Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice

LORE receptor homomerization is required for 3-hydroxydecanoic acid-induced immune signaling and determines the natural variation of immunosensitivity within the Arabidopsis genus

The S-domain-type receptor-like kinase (SD-RLK) LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION (LORE) from Arabidopsis thaliana is a pattern recognition receptor that senses medium-chain 3-hydroxy fatty acids, such as 3-hydroxydecanoic acid (3-OH-C10:0), to activate pattern-triggered immunity. Here, we show that LORE homomerization is required to activate 3-OH-C10:0-induced immune signaling. Fluorescence lifetime imaging in Nicotiana benthamiana demonstrates that AtLORE homomerizes via the extracellular and transmembrane domains. Co-expression of AtLORE truncations lacking the intracellular domain exerts a dominant negative effect on AtLORE signaling in both N. benthamiana and A. thaliana, highlighting that homomerization is essential for signaling. Screening for 3-OH-C10:0-induced reactive oxygen species production revealed natural variation within the Arabidopsis genus. Arabidopsis lyrata and Arabidopsis halleri do not respond to 3-OH-C10:0, although both possess a putative LORE ortholog. Both LORE orthologs have defective extracellular domains that bind 3-OH-C10:0 to a similar level as AtLORE, but lack the ability to homomerize. Thus, ligand binding is independent of LORE homomerization. Analysis of AtLORE and AlyrLORE chimera suggests that the loss of AlyrLORE homomerization is caused by several amino acid polymorphisms across the extracellular domain. Our findings shed light on the activation mechanism of LORE and the loss of 3-OH-C10:0 perception within the Arabidopsis genus.

C-Type LECTIN receptor-like kinase 1 and ACTIN DEPOLYMERIZING FACTOR 3 are key components of plasmodesmata callose modulation

Plasmodesmata (PDs) are intercellular organelles carrying multiple membranous nanochannels that allow the trafficking of cellular signalling molecules. The channel regulation of PDs occurs dynamically and is required in various developmental and physiological processes. It is well known that callose is a critical component in regulating PD permeability or symplasmic connectivity, but the understanding of the signalling pathways and mechanisms of its regulation is limited. Here, we used the reverse genetic approach to investigate the role of C-type lectin receptor-like kinase 1 (CLRLK1) in the aspect of PD callose-modulated symplasmic continuity. Here, we found that loss-of-function mutations in CLRLK1 resulted in excessive PD callose deposits and reduced symplasmic continuity, resulting in an accelerated gravitropic response. The protein interactome study also found that CLRLK1 interacted with actin depolymerizing factor 3 (ADF3) in vitro and in plants. Moreover, mutations in ADF3 result in elevated PD callose deposits and faster gravitropic response. Our results indicate that CLRLK1 and ADF3 negatively regulate PD callose accumulation, contributing to fine-tuning symplasmic opening apertures. Overall, our studies identified two key components involved in the deposits of PD callose and provided new insights into how symplasmic connectivity is maintained by the control of PD callose homoeostasis.

Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.)

Lectin receptor-like kinases (LecRLKs) are a significant subgroup of the receptor-like kinases (RLKs) protein family. They play crucial roles in plant growth, development, immune responses, signal transduction, and stress tolerance. However, the genome-wide identification and characterization of LecRLK genes and their regulatory elements have not been explored in a major cereal crop, barley (Hordeum vulgare L.). Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 LecRLK genes were identified in the barley genome (referred to as HvlecRLK) corresponding to the LecRLK genes of Arabidopsis thaliana. These putative HvlecRLK genes were classified into three groups: 62 G-type LecRLKs, 1 C-type LecRLK, and 50 L-type LecRLKs. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type HvlecRLK (96.8%), C-type HvlecRLK (100%), and L-type HvlecRLK (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of AtlecRLK. Notably, most of the HvlecRLKs (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that HvlecRLK gene pairs evolved through purifying selection and gene duplication was the major factor for the expansion of the HvlecRLK gene family. Exploration of gene ontology (GO) enrichment indicated that the identified HvlecRLK genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of HvlecRLK gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type HvleckRLK64 and HvleckRLK86. The promoter cis-acting regulatory element (CARE) analysis of barley identified a total of 75 CARE motifs responsive to light responsiveness (LR), tissue-specific (TS), hormone responsiveness (HR), and stress responsiveness (SR). The maximum number of CAREs was identified in HvleckRLK11 (25 for LR), HvleckRLK69 (17 for TS), and HvleckRLK80 (12 for HR). Additionally, HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110 were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 HvlecRLK genes and HvlecRLK13 was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 Arabidopsis STRING proteins. Our overall findings provide valuable information on the LecRLK gene family which might pave the way to advanced research on the functional mechanism of the candidate genes as well as to develop new barley cultivars in breeding programs.

PWL1, a G-type lectin receptor-like kinase, positively regulates leaf senescence and heat tolerance but negatively regulates resistance to Xanthomonas oryzae in rice

Plant leaf senescence, caused by multiple internal and environmental factors, has an important impact on agricultural production. The lectin receptor-like kinase (LecRLK) family members participate in plant development and responses to biotic and abiotic stresses, but their roles in regulating leaf senescence remain elusive. Here, we identify and characterize a rice premature withered leaf 1 (pwl1) mutant, which exhibits premature leaf senescence throughout the plant life cycle. The pwl1 mutant displayed withered and whitish leaf tips, decreased chlorophyll content, and accelerated chloroplast degradation. Map-based cloning revealed an amino acid substitution (Gly412Arg) in LOC_Os03g62180 (PWL1) was responsible for the phenotypes of pwl1. The expression of PWL1 was detected in all tissues, but predominantly in tillering and mature leaves. PWL1 encodes a G-type LecRLK with active kinase and autophosphorylation activities. PWL1 is localized to the plasma membrane and can self-associate, mainly mediated by the plasminogen-apple-nematode (PAN) domain. Substitution of the PAN domain significantly diminished the self-interaction of PWL1. Moreover, the pwl1 mutant showed enhanced reactive oxygen species (ROS) accumulation, cell death, and severe DNA fragmentation. RNA sequencing analysis revealed that PWL1 was involved in the regulation of multiple biological processes, like carbon metabolism, ribosome, and peroxisome pathways. Meanwhile, interfering of biological processes induced by the PWL1 mutation also enhanced heat sensitivity and resistance to bacterial blight and bacterial leaf streak with excessive accumulation of ROS and impaired chloroplast development in rice. Natural variation analysis indicated more variations in indica varieties, and the vast majority of japonica varieties harbour the PWL1Hap1 allele. Together, our results suggest that PWL1, a member of LecRLKs, exerts multiple roles in regulating plant growth and development, heat-tolerance, and resistance to bacterial pathogens.

L-type lectin receptor-like kinase OsCORK1 as an important negative regulator confers copper stress tolerance in rice

Copper (Cu) is vital for plant growth but becomes toxic in excess, posing potential threats to human health. Although receptor-like kinases (RLKs) have been studied in plant response to abiotic stresses, their roles in Cu stress response remain poorly understood. Therefore, we aimed to evaluate Cu toxicity effects on rice and elucidate its potential molecular mechanisms. Specifically, rice lectin-type RLK OsCORK1 (Copper-response receptor-like kinase 1) function in Cu stress response was investigated. RNA sequencing and expression assays revealed that OsCORK1 is mainly expressed in roots and leaves, and its expression was significantly induced by Cu stress time- and dose-dependently. Kinase activity assays demonstrated OsCORK1 as a Mn2+-preferred functional kinase. Genetically, OsCORK1 gene-edited mutants exhibited increased tolerance to Cu stress and reduced Cu accumulation compared to the wild type (WT). Conversely, OsCORK1 overexpression compromised the Cu stress tolerance observed in OsCORK1 gene-edited mutants. OsCORK1 gene-edited mutants slightly damaged the root tips compared to the WT under Cu stress. Furthermore, OsCORK1 was demonstrated to modulate Cu stress tolerance by mainly altering cell wall components, particularly lignin, in rice. Overall, OsCORK1 is an important negative regulator of Cu stress tolerance, providing a potential gene target to reduce Cu pollution in rice production.

Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses

The productivity of plants is hindered by unfavorable conditions. To perceive stress signals and to transduce these signals to intracellular responses, plants rely on membrane-bound receptor-like kinases (RLKs). These play a pivotal role in signaling events governing growth, reproduction, hormone perception, and defense responses against biotic stresses; however, their involvement in abiotic stress responses is poorly documented. Plant RLKs harbor an N-terminal extracellular domain, a transmembrane domain, and a C-terminal intracellular kinase domain. The ectodomains of these RLKs are quite diverse, aiding their responses to various stimuli. We summarize here the sub-classes of RLKs based on their domain structure and discuss the available information on their specific role in abiotic stress adaptation. Furthermore, the current state of knowledge on RLKs and their significance in abiotic stress responses is highlighted in this review, shedding light on their role in influencing plant-environment interactions and opening up possibilities for novel approaches to engineer stress-tolerant crop varieties.

G-type receptor-like kinase AsNIP43 interacts with rhizobia effector nodulation outer protein P and is required for symbiosis

In the Rhizobium-Legume symbiosis, the nodulation outer protein P (NopP) effector is one of the key regulators for rhizobial infection and nodule organogenesis. However, the molecular mechanism through which host legume plants sense NopP remains largely unknown. Here, we constructed an nopP deletion mutant of Mesorhizobium huakuii and found that nopP negatively regulates nodulation on Chinese milk vetch (Astragalus sinicus). Screening for NopP interacting proteins in host plants using the yeast 2-hybrid system identified NopP interacting protein 43 (AsNIP43), which encodes a G-type receptor-like kinase (LecRLK). The B-lectin domain at the N terminus of AsNIP43 was essential in mediating its interaction with NopP, which was confirmed in vitro and in vivo. Subcellular localization, co-localization, and gene expression analyses showed that AsNIP43 and NopP function tightly associated with earlier infection events. RNA interference (RNAi) knockdown of AsNIP43 expression by hairy root transformation led to decreased nodule formation. AsNIP43 plays a positive role in symbiosis, which was further verified in the model legume Medicago truncatula. Transcriptome analysis indicated that MtRLK (a homolog of AsNIP43 in M. truncatula) may function to affect defense gene expression and thus to regulate early nodulation. Taken together, we show that LecRLK AsNIP43 is a legume host target that interacts with rhizobia effector NopP is essential for rhizobial infection and nodulation.

A G-type lectin receptor kinase negatively regulates Arabidopsis immunity against root-knot nematodes

Root-knot nematodes (Meloidogyne spp., RKN) are responsible for extensive crop losses worldwide. During infection, they penetrate plant roots, migrate between plant cells, and establish feeding sites, known as giant cells, near the root vasculature. Previously, we found that nematode perception and early responses in plants were similar to those of microbial pathogens and required the BRI1-ASSOCIATED KINASE1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE3 (BAK1/SERK3) coreceptor in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum). Here, we implemented a reverse genetic screen for resistance or sensitivity to RKN using Arabidopsis T-DNA alleles of genes encoding transmembrane receptor-like kinases to identify additional receptors involved in this process. This screen identified a pair of allelic mutations with enhanced resistance to RKN in a gene we named ENHANCED RESISTANCE TO NEMATODES1 (ERN1). ERN1 encodes a G-type lectin receptor kinase (G-LecRK) with a single-pass transmembrane domain. Further characterization showed that ern1 mutants displayed stronger activation of MAP kinases, elevated levels of the defense marker MYB51, and enhanced H2O2 accumulation in roots upon RKN elicitor treatments. Elevated MYB51 expression and ROS bursts were also observed in leaves of ern1 mutants upon flg22 treatment. Complementation of ern1.1 with 35S- or native promoter-driven ERN1 rescued the RKN infection and enhanced defense phenotypes. Our results indicate that ERN1 is an important negative regulator of immunity.

Ligand recognition and signal transduction by lectin receptor-like kinases in plant immunity

Lectin receptor-like kinases (LecRKs) locate on the cell membrane and play diverse roles in perceiving environmental factors in higher plants. Studies have demonstrated that LecRKs are involved in plant development and response to abiotic and biotic stresses. In this review, we summarize the identified ligands of LecRKs in Arabidopsis, including extracellular purine (eATP), extracellular pyridine (eNAD⁺), extracellular NAD⁺ phosphate (eNADP⁺) and extracellular fatty acids (such as 3-hydroxydecanoic acid). We also discussed the posttranslational modification of these receptors in plant innate immunity and the perspectives of future research on plant LecRKs.

The enhanced Valsa canker resistance conferred by MdLecRK-S.4.3 in Pyrus betulifolia can be largely suppressed by PbePUB36

L-type lectin receptor-like kinases (L-LecRKs) act as a sensor of extracellular signals and an initiator for plant immune responses. However, the function of LecRK-S.4 on plant immunity has not been extensively investigated. At present, in the apple (Malus domestica) genome, we identified that MdLecRK-S.4.3, a homologous gene of LecRK-S.4, was differentially expressed during the occursion of Valsa canker. Over-expression of MdLecRK-S.4.3 facilitated the induction of immune response and enhanced the Valsa canker resistance of apple and pear fruit, and 'Duli-G03' (Pyrus betulifolia) suspension cells. On the contrary, the expression of PbePUB36, RLCK XI subfamily member, was significantly repressed in the MdLecRK-S.4.3 overexpressed cell lines. Over-expression of PbePUB36 interfered with the Valsa canker resistance and immune response caused by up-regulation of MdLecRK-S.4.3. Furthermore, MdLecRK-S.4.3 interacted with BAK1 or PbePUB36 in vivo. In conclusion, MdLecRK-S.4.3 activated various immune responses and positively regulate Valsa canker resistance, which could be largely compromised by PbePUB36. MdLecRK-S.4.3 interacted with PbePUB36 and/or MdBAK1 to mediate the immune responses. This finding provides a reference for studying the molecular mechanism of resistance to Valsa canker and resistance breeding.

System network analysis of Rosmarinus officinalis transcriptome and metabolome-Key genes in biosynthesis of secondary metabolites

Medicinal plants contain valuable compounds that have attracted worldwide interest for their use in the production of natural drugs. The presence of compounds such as rosmarinic acid, carnosic acid, and carnosol in Rosmarinus officinalis has made it a plant with unique therapeutic effects. The identification and regulation of the biosynthetic pathways and genes will enable the large-scale production of these compounds. Hence, we studied the correlation between the genes involved in biosynthesis of the secondary metabolites in R. officinalis using proteomics and metabolomics data by WGCNA. We identified three modules as having the highest potential for the metabolite engineering. Moreover, the hub genes highly connected to particular modules, TFs, PKs, and transporters were identified. The TFs of MYB, C3H, HB, and C2H2 were the most likely candidates associated with the target metabolic pathways. The results indicated that the hub genes including Copalyl diphosphate synthase (CDS), Phenylalanine ammonia lyase (PAL), Cineole synthase (CIN), Rosmarinic acid synthase (RAS), Tyrosine aminotransferase (TAT), Cinnamate 4-hydroxylase (C4H), and MYB58 are responsible for biosynthesis of important secondary metabolites. Thus, we confirmed these results using qRT-PCR after treating R. officinalis seedlings with methyl jasmonate. These candidate genes may be employed for genetic and metabolic engineering research to increase R. officinalis metabolite production.

Phosphate-deprivation and damage signalling by extracellular ATP

Phosphate deprivation compromises plant productivity and modulates immunity. DAMP signalling by extracellular ATP (eATP) could be compromised under phosphate deprivation by the lowered production of cytosolic ATP and the need to salvage eATP as a nutritional phosphate source. Phosphate-starved roots of Arabidopsis can still sense eATP, indicating robustness in receptor function. However, the resultant cytosolic free Ca²⁺ signature is impaired, indicating modulation of downstream components. This perspective on DAMP signalling by extracellular ATP (eATP) addresses the salvage of eATP under phosphate deprivation and its promotion of immunity, how Ca²⁺ signals are generated and how the Ca²⁺ signalling pathway could be overcome to allow beneficial fungal root colonization to fulfill phosphate demands. Safe passage for an endophytic fungus allowing root colonization could be achieved by its down-regulation of the Ca²⁺ channels that act downstream of the eATP receptors and by also preventing ROS accumulation, thus further impairing DAMP signalling.

Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean (Phaseolus vulgaris L.) in Response to Terminal Drought Stress

We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.

Evolutionary and functional analysis reveals the crucial roles of receptor-like proteins in resistance to Valsa canker in Rosaceae

Rosaceae is an economically important plant family that can be affected by a multitude of pathogenic microbes, some of which can cause dramatic losses in production. As a type of pattern-recognition receptor, receptor-like proteins (RLPs) are considered vital regulators of plant immunity. Based on genome-wide identification, bioinformatic analysis, and functional determination, we investigated the evolutionary characteristics of RLPs, and specifically those that regulate Valsa canker, a devastating fungal disease affecting apple and pear production. A total of 3028 RLPs from the genomes of 19 species, including nine Rosaceae, were divided into 24 subfamilies. Five subfamilies and seven co-expression modules were found to be involved in the responses to Valsa canker signals of the resistant pear rootstock Pyrus betulifolia 'Duli-G03'. Fourteen RLPs were subsequently screened as candidate genes for regulation of resistance. Among these, PbeRP23 (Chr13.g24394) and PbeRP27 (Chr16.g31400) were identified as key resistance genes that rapidly enhance the resistance of 'Duli-G03' and strongly initiate immune responses, and hence they have potential for further functional exploration and breeding applications for resistance to Valsa canker. In addition, as a consequence of this work we have established optimal methods for the classification and screening of disease-resistant RLPs.

Genome-wide association studies revealed complex genetic architecture and breeding perspective of maize ear traits

BACKGROUND

Maize (Zea Mays) is one of the world's most important crops. Hybrid maize lines resulted a major improvement in corn production in the previous and current centuries. Understanding the genetic mechanisms of the corn production associated traits greatly facilitate the development of superior hybrid varieties.

RESULT

In this study, four ear traits associated with corn production of Nested Association Mapping (NAM) population were analyzed using a full genetic model, and further, optimal genotype combinations and total genetic effects of current best lines, superior lines, and superior hybrids were predicted for each of the traits at four different locations. The analysis identified 21-34 highly significant SNPs (-log₁₀P > 5), with an estimated total heritability of 37.31-62.34%, while large contributions to variations was due to dominance, dominance-related epistasis, and environmental interaction effects ([Formula: see text] 14.06% ~ 49.28%), indicating these factors contributed significantly to phenotypic variations of the ear traits. Environment-specific genetic effects were also discovered to be crucial for maize ear traits. There were four SNPs found for three ear traits: two for ear length and weight, and two for ear row number and length. Using the Enumeration method and the stepwise tuning technique, optimum multi-locus genotype combinations for superior lines were identified based on the information obtained from GWAS.

CONCLUSIONS

Predictions of genetic breeding values showed that different genotype combinations in different geographical regions may be better, and hybrid-line variety breeding with homozygote and heterozygote genotype combinations may have a greater potential to improve ear traits.

Molecular evolution of the Pi-d2 gene conferring resistance to rice blast in Oryza

The exploitation of plant disease resistance (R) genes in breeding programs is an effective strategy for coping with pathogens. An understanding of R gene variation is the basis for this strategy. Rice blast disease, caused by the Magnaporthe oryzae fungus, is a destructive disease of rice. The rice blast resistance gene Pi-d2 represents a new class of plant R gene because of its novel extracellular domain. We investigated the nucleotide polymorphism, phylogenetic topology and evolution patterns of the Pi-d2 gene among 67 cultivated and wild rice relatives. The Pi-d2 gene originated early in the basal Poales and has remained as a single gene without expansion. The striking finding is that susceptible Pi-d2 alleles might be derived from a single nucleotide substitution of the resistant alleles after the split of Oryza subspecies. Functional pleiotropy and linkage effects are proposed for the evolution and retention of the disease-susceptible alleles in rice populations. One set of DNA primers was developed from the polymorphic position to detect the functional nucleotide polymorphism for disease resistance of the Pi-d2 gene based on conventional Polymerase Chain Reaction. The nucleotide diversity level varied between different domains of the Pi-d2 gene, which might be related to distinct functions of each domain in the disease defense response. Directional (or purifying) selection appears dominant in the molecular evolution of the Pi-d2 gene and has shaped its conserved variation pattern.

Cell wall integrity regulation across plant species

Plant cell walls are highly dynamic and chemically complex structures surrounding all plant cells. They provide structural support, protection from both abiotic and biotic stress as well as ensure containment of turgor. Recently evidence has accumulated that a dedicated mechanism exists in plants, which is monitoring the functional integrity of cell walls and initiates adaptive responses to maintain integrity in case it is impaired during growth, development or exposure to biotic and abiotic stress. The available evidence indicates that detection of impairment involves mechano-perception, while reactive oxygen species and phytohormone-based signaling processes play key roles in translating signals generated and regulating adaptive responses. More recently it has also become obvious that the mechanisms mediating cell wall integrity maintenance and pattern triggered immunity are interacting with each other to modulate the adaptive responses to biotic stress and cell wall integrity impairment. Here we will review initially our current knowledge regarding the mode of action of the maintenance mechanism, discuss mechanisms mediating responses to biotic stresses and highlight how both mechanisms may modulate adaptive responses. This first part will be focused on Arabidopsis thaliana since most of the relevant knowledge derives from this model organism. We will then proceed to provide perspective to what extent the relevant molecular mechanisms are conserved in other plant species and close by discussing current knowledge of the transcriptional machinery responsible for controlling the adaptive responses using selected examples.

GmLecRlk, a Lectin Receptor-like Protein Kinase, Contributes to Salt Stress Tolerance by Regulating Salt-Responsive Genes in Soybean

Soybean [Glycine max (L.) Merr.] is an important oil crop that provides valuable resources for human consumption, animal feed, and biofuel. Through the transcriptome analysis in our previous study, GmLecRlk (Glyma.07G005700) was identified as a salt-responsive candidate gene in soybean. In this study, qRT-PCR analysis showed that the GmLecRlk gene expression level was significantly induced by salt stress and highly expressed in soybean roots. The pCAMBIA3300-GmLecRlk construct was generated and introduced into the soybean genome by Agrobacterium rhizogenes. Compared with the wild type (WT), GmLecRlk overexpressing (GmLecRlk-ox) soybean lines had significantly enhanced fresh weight, proline (Pro) content, and catalase (CAT) activity, and reduced malondialdehyde (MDA) and H2O2 content under salt stress. These results show that GmLecRlk gene enhanced ROS scavenging ability in response to salt stress in soybean. Meanwhile, we demonstrated that GmLecRlk gene also conferred soybean salt tolerance when it was overexpressed alone in soybean hairy root. Furthermore, the combination of RNA-seq and qRT-PCR analysis was used to determine that GmLecRlk improves the salt tolerance of soybean by upregulating GmERF3, GmbHLH30, and GmDREB2 and downregulating GmGH3.6, GmPUB8, and GmLAMP1. Our research reveals a new mechanism of salt resistance in soybean, which exposes a novel avenue for the cultivation of salt-resistant varieties.

The Diesel Tree Sindora glabra Genome Provides Insights Into the Evolution of Oleoresin Biosynthesis

Sindora glabra is an economically important tree that produces abundant oleoresin in the trunk. Here, we present a high-quality chromosome-scale assembly of S. glabra genome by combining Illumina HiSeq, Pacific Biosciences sequencing, and Hi-C technologies. The size of S. glabra genome was 1.11 Gb, with a contig N50 of 1.27 Mb and 31,944 predicted genes. This is the first sequenced genome of the subfamily Caesalpinioideae. As a sister taxon to Papilionoideae, S. glabra underwent an ancient genome triplication shared by core eudicots and further whole-genome duplication shared by early-legume in the last 73.3 million years. S. glabra harbors specific genes and expanded genes largely involved in stress responses and biosynthesis of secondary metabolites. Moreover, 59 terpene backbone biosynthesis genes and 64 terpene synthase genes were identified, which together with co-expressed transcription factors could contribute to the diversity and specificity of terpene compounds and high terpene content in S. glabra stem. In addition, 63 disease resistance NBS-LRR genes were found to be unique in S. glabra genome and their expression levels were correlated with the accumulation of terpene profiles, suggesting potential defense function of terpenes in S. glabra. These together provide new resources for understanding genome evolution and oleoresin production.

35 years in plant lectin research: a journey from basic science to applications in agriculture and medicine

Plants contain an extended group of lectins differing from each other in their molecular structures, biochemical properties and carbohydrate-binding specificities. The heterogeneous group of plant lectins can be classified in several families based on the primary structure of the lectin domain. All proteins composed of one or more lectin domains, or having a domain architecture including one or more lectin domains in combination with other protein domains can be defined as lectins. Plant lectins reside in different cell compartments, and depending on their location will encounter a large variety carbohydrate structures, allowing them to be involved in multiple biological functions. Over the years lectins have been studied intensively for their carbohydrate-binding properties and biological activities, which also resulted in diverse applications. The present overview on plant lectins especially focuses on the structural and functional characteristics of plant lectins and their applications for crop improvement, glycobiology and biomedical research.

Review: The multiple roles of plant lectins

For decades, the biological roles of plant lectins remained obscure and subject to speculation. With the advent of technological and scientific progress, researchers have compiled a vast amount of information regarding the structure, biological activities and functionality of hundreds of plant lectins. Data mining of genomes and transcriptome sequencing and high-throughput analyses have resulted in new insights. This review aims to provide an overview of what is presently known about plant lectins, highlighting their versatility and the importance of plant lectins for a multitude of biological processes, such as plant development, immunity, stress signaling and regulation of gene expression. Though lectins primarily act as readers of the glycocode, the multiple roles of plant lectins suggest that their functionality goes beyond carbohydrate-recognition.

Identification and Analysis of Genes Involved in Double Fertilization in Rice

Double fertilization is a key determinant of grain yield, and the failure of fertilization during hybridization is one important reason for reproductive isolation. Therefore, fertilization has a very important role in the production of high-yield and well-quality hybrid of rice. Here, we used RNA sequencing technology to study the change of the transcriptome during double fertilization with the help of the mutant fertilization barrier (feb) that failed to finish fertilization process and led to seed abortion. The results showed that 1669 genes were related to the guided growth of pollen tubes, 332 genes were involved in the recognition and fusion of the male–female gametes, and 430 genes were associated with zygote formation and early free endosperm nuclear division. Among them, the genes related to carbohydrate metabolism; signal transduction pathways were enriched in the guided growth of pollen tubes, the genes involved in the photosynthesis; fatty acid synthesis pathways were activated by the recognition and fusion of the male–female gametes; and the cell cycle-related genes might play an essential role in zygote formation and early endosperm nuclear division. Furthermore, among the 1669 pollen tube-related genes, it was found that 7 arabinogalactan proteins (AGPs), 1 cysteine-rich peptide (CRP), and 15 receptor-like kinases (RLKs) were specifically expressed in anther, while 2 AGPs, 7 CRPs, and 5 RLKs in pistil, showing obvious unequal distribution which implied they might play different roles in anther and pistil during fertilization. These studies laid a solid foundation for revealing double fertilization mechanism of rice and for the follow-up investigation.

Identification and characterization of L-type lectin receptor-like kinases involved in Glycine max-Phytophthora sojae interaction

MAIN CONCLUSION

Soybean contains a group of 64 L-type lectin receptor-like kinases. Three LecRKs were involved in the interactions with Phytophthora sojae and Bradyrhizobium diazoefficiens. L-type lectin receptor-like kinases (LecRKs) comprise an important class of membrane-localized receptor-like kinases that are involved in plant adaptation. In this study, we performed an inventory analysis of LecRKs in Glycine max (soybean). In total, 64 GmLecRKs containing the canonical LecRK feature were identified. Phylogenetic analysis revealed that 48 GmLecRKs have close orthologs in Arabidopsis or Solanum lycopersicum, while 16 are likely present only in the leguminous plant species. Transcriptome analyses revealed that expressions of multiple GmLecRK genes are either induced or suppressed during infection by the soybean root rot pathogen Phytophthora sojae. In addition, overexpression of the three LecRKs (Glyma.17G085000, Glyma.05G041300 or Glyma.17G224600) in the soybean hairy roots enhanced resistance to P. sojae. Upon inoculation with Bradyrhizobium diazoefficiens, overexpression of Glyma.17G085000 in the soybean hairy roots does not significantly influence the nodulation, while overexpression of Glyma.05G041300 or Glyma.17G224600 slightly reduced the number and dry weight of nodules. This study highlights the importance of LecRKs in regulating plant-microbe interactions and provides new knowledge on the deployment of LecRKs to increase resistance in soybean.

Lectin receptor-like kinase LecRK-VIII.2 is a missing link in MAPK signaling-mediated yield control

The energy allocation for vegetative and reproductive growth is regulated by developmental signals and environmental cues, which subsequently affects seed output. However, the molecular mechanism underlying how plants coordinate yield-related traits to control yield in changing source-sink relationships remains largely unknown. Here, we discovered the lectin receptor-like kinase LecRK-VIII.2 as a specific receptor-like kinase that coordinates silique number, seed size, and seed number to determine seed yield in Arabidopsis (Arabidopsis thaliana). The lecrk-VIII.2 mutants develop smaller seeds, but more siliques and seeds, leading to increased yield. In contrast, the plants overexpressing LecRK-VIII.2 form bigger seeds, but less siliques and seeds, which results in similar yield to that of wild-type plants. Interestingly, LecRK-VIII.2 promotes the growth of the rosette, root, and stem by coordinating the source-sink relationship. Additionally, LecRK-VIII.2 positively regulates cell expansion and proliferation in the seed coat, and maternally controls seed size. The genetic and biochemical analyses demonstrated that LecRK-VIII.2 acts upstream of the mitogen-activated protein kinase (MAPK) gene MPK6 to regulate silique number, seed size, and seed number. Collectively, these findings uncover LecRK-VIII.2 as an upstream component of the MAPK signaling pathway to control yield-related traits and suggest its potential for crop improvement aimed at developing plants with stable yield, a robust root system, and improved lodging resistance.

Transcriptome and DNA Methylome Reveal Insights Into Phytoplasma Infection Responses in Mulberry (Morus multicaulis Perr.)

To reveal whether the response of mulberry to phytoplasma infection is associated with genome-wide DNA methylation changes, the methylome and transcriptome patterns of mulberry in response to phytoplasma infection were explored. Though the average methylation level of the infected leaves showed no significant difference from that of healthy leaves, there were 1,253 differentially methylated genes (DMGs) and 1,168 differentially expressed genes (DEGs) in the infected leaves, and 51 genes were found simultaneously to be differently methylated and expressed. It was found that the expression of G-type lectin S-receptor-like serine/threonine protein kinase gene (Mu-GsSRK) was increased, but its methylation level was decreased in the pathogen-infected or salicylic acid (SA)-treated leaves. Overexpression of Mu-GsSRK in Arabidopsis and in the hairy roots of mulberry enhanced transgenic plant resistance to the phytoplasma. Moreover, overexpression of Mu-GsSRK enhanced the expressions of pathogenesis-related protein 1, plant defensin, and cytochrome P450 protein CYP82C2 genes in transgenic plants inoculated with pathogens, which may contribute to the enhanced disease resistance against various pathogens. Finally, the DNA methylation dynamic patterns and functions of the differentially expressed and methylated genes were discussed. The results suggested that DNA methylation has important roles in mulberry responses to phytoplasma infection.

Identification of LecRLK gene family in Cerasus humilis through genomic-transcriptomic data mining and expression analyses

Lectin receptor-like protein kinases (LecRLKs) have been shown to be involved in plants’ responses to various biotic and abiotic stresse factors. Cerasus humilis is an important fruit species widely planted for soil and water conservation in northern China due to its strong tolerance to drought and salinity stresses. In this study, a total of 170 LecRLK family genes (125 G-types, 43 L-types and 2 C-types) were identified in the newly released whole-genome sequences of C. humilis. Furthermore, nine representative LecRLK genes in young plants of C. humilis under varying drought and salinity stresses were selected for qRT-PCR analysis. Our systematic comparative analyses revealed the active participation of these nine LecRLK genes in the salt and drought stress responses of C. humilis. The results from our study have provided a solid foundation for future functional verification of these LecRLK family genes and will likely help facilitate the more rapid and effective development of new stress resistant Cerasus humilis cultivars.

An L-type lectin receptor-like kinase promotes starch accumulation during rice pollen maturation

Starch accumulation is key for the maturity of rice pollen grains; however, the regulatory mechanism underlying this process remains unknown. Here, we have isolated a male-sterile rice mutant, abnormal pollen 1 (ap1), which produces nonviable pollen grains with defective starch accumulation. Functional analysis revealed that AP1 encodes an active L-type lectin receptor-like kinase (L-LecRLK). AP1 is localized to the plasma membrane and its transcript is highly accumulated in pollen during the starch synthesis phase. RNA-seq and phosphoproteomic analysis revealed that the expression/phosphorylation levels of numerous genes/proteins involved in starch and sucrose metabolism pathway were significantly altered in the mutant pollen, including a known rice UDP-glucose pyrophosphorylase (OsUGP2). We further found that AP1 physically interacts with OsUGP2 to elevate its enzymatic activity, likely through targeted phosphorylation. These findings revealed a novel role of L-LecRLK in controlling pollen maturity via modulating sucrose and starch metabolism.

Regulatory role of receptor-like cytoplasmic kinases in early immune signaling events in plants

Receptor-like cytoplasmic kinases (RLCKs) play crucial roles in regulating plant development and immunity. Conserved pathogen-associated molecular patterns (PAMPs) derived from microbes are recognized by plant pattern recognition receptors to activate PAMP-triggered immunity (PTI). Microbial effectors, whose initial function is to promote virulence, are recognized by plant intracellular nucleotide-binding domain and leucine-rich repeat receptors (NLRs) to initiate effector-triggered immunity (ETI). Both PTI and ETI trigger early immune signaling events including the production of reactive oxygen species, induction of calcium influx and activation of mitogen-activated protein kinases. Research progress has revealed the important roles of RLCKs in the regulation of early PTI signaling. Accordingly, RLCKs are often targeted by microbial effectors that are evolved to evade PTI via diverse modulations. In some cases, modulation of RLCKs by microbial effectors triggers the activation of NLRs. This review covers the mechanisms by which RLCKs engage diverse substrates to regulate early PTI signaling and the regulatory roles of RLCKs in triggering NLR activation. Accumulating evidence suggests evolutionary links and close connections between PAMP- and effector-triggered early immune signaling that are mediated by RLCKs. As key immune regulators, RLCKs can be considered targets with broad prospects for the improvement of plant resistance via genetic engineering.

Genome-Wide Characterization of Lectin Receptor Kinases in Saccharum spontaneum L. and Their Responses to Stagonospora tainanensis Infection

Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants.

Characterization of CHARK, an unusual cytokinin receptor of rice

The signal transduction of the plant hormone cytokinin is mediated by a His-to-Asp phosphorelay. The canonical cytokinin receptor consists of an extra cytoplasmic hormone binding domain named cyclase/histidine kinase associated sensory extracellular (CHASE) and cytoplasmic histidine kinase and receiver domains. In addition to classical cytokinin receptors, a different type receptor—named CHASE domain receptor serine/threonine kinase (CHARK)—is also present in rice. It contains the same ligand binding domain as other cytokinin receptors but has a predicted Ser/Thr—instead of a His-kinase domain. Bioinformatic analysis indicates that CHARK is a retrogene and a product of trans-splicing. Here, we analyzed whether CHARK can function as a bona fide cytokinin receptor. A biochemical assay demonstrated its ability to bind cytokinin. Transient expression of CHARK in protoplasts increased their response to cytokinin. Expression of CHARK in an Arabidopsis receptor double mutant complemented its growth defects and restored the ability to activate cytokinin response genes, clearly demonstrating that CHARK functions as a cytokinin receptor. We propose that the CHARK gene presents an evolutionary novelty in the cytokinin signaling system.

Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.

Data-mining bioinformatics: suggesting Arabidopsis thaliana L-type lectin receptor kinase IX.2 (LecRK-IX.2) modulate metabolites and abiotic stress responses

The central role of the Arabidopsis LecRK-IX.2 gene in response to biotic stress has been well established by an array of workers. So far, the role of LecRK-IX.2 in abiotic stresses has not been investigated systematically. Here, we have first investigated a comprehensive in silico survey to explore the regulation, expression pattern in responses to a wide range of abiotic stresses. The present study reveals that the LecRK-IX.2 promoter has numerous potential cis-regulatory elements (CREs) that are regulated by different stresses. AtGenExpress data elucidate that LecRK-IX.2 gene plays a potential role in responses to cold, osmotic, drought, salt, UV-B, heat, wound, and genotoxic compound. The expression profile of the co-expressed genes suggests that Arabidopsis LecRK-IX.2 gene might have a potential role in stress responses in a tissue-specific manner. Furthermore, a probable signal transduction mechanism has been described by using protein-protein interaction (PPI) dataset. Moreover, the present data-mining investigations have suggested that LecRK-IX.2 gene modulates cellular metabolites and abiotic stress responses.

A Plant Lectin Receptor-like Kinase Phosphorylates the Bacterial Effector AvrPtoB to Dampen Its Virulence in Arabidopsis

Plasma membrane-localized receptor-like kinases (RLKs) perceive conserved pathogen-associated molecular patterns (PAMPs) in plants, leading to PAMP-triggered immunity (PTI). The Arabidopsis thaliana lectin RLK LecRK-IX.2 has been shown to regulate the bacterial flagellin-derived peptide flg22-induced PTI. Here, we discover that Pseudomonas syringae effector AvrPtoB targets LecRK-IX.2 for degradation, which subsequently suppresses LecRK-IX.2-mediated PTI and disease resistance. However, LecRK-IX.2 can interact with and phosphorylate AvrPtoB at serine site 335 (S335). AvrPtoB self-associates in vitro and in vivo, and the association appears to be essential for its E3 ligase activity in ubiquitinating substrate in plants. Phosphorylation of S335 disrupts the self-association and as a result, phosphomimetic AvrPtoB^S335D cannot ubiquitinate LecRK-IX.2 efficiently, leading to the compromised virulence of AvrPtoB in suppressing PTI responses. flg22 enhances AvrPtoB S335 phosphorylation by inducing the expression and activating of LecRK-IX.2. Our study demonstrates that host RLKs can modify pathogen effectors to dampen their virulence and undermine their ability in suppressing PTI.

Genome-Wide Identification and Characterization of Lectin Receptor-Like Kinase Gene Family in Cucumber and Expression Profiling Analysis under Different Treatments

Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). In this study, 46 putative LecRLK genes were identified in the cucumber genome, including 23 G-type and 22 L-type, and one C-type LecRLK gene. They were unequally distributed on all seven chromosomes, with a clustering tendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormones and stress on these genes’ promoters. Transcriptome data demonstrated distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real-time PCR (qRT-PCR) analysis. This study provides a better understanding of the character and function of the LecRLK gene family in cucumber and opens up the possibility to exploring the roles that LecRLKs might play in the life cycle of cucumber.

130 years of Plant Lectin Research

Lectins are proteins with diverse molecular structures that share the ability to recognize and bind specifically and reversibly to carbohydrate structures without changing the carbohydrate moiety. The history of lectins started with the discovery of ricin about 130 years ago but since then our understanding of lectins has dramatically changed. Over the years the research focus was shifted from 'the characterization of carbohydrate-binding proteins' to 'understanding the biological function of lectins'. Nowadays plant lectins attract a lot of attention especially because of their potential for crop improvement and biomedical research, as well as their application as tools in glycobiology. The present review aims to give an overview of plant lectins and their applications, and how the field evolved in the last decades.

Lectin receptor kinase OsLecRK-S.7 is required for pollen development and male fertility

Pollen grains are covered by exine that protects the pollen from stress and facilitates pollination. Here we isolated a male sterile mutant s13283 in rice exhibiting aborted pollen with abnormal exine and defective aperture. The mutant gene encodes a novel plasma membrane-localized legume-lectin receptor kinase that we named OsLecRK-S.7. OsLecRK-S.7 was expressed at different levels in all tested tissues and throughout anther development. In vitro kinase assay showed OsLecRK-S.7 capable of autophosporylation. Mutation in s13283 (E560K) and mutation of the conserved ATP binding site (K418E) both knocked out the kinase activity. Mass spectrometry showed Thr₃₇₆ , Ser₃₇₈ , Thr₃₈₆ , Thr₄₀₃ , and Thr₆₅₇ to be the autophosphorylation sites. Mutation of individual autophosphorylation site affected the in vitro kinase activity to different degrees, but did not abolish the gene function in fertility complementation. oslecrk-s.7 mutant plant overexpressing OsLecRK-S.7 recovered male fertility but showed severe growth retardation with reduced number of tillers, and these phenotypes were abolished by E560K or K418E mutation. The results indicated that OsLecRK-S.7 was a key regulator of pollen development.

Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.)

Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.

Origin and Diversity of Plant Receptor-Like Kinases

Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics. We discuss when these different domain associations first occurred and how they evolved, based on a literature review complemented by some of our unpublished results.

Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley

Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.

Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface

Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.

Functional Haplotype and eQTL Analyses of Genes Affecting Cadmium Content in Cultivated Rice

BACKGROUND

Rice is a major food resource for Asian countries including Korea. However, most Asian countries are facing food safety problems due to cropland contamination by heavy metals. Thus, this study was conducted to investigate genetic factors affecting the expression of cadmium (Cd) gene, and to confirm differences in Cd translocation among cultivars because the current molecular understanding of Cd uptake-transport mechanisms remains insufficient. Associations between genotypes and gene expression level of Cd-related genes such as NRAMP, MTP, and HMA gene families in the rice core collection were analyzed at the genomic level.

RESULTS

Os01g0956700, Os05g0128400 and Os11g0485200 showed strong associations between expression level and genotype in the rice core collection, the regulatory factors that associated with these genes in cis and trans were founded. The association between the expression level and genotype of the candidate gene (Os01g0611300: metal tolerance protein) predicted to affect Cd content in rice by a previous genome-wide association study (GWAS) was also analyzed. Furthermore, as a result of the phylogeny and haplotype analyses of the candidate gene, high-Cd tolerance cultivars were selected. The correlations between Cd and other inorganic components (Mg, Mn, Fe, Cu and Zn) in the roots, stems, leaves and unpolished grain of selected rice cultivars were analyzed.

CONCLUSION

Therefore, these results may be useful for understanding the uptake-transport mechanisms of Cd and other inorganic components via molecular genetics and may help rice breeders develop new low-Cd cultivars in the near future.

Extracellular pyridine nucleotides trigger plant systemic immunity through a lectin receptor kinase/BAK1 complex

Systemic acquired resistance (SAR) is a long-lasting broad-spectrum plant immunity induced by mobile signals produced in the local leaves where the initial infection occurs. Although multiple structurally unrelated signals have been proposed, the mechanisms responsible for perception of these signals in the systemic leaves are unknown. Here, we show that exogenously applied nicotinamide adenine dinucleotide (NAD⁺) moves systemically and induces systemic immunity. We demonstrate that the lectin receptor kinase (LecRK), LecRK-VI.2, is a potential receptor for extracellular NAD⁺ (eNAD⁺) and NAD⁺ phosphate (eNADP⁺) and plays a central role in biological induction of SAR. LecRK-VI.2 constitutively associates with BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1 (BAK1) in vivo. Furthermore, BAK1 and its homolog BAK1-LIKE1 are required for eNAD(P)⁺ signaling and SAR, and the kinase activities of LecR-VI.2 and BAK1 are indispensable to their function in SAR. Our results indicate that eNAD⁺ is a putative mobile signal, which triggers SAR through its receptor complex LecRK-VI.2/BAK1 in Arabidopsis thaliana.

Systemic signals allows plants to mount immune responses in sites that are distal from the local infection site. Here, the authors provide evidence that nicotinamide adenine dinucleotide (NAD ⁺ ) is a potential systemic signal that induces immunity via the lectin receptor kinase LecRK-VI.2 and BAK1.

Magnesium Deficiency Induced Global Transcriptome Change in Citrus sinensis Leaves Revealed by RNA-Seq

Magnesium (Mg) deficiency is one of the major constraining factors that limit the yield and quality of agricultural products. Uniform seedlings of the Citrus sinensis were irrigated with Mg deficient (0 mM MgSO₄) and Mg sufficient (1 mM MgSO₄) nutrient solutions for 16 weeks. CO₂ assimilation, starch, soluble carbohydrates, TBARS content and H₂O₂ production were measured. Transcriptomic analysis of C. sinensis leaves was performed by Illumina sequencing. Our results showed that Mg deficiency decreased CO₂ assimilation, but increased starch, sucrose, TBARS content and H₂O₂ production in C. sinensis leaves. A total of 4864 genes showed differential expression in response to Mg deficiency revealed by RNA-Seq and the transcriptomic data were further validated by real-time quantitative PCR (RT-qPCR). Gene ontology (GO) enrichment analysis indicated that the mechanisms underlying Mg deficiency tolerance in C. sinensis may be attributed to the following aspects: (a) enhanced microtubule-based movement and cell cycle regulation; (b) elevated signal transduction in response to biotic and abiotic stimuli; (c) alteration of biological processes by tightly controlling phosphorylation especially protein phosphorylation; (d) down-regulation of light harvesting and photosynthesis due to the accumulation of carbohydrates; (e) up-regulation of cell wall remodeling and antioxidant system. Our results provide a comprehensive insight into the transcriptomic profile of key components involved in the Mg deficiency tolerance in C. sinensis and enrich our understanding of the molecular mechanisms by which plants adapted to a Mg deficient condition.

miR393 regulation of lectin receptor-like kinases associated with LPS perception in Arabidopsis thaliana

microRNAs regulate dynamic aspects of innate immunity in Arabidopsis thaliana in response to lipopolysaccharides. Lectin-domain receptor-like kinases function as surveillance proteins and miR393 targets transcripts of an L-type LecRK (LECRK-V.7, At3g59740). This study investigated miR393 regulation of LecRLKs associated with LPS perception. Following pre-treatment of wild type -, miR393 ab double mutant - and miR393 overexpressor plants with LPS, the expression of miR393 and two other LecRLK genes (G-type lectin S-receptor-like protein kinases, SD1-13 (At1g11330) and SD1-29 (At1g61380) were evaluated. Overexpression and repression of miR393 respectively suppressed and induced transcripts of the LecRLK genes. The results indicate that miR393 regulates the three LecRLKs following perception of bacterial LPS, in support of immunity and basal resistance.

Quantitative phosphoproteomics of lectin receptor-like kinase VI.4 dependent abscisic acid response in Arabidopsis thaliana

Lectin receptor-like kinases (LecRKs) play important roles in the responses to adverse environment stress. Abscisic acid (ABA) is a plant hormone involved in plant growth, development and adverse environmental stress responses. Although some studies of ABA response LecRK genes have been reported, the molecular mechanisms of LecRKs regulation of downstream pathways under ABA induction are not well understood. The present study showed that LecRK-VI.4 responded to ABA and negatively regulated stomatal closure. Here, a quantitative phosphoproteomics approach based on mass spectrometry was employed to study the roles of LecRK-VI.4 in the ABA signaling pathway. Metal oxide affinity beads and C18 chromatography were used for phosphopeptide enrichment and separation. The isobaric tags for relative and absolute quantitation were used for profiling the phosphoproteome of mutant lecrk-vi.4-1 and wild-type Col-0 Arabidopsis under normal growth conditions or ABA treatments. In total, 475 unique phosphopeptides were quantified, including 81 phosphopeptides related to LecRK-VI.4 regulation. Gene ontology, protein-protein interaction and motif analysis were performed. The bioinformatics data showed that phosphorylated proteins regulated by LecRK-VI.4 had close relations with factors of stomatal function, which included aquaporin activity, H⁺ pump activity and the Ca²⁺ concentration in the cytoplasm. These data have expanded our understanding of how LecRK-VI.4 regulates ABA-mediated stomatal movements.

AtPR5K2, a PR5-Like Receptor Kinase, Modulates Plant Responses to Drought Stress by Phosphorylating Protein Phosphatase 2Cs

Cell surface receptors perceive signals from the environment and transfer them to the interior of the cell. The Arabidopsis thaliana PR5 receptor-like kinase (AtPR5K) subfamily consists of three members with extracellular domains that share sequence similarity with the PR5 proteins. In this study, we characterized the role of AtPR5K2 in plant drought-stress signaling. AtPR5K2 is predominantly expressed in leaves and localized to the plasma membrane. The atpr5k2-1 mutant showed tolerance to dehydration stress, while AtPR5K2-overexpressing plants was hypersensitive to drought. Bimolecular fluorescence complementation assays showed that AtPR5K2 physically interacted with the type 2C protein phosphatases ABA-insensitive 1 (ABI1) and ABI2 and the SNF1-related protein kinase 2 (SnRK2.6) proteins, all of which are involved in the initiation of abscisic acid (ABA) signaling; however, these interactions were inhibited by treatments of exogenous ABA. Moreover, AtPR5K2 was found to phosphorylate ABI1 and ABI2, but not SnRK2.6. Taken together, these results suggest that AtPR5K2 participates in ABA-dependent drought-stress signaling through the phosphorylation of ABI1 and ABI2.

Regulation through MicroRNAs in Response to Low-Energy N+ Ion Irradiation in Oryza sativa

MicroRNAs (miRNAs) are a non-coding regulatory RNAs that play significant roles in plant growth and development, especially in the stress response. Low-energy ion radiation, a type of environmental stress, can cause multiple biological effects. To understand the roles of miRNAs in response to low-energy N⁺ ion radiation in Oryza sativa, high-throughput sequencing of small RNAs was carried out to detect the expression of miRNAs in the shoots of the rice after 2 × 10¹⁷ N+/cm² irradiation. The differentially expressed 28 known miRNAs were identified, 17 of these identified miRNAs were validated by real-time quantitative fluorescent PCR (q-PCR), including 9 up-regulated miRNAs (miR1320-3p, miR1320-5p, miR156b-3p, miR156c-5p, miR156c-3p/g-3p, miR1561-5p, miR398b and miR6250) and 8 down-regulated miRNAs (miR156a/e/i, miR156k, miR160f-5p, miR166j-5p, miR1846e and miR399d). In addition, 45 novel radiationresponsive miRNAs were predicted, and 8 of them were verified by q-PCR. The target genes of radiation-responsive miRNAs were predicted and gene function enrichment analysis was performed with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of 9 targets of 4 known miRNA families (miR156, miR399, miR1320 and miR398) and 2 targets of 2 novel miRNAs were quantified by q-PCR, and a strong negative regulation relation between miRNAs and their targets were observed. Those targets including SQUAMOSA promoterbinding-like protein (SPL) genes, copper/zinc superoxide dismutase (Cu/Zn-SOD), copper chaperone for SOD (CCS1) and electron transporter/ heat-shock protein binding protein (HSP), which are involved in growth and defense against various stresses, especially associated with reactive oxygen species (ROS) scavenging. This work provides important information for understanding the ROS generation and elimination mechanisms closely related to miRNAs in rice seedlings after low-energy N⁺ radiation exposure.

Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree

International trade has resulted in the introduction of plant diseases into natural ecosystems around the world. These introductions have potentially catastrophic impacts on ecosystem structure and function. Leveraging genomic tools, natural variation within a tree species, and a high-throughput phenotyping platform, we present a framework that can be broadly applied to rapidly identify candidate genes associated with resistance and susceptibility to introduced plant diseases. The unprecedented speed and accuracy with which the candidate genes can be identified in woody trees demonstrates the potential of genomics to mitigate the impacts of invasive diseases on forest health.

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated, we employed a genome-wide association mapping of ca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among significant associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.

Plant cell surface molecular cypher: Receptor-like proteins and their roles in immunity and development

Plant receptor-like proteins (RLPs) are a family of transmembrane receptors which are distinguished from receptor-like kinases (RLKs) by their lack of a cytoplasmic kinase domain. RLPs continue to be implicated in a broad range of plant immunological and developmental processes as critical sensors or participants in receptor complexes on the plasma membrane. RLPs often associate with RLKs to activate or attenuate signal perception and relay. Some RLPs also physically cluster with RLKs and bear similar expression patterns. Here, we discuss the characteristics, function, and expression of characterized RLPs in the context of their associated RLKs in plant immunity and development.