Resistance gene-dependent activation of a calcium-dependent protein kinase in the plant defense response

Comparative transcriptome profiling reveals differential defense responses among Alternaria brassicicola resistant Sinapis alba and susceptible Brassica rapa

Alternaria blight is a devastating disease that causes significant crop losses in oilseed Brassicas every year. Adoption of conventional breeding to generate disease-resistant varieties has so far been unsuccessful due to the lack of suitable resistant source germplasms of cultivated Brassica spp. A thorough understanding of the molecular basis of resistance, as well as the identification of defense-related genes involved in resistance responses in closely related wild germplasms, would substantially aid in disease management. In the current study, a comparative transcriptome profiling was performed using Illumina based RNA-seq to detect differentially expressed genes (DEGs) specifically modulated in response to Alternaria brassicicola infection in resistant Sinapis alba, a close relative of Brassicas, and the highly susceptible Brassica rapa. The analysis revealed that, at 48 hpi (hours post inoculation), 3396 genes were upregulated and 23239 were downregulated, whereas at 72 hpi, 4023 genes were upregulated and 21116 were downregulated. Furthermore, a large number of defense response genes were detected to be specifically regulated as a result of Alternaria infection. The transcriptome data was validated using qPCR-based expression profiling for selected defense-related DEGs, that revealed significantly higher fold change in gene expression in S. alba when compared to B. rapa. Expression of most of the selected genes was elevated across all the time points under study with significantly higher expression towards the later time point of 72 hpi in the resistant germplasm. S. alba activates a stronger defense response reaction against the disease by deploying an array of genes and transcription factors involved in a wide range of biological processes such as pathogen recognition, signal transduction, cell wall modification, antioxidation, transcription regulation, etc. Overall, the study provides new insights on resistance of S. alba against A. brassicicola, which will aid in devising strategies for breeding resistant varieties of oilseed Brassica.

First Vanilla planifolia High-Density Genetic Linkage Map Provides Quantitative Trait Loci for Resistance to Fusarium oxysporum

Fusarium oxysporum f. sp. radicis-vanillae (Forv), the causal agent of root and stem rot disease, is the main pathogen affecting vanilla production. Sources of resistance have been reported in Vanilla planifolia G. Jackson ex Andrews, the main cultivated vanilla species. In this study, we developed the first high-density genetic map in this species with 1,804 genotyping-by-sequencing (GBS)-generated single nucleotide polymorphism (SNP) markers using 125 selfed progenies of the CR0040 traditional vanilla cultivar. Sixteen linkage groups (LG) were successfully constructed, with a mean of 113 SNPs and an average length of 207 cM per LG. The map had a high density with an average of 5.45 SNP every 10 cM and an average distance of 1.85 cM between adjacent markers. The first three LG were aligned against the first assembled chromosome of CR0040, and the other 13 LG were correctly associated with the other 13 assembled chromosomes. The population was challenged with the highly pathogenic Forv strain Fo072 using the root-dip inoculation method. Five traits were mapped, and 20 QTLs were associated with resistance to Fo072. Among the genes retrieved in the CR0040 physical regions associated with QTLs, genes potentially involved in biotic resistance mechanisms, coding for kinases, E3 ubiquitin ligases, pentatricopeptide repeat-containing proteins, and one leucine-rich repeat receptor underlying the qFo72_08.1 QTL have been highlighted. This study should provide useful resources for marker-assisted selection in V. planifolia.

The Re-Localization of Proteins to or Away from Membranes as an Effective Strategy for Regulating Stress Tolerance in Plants

The membranes of plant cells are dynamic structures composed of phospholipids and proteins. Proteins harboring phospholipid-binding domains or lipid ligands can localize to membranes. Stress perception can alter the subcellular localization of these proteins dynamically, causing them to either associate with or detach from membranes. The mechanisms behind the re-localization involve changes in the lipidation state of the proteins and interactions with membrane-associated biomolecules. The functional significance of such re-localization includes the regulation of molecular transport, cell integrity, protein folding, signaling, and gene expression. In this review, proteins that re-localize to or away from membranes upon abiotic and biotic stresses will be discussed in terms of the mechanisms involved and the functional significance of their re-localization. Knowledge of the re-localization mechanisms will facilitate research on increasing plant stress adaptability, while the study on re-localization of proteins upon stresses will further our understanding of stress adaptation strategies in plants.

Nutrient Elements Promote Disease Resistance in Tomato by Differentially Activating Immune Pathways

Nutrient elements play essential roles in plant growth, development, and reproduction. Balanced nutrition is critical for plant health and the ability to withstand biotic stress. Treatment with essential elements has been shown to induce disease resistance in certain cases. Understanding the functional mechanisms underlying plant immune responses to nutritional elements has the potential to provide new insights into crop improvement. In the present study, we investigated the effect of various elements-potassium (K), calcium (Ca), magnesium (Mg), and sodium (Na)-in promoting resistance against the necrotrophic fungus Botrytis cinerea and the hemibiotrophic bacterium Xanthomonas euvesicatoria in tomato. We demonstrate that spray treatment of essential elements was sufficient to activate immune responses, inducing defense gene expression, cellular leakage, reactive oxygen species, and ethylene production. We report that different defense signaling pathways are required for induction of immunity in response to different elements. Our results suggest that genetic mechanisms that are modulated by nutrient elements can be exploited in agricultural practices to promote disease resistance.

The role of CDPKs in plant development, nutrient and stress signaling

The second messenger calcium (Ca2+) is a ubiquitous intracellular signaling molecule found in eukaryotic cells. In plants, the multigene family of calcium-dependent protein kinases (CDPKs) plays an important role in regulating plant growth, development, and stress tolerance. CDPKs sense changes in intracellular Ca2+ concentration and translate them into phosphorylation events that initiate downstream signaling processes. Several functional and expression studies on different CDPKs and their encoding genes have confirmed their multifunctional role in stress. Here, we provide an overview of the signal transduction mechanisms and functional roles of CDPKs. This review includes details on the regulation of secondary metabolites, nutrient uptake, regulation of flower development, hormonal regulation, and biotic and abiotic stress responses.

Molecular Interactions Between Leptosphaeria maculans and Brassica Species

Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete Leptosphaeria maculans, causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the Brassica napus-L. maculans interaction has rapidly increased, with numerous Avr and R genes cloned, setting this system up as a model organism for studying plant-pathogen associations. Although the B. napus-L. maculans interaction follows Flor's gene-for-gene hypothesis for qualitative resistance, it also puts some unique spins on the interaction. This review discusses the current status of the host-pathogen interaction and highlights some of the future gaps that need addressing moving forward.

Thirty years of resistance: Zig-zag through the plant immune system

Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.

Nutrient Status of Cucumber Plants Affects Powdery Mildew (Podosphaera xanthii)

We examined the effects of applications of N, P, K, Mg, and Ca through an irrigation solution and spraying K, Ca, and Mg salts on cucumber powdery mildew (CPM, Podosphaera xanthii) in potted plants and under commercial-like conditions. Spraying CaCl₂ and MgCl₂, or KCl and K₂SO₄, decreased CPM. There were significant negative correlations between the anion-related molar concentrations of the salts and disease severity. Among the sprayed treatments, NaCl provided significantly less CPM control when applied at a low (0.05 M) concentration, as compared with CaCl₂ and MgCl₂. When sprayed applications of Mg and K salts were analyzed separately from the untreated control, the Cl⁻ salts were found to be more effective than the SO₄⁻² salts. High N and Mg concentrations in the irrigation water delivered to young, fruit-less cucumber plants reduced CPM, whereas more CPM was observed when the irrigation solution contained a medium amount of P and a high amount of K. In contrast, mature, fruit-bearing plants had less severe CPM at higher N, lower P, and higher K levels. Spraying mature plants with monopotassium phosphate, polyhalite (K₂Ca₂Mg(SO₄)₄·2H₂O), and the salts mentioned above over an entire growing season suppressed CPM. CPM severity was also reduced by spray applications of Ca, Mg, and KSO₄⁻² and Cl⁻ salts. Spray applications provided better CPM control than fertigation treatments. Induced resistance is probably involved in the effects of nutrients on CPM.

Protein kinase sensors: an overview of new designs for visualizing kinase dynamics in single plant cells

Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor's working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO2 merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae

Phytophthora nicotianae is highly pathogenic to Solanaceous crops and is a major problem in tobacco production. The tobacco cultivar Beihart1000-1 (BH) is resistant, whereas the Xiaohuangjin 1025 (XHJ) cultivar is susceptible to infection. Here, BH and XHJ were used as models to identify resistant and susceptible genes using RNA sequencing (RNA-seq). Roots were sampled at 0, 6, 12, 24, and 60 h post infection. In total, 23,753 and 25,187 differentially expressed genes (DEGs) were identified in BH and XHJ, respectively. By mapping upregulated DEGs to the KEGG database, changes of the rich factor of "plant pathogen interaction pathway" were corresponded to the infection process. Of all the DEGs in this pathway, 38 were specifically regulated in BH. These genes included 11 disease-resistance proteins, 3 pathogenesis-related proteins, 4 RLP/RLKs, 2 CNGCs, 7 calcium-dependent protein kinases, 4 calcium-binding proteins, 1 mitogen-activated protein kinase kinase, 1 protein EDS1L, 2 WRKY transcription factors, 1 mannosyltransferase, and 1 calmodulin-like protein. By combining the analysis of reported susceptible (S) gene homologs and DEGs in XHJ, 9 S gene homologs were identified, which included 1 calmodulin-binding transcription activator, 1 cyclic nucleotide-gated ion channel, 1 protein trichome birefringence-like protein, 1 plant UBX domain-containing protein, 1 ADP-ribosylation factor GTPase-activating protein, 2 callose synthases, and 2 cellulose synthase A catalytic subunits. qRT-PCR was used to validate the RNA-seq data. The comprehensive transcriptome dataset described here, including candidate resistant and susceptible genes, will provide a valuable resource for breeding tobacco plants resistant to P. nicotianae infections.

Comparative genomic and transcriptomic analyses reveal different pathogenicity-related genes among three eucalyptus fungal pathogens

Ceratocystis fimbriata is an important plant pathogen known to cause Ceratocystis Wilt (CW), a prevalent fungal disease known to affect Eucalyptus spp. plantations in Brazil. To better understand the molecular mechanisms related to pathogenicity in eucalyptus, we generated a high-quality assembly and annotation of the Ce. fimbriata LPF1912 isolate (LPF1912) genome, as well as the first transcriptome of LPF1912 from 16 eucalyptus clones at three infection incubation periods (12, 18, and 24 h). The LPF1912 genome assembly contains 805 scaffolds, totaling 31.8 Mb, with 43% of the genome estimated to be coding sequence comprised of 7,390 protein-coding genes of which 626 (8.5%) were classified as secreted proteins, 120 ribosomal RNAs, and 532 transfer RNAs. Comparative genomic analysis among three eucalyptus fungal pathogens (Ce. fimbriata, Ce. eucalypticola, and Calonectria pseudoreteaudii), showed high similarity in the proteome (21.81%) and secretome (52.01%) of LPF1912 and Ce. eucalypticola. GO annotation of pathogenicity-related genes of LPF1912 and Ce. eucalypticola, revealed enrichment in cell wall degrading enzymes (CWDEs), and lipid/cutin metabolism for Ca. pseudoreteaudii. Additionally, a transcriptome analysis between resistant and susceptible eucalyptus clones to CW infection indicated that a majority (11) of LPF1912 differentially expressed genes had GO terms associated with enzymatic functions, such as the polygalacturonase gene family, confirming the crucial role of CWDEs for Ce. fimbriata pathogenicity. Finally, our genomic and transcriptomic analysis approach provides a better understanding of the mechanisms involved in Ce. fimbriata pathogenesis, as well as a framework for further studies.

Calcium-dependent protein kinase 5 links calcium signaling with N-hydroxy-l-pipecolic acid- and SARD1-dependent immune memory in systemic acquired resistance

Systemic acquired resistance (SAR) prepares infected plants for faster and stronger defense activation upon subsequent attacks. SAR requires an information relay from primary infection to distal tissue and the initiation and maintenance of a self-maintaining phytohormone salicylic acid (SA)-defense loop. In spatial and temporal resolution, we show that calcium-dependent protein kinase CPK5 contributes to immunity and SAR. In local basal resistance, CPK5 functions upstream of SA synthesis, perception, and signaling. In systemic tissue, CPK5 signaling leads to accumulation of SAR-inducing metabolite N-hydroxy-L-pipecolic acid (NHP) and SAR marker genes, including Systemic Acquired Resistance Deficient 1 (SARD1) Plants of increased CPK5, but not CPK6, signaling display an 'enhanced SAR' phenotype towards a secondary bacterial infection. In the sard1-1 background, CPK5-mediated basal resistance is still mounted, but NHP concentration is reduced and enhanced SAR is lost. The biochemical analysis estimated CPK5 half maximal kinase activity for calcium, K50 [Ca²⁺ ], to be c. 100 nM, close to the cytoplasmic resting level. This low threshold uniquely qualifies CPK5 to decode subtle changes in calcium, a prerequisite to signal relay and onset and maintenance of priming at later time points in distal tissue. Our data explain why CPK5 functions as a hub in basal and systemic plant immunity.

Enhanced resistance to Verticillium dahliae mediated by an F-box protein GhACIF1 from Gossypium hirsutum

Avr9/Cf-9-INDUCED F-BOX1 (ACIF1) was first identified during screening of Avr9/Cf-9-elicited genes in tobacco. Further analysis revealed that ACIF1 was required for hypersensitive responses triggered by various elicitors in tobacco and tomato, indicating that it may be involved in various disease resistance. Here, we cloned its cotton (Gossypium hirsutum) homolog GhACIF1, which encodes an F-box protein. We show that GhACIF1 interacts with the putative SKP1-like protein, named GhSKP1. Disease resistance assays show that GhACIF1 enhances resistance to Verticillium dahliae in Arabidopsis plants, while silencing of GhACIF1 confers sensitivity to V. dahliae in cotton. Further analysis show that PevD1 elicitor activates hypersensitive and acquired immune response mediated by GhACIF1. Collectively, these results indicate that GhACIF1 contributes to protection against V. dahliae infection.

Plant Immunity: Thinking Outside and Inside the Box

Models are extensively used to describe the coevolution of plants and microbial attackers. Such models distinguish between different classes of plant immune responses, based on the type of danger signal that is recognized or on the strength of the defense response that the danger signal provokes. However, recent molecular and biochemical advances have shown that these dichotomies are blurred. With molecular proof in hand, we propose here to abandon the current classification of plant immune responses, and to define the different forms of plant immunity solely based on the site of microbe recognition - either extracellular or intracellular. Using this spatial partition, our 'spatial immunity model' facilitates a broadly inclusive, but clearly distinguishing nomenclature to describe immune signaling in plant-microbe interactions.

Regulation of Plant Immune Signaling by Calcium-Dependent Protein Kinases

Activation of Ca²⁺ signaling is a universal response to stress that allows cells to quickly respond to environmental cues. Fluctuations in cytosolic Ca²⁺ are decoded in plants by Ca²⁺-sensing proteins such as Ca²⁺-dependent protein kinases (CDPKs). The perception of microbes results in an influx of Ca²⁺ that activates numerous CDPKs responsible for propagating immune signals required for resistance against disease-causing pathogens. This review describes our current understanding of CDPK activation and regulation, and provides a comprehensive overview of CDPK-mediated immune signaling through interaction with various substrates.

Nitrogen Metabolism is Affected in the Nitrogen-Deficient Rice Mutant esl4 with a Calcium-Dependent Protein Kinase Gene Mutation

Calcium-dependent protein kinases are involved in various biological processes, including hormone response, growth and development, abiotic stress response, disease resistance, and nitrogen metabolism. We identified a novel mutant of a calcium-dependent protein-kinase-encoding gene, esl4, by performing map cloning. The esl4 mutant was nitrogen deficient, and expression and enzyme activities of genes related to nitrogen metabolism were down-regulated. ESL4 was mainly expressed in the vascular bundles of roots, stems, leaves, and sheaths. The ESL4 protein was localized in the cell membranes. Enzyme activity and physiological index analyzes and analysis of the expression of nitrogen metabolism and senescence-related genes indicated that ESL4 was involved in nitrogen metabolism. ESL4 overexpression in transgenic homozygous T2 plants increased nitrogen-use efficiency, improving yields when little nitrogen was available. The seed-set rates, yields per plant, numbers of grains per plant, grain nitrogen content ratios, and total nitrogen content per plant were significantly or very significantly higher for two ESL4 overexpression lines than for the control plants. These results suggest that ESL4 may function upstream of nitrogen-metabolism genes. The results will allow ESL4 to be used to breed novel cultivars for growing in low-nitrogen conditions.

The role of chloroplasts in plant pathology

Plants have evolved complex tolerance systems to survive abiotic and biotic stresses. Central to these programmes is a sophisticated conversation of signals between the chloroplast and the nucleus. In this review, we examine the antagonism between abiotic stress tolerance (AST) and immunity: we propose that to generate immunogenic signals, plants must disable AST systems, in particular those that manage reactive oxygen species (ROS), while the pathogen seeks to reactivate or enhance those systems to achieve virulence. By boosting host systems of AST, pathogens trick the plant into suppressing chloroplast immunogenic signals and steer the host into making an inappropriate immune response. Pathogens disrupt chloroplast function, both transcriptionally-by secreting effectors that alter host gene expression by interacting with defence-related kinase cascades, with transcription factors, or with promoters themselves-and post-transcriptionally, by delivering effectors that enter the chloroplast or alter the localization of host proteins to change chloroplast activities. These mechanisms reconfigure the chloroplast proteome and chloroplast-originating immunogenic signals in order to promote infection.

The early response during the interaction of fungal phytopathogen and host plant

Plants can be infected by a variety of pathogens, most of which can cause severe economic losses. The plants resist the invasion of pathogens via the innate or acquired immune system for surviving biotic stress. The associations between plants and pathogens are sophisticated beyond imaging and the interactions between them can occur at a very early stage after their touching each other. A number of researchers in the past decade have shown that many biochemical events appeared even as early as 5 min after their touching for plant disease resistance response. The early molecular interactions of plants and pathogens are likely to involve protein phosphorylation, ion fluxes, reactive oxygen species (ROS) and other signalling transduction. Here, we reviewed the recent progress in the study for molecular interaction response of fungal pathogens and host plant at the early infection stage, which included many economically important crop fungal pathogens such as cereal rust fungi, tomato Cladosporium fulvum, rice blast and so on. By dissecting the earlier infection stage of the diseases, the avirulent/virulent genes of pathogen or resistance genes of plant could be defined more clearly and accurately, which would undoubtedly facilitate fungal pathogenesis study and resistant crop breeding.

Physiological and RNA-seq analyses provide insights into the response mechanism of the Cf-10-mediated resistance to Cladosporium fulvum infection in tomato

Based on the physiological and RNA-seq analysis, some progress has been made in elucidating the Cf-10-mediated resistance responses to C. fulvum infection in tomato. GO and KEGG enrichment analysis revealed that the DEGs were significantly associated with defense-signaling pathways like oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Leaf mold, caused by the fungus Cladosporium fulvum, is one of the most common diseases affecting tomatoes worldwide. Cf series genes including Cf-2, Cf-4, Cf-5, Cf-9 and Cf-10 play very important roles in resisting tomato leaf mold. Understanding the molecular mechanism of Cf gene-mediated resistance is thus the key to facilitating genetic engineering of resistance to C. fulvum infection. Progress has been made in elucidating two Cf genes, Cf -19 and Cf -12, and how they mediate resistance responses to C. fulvum infection in tomato. However, the mechanism of the Cf-10- mediated resistance response is still unclear. In the present study, RNA-seq was used to analyze changes in the transcriptome at different stages of C. fulvum infection. A total of 2,242 differentially expressed genes (DEGs) responsive to C. fulvum between 0 and 16 days post infection (dpi) were identified, including 1,501 upregulated and 741 downregulated genes. The majority of DEGs were associated with defense-signaling pathways including oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Four DEGs associated with plant-pathogen interaction were uniquely activated in Cf-10 tomato and validated by qRT-PCR. In addition, physiological indicators including reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were measured at 0-21 dpi, and hormone expression [Jasmonic acid (JA) and salicylic acid (SA)] was estimated at 0 and 16 dpi to elucidate the mechanism of the Cf-10-mediated resistance response. C. fulvum infection induced the activities of POD, CAT and SOD, and decreased ROS levels. JA was determined to participate in the resistance response to C. fulvum during the initial infection period. The results of this study provide accountable evidence for the physiological and transcriptional regulation of the Cf-10-mediated resistance response to C. fulvum infection, facilitating further understanding of the molecular mechanism of Cf-10-mediated resistance to C. fulvum infection.

The Kinase OsCPK4 Regulates a Buffering Mechanism That Fine-Tunes Innate Immunity

The calcium-dependent protein kinase OsCPK4 has been demonstrated to play important roles in salt and drought tolerance, plant growth, and development in rice (Oryza sativa). However, little is known about molecular mechanisms underlying OsCPK4 function in rice immunity. In this study, we demonstrated that the generation of oxidative burst and pathogenesis-related gene expression triggered by microbe-associated molecular patterns were significantly enhanced in the oscpk4 mutants. These mutant lines are more resistant to bacterial blight and fungal blast diseases than the wild-type plants, indicating that OsCPK4 negatively regulates innate immunity in rice. OsCPK4 was further identified to interact with a receptor-like cytoplasmic kinase OsRLCK176. OsRLCK176 accumulation is negatively regulated by OsCPK4. Interestingly, the kinase-dead OsCPK4 promotes OsRLCK176 degradation more strongly than the wild-type protein. OsCPK4 and OsRLCK176 mutually phosphorylate each other and form a feedback loop. Moreover, the kinase activity and phosphorylation of OsCPK4 and OsRLCK176 contribute to the stability of OsRLCK176. These findings indicate that the kinase-inactive OsCPK4 promotes OsRLCK176 degradation and restricts plant defenses, whereas the activation of OsCPK4-OsRLCK176 phosphorylation circuit invalidates the OsRLCK176 degradation machinery, thus enhancing plant immunity. Collectively, the study proposes a novel defense buffering mechanism mediated by OsCPK4, which fine-tunes microbe-associated molecular pattern-triggered immunity in rice.

The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications

Plant calcium-dependent protein kinases (CDPKs) are key proteins implicated in calcium-mediated signaling pathways of a wide range of biological events in the organism. The action of each particular CDPK is strictly regulated by many mechanisms in order to ensure an accurate signal translation and the activation of the adequate response processes. In this work, we investigated the regulation of a CDPK involved in rice cold stress response, OsCPK17, to better understand its mode of action. We identified two new alternative splicing (AS) mRNA forms of OsCPK17 encoding truncated versions of the protein, missing the CDPK activation domain. We analyzed the expression patterns of all AS variants in rice tissues and examined their subcellular localization in onion epidermal cells. The results indicate that the AS of OsCPK17 putatively originates truncated forms of the protein with distinct functions, and different subcellular and tissue distributions. Additionally, we addressed the regulation of OsCPK17 by post-translational modifications in several in vitro experiments. Our analysis indicated that OsCPK17 activity depends on its structural rearrangement induced by calcium binding, and that the protein can be autophosphorylated. The identified phosphorylation sites mostly populate the OsCPK17 N-terminal domain. Exceptions are phosphosites T107 and S136 in the kinase domain and S558 in the C-terminal domain. These phosphosites seem conserved in CDPKs and may reflect a common regulatory mechanism for this protein family.

Genetic Architecture of Charcoal Rot (Macrophomina phaseolina) Resistance in Soybean Revealed Using a Diverse Panel

Charcoal rot (CR) disease caused by Macrophomina phaseolina is responsible for significant yield losses in soybean production. Among the methods available for controlling this disease, breeding for resistance is the most promising. Progress in breeding efforts has been slow due to the insufficient information available on the genetic mechanisms related to resistance. Genome-wide association studies (GWAS) enable unraveling the genetic architecture of resistance and identification of causal genes. The aims of this study were to identify new sources of resistance to CR in a collection of 459 diverse plant introductions from the USDA Soybean Germplasm Core Collection using field and greenhouse screenings, and to conduct GWAS to identify candidate genes and associated molecular markers. New sources for CR resistance were identified from both field and greenhouse screening from maturity groups I, II, and III. Five significant single nucleotide polymorphism (SNP) and putative candidate genes related to abiotic and biotic stress responses are reported from the field screening; while greenhouse screening revealed eight loci associated with eight candidate gene families, all associated with functions controlling plant defense response. No overlap of markers or genes was observed between field and greenhouse screenings suggesting a complex molecular mechanism underlying resistance to CR in soybean with varied response to different environments; but our findings provide useful information for advancing breeding for CR resistance as well as the genetic mechanism of resistance.

Transcriptome Analysis of the Sm-Mediated Hypersensitive Response to Stemphylium lycopersici in Tomato

Gray leaf spot disease caused by Stemphylium lycopersici is a major disease in cultivated tomato plants and threatens tomato-growing areas worldwide. Sm is a single dominant gene that confers resistance to tomato gray leaf spot disease agent. However, the underlying molecular mechanism remains unclear. Here, resistant (cv. Motelle, containing the Sm gene) and susceptible (cv. Moneymaker) plants were inoculated with virulent Stemphylium lycopersici isolate at a time point at which both cultivars showed a strong response to S. lycopersici infection. Transcriptome analyses were performed in both cultivars using RNA-seq. The number of differentially expressed genes (DEGs) was higher in Motelle than Moneymaker. Functional classification revealed that most DEGs were involved in plant-pathogen interactions, plant hormone signal transduction, regulation of autophagy, glycerophospholipid metabolism, and α-linolenic acid metabolism. Moreover, the genes that were significantly up-regulated in Sm tomatoes were involved in plant-pathogen interaction pathways. A total of 26 genes were selected for confirmation of differentially expressed levels by quantitative real-time PCR. This knowledge will yield new insights into the molecular mechanism of Sm responses to S. lycopersici infection.

CALCIUM-DEPENDENT PROTEIN KINASE5 Associates with the Truncated NLR Protein TIR-NBS2 to Contribute to exo70B1-Mediated Immunity

Calcium-dependent protein kinases (CPKs) function as calcium sensors and play important roles in plant immunity. Loss of function of the exocyst complex subunit EXO70B1 leads to autoimmunity caused by activation of TN2, a truncated Toll/interleukin-1 receptor-nucleotide binding sequence protein. Here we show, based on a screen for suppressors of exo70B1, that exo70B1-activated autoimmune responses require CPK5 However, the CPK5 homologs CPK4, CPK6, and CPK11, which were previously reported to function redundantly with CPK5 in effector-triggered immunity, did not contribute to exo70B1-associated phenotypes, indicating that CPK5 plays a unique role in plant immunity. Overexpressing CPK5 results in TN2-dependent autoimmunity and enhanced disease resistance, reminiscent of the exo70B1 phenotypes. Ectopic expression of CPK5 in the exo70B1 mutant led to constitutive CPK5 protein kinase activity, which was not detectable in tn2 mutants. Furthermore, TN2 interacts with the CPK5 N-terminal variable and kinase domains, stabilizing CPK5 kinase activity in vitro. This work uncovers a direct functional link between an atypical immune receptor and a crucial component of early immune signaling: increased immunity in exo70B1 depends on TN2 and CPK5 and, in a positive feedback loop, TN2 keeps CPK5 enzymatically active beyond the initiating stimulus.

Comprehensive Analysis of the CDPK-SnRK Superfamily Genes in Chinese Cabbage and Its Evolutionary Implications in Plants

The CDPK-SnRK (calcium-dependent protein kinase/Snf1-related protein kinase) gene superfamily plays important roles in signaling pathways for disease resistance and various stress responses, as indicated by emerging evidence. In this study, we constructed comparative analyses of gene structure, retention, expansion, whole-genome duplication (WGD) and expression patterns of CDPK-SnRK genes in Brassica rapa and their evolution in plants. A total of 49 BrCPKs, 14 BrCRKs, 3 BrPPCKs, 5 BrPEPRKs, and 56 BrSnRKs were identified in B. rapa. All BrCDPK-SnRK proteins had highly conserved kinase domains. By statistical analysis of the number of CDPK-SnRK genes in each species, we found that the expansion of the CDPK-SnRK gene family started from angiosperms. Segmental duplication played a predominant role in CDPK-SnRK gene expansion. The analysis showed that PEPRK was more preferentially retained than other subfamilies and that CPK was retained similarly to SnRK. Among the CPKs and SnRKs, CPKIII and SnRK1 genes were more preferentially retained than other groups. CRK was closest to CPK, which may share a common evolutionary origin. In addition, we identified 196 CPK genes and 252 SnRK genes in 6 species, and their different expansion and evolution types were discovered. Furthermore, the expression of BrCDPK-SnRK genes is dynamic in different tissues as well as in response to abiotic stresses, demonstrating their important roles in development in B. rapa. In summary, this study provides genome-wide insight into the evolutionary history and mechanisms of CDPK-SnRK genes following whole-genome triplication in B. rapa.

CDPK Activation in PRR Signaling

Calcium-dependent protein kinases undergo a rapid biochemical activation in response to an intracellular Ca increase induced by the PRR-dependent perception of a pathogen-related stimulus. Based on SDS gel resolution, the in-gel kinase assay allows the analysis of multiple in vivo protein samples in parallel, combining the advantage of protein separation according to molecular mass with the activity read-out of a protein kinase assay. It thus enables to follow the transient CDPK activation and inactivation in response to in vivo elicitation with a time-wise resolution. In addition, changes of CDPK phosphorylation activity often correlate with slight shifts in the enzyme's apparent molecular mass, indicating posttranslational modifications and a conformational change of the active enzyme compared to its inactive resting form. These band shifts can be detected by a simple immunoblotting to monitor CDPK activation.

A Role for Barley Calcium-Dependent Protein Kinase CPK2a in the Response to Drought

Increasing the drought tolerance of crops is one of the most challenging goals in plant breeding. To improve crop productivity during periods of water deficit, it is essential to understand the complex regulatory pathways that adapt plant metabolism to environmental conditions. Among various plant hormones and second messengers, calcium ions are known to be involved in drought stress perception and signaling. Plants have developed specific calcium-dependent protein kinases that convert calcium signals into phosphorylation events. In this study we attempted to elucidate the role of a calcium-dependent protein kinase in the drought stress response of barley (Hordeum vulgare L.), one of the most economically important crops worldwide. The ongoing barley genome project has provided useful information about genes potentially involved in the drought stress response, but information on the role of calcium-dependent kinases is still limited. We found that the gene encoding the calcium-dependent protein kinase HvCPK2a was significantly upregulated in response to drought. To better understand the role of HvCPK2a in drought stress signaling, we generated transgenic Arabidopsis plants that overexpressed the corresponding coding sequence. Overexpressing lines displayed drought sensitivity, reduced nitrogen balance index (NBI), an increase in total chlorophyll content and decreased relative water content. In addition, in vitro kinase assay experiments combined with mass spectrometry allowed HvCPK2a autophosphorylation sites to be identified. Our results suggest that HvCPK2a is a dual-specificity calcium-dependent protein kinase that functions as a negative regulator of the drought stress response in barley.

Genome-Wide Association Study of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja)

Soybean cyst nematode (SCN) is the most destructive soybean pest worldwide. Host plant resistance is the most environmentally friendly and cost-effective way of mitigating SCN damage to soybeans. However, overuse of the resistant soybean [Glycine max (L.) Merr.] cultivars from limited genetic resources has resulted in SCN race shifts in many soybean-growing areas. Thus, exploration of novel sources of SCN resistance and dissection of the genetic basis are urgently needed. In this study, we screened 235 wild soybean (Glycine soja Sieb. & Zucc.) accessions to identify genotypes resistant to SCN HG Type 2.5.7 (race 5), a less investigated type but is prevalent in the southeastern US. We also dissected the genetic basis of SCN resistance using a genome-wide association study with SNPs genotyped by SoySNP50k iSelect BeadChip. In total, 43 resistant accessions (female index < 30) were identified, with 10 SNPs being significantly associated with SCN HG 2.5.7 resistance in this wild species. Furthermore, four significant SNPs were localized to linked regions of the known quantitative trait locus (QTL) rhg1 on chromosome 18. The other four SNPs on chromosome 18 and two SNPs on chromosome 19 are novel. Genes encoding disease resistance-related proteins with a leucine-rich region, a mitogen-activated protein kinase (MAPK) on chromosome 18, and a MYB transcription factor on chromosome 19 were identified as promising candidate genes. The identified SNPs and candidate genes will benefit future marker-assisted breeding and dissection of the molecular mechanisms underlying the soybean-SCN interaction.

A mutational analysis of the cytosolic domain of the tomato Cf-9 disease-resistance protein shows that membrane-proximal residues are important for Avr9-dependent necrosis

The tomato Cf-9 gene encodes a membrane-anchored glycoprotein that imparts race-specific resistance against the tomato leaf mould fungus Cladosporium fulvum in response to the avirulence protein Avr9. Although the N-terminal half of the extracellular leucine-rich repeat (eLRR) domain of the Cf-9 protein determines its specificity for Avr9, the C-terminal half, including its small cytosolic domain, is postulated to be involved in signalling. The cytosolic domain of Cf-9 carries several residues that are potential sites for ubiquitinylation or phosphorylation, or signals for endocytic uptake. A targeted mutagenesis approach was employed to investigate the roles of these residues and cellular processes in Avr9-dependent necrosis triggered by Cf-9. Our results indicate that the membrane-proximal region of the cytosolic domain of Cf-9 plays an important role in Cf-9-mediated necrosis, and two amino acids within this region, a threonine (T835) and a proline (P838), are particularly important for Cf-9 function. An alanine mutation of T835 had no effect on Cf-9 function, but an aspartic acid mutation, which mimics phosphorylation, reduced Cf-9 function. We therefore postulate that phosphorylation/de-phosphorylation of T835 could act as a molecular switch to determine whether Cf-9 is in a primed or inactive state. Yeast two-hybrid analysis was used to show that the cytosolic domain of Cf-9 interacts with the cytosolic domain of tomato VAP27. This interaction could be disrupted by an alanine mutation of P838, whereas interaction with CITRX remained unaffected. We therefore postulate that a proline-induced kink in the membrane-proximal region of the cytosolic domain of Cf-9 may be important for interaction with VAP27, which may, in turn, be important for Cf-9 function.

Assessing Kinase Activity in Plants with In-Gel Kinase Assays

The in-gel protein kinase assay is a powerful method to measure the protein phosphorylation activity of specific protein kinases. Any protein substrate can be embedded in polyacrylamide gels where they can be phosphorylated by protein kinases that are separated in the gel under denaturing conditions and then renatured. The kinase activity can be visualized in situ in the gels by autoradiography. This method has been used to compare the activities of protein kinases in parallel samples or to identify their potential substrates. Here, we describe in detail an in-gel kinase assay to measure the activity of some protein kinases in plants.

Genome-wide association and genomic prediction of resistance to maize lethal necrosis disease in tropical maize germplasm

KEY MESSAGE

Genome-wide association analysis in tropical and subtropical maize germplasm revealed that MLND resistance is influenced by multiple genomic regions with small to medium effects. The maize lethal necrosis disease (MLND) caused by synergistic interaction of Maize chlorotic mottle virus and Sugarcane mosaic virus, and has emerged as a serious threat to maize production in eastern Africa since 2011. Our objective was to gain insights into the genetic architecture underlying the resistance to MLND by genome-wide association study (GWAS) and genomic selection. We used two association mapping (AM) panels comprising a total of 615 diverse tropical/subtropical maize inbred lines. All the lines were evaluated against MLND under artificial inoculation. Both the panels were genotyped using genotyping-by-sequencing. Phenotypic variation for MLND resistance was significant and heritability was moderately high in both the panels. Few promising lines with high resistance to MLND were identified to be used as potential donors. GWAS revealed 24 SNPs that were significantly associated (P < 3 × 10(-5)) with MLND resistance. These SNPs are located within or adjacent to 20 putative candidate genes that are associated with plant disease resistance. Ridge regression best linear unbiased prediction with five-fold cross-validation revealed higher prediction accuracy for IMAS-AM panel (0.56) over DTMA-AM (0.36) panel. The prediction accuracy for both within and across panels is promising; inclusion of MLND resistance associated SNPs into the prediction model further improved the accuracy. Overall, the study revealed that resistance to MLND is controlled by multiple loci with small to medium effects and the SNPs identified by GWAS can be used as potential candidates in MLND resistance breeding program.

Digital Gene Expression Analysis to Screen Disease Resistance-Relevant Genes from Leaves of Herbaceous Peony (Paeonia lactiflora Pall.) Infected by Botrytis cinerea

Herbaceous peony (Paeonia lactiflora Pall.) is a well-known traditional flower in China and is widely used for landscaping and garden greening due to its high ornamental value. However, disease spots usually appear after the flowering of the plant and may result in the withering of the plant in severe cases. This study examined the disease incidence in an herbaceous peony field in the Yangzhou region, Jiangsu Province. Based on morphological characteristics and molecular data, the disease in this area was identified as a gray mold caused by Botrytis cinerea. Based on previously obtained transcriptome data, eight libraries generated from two herbaceous peony cultivars ‘Zifengyu’ and ‘Dafugui’ with different susceptibilities to the disease were then analyzed using digital gene expression profiling (DGE). Thousands of differentially expressed genes (DEGs) were screened by comparing the eight samples, and these genes were annotated using the Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) database. The pathways related to plant-pathogen interaction, secondary metabolism synthesis and antioxidant system were concentrated, and 51, 76, and 13 disease resistance-relevant candidate genes were identified, respectively. The expression patterns of these candidate genes differed between the two cultivars: their expression of the disease-resistant cultivar ‘Zifengyu’ sharply increased during the early stages of infection, while it was relatively subdued in the disease-sensitive cultivar ‘Dafugui’. A selection of ten candidate genes was evaluated by quantitative real-time PCR (qRT-PCR) to validate the DGE data. These results revealed the transcriptional changes that took place during the interaction of herbaceous peony with B. cinerea, providing insight into the molecular mechanisms of host resistance to gray mold.

Calcium signaling during reproduction and biotrophic fungal interactions in plants

Many recent studies have indicated that cellular communications during plant reproduction, fungal invasion, and defense involve identical or similar molecular players and mechanisms. Indeed, pollen tube invasion and sperm release shares many common features with infection of plant tissue by fungi and oomycetes, as a tip-growing intruder needs to communicate with the receptive cells to gain access into a cell and tissue. Depending on the compatibility between cells, interactions may result in defense, invasion, growth support, or cell death. Plant cells stimulated by both pollen tubes and fungal hyphae secrete, for example, small cysteine-rich proteins and receptor-like kinases are activated leading to intracellular signaling events such as the production of reactive oxygen species (ROS) and the generation of calcium (Ca(2+)) transients. The ubiquitous and versatile second messenger Ca(2+) thereafter plays a central and crucial role in modulating numerous downstream signaling processes. In stimulated cells, it elicits both fast and slow cellular responses depending on the shape, frequency, amplitude, and duration of the Ca(2+) transients. The various Ca(2+) signatures are transduced into cellular information via a battery of Ca(2+)-binding proteins. In this review, we focus on Ca(2+) signaling and discuss its occurrence during plant reproduction and interactions of plant cells with biotrophic filamentous microbes. The participation of Ca(2+) in ROS signaling pathways is also discussed.

Comparative Transcriptome Analysis of Resistant and Susceptible Tomato Lines in Response to Infection by Xanthomonas perforans Race T3

Bacterial spot, incited by several Xanthomonas sp., is a serious disease in tomato (Solanum lycopersicum L.). Although genetics of resistance has been widely investigated, the interactions between the pathogen and tomato plants remain unclear. In this study, tanscriptomes of X. perforans race T3 infected tomato lines were compared to those of controls. An average of 7 million reads were generated with approximately 21,526 genes mapped in each sample post-inoculation at 6 h (6 HPI) and 6 days (6 DPI) using RNA-sequencing technology. Overall, the numbers of differentially expressed genes (DEGs) were higher in the resistant tomato line PI 114490 than in the susceptible line OH 88119, and the numbers of DEGs were higher at 6 DPI than at 6 HPI. Fewer genes (78 in PI 114490 and 15 in OH 88119) were up-regulated and most DEGs were down-regulated, suggesting that the inducible defense response might not be fully activated at 6 HPI. Accumulation expression levels of 326 co-up regulated genes in both tomato lines at 6 DPI might be involved in basal defense, while the specific and strongly induced genes at 6 DPI might be correlated with the resistance in PI 114490. Most DEGs were involved in plant hormone signal transduction, plant-pathogen interaction and phenylalanine metabolism, and the genes significantly up-regulated in PI 114490 at 6 DPI were associated with defense response pathways. DEGs containing NBS-LRR domain or defense-related WRKY transcription factors were also identified. The results will provide a valuable resource for understanding the interactions between X. perforans and tomato plants.

From local to global: CDPKs in systemic defense signaling upon microbial and herbivore attack

Calcium-dependent protein kinases (CDPKs) are multifunctional proteins in which a calmodulin-like calcium-sensor and a protein kinase effector domain are combined in one molecule. Not surprisingly, CDPKs were primarily recognized as signaling mediators, which perceive rapid intracellular changes of Ca(2+) ion concentration, for example triggered by environmental stress cues, and relay them into specific phosphorylation events to induce further downstream stress responses. In the context of both, plant exposure to biotrophic pathogens-derived signals as well as plant attack by herbivores and wounding, CDPKs were shown to undergo rapid biochemical activation within seconds to minutes after stimulation and to induce local defence-responses including respective changes in gene expression patterns. In addition, CDPK function was correlated with the control of either salicylic acid-mediated or jasmonic acid-mediated phytohormone signaling pathways, mediating long term resistance to either biotrophic bacterial pathogens or herbivores also in distal parts of a plant. It has long been unclear how an individual enzyme can affect both rapid local as well as long-term distal immune responses. Here, we discuss recently raised topics from the field of CDPK research, in particular with a view on the identification of in vivo phosphorylation targets, which provide first mechanistic insights into the dual role of these enzymes: On the one hand as component of a self-activating circuit responsible for rapid plasma-membrane anchored cell-to-cell signal propagation from local to distal plant sites. On the other hand as nuclear-located regulators of transcription factor activity. Finally, we will highlight the dual function of calcium sensors in plasma-membrane/calcium-mediated signal propagation and in phytohormone signaling-dependent systemic resistance in immune responses to both, bacterial pathogens and herbivores.

Identification of interacting proteins for calcium-dependent protein kinase 8 by a novel screening system based on bimolecular fluorescence complementation

Protein kinases are key regulators of cell function that constitute one of the largest and most functionally diverse gene families. We developed a novel assay system, based on the bimolecular fluorescence complementation (BiFC) technique in Escherichia coli, for detecting transient interactions such as those between kinases and their substrates. This system detected the interaction between OsMEK1 and its direct target OsMAP1. By contrast, BiFC fluorescence was not observed when OsMAP2 or OsMAP3, which are not substrates of OsMEK1, were used as prey proteins. We also screened for interacting proteins of calcium-dependent protein kinase 8 (OsCPK8), a regulator of plant immune responses, and identified three proteins as interacting molecules of OsCPK8. The interaction between OsCPK8 and two of these proteins (ARF-GEF and peptidyl prolyl isomerase) was confirmed in rice cells by means of BiFC technology. These results indicate that our new assay system has the potential to screen for protein kinase target molecules.

Overexpression of constitutively active OsCPK10 increases Arabidopsis resistance against Pseudomonas syringae pv. tomato and rice resistance against Magnaporthe grisea

Calcium-dependent protein kinases (CDPKs) are crucial calcium sensors involved in plant responses to pathogen infection. Here, we report isolation and functional characterization of the pathogen-responsive rice OsCPK10 gene. The expression of OsCPK10 was strongly induced following treatment with a Magnaporthe grisea elicitor. Kinase activity assay showed that the functional OsCPK10 protein not only autophosphorylated, but also phosphorylated Casein in a calcium-dependent manner. Overexpression of constitutively active OsCPK10 in Arabidopsis enhanced the resistance to infection with Pseudomonas syringae pv. tomato, associated with elevated expression of both SA- and JA-related defense genes. Similarly, transgenic rice plants containing constitutively active OsCPK10 exhibited enhanced resistance to blast fungus M. grisea. The enhanced resistance in the transgenic lines was associated with activated expression of SA- and JA-related defense genes. Collectively, our results indicate that rice OsCPK10 is a crucial regulator in plant immune responses, and that it may regulate disease resistance by activating both SA- and JA-dependent defense responses.

Overexpression of constitutively active OsCPK10 increases Arabidopsis resistance against Pseudomonas syringae pv. tomato and rice resistance against Magnaporthe grisea

Calcium-dependent protein kinases (CDPKs) are crucial calcium sensors involved in plant responses to pathogen infection. Here, we report isolation and functional characterization of the pathogen-responsive rice OsCPK10 gene. The expression of OsCPK10 was strongly induced following treatment with a Magnaporthe grisea elicitor. Kinase activity assay showed that the functional OsCPK10 protein not only autophosphorylated, but also phosphorylated Casein in a calcium-dependent manner. Overexpression of constitutively active OsCPK10 in Arabidopsis enhanced the resistance to infection with Pseudomonas syringae pv. tomato, associated with elevated expression of both SA- and JA-related defense genes. Similarly, transgenic rice plants containing constitutively active OsCPK10 exhibited enhanced resistance to blast fungus M. grisea. The enhanced resistance in the transgenic lines was associated with activated expression of SA- and JA-related defense genes. Collectively, our results indicate that rice OsCPK10 is a crucial regulator in plant immune responses, and that it may regulate disease resistance by activating both SA- and JA-dependent defense responses.

Calcium-dependent protein kinases: hubs in plant stress signaling and development

These kinases are identified as integrators in plant signaling, with distinct as well as shared phosphorylation substrates mediating pathway specificity.

An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis

The failure of gene-for-gene resistance traits to provide durable and broad-spectrum resistance in an agricultural context has led to the search for genes underlying quantitative resistance in plants. Such genes have been identified in only a few cases, all for fungal or nematode resistance, and encode diverse molecular functions. However, an understanding of the molecular mechanisms of quantitative resistance variation to other enemies and the associated evolutionary forces shaping this variation remain largely unknown. We report the identification, map-based cloning and functional validation of QRX3 (RKS1, Resistance related KinaSe 1), conferring broad-spectrum resistance to Xanthomonas campestris (Xc), a devastating worldwide bacterial vascular pathogen of crucifers. RKS1 encodes an atypical kinase that mediates a quantitative resistance mechanism in plants by restricting bacterial spread from the infection site. Nested Genome-Wide Association mapping revealed a major locus corresponding to an allelic series at RKS1 at the species level. An association between variation in resistance and RKS1 transcription was found using various transgenic lines as well as in natural accessions, suggesting that regulation of RKS1 expression is a major component of quantitative resistance to Xc. The co-existence of long lived RKS1 haplotypes in A. thaliana is shared with a variety of genes involved in pathogen recognition, suggesting common selective pressures. The identification of RKS1 constitutes a starting point for deciphering the mechanisms underlying broad spectrum quantitative disease resistance that is effective against a devastating and vascular crop pathogen. Because putative RKS1 orthologous have been found in other Brassica species, RKS1 provides an exciting opportunity for plant breeders to improve resistance to black rot in crops.

During the evolution of plant-pathogen interactions, plants have evolved the capability to defend themselves from pathogen infection by different overlapping mechanisms. Disease resistance is constituted by an elaborate, multilayered system of defense. Among these responses, quantitative resistance is a prevalent form of resistance in crops and natural plant populations, for which the genetic and molecular bases remain largely unknown. Thus, identification of the genes underlying quantitative resistance constitutes a major challenge in plant breeding and evolutionary biology, and might have enormous practical implications for human health by increasing crop yield and quality. Our work contributes to understanding the molecular bases of quantitative resistance to the vascular pathogen Xanthomonas campestris (Xc), which is responsible for black rot, an important disease of crucifers worldwide. By multiple approaches, we demonstrate that RKS1 is a quantitative resistance gene in Arabidopsis thaliana conferring broad-spectrum resistance to Xc and that this resistance mechanism in plants is associated with regulation of RKS1 expression. We also provide evidence that RKS1 allelic variation is a major component of quantitative resistance to Xc at the species level. Finally, the long-lived polymorphism associated with RKS1 suggests that evolutionary stable broad-spectrum resistance to Xc may be achieved in natural populations of A. thaliana.

CPK3-phosphorylated RhoGDI1 is essential in the development of Arabidopsis seedlings and leaf epidermal cells

The regulation of Rho of plants (ROP) in morphogenesis of leaf epidermal cells has been well studied, but the roles concerning regulators of ROPs such as RhoGDIs are poorly understood. This study reports that AtRhoGDI1 (GDI1) acts as a versatile regulator to modulate development of seedlings and leaf pavement cells. In mutant gdi1, leaf pavement cells showed shorter lobes in comparison with those in wild type. In GDI1-14 seedlings (GDI1-overexpression line) the growth of lobes in pavement cells was severely suppressed and the development of seedlings was altered. These results indicate that GDI1 plays an essential role in morphogenesis of epidermal pavement cells through modulating the ROP signalling pathways. The interaction between GDI1 and ROP2 or ROP6 was detected in the leaf pavement cells using FRET analysis. Dominant negative, not constitutively active, DN-rop6 could weaken the effect caused by overexpression of GDI1; because the pleiotropic phenotype of GDI1-14 plants was eliminated in the hybrid line GDI1-14 DN-rop6. GDI1 could be phosphorylated by CPK3. Three conserved Ser/Thr residues in GDI1 were determined as targeted amino acids for CPK3. Overexpression of GDI1(3D), not GDI1(3A), could rescue the abnormal growth phenotypes of gdi1-1 seedlings, demonstrating the impact of GDI1 phosphorylation in the development of Arabidopsis. In summary, these results suggest that GDI1 regulation in morphogenesis of seedlings and leaf pavement cells could be undergone through modulating the ROP signalling pathways and the phosphorylation of GDI1 by CPK3 was required for the developmental modulation in Arabidopsis.

The myristoylated amino-terminus of an Arabidopsis calcium-dependent protein kinase mediates plasma membrane localization

Calcium-dependent protein kinases (CDPK) are a major group of calcium-stimulated kinases found in plants and some protists. Many CDPKs are membrane-associated, presumably because of lipid modifications at their amino termini. We investigated the subcellular location and myristoylation of AtCPK5, a member of the Arabidopsis CDPK family. Most AtCPK5 was associated with the plasma membrane as demonstrated by two-phase fractionation of plant microsomes and by in vivo detection of AtCPK5-GFP fusion proteins. AtCPK5 was a substrate for plant N-myristoyltransferase and myristoylation was prevented by converting the glycine at the proposed site of myristate attachment to alanine (G2A). In transgenic plants, a G2A mutation completely abolished AtCPK5 membrane association, indicating that myristoylation was essential for membrane binding. The first sixteen amino acids of AtCPK5 were sufficient to direct plasma membrane localization. In addition, differentially phosphorylated forms of AtCPK5 were detected both in planta and after expression of AtCPK5 in a cell-free plant extract. Our results demonstrate that AtCPK5 is myristoylated at its amino terminus and that myristoylation is required for membrane binding.

Calcium-dependent protein kinase/NADPH oxidase activation circuit is required for rapid defense signal propagation

In animals and plants, pathogen recognition triggers the local activation of intracellular signaling that is prerequisite for mounting systemic defenses in the whole organism. We identified that Arabidopsis thaliana isoform CPK5 of the plant calcium-dependent protein kinase family becomes rapidly biochemically activated in response to pathogen-associated molecular pattern (PAMP) stimulation. CPK5 signaling resulted in enhanced salicylic acid-mediated resistance to the bacterial pathogen Pst DC3000, differential plant defense gene expression, and synthesis of reactive oxygen species (ROS). Using selected reaction monitoring MS, we identified the plant NADPH oxidase, respiratory burst oxidase homolog D (RBOHD), as an in vivo phosphorylation target of CPK5. Remarkably, CPK5-dependent in vivo phosphorylation of RBOHD occurs on both PAMP- and ROS stimulation. Furthermore, rapid CPK5-dependent biochemical and transcriptional activation of defense reactions at distal sites is compromised in cpk5 and rbohd mutants. Our data not only identify CPK5 as a key regulator of innate immune responses in plants but also support a model of ROS-mediated cell-to-cell communication, where a self-propagating mutual activation circuit consisting of the protein kinase, CPK5, and the NADPH oxidase RBOHD facilitates rapid signal propagation as a prerequisite for defense response activation at distal sites within the plant.

Calcium-dependent protein kinase/NADPH oxidase activation circuit is required for rapid defense signal propagation

In animals and plants, pathogen recognition triggers the local activation of intracellular signaling that is prerequisite for mounting systemic defenses in the whole organism. We identified that Arabidopsis thaliana isoform CPK5 of the plant calcium-dependent protein kinase family becomes rapidly biochemically activated in response to pathogen-associated molecular pattern (PAMP) stimulation. CPK5 signaling resulted in enhanced salicylic acid-mediated resistance to the bacterial pathogen Pst DC3000, differential plant defense gene expression, and synthesis of reactive oxygen species (ROS). Using selected reaction monitoring MS, we identified the plant NADPH oxidase, respiratory burst oxidase homolog D (RBOHD), as an in vivo phosphorylation target of CPK5. Remarkably, CPK5-dependent in vivo phosphorylation of RBOHD occurs on both PAMP- and ROS stimulation. Furthermore, rapid CPK5-dependent biochemical and transcriptional activation of defense reactions at distal sites is compromised in cpk5 and rbohd mutants. Our data not only identify CPK5 as a key regulator of innate immune responses in plants but also support a model of ROS-mediated cell-to-cell communication, where a self-propagating mutual activation circuit consisting of the protein kinase, CPK5, and the NADPH oxidase RBOHD facilitates rapid signal propagation as a prerequisite for defense response activation at distal sites within the plant.

Ca2+-dependent protein kinase11 and 24 modulate the activity of the inward rectifying K+ channels in Arabidopsis pollen tubes

Potassium (K(+)) influx into pollen tubes via K(+) transporters is essential for pollen tube growth; however, the mechanism by which K(+) transporters are regulated in pollen tubes remains unknown. Here, we report that Arabidopsis thaliana Ca(2+)-dependent protein kinase11 (CPK11) and CPK24 are involved in Ca(2+)-dependent regulation of the inward K(+) (K(+)in) channels in pollen tubes. Using patch-clamp analysis, we demonstrated that K(+)in currents of pollen tube protoplasts were inhibited by elevated [Ca(2+)]cyt. However, disruption of CPK11 or CPK24 completely impaired the Ca(2+)-dependent inhibition of K(+)in currents and enhanced pollen tube growth. Moreover, the cpk11 cpk24 double mutant exhibited similar phenotypes as the corresponding single mutants, suggesting that these two CDPKs function in the same signaling pathway. Bimolecular fluorescence complementation and coimmunoprecipitation experiments showed that CPK11 could interact with CPK24 in vivo. Furthermore, CPK11 phosphorylated the N terminus of CPK24 in vitro, suggesting that these two CDPKs work together as part of a kinase cascade. Electrophysiological assays demonstrated that the Shaker pollen K(+)in channel is the main contributor to pollen tube K(+)in currents and acts as the downstream target of the CPK11-CPK24 pathway. We conclude that CPK11 and CPK24 together mediate the Ca(2+)-dependent inhibition of K(+)in channels and participate in the regulation of pollen tube growth in Arabidopsis.

Bifurcation of Arabidopsis NLR immune signaling via Ca²⁺-dependent protein kinases

Nucleotide-binding domain leucine-rich repeat (NLR) protein complexes sense infections and trigger robust immune responses in plants and humans. Activation of plant NLR resistance (R) proteins by pathogen effectors launches convergent immune responses, including programmed cell death (PCD), reactive oxygen species (ROS) production and transcriptional reprogramming with elusive mechanisms. Functional genomic and biochemical genetic screens identified six closely related Arabidopsis Ca²⁺-dependent protein kinases (CPKs) in mediating bifurcate immune responses activated by NLR proteins, RPS2 and RPM1. The dynamics of differential CPK1/2 activation by pathogen effectors controls the onset of cell death. Sustained CPK4/5/6/11 activation directly phosphorylates a specific subgroup of WRKY transcription factors, WRKY8/28/48, to synergistically regulate transcriptional reprogramming crucial for NLR-dependent restriction of pathogen growth, whereas CPK1/2/4/11 phosphorylate plasma membrane-resident NADPH oxidases for ROS production. Our studies delineate bifurcation of complex signaling mechanisms downstream of NLR immune sensors mediated by the myriad action of CPKs with distinct substrate specificity and subcellular dynamics.

Distinguishing self from non-self is the fundamental principle of immunity. Nucleotide-binding leucine-rich repeat (NLR) proteins were first identified in plants as disease resistance proteins and were recently found to play essential roles in mammalian innate immunity and inflammation. NLR protein complexes sense intracellular pathogenic effectors in plants and microbial patterns and danger signals in humans, but the signaling mechanisms upon NLR activation remain elusive. Using the Arabidopsis-Pseudomonas interaction as a model system, we discovered the molecular link between NLR immune sensors and the convergent immune responses triggered by distinct pathogen effectors. Integrated functional genomic and biochemical genetic screens identified six closely related Ca²⁺-dependent protein kinases (CPKs) that orchestrate bifurcate NLR immune signaling via distinct substrate specificity and subcellular dynamics. The CPK1/2 regulate the onset of programmed cell death; CPK4/5/6/11 phosphorylate specific WRKY transcription factors to regulate immune gene expression crucial for NLR-dependent restriction of pathogen growth, whereas CPK1/2/4/11 phosphorylate NADPH oxidases for the production of reactive oxygen species. Our studies decode the complex signaling mechanisms via the myriad action of CPKs downstream of NLR immune sensors.

CDPKs in immune and stress signaling

Ca(2+) has long been recognized as a conserved second messenger and principal mediator in plant immune and stress responses. How Ca(2+) signals are sensed and relayed into diverse primary and global signaling events is still largely unknown. Comprehensive analyses of the plant-specific multigene family of Ca(2+)-dependent protein kinases (CDPKs) are unraveling the molecular, cellular and genetic mechanisms of Ca(2+) signaling. CDPKs, which exhibit overlapping and distinct expression patterns, sub-cellular localizations, substrate specificities and Ca(2+) sensitivities, play versatile roles in the activation and repression of enzymes, channels and transcription factors. Here, we review the recent advances on the multifaceted functions of CDPKs in the complex immune and stress signaling networks, including oxidative burst, stomatal movements, hormonal signaling and gene regulation.