Plant innate immunity – direct and indirect recognition of general and specific pathogen-associated molecules

ATR2C ala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition

Arabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. To reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2 and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. ATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. Two additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. We compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all four genes are present in all ATR2Cala2-recognizing accessions.

Two structurally different oomycete lipophilic microbe-associated molecular patterns induce distinctive plant immune responses

Plants recognize a variety of external signals and induce appropriate mechanisms to increase their tolerance to biotic and abiotic stresses. Precise recognition of attacking pathogens and induction of effective resistance mechanisms are critical functions for plant survival. Some molecular patterns unique to a certain group of microbes, microbe-associated molecular patterns (MAMPs), are sensed by plant cells as nonself molecules via pattern recognition receptors. While MAMPs of bacterial and fungal origin have been identified, reports on oomycete MAMPs are relatively limited. This study aimed to identify MAMPs from an oomycete pathogen Phytophthora infestans, the causal agent of potato late blight. Using reactive oxygen species (ROS) production and phytoalexin production in potato (Solanum tuberosum) as markers, two structurally different groups of elicitors, namely ceramides and diacylglycerols, were identified. P. infestans ceramides (Pi-Cer A, B, and D) induced ROS production, while diacylglycerol (Pi-DAG A and B), containing eicosapentaenoic acid (EPA) as a substructure, induced phytoalexins production in potato. The molecular patterns in Pi-Cers and Pi-DAGs essential for defense induction were identified as 9-methyl-4,8-sphingadienine (9Me-Spd) and 5,8,11,14-tetraene-type fatty acid (5,8,11,14-TEFA), respectively. These structures are not found in plants, but in oomycetes and fungi, indicating that they are microbe molecular patterns recognized by plants. When Arabidopsis (Arabidopsis thaliana) was treated with Pi-Cer D and EPA, partially overlapping but different sets of genes were induced. Furthermore, expression of some genes is upregulated only after the simultaneous treatment with Pi-Cer D and EPA, indicating that plants combine the signals from simultaneously recognized MAMPs to adapt their defense response to pathogens.

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.

Pathogen-induced m6A dynamics affect plant immunity

Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term responses to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses.

Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt in Gossypium barbadense L

Duplication events occur very frequently during plant evolution. The genes in the duplicated pathway or network can evolve new functions through neofunctionalization and subfunctionalization. Flavonoids are secondary metabolites involved in plant development and defense. Our previous transcriptomic analysis of F6 recombinant inbred lines (RILs) and the parent lines after Fusarium oxysporum f. sp. vasinfectum (Fov) infection showed that CHI genes have important functions in cotton. However, there are few reports on the possible neofunctionalization differences of CHI family paralogous genes involved in Fusarium wilt resistance in cotton. In this study, the resistance to Fusarium wilt, expression of metabolic pathway-related genes, metabolite content, endogenous hormone content, reactive oxygen species (ROS) content and subcellular localization of four paralogous CHI family genes in cotton were investigated. The results show that the four paralogous CHI family genes may play a synergistic role in Fusarium wilt resistance. These results revealed a genetic channelization mechanism that can regulate the metabolic flux homeostasis of flavonoids under the mediation of endogenous salicylic acid (SA) and methyl jasmonate (MeJA) via the four paralogous CHI genes, thereby achieving disease resistance. Our study provides a theoretical basis for studying the evolutionary patterns of homologous plant genes and using homologous genes for molecular breeding.

Comparative Transcriptomic and Metabolomic Analyses of Differences in Trunk Spiral Grain in Pinus yunnanensis

Having a spiral grain is considered to be one of the most important wood properties influencing wood quality. Here, transcriptome profiles and metabolome data were analyzed in the straight grain and twist grain of Pinus yunnanensis. A total of 6644 differential expression genes were found between the straight type and the twist type. A total of 126 differentially accumulated metabolites were detected. There were 24 common differential pathways identified from the transcriptome and metabolome, and these pathways were mainly annotated in ABC transporters, arginine and proline metabolism, flavonoid biosynthesis, isoquinoline alkaloid biosynthesis, linoleic acid metabolism, phenylpropanoid, tryptophan metabolism, etc. A weighted gene coexpression network analysis showed that the lightblue4 module was significantly correlated with 2'-deoxyuridine and that transcription factors (basic leucine zipper (bZIP), homeodomain leucine zipper (HD-ZIP), basic helix-loop-helix (bHLH), p-coumarate 3-hydroxylase (C3H), and N-acetylcysteine (NAC)) play important roles in regulating 2'-deoxyuridine, which may be involved in the formation of spiral grains. Meanwhile, the signal transduction of hormones may be related to spiral grain, as previously reported. ARF7 and MKK4_5, as indoleacetic acid (IAA)- and ethylene (ET)-related receptors, may explain the contribution of plant hormones in spiral grain. This study provided useful information on spiral grain in P. yunnanensis by transcriptome and metabolome analyses and could lay the foundation for future molecular breeding.

Induction of plant disease resistance by mixed oligosaccharide elicitors prepared from plant cell wall and crustacean shells

Basal plant immune responses are activated by the recognition of conserved microbe-associated molecular patterns (MAMPs), or breakdown molecules released from the plants after damage by pathogen penetration, so-called damage-associated molecular patterns (DAMPs). While chitin-oligosaccharide (CHOS), a primary component of fungal cell walls, is most known as MAMP, plant cell wall-derived oligosaccharides, cello-oligosaccharides (COS) from cellulose, and xylo-oligosaccharide (XOS) from hemicellulose are representative DAMPs. In this study, elicitor activities of COS prepared from cotton linters, XOS prepared from corn cobs, and chitin-oligosaccharide (CHOS) from crustacean shells were comparatively investigated. In Arabidopsis, COS, XOS, or CHOS treatment triggered typical defense responses such as reactive oxygen species (ROS) production, phosphorylation of MAP kinases, callose deposition, and activation of the defense-related transcription factor WRKY33 promoter. When COS, XOS, and CHOS were used at concentrations with similar activity in inducing ROS production and callose depositions, CHOS was particularly potent in activating the MAPK kinases and WRKY33 promoters. Among the COS and XOS with different degrees of polymerization, cellotriose and xylotetraose showed the highest activity for the activation of WRKY33 promoter. Gene ontology enrichment analysis of RNAseq data revealed that simultaneous treatment of COS, XOS, and CHOS (oligo-mix) effectively activates plant disease resistance. In practice, treatment with the oligo-mix enhanced the resistance of tomato to powdery mildew, but plant growth was not inhibited but rather tended to be promoted, providing evidence that treatment with the oligo-mix has beneficial effects on improving disease resistance in plants, making them a promising class of compounds for practical application.

Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass

Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant-pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass.

Extracción y análisis de metabolitos fenólicos apoplásticos en raíz y tallo de clavel (Dianthus caryophyllus L)

En el presente estudio se describe el acondicionamiento de algunos parámetros con fines de obtención eficiente de extractos apoplásticos enriquecidos en compuestos polares, principalmente fenólicos. Este flujo de trabajo descrito, incluso, puede ser aplicado a diferentes especies vegetales para ser empleado en el análisis particular o global de metabolitos en este espacio extracelular periférico. Para ello, usando raíces y tallos de clavel (Dianthus cariophyllus L), se evaluaron diferentes soluciones de infiltración para la extracción de los metabolitos apoplásticos. El mejor resultado se logró con la disolución amortiguadora NaH2PO4-Na2HPO4 0,1 M pH 6,5/NaCl 50 mM, porque se obtiene la mayor cantidad de metabolitos fenólicos apoplásticos, con la menor contaminación de compuestos intracelulares. Los metabolitos se separaron mediante HPLC-DAD-ESI-MS, obteniendo perfiles cromatográficos con parámetros de calidad razonables basados en resolución, selectividad y número de platos teóricos. Con estas condiciones, fue posible identificar ocho compuestos diferenciales (una flavona y siete flavonoles), cuyas estructuras básicas comprendían flavonoides del tipo (iso)pratol, kaempférido, (dihidro)kaempferol, quercetina y miricetina, según el órgano de prueba y la variedad. Los flavonoides identificados están relacionados con metabolitos de tipo fitoanticipina en el clavel, como hidroxi-metoxiflavona, di-o-benzoilquercetina y kaempférido disaliciloilrhamnósido, abundantemente presentes en la variedad resistente. Las condiciones descritas en este trabajo son fundamentales para profundizar en el papel de los metabolitos fenólicos apoplásticos relacionados con los mecanismos de defensa de esta planta ornamental.  

Triticale Improvement: Mining of Genes Related to Yellow Rust Resistance in Triticale Based on Transcriptome Sequencing

Yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (Pst) is a major destructive fungal disease of small grain cereals, leading to large yield losses. The breeding of resistant varieties is an effective, sustainable way to control yellow rust. Elucidation of resistance mechanisms against yellow rust and identification of candidate genes associated with rust resistance are thus crucial. In this study, seedlings of two Triticosecale Wittmack cultivars, highly resistant Gannong No. 2 and susceptible Shida No. 1, were inoculated with Pst race CYR34. Transcriptome sequencing (RNA-seq) was then used to investigate their transcriptional responses against pathogen infection before and after the appearance of symptoms-10 and 20 days after inoculation, respectively. According to the RNA-seq data, the number of upregulated and downregulated differentially expressed genes (DEGs) in the resistant cultivar was greater than in the susceptible cultivar. A total of 2,560 DEGs commonly expressed in the two cultivars on two sampling dates were subjected to pathway analysis, which revealed that most DEGs were closely associated with defense and metabolic activities. Transcription factor enrichment analysis indicated that the expressions of NAC, WRKY, and FAR1 families were also significantly changed. Further in-depth analysis of resistance genes revealed that almost all serine/threonine-protein kinases were upregulated in the resistant cultivar. Other genes related to disease resistance, such as those encoding disease-resistance- and pathogenesis-related proteins were differentially regulated in the two cultivars. Our findings can serve as a resource for gene discovery and facilitate elucidation of the complex defense mechanisms involved in triticale resistance to Pst.

Gene expression analysis of resistant and susceptible rice cultivars to sheath blight after inoculation with Rhizoctonia solani

BACKGROUND

Rice sheath blight, caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris), is one of the most severe diseases in rice (Oryza sativa L.) worldwide. Studies on resistance genes and resistance mechanisms of rice sheath blight have mainly focused on indica rice. Rice sheath blight is a growing threat to rice production with the increasing planting area of japonica rice in Northeast China, and it is therefore essential to explore the mechanism of sheath blight resistance in this rice subspecies.

RESULTS

In this study, RNA-seq technology was used to analyse the gene expression changes of leaf sheath at 12, 24, 36, 48, and 72 h after inoculation of the resistant cultivar 'Shennong 9819' and susceptible cultivar 'Koshihikari' with R. solani. In the early stage of R. solani infection of rice leaf sheaths, the number of differentially expressed genes (DEGs) in the inoculated leaf sheaths of resistant and susceptible cultivars showed different regularity. After inoculation, the number of DEGs in the resistant cultivar fluctuated, while the number of DEGs in the susceptible cultivar increased first and then decreased. In addition, the number of DEGs in the susceptible cultivar was always higher than that in the resistant cultivar. After inoculation with R. solani, the overall transcriptome changes corresponding to multiple biological processes, molecular functions, and cell components were observed in both resistant and susceptible cultivars. These included metabolic process, stimulus response, biological regulation, catalytic activity, binding and membrane, and they were differentially regulated. The phenylalanine metabolic pathway; tropane, piperidine, and pyridine alkaloid biosynthesis pathways; and plant hormone signal transduction were significantly enriched in the early stage of inoculation of the resistant cultivar Shennong 9819, but not in the susceptible cultivar Koshihikari. This indicates that the response of the resistant cultivar Shennong 9819 to pathogen stress was faster than that of the susceptible cultivar. The expression of plant defense response marker PR1b gene, transcription factor OsWRKY30 and OsPAL1 and OsPAL6 genes that induce plant resistance were upregulated in the resistant cultivar. These data suggest that in the early stage of rice infection by R. solani, there is a pathogen-induced defence system in resistant rice cultivars, involving the expression of PR genes, key transcription factors, PAL genes, and the enrichment of defence-related pathways.

CONCLUSION

The transcriptome data revealed the molecular and biochemical differences between resistant and susceptible cultivars of rice after inoculation with R. solani, indicating that resistant cultivars have an immune response mechanism in the early stage of pathogen infection. Disease resistance is related to the overexpression of PR genes, key transcriptome factors, and PAL genes, which are potential targets for crop improvement.

Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction

BACKGROUND

Soybean mosaic virus (SMV) is one of the most devastating pathogens of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) which are endogenously produced by the plant host as part of a general gene expression regulatory mechanisms, but also play roles in regulating plant defense against pathogens. However, miRNA-mediated plant response to SMV in soybean is not as well documented.

RESULT

In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1 × Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs profile changes during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. The expression patterns of several miRNAs were validated by quantitative real-time PCR. We also validated the miRNA-target gene interaction by agrobacterium-mediated transient expression in Nicotiana benthamiana.

CONCLUSION

We have identified a large number of miRNAs and their target genes and also functional annotations. We found that multiple miRNAs were differentially expressed in the two lines and targeted a series of NBS-LRR resistance genes. It is worth mentioning that many of these genes exist in the previous fine-mapping interval of the resistance gene locus. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

Identification of the CesA Subfamily and Functional Analysis of GhMCesA35 in Gossypium Hirsutum L

The cellulose synthase genes control the biosynthesis of cellulose in plants. Nonetheless, the gene family members of CesA have not been identified in the newly assembled genome of Gossypiumhirsutum (AD1, HEBAU_NDM8). We identified 38 CesA genes in G. hirsutum (NDM8) and found that the protein sequence of GhMCesA35 is 100% identical to CelA1 in a previous study. It is already known that CelA1 is involved in cellulose biosynthesis in vitro. However, the function of this gene in vivo has not been validated. In this study, we verified the function of GhMCesA35 in vivo based on overexpressed Arabidopsis thaliana. In addition, we found that it interacted with GhCesA7 through the yeast two-hybrid assay. This study provides new insights for studying the biological functions of CesA genes in G. hirsutum, thereby improving cotton fiber quality and yield.

Specialized metabolites: Physiological and biochemical role in stress resistance, strategies to improve their accumulation, and new applications in crop breeding and management

Specialized plant metabolites (SPMs), traditionally referred to as 'secondary metabolites', are chemical compounds involved in a broad range of biological functions, including plant responses to abiotic and biotic stresses. Moreover, some of them have a role in end-product quality with potential health benefits in humans. For this reason, they became an important target of studies focusing on their mechanisms of action and use in crop breeding and management. In this review we summarize the specific role of SPMs in physiological processes and in plant resistance to abiotic and biotic stresses, and the different strategies to enhance their production/accumulation in plant tissues under stress, including genetic approaches (marker-assisted selection and biotechnological tools) and agronomic management (fertilizer applications, cultivation method and beneficial microorganisms). New crop management strategies based on the direct application of the most promising compounds in form of plant residuals or liquid formulations are also described.

The tomato Mediator subunit MED8 positively regulates plant response to Botrytis cinerea

The Mediator complex acts as a bridge between specific transcription factors and the RNA polymerase II transcriptional machinery and plays a central role in plant immunity. Biological induction of plant resistance against pathogens requires endogenous hormone jasmonic acid (JA) and involves profound transcriptional changes controlled by the key transcription factor MYC2. Arabidopsis thaliana Mediator subunit 25 (AtMED25) regulates JA-dependent defense response through interacting with MYC2. Here, we report that the tomato (Solanum lycopersicum, Sl) Mediator subunit 8 (SlMED8) is another essential component in JA-dependent defense response. The transcript levels of SlMED8 could not be affected by treatment with MeJA, SA, ABA, and mechanical wounding. Yeast two-hybrid assays showed that SlMED8 could interact with itself, SlMYC2, and SlMED25, respectively. In addition, ectopic overexpression of SlMED8 complemented the late flowering and pathogen hypersensitivity phenotypes of Arabidopsis med8 mutant. Overexpression of SlMED8 rendered transgenic plants higher tolerance to necrotrophic pathogen Botrytis cinerea. Meanwhile, SlMED8 antisense plants displayed compromised resistance to Botrytis cinerea. Consistent with this, differential expression levels of several JA-responsive genes were detected within the transgenic plants. Overall, our results identified an important control point in the regulation of the JA signaling pathway within the transcriptional machinery.

Signals in systemic acquired resistance of plants against microbial pathogens

After a local infection by the microbial pathogens, plants will produce strong resistance in distal tissues to cope with the subsequent biotic attacks. This type of the resistance in the whole plant is termed as systemic acquired resistance (SAR). The priming of SAR can confer the robust defense responses and the broad-spectrum disease resistances in plants. In general, SAR is activated by the signal substances generated at the local sites of infection, and these small signaling molecules can be rapidly transported to the systemic tissues through the phloem. In the last two decades, numerous endogenous metabolites were proved to be the potential elicitors of SAR, including methyl salicylate (MeSA), azelaic acid (AzA), glycerol-3-phosphate (G3P), free radicals (NO and ROS), pipecolic acid (Pip), N-hydroxy-pipecolic acid (NHP), dehydroabietinal (DA), monoterpenes (α-pinene and β-pinene) and NAD(P). In the meantime, the proteins associated with the transport of these signaling molecules were also identified, such as DIR1 (DEFECTIVE IN INDUCED RESISTANCE 1) and AZI1 (AZELAIC ACID INDUCED 1). This review summarizes the recent findings related to synthesis, transport and interaction of the different signal substances in SAR.

Tomato protein Rx4 mediates the hypersensitive response to Xanthomonas euvesicatoria pv. perforans race T3

Bacterial spot, which is caused by several Xanthomonas species, is an economically important disease in tomato (Solanum lycopersicum). Great efforts have been made for the identification of resistant sources and the genetic analysis of resistance. However, the development of resistant commercial varieties is slow due to the existence of multiple species of the pathogen and a poor understanding of the resistance mechanism in tomato. The current study revealed that the Rx4 gene encodes a nucleotide-binding leucine-rich repeat protein in the wild tomato species Solanum pimpinellifolium and specifically recognizes and confers a hypersensitive response (HR) to Xanthomonas euvesicatoria pv. perforans race T3 expressing the AvrXv3 avirulence protein. Complementation of the Rx4 gene in the susceptible tomato line Ohio 88119 using a transgenic approach resulted in HR, whereas knockout of the gene through CRISPR/Cas9 editing in resistant lines Hawaii 7981 and PI 128216 led to non-HR to race T3. Transcription of Rx4 was not induced by the presence of race T3. Furthermore, the Rx4 protein did not show physical interaction with AvrXv3 but interacted with SGT1-1 and RAR1. Virus-induced gene silencing of SGT1-1 and RAR1 in the resistant line PI128216 suppressed the HR to race T3. Taken together, our study confirms Rx4 is the gene conferring the HR to bacterial spot race T3 and reveals the potential roles of SGT1-1 and RAR1 as signals in the Rx4-mediated HR. This discovery represents a step forward in our understanding of the mechanism of resistance to bacterial spot in tomato and may have important implications for understanding plant-bacterial interactions.

A Rice NBS-ARC Gene Conferring Quantitative Resistance to Bacterial Blight Is Regulated by a Pathogen Effector-Inducible miRNA

The bacterium Xanthomonas oryzae pv. Oryzae (Xoo) causes blight in rice worldwide, resulting in significant crop loss. However, no gene underlying a quantitative trait locus (QTL) for resistance against Xoo has been cloned yet. Here, we report the map-based cloning of a QTL, in which the NBS8R gene confers quantitative resistance to Xoo. NBS8R encodes an NB-ARC protein, which is involved in pathogen/microbe-associated molecular pattern-triggered immunity and whose expression is regulated by non-TAL effector XopQ-inducible Osa-miR1876 through DNA methylation. Sequence analysis of NBS8R in wild rice species and rice cultivars suggests that the Osa-miR1876 binding sites in the 5' UTR of NBS8R are inserted by chance and have undergone variations with Osa-miR1876 throughout evolution. The interaction between NBS8R and XopQ-inducible Osa-miR1876 is partially in keeping with the zigzag model, revealing that quantitative genes may also follow this model to control the innate immune response or basal disease resistance, and may prove valuable in utilizing the existing landraces that harbor the NBS8R gene but with no Osa-miR1876 binding site in rice breeding for bacterial blight resistance.

Modulation of Plant Defense System in Response to Microbial Interactions

At different stages throughout their life cycle, plants often encounter several pathogenic microbes that challenge plant growth and development. The sophisticated innate plant immune system prevents the growth of harmful microbes via two interconnected defense strategies based on pathogen perception. These strategies involve microbe-associated molecular pattern-triggered immunity and microbial effector-triggered immunity. Both these immune responses induce several defense mechanisms for restricting pathogen attack to protect against pathogens and terminate their growth. Plants often develop immune memory after an exposure to pathogens, leading to systemic acquired resistance. Unlike that with harmful microbes, plants make friendly interactions with beneficial microbes for boosting their plant immune system. A spike in recent publications has further improved our understanding of the immune responses in plants as triggered by interactions with microbes. The present study reviews our current understanding of how plant–microbe interactions can activate the sophisticated plant immune system at the molecular level. We further discuss how plant-microbe interaction boost the immune system of plants by demonstrating the examples of Mycorrhizal and Rhizobial association and how these plant-microbe interactions can be exploited to engineer disease resistance and crop improvement.

A novel effector CfEC92 of Colletotrichum fructicola contributes to glomerella leaf spot virulence by suppressing plant defences at the early infection phase

The ascomycete fungus Colletotrichum fructicola causes diseases on a broad range of plant species. On susceptible cultivars of apple, it induces severe early defoliation and fruit spots, named glomerella leaf spot (GLS), but the mechanisms of pathogenicity have remained elusive. Phytopathogens exhibit small secreted effectors to advance host infection by manipulating host immune reactions. We report the identification and characterization of CfEC92, an effector required for C. fructicola virulence. CfEC92 is a Colletotrichum-specific small secreted protein that suppresses BAX-triggered cell death in Nicotiana benthamiana. Accumulation of the gene transcript was barely detectable in conidia or vegetative hyphae, but was highly up-regulated in appressoria formed during early apple leaf infection. Gene deletion mutants were not affected in vegetative growth, appressorium formation, or appressorium-mediated cellophane penetration. However, the mutants were significantly reduced in virulence toward apple leaves and fruits. Microscopic examination indicated that infection by the deletion mutants elicited elevated deposition of papillae at the penetration sites, and formation of infection vesicles and primary hyphae was retarded. Signal peptide activity, subcellular localization, and cell death-suppressive activity (without signal peptide) assays suggest that CfEC92 could be secreted and perform virulence functions inside plant cells. RNA sequencing and quantitative reverse transcription PCR results confirmed that the deletion mutants triggered elevated host defence reactions. Our results strongly support the interpretation that CfEC92 contributes to C. fructicola virulence as a plant immunity suppressor at the early infection phase.

OsNPR3.3-dependent salicylic acid signaling is involved in recessive gene xa5-mediated immunity to rice bacterial blight

Salicylic acid (SA) is a key natural component that mediates local and systemic resistance to pathogens in many dicotyledonous species. However, its function is controversial in disease resistance in rice plants. Here, we show that the SA signaling is involved in both pathogen-associated-molecular-patterns triggered immunity (PTI) and effector triggered immunity (ETI) to Xanthomonas oryzae pv. Oryzae (Xoo) mediated by the recessive gene xa5, in which OsNPR3.3 plays an important role through interacting with TGAL11. Rice plants containing homozygous xa5 gene respond positively to exogenous SA, and their endogenous SA levels are also especially induced upon infection by the Xoo strain, PXO86. Depletion of endogenous SA can significantly attenuate plant resistance to PXO86, even to 86∆HrpXG (mutant PXO86 with a damaged type III secretion system). These results indicated that SA plays an important role in disease resistance in rice plants, which can be clouded by high levels of endogenous SA and the use of particular rice varieties.

Transcriptomic Insights into Innate Immunity Responding to Red Rot Disease in Red Alga Pyropia yezoensis

Pyropia yezoensis, one of the most economically important marine algae, suffers from the biotic stress of the oomycete necrotrophic pathogen Pythium porphyrae. However, little is known about the molecular defensive mechanisms employed by Pyr. yezoensis during the infection process. In the present study, we defined three stages of red rot disease based on histopathological features and photosynthetic physiology. Transcriptomic analysis was carried out at different stages of infection to identify the genes related to the innate immune system in Pyr. yezoensis. In total, 2139 up-regulated genes and 1672 down-regulated genes were identified from all the infected groups. Pathogen receptor genes, including three lectin genes (pattern recognition receptors (PRRs)) and five genes encoding typical plant R protein domains (leucine rich repeat (LRR), nucleotide binding site (NBS), or Toll/interleukin-1 receptor (TIR)), were found to be up-regulated after infection. Several defense mechanisms that were typically regarded as PAMP-triggered immunity (PTI) in plants were induced during the infection. These included defensive and protective enzymes, heat shock proteins, secondary metabolites, cellulase, and protease inhibitors. As a part of the effector-triggered immunity (ETI), the expression of genes related to the ubiquitin-proteasome system (UPS) and hypersensitive cell death response (HR) increased significantly during the infection. The current study suggests that, similar to plants, Pyr. yezoensis possesses a conserved innate immune system that counters the invasion of necrotrophic pathogen Pyt. porphyrae. However, the innate immunity genes of Pyr. yezoensis appear to be more ancient in origin compared to those in higher plants.

Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis

Background

Grapevine is an important fruit crop grown worldwide, and its cultivars are mostly derived from the European species Vitis vinifera, which has genes for high fruit quality and adaptation to a wide variety of climatic conditions. Disease resistance varies substantially across grapevine species; however, the molecular mechanisms underlying such variation remain uncharacterized.

Results

The anatomical structure and disease symptoms of grapevine leaves were analyzed for two grapevine species, and the critical period of resistance of grapevine to pathogenic bacteria was determined to be 12 h post inoculation (hpi). Differentially expressed genes (DEGs) were identified from transcriptome analysis of leaf samples obtained at 12 and 36 hpi, and the transcripts in four pathways (cell wall genes, LRR receptor-like genes, WRKY genes, and pathogenesis-related (PR) genes) were classified into four co-expression groups by using weighted correlation network analysis (WGCNA). The gene VdWRKY53, showing the highest transcript level, was introduced into Arabidopsis plants by using a vector containing the CaMV35S promoter. These procedures allowed identifying the key genes contributing to differences in disease resistance between a strongly resistant accession of a wild grapevine species Vitis davidii (VID) and a susceptible cultivar of V. vinifera, ‘Manicure Finger’ (VIV). Vitis davidii, but not VIV, showed a typical hypersensitive response after infection with a fungal pathogen (Coniella diplodiella) causing white rot disease. Further, 20 defense-related genes were identified, and their differential expression between the two grapevine species was confirmed using quantitative real-time PCR analysis. VdWRKY53, showing the highest transcript level, was selected for functional analysis and therefore over-expressed in Arabidopsis under the control of the CaMV35S promoter. The transgenic plants showed enhanced resistance to C. diplodiella and to two other pathogens, Pseudomonas syringae pv. tomato DC3000 and Golovinomyces cichoracearum.

Conclusion

The consistency of the results in VID and transgenic Arabidopsis indicated that VdWRKY53 might be involved in the activation of defense-related genes that enhance the resistance of these plants to pathogens. Thus, the over-expression of VdWRKY53 in transgenic grapevines might improve their resistance to pathogens.

Electronic supplementary material

The online version of this article (10.1186/s41065-019-0089-5) contains supplementary material, which is available to authorized users.

Identification of Soybean Genes Whose Expression is Affected by the Ensifer fredii HH103 Effector Protein NopP

In some legume⁻rhizobium symbioses, host specificity is influenced by rhizobial nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. We generated an Ensifer fredii HH103 NopP mutant (HH103ΩNopP), and analyzed the nodule number (NN) and nodule dry weight (NDW) of 10 soybean germplasms inoculated with the wild-type E. fredii HH103 or the mutant strain. An analysis of recombinant inbred lines (RILs) revealed the quantitative trait loci (QTLs) associated with NopP interactions. A soybean genomic region containing two overlapping QTLs was analyzed in greater detail. A transcriptome analysis and qRT-PCR assay were used to identify candidate genes encoding proteins that interact with NopP. In some germplasms, NopP positively and negatively affected the NN and NDW, while NopP had different effects on NN and NDW in other germplasms. The QTL region in chromosome 12 was further analyzed. The expression patterns of candidate genes Glyma.12g031200 and Glyma.12g073000 were determined by qRT-PCR, and were confirmed to be influenced by NopP.

The cotton MAPK kinase GhMPK20 negatively regulates resistance to Fusarium oxysporum by mediating the MKK4-MPK20-WRKY40 cascade

Fusarium wilt is one of the most serious diseases affecting cotton. However, the pathogenesis and mechanism by which Fusarium oxysporum overcomes plant defence responses are unclear. Here, a new group D mitogen-activated protein kinase (MAPK) gene, GhMPK20, was identified and functionally analysed in cotton. GhMPK20 expression was significantly induced by F. oxysporum. Virus-induced gene silencing (VIGS) of GhMPK20 in cotton increased the tolerance to F. oxysporum, whereas ectopic GhMPK20 overexpression in Nicotiana benthamiana reduced F. oxysporum resistance via disruption of the salicylic acid (SA)-mediated defence pathway. More importantly, an F. oxysporum-induced MAPK cascade pathway composed of GhMKK4, GhMPK20 and GhWRKY40 was identified. VIGS of GhMKK4 and GhWRKY40 also enhanced F. oxysporum resistance in cotton, and the function of GhMKK4-GhMPK20 was shown to be essential for F. oxysporum-induced GhWRKY40 expression. Together, our results indicate that the GhMKK4-GhMPK20-GhWRKY40 cascade in cotton plays an important role in the pathogenesis of F. oxysporum. This research broadens our knowledge of the negative role of the MAPK cascade in disease resistance in cotton and provides an important scientific basis for the formulation of Fusarium wilt prevention strategies.

Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity

NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.

Bacillus cereus AR156 Activates Defense Responses to Pseudomonas syringae pv. tomato in Arabidopsis thaliana Similarly to flg22

Bacillus cereus AR156 (AR156) is a plant growth-promoting rhizobacterium capable of inducing systemic resistance to Pseudomonas syringae pv. tomato in Arabidopsis thaliana. Here, we show that, when applied to Arabidopsis leaves, AR156 acted similarly to flg22, a typical pathogen-associated molecular pattern (PAMP), in initiating PAMP-triggered immunity (PTI). AR156-elicited PTI responses included phosphorylation of MPK3 and MPK6, induction of the expression of defense-related genes PR1, FRK1, WRKY22, and WRKY29, production of reactive oxygen species, and callose deposition. Pretreatment with AR156 still significantly reduced P. syringae pv. tomato multiplication and disease severity in NahG transgenic plants and mutants sid2-2, jar1, etr1, ein2, npr1, and fls2. This suggests that AR156-induced PTI responses require neither salicylic acid, jasmonic acid, and ethylene signaling nor flagella receptor kinase FLS2, the receptor of flg22. On the other hand, AR156 and flg22 acted in concert to differentially regulate a number of AGO1-bound microRNAs that function to mediate PTI. A full-genome transcriptional profiling analysis indicated that AR156 and flg22 activated similar transcriptional programs, coregulating the expression of 117 genes; their concerted regulation of 16 genes was confirmed by real-time quantitative polymerase chain reaction analysis. These results suggest that AR156 activates basal defense responses to P. syringae pv. tomato in Arabidopsis, similarly to flg22.

Candidate Effector Pst_8713 Impairs the Plant Immunity and Contributes to Virulence of Puccinia striiformis f. sp. tritici

Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust, is an obligate biotrophic pathogen responsible for severe wheat disease epidemics worldwide. Pst and other rust fungi are acknowledged to deliver many effector proteins to the host, but little is known about the effectors' functions. Here, we report a candidate effector Pst_8713 isolated based on the genome data of CY32 and the expression of Pst_8713 is highly induced during the early infection stage. The Pst_8713 gene shows a low level of intra-species polymorphism. It has a functional N-terminal signal peptide and its product was found in the host cytoplasm and nucleus. Co-infiltrations in Nicotiana benthamiana demonsrated that Pst_8713 was capable of suppressing cell death triggered by mouse pro-apoptotic protein-BAX or Phytophthora infestans PAMP-INF1. Overexpression of Pst_8713 in plants suppressed pattern-triggered immunity (PTI) -associated callose deposition and expression of PTI-associated marker genes and promoted bacterial growth in planta. Effector-triggered immunity (ETI) induced by an avirulent Pst isolate was weakened when we overexpressed Pst_8713 in wheat leaves which accompanied by reduction of reactive oxygen species (ROS) accumulation and hypersensitive response (HR). In addition, the host induced gene silencing (HIGS) experiment showed that knockdown of Pst_8713 weakened the virulence of Pst by producing fewer uredinia. These results indicated that candidate effector Pst_8713 is involved in plant defense suppression and contributes to enhancing the Pst virulence.

Transcriptional analysis and histochemistry reveal that hypersensitive cell death and H2O2 have crucial roles in the resistance of tea plant (Camellia sinensis (L.) O. Kuntze) to anthracnose

Anthracnose causes severe losses of tea production in China. Although genes and biological processes involved in anthracnose resistance have been reported in other plants, the molecular response to anthracnose in tea plant is unknown. We used the susceptible tea cultivar Longjing 43 and the resistant cultivar Zhongcha 108 as materials and compared transcriptome changes in the leaves of both cultivars following Colletotrichum fructicola inoculation. In all, 9015 and 8624 genes were differentially expressed between the resistant and susceptible cultivars and their controls (0 h), respectively. In both cultivars, the differentially expressed genes (DEGs) were enriched in 215 pathways, including responses to sugar metabolism, phytohormones, reactive oxygen species (ROS), biotic stimuli and signalling, transmembrane transporter activity, protease activity and signalling receptor activity, but DEG expression levels were higher in Zhongcha 108 than in Longjing 43. Moreover, functional enrichment analysis of the DEGs showed that hydrogen peroxide (H₂O₂) metabolism, cell death, secondary metabolism, and carbohydrate metabolism are involved in the defence of Zhongcha 108, and 88 key genes were identified. Protein-protein interaction (PPI) network demonstrated that putative mitogen-activated protein kinase (MAPK) cascades are activated by resistance (R) genes and mediate downstream defence responses. Histochemical analysis subsequently validated the strong hypersensitive response (HR) and H₂O₂ accumulation that occurred around the hyphal infection sites in Zhongcha 108. Overall, our results indicate that the HR and H₂O₂ are critical mechanisms in tea plant defence against anthracnose and may be activated by R genes via MAPK cascades.

Elongation factor Tu is a multifunctional and processed moonlighting protein

Many bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (Sa_Ef-Tu) and Mycoplasma pneumoniae (Mpn_Ef-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (Mhp_Ef-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline. Recombinant Mpn_Ef-Tu bound strongly to a diverse range of host molecules, and when bound to plasminogen, was able to convert plasminogen to plasmin in the presence of plasminogen activators. Fragments of Ef-Tu retain binding capabilities to host proteins. Bioinformatics and structural modelling studies indicate that the accumulation of positively charged amino acids in short linear motifs (SLiMs), and protein processing promote multifunctional behaviour. Codon bias engendered by an A + T rich genome may influence how positively-charged residues accumulate in SLiMs.

A candidate RxLR effector from Plasmopara viticola can elicit immune responses in Nicotiana benthamiana

BACKGROUND

Diverse plant pathogens deliver effectors into plant cells to alter host processes. Oomycete pathogen encodes a large number of putative RxLR effectors which are likely to play a role in manipulating plant defense responses. The secretome of Plasmopara viticola (downy mildew of grapevine) contains at least 162 candidate RxLR effectors discovered in our recent studies, but their roles in infection and pathogenicity remain to be determined. Here, we characterize in depth one of the putative RxLR effectors, PvRxLR16, which has been reported to induce cell death in Nicotiana benthamiana in our previous study.

RESULTS

The nuclear localization, W/Y/L motifs, and a putative N-glycosylation site in C-terminal of PvRxLR16 were essential for cell death-inducing activity. Suppressor of G-two allele of Skp1 (SGT1), heat shock protein 90 (HSP90) and required for Mla12 resistance (RAR1), but not somatic embryogenesis receptor-like kinase (SERK3), were required for the cell death response triggered by PvRxLR16 in N. benthamiana. Some mitogen-activated protein kinases and transcription factors were also involved in the perception of PvRxLR16 by N. benthamiana. PvRxLR16 could also significantly enhance plant resistance to Phytophthora capsici and the nuclear localization was required for this ability. However, some other PvRxLR effectors could suppress defense responses and disease resistance induced by PvRxLR16, suggesting that it may not trigger host cell death or immune responses during physiological infection under natural conditions.

CONCLUSION

These data demonstrate that PvRxLR16 may be recognized by endogenous proteins in nucleus to trigger immune responses in N. benthamiana, which in turn can be suppressed by other PvRxLR effectors.

Virus-induced gene silencing (VIGS)-mediated functional characterization of two genes involved in lignocellulosic secondary cell wall formation

KEY MESSAGE

Functional characterization of two tobacco genes, one involved in xylan synthesis and the other, a positive regulator of secondary cell wall formation, is reported. Lignocellulosic secondary cell walls (SCW) provide essential plant materials for the production of second-generation bioethanol. Therefore, thorough understanding of the process of SCW formation in plants is beneficial for efficient bioethanol production. Recently, we provided the first proof-of-concept for using virus-induced gene silencing (VIGS) approach for rapid functional characterization of nine genes involved in cellulose, hemicellulose and lignin synthesis during SCW formation. Here, we report VIGS-mediated functional characterization of two tobacco genes involved in SCW formation. Stems of VIGS plants silenced for both selected genes showed increased amount of xylem formation but thinner cell walls than controls. These results were further confirmed by production of stable transgenic tobacco plants manipulated in expression of these genes. Stems of stable transgenic tobacco plants silenced for these two genes showed increased xylem proliferation with thinner walls, whereas transgenic tobacco plants overexpressing these two genes showed increased fiber cell wall thickness but no change in xylem proliferation. These two selected genes were later identified as possible members of DUF579 family involved in xylan synthesis and KNAT7 transcription factor family involved in positive regulation of SCW formation, respectively. Glycome analyses of cell walls showed increased polysaccharide extractability in 1 M KOH extracts of both VIGS-NbDUF579 and VIGS-NbKNAT7 lines suggestive of cell wall loosening. Also, VIGS-NbDUF579 and VIGS-NbKNAT7 lines showed increased saccharification rates (74.5 and 40 % higher than controls, respectively). All these properties are highly desirable for producing higher quantities of bioethanol from lignocellulosic materials of bioenergy plants.

Extraction and Characterization of Extracellular Proteins and Their Post-Translational Modifications from Arabidopsis thaliana Suspension Cell Cultures and Seedlings: A Critical Review

Proteins secreted by plant cells into the extracellular space, consisting of the cell wall, apoplastic fluid, and rhizosphere, play crucial roles during development, nutrient acquisition, and stress acclimation. However, isolating the full range of secreted proteins has proven difficult, and new strategies are constantly evolving to increase the number of proteins that can be detected and identified. In addition, the dynamic nature of the extracellular proteome presents the further challenge of identifying and characterizing the post-translational modifications (PTMs) of secreted proteins, particularly glycosylation and phosphorylation. Such PTMs are common and important regulatory modifications of proteins, playing a key role in many biological processes. This review explores the most recent methods in isolating and characterizing the plant extracellular proteome with a focus on the model plant Arabidopsis thaliana, highlighting the current challenges yet to be overcome. Moreover, the crucial role of protein PTMs in cell wall signalling, development, and plant responses to biotic and abiotic stress is discussed.

Bacillus cereus AR156 Extracellular Polysaccharides Served as a Novel Micro-associated Molecular Pattern to Induced Systemic Immunity to Pst DC3000 in Arabidopsis

Non-host resistance (NHR) is a broad-spectrum plant defense. Upon colonizing on the surface on the root or leaves of non-host species, pathogens initial encounter preform and induce defense response in plant, such as induced hypersensitive response, PAMPs triggered immunity (PTI), and effector triggered immunity (ETI). The ability of plants to develop an induced systemic response (ISR) in reaction to the colonization by non-pathogenic rhizobacterium depends on interactions between host plants and the colonizing rhizobacterium, and the ISR also can be defined as a NHR. However, how the colonization signal is and how systemic resistance to pathogens is developed is still unclear. In this study, we demonstrated that the extracellular polysaccharides (EPSs) of Bacillus cereus AR156 could act as novel microbe-associated molecular patterns (MAMPs) and function in the early perception status of the ISR of B. cereus AR156. The results revealed that B. cereus AR156 EPS could induce systemic resistance to Pst DC3000 in Arabidopsis. Cellular defense response markers such as hydrogen peroxide accumulation, callose deposition, and defense-associated enzyme were induced upon challenge inoculation in the leaves primed by EPS. Moreover, the defense-related genes PR1, PR2, and PR5 and mitogen-activated kinases (MAPK) cascade marker gene MPK6 were concurrently expressed in the leaves of EPS-treated plants and induced higher resistance to Pst DC3000 in Col-0 than that in the jar1 or etr1 mutants. The protection was absent in the NahG transgenic plants and npr1 mutant, suggesting an activation of the salicylic acid (SA)- and the MAPK-dependent signaling pathways with NPR1-dependent by B. cereus AR156 EPS. In conclusion, B. cereus AR156 EPS play an important role in MAMP perception during the process of rhizobacteria-triggered NHR. This study is the first to illustrate how AR156 induces systemic resistance to Pst DC3000 in Arabidopsis. It also provides the first explanation of how plants perceive colonization of non-pathogenic bacteria and how rhizobacteria trigger ISR to plant pathogens.

Arabidopsis thaliana: A Model Host Plant to Study Plant-Pathogen Interaction Using Rice False Smut Isolates of Ustilaginoidea virens

Rice false smut fungus which is a biotrophic fungal pathogen causes an important rice disease and brings a severe damage where rice is cultivated. We established a new fungal-plant pathosystem where Ustilaginoidea virens was able to interact compatibly with the model plant Arabidopsis thaliana. Disease symptoms were apparent on the leaves of the plants after 6 days of post inoculation in the form of chlorosis. Cytological studies showed that U. virens caused a heavy infestation inside the cells of the chlorotic tissues. Development and colonization of aerial mycelia in association with floral organ, particularly on anther and stigma of the flowers after 3 weeks of post inoculation was evident which finally caused infection on the developing seeds and pod tissues. The fungus adopts a uniquely biotrophic infection strategy in roots and spreads without causing a loss of host cell viability. We have also demonstrated that U. virens isolates infect Arabidopsis and the plant subsequently activates different defense response mechanisms which are witnessed by the expression of pathogenesis-related genes, PR-1, PR-2, PR-5, PDF1.1, and PDF1.2. The established A. thaliana-U. virens pathosystem will now permit various follow-up molecular genetics and gene expression experiments to be performed to identify the defense signals and responses that restrict fungal hyphae colonization in planta and also provide initial evidence for tissue-adapted fungal infection strategies.

Bacterial Leaf Infiltration Assay for Fine Characterization of Plant Defense Responses using the Arabidopsis thaliana-Pseudomonas syringae Pathosystem

In the absence of specialized mobile immune cells, plants utilize their localized programmed cell death and Systemic Acquired Resistance to defend themselves against pathogen attack. The contribution of a specific Arabidopsis gene to the overall plant immune response can be specifically and quantitatively assessed by assaying the pathogen growth within the infected tissue. For over three decades, the hemibiotrophic bacterium Pseudomonas syringae pv. maculicola ES4326 (Psm ES4326) has been widely applied as the model pathogen to investigate the molecular mechanisms underlying the Arabidopsis immune response. To deliver pathogens into the leaf tissue, multiple inoculation methods have been established, e.g., syringe infiltration, dip inoculation, spray, vacuum infiltration, and flood inoculation. The following protocol describes an optimized syringe infiltration method to deliver virulent Psm ES4326 into leaves of adult soil-grown Arabidopsis plants and accurately screen for enhanced disease susceptibility (EDS) towards this pathogen. In addition, this protocol can be supplemented with multiple pre-treatments to further dissect specific immune defects within different layers of plant defense, including Salicylic Acid (SA)-Triggered Immunity (STI) and MAMP-Triggered Immunity (MTI).

Disease resistance in rice and the role of molecular breeding in protecting rice crops against diseases

Rice diseases (bacterial, fungal, or viral) threaten food productivity. Host resistance is the most efficient, environmentally friendly method to cope with such diverse pathogens. Quantitative resistance conferred by quantitative trait loci (QTLs) is a valuable resource for rice disease resistance improvement. Although QTLs confer partial but durable resistance to many pathogen species in different crop plants, the molecular mechanisms of quantitative disease resistance remain mostly unknown. Quantitative resistance and non-host resistance are types of broad-spectrum resistance, which are mediated by resistance (R) genes. Because R genes activate different resistance pathways, investigating the genetic spectrum of resistance may lead to minimal losses from harmful diseases. Genome studies can reveal interactions between different genes and their pathways and provide insight into gene functions. Protein–protein interaction (proteomics) studies using molecular and bioinformatics tools may further enlighten our understanding of resistance phenomena.

The receptor-like cytoplasmic kinase PCRK1 contributes to pattern-triggered immunity against Pseudomonas syringae in Arabidopsis thaliana

In this paper we describe PATTERN-TRIGGERED IMMUNITY (PTI) COMPROMISED RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (PCRK1) of Arabidopsis thaliana, an RLCK that is important for defense against the pathogen Pseudomonas syringae pv. maculicola ES4326 (Pma ES4326). We examined defense responses such as bacterial growth, production of reactive oxygen species (ROS) and callose deposition in pcrk1 mutant plants to determine the role of PCRK1 during pathogen infection. Expression of PCRK1 was induced following pathogen infection. Pathogen growth was significantly higher in pcrk1 mutant lines than in wild-type Col-0. Mutant pcrk1 plants showed reduced pattern-triggered immunity (PTI) against Pma ES4326 after pretreatment with peptides derived from flagellin (flg22), elongation factor-Tu (elf18), or an endogenous protein (pep1). Deposition of callose was reduced in pcrk1 plants, indicating a role of PCRK1 in activation of early immune responses. A PCRK1 transgene containing a mutation in a conserved lysine residue important for phosphorylation activity of kinases (K118E) failed to complement a pcrk1 mutant for the Pma ES4326 growth phenotype. Our study shows that PCRK1 plays an important role during PTI and that a conserved lysine residue in the putative kinase domain is important for PCRK1 function.

Unmasking host and microbial strategies in the Agrobacterium-plant defense tango

Coevolutionary forces drive adaptation of both plant-associated microbes and their hosts. Eloquently captured in the Red Queen Hypothesis, the complexity of each plant-pathogen relationship reflects escalating adversarial strategies, but also external biotic and abiotic pressures on both partners. Innate immune responses are triggered by highly conserved pathogen-associated molecular patterns, or PAMPs, that are harbingers of microbial presence. Upon cell surface receptor-mediated recognition of these pathogen-derived molecules, host plants mount a variety of physiological responses to limit pathogen survival and/or invasion. Successful pathogens often rely on secretion systems to translocate host-modulating effectors that subvert plant defenses, thereby increasing virulence. Host plants, in turn, have evolved to recognize these effectors, activating what has typically been characterized as a pathogen-specific form of immunity. Recent data support the notion that PAMP-triggered and effector-triggered defenses are complementary facets of a convergent, albeit differentially regulated, set of immune responses. This review highlights the key players in the plant's recognition and signal transduction pathways, with a focus on the aspects that may limit Agrobacterium tumefaciens infection and the ways it might overcome those defenses. Recent advances in the field include a growing appreciation for the contributions of cytoskeletal dynamics and membrane trafficking to the regulation of these exquisitely tuned defenses. Pathogen counter-defenses frequently manipulate the interwoven hormonal pathways that mediate host responses. Emerging systems-level analyses include host physiological factors such as circadian cycling. The existing literature indicates that varying or even conflicting results from different labs may well be attributable to environmental factors including time of day of infection, temperature, and/or developmental stage of the host plant.

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.

Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)

BACKGROUND

Hybrids of larch (Larix kaempferi × Larix olgensis) are important afforestation species in northeastern China. They are routinely propagated via rooted stem cuttings. Despite the importance of rooting, little is known about the regulation of adventitious root development in larch hybrids. 454 GS FLX Titanium technology represents a new method for characterizing the transcriptomes of non-model species. This method can be used to identify differentially expressed genes, and then two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analyses can be used to analyze their corresponding proteins. In this study, we analyzed semi-lignified cuttings of two clones of L. kaempferi × L. olgensis with different rooting capacities to study the molecular basis of adventitious root development.

RESULTS

We analyzed two clones; clone 25-5, with strong rooting capacity, and clone 23-12, with weak rooting capacity. We constructed four cDNA libraries from 25-5 and 23-12 at two development stages. Sequencing was conducted using the 454 pyrosequencing platform. A total of 957832 raw reads was produced; 95.07% were high-quality reads, and were assembled into 45137 contigs and 61647 singletons. The functions of the unigenes, as indicated by their Gene Ontology annotation, included diverse roles in the molecular functions, biological processes, and cellular component categories. We analyzed 75 protein spots (-fold change ≥ 2, P ≤ 0.05) by 2D-DIGE, and identified the differentially expressed proteins using MALDI-TOF/TOF MS. A joint analysis of transcriptome and proteome showed genes related to two pathways, polyamine synthesis and stress response, might play an important role on adventitious root development.

CONCLUSIONS

These results provide fundamental and important information for research on the molecular mechanism of adventitious root development. We also demonstrated for the first time the combined use of two important technologies as a powerful approach to advance research on non-model, but otherwise important, larch species.

Self/nonself perception in plants in innate immunity and defense

The ability to distinguish 'self' from 'nonself' is the most fundamental aspect of any immune system. The evolutionary solution in plants to the problems of perceiving and responding to pathogens involves surveillance of nonself, damaged-self and altered-self as danger signals. This is reflected in basal resistance or non-host resistance, which is the innate immune response that protects plants against the majority of pathogens. In the case of surveillance of nonself, plants utilize receptor-like proteins or -kinases (RLP/Ks) as pattern recognition receptors (PRRs), which can detect conserved pathogen/microbe-associated molecular pattern (P/MAMP) molecules. P/MAMP detection serves as an early warning system for the presence of a wide range of potential pathogens and the timely activation of plant defense mechanisms. However, adapted microbes express a suite of effector proteins that often interfere or act as suppressors of these defenses. In response, plants have evolved a second line of defense that includes intracellular nucleotide binding leucine-rich repeat (NB-LRR)-containing resistance proteins, which recognize isolate-specific pathogen effectors once the cell wall has been compromised. This host-immunity acts within the species level and is controlled by polymorphic host genes, where resistance protein-mediated activation of defense is based on an 'altered-self' recognition mechanism.

Benzothiadiazole effect in the compatible tomato-Meloidogyne incognita interaction: changes in giant cell development and priming of two root anionic peroxidases

BTH application is effective in root-knot nematode-tomato interaction in a way that involves a delay in the formation of nematode feeding site and triggers molecular responses at several levels. The compatible interaction between root-knot nematodes and their hosts requires the nematode to overcome plant defense systems so that a sophisticated permanent feeding site (giant cells) can be produced within the host roots. It has been suggested that activators of plant defenses may provide a novel management strategy for controlling root-knot nematodes but little is known about the molecular basis by which these elicitors operate. The role of pre-treatment with Benzothiadiazole (BTH), a salicylic acid analog, in inducing resistance against Meloidogyne incognita infection was investigated in tomato roots. A decrease in galling in roots and feeding site numbers was observed following BTH treatment. Histological investigations showed a delay in formation of feeding sites in treated plants. BTH-treated galls had higher H2O2 production, lignin accumulation, and increased peroxidase activity than untreated galls. The expression of two tomato genes, Tap1 and Tap2, coding for anionic peroxidases, was examined by qRT-PCR and in situ hybridization in response to BTH. Tap1 was induced at all infection points, reaching the highest level at 15 dpi. Tap2 expression, although slightly delayed in untreated galls, increased during infection in both treated and untreated galls. The expression of Tap1 and Tap2 was observed in giant cells of untreated roots, whereas the transcripts were localized in both giant cells and in parenchyma cells surrounding the developing feeding sites in treated plants. These results show that BTH applied to tomato plants makes them more resistant to infection by nematodes, which become less effective in overcoming root defense pathway.

QTL mapping of black rot (Guignardia bidwellii) resistance in the grapevine rootstock 'Börner' (V. riparia Gm183 × V. cinerea Arnold)

In the grapevine cultivar 'Börner' QTLs for black rot resistance were detected consistently in several independent experiments. For one QTL on chromosome 14 closely linked markers were developed and a detailed map provided. Black rot is a serious grapevine disease that causes substantial yield loss under unfavourable conditions. All traditional European grapevine cultivars are susceptible to the causative fungus Guignardia bidwellii which is native to North America. The cultivar 'Börner', an interspecific hybrid of V. riparia and V. cinerea, shows a high resistance to black rot. Therefore, a mapping population derived from the cross of the susceptible breeding line V3125 ('Schiava grossa' × 'Riesling') with 'Börner' was used to carry out QTL analysis. A resistance test was established based on potted plants which were artificially inoculated in a climate chamber with in vitro produced G. bidwellii spores. Several rating systems were developed and tested. Finally, a five class scheme was applied for scoring the level of resistance. A major QTL was detected based on a previously constructed genetic map and data from six independent resistance tests in the climate chamber and one rating of natural infections in the field. The QTL is located on linkage group 14 (Rgb1) and explained up to 21.8 % of the phenotypic variation (LOD 10.5). A second stable QTL mapped on linkage group 16 (Rgb2; LOD 4.2) and explained 8.5 % of the phenotypic variation. These two QTLs together with several minor QTLs observed on the integrated map indicate a polygenic nature of the black rot resistance in 'Börner'. A detailed genetic map is presented for the locus Rgb1 with tightly linked markers valuable for the development for marker-assisted selection for black rot resistance in grapevine breeding.

Preparing to fight back: generation and storage of priming compounds

Immune-stimulated plants are able to respond more rapidly and adequately to various biotic stresses allowing them to efficiently combat an infection. During the priming phase, plant are stimulated in absence of a challenge, and can accumulate and store conjugates or precursors of molecules as well as other compounds that play a role in defense. These molecules can be released during the defensive phase following stress. These metabolites can also participate in the first stages of the stress perception. Here, we report the metabolic changes occuring in primed plants during the priming phase. β-aminobutyric acid (BABA) causes a boost of the primary metabolism through the tricarboxylic acids (TCA) such as citrate, fumarate, (S)-malate and 2-oxoglutarate, and the potentiation of phenylpropanoid biosynthesis and the octodecanoic pathway. On the contrary, Pseudomonas syringae pv tomato (PstAvrRpt2) represses the same pathways. Both systems used to prime plants share some common signals like the changes in the synthesis of amino acids and the production of SA and its glycosides, as well as IAA. Interestingly, a product of the purine catabolism, xanthosine, was found to accumulate following both BABA- and PstAvrRpt2-treatement. The compounds that are strongly affected in this stage are called priming compounds, since their effect on the metabolism of the plant is to induce the production of primed compounds that will help to combat the stress. At the same time, additional identified metabolites suggest the possible defense pathways that plants are using to get ready for the battle.

Hypervirulent Diuraphis noxia (Hemiptera: Aphididae) biotype SAM avoids triggering defenses in its host (Triticum aestivum) (Poales: Poaceae) during feeding

In the molecular arms race between aphids and plants, both organisms rely on adaptive strategies to outcompete their evolutionary rival. In the current study, we investigated the difference in elicited defense responses of wheat (Triticum aestivum L.) near-isogenic lines with different Dn resistance genes, upon feeding by an avirulent and hypervirulent Diuraphis noxia Kurdjumov biotype. After measuring the activity of a suite of enzymes associated with plant defense, it became apparent that the host does not recognize the invasion by the hypervirulent aphid because none of these were induced, while feeding by the avirulent biotype did result in induction of enzyme activity. Genomic plasticity in D. noxia may be a likely explanation for the observed differences in virulence between D. noxia biotype SA1 and SAM, as demonstrated in the current study.

SEC14 phospholipid transfer protein is involved in lipid signaling-mediated plant immune responses in Nicotiana benthamiana

We previously identified a gene related to the SEC14-gene phospholipid transfer protein superfamily that is induced in Nicotiana benthamiana (NbSEC14) in response to infection with Ralstonia solanacearum. We here report that NbSEC14 plays a role in plant immune responses via phospholipid-turnover. NbSEC14-silencing compromised expression of defense-related PR-4 and accumulation of jasmonic acid (JA) and its derivative JA-Ile. Transient expression of NbSEC14 induced PR-4 gene expression. Activities of diacylglycerol kinase, phospholipase C and D, and the synthesis of diacylglycerol and phosphatidic acid elicited by avirulent R. solanacearum were reduced in NbSEC14-silenced plants. Accumulation of signaling lipids and activation of diacylglycerol kinase and phospholipases were enhanced by transient expression of NbSEC14. These results suggest that the NbSEC14 protein plays a role at the interface between lipid signaling-metabolism and plant innate immune responses.