The distribution and density of RGAs across chromosomes were examined. RGA distribution was skewed towards chromosomal ends, with patterns differing across RGA types. Sequence hierarchical pairwise similarity analysis revealed distinct gene clusters, suggesting evolutionary relationships. The study also identified homologous genes among RGAs and non-RGAs in each species, providing insights into disease resistance mechanisms. Finally, RLKs and RLPs were co-localised with reported disease resistance loci in Brassica, indicating significant associations. Phylogenetic analysis of cloned RGAs and QTL-mapped RLKs and RLPs identified distinct clusters, enhancing our understanding of their evolutionary trajectories. These findings provide a comprehensive view of RGA diversity and genomics in these Brassicaceae species, providing valuable insights for future research in plant disease resistance and crop improvement. Full article

Rice blast disease is a major threat to rice yields. Sustainable control relies on resistant varieties, where plant immunity is triggered by pattern recognition receptors like receptor-like proteins (RLPs). The rice RLP chitin-elicitor binding protin (CEBiP) recognizes fungal chitin and confers blast resistance to pathogen Magnaporthe oryzae. However, understanding of the broader signaling and metabolomic pathways associated with CEBiP activation remains limited. Here, we performed an integrated transcriptomic and metabolomic analysis of the rice Zhonghua 11 genotype and CEBiP knockout plants. Both plants were infected with M. oryzae, and infected leaves were harvested at 24, 48, and 72 hpi for RNA sequencing and Liquid Chromatography-Tandem Mass Spectrometry analysis. Transcriptomics identified a total of 655 genes that were differentially regulated upon knockout of CEBiP; they were mainly related to diterpenoid/phenylpropanoid biosynthesis, nitrogen metabolism, the mitogen-activated protein kinasesignaling pathway, plant–pathogen interaction, and plant hormone signal transduction. The presence of a large number of pathogenesis-related protein 1 family genes indicates the key role of salicylic acid (SA) in CEBiP immunity. Metabolomics detected a total of 962 differentially accumulated metabolites and highlights the roles of caffeine and glutathione metabolism in CEBiP-mediated immunity. Since caffeine and glutathione metabolism can regulate SA signaling, we propose that SA signaling plays a central role in the CEBiP immune function. Full article

Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice. Full article

Brassica napus is one of the most extensively cultivated oilseed crops in China, but its yield is significantly impacted by stem rot caused by Sclerotinia sclerotiorum. Receptor-like proteins (RLPs) and receptor-like kinases (RLKs) play essential roles in plant–pathogen interactions; however, their regulatory mechanisms remain largely unknown in B. napus. In this study, we investigated the function of the leucine-rich repeat receptor-like protein BnaRLP-G13-1 in Brassica napus immunity. Previous observations indicated that B. napus plants expressing BnaRLP-G13-1 exhibited enhanced resistance to Sclerotinia sclerotiorum. We hypothesized that BnaRLP-G13-1 mediates pathogen recognition and immune signaling. To test this, we employed mitogen-activated protein kinase (MAPK) activity assays, transgenic overexpression analyses, and pathogen infection assays. Our results demonstrated that BnaRLP-G13-1 recognizes the conserved necrosis- and ethylene-inducing peptide Ssnlp24_SsNEP2 derived from S. sclerotiorum, triggering MAPK cascades and subsequent immune responses. Furthermore, protein interaction studies revealed that BnaRLP-G13-1 physically interacts with the receptor-like kinase BnaSOBIR1, which is essential for full antifungal defense activation. These results elucidate the molecular basis of BnaRLP-G13-1-mediated immunity, providing insights into improving disease resistance in oilseed crops. Full article

Plants utilize plasma membrane localized receptors like kinases (RLKs) or receptor-like proteins (RLPs) to recognize pathogens and activate pattern-triggered immunity (PTI) responses. A gain-of-function mutation in the Arabidopsis RLP SNC2 (SUPPRESSOR OF NPR1-1, CONSTITUTIVE 2) leads to constitutive activation of defense responses in snc2-1D mutant plants. Transcription factors, SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1) and CALMODULIN-BINDING PROTEIN 60g (CBP60g), define two parallel pathways downstream of SNC2. The autoimmunity of snc2-1D was partially affected by single mutations in SARD1 or CBP60g but completely suppressed by the sard1 cbp60g double mutant. From a suppressor screen using sard1-1 snc2-1D, we identified a deubiquitinating enzyme ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM 1 (AMSH1) as a key component in SNC2-mediated plant immunity. A loss-of-function mutation in AMSH1 can suppress the autoimmune responses of sard1-1 snc2-1D. In eukaryotes, selective protein degradation often occurs through the ubiquitination/deubiquitination system. The deubiquitinating enzymes that remove ubiquitin from target proteins play essential roles in controlling the level of target protein ubiquitination and degradation. As loss of AMSH1 results in decreased BDA1 abundance and BDA1 is a transmembrane protein required for SNC2-mediated immunity, AMSH1 likely contributes to immunity regulation through controlling BDA1 stability. Full article

Greenbug, Schizaphis graminum, is one of the important cereal aphid pests of sorghum in the United States and other parts of the world. Sorghum bicolor variety PI 607900 carries the Schizaphis graminum resistance (SgR1) gene that underlies plant resistance to greenbug biotype I (GBI). Now, the SgR1 has been determined as the major gene conferring greenbug resistance based on the strong association of its presence with the resistance phenotype in sorghum. In this study, we have successfully isolated the SgR1 gene using a map-based cloning approach, and subsequent molecular characterization revealed it encodes a leucine-rich repeat containing receptor-like protein (LRR-RLP). According to DNA sequence analysis, the SgR1 gene are conserved among GBI-resistance sorghum accessions but are variable within susceptible lines. Furthermore, an InDel (−965 nt) at its promoter region and a single-nucleotide polymorphism (SNP, 592 nt) in the CDS of the SgR1 were detected and they are well conserved within resistant genotypes. When the SgR1 gene was cloned and transferred into Arabidopsis plants, the SgR1 was activated in the transgenic Arabidopsis plants in response to attack by green peach aphids according to the results of the histochemical assay, and GUS activity was detected in situ in spots around the vasculature of the leaf where the phloem is located, suggesting its biological function in those transgenic Arabidopsis plants. Overall, this study confirms that the SgR1 gene coding for an LRR-RLP is the major resistance gene to greenbug, a destructive pest in sorghum and wheat. This represents the first greenbug resistance gene cloned so far and indicates that the simple-inherited GBI resistance gene can be used for sorghum improvement with genetic resistance to GBI via molecular breeding or cross-based conventional breeding technologies. Full article

Passion fruit (Passiflora edulis Sims) is a Passifloraceae plant with high economic value. Crown rot caused by Rhizoctonia solani is a major fungal disease, which can seriously reduce the yield and quality of passion fruit. Receptor-like proteins (RLPs), which act as pathogen recognition receptors, are widely involved in plant immune responses and developmental processes. However, the role of RLP family members of passion fruit in resistance to crown rot remains unclear. In this study, evolutionary dynamics analysis and comprehensive genomic characterization of the RLP genes family were performed on passion fruit. A total of 141 PeRLPs in the genome of the ‘Zixiang’ cultivar and 79 PesRLPs in the genome of the ‘Tainong’ cultivar were identified, respectively. Evolutionary analysis showed that proximal and dispersed duplication events were the primary drivers of RLP family expansion. RNA-seq data and RT-qPCR analysis showed that PeRLPs were constitutively expressed in different tissues and induced by low temperature, JA, MeJA, and SA treatments. The PeRLP8 gene was identified as the hub gene by RNA-seq analysis of passion fruit seedlings infected by Rhizoctonia solani. The expression levels of PeRLP8 of the resistant variety Passiflora maliformis (LG) were significantly higher than those of the sensitive variety Passiflora edulis f. flavicarpa (HG). Transient overexpression of PeRLP8 tobacco and passion fruit leaves enhanced the resistance to Rhizoctonia solani, resulting in reduced lesion areas by 52.06% and 54.17%, respectively. In addition, it can increase reactive oxygen species levels and upregulated expression of genes related to active oxygen biosynthesis and JA metabolism in passion fruit leaves. Our research provides new insights into the molecular mechanism and breeding strategy of passion fruit resistance to crown rot. Full article

Plants are challenged by different microbial pathogens that affect their growth and productivity. However, to defend pathogen attack, plants use diverse immune responses, such as pattern-triggered immunity (PTI), effector-triggered immunity (ETI), RNA silencing and autophagy, which are intricate and regulated by diverse signaling cascades. Pattern-recognition receptors (PRRs) and nucleotide-binding leucine-rich repeat (NLR) receptors are the hallmarks of plant innate immunity because they can detect pathogen or related immunogenic signals and trigger series of immune signaling cascades at different cellular compartments. In plants, most commonly, PRRs are receptor-like kinases (RLKs) and receptor-like proteins (RLPs) that function as a first layer of inducible defense. In this review, we provide an update on how plants sense pathogens, microbe-associated molecular patterns (PAMPs or MAMPs), and effectors as a danger signals and activate different immune responses like PTI and ETI. Further, we discuss the role RNA silencing, autophagy, and systemic acquired resistance as a versatile host defense response against pathogens. We also discuss early biochemical signaling events such as calcium (Ca²⁺), reactive oxygen species (ROS), and hormones that trigger the activation of different plant immune responses. This review also highlights the impact of climate-driven environmental factors on host–pathogen interactions. Full article

Leucine-rich repeat receptor-like proteins (LRR-RLPs), a major group of receptor-like proteins in plants, have diverse functions in plant physiology, including growth, development, signal transduction, and stress responses. Despite their importance, the specific roles of kiwifruit LRR-RLPs in response to biotic and abiotic stresses remain poorly understood. In this study, we performed family identification, characterization, transcriptome data analysis, and differential gene expression analysis of kiwifruit LRR-RLPs. We identified totals of 101, 164, and 105 LRR-RLPs in Actinidia chinensis ‘Hongyang’, Actinidia eriantha ‘Huate’, and Actinidia chinensis ‘Red5’, respectively. Synteny analysis revealed that the expansion of kiwifruit LRR-RLPs was primarily attributed to segmental duplication events. Based on RNA-seq data from pathogen-infected kiwifruits, we identified specific LRR-RLP genes potentially involved in different stages of pathogen infection. Additionally, we observed the potential involvement of kiwifruit LRR-RLPs in abiotic stress responses, with upstream transcription factors possibly regulating their expression. Furthermore, protein interaction network analysis unveiled the participation of kiwifruit LRR-RLP in the regulatory network of abiotic stress responses. These findings highlight the crucial roles of LRR-RLPs in mediating both biotic and abiotic stress responses in kiwifruit, offering valuable insights for the breeding of stress-resistant kiwifruit varieties. Full article

Fresh horticultural products are economically significant foods that are highly demanded by consumers worldwide; however, they are highly perishable and susceptible to deterioration by fungi, which contribute to their short shelf-life and cause significant post-harvest losses. Among the alternatives suggested for fungal control in plants is the elicitation of the innate plant defense mechanism, which may be activated when specific molecules of the phytopathogen, such as chitin, are recognized. Chitin is a long-chain polymer of N-acetyl-α-D-glucosamine of the fungal cell wall; it possesses biological activity by eliciting the plant immune response. This molecule and its oligosaccharides are recognized through transmembrane receptors known as receptor-like kinases (RLKs) and receptor-like proteins (RLPs). Mediated by receptor-like cytoplasmic kinases (RLCKs), which bind to the intracellular domain of these receptors, they initiate intracellular signal transduction via MAP kinases, triggering the plant defense response. In model plants, such as Oryza sativa (rice) and Arabidopsis thaliana, the set of RLK/RLP-RLCK-MAP kinases is involved in plant immunity triggered by chitin. Furthermore, in horticultural products, research into the molecular events between these three elements has suggested that similar processes occur. However, little is known about these molecular events in fruits. Against this background, the present review provides the most recent and relevant findings on the molecular associations of these three elements in the response to fungal chitin in plants and outlines which elements could participate in this signaling process in horticultural crops. Full article

Rice is an important cereal crop worldwide, the growth of which is affected by rice blast disease, caused by the fungal pathogen Magnaporthe oryzae. As climate change increases the diversity of pathogens, the disease resistance genes (R genes) in plants must be identified. The major blast-resistance genes have been identified in indica rice varieties; therefore, japonica rice varieties with R genes now need to be identified. Because leucine-rich repeat (LRR) domain proteins possess R-gene properties, we used bioinformatics analysis to identify the rice candidate LRR domain receptor-like proteins (OsLRR-RLPs). OsLRR-RLP2, which contains six LRR domains, showed differences in the DNA sequence, containing 43 single-nucleotide polymorphisms (SNPs) in indica and japonica subpopulations. The results of the M. oryzae inoculation analysis indicated that indica varieties with partial deletion of OsLRR-RLP2 showed susceptibility, whereas japonica varieties with intact OsLRR-RLP2 showed resistance. The oslrr-rlp2 mutant, generated using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), showed increased pathogen susceptibility, whereas plants overexpressing this gene showed pathogen resistance. These results indicate that OsLRR-RLP2 confers resistance to rice, and OsLRR-RLP2 may be useful for breeding resistant cultivars. Full article

Starfish relaxin-like gonad-stimulating peptide (RGP) is the first identified peptide hormone with gonadotropin-like activity in invertebrates. RGP is a heterodimeric peptide, comprising A and B chains with disulfide cross-linkages. Although RGP had been named a gonad-stimulating substance (GSS), the purified peptide is a member of relaxin-type peptide family. Thus, GSS was renamed as RGP. The cDNA of RGP encodes not only the A and B chains, but also signal and C-peptides. After the rgp gene is translated as a precursor, mature RGP is produced by eliminating the signal and C-peptides. Hitherto, twenty-four RGP orthologs have been identified or predicted from starfish in the orders Valvatida, Forcipulatida, Paxillosida, Spinulosida, and Velatida. The molecular evolution of the RGP family is in good accordance with the phylogenetic taxonomy in Asteroidea. Recently, another relaxin-like peptide with gonadotropin-like activity, RLP2, was found in starfish. RGP is mainly present in the radial nerve cords and circumoral nerve rings, but also in the arm tips, the gonoducts, and the coelomocytes. RGP acts on ovarian follicle cells and testicular interstitial cells to induce the production of 1-methyladenine (1-MeAde), a starfish maturation-inducing hormone. RGP-induced 1-MeAde production is accompanied by an increase in intracellular cyclic AMP levels. This suggests that the receptor for RGP (RGPR) is a G protein-coupled receptor (GPCR). Two types of GPCRs, RGPR1 and RGPR2, have been postulated as candidates. Furthermore, 1-MeAde produced by RGP not only induces oocyte maturation, but also induces gamete shedding, possibly by stimulating the secretion of acetylcholine in the ovaries and testes. Thus, RGP plays an important role in starfish reproduction, but its secretion mechanism is still unknown. It has also been revealed that RGP is found in the peripheral adhesive papillae of the brachiolaria arms. However, gonads are not developed in the larvae before metamorphosis. It may be possible to discover new physiological functions of RGP other than gonadotropin-like activity. Full article

Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars. Full article

Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes. Full article

Protein-protein interaction studies provide valuable insights into cellular signaling. Brassinosteroid (BR) signaling is initiated by the hormone-binding receptor Brassinosteroid Insensitive 1 (BRI1) and its co-receptor BRI1 Associated Kinase 1 (BAK1). BRI1 and BAK1 were shown to interact independently with the Receptor-Like Protein 44 (RLP44), which is implicated in BRI1/BAK1-dependent cell wall integrity perception. To demonstrate the proposed complex formation of BRI1, BAK1 and RLP44, we established three-fluorophore intensity-based spectral Förster resonance energy transfer (FRET) and FRET-fluorescence lifetime imaging microscopy (FLIM) for living plant cells. Our evidence indicates that RLP44, BRI1 and BAK1 form a ternary complex in a distinct plasma membrane nanodomain. In contrast, although the immune receptor Flagellin Sensing 2 (FLS2) also forms a heteromer with BAK1, the FLS2/BAK1 complexes are localized to other nanodomains. In conclusion, both three-fluorophore FRET approaches provide a feasible basis for studying the in vivo interaction and sub-compartmentalization of proteins in great detail. Full article