Dual metabolomics: a novel approach to understanding plant-pathogen interactions

Decoding the biochemical dialogue: metabolomic insights into soybean defense strategies against diverse pathogens

Soybean, a crucial global leguminous crop, confronts persistent threats from diverse pathogens, exerting a profound impact on global yields. While genetic dimensions of soybean-pathogen interactions have garnered attention, the intricate biochemical responses remain poorly elucidated. In this study, we applied targeted and untargeted liquid chromatography coupled to mass spectrometry (LC-MS) metabolite profiling to dissect the complex interplay between soybeans and five distinct pathogens. Our analysis uncovered 627 idMS/MS spectra, leading to the identification of four main modules, encompassing flavonoids, isoflavonoids, triterpenoids, and amino acids and peptides, alongside other compounds such as phenolics. Profound shifts were observed in both primary and secondary metabolism in response to pathogenic infections. Particularly notable were the bidirectional changes in total flavonoids across diverse pathogenic inoculations, while triterpenoids exhibited a general declining trend. Noteworthy among the highly inducible total flavonoids were known representative anti-pathogen compounds (glyceollin I), backbone forms of isoflavonoids (daidzein, genistein, glycitein, formononetin), and newly purified compounds in this study (prunin). Subsequently, we delved into the biological roles of these five compounds, validating their diverse functions against pathogens: prunin significantly inhibited the vegetative growth and virulence of Phytophthora sojae; genistein exhibited a pronounced inhibitory effect on the vegetative growth and virulence of Phomopsis longicolla; daidzein and formononetin displayed significant repressive effects on the virulence of P. longicolla. This study underscores the potent utility of metabolomic tools, providing in-depth insights into plant-pathogen interactions from a biochemical perspective. The findings not only contribute to plant pathology but also offer strategic pathways for bolstering plant resistance against diseases on a broader scale.

Induced responses to the wheat pathogen: Tan Spot-(Pyrenophora tritici-repentis) in wheat (Triticum aestivum) focus on changes in defence associated and sugar metabolism

INTRODUCTION

Tan Spot (TS) disease of wheat is caused by Pyrenophora tritici-repentis (Ptr), where most of the yield loss is linked to diseased flag leaves. As there are no fully resistant cultivars available, elucidating the responses of wheat to Ptr could inform the derivation of new resistant genotypes.

OBJECTIVES

The study aimed to characterise the flag-leaf metabolomes of two spring wheat cultivars (Triticum aestivum L. cv. PF 080719 [PF] and cv. Fundacep Horizonte [FH]) following challenge with Ptr to gain insights into TS disease development.

METHODS

PF and FH plants were inoculated with a Ptr strain that produces the necrotrophic toxin ToxA. The metabolic changes in flag leaves following challenge (24, 48, 72, and 96 h post-inoculation [hpi]) with Ptr were investigated using untargeted flow infusion ionisation-high resolution mass spectroscopy (FIE-HRMS).

RESULTS

Both cultivars were susceptible to Ptr at the flag-leaf stage. Comparisons of Ptr- and mock-inoculated plants indicated that a major metabolic shift occurred at 24 hpi in FH, and at 48 hpi in PF. Although most altered metabolites were genotype specific, they were linked to common pathways; phenylpropanoid and flavonoid metabolism. Alterations in sugar metabolism as well as in glycolysis and glucogenesis pathways were also observed. Pathway enrichment analysis suggested that Ptr-triggered alterations in chloroplast and photosynthetic machinery in both cultivars, especially in FH at 96 hpi. In a wheat-Ptr interactome in integrative network analysis, "flavone and flavonol biosynthesis" and "starch and sucrose metabolism" were targeted as the key metabolic processes underlying PF-FH-Ptr interactions.

CONCLUSION

These observations suggest the potential importance of flavone and flavonol biosynthesis as well as bioenergetic shifts in susceptibility to Ptr. This work highlights the value of metabolomic approaches to provide novel insights into wheat pathosystems.

Determining Macromolecular Structures Using Cryo-Electron Microscopy

Structural insights into macromolecular and protein complexes provide key clues about the molecular basis of the function. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful structural biology method for studying protein and macromolecular structures at high resolution in both native and near-native states. Despite the ability to get detailed structural insights into the processes underlying protein function using cryo-EM, there has been hesitancy amongst plant biologists to apply the method for biomolecular interaction studies. This is largely evident from the relatively fewer structural depositions of proteins and protein complexes from plant origin in electron microscopy databank. Even though the progress has been slow, cryo-EM has significantly contributed to our understanding of the molecular biology processes underlying photosynthesis, energy transfer in plants, besides viruses infecting plants. This chapter introduces sample preparation for both negative-staining electron microscopy (NSEM) and cryo-EM for plant proteins and macromolecular complexes and data analysis using single particle analysis for beginners.

Uncovering Phytotoxic Compounds Produced by Colletotrichum spp. Involved in Legume Diseases Using an OSMAC-Metabolomics Approach

Different fungal species belonging to the Colletotrichum genus cause anthracnose disease in a range of major crops, resulting in huge economic losses worldwide. Typical symptoms include dark, sunken lesions on leaves, stems, or fruits. Colletotrichum spp. have synthesized, in vitro, a number of biologically active and structurally unusual metabolites that are involved in their host's infection process. In this study, we applied a one strain many compounds (OSMAC) approach, integrated with targeted and non-targeted metabolomics profiling, to shed light on the secondary phytotoxic metabolite panels produced by pathogenic isolates of Colletotrichum truncatum and Colletotrichum trifolii. The phytotoxicity of the fungal crude extracts was also assessed on their primary hosts and related legumes, and the results correlated with the metabolite profile that arose from the different cultural conditions. To the best of our knowledge, this is the first time that the OSMAC strategy integrated with metabolomics approaches has been applied to Colletotrichum species involved in legume diseases.

Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications

In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.

Untargeted profiling of secondary metabolites and phytotoxins associated with stemphylium blight of lentil

Stemphylium botryosum alters lentil secondary metabolism and differentially affects resistant and susceptible genotypes. Untargeted metabolomics identifies metabolites and their potential biosynthetic pathways that play a crucial role in resistance to S. botryosum. The molecular and metabolic processes that mediate resistance to stemphylium blight caused by Stemphylium botryosum Wallr. in lentil are largely unknown. Identifying metabolites and pathways associated with Stemphylium infection may provide valuable insights and novel targets to breed for enhanced resistance. The metabolic changes following infection of four lentil genotypes by S. botryosum were investigated by comprehensive untargeted metabolic profiling employing reversed-phase or hydrophilic interaction liquid chromatography (HILIC) coupled to a Q-Exactive mass spectrometer. At the pre-flowering stage, plants were inoculated with S. botryosum isolate SB19 spore suspension and leaf samples were collected at 24, 96 and 144 h post-inoculation (hpi). Mock-inoculated plants were used as negative controls. After analyte separation, high-resolution mass spectrometry data was acquired in positive and negative ionization modes. Multivariate modeling revealed significant treatment, genotype and hpi effects on metabolic profile changes that reflect lentil response to Stemphylium infection. In addition, univariate analyses highlighted numerous differentially accumulated metabolites. By contrasting the metabolic profiles of SB19-inoculated and mock-inoculated plants and among lentil genotypes, 840 pathogenesis-related metabolites were detected including seven S. botryosum phytotoxins. These metabolites included amino acids, sugars, fatty acids and flavonoids in primary and secondary metabolism. Metabolic pathway analysis revealed 11 significant pathways including flavonoid and phenylpropanoid biosynthesis, which were affected upon S. botryosum infection. This research contributes to ongoing efforts toward a comprehensive understanding of the regulation and reprogramming of lentil metabolism under biotic stress, which will provide targets for potential applications in breeding for enhanced disease resistance.

From prediction to function: Current practices and challenges towards the functional characterization of type III effectors

The type III secretion system (T3SS) is a well-studied pathogenicity determinant of many bacteria through which effectors (T3Es) are translocated into the host cell, where they exercise a wide range of functions to deceive the host cell's immunity and to establish a niche. Here we look at the different approaches that are used to functionally characterize a T3E. Such approaches include host localization studies, virulence screenings, biochemical activity assays, and large-scale omics, such as transcriptomics, interactomics, and metabolomics, among others. By means of the phytopathogenic Ralstonia solanacearum species complex (RSSC) as a case study, the current advances of these methods will be explored, alongside the progress made in understanding effector biology. Data obtained by such complementary methods provide crucial information to comprehend the entire function of the effectome and will eventually lead to a better understanding of the phytopathogen, opening opportunities to tackle it.

Forage grass growth under future climate change scenarios affects fermentation and ruminant efficiency

With an increasing human population access to ruminant products is an important factor in global food supply. While ruminants contribute to climate change, climate change could also affect ruminant production. Here we investigated how the plant response to climate change affects forage quality and subsequent rumen fermentation. Models of near future climate change (2050) predict increases in temperature, CO₂, precipitation and altered weather systems which will produce stress responses in field crops. We hypothesised that pre-exposure to altered climate conditions causes compositional changes and also primes plant cells such that their post-ingestion metabolic response to the rumen is altered. This “stress memory” effect was investigated by screening ten forage grass varieties in five differing climate scenarios, including current climate (2020), future climate (2050), or future climate plus flooding, drought or heat shock. While varietal differences in fermentation were detected in terms of gas production, there was little effect of elevated temperature or CO₂ compared with controls (2020). All varieties consistently showed decreased digestibility linked to decreased methane production as a result of drought or an acute flood treatment. These results indicate that efforts to breed future forage varieties should target tolerance of acute stress rather than long term climate.

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant-microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

Implications of mistletoe parasitism for the host metabolome: A new plant identity in the forest canopy

Mistletoe-host systems exemplify an intimate and chronic relationship where mistletoes represent protracted stress for hosts, causing long-lasting impact. Although host changes in morphological and reproductive traits due to parasitism are well known, shifts in their physiological system, altering metabolite concentrations, are less known due to the difficulty of quantification. Here, we use ecometabolomic techniques in the plant-plant interaction, comparing the complete metabolome of the leaves from mistletoe (Viscum album) and needles from their host (Pinus nigra), both parasitized and unparasitized, to elucidate host responses to plant parasitism. Our results show that mistletoe acquires metabolites basically from the primary metabolism of its host and synthesizes its own defence compounds. In response to mistletoe parasitism, pines modify a quarter of their metabolome over the year, making the pine canopy metabolome more homogeneous by reducing the seasonal shifts in top-down stratification. Overall, host pines increase antioxidant metabolites, suggesting oxidative stress, and also increase part of the metabolites required by mistletoe, which act as a permanent sink of host resources. In conclusion, by exerting biotic stress and thereby causing permanent systemic change, mistletoe parasitism generates a new host-plant metabolic identity available in forest canopy, which could have notable ecological consequences in the forest ecosystem.

Metabolic Analysis of the Development of the Plant-Parasitic Cyst Nematodes Heterodera schachtii and Heterodera trifolii by Capillary Electrophoresis Time-of-Flight Mass Spectrometry

The cyst nematodes Heterodera schachtii and Heterodera trifolii, whose major hosts are sugar beet and clover, respectively, damage a broad range of plants, resulting in significant economic losses. Nematodes synthesize metabolites for organismal development and social communication. We performed metabolic profiling of H. schachtii and H. trifolii in the egg, juvenile 2 (J2), and female stages. In all, 392 peaks were analyzed by capillary electrophoresis time-of-flight mass spectrometry, which revealed a lot of similarities among metabolomes. Aromatic amino acid metabolism, carbohydrate metabolism, choline metabolism, methionine salvage pathway, glutamate metabolism, urea cycle, glycolysis, gluconeogenesis, coenzyme metabolism, purine metabolism, pyrimidine metabolism, and tricarboxylic acid (TCA) cycle for energy conversion (β-oxidation and branched-chain amino acid metabolism) energy storage were involved in all stages studied. The egg and female stages synthesized higher levels of metabolites compared to the J2 stage. The key metabolites detected were glycerol, guanosine, hydroxyproline, citric acid, phosphorylcholine, and the essential amino acids Phe, Leu, Ser, and Val. Metabolites, such as hydroxyproline, acetylcholine, serotonin, glutathione, and glutathione disulfide, which are associated with growth and reproduction, mobility, and neurotransmission, predominated in the J2 stage. Other metabolites, such as SAM, 3PSer, 3-ureidopropionic acid, CTP, UDP, UTP, 3-hydroxy-3-methylglutaric acid, 2-amino-2-(hydroxymethyl-1,3-propanediol, 2-hydroxy-4-methylvaleric acid, Gly Asp, glucuronic acid-3 + galacturonic acid-3 Ser-Glu, citrulline, and γ-Glu-Asn, were highly detected in the egg stage. Meanwhile, nicotinamide, 3-PG, F6P, Cys, ADP-Ribose, Ru5P, S7P, IMP, DAP, diethanolamine, p-Hydroxybenzoic acid, and γ-Glu-Arg_divalent were unique to the J2 stage. Formiminoglutamic acid, nicotinaminde riboside + XC0089, putrescine, thiamine 2,3-dihydroxybenzoic acid, 3-methyladenine, caffeic acid, ferulic acid, m-hydrobenzoic acid, o- and p-coumaric acid, and shikimic acid were specific to the female stage. Overall, highly similar identities and quantities of metabolites between the corresponding stages of the two species of nematode were observed. Our results will be a valuable resource for further studies of physiological changes related to the development of nematodes and nematode-plant interactions.

Unravelling Plant Responses to Stress-The Importance of Targeted and Untargeted Metabolomics

Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global crop losses, as well as mounting abiotic stress pressures, due to climate change. Metabolomics approaches have previously contributed to our knowledge within the fields of molecular plant pathology and plant-insect interactions. However, these remain incredibly challenging targets, due to the vast diversity in metabolite volatility and polarity, heterogeneous mixtures of pathogen and plant cells, as well as rapid rates of metabolite turn-over. Unravelling the systematic biochemical responses of plants to various individual and combined stresses, involves monitoring signaling compounds, secondary messengers, phytohormones, and defensive and protective chemicals. This demands both targeted and untargeted metabolomics approaches, as well as a range of enzymatic assays, protein assays, and proteomic and transcriptomic technologies. In this review, we focus upon the technical and biological challenges of measuring the metabolome associated with plant stress. We illustrate the challenges, with relevant examples from bacterial and fungal molecular pathologies, plant-insect interactions, and abiotic and combined stress in the environment. We also discuss future prospects from both the perspective of key innovative metabolomic technologies and their deployment in breeding for stress resistance.

Untargeted metabolite profiling of petal blight in field-grown Rhododendron agastum using GC-TOF-MS and UHPLC-QTOF-MS/MS

Petal blight caused by fungi is among the most destructive diseases of Rhododendron, especially Rhododendron agastum. Nonetheless, the metabolite changes that occur during petal blight are unknown. We used untargeted gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and ultra-high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) to compare the metabolite profiles of healthy and petal blight R. agastum flowers. Using GC-TOF-MS, 571 peaks were extracted, of which 189 metabolites were tentatively identified. On the other hand, 364 and 277 metabolites were tentatively identified in the positive and negative ionization modes of the UHPLC-QTOF-MS/MS, respectively. Principal component analysis (PCA) and orthogonal projections to latent structures-discriminant analysis (OPLS-DA) were able to clearly discriminate between healthy and petal blight flowers. Differentially abundant metabolites were primarily enriched in the biosynthesis of specialized metabolites. 17 accumulated specialized metabolites in petal blight flowers have been reported to have antifungal activity, and literature indicates that 9 of them are unique to plants. 3 metabolites (chlorogenic acid, medicarpin, and apigenin) are reportedly involved in resistance to blight caused by pathogens. We therefore speculate that the accumulation of chlorogenic acid, medicarpin, and apigenin may be involved in the resistance to petal blight. Our results suggest that these metabolites may be used as candidate biocontrol agents for the control fungal petal blight in Rhododendron.

Using Metabolomics to Assist Plant Breeding

Recent methodological advances in both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) have provided a deep understanding of metabolic regulation occurring in plant cells. The application of these techniques to agricultural systems is, however, subject to more complex interactions. Here we summarize a step-by-step modern metabolomics methodology that generates metabolome data toward the implementation of metabolomics in crop breeding. We describe a metabolic workflow, and provide guidelines for handling large sample numbers for the specific purpose of metabolic quantitative trait loci approaches.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Plant-microbe Interactions for Sustainable Agriculture in the Post-genomic Era

Plant-microbe interactions are both symbiotic and antagonistic, and the knowledge of both these interactions is equally important for the progress of agricultural practice and produce. This review gives an insight into the recent advances that have been made in the plant-microbe interaction study in the post-genomic era and the application of those for enhancing agricultural production. Adoption of next-generation sequencing (NGS) and marker assisted selection of resistant genes in plants, equipped with cloning and recombination techniques, has progressed the techniques for the development of resistant plant varieties by leaps and bounds. Genome-wide association studies (GWAS) of both plants and microbes have made the selection of desirable traits in plants and manipulation of the genomes of both plants and microbes effortless and less time-consuming. Stress tolerance in plants has been shown to be accentuated by association of certain microorganisms with the plant, the study and application of the same have helped develop stress-resistant varieties of crops. Beneficial microbes associated with plants are being extensively used for the development of microbial consortia that can be applied directly to the plants or the soil. Next-generation sequencing approaches have made it possible to identify the function of microbes associated in the plant microbiome that are both culturable and non-culturable, thus opening up new doors and possibilities for the use of these huge resources of microbes that can have a potential impact on agriculture.

Metabolomic applications for understanding complex tripartite plant-microbes interactions: Strategies and perspectives

Phytopathogens from the Alternaria sp., Fusarium sp., Penicillium sp., and Pseudomonas sp. and their toxigenic metabolites - alternariol, fumonisin, citrinin, and coronatine respectively, negatively impact crop yields and sales by eliciting plant diseases and/or causing human and veterinary toxicoses upon the consumption of contaminated food. These phytopathogens and their associated toxins, however, are present and most likely in undetectable concentrations pre-harvest and post-harvest of many major staple crops. Metabolomic approaches have been used extensively for better characterizing and diagnosing human disease, plant disease and, their etiological agents. Their use in agro-industrial research focusing specifically on tripartite (plant - toxicogenic microbe - beneficial microbe) interactions is, however, limited. Since new approaches for eradicating food-borne pathogens, increasing crop productivity and improving agro-international trade are being sought worldwide, the consequent integration of metabolomic approaches and perspectives in crop protection strategies for better understanding plant - toxicogenic microbe - beneficial microbe interaction in tandem is discussed.

Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

Adaptation of the metabolomics profile of rice after Pyricularia oryzae infection

Pyricularia oryzae (P. oryzae), one of the most devastating fungal pathogens, is the cause of blast disease in rice. Infection with a blast fungus induces biological responses in the host plant that lead to its survival through the termination or suppression of pathogen growth, and metabolite compounds play vital roles in plant interactions with a wide variety of other organisms. Numerous studies have indicated that rice has a multi-layered plant immune system that includes pre-developed (e.g., cell wall and phytoanticipins), constitutive and inducible (phytoalexins) defence barriers against stresses. Significant progress towards understanding the basis of the molecular mechanisms underlying the defence responses of rice to P. oryzae has been achieved. Nonetheless, even though the important metabolites in the responses of rice to pathogens have been identified, their exact mechanisms and their contributions to plant immunity against blast fungi have not been elucidated. The purpose of this review is to summarize and discuss recent advances towards the understanding of the integrated metabolite variations in rice after P. oryzae invasion.

Development of a Pseudomonas syringae-Arabidopsis Suspension Cell Infection System for Investigating Host Metabolite-Dependent Regulation of Type III Secretion and Pattern-Triggered Immunity

The importance of pattern-triggered immunity (PTI) in plant defense has been clearly established through genetic studies of mutants lacking functional pattern recognition receptors (PRRs) and signaling components downstream of PRR activation. Despite extensive knowledge of PRR-mediated signaling responses to pathogen-associated molecular patterns (PAMPs), little is known about which of these responses, if any, are directly responsible for limiting bacterial growth. In this work, we established a protocol for coculturing the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 and Arabidopsis suspension cells. The system closely mirrors infection processes that occur in leaves, with bacteria relying on the type III secretion system (T3SS) for maximal growth and PAMP-induced plant defenses effectively limiting bacterial growth. To demonstrate the utility of this system, we investigated the molecular basis of PAMP-induced growth inhibition and discovered that T3SS-associated genes are inhibited when DC3000 is cocultured with PAMP-treated plant suspension cells. To determine the underlying mechanism of decreased T3SS gene expression, we performed metabolomics and biochemical analyses of suspension cell exudates and identified 14 metabolites that significantly increased or decreased following PAMP treatment. Citric acid, a known inducer of T3SS gene expression in DC3000, was among several organic acids decreased in exudates from PAMP-treated plant cells. Exogenous addition of citric acid increased T3SS gene expression and partially recovered growth of DC3000 in the presence of PAMP-treated cells, indicating that a portion of PAMP-induced defense in this system is decreased extracellular release of this metabolite. We envision that the well-defined infection conditions of this coculture system will be valuable for quantitative studies of type III effector delivery by P. syringae. Furthermore, this system provides a unique 'top-down' approach to unravel the molecular basis of PTI against P. syringae.

Dual Analysis of Virus-Host Interactions: The Case of Ostreid herpesvirus 1 and the Cupped Oyster Crassostrea gigas

Dual analyses of the interactions between Ostreid herpesvirus 1 (OsHV-1) and the bivalve Crassostrea gigas during infection can unveil events critical to the onset and progression of this viral disease and can provide novel strategies for mitigating and preventing oyster mortality. Among the currently used “omics” technologies, dual transcriptomics (dual RNA-seq) coupled with the analysis of viral DNA in the host tissues has greatly advanced the knowledge of genes and pathways mostly contributing to host defense responses, expression profiles of annotated and unknown OsHV-1 open reading frames (ORFs), and viral genome variability. In addition to dual RNA-seq, proteomics and metabolomics analyses have the potential to add complementary information, needed to understand how a malacoherpesvirus can redirect and exploit the vital processes of its host. This review explores our current knowledge of “omics” technologies in the study of host-pathogen interactions and highlights relevant applications of these fields of expertise to the complex case of C gigas infections by OsHV-1, which currently threaten the mollusk production sector worldwide.

Guidelines for Sample Normalization to Minimize Batch Variation for Large-Scale Metabolic Profiling of Plant Natural Genetic Variance

Recent methodological advances in both liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) have facilitated the profiling highly complex mixtures of primary and secondary metabolites in order to investigate a diverse range of biological questions. These techniques usually face a large number of potential sources of technical and biological variation. In this chapter we describe guidelines and normalization procedures to reduce the analytical variation, which are essential for the high-throughput evaluation of metabolic variance used in broad genetic populations which commonly entail the evaluation of hundreds or thousands of samples. This chapter specifically deals with handling of large-scale plant samples for metabolomics analysis of quantitative trait loci (mQTL) in order to reduce analytical error as well as batch-to-batch variation.

Alterations in plant sugar metabolism: signatory of pathogen attack

This review summarizes the current understanding, future challenges and ongoing quest on sugar metabolic alterations that influence the outcome of plant-pathogen interactions. Intricate cellular and molecular events occur during plant-pathogen interactions. They cause major metabolic perturbations in the host and alterations in sugar metabolism play a pivotal role in governing the outcome of various kinds of plant-pathogen interactions. Sugar metabolizing enzymes and transporters of both host and pathogen origin get differentially regulated during the interactions. Both plant and pathogen compete for utilizing the host sugar metabolic machinery and in turn promote resistant or susceptible responses. However, the kind of sugar metabolism alteration that is beneficial for the host or pathogen is yet to be properly understood. Recently developed tools and methodologies are facilitating research to understand the intricate dynamics of sugar metabolism during the interactions. The present review elaborates current understanding, future challenges and ongoing quest on sugar metabolism, mobilization and regulation during various plant-pathogen interactions.

The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance

Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant-plant and plant-microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground 'signalomics', and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial - and priming events.

Primed primary metabolism in systemic leaves: a functional systems analysis

Plants evolved mechanisms to counteract bacterial infection by preparing yet uninfected systemic tissues for an enhanced defense response, so-called systemic acquired resistance or priming responses. Primed leaves express a wide range of genes that enhance the defense response once an infection takes place. While hormone-driven defense signalling and defensive metabolites have been well studied, less focus has been set on the reorganization of primary metabolism in systemic leaves. Since primary metabolism plays an essential role during defense to provide energy and chemical building blocks, we investigated changes in primary metabolism at RNA and metabolite levels in systemic leaves of Arabidopsis thaliana plants that were locally infected with Pseudomonas syringae. Known defense genes were still activated 3–4 days after infection. Also primary metabolism was significantly altered. Nitrogen (N)-metabolism and content of amino acids and other N-containing metabolites were significantly reduced, whereas the organic acids fumarate and malate were strongly increased. We suggest that reduction of N-metabolites in systemic leaves primes defense against bacterial infection by reducing the nutritional value of systemic tissue. Increased organic acids serve as quickly available metabolic resources of energy and carbon-building blocks for the production of defense metabolites during subsequent secondary infections.

Metabolomics of Early Stage Plant Cell-Microbe Interaction Using Stable Isotope Labeling

Metabolomics has been used in unraveling metabolites that play essential roles in plant-microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms.

Chemometric analysis reveals links in the formation of fragrant bio-molecules during agarwood (Aquilaria malaccensis) and fungal interactions

Fragrant agarwood, arguably the costliest wood in the world, is formed by plant-fungal interactions in Aquilaria spp. However, very little is known about this fragrant outcome of interaction. Therefore, mimicking the ancient traditions of agarwood production in Assam (Northeast India), a chemometric assessment of the agarwood-fungus interaction was made by chemical profiling (GC-MS) coupled with statistical analysis (principal component, correlation network analysis) across three platforms, viz. callus, juvenile plants and resinous wood-chips with an associated Fusarium. In the study of callus-fungus interaction, increased accumulation of key aroma compounds such as pentatriacontane {fold change (log2FC) = 3.47)}, 17-pentatriacontene (log2FC = 2.95), tetradecane, 2-methyl- (log2FC = 1.10) over callus and activation of pathways related to defense and secondary metabolism indicated links to aroma production. Study on fungal interactions in juvenile plants and resinous wood-chips indicated formation of terpenoid precursors (e.g. farnesol, geranylgeraniol acetate) and agarwood sesquiterpenes (e.g. agarospirol, γ-eudesmol). Correlation network analysis revealed the possible regulation of sesquiterpene biosynthesis involving squalene. Also a direct role of fungus in aroma (e.g. dodecane, 4-methyl-, tetracosane) was highlighted. Appearance of fragrant molecules unknown to agarwood during interaction featured as a new possibility for future research.

Control of Endophytic Frankia Sporulation by Alnus Nodule Metabolites

A unique case of microbial symbiont capable of dormancy within its living host cells has been reported in actinorhizal symbioses. Some Frankia strains, named Sp+, are able to sporulate inside plant cells, contrarily to Sp- strains. The presence of metabolically slowed-down bacterial structures in host cells alters our understanding of symbiosis based on reciprocal benefits between both partners, and its impact on the symbiotic processes remains unknown. The present work reports a metabolomic study of Sp+ and Sp- nodules (from Alnus glutinosa), in order to highlight variabilities associated with in-planta sporulation. A total of 21 amino acids, 44 sugars and organic acids, and 213 secondary metabolites were detected using UV and mass spectrometric-based profiling. Little change was observed in primary metabolites, suggesting that in-planta sporulation would not strongly affect the primary functionalities of the symbiosis. One secondary metabolite (M27) was detected only in Sp+ nodules. It was identified as gentisic acid 5-O-β-d-xylopyranoside, previously reported as involved in plant defenses against microbial pathogens. This metabolite significantly increased Frankia in-vitro sporulation, unlike another metabolite significantly more abundant in Sp- nodules [M168 = (5R)-1,7-bis-(3,4-dihydroxyphenyl)-heptane-5-O-β-d-glucopyranoside]. All these results suggest that the plant could play an important role in the Frankia ability to sporulate in planta and allow us to discuss a possible sanction emitted by the host against less cooperative Sp+ symbionts.

Ectopic expression and functional characterization of type III polyketide synthase mutants from Emblica officinalis Gaertn

KEY MESSAGE

Functional characterization and ectopic expression studies of chalcone synthase mutants implicate the role of phenylalanine in tailoring the substrate specificity of type III polyketide synthase. Chalcone synthase (CHS) is a plant-specific type III polyketide synthase that catalyzes the synthesis of flavonoids. Native CHS enzyme does not possess any functional activity on N-methylanthraniloyl-CoA, which is the substrate for acridione/quinolone alkaloid biosynthesis. Here, we report the functional transformation of chalcone synthase protein from Emblica officinalis (EoCHS) to quinolone and acridone synthase (ACS) with single amino acid substitutions. A cDNA of 1173 bp encoding chalcone synthase was isolated from E. officinalis and mutants (F215S and F265V) were generated by site-directed mutagenesis. Molecular modeling studies of EoCHS did not show any active binding with N-methylanthraniloyl-CoA, but the mutants of EoCHS showed strong affinity to the same. As revealed by the modeling studies, functional analysis of CHS mutants showed that they could utilize p-coumaroyl-CoA as well as N-methylanthraniloyl-CoA as substrates and yield active products such as naringenin, 4-hydroxy 1-methyl 2(H) quinolone and 1,3-dihydroxy-n-methyl acridone. Exchange of a single amino acid in EoCHS (F215S and F265V) resulted in functionally active mutants that preferred N-methylanthraniloyl-CoA over p-coumaroyl-CoA. This can be attributed to the increase in the relative volume of active sites in mutants by mutation. Moreover, metabolomic and MS analyses of tobacco leaves transiently expressing mutant genes showed high levels of naringenin, acridones and quinolone derivatives compared to wild-type CHS. This is the first report demonstrating the functional activity of EoCHS mutants with N-methylanthraniloyl-CoA and these results indicate the role of phenylalanine in altering the substrate specificity and in the evolution of type III PKSs.

Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions

Many aspects of the way plants protect themselves against pathogen attack, or react upon such an attack, are realized by metabolites. The ambitious aim of metabolomics, namely the identification and annotation of the entire cellular metabolome, still poses a considerable challenge due to the high diversity of the metabolites in the cell. Recent advances in analytical methods and data analysis have resulted in improved sensitivity, accuracy, and capacity, allowing the analysis of several hundreds or even thousands of compounds within one sample. Investigators have only recently begun to acknowledge and harness the power of metabolomics to elucidate key questions in the study of plant biotic interactions; we review trends and developments in the field.

Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions

The control and interaction between nitrogen and carbon assimilatory pathways is essential in both photosynthetic and non-photosynthetic tissue in order to support metabolic processes without compromising growth. Physiological differences between the basal and mature region of wheat (Triticum aestivum) primary leaves confirmed that there was a change from heterotrophic to autotrophic metabolism. Fourier Transform Infrared (FT-IR) spectroscopy confirmed the suitability and phenotypic reproducibility of the leaf growth conditions. Principal Component-Discriminant Function Analysis (PC-DFA) revealed distinct clustering between base, and tip sections of the developing wheat leaf, and from plants grown in the presence or absence of nitrate. Gas Chromatography-Time of Flight/Mass Spectrometry (GC-TOF/MS) combined with multivariate and univariate analyses, and Bayesian network (BN) analysis, distinguished different tissues and confirmed the physiological switch from high rates of respiration to photosynthesis along the leaf. The operation of nitrogen metabolism impacted on the levels and distribution of amino acids, organic acids and carbohydrates within the wheat leaf. In plants grown in the presence of nitrate there was reduced levels of a number of sugar metabolites in the leaf base and an increase in maltose levels, possibly reflecting an increase in starch turnover. The value of using this combined metabolomics analysis for further functional investigations in the future are discussed.

1H nuclear magnetic resonance-based extracellular metabolomic analysis of multidrug resistant Tca8113 oral squamous carcinoma cells

A major obstacle of successful chemotherapy is the development of multidrug resistance (MDR) in the cancer cells, which is difficult to reverse. Metabolomic analysis, an emerging approach that has been increasingly applied in various fields, is able to reflect the unique chemical fingerprints of specific cellular processes in an organism. The assessment of such metabolite changes can be used to identify novel therapeutic biomarkers. In the present study, ¹H nuclear magnetic resonance (NMR) spectroscopy was used to analyze the extracellular metabolomic spectrum of the Tca8113 oral squamous carcinoma cell line, in which MDR was induced using the carboplatin (CBP) and pingyangmycin (PYM) chemotherapy drugs in vitro. The data were analyzed using the principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) methods. The results demonstrated that the extracellular metabolomic spectrum of metabolites such as glutamate, glycerophosphoethanol amine, α-Glucose and β-Glucose for the drug-induced Tca8113 cells was significantly different from the parental Tca8113 cell line. A number of biochemicals were also significantly different between the groups based on their NMR spectra, with drug-resistant cells presenting relatively higher levels of acetate and lower levels of lactate. In addition, a significantly higher peak was observed at δ 3.35 ppm in the spectrum of the PYM-induced Tca8113 cells. Therefore, ¹H NMR-based metabolomic analysis has a high potential for monitoring the formation of MDR during clinical tumor chemotherapy in the future.

Gas chromatography-mass spectrometry of biofluids and extracts

Gas chromatography-mass spectrometry (GC-MS) has been widely used in metabonomics analyses of biofluid samples. Biofluids provide a wealth of information about the metabolism of the whole body and from multiple regions of the body that can be used to study general health status and organ function. Blood serum and blood plasma, for example, can provide a comprehensive picture of the whole body, while urine can be used to monitor the function of the kidneys, and cerebrospinal fluid (CSF) will provide information about the status of the brain and central nervous system (CNS). Different methods have been developed for the extraction of metabolites from biofluids, these ranging from solvent extracts, acids, heat denaturation, and filtration. These methods vary widely in terms of efficiency of protein removal and in the number of metabolites extracted. Consequently, for all biofluid-based metabonomics studies, it is vital to optimize and standardize all steps of sample preparation, including initial extraction of metabolites. In this chapter, recommendations are made of the optimum experimental conditions for biofluid samples for GC-MS, with a particular focus on blood serum and plasma samples.

Sample collection and preparation of biofluids and extracts for gas chromatography-mass spectrometry

To maximize the utility of gas chromatography-mass spectrometry (GC-MS) in metabonomics research, all stages of the experimental design should be standardized, including sample collection, storage, preparation, and sample separation. Moreover, the prerequisite for any GC-MS analysis is that a compound must be volatile and thermally stable if it is to be analyzed using this technique. Since many metabolites are nonvolatile and polar in nature, they are not readily amenable to analysis by GC-MS and require initial chemical derivatization of the polar functional groups in order to reduce the polarity and to increase the thermal stability and volatility of the analytes. In this chapter, an overview is presented of the optimum approach to sample collection, storage, and preparation for gas chromatography-mass spectrometry-based metabonomics with particular focus on urine samples as example of biofluids.

Experimental approaches to study plant cell walls during plant-microbe interactions

Plant cell walls provide physical strength, regulate the passage of bio-molecules, and act as the first barrier of defense against biotic and abiotic stress. In addition to providing structural integrity, plant cell walls serve an important function in connecting cells to their extracellular environment by sensing and transducing signals to activate cellular responses, such as those that occur during pathogen infection. This mini review will summarize current experimental approaches used to study cell wall functions during plant-pathogen interactions. Focus will be paid to cell imaging, spectroscopic analyses, and metabolic profiling techniques.

Ergosterol, an orphan fungal microbe-associated molecular pattern (MAMP)

Fungal pathogens continue to pose a significant threat to crop production and food supply. The early stages of plant-fungus interactions are mostly mediated by microbe-associated molecular pattern (MAMP) molecules, perceived by plant pattern recognition receptors (PRRs). Currently, the identified fungal MAMP molecules include chitin, chitosan, β-glucans, elicitins and ergosterol. Although the molecular battles between host plants and infecting fungal phytopathogens have been studied extensively, many aspects still need to be investigated to obtain a holistic understanding of the intrinsic mechanisms, which is paramount in combating fungal plant diseases. Here, an overview is given of the most recent findings concerning an 'orphan' fungal MAMP molecule, ergosterol, and we present what is currently known from a synopsis of different genes, proteins and metabolites found to play key roles in induced immune responses in plant-fungus interactions. Clearly, integrative investigations are still needed to provide a comprehensive systems-based understanding of the dynamics associated with molecular mechanisms in plant-ergosterol interactions and associated host responses.

Plant systems biology: insights, advances and challenges

Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.

Comparative metabolite fingerprinting of the rumen system during colonisation of three forage grass (Lolium perenne L.) varieties

The rumen microbiota enable ruminants to degrade complex ligno-cellulosic compounds to produce high quality protein for human consumption. However, enteric fermentation by domestic ruminants generates negative by-products: greenhouse gases (methane) and environmental nitrogen pollution. The current lack of cultured isolates representative of the totality of rumen microbial species creates an information gap about the in vivo function of the rumen microbiota and limits our ability to apply predictive biology for improvement of feed for ruminants. In this work we took a whole ecosystem approach to understanding how the metabolism of the microbial population responds to introduction of its substrate. Fourier Transform Infra Red (FTIR) spectroscopy-based metabolite fingerprinting was used to discriminate differences in the plant-microbial interactome of the rumen when using three forage grass varieties (Lolium perenne L. cv AberDart, AberMagic and Premium) as substrates for microbial colonisation and fermentation. Specific examination of spectral regions associated with fatty acids, amides, sugars and alkanes indicated that although the three forages were apparently similar by traditional nutritional analysis, patterns of metabolite flux within the plant-microbial interactome were distinct and plant genotype dependent. Thus, the utilisation pattern of forage nutrients by the rumen microbiota can be influenced by subtleties determined by forage genotypes. These data suggest that our interactomic approach represents an important means to improve forages and ultimately the livestock environment.

High-throughput phenotyping of uropathogenic E. coli isolates with Fourier transform infrared spectroscopy

Fourier transform infrared (FT-IR) spectroscopy is an established rapid whole-organism fingerprinting method that generates metabolic fingerprints from bacteria that reflect the phenotype of the microorganism under investigation. However, whilst FT-IR spectroscopy is fast (typically 10 s to 1 min per sample), the approaches for microbial sample preparation can be time consuming as plate culture or shake flasks are used for growth of the organism. We report a new approach that allows micro-cultivation of bacteria from low volumes (typically 200 μL) to be coupled with FT-IR spectroscopy. This approach is fast and easy to perform and gives equivalent data to the lengthier and more expensive shake flask cultivations (sample volume = 20 mL). With this micro-culture approach we also demonstrate high reproducibility of the metabolic fingerprints. The approach allowed separation of different isolates of Escherichia coli involved in urinary tract infection, including members of the globally disseminated ST131 clone, with respect to both genotype and resistance or otherwise to the antibiotic Ciprofloxacin.

Metabolomic analysis of isonitrosoacetophenone-induced perturbations in phenolic metabolism of Nicotiana tabacum cells

Plants have developed biochemical and molecular responses to adapt to different stress environments. One of the characteristics of the multi-component defence response is the production of defence-related metabolites. Plant defences can be triggered by various stimuli, including synthetic or naturally occurring molecules, especially those derived from pathogens. In the current study, Nicotiana tabacum cell suspensions were treated with isonitrosoacetophenone (INAP), a subcomponent of a plant-derived stress metabolite with anti-fungal and anti-oxidant properties, in order to investigate the effect thereof on cellular metabolism. Subsequent metabolomic-based analyses were employed to evaluate changes in the metabolome. UPLC-MS in conjunction with multivariate data analyses was found to be an appropriate approach to study the effect of chemical inducers like INAP on plant metabolism in this model system. Principal component analysis (PCA) indicated that INAP is capable of inducing time-dependent metabolic perturbations in the cultured cells. Orthogonal projection to latent structures discriminant analysis (OPLS-DA) revealed metabolites of which the levels are affected by INAP, and eight of these were tentatively annotated from the mass spectral data and online databases. These metabolites are known in the context of plant stress- and defence responses and include benzoic- or cinnamic acid derivatives that are either glycosylated or quinilated as well as flavonoid derivatives. The results indicate that INAP affects the shikimate-, phenylpropanoid- and flavonoid pathways, the products of which may subsequently lead to an anti-oxidant environment in vivo.

Glutamate Metabolism in Plant Disease and Defense: Friend or Foe?

Plant glutamate metabolism (GM) plays a pivotal role in amino acid metabolism and orchestrates crucial metabolic functions, with key roles in plant defense against pathogens. These functions concern three major areas: nitrogen transportation via the glutamine synthetase and glutamine-oxoglutarate aminotransferase cycle, cellular redox regulation, and tricarboxylic acid cycle-dependent energy reprogramming. During interactions with pathogens, the host GM is markedly altered, leading to either a metabolic state, termed “endurance”, in which cell viability is maintained, or to an opposite metabolic state, termed “evasion”, in which the process of cell death is facilitated. It seems that endurance-natured modulations result in resistance to necrotrophic pathogens and susceptibility to biotrophs, whereas evasion-related reconfigurations lead to resistance to biotrophic pathogens but stimulate the infection by necrotrophs. Pathogens, however, have evolved strategies such as toxin secretion, hemibiotrophy, and selective amino acid utilization to exploit the plant GM to their own benefit. Collectively, alterations in the host GM in response to different pathogenic scenarios appear to function in two opposing ways, either backing the ongoing defense strategy to ultimately shape an efficient resistance response or being exploited by the pathogen to promote and facilitate infection.

The Metabolic Interplay between Plants and Phytopathogens

Plant diseases caused by pathogenic bacteria or fungi cause major economic damage every year and destroy crop yields that could feed millions of people. Only by a thorough understanding of the interaction between plants and phytopathogens can we hope to develop strategies to avoid or treat the outbreak of large-scale crop pests. Here, we studied the interaction of plant-pathogen pairs at the metabolic level. We selected five plant-pathogen pairs, for which both genomes were fully sequenced, and constructed the corresponding genome-scale metabolic networks. We present theoretical investigations of the metabolic interactions and quantify the positive and negative effects a network has on the other when combined into a single plant-pathogen pair network. Merged networks were examined for both the native plant-pathogen pairs as well as all other combinations. Our calculations indicate that the presence of the parasite metabolic networks reduce the ability of the plants to synthesize key biomass precursors. While the producibility of some precursors is reduced in all investigated pairs, others are only impaired in specific plant-pathogen pairs. Interestingly, we found that the specific effects on the host's metabolism are largely dictated by the pathogen and not by the host plant. We provide graphical network maps for the native plant-pathogen pairs to allow for an interactive interrogation. By exemplifying a systematic reconstruction of metabolic network pairs for five pathogen-host pairs and by outlining various theoretical approaches to study the interaction of plants and phytopathogens on a biochemical level, we demonstrate the potential of investigating pathogen-host interactions from the perspective of interacting metabolic networks that will contribute to furthering our understanding of mechanisms underlying a successful invasion and subsequent establishment of a parasite into a plant host.

Reactive oxygen species and their role in plant defence and cell wall metabolism

Harnessing the toxic properties of reactive oxygen species (ROS) to fight off invading pathogens can be considered a major evolutionary success story. All aerobic organisms have evolved the ability to regulate the levels of these toxic intermediates, whereas some have evolved elaborate signalling pathways to dramatically increase the levels of ROS and use them as weapons in mounting a defence response, a process commonly referred to as the oxidative burst. The balance between steady state levels of ROS and the exponential increase in these levels during the oxidative burst has begun to shed light on complex signalling networks mediated by these molecules. Here, we discuss the different sources of ROS that are present in plant cells and review their role in the oxidative burst. We further describe two well-studied ROS generating systems, the NADPH oxidase and apoplastic peroxidase proteins, and their role as the primary producers of ROS during pathogen invasion. We then discuss what is known about the metabolic and proteomic fluxes that occur in plant cells during the oxidative burst and after pathogen recognition, and try to highlight underlying biochemical processes that may provide more insight on the complex regulation of ROS in plants.

FT-ICR/MS and GC-EI/MS metabolomics networking unravels global potato sprout's responses to Rhizoctonia solani infection

The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents.

GC-MS metabolomic differentiation of selected citrus varieties with different sensitivity to citrus huanglongbing

Huanglongbing (HLB) is the most destructive disease of citrus worldwide. The rapid identification of tolerant varieties is considered a critical step towards controlling HLB. GC-MS metabolite profiles were used to differentiate HLB-tolerant citrus varieties 'Poncirus trifoliata' (TR) and 'Carrizo citrange' (CAR) from HLB-sensitive varieties 'Madam Vinous sweet orange' (MV) and 'Duncan' grapefruit (DG). PCR analyses revealed that MV was the most sensitive variety followed by DG and the tolerant varieties CAR and TR. Metabolomic multivariate analysis allowed classification of the cultivars in apparent agreement with PCR results. Higher levels of the amino acids l-proline, l-serine, and l-aspartic acid, as well as the organic acids butanedioic and tetradecanoic acid, and accumulation of galactose in healthy plants were characteristic of the most sensitive variety MV when compared to all other varieties. Only galactose was significantly higher in DG when compared to the tolerant varieties TR and CAR. The tolerant varieties showed higher levels of l-glycine and mannose when compared to sensitive varieties MV and DG. Profiling of the sensitive varieties MV and DG over a 20-week period after inoculation of those with the HLB-containing material revealed strong responses of metabolites to HLB infection that differed from the response of the tolerant varieties. Significant changes of l-threonine level in the leaves from old mature flushes and l-serine, l-threonine, scyllo-inositol, hexadecanoic acid, and mannose in the leaves from young developing flushes were observed in MV. Significant changes in myo-inositol in old flushes and l-proline, indole, and xylose in new flushes were observed in DG.

Future prospects for ascochyta blight resistance breeding in cool season food legumes

Legume cultivation is strongly hampered by the occurrence of ascochyta blights. Strategies of control have been developed but only marginal successes achieved. Breeding for disease resistance is regarded the most cost efficient method of control. Significant genetic variation for disease resistance exists in most legume crops with numerous germplasm lines maintained, providing an excellent resource for plant breeders. Fast and reliable screening methods have been adjusted to fulfill breeding program needs. However, the complex inheritance controlled quantitatively by multiple genes, has been difficult to manipulate. Successful application of biotechnology to ascochyta blight resistance breeding in legume crops will facilitate a good biological knowledge both of the crops-pathogen interaction and of the mechanisms underlying resistance. The current focus in applied breeding is leveraging biotechnological tools to develop more and better markers to speed up the delivery of improved cultivars to the farmer. To date, however, progress in marker development and delivery of useful markers has been slow in most legumes. The limited saturation of the genomic regions bearing putative QTLs in legume crops makes difficult to identify the most tightly linked markers and to determine the accurate position of QTLs. The application of next generation sequencing technologies will contribute to the development of new markers and the identification of candidate genes for ascochyta blight resistance.

Metabolomic approaches reveal that cell wall modifications play a major role in ethylene-mediated resistance against Botrytis cinerea

In Arabidopsis, resistance to the necrotrophic fungus Botrytis cinerea is conferred by ethylene via poorly understood mechanisms. Metabolomic approaches compared the responses of the wild-type, the ethylene-insensitive mutant etr1-1, which showed increased susceptibility, and the constitutively active ethylene mutants ctr1-1 and eto2 both exhibited decreased susceptibility to B. cinerea. Fourier transform-infrared (FT-IR) spectroscopy demonstrated reproducible biochemical differences between treatments and genotypes. To identify discriminatory mass-to-charge ratios (m/z) associated with resistance, discriminant function analysis was employed on spectra derived from direct injection electrospray ionisation-mass spectrometry on the derived principal components of these data. Ethylene-modulated m/z were mapped onto Arabidopsis biochemical pathways and many were associated with hydroxycinnamate and monolignol biosynthesis, both linked to cell wall modification. A high-resolution linear triple quadrupole-Orbitrap hybrid system confirmed the identity of key metabolites in these pathways. The contribution of these pathways to defence against B. cinerea was validated through the use of multiple Arabidopsis mutants. The FT-IR microspectroscopy indicated that spatial accumulation of hydroxycinnamates and monolignols at the cell wall to confine disease was linked ot ethylene. These data demonstrate the power of metabolomic approaches in elucidating novel biological phenomena, especially when coupled to validation steps exploiting relevant mutant genotypes.