Arabidopsis Mutant bik1 Exhibits Strong Resistance to Plasmodiophora brassicae

Comparative Analysis of Transcriptomes Reveals Pathways and Verifies Candidate Genes for Clubroot Resistance in Brassica oleracea

Clubroot, a soil-borne disease caused by Plasmodiophora brassicae, is one of the most destructive diseases of Brassica oleracea all over the world. However, the mechanism of clubroot resistance remains unclear. In this research, transcriptome sequencing was conducted on root samples from both resistant (R) and susceptible (S) B. oleracea plants infected by P. brassicae. Then the comparative analysis was carried out between the R and S samples at different time points during the infection stages to reveal clubroot resistance related pathways and candidate genes. Compared with 0 days after inoculation, a total of 4991 differential expressed genes were detected from the S pool, while only 2133 were found from the R pool. Gene function enrichment analysis found that the effector-triggered immunity played a major role in the R pool, while the pathogen-associated molecular pattern triggered immune response was stronger in the S pool. Simultaneously, candidate genes were identified through weighted gene co-expression network analysis, with Bol010786 (CNGC13) and Bol017921 (SD2-5) showing potential for conferring resistance to clubroot. The findings of this research provide valuable insights into the molecular mechanisms underlying clubroot resistance and present new avenues for further research aimed at enhancing the clubroot resistance of B. oleracea through breeding.

Identification and Characterization of High-Molecular-Weight Proteins Secreted by Plasmodiophora brassicae That Suppress Plant Immunity

Plasmodiophora brassicae is an obligate intracellular parasitic protist that causes clubroot disease on cruciferous plants. So far, some low-molecular-weight secreted proteins from P. brassicae have been reported to play an important role in plant immunity regulation, but there are few reports on its high-molecular-weight secreted proteins. In this study, 35 putative high-molecular-weight secreted proteins (>300 amino acids) of P. brassicae (PbHMWSP) genes that are highly expressed during the infection stage were identified using transcriptome analysis and bioinformatics prediction. Then, the secretory activity of 30 putative PbHMWSPs was confirmed using the yeast signal sequence trap system. Furthermore, the genes encoding 24 PbHMWSPs were successfully cloned and their functions in plant immunity were studied. The results showed that ten PbHMWSPs could inhibit flg22-induced reactive oxygen burst, and ten PbHMWSPs significantly inhibited the expression of the SA signaling pathway marker gene PR1a. In addition, nine PbHMWSPs could inhibit the expression of a marker gene of the JA signaling pathway. Therefore, a total of 19 of the 24 tested PbHMWSPs played roles in suppressing the immune response of plants. Of these, it is worth noting that PbHMWSP34 can inhibit the expression of JA, ET, and several SA signaling pathway marker genes. The present study is the first to report the function of the high-molecular-weight secreted proteins of P. brassicae in plant immunity, which will enrich the theory of interaction mechanisms between the pathogens and plants.

Disease-resistant varieties of Chinese cabbage (Brassica rapa L. ssp. pekinensis) inhibit Plasmodiophora brassicae infestation by stabilising root flora structure

The application of disease-resistant varieties is the most cost-effective method for solving the problem of clubroot. "Shangpin," a disease-resistant variety of Chinese cabbage with broad-spectrum immunity to Plasmodiophora brassicae (P. brassicae), was screened in a previous study. Based on 16S rRNA sequencing technology, we annotated the compositional differences between the rhizosphere, rhizoplane, and endosphere bacterial communities of "Shangpin" and "83-1" under P. brassicae stress. Alpha diversity analysis showed that the abundance of microorganisms in the root system of "83-1" changed more than that of "Shangpin" after P. brassicae infestation, and Beta diversity analysis indicated that Flavobacterium and Sphingomonas may mediate clubroot resistance, while Nitrospira, Nitrosospira, and Pseudomonas may mediate P. brassicae infestation among the bacteria in the Top 10 abundances. Microbial functional analyses showed that the root microorganisms of "83-1" were metabolically weakened after P. brassicae inoculation and were inhibited in competition with pathogenic bacteria. Conversely, the root microorganisms of "Shangpin" maintained the strength of their metabolic capacity, which took a favorable position in competition with the pathogen and inhibited the growth and development of the pathogen, thus showing resistance. Root secretions of "Shangpin" significantly inhibited the incidence and disease index of clubroot, which indicated that under clubroot stress, resistant varieties maintain root microbial diversity and microbial community functions through specific root exudates, enriching the genera Flavobacterium and Sphingomonas, thus showing resistance. The results of this study reveal the resistance mechanism of resistant varieties to clubroot and provide new insights into the prevention and control of clubroot in Chinese cabbage.

Protist ubiquitin ligase effector PbE3-2 targets cysteine protease RD21A to impede plant immunity

Clubroot, caused by the soil-borne protist pathogen Plasmodiophora brassicae, is one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, because of its obligate biotrophic nature, the molecular mechanism by which this pathogen promotes infection remains largely unknown. P. brassicae E3 ubiquitin ligase 2 (PbE3-2) is a Really Interesting New Gene (RING)-type E3 ubiquitin ligase in P. brassicae with E3 ligase activity in vitro. Yeast (Saccharomyces cerevisiae) invertase assay and apoplast washing fluid extraction showed that PbE3-2 harbors a functional signal peptide. Overexpression of PbE3-2 in Arabidopsis (Arabidopsis thaliana) resulted in higher susceptibility to P. brassicae and decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated host cysteine protease RESPONSIVE TO DEHYDRATION 21A (RD21A) in vitro and in vivo. Mutant plants deficient in RD21A exhibited similar susceptibility and compromised immune responses as in PbE3-2 overexpression plants. We show that PbE3-2, which targets RD21A, is an important virulence factor for P. brassicae. Two other secretory RING-type E3 ubiquitin ligases in P. brassicae performed the same function as PbE3-2 and ubiquitinated RD21A. This study reveals a substantial virulence functional role of protist E3 ubiquitin ligases and demonstrates a mechanism by which protist E3 ubiquitin ligases degrade host immune-associated cysteine proteases to impede host immunity.

Genomic Analysis Highlights Putative Defective Susceptibility Genes in Tomato Germplasm

Tomato (Solanum lycopersicum L.) is one of the most widely grown vegetables in the world and is impacted by many diseases which cause yield reduction or even crop failure. Breeding for disease resistance is thus a key objective in tomato improvement. Since disease arises from a compatible interaction between a plant and a pathogen, a mutation which alters a plant susceptibility (S) gene facilitating compatibility may induce broad-spectrum and durable plant resistance. Here, we report on a genome-wide analysis of a set of 360 tomato genotypes, with the goal of identifying defective S-gene alleles as a potential source for the breeding of resistance. A set of 125 gene homologs of 10 S-genes (PMR 4, PMR5, PMR6, MLO, BIK1, DMR1, DMR6, DND1, CPR5, and SR1) were analyzed. Their genomic sequences were examined and SNPs/indels were annotated using the SNPeff pipeline. A total of 54,000 SNPs/indels were identified, among which 1300 were estimated to have a moderate impact (non-synonymous variants), while 120 were estimated to have a high impact (e.g., missense/nonsense/frameshift variants). The latter were then analyzed for their effect on gene functionality. A total of 103 genotypes showed one high-impact mutation in at least one of the scouted genes, while in 10 genotypes, more than 4 high-impact mutations in as many genes were detected. A set of 10 SNPs were validated through Sanger sequencing. Three genotypes carrying high-impact homozygous SNPs in S-genes were infected with Oidium neolycopersici, and two highlighted a significantly reduced susceptibility to the fungus. The existing mutations fall within the scope of a history of safe use and can be useful to guide risk assessment in evaluating the effect of new genomic techniques.

WeiTsing, a pericycle-expressed ion channel, safeguards the stele to confer clubroot resistance

Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on cruciferous crops worldwide. Here, we report the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS is transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. Brassica napus carrying the WTS transgene displayed strong resistance to Pb. WTS encodes a small protein localized in the endoplasmic reticulum (ER), and its expression in plants induces immune responses. The cryoelectron microscopy (cryo-EM) structure of WTS revealed a previously unknown pentameric architecture with a central pore. Electrophysiology analyses demonstrated that WTS is a calcium-permeable cation-selective channel. Structure-guided mutagenesis indicated that channel activity is strictly required for triggering defenses. The findings uncover an ion channel analogous to resistosomes that triggers immune signaling in the pericycle.

Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis

Introduction

Receptor-like cytoplastic kinases (RLCKs) are known in many plants to be involved in various processes of plant growth and development and regulate plant immunity to pathogen infection. Environmental stimuli such as pathogen infection and drought restrict the crop yield and interfere with plant growth. However, the function of RLCKs in sugarcane remains unclear.

Methods and results

In this study, a member of the RLCK VII subfamily, ScRIPK, was identified in sugarcane based on sequence similarity to the rice and Arabidopsis RLCKs. ScRIPK was localized to the plasma membrane, as predicted, and the expression of ScRIPK was responsive to polyethylene glycol treatment and Fusarium sacchari infection. Overexpression of ScRIPK in Arabidopsis enhanced drought tolerance and disease susceptibility of seedlings. Moreover, the crystal structure of the ScRIPK kinase domain (ScRIPK KD) and the mutant proteins (ScRIPK-KD K124R and ScRIPK-KD S253A|T254A) were characterized in order to determine the activation mechanism. We also identified ScRIN4 as the interacting protein of ScRIPK.

Discussion

Our work identified a RLCK in sugarcane, providing a potential target for sugarcane responses to disease infection and drought, and a structural basis for kinase activation mechanisms.

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L

Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

Application of Trichoderma Hz36 and Hk37 as Biocontrol Agents against Clubroot Caused by Plasmodiophora brassicae

Clubroot, a soil-infective disease caused by Plasmodiophora brassicae, is a serious disease affecting cruciferous plants around the world. There is no effective control measure to completely remove this pathogen from fields after infection. Here, we screened and identified two strains (Hz36, Trichoderma guizhouense; Hk37, Trichoderma koningiopsis) of Trichoderma from the gall of clubroot in rapeseed fields with biocontrol potential for clubroot. The fermentation broth of Hz36 could significantly inhibit the germination of resting spores of P. brassicae, and promote the seed germination and root growth of rapeseed. The biocontrol efficiency of Hz36 strain on clubroot for rapeseed and Arabidopsis thaliana was 44.29% and 52.18%, respectively. The qPCR results revealed that strain Hz36 treatment could significantly reduce the content of P. brassicae in root cells, and paraffin section analysis revealed that it could delay the development of P. brassicae. Strain Hk37 showed similar effects to strain Hz36, whose biocontrol efficiency of clubroot could reach 57.30% in rapeseed and 68.01% in A. thaliana. These results indicate that strains Hz36 and Hk37 have the potential for the biocontrol of clubroot.

Ethylene Plays a Dual Role during Infection by Plasmodiophora brassicae of Arabidopsis thaliana

Plasmodiophora brassicae infection leads to hypertrophy of host roots and subsequent formation of galls, causing huge economic losses to agricultural producers of Cruciferae plants. Ethylene (ET) has been reported to play a vital role against necrotrophic pathogens in the classic immunity system. More clues suggested that the defense to pathogens in roots may be different from the acrial. The ET pathway may play a positive role in the infection of P. brassicae, as shown by recent transcriptome profiling. However, the molecular basis of ET remains poorly understood. In this study, we investigated the potential role of ethylene against P. brassicae infection in an ein3/eil1 double-mutant of Arabidopsis thaliana (A. thaliana). After infection, ein3/eil1 (Disease Index/DI: 93) showed more susceptibility compared with wild type (DI: 75). Then, we inoculated A. thaliana Columbia-0 (Col-0) with P. brassicae by 1-aminocyclopropane-1-carboxylic acid (ACC) and pyrazinamide (PZA), respectively. It was found that the symptoms of infected roots with ACC were more serious than those with PZA at 20 dpi (day post infection). However, the DI were almost the same in different treatments at 30 dpi. WRKY75 can be directly regulated by ET and was upregulated at 7 dpi with ACC, as shown by qRT-PCR. The wrky75-c mutant of A. thaliana (DI: 93.75) was more susceptible than the wild type in Arabidopsis. Thus, our work reveals the dual roles of ET in infection of P. brassicae and provides evidence of ET in root defense against pathogens.

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.

Root Transcriptome and Metabolome Profiling Reveal Key Phytohormone-Related Genes and Pathways Involved Clubroot Resistance in Brassica rapa L

Plasmodiophora brassicae, an obligate biotrophic pathogen-causing clubroot disease, can seriously affect Brassica crops worldwide, especially Chinese cabbage. Understanding the transcriptome and metabolome profiling changes during the infection of P. brassicae will provide key insights in understanding the defense mechanism in Brassica crops. In this study, we estimated the phytohormones using targeted metabolome assays and transcriptomic changes using RNA sequencing (RNA-seq) in the roots of resistant (BrT24) and susceptible (Y510-9) plants at 0, 3, 9, and 20 days after inoculation (DAI) with P. brassicae. Differentially expressed genes (DEGs) in resistant vs. susceptible lines across different time points were identified. The weighted gene co-expression network analysis of the DEGs revealed six pathways including "Plant-pathogen interaction" and "Plant hormone signal transduction" and 15 hub genes including pathogenic type III effector avirulence factor gene (RIN4) and auxin-responsive protein (IAA16) to be involved in plants immune response. Inhibition of Indoleacetic acid, cytokinin, jasmonate acid, and salicylic acid contents and changes in related gene expression in R-line may play important roles in regulation of clubroot resistance (CR). Based on the combined metabolome profiling and hormone-related transcriptomic responses, we propose a general model of hormone-mediated defense mechanism. This study definitely enhances our current understanding and paves the way for improving CR in Brassica rapa.

Exogenous inoculation of endophytic bacterium Bacillus cereus suppresses clubroot (Plasmodiophora brassicae) occurrence in pak choi (Brassica campestris sp. chinensis L.)

The presence of Bacillus cereus plays a key role in clubroot suppression and improves plant biomass in pak choi. B. cereus is reported for the first time as a novel biocontrol agent against clubroot. Plasmodiophora brassicae Woronin causes a devastating infectious disease known as clubroot that is damaging to cruciferous vegetables. This study aimed to isolate beneficial bacteria from the rhizosphere soil of pak choi (Brassica campestris sp. chinensis) and to evaluate the ability of the isolate to reduce the severity of clubroot. Strains obtained from the rhizosphere of symptomless pak choi were first selected on the basis of their germination inhibition rate and effects on the viability of P. brassicae resting spores. Eight bacterial isolates had inhibitory effects against the resting spores of clubroot causing pathogen. However, MZ-12 showed the highest inhibitory effect at 73.4%. Inoculation with MZ-12 enhanced the plant biomass relative to plants grown without MZ-12 as well as P. brassicae infected plants. Furthermore, enhanced antioxidant enzymatic activities were observed in clubroot-infected plants during bacterial association. Co-inoculation of the plant with both P. brassicae and MZ-12 resulted in a 64% reduction of gall formation in comparison to plants inoculated with P. brassicae only. Three applications of MZ-12 to plants infected with P. brassicae at 7, 14 and 21 days after seeding (DAS) were more effective than one application and repressed root hair infection. According to 16S rDNA sequence analysis, strain MZ-12 was identified as had a 100% sequence similarity with type strain Bacillus cereus. The findings of the present study will facilitate further investigation into biological mechanisms of cruciferous clubroot control.

Comparing the Infection Biology of Plasmodiophora brassicae in Clubroot Susceptible and Resistant Hosts and Non-hosts

The potential infection biology of Plasmodiophora brassicae in resistant hosts and non-hosts is still not completely understood. Clubroot resistance assay on European clubroot differentials (ECD) set revealed that ECD10 (Brassica napus) and ECD4 (Brassica rapa) show a complete resistance to the tested P. brassicae isolate in contrast to highly susceptible hosts Westar (B. napus) and ECD5 (B. rapa). Previously, we used fluorescent probe-based confocal microscopy (FCM) to refine the life cycle of P. brassicae and indicate the important time points during its infection in Arabidopsis. Here, we used FCM to systematically investigate the infection of P. brassicae in two resistant host species ECD10 and ECD4 and two non-host crops wheat and barley at each indicated time points, compared with two susceptible hosts Westar and ECD5. We found that P. brassicae can initiate the primary infection phase and produce uninucleate primary plasmodia in both resistant hosts and non-hosts just like susceptible hosts at 2 days post-inoculation (dpi). Importantly, P. brassicae can develop into zoosporangia and secondary zoospores and release the secondary zoospores from the zoosporangia in resistant hosts at 7 dpi, comparable to susceptible hosts. However, during the secondary infection phase, no secondary plasmodium was detected in the cortical cells of both resistant hosts in contrast to massive secondary plasmodia present in the cortex tissue of two susceptible hosts leading to root swelling at 15 dpi. In both non-host crops, only uninucleate primary plasmodia were observed throughout roots at 7 and 15 dpi. Quantitative PCR based on DNA revealed that the biomass of P. brassicae has no significant increase from 2 dpi in non-host plants and from 7 dpi in resistant host plants, compared to the huge biomass increase in susceptible host plants from 2 to 25 dpi. Our study reveals that the primary infection phase in the root epidermis and the secondary infection phase in the cortex tissue are, respectively, blocked in non-hosts and resistant hosts, contributing to understanding of cellular and molecular mechanisms underlying clubroot non-host and host resistance.

Response of Brassica napus to Plasmodiophora brassicae Involves Salicylic Acid-Mediated Immunity: An RNA-Seq-Based Study

Clubroot, caused by the obligate parasite Plasmodiophora brassicae, is an important disease of the Brassicaceae and poses a significant threat to the $26.7 billion canola/oilseed rape (Brassica napus) industry in western Canada. While clubroot is managed most effectively by planting resistant host varieties, new pathotypes of P. brassicae have emerged recently that can overcome this resistance. Whole genome analyses provide both a toolbox and a systemic view of molecular mechanisms in host-pathogen interactions, which can be used to design new breeding strategies to increase P. brassicae resistance. We used RNA-seq to evaluate differential gene expression at 7, 14 and 21 days after inoculation (dai) of two B. napus genotypes with differential responses to P. brassicae pathotype 5X. Gall development was evident at 14 dai in the susceptible genotype (the oilseed rape 'Brutor'), while gall development in the resistant genotype (the rutabaga (B. napus) 'Laurentian') was limited and not visible until 21 dai. Immune responses were better sustained through the time-course in 'Laurentian', and numerous genes from immune-related functional categories were associated with salicylic acid (SA)-mediated responses. Jasmonic acid (JA)-mediated responses seemed to be mostly inhibited, especially in the resistant genotype. The upregulation of standard defense-related proteins, like chitinases and thaumatins, was evident in 'Laurentian'. The enrichment, in both host genotypes, of functional categories for syncytium formation and response to nematodes indicated that cell enlargement during P. brassicae infection, and the metabolic processes therein, share similarities with the response to infection by nematodes that produce similar anatomical symptoms. An analysis of shared genes between the two genotypes at different time-points, confirmed that the nematode-like responses occurred earlier for 'Brutor', along with cell metabolism and growth changes. Additionally, the susceptible cultivar turned off defense mechanisms earlier than 'Laurentian'. Collectively, this study showed the importance of SA in triggering immune responses and suggested some key resistance and susceptibility factors that can be used in future studies for resistance breeding through gene-editing approaches.

Prospects of Gene Knockouts in the Functional Study of MAMP-Triggered Immunity: A Review

Plants depend on both preformed and inducible defence responses to defend themselves against biotic stresses stemming from pathogen attacks. In this regard, plants perceive pathogenic threats from the environment through pattern recognition receptors (PRRs) that recognise microbe-associated molecular patterns (MAMPs), and so induce plant defence responses against invading pathogens. Close to thirty PRR proteins have been identified in plants, however, the molecular mechanisms underlying MAMP perception by these receptors/receptor complexes are not fully understood. As such, knockout (KO) of genes that code for PRRs and co-receptors/defence-associated proteins is a valuable tool to study plant immunity. The loss of gene activity often causes changes in the phenotype of the model plant, allowing in vivo studies of gene function and associated biological mechanisms. Here, we review the functions of selected PRRs, brassinosteroid insensitive 1 (BRI1) associated receptor kinase 1 (BAK1) and other associated defence proteins that have been identified in plants, and also outline KO lines generated by T-DNA insertional mutagenesis as well as the effect on MAMP perception—and triggered immunity (MTI). In addition, we further review the role of membrane raft domains in flg22-induced MTI in Arabidopsis, due to the vital role in the activation of several proteins that are part of the membrane raft domain theory in this regard.

Transcriptomic response in symptomless roots of clubroot infected kohlrabi (Brassica oleracea var. gongylodes) mirrors resistant plants

BACKGROUND

Clubroot disease caused by Plasmodiophora brassicae (Phytomyxea, Rhizaria) is one of the economically most important diseases of Brassica crops. The formation of hypertrophied roots accompanied by altered metabolism and hormone homeostasis is typical for infected plants. Not all roots of infected plants show the same phenotypic changes. While some roots remain uninfected, others develop galls of diverse size. The aim of this study was to analyse and compare the intra-plant heterogeneity of P. brassicae root galls and symptomless roots of the same host plants (Brassica oleracea var. gongylodes) collected from a commercial field in Austria using transcriptome analyses.

RESULTS

Transcriptomes were markedly different between symptomless roots and gall tissue. Symptomless roots showed transcriptomic traits previously described for resistant plants. Genes involved in host cell wall synthesis and reinforcement were up-regulated in symptomless roots indicating elevated tolerance against P. brassicae. By contrast, genes involved in cell wall degradation and modification processes like expansion were up-regulated in root galls. Hormone metabolism differed between symptomless roots and galls. Brassinosteroid-synthesis was down-regulated in root galls, whereas jasmonic acid synthesis was down-regulated in symptomless roots. Cytokinin metabolism and signalling were up-regulated in symptomless roots with the exception of one CKX6 homolog, which was strongly down-regulated. Salicylic acid (SA) mediated defence response was up-regulated in symptomless roots, compared with root gall tissue. This is probably caused by a secreted benzoic acid/salicylic acid methyl transferase from the pathogen (PbBSMT), which was one of the highest expressed pathogen genes in gall tissue. The PbBSMT derived Methyl-SA potentially leads to increased pathogen tolerance in uninfected roots.

CONCLUSIONS

Infected and uninfected roots of clubroot infected plants showed transcriptomic differences similar to those previously described between clubroot resistant and susceptible hosts. The here described intra-plant heterogeneity suggests, that for a better understanding of clubroot disease targeted, spatial analyses of clubroot infected plants will be vital in understanding this economically important disease.

Proto-oncogenes in a eukaryotic unicellular organism play essential roles in plasmodial growth in host cells

BACKGROUND

The eukaryotic unicellular protist Plasmodiophora brassicae is an endocellular parasite of cruciferous plants. In host cortical cells, this protist develops a unicellular structure that is termed the plasmodium. The plasmodium is actually a multinucleated cell, which subsequently splits and forms resting spores. The mechanism for the growth of this endocellular parasite in host cell is unclear.

RESULTS

Here, combining de novo genome sequence and transcriptome analysis of strain ZJ-1, we identified top five significant enriched KEGG pathways of differentially expressed genes (DEGs), namely translation, cell growth and death, cell communication, cell motility and cancers. We detected 171 proto-oncogenes from the genome of P. brassicae that were implicated in cancer-related pathways, of which 46 were differential expression genes. Three predicted proto-oncogenes (Pb-Raf1, Pb-Raf2, and Pb-MYB), which showed homology to the human proto-oncogenes Raf and MYB, were specifically activated during the plasmodial growth in host cortical cells, demonstrating their involvement in the multinucleate development stage of the unicellular protist organism. Gene networks involved in the tumorigenic-related signaling transduction pathways and the activation of 12 core genes were identified. Inhibition of phosphoinositol-3-kinase relieved the clubroot symptom and significantly suppressed the development process of plasmodia.

CONCLUSIONS

Proto-oncogene-related regulatory mechanisms play an important role in the plasmodial growth of P. brassicae.

MAPKK Inhibitor U0126 Inhibits Plasmodiophora brassicae Development

Mitogen-activated protein kinase (MAPK) cascades play a central role in cellular growth, proliferation, and survival. MAPK cascade genes have been extensively investigated in model plants, mammals, yeast, and fungi but are not characterized in Plasmodiophora brassicae, which causes clubroot disease in cruciferous plants. Here, we identified 7 PbMAPK, 3 PbMAPKK, and 9 PbMAPKKK genes in the P. brassicae genome. Transcriptional profiling analysis demonstrated that several MAPK, MAPK kinase (MAPKK), and MAPK kinase kinase (MAPKKK) genes were preferentially expressed in three different zoosporic stages. Based on yeast two-hybrid assays, PbMAKKK7 interacted with PbMAKK3 and PbMAKK3 interacted with PbMAK1/PbMAK3. The PbMAKKK7-PbMAKK3-PbMAK1/PbMAK3 cascade may be present in P. brassicae. U0126, a potent and specific inhibitor of MAPKK, could inhibit the germination of P. brassicae resting spores. U0126 was used to treat the resting spores of P. brassicae and coinoculate rapeseed, and was proven to significantly relieve the severity of clubroot symptoms in the host plant and delay the life cycle of P. brassicae. These results suggest that MAPK signaling pathways may play important roles in P. brassicae growth, development, and pathogenicity.

Defence signalling marker gene responses to hormonal elicitation differ between roots and shoots

Phytohormones such as jasmonic acid (JA), salicylic acid (SA), ethylene (ET) and abscisic acid (ABA) play a key role in regulation of plant immune responses to different attackers. Extensive research over recent years has led to the identification of molecular markers for specific hormonal-regulated defence pathways. However, most of our current knowledge on the regulation of plant immunity derives from studies focused on above-ground organs, mainly on the model plant Arabidopsis thaliana. Therefore, it is unclear whether the paradigms based on experiments on above-ground organs are entirely transferable to roots. Here, we used the non-model plant Brassica rapa to study the regulation dynamics of hormonal-related marker genes in both roots and shoots. These markers were identified in Arabidopsis shoots after elicitation of the JA-, SA-, ET- or ABA-signalling pathways, and are commonly used to study induced responses. We assessed whether the regulation of those genes by hormonal elicitation differs between roots and shoots. To discern whether the differences in marker gene expression between roots and shoots are related to differences in hormone production or to differential responsiveness, we also measured actual hormone content in the treated tissue after elicitation. Our results show that some of the widely used markers did not show specific responsiveness to single hormone applications in B. rapa. We further found that hormonal elicitation led to different response patterns of the molecular markers in shoots and roots. Our results suggest that the regulation of some hormonal-related marker genes in B. rapa is organ specific and differs from the Arabidopsis-derived paradigms.

Receptor-Like Cytoplasmic Kinases: Central Players in Plant Receptor Kinase-Mediated Signaling

Receptor kinases (RKs) are of paramount importance in transmembrane signaling that governs plant reproduction, growth, development, and adaptation to diverse environmental conditions. Receptor-like cytoplasmic kinases (RLCKs), which lack extracellular ligand-binding domains, have emerged as a major class of signaling proteins that regulate plant cellular activities in response to biotic/abiotic stresses and endogenous extracellular signaling molecules. By associating with immune RKs, RLCKs regulate multiple downstream signaling nodes to orchestrate a complex array of defense responses against microbial pathogens. RLCKs also associate with RKs that perceive brassinosteroids and signaling peptides to coordinate growth, pollen tube guidance, embryonic and stomatal patterning, floral organ abscission, and abiotic stress responses. The activity and stability of RLCKs are dynamically regulated not only by RKs but also by other RLCK-associated proteins. Analyses of RLCK-associated components and substrates have suggested phosphorylation relays as a major mechanism underlying RK-mediated signaling.

Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation

In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae

Clubroot caused by Plasmodiophora brassicae, is a severe disease of cruciferous crops that causes large hypertrophic galls in the roots. The plant microbiome is important for growth promotion and disease suppression. In this study, using 16S rRNA and internal transcribed spacer (ITS) sequencing techniques, we compared the endosphere microbiome of symptomatic and asymptomatic B. napus roots infected with P. brassicae collected from the same natural clubroot field. The results showed that the microbial population and its relative abundance in the asymptomatic roots was far higher than that in the symptomatic roots, and that many microorganisms in asymptomatic roots have biological control and plant growth promotion functions that may be related to clubroot symptoms. These results suggest the importance of the endosphere microbiome in clubroot disease and provide potential bio-control resources for its prevention.

Transcriptome Analysis of Arabidopsis thaliana in Response to Plasmodiophora brassicae during Early Infection

Clubroot disease is a serious threat to cruciferous plants worldwide, especially to oilseed rape. However, knowledge on pathogenic molecular mechanisms and host interaction is limited. We presume that the recognition between Arabidopsis thaliana and Plasmodiophora brassicae occurs at the early stage of infection and within a relatively short period. In this study, we demonstrated changes on gene expression and pathways in A. thaliana during early infection with P. brassicae using transcriptome analysis. We identified 1,903 and 1,359 DEGs at 24 and 48 h post-inoculation (hpi), respectively. Flavonoids and the lignin synthesis pathways were enhanced, glucosinolates, terpenoids, and proanthocyanidins accumulated and many hormonal- and receptor-kinase related genes were expressed, caused by P. brassicae infection during its early phase. Therefore, the early interaction between A. thaliana and P. brassicae plays an important role in the entire infection process. The results provide a new contribution to a better understanding of the interaction between host plants and P. brassicae, as well as the development of future measures for the prevention of clubroot.

Integrated omics study of lipid droplets from Plasmodiophora brassicae

Plasmodiophora brassicae causes clubroot disease in cruciferous. In this report, lipid droplets were observed in the resting spores of P. brassicae. 295 lipid droplet-associated proteins were identified and categorized into nine groups. Transcriptome analysis of these proteins during three different zoosporic stages revealed differences in gene expression pattern. GO enrichment analysis revealed that these proteins associated with lipid droplets were mainly linked to biosynthesis and metabolism. GC-MS analysis revealed that lipid droplets contain seven types of free fatty acids: saturated fatty acids C16:0 and C18:0, and unsaturated fatty acids C18:1Δ9, C18:1Δ11, C18:2, C20:4 and C20:5. P. brassicae accumulated a large amount of triacylglycerols (TAGs). We systematically analyzed the putative proteins involved in TAG biosynthesis and its metabolic pathway. KEGG pathway analysis defined 3390 genes, including 167 genes involved in lipid metabolism. Transcriptome analysis revealed that 162 candidate enzymes involved in lipid metabolism were differential expressed. Our omics studies are the first to investigate the lipid droplet organelles in P. brassicae, providing a reference resource to study protist lipid droplets.