Plant-Fungal Pathogen Interaction: A Classical and Molecular View

Request PDF on ResearchGate | On May 1, , Pietro Spanu and others published Plant–Fungal Pathogen Interaction: A Classical and Molecular View.
Table of contents

This book offers insight into the state of present knowledge. Special emphasis is placed on recognition phenomena between plants and fungi, parasitization strategies employed by the phytopathogenic fungi, the action of phytotoxins, the compatibility of pathogens with host plants and the basic resistance of non-host plants as well as cultivar-specific resistance of host plants.

Special attention is paid to the gene-for-gene hypothesis for the determination of race-specific resistance, its molecular models and to the nature of race non-specific resistance as well as the population dynamics of plants and the evolution of their basic resistance. Advances in Plant Biopesticides. Use in Sustainable Agriculture and Land Restoration. Reproductive Biology of Plants. Plant Growth and Health Promoting Bacteria. The Iceman and his Natural Environment. Legume Nitrogen Fixation in a Changing Environment. Bioremediation of Salt Affected Soils: Biological Control of Plant-Parasitic Nematodes:.

Bioaugmentation, Biostimulation and Biocontrol. High-Tech and Micropropagation VI. The Bamboos of the World. Identification and Control of Common Weeds: Silviculture in the Tropics. Belowground Defence Strategies in Plants. Endophytes of Forest Trees. Genetic Modification of Plants. These tests analyze individual spots instead of the complete set, omitting information about correlated variables.

In expression studies, many thousands of statistical tests are conducted, one for each protein species. A substantial number of false positives may accumulate which is termed the multiple testing problem and is a general property of a confidence-based statistical test when applied many times [ ]. One approach to addressing the multiple testing problem is to control the family wise error rate FWER , which control the probability of one or more false rejections among all the tests conducted.

The simplest and most conservative approach is the Bonferroni correction, which adjusts the threshold of significance by dividing the per comparison error rate PCER by the number of comparisons being completed [ ]. This has led to the application of methodologies to control the false discovery rate FDR , where the focus is on achieving an acceptable ratio of true- and false-positives. The FDR is a proportion of changes identified as significant that are false [ ].

An extension to the FDR calculates a -value for each tested feature and is the expected proportion of false positives incurred when making a call that this feature has a significant change in the expression [ ]. For each -value, a -value will be reported on an overall estimation for the proportion of species changing in the study. Multiple testing correction methods, such as the Bonferroni correction and testing for the false discovery rate FDR [ ], fit the Student -test or ANOVA values for each protein spot to keep the overall error rate as low as possible.

Multivariate data analysis methods, such as PCA, are now used to pinpoint spots that differ between samples. These multivariate methods focus not only on differences in individual spots but also on the covariance structure between proteins [ ]. However, the results of these methods are sensitive to data scaling, and they may fail to produce valid multivariate models due to the large number of spots in the gels that do not contribute to the discrimination process [ ].

One of the limitations of PCA analysis is that it does not allow to miss values, a problem that can be avoided by imputing them when possible if enough replicates are available [ ]. The huge amount of data generated are being deposited and organized in several databases available to the scientific community: After 20 years of Proteomics research, it is possible to look back at previous research and publications, identifying errors from the experimental design, the analysis, and the interpretation of the data [ ].

In addition, data validation is done in a purely descriptive or speculative manner, as well as it is common to find low-confidence protein identification in the literature, especially in the case of unsequenced organisms and inappropriate statistical analyses of results have often been performed. The MIAPE documents recommend proteomic techniques that should be considered and followed when conducting a proteomic experiment. Proteomics journals should be, and in fact are, extremely strict when recommending that investigators follow the MIAPE standards for publishing a proteomic experiment.

On the other hand, many journals recommend or require the original data generated in a proteomic experiment to be submitted to public repositories [ , ]. A shift in the protein identification paradigm is currently underway, moving from sequencing and database searching to spectrum searching in spectral libraries. This underscores the importance of repositories for Proteomics [ — ]. Several proteomic studies have been carried out in order to understand fungal pathogenicity or plant-fungus interactions for reviews see [ — ] , although the plant-fungus association has been the one most studied by Proteomics approaches Table 6 , which is outside the scope of this review.

On the other hand, some fungal species have attracted an increasing interest in the biotechnological industry, in food science, or in agronomy as biocontrol agents Table 7 , which is also beyond the objectives of this work. At this point, this review describes studies published up to December in plant pathogenic fungi in descriptive proteomics intracellular proteomics, subproteomics, and secretomics , differential expression proteomics, as well as some basic knowledge about the Interactomics in fungi Table 3.

Within this section, papers devoted to establishing reference proteome maps of fungal cells and structures and subcellular fractions, and to study changes in the protein profile between species, races, populations, mutants, growth and developmental stages, as well as growth conditions, are discussed, paying special attention to proteins related to pathogenicity and virulence. Most of the reported work mainly uses mycelia from in vitro grown fungi, and 2-DE coupled to MS as proteomic strategy.

Thus, a partial proteome map has been reported for the ascomycete B. They have reported the detection of spots in Coomassie-stained 2-DE gels, covering the 5. In a second study, comparative proteomic analysis of two B. Some of them were the same proteins mentioned above and they appeared overexpressed or exclusively in the most virulent strain [ 46 ].

A third and more exhaustive work tried to establish a proteomic map of B. The authors conclude that since cellulose is one of the major components of the plant cell wall, many of the identified proteins may have a crucial role in the pathogenicity process, be involved in the infection cycle, and be potential antifungal targets. A close relative to B. Yajima and Kav [ 64 ] performed the first comprehensive proteome-level study in this important phytopathogenic fungus, in order to gain a better understanding of its life cycle and its ability to infect susceptible plants.

Eighteen secreted and 95 mycelial proteins were identified. Many of the annotated secreted proteins were cell wall-degrading enzymes that had been previously identified as pathogenicity or virulence factors of S. Furthermore, this study has allowed the annotation of a number of proteins that were unnamed, predicted, or hypothetical proteins with undetermined functions in the available databases.

According to the 1-DE band pattern, isolates were clustered into three groups consisting of different virulent types. By 2-DE spots were resolved with 29 of them being isolate-specific, and 39 showed quantitative differences. One of them was identified as Brn1 protein which has been reported to be related to melanin biosynthesis and the virulence differentiation in fungi. The fungal pathogen F. It synthesizes trichothecene mycotoxins during plant host attack to facilitate spread within the host. In order to study proteins and pathways that are important for successful host invasion, Taylor et al.

Protein samples were extracted from three biological replicates of a time course study and subjected to iTRAQ isobaric tags for relative and absolute quantification analysis. Statistical analysis of a filtered dataset of proteins revealed F. RT-PCR and northern hybridization confirmed that genes encoding proteins that were upregulated based on iTRAQ were also transcriptionally active under mycotoxin-producing conditions. Numerous candidate pathogenicity proteins were identified using this technique, including many predicted secreted proteins. Curiously, enzymes catalyzing reactions in the mevalonate pathway leading to trichothecene precursors were either not identified or only identified in one replicate, indicating that proteomics approaches cannot always probe biological characteristics.

The virus perturbs fungal developmental processes such as sporulation, morphology, and pigmentation and attenuates its virulence. A total of spots showing differences in abundance were identified. Seven proteins including sporulation-specific gene SPS2, triose phosphate isomerase, nucleoside diphosphate kinase, and woronin body major protein precursor were upaccumulated while 16, including enolase, saccharopine dehydrogenase, flavohemoglobin, mannitol dehydrogenase, and malate dehydrogenase, were downaccumulated.

Variations in protein abundance were investigated at the mRNA level by real-time RT-PCR analysis, which confirmed the proteomic data for 9 out of the representative 11 selected proteins. There are a few proteomics studies on fungal spores published. Recently, Sulc et al. Thus, these mass finger-printing generated by MS can be used for typing and characterizing different fungal strains and finding new biomarkers in host-pathogen interactions.

Plant-Fungal Pathogen Interaction : Peter Day :

Another study on B. The identity of distinct fungal gene products was determined, most of them with a predicted function in carbohydrate, lipid, or protein metabolism indicating that the conidiospore is geared for the breakdown of storage compounds and protein metabolites during germination correlating with previously reported transcriptomic data [ , ].

These results allowed a functionally annotated reference proteome for Bgh conidia. The technique is of relevance in the study of the molecular bases of biotrophy considering that biotrophic fungi, including downy mildews Oomycota , powdery mildews Ascomycota , and rust fungi Basidiomycota , are some of the most destructive pathogens on many plants. The majority of the proteins appeared to have roles in protein metabolic pathways and biological energy production.

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Surprisingly, pyruvate decarboxylase PDC , involved in alcoholic fermentation and commonly abundant in fungi and plants, was absent in both their Bgh proteome data set and in their EST sequence database. Significantly, BLAST searches of the recently available Bgh genome sequence data also failed to identify a sequence encoding this enzyme, strongly indicating that Bgh does not have a gene for PDC [ 44 ].

In order to overcome the low proteome coverage of most of the proteomic platforms available, this being related to the physicochemical and biological complexity and high dynamism range of proteins, different strategies directed at subfractionating the whole proteome have been developed, most of them involving cell fractionation. The analysis of the subcellular proteomes [ ] not only allows a deeper proteome coverage but also provides relevant informaction on the biology of the different organules, protein location, and trafficking.

The number of intracellular subproteomic studies carried out with fungal plant pathogens is minimum. Next we introduce a couple of papers appearing in the literature. The number of them devoted to the cell wall and extracellular fraction is much higher, and because of that a specific section is devoted to them. Mitochondria have also received attention. Based on protein databases of N.

More recently, the same researchers separated and identified 13 of the 14 subunits of the T. Relevant information on biological systems and processes comes from comparative studies in which genotypes, including mutants, developmental stages, or environmental conditions supply the knowledge inferred from the observed differences. Fungal pathogenicity requires the coordinated regulation of multiple genes and their protein products involved in host recognition, spore germination, hyphal penetration, appressorium formation, toxin production, and secretion.


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To study the infection cycle and to identify virulence factors, proteomics provides us with a powerful tool for analyzing changes in protein expression between races and stages. However, most of these studies are made in planta after the plant inoculation, which is outside the scope of this review.

In the case of plant fungal pathogens at least four papers have reported changes in the proteome at different developmental stages or strains. The dimorphic phytopathogenic fungus Ustilago maydis has been established as a valuable model system to study fungal dimorphism and pathogenicity. In its haploid stage, the fungus is unicellular and multiplies vegetatively by budding and undergoing a dimorphic transition infective filamentous growth. The majority of the identified proteins might have putative roles in energy and general metabolism. Comparison of Rac1- and -b-regulated protein sets supports the hypothesis that filament formation during pathogenic development occurs via stimulation of a Rac1-containing signalling module.

The proteins identified in this study might prove to be potential targets for antibiotic substances specifically targeted at dimorphic fungal pathogens. The reference map generated from U. From cyst and germinated cyst to sporangial could be resolved. Moreover, they made the protein profiles of parallel samples of P. In this work, only three identified proteins were reported, corresponding to actin isoforms.

More recently, Ebstrup et al. These identified proteins were most likely important for disease establishment and some of the proteins could therefore be putative targets for disease control. For example, downregulation of the crinkling- and necrosis-inducing CRN2 protein in appressoria compared to germinated cysts and the discovery of upregulation of a putative elongation factor EF-3 are of great interest. On the one hand, CRN2 protein might have an important function in the interaction with the host-plant before and after penetration into the leaf, this being a putative target for disease control.

Since plants presumably do not contain EF-3, it could represent a putative antioomycete as well as a putative antifungal target. Furthermore, several representatives of housekeeping systems were upaccumulated, and these changes are most likely involved in the runup to the establishment of the infection of the host plant. The biotrophic fungal pathogen U. The proteins identified revealed that uredospores require high energy and structural proteins during germination, indicating a metabolic transition from dormancy to germination.

Proteomics of Plant Pathogenic Fungi

The role of signal transduction in the pathogenecity of Stagonospora nodorum is well established and the inactivation of heterotrimeric G protein signaling caused developmental defects and reduced pathogenicity [ ]. In a follow-up study, the S. By matching the protein mass spectra to the translate S. This fungus causes tan spot, an important foliar disease of wheat, and produces multiple host-specific toxins, including Ptr ToxB, which is also found in avirulent isolates of the fungus.

In order to improve the understanding of the role of this homolog and evaluate the general pathogenic ability of P. The proteomic analysis revealed a number of the proteins found to be upregulated in a virulent race, which has been implicated in microbial virulence in other pathosystems, such as the secreted enzymes a-mannosidase and exo-b-1,3-glucanase, heat-shock and bip proteins, and various metabolic enzymes, which suggests a reduced general pathogenic ability in avirulent race of P.

Most eukaryotic plant pathogens initially invade the space between host cell walls the apoplastic space , and much of the initial host defence and pathogen counter defence happens in the apoplast and commonly involves secreted pathogen and host-derived proteins and metabolites [ ].

While some pathogens remain exclusively in the apoplast, such as Cladosporium fulvum , others, including mildews, rusts smuts, Phytophthora , and Magnaporthe species, breach host cell walls but remain external to and separated from the host cytoplasm by host and pathogen cell membranes. Some host wall-breaching pathogens, like rusts, mildews, and oomycetes, form specialised expanded hyphal protuberances called haustoria whereas others, like maize smut and the rice blast fungi, use unexpanded but probably specialised intrahost cell wall hyphae [ ].

The role of these structures was initially thought to be primarily nutrient acquisition, but recently their additional role in secretion of effectors, some of which are translocated to the host cytoplasm, has become more apparent. These issues have been recently reviewed by Ellis et al. The secretome has been defined as being the combination of native secreted proteins and the cell machinery involved in their secretion [ ]. A defining characteristic of plant pathogenic fungi is the secretion of a large number of degradative enzymes and other proteins, which have diverse functions in nutrient acquisition, substrate colonization, and ecological interactions [ — ].

Several extracellular fungal enzymes, such as polygalacturonase, pectate lyase, xylanase, and lipase, have been shown or postulated to be required for virulence in at least one host-pathogen interaction [ — ]. Proteomics is the right approach to study the interaction between plants and microbes mediated by excreted molecules, the role of the cell wall and the interface, and to identify fungal protein effectors facilitating either infection virulence factors, enzymes of the toxin biosynthesis pathways or trigger defence responses avirulence factors.

Therefore, many of these proteins are of special interest in the study of plant pathogens [ 46 , 64 ]. This might also be owing to the fact that secretome sample preparation is much faster and simpler than extraction and preparation of intracellular proteins. Next, a number of papers covering this topic are presented, including those dealing with the secretome of Trichoderma spp, a study directed at identifying proteins related to its biofungicidal activity. Pioneering work on this field comes before the arrival of proteomics during the s, with typical studies focused on the identification, purification, and characterization of single secreted proteins, under the influence of the biotechnology industry for the production of enzymes for commercial and industrial use [ ].

The first complete proteomic study of secreted proteins was released on the filamentous fungus A. The interest of this study was the ability of both A. The secreted proteins were analyzed by 2-DE and MALDI-TOF mass spectrometry, with 15 rutin-induced proteins and 7 noninduced proteins identified, among them enzymes of routine catabolism pathway and glycosidases. The culture medium was found to contain a larger amount of proteins and these were more diverse when the fungus grew on the cell wall. These cell wall-degradating enzymes were predominantly matches to putative carbohydrate active enzymes implicated in cellulose, hemicelluloses, and pectin, catabolism.

These results indicated that fungal metabolism becomes oriented towards the synthesis and secretion of a whole arsenal of enzymes able to digest almost the complete plant cell wall. The secretome has also been analyzed in S. In this study, 52 secreted proteins were identified and many of the annotated secreted proteins were cell wall-degrading enzymes that had been identified previously as pathogenic or virulence factors of S.

Two studies have been published reporting the B. First, secretions were collected from fungus grown on a solid substrate of cellophane membrane while mock infecting media supplemented with the extract of full red tomato, ripened strawberry, or Arabidopsis leaf extract. Sixty of these proteins were predicted to contain a SignalP motif indicating the extracellular location of the proteins.

In the second work, the impact of degree of esterification of pectin on secreted enzyme of B. All the major components of the fruit cell wall pectin, cellulose, hemicellulose undergo these changes. The results showed that the growth of B. Therefore, future studies of the B. Using the plant pathogenic fungus L. These authors used both broad and narrow acidic and basic pH range in IEF. Compared with the previously published protocols for which only dozens of 2-DE spots were recovered from fungal secretome samples, in this study, up to approximately 2-DE spots were resolved.

This high resolution was confirmed with the identification of proteins along several pH gradients as well as the presence of major secretome markers such as endopolygalacturonases, beta-glucanosyltransferases, pectate lyases, and endoglucanases. Thus, shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium.

One of the earliest works was released on Trichoderma reesei mycelium cell wall, one of the most powerful producers of extracellular proteins, this study being justified in order to find out the protein secretory pathways and the effect of the fungal genus, strain, and media condition on the excretion through the cell wall [ ].

A total of cell envelope-associated proteins were successfully extracted and separated by 2-DE from Trichoderma reesei mycelia actively secreting proteins and from mycelia in which the secretion of proteins is low. For each different substrate, they found significant differences in 2-DE maps of extracellular proteins. However, despite these differences, the most abundant protein under all conditions was a novel aspartic protease P , which showed a strong homology with polyporopepsin from Irpex lacteus. This led to speculation that this protein plays a fundamental role in the parasitic activity of Trichoderma spp.

Two-DE was used to analyze separately collected proteomes from each single, two- or three-partner interaction. Thus, a large number of protein factors associated with the multiplayer interactions examined were identified, including protein kinases, cyclophilines, chitine synthase, and ABC transporters. Recently, another similar study was released between T. A cell wall proteome has been proposed for the oomycete Phytophthora ramorum , the causal agent of sudden oak death, in order to study its pathogenic factors [ 60 ]. This study showed an inventory of cell wall-associated proteins based on MS sequence analysis.

Seventeen secreted proteins were identified by homology searches. The functional classification revealed several cell wall-associated proteins, thus suggesting that cell wall proteins may also be important for fungal pathogenicity. The filamentous fungus Neurospora crassa is a model laboratory organism but in nature is commonly found growing on dead plant material, particularly grasses. Using functional genomics resources available for N. An overlap set of genes was identified from expression analysis of N.


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    • Moreover, the in-vitro secretome analysis may not illustrate the real state of host-pathogen interaction, thereby necessitating extraction of apoplastic proteins from the in-planta systems. In this mini-review, we have summarized the progress made so far in this area to present the current scenario of secretomics during the plant-pathogen interaction.

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    Due to the biochemical and technical advances, it is possible to isolate the proteins directly from the apoplast which can be analyzed by gel-based or gel-free proteomics approaches. However, relatively limited number of studies have been conducted so far, to identify the pathogen-secreted proteins in-planta Table 1. The successful isolation of apoplastic proteins is the most critical step prior to utilizing the samples for proteome analysis.

    For the isolation of apoplastic proteins, a number of methods including vacuum infiltration VIC and gravity extraction methods are available reviewed in Agrawal et al. However, only VIC method along with its modified version termed CA-VIC , has been used for the isolation of apoplastic proteins in response to pathogen infection Floerl et al.

    In the VIC method, leaves are cut into small sections followed by extensive washings of these sections to remove cytoplasmic proteins from the cut ends. The washed leaves sections are then incubated in the extraction buffer which is allowed to infiltrate into the cells through a pressure change induced by vacuum. Finally, apoplastic proteins are recovered by centrifugation at low speed. This method was used to isolate the apoplastic proteins from the leaves of Arabidopsis and tobacco De-la-Pena et al. However, this VIC method is less efficient in isolating the apoplastic proteins from the waxy coated leaves, like leaves of rice and maize.

    Moreover, previous studies in which apoplastic proteins were extracted from Arabidopsis and Brassica leaves by VIC method, showed identification of only few differential proteins in response to Verticillium longisporum infection, indicating the limitation of this method for comparative proteome analysis Floerl et al. Furthermore, this VIC method yields much lower amount of apoplastic proteins which is a major constrain for large scale proteome analysis.

    This method involves shaking of the cut segments of the leaves in a calcium based buffer for 1 h on ice, followed by vacuum infiltration, centrifugation, and phenol precipitation Kim et al. This method yields higher amount of apoplastic proteins than classical VIC method, may be due to the addition of calcium, which facilitates the extraction of loosely bound cell wall proteins Watson et al.

    A comparative analysis was carried out to select the best buffer for isolation of apoplastic proteins. Among all the extraction buffers tested, sodium phosphate or ascorbic acid with calcium chloride were the most efficient, while extraction with water or Tris showed contamination from vacuole and other organelles Witzel et al.

    Plant-Fungal Pathogen Interaction : A Classical and Molecular View

    Therefore, the selection of an appropriate extraction method is crucial for apoplastic protein extraction in different plant species. List of published in-planta secretome studies on plant-microbe interactions. Experimental strategy of the in-planta secretome studies during the host-pathogen interactions. Details are in the text. After isolation of apoplastic proteins, the next step is to assess the purity of isolated proteins as contamination from cytoplasm and other organelles can lead to the false positive results.

    To assess the purity of extracted apoplastic proteins, several methods including cytoplasmic marker enzymes activity assays and Western blot analysis of marker proteins, can be performed Figure 1. Glucosephosphate dehydrogenase G6PDH , glyceraldehydephosphate dehydrogenase GAPDH , and malate dehydrogenase MDH are some of the common cytoplasmic enzymes which are being widely used as biomarkers for cytoplasmic contamination, while RuBisCO antibodies are used for assessing the chloroplastic contamination in the apoplastic proteins.

    Moreover, this approach can also be employed to measure the contamination ratio with other cellular organelle markers. In addition, Western blots of intracellular proteins, OsPR and PBZ1, did not detect any signal, suggesting the low levels of cytoplasmic contamination in isolated apoplastic proteins. Furthermore, the enrichment of apoplastic proteins was also shown by assessing the expression of apoplastic marker proteins glucanse-2 and thaumatin-like protein using Western blotting, indicating the efficacy of calcium based buffer in isolation of apoplastic proteins Kim et al.

    Taken together, assessing the enrichment of apoplastic proteins and contaminations are the essential steps in the analysis of secretome. To examine the differences in global protein secretion upon pathogen infection, sufficient normalization of protein samples is necessary.

    Based on previous studies, two possible normalization methods were applied to evaluate the protein abundances Figure 1. In the first method, protein abundance is normalized with same amount of isolated proteins Kaffarnik et al. As it is possible that the rate of protein secretion would also be affected in addition to changes in which proteins were secreted, normalization with protein concentration would provide absolute changes in protein identities or proteins that changed dramatically in concentrations. However, as infection of pathogen could enhance the protein secretion in plants Watanabe et al.

    Another choice for sample normalization is on the fresh tissue amount. A significant increase of protein secretion was detected comparing with non-infected tissues Kim et al. These results indicated that upon pathogen infection the overall protein secretion might be enhanced.

    Moreover, the selection of extraction buffer and protein loss during extraction procedures may strongly affect the final proteomics results. Therefore, normalization with fresh tissue amount may illustrate the real case of protein secretion upon pathogen infection. However, as it is difficult to distinguish the cytoplasmic and apoplastic proteins when normalized with the fresh tissue amount, use of cytoplasmic and apoplastic marker is highly recommended in order to check the cytoplasmic contamination.

    Taken together, the issue of how the amount of apoplastic proteins should be normalized has to be considered prior to the proteomics analysis. A gel-based proteomics approach was used to identify the rice- M. In addition, a M. Furthermore, a higher level of up-regulation of glycosylhydrolase and chitinase proteins was observed in case of incompatible interactions as compared to the compatible, suggesting the involvement of these proteins in the resistance against rice blast fungus.

    These studies indicated that the pathogenic fungus also secretes numerous proteins into the apoplastic space. Plant secreted proteins were mainly glycosyl hydrolase family proteins, esterases, proteases and peptidases, suggesting that the cell wall and protein modifications are important aspects for the resistance against M. Identification of apoplastic proteins during rice- Cochliobolus miyabeanus a necrotrophic fungus infection led to the identification of proteins, of which only 31 6. These results suggest that the host-secreted proteins are more abundant during the C.

    Kirkhouse Trust - Isolation of a fungal pathogen and producing inoculum

    Proteins with decreased abundance were mainly related to the Calvin cycle and glycolysis, whereas abundance of the proteins involved in the TCA cycle, amino acids, and ethylene biosynthesis was increased Kim et al. Analysis of plant- V. A lectin-like, chitin-inducible protein was down-regulated upon V.