Metabolic networks of Cucurbita maxima phloem

Regulation of carbohydrate metabolism during anther development in a thermo-sensitive genic male-sterile wheat line

Bainong sterility (BNS) is a thermo-sensitive genic male sterile wheat line, characterised by anther fertility transformation in response to low temperature (LT) stress during meiosis, the failure of vacuole decomposition and the absence of starch accumulation in sterile bicellular pollen. Our study demonstrates that the late microspore (LM) stage marks the transition from the anther growth to anther maturation phase, characterised by the changes in anther structure, carbohydrate metabolism and the main transport pathway of sucrose (Suc). Fructan is a main storage polysaccharide in wheat anther, and its synthesis and remobilisation are crucial for anther development. Moreover, the process of pollen amylogenesis and the fate of the large vacuole in pollen are closely intertwined with fructan synthesis and remobilisation. LT disrupts the normal physiological metabolism of BNS anthers during meiosis, particularly affecting carbohydrate metabolism, thus determining the fate of male gametophytes and pollen abortion. Disruption of fructan synthesis and remobilisation regulation serves as a decisive event that results in anther abortion. Sterile pollen exhibits common traits of pollen starvation and impaired starch accumulation due to the inhibition of apoplastic transport starting from the LM stage, which is regulated by cell wall invertase TaIVR1 and Suc transporter TaSUT1.

Aphid adaptation to cucurbits: sugars, cucurbitacin and phloem structure in resistant and susceptible melons

BACKGROUND

Aphis gossypii, a strictly phloemophagaous aphid, colonize hundreds of plant families, and a group of clones formed a cucurbit-specialised host-race. Cucurbits are unique in having evolved a specific extra-fascicular phloem (EFP), which carries defence-related metabolites such as cucurbitacin, whereas the fascicular phloem (FP) is common to all higher plants and carries primary metabolites, such as raffinose-family oligosaccharides (RFOs). Both cucurbitacins (in the EFP) and galactinol (in the FP) have been suggested to be toxic to aphids. We investigated these hypotheses in cucurbit-specialized A. gossypii fed on melon plants with or without aphid-resistance conferred by the NLR gene Vat. We selected a plant-aphid system with (i) Vat-mediated resistance not triggered, (ii) Vat-mediated resistance triggered by an aphid clone adapted to the presence of Vat resistant alleles and (iii) Vat-mediated resistance triggered by a non-adapted aphid clone.

RESULTS

We quantified cucurbitacin B, its glycosylated derivative, and sugars, in melon plants and aphids that fed on. The level of cucurbitacin in plants was unrelated to both aphid infestation and aphid resistance. Galactinol was present at higher quantities in plants when Vat-mediated resistance was triggered, but its presence did not correlate with aphid performance. Finally, we showed that cucurbit-specialized A. gossypii fed from the FP but could also occasionally access the EFP without sustainably feeding from it. However, the clone not adapted to Vat-mediated resistance were less able to access the FP when the Vat resistance was triggered.

CONCLUSION

We concluded that galactinol accumulation in resistant plants does not affect aphids, but may play a role in aphid adaptation to fasting and that Cucurbitacin in planta is not a real threat to Aphis gossypii. Moreover, the specific phloem of Cucurbits is involved neither in A. gossypii cucurbit specialisation nor in adaptation to Vat-dependent resistance.

Phloem Sap Composition: What Have We Learnt from Metabolomics?

Phloem sap transport is essential for plant nutrition and development since it mediates redistribution of nutrients, metabolites and signaling molecules. However, its biochemical composition is not so well-known because phloem sap sampling is difficult and does not always allow extensive chemical analysis. In the past years, efforts have been devoted to metabolomics analyses of phloem sap using either liquid chromatography or gas chromatography coupled with mass spectrometry. Phloem sap metabolomics is of importance to understand how metabolites can be exchanged between plant organs and how metabolite allocation may impact plant growth and development. Here, we provide an overview of our current knowledge of phloem sap metabolome and physiological information obtained therefrom. Although metabolomics analyses of phloem sap are still not numerous, they show that metabolites present in sap are not just sugars and amino acids but that many more metabolic pathways are represented. They further suggest that metabolite exchange between source and sink organs is a general phenomenon, offering opportunities for metabolic cycles at the whole-plant scale. Such cycles reflect metabolic interdependence of plant organs and shoot-root coordination of plant growth and development.

Comparison of Widely Targeted Metabolomics and Untargeted Metabolomics of Wild Ophiocordyceps Sinensis

The authors of this paper conducted a comparative metabolomic analysis of Ophiocordyceps sinensis (OS), providing the metabolic profiles of the stroma (OSBSz) and sclerotia (OSBSh) of OS by widely targeted metabolomics and untargeted metabolomics. The results showed that 778 and 1449 metabolites were identified by the widely targeted metabolomics and untargeted metabolomics approaches, respectively. The metabolites in OSBSz and OSBSh are significantly differentiated; 71 and 96 differentially expressed metabolites were identified by the widely targeted metabolomics and untargeted metabolomics approaches, respectively. This suggests that these 71 metabolites (riboflavine, tripdiolide, bromocriptine, lumichrome, tetrahymanol, citrostadienol, etc.) and 96 metabolites (sancycline, vignatic acid B, pirbuterol, rubrophen, epalrestat, etc.) are potential biomarkers. 4-Hydroxybenzaldehyde, arginine, and lumichrome were common differentially expressed metabolites. Using the widely targeted metabolomics approach, the key pathways identified that are involved in creating the differentiation between OSBSz and OSBSh may be nicotinate and nicotinamide metabolism, thiamine metabolism, riboflavin metabolism, glycine, serine, and threonine metabolism, and arginine biosynthesis. The differentially expressed metabolites identified using the untargeted metabolomics approach were mainly involved in arginine biosynthesis, terpenoid backbone biosynthesis, porphyrin and chlorophyll metabolism, and cysteine and methionine metabolism. The purpose of this research was to provide support for the assessment of the differences between the stroma and sclerotia, to furnish a material basis for the evaluation of the physical effects of OS, and to provide a reference for the selection of detection methods for the metabolomics of OS.

Cellular export of sugars and amino acids: role in feeding other cells and organisms

Sucrose, hexoses, and raffinose play key roles in the plant metabolism. Sucrose and raffinose, produced by photosynthesis, are translocated from leaves to flowers, developing seeds and roots. Translocation occurs in the sieve elements or sieve tubes of angiosperms. But how is sucrose loaded into and unloaded from the sieve elements? There seem to be two principal routes: one through plasmodesmata and one via the apoplasm. The best-studied transporters are the H+/SUCROSE TRANSPORTERs (SUTs) in the sieve element-companion cell complex. Sucrose is delivered to SUTs by SWEET sugar uniporters that release these key metabolites into the apoplasmic space. The H+/amino acid permeases and the UmamiT amino acid transporters are hypothesized to play analogous roles as the SUT-SWEET pair to transport amino acids. SWEETs and UmamiTs also act in many other important processes-for example, seed filling, nectar secretion, and pollen nutrition. We present information on cell type-specific enrichment of SWEET and UmamiT family members and propose several members to play redundant roles in the efflux of sucrose and amino acids across different cell types in the leaf. Pathogens hijack SWEETs and thus represent a major susceptibility of the plant. Here, we provide an update on the status of research on intercellular and long-distance translocation of key metabolites such as sucrose and amino acids, communication of the plants with the root microbiota via root exudates, discuss the existence of transporters for other important metabolites and provide potential perspectives that may direct future research activities.

Organic Waste-Based Fertilizer in Hydroponics Increases Tomato Fruit Size but Reduces Fruit Quality

In regions with intensive agricultural production, large amounts of organic waste are produced by livestock animals. Liquid digestate from manure-based biogas production could potentially serve as fertilizer if integrated with closed horticultural irrigation systems. The aim of this experiment was to investigate how fertilizer based on liquid biogas by-products of pig manure digestion can affect the growth and production of tomato plants. Integration of a nitrification bioreactor presumes a significantly lower concentration of nutrient solutions and a higher level of oxygenation than classical mineral cultivation. Therefore, additional controls were included. We compared plant growth and fruit quality traits of tomato plants grown in a hydroponic solution with organic fertilizer with two levels of mineral fertilizer. The tomatoes grown with organic waste-based liquid fertilizer showed reduced growth rates but increased mean fruit size, resulting in no significant change in total yield compared with high-mineral cultivation. The growth rate was similarly reduced in plants cultivated with low-mineral fertilizer. Plants cultivated with organic waste-based fertilizer had high Cl^- concentration in xylem sap, leaves, and, ultimately, fruits. The leaves of plants cultivated with organic waste-based fertilizer contained higher concentrations of starch and soluble carbohydrate and low concentrations of phosphorous (P) and sulfur (S). The plants grown with organic waste-based or low-mineral medium showed significantly poorer fruit quality than the plants cultivated with the high-mineral solution. The low-mineral treatment increased xylem sap contribution to fruit weight because of higher root power. The organic waste-based fertilization did not change the root power but increased fruit size. In conclusion, organic waste-based cultivation is a possible solution for sustainable plant production in greenhouses. However, additional adjustment of nutrient supply is required to improve fruit quality.

Unraveling the Roles of Vascular Proteins Using Proteomics

Vascular bundles play important roles in transporting nutrients, growth signals, amino acids, and proteins between aerial and underground tissues. In order to understand these sophisticated processes, a comprehensive analysis of the roles of the components located in the vascular tissues is required. A great deal of data has been obtained from proteomic analyses of vascular tissues in plants, which mainly aim to identify the proteins moving through the vascular tissues. Here, different aspects of the phloem and xylem proteins are reviewed, including their collection methods, and their main biological roles in growth, and biotic and abiotic stress responses. The study of vascular proteomics shows great potential to contribute to our understanding of the biological mechanisms related to development and defense in plants.

Liquid Chromatography/Mass Spectrometry based serum metabolomics study on recurrent abortion women with antiphospholipid syndrome

Objective

The antiphospholipid syndrome (APS) is an important cause of acquired thromboembolic complications and pregnancy morbidity. The pathogenic mechanisms that damage the fetal–maternal unit and cause abnormal placental development are incompletely understood in APS patients. Liquid Chromatography/Mass Spectrometry (LC/MS) based metabolomics are applied for the mechanism of disease and further supporting the research of diagnosis and management in recent years. The aim of this research was to investigate the difference of serum metabolic profiles in recurrent abortion women with APS and healthy women to explore the mechanism of this disease.

Methods

Serum samples of 25 recurrent abortion women with APS and 25 healthy women were collected and analyzed by LC/MS in this study. Potential biomarkers were discovered by multivariate statistical analysis and then identified based on analysis results.

Results

Totally, we identified five biomarkers that involved in different metabolic pathway such as purine metabolism, amino acid metabolism and tyrosine metabolism. These biomarkers showed different roles in disease development.

Conclusion

Metabolomics was proved as a powerful tool in understanding the mechanism of recurrent abortion caused by APS.

Application of capillary electrophoretic methods for the analysis of plant phloem and xylem saps composition: A review

Plant vascular tissue is essential for the exchange of water, nutrients, metabolic products, and signals among distant organs in cormophytes. The compositions of phloem and xylem saps are highly dependent on many internal and external factors, and thus their analysis provides a valuable insight into plant physiology, growth, and development as well as nutrition status or presence of biotic or abiotic stresses. Capillary electrophoresis characterized by highly efficient separations and minuscule sample requirements represents a suitable analytical technique for this purpose because the sap constitutes a complex mixture with generally minimal availability. This review aims at providing a comprehensive overview of published capillary electrophoretic methods for the analysis of primary components present in the phloem and xylem saps of higher plants.

Metabolomics responses of Bambusa pervariabilis × Dendrocalamopsis grandis varieties to Biotic (pathogenic fungus) stress

Bambusa pervariabilis × Dendrocalamopsis grandis blight, caused by Arthrinium phaeospermum, is one of the most common and serious diseases in bamboo and occurs in the newly born twigs. Bamboo has suffered large dead areas, including more than 3000 hm², which greatly threatens the process of returning farmlands to forests and the construction of ecological barriers. To identify differential metabolites and metabolic pathways associated with B. pervariabilis × D. grandis to A. phaeospermum, ultra-performance liquid chromatography (UPLC) and quadrupole-time of flight (Q-TOF) Mass Spectrometry (MS) combined with a data-dependent acquisition method was used to analyse the entire sample spectrum. In total, 13223 positive ion peaks and 10616 negative ion peaks were extracted. OPLS-DA and several other analyses were performed using the original data. The OPLS-DA models showed good quality and had strong predictive power, indicating clear trends in the analyses of the treatment and control groups. Clustering and KEGG pathway analyses were used to screen the differential metabolites in the treatment and control groups from the three B. pervariabilis × D. grandis varieties and reflected their metabolic responses induced by A. phaeospermum infection. The results showed that the three B. pervariabilis × D. grandis varieties mode showed significant changes in the following six resistance-related metabolites after A. phaeospermum invasion in positive and negative ion modes: proline, glutamine, dictamnine, apigenin 7-O-neohesperidoside, glutamate, and cis-Aconitate. The following four main metabolic pathways are involved: Arginine and proline metabolism, Glyoxylate and dicarboxylate metabolism, Biosynthesis of alkaloids derived from shikimate pathway, and Flavone and flavonol biosynthesis. This study lays a foundation for the later detection of differential metabolites and metabolic pathways for targeting, and provides a theoretical basis for disease-resistant breeding and the control of B. pervariabilis × D. grandis blight.

Fruit Salad in the Lab: Comparing Botanical Species to Help Deciphering Fruit Primary Metabolism

Although fleshy fruit species are economically important worldwide and crucial for human nutrition, the regulation of their fruit metabolism remains to be described finely. Fruit species differ in the origin of the tissue constituting the flesh, duration of fruit development, coordination of ripening changes (climacteric vs. non-climacteric type) and biochemical composition at ripeness is linked to sweetness and acidity. The main constituents of mature fruit result from different strategies of carbon transport and metabolism. Thus, the timing and nature of phloem loading and unloading can largely differ from one species to another. Furthermore, accumulations and transformations of major soluble sugars, organic acids, amino acids, starch and cell walls are very variable among fruit species. Comparing fruit species therefore appears as a valuable way to get a better understanding of metabolism. On the one hand, the comparison of results of studies about species of different botanical families allows pointing the drivers of sugar or organic acid accumulation but this kind of comparison is often hampered by heterogeneous analysis approaches applied in each study and incomplete dataset. On the other hand, cross-species studies remain rare but have brought new insights into key aspects of primary metabolism regulation. In addition, new tools for multi-species comparisons are currently emerging, including meta-analyses or re-use of shared metabolic or genomic data, and comparative metabolic flux or process-based modeling. All these approaches contribute to the identification of the metabolic factors that influence fruit growth and quality, in order to adjust their levels with breeding or cultural practices, with respect to improving fruit traits.

Exploring the pharmacological effects and potential targets of paeoniflorin on the endometriosis of cold coagulation and blood stasis model rats by ultra-performance liquid chromatography tandem mass spectrometry with a pattern recognition approach

This study was employed to explore the potential biomarkers of endometriosis of cold coagulation and blood stasis (ECB) model rats and the effective mechanism of action of paeoniflorin (PF). The serum metabolomics approach was carried out using the UPLC-MS technique with a pattern recognition approach to prove the possible biomarkers of the ECB model rats and the perturbed pathways. Subsequently, the mechanism of PF treatment of this disease model was elucidated. The results revealed that the serum metabolism profiles in two groups were also separated significantly. Moreover, 8 biomarkers were found in the positive mode, and 5 biomarkers were found in the negative mode. Totally, 13 biomarkers participated in the metabolism of phenylalanine, arachidonic acid, etc. After treatment with PF, 10 biomarkers were regulated. Among the 10 biomarkers, 4 were statistically significant: l-phenylalanine, l-tryptophan, LysoPC (18:4(6Z,9Z,12Z,15Z)), and LysoPC (16:1(9Z)). We initially confirmed that PF could significantly regulate the metabolic expression of multiple metabolic pathways in the ECB model rats. For the first time, this study explored the mechanism of action of PF treatment based on the metabolic pathways of the organism and demonstrated the potential of the metabolomics techniques for the study of drug action mechanisms.

Central Metabolism Is Tuned to the Availability of Oxygen in Developing Melon Fruit

Respiration of bulky plant organs such as fleshy fruits depends on oxygen (O₂) availability and often decreases with O₂ concentration to avoid anoxia, but the relationship between O₂ diffusional resistance and metabolic adjustments remains unclear. Melon fruit (Cucumis melo L.) was used to study relationships between O₂ availability and metabolism in fleshy fruits. Enzyme activities, primary metabolites and O₂ partial pressure were quantified from the periphery to the inner fruit mesocarp, at three stages of development. Hypoxia was gradually established during fruit development, but there was no strong oxygen gradient between the outer- and the inner mesocarp. These trends were confirmed by a mathematical modeling approach combining O₂ diffusion equations and O₂ demand estimates of the mesocarp tissue. A multivariate analysis of metabolites, enzyme activities, O₂ demand and concentration reveals that metabolite gradients and enzyme capacities observed in melon fruits reflect continuous metabolic adjustments thus ensuring a timely maturation of the mesocarp. The present results suggest that the metabolic adjustments, especially the tuning of the capacity of cytochrome c oxidase (COX) to O₂-availability that occurs during growth development, contribute to optimizing the O₂-demand and avoiding the establishment of an O₂ gradient within the flesh.

A non-persistent aphid-transmitted Potyvirus differentially alters the vector and non-vector biology through host plant quality manipulation

The association of plant viruses with their vectors has significant implications for virus transmission and spread. Only a few studies, with even fewer pathosystems, have explored non-persistent (NP) virus-vector interactions that are presumed to be transient. We studied how a NP virus, Papaya ringspot virus (PRSV) influenced the behavior and biology of its vector, the melon aphid (Aphis gossypii Glover) and the non-vector, silverleaf whitefly (Bemisia tabaci Gennadius). We also assessed whether the fitness effects on aphids are modulated through changes in the host plant, squash (Cucurbita pepo L.) nutrient profile. The overall performance of A. gossypii was substantially higher on PRSV-infected plants, along with increased arrestment on PRSV-infected than non-infected plants. No such PRSV-modulated fitness effects were observed with B. tabaci. PRSV-infected plants had increased concentrations of free essential amino acids: threonine, arginine and lysine; non-essential amino acids: glycine and homocysteine; and soluble carbohydrates: galactose, raffinose and cellobiose. In general, PRSV encouraged long-term feeding and enhanced fitness of A. gossypii through host plant nutrient enrichment. These findings provide evidence for a NP virus mediated positive fitness effects on its vector, with no spillover fitness benefits to the non-vector within the same feeding guild.

Review of recent developments in GC-MS approaches to metabolomics-based research

BACKGROUND

Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC-MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and 'in house' metabolite databases available.

AIM OF REVIEW

This review provides an overview of developments in GC-MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC-MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The purpose of this review is to both highlight and provide an update on GC-MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC-MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.

Metabolomic profiling of matured coconut water during post-harvest storage revealed discrimination and distinct changes in metabolites

The metabolites of coconut water stored at room temperature were analyzed using UPLC-MS/MS and multivariate statistical analysis to identify the differential biomarkers and metabolic pathways during post-harvest storage. Principal component analysis (PCA), partial least squares-discriminate analysis (PLS-DA), and orthogonal projections to latent structures discriminant analysis (OPLS-DA) were employed to analyze the UPLC-MS/MS data set of 34 matured coconut water samples collected after 0, 1, 2, 3, 4, and 5 months of storage (MOS); moreover, the p-value and fold change were chosen to identify the differential biomarkers; furthermore, a KEGG pathway was applied to analyze the metabolic pathways. All samples were discriminated well in the OPLS-DA model and were divided into two clusters: groups A (0 MOS, and so on), B, C, and D were in one cluster, and groups E and F were in another. A total of 18 biomarkers were identified among all groups and 12 biomarkers between groups A and E, from which we concluded that the post-harvest storage life of matured coconut water shall not exceed 3 months and the pathways of the TCA cycle, protein hydrolysis from coconut meat, and interconversion among amino acids were mainly enriched during the post-harvest storage.

Illuminating the dark metabolome to advance the molecular characterisation of biological systems

BACKGROUND

The latest version of the Human Metabolome Database (v4.0) lists 114,100 individual entries. Typically, however, metabolomics studies identify only around 100 compounds and many features identified in mass spectra are listed only as 'unknown compounds'. The lack of ability to detect all metabolites present, and fully identify all metabolites detected (the dark metabolome) means that, despite the great contribution of metabolomics to a range of areas in the last decade, a significant amount of useful information from publically funded studies is being lost or unused each year. This loss of data limits our potential gain in knowledge and understanding of important research areas such as cell biology, environmental pollution, plant science, food chemistry and health and biomedical research. Metabolomics therefore needs to develop new tools and methods for metabolite identification to advance as a field.

AIM OF REVIEW

In this critical review, some potential issues with metabolite identification are identified and discussed. New and novel emerging technologies and tools which may contribute to expanding the number of compounds identified in metabolomics studies (thus illuminating the dark metabolome) are reviewed. The aim is to stimulate debate and research in the molecular characterisation of biological systems to drive forward metabolomic research.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The work specifically discusses dynamic nuclear polarisation nuclear magnetic resonance spectroscopy (DNP-NMR), non-proton NMR active nuclei, two-dimensional liquid chromatography (2DLC) and Raman spectroscopy (RS). It is suggested that developing new methods for metabolomics with these techniques could lead to advances in the field and better characterisation of biological systems.

Cucurbit extrafascicular phloem has strong negative impacts on aphids and is not a preferred feeding site

Cucurbits have long been known to possess two types of phloem: fascicular (FP) within vascular bundles and extrafascicular phloem (EFP) surrounding vascular bundles and scattered through the cortex. Recently, their divergent composition was revealed, with FP having high sugar content consistent with conventional phloem, but EFP having much lower sugar levels and a very different proteome. However, the evolutionary advantages of possessing both FP and EFP have remained unclear. Here, we present four lines of quantitative evidence that together support the hypothesis that FP represents a typical phloem and is an attractive diet for aphids, whereas aphids avoid feeding on EFP. First, aphid stylet track endings were more abundant near the abaxial FP element of minor veins, suggesting a feeding preference for FP over EFP. Second, sugar profiles from stylet exudates were wholly consistent with FP origins, further supporting preference for FP and avoidance of EFP. Third, supplementation of EFP exudate into artificial diets confirmed an aversion to EFP in choice experiments. Finally, EFP exudate had negative effects on aphid performance. On the basis of aphids' inability to thrive on EFP, we conclude that EFP is atypical and perhaps should not be classed as a phloem system.

Behavioral Sabotage of Plant Defenses by Insect Folivores

Plant susceptibility to herbivore attack is determined not just by the suite of defenses present in different tissues of the plant, but also by the capabilities of the herbivore for tolerating, circumventing, or disarming the defenses. This article reviews the elaborate behaviors exhibited by leaf-chewing insects that appear to function specifically to deactivate hostplant defenses. Shortcomings in our understanding and promising areas for future research are highlighted. Behaviors covered include vein cutting, trenching, girdling, leaf clipping, and application of fluids from exocrine glands. Many of these behaviors have a widespread distribution, having evolved independently in multiple insect lineages. Insects utilizing the behaviors include significant agricultural, horticultural, and forestry pests, as well as numerous species important in natural ecosystems. Behavioral, ecological, and phylogenetic studies have documented the importance of the behaviors and their ancient history, but the molecular analysis of how the behaviors affect plant physiology has scarcely begun.

Comparative proteomics of cucurbit phloem indicates both unique and shared sets of proteins

Cucurbits are well-studied models for phloem biology but unusually possess both fascicular phloem (FP) within vascular bundles and additional extrafascicular phloem (EFP). Although the functional differences between the two systems are not yet clear, sugar analysis and limited protein profiling have established that FP and EFP have divergent compositions. Here we report a detailed comparative proteomics study of FP and EFP in two cucurbits, pumpkin and cucumber. We re-examined the sites of exudation by video microscopy, and confirmed that in both species, the spontaneous exudate following tissue cutting derives almost exclusively from EFP. Comparative gel electrophoresis and mass spectrometry-based proteomics of exudates, sieve element contents and microdissected stem tissues established that EFP and FP profiles are highly dissimilar, and that there are also species differences. Searches against cucurbit databases enabled identification of more than 300 FP proteins from each species. Few of the detected proteins (about 10%) were shared between the sieve element contents of FP and EFP, and enriched Gene Ontology categories also differed. To explore quantitative differences in the proteomes, we developed multiple reaction monitoring methods for cucumber proteins that are representative markers for FP or EFP and assessed exudate composition at different times after tissue cutting. Based on failure to detect FP markers in exudate samples, we conclude that FP is blocked very rapidly and therefore makes a minimal contribution to the exudates. Overall, the highly divergent contents of FP and EFP indicate that they are substantially independent vascular compartments.

Proteomics and metabolomics analyses reveal the cucurbit sieve tube system as a complex metabolic space

The plant vascular system, and specifically the phloem, plays a pivotal role in allocation of fixed carbon to developing sink organs. Although the processes involved in loading and unloading of sugars and amino acids are well characterized, little information is available regarding the nature of other metabolites in the sieve tube system (STS) at specific sites along the pathway. Here, we elucidate spatial features of metabolite composition mapped with phloem enzymes along the cucurbit STS. Phloem sap (PS) was collected from the loading (source), unloading (apical sink region) and shoot-root junction regions of cucumber, watermelon and pumpkin. Our PS analyses revealed significant differences in the metabolic and proteomic profiles both along the source-sink pathway and between the STSs of these three cucurbits. In addition, metabolite profiles established for PS and vascular tissue indicated the presence of distinct compositions, consistent with the operation of the STS as a unique symplasmic domain. In this regard, at various locations along the STS we could map metabolites and their related enzymes to specific metabolic pathways. These findings are discussed with regard to the function of the STS as a unique and highly complex metabolic space within the plant vascular system.

Connecting Source with Sink: The Role of Arabidopsis AAP8 in Phloem Loading of Amino Acids

Allocation of large amounts of nitrogen to developing organs occurs in the phloem and is essential for plant growth and seed development. In Arabidopsis (Arabidopsis thaliana) and many other plant species, amino acids represent the dominant nitrogen transport forms in the phloem, and they are mainly synthesized in photosynthetically active source leaves. Following their synthesis, a broad spectrum of the amino nitrogen is actively loaded into the phloem of leaf minor veins and transported within the phloem sap to sinks such as developing leaves, fruits, or seeds. Controlled regulation of the source-to-sink transport of amino acids has long been postulated; however, the molecular mechanism of amino acid phloem loading was still unknown. In this study, Arabidopsis AMINO ACID PERMEASE8 (AAP8) was shown to be expressed in the source leaf phloem and localized to the plasma membrane, suggesting its function in phloem loading. This was further supported by transport studies with aap8 mutants fed with radiolabeled amino acids and by leaf exudate analyses. In addition, biochemical and molecular analyses revealed alterations in leaf nitrogen pools and metabolism dependent on the developmental stage of the mutants. Decreased amino acid phloem loading and partitioning to sinks led to decreased silique and seed numbers, but seed protein levels were unchanged, demonstrating the importance of AAP8 function for sink development rather than seed quality. Overall, these results show that AAP8 plays an important role in source-to-sink partitioning of nitrogen and that its function affects source leaf physiology and seed yield.

Plant fluid proteomics: Delving into the xylem sap, phloem sap and apoplastic fluid proteomes

The phloem sap, xylem sap and apoplastic fluid play key roles in long and short distance transport of signals and nutrients, and act as a barrier against local and systemic pathogen infection. Among other components, these plant fluids contain proteins which are likely to be important players in their functionalities. However, detailed information about their proteomes is only starting to arise due to the difficulties inherent to the collection methods. This review compiles the proteomic information available to date in these three plant fluids, and compares the proteomes obtained in different plant species in order to shed light into conserved functions in each plant fluid. Inter-species comparisons indicate that all these fluids contain the protein machinery for self-maintenance and defense, including proteins related to cell wall metabolism, pathogen defense, proteolysis, and redox response. These analyses also revealed that proteins may play more relevant roles in signaling in the phloem sap and apoplastic fluid than in the xylem sap. A comparison of the proteomes of the three fluids indicates that although functional categories are somewhat similar, proteins involved are likely to be fluid-specific, except for a small group of proteins present in the three fluids, which may have a universal role, especially in cell wall maintenance and defense. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Plant and pathogen nutrient acquisition strategies

Nutrients are indispensable elements required for the growth of all living organisms including plants and pathogens. Phyllosphere, rhizosphere, apoplast, phloem, xylem, and cell organelles are the nutrient niches in plants that are the target of bacterial pathogens. Depending upon nutrients availability, the pathogen adapts various acquisition strategies and inhabits the specific niche. In this review, we discuss the nutrient composition of different niches in plants, the mechanisms involved in the recognition of nutrient niche and the sophisticated strategies used by the bacterial pathogens for acquiring nutrients. We provide insight into various nutrient acquisition strategies used by necrotrophic, biotrophic, and hemibiotrophic bacteria. Specifically we discuss both modulation of bacterial machinery and manipulation of host machinery. In addition, we highlight the current status of our understanding about the nutrient acquisition strategies used by bacterial pathogens, namely targeting the sugar transporters that are dedicated for the plant's growth and development. Bacterial strategies for altering the plant cell membrane permeability to enhance the release of nutrients are also enumerated along with in-depth analysis of molecular mechanisms behind these strategies. The information presented in this review will be useful to understand the plant-pathogen interaction in nutrient perspective.

Biochemical and physiological mechanisms underlying effects of Cucumber mosaic virus on host-plant traits that mediate transmission by aphid vectors

The transmission of insect-vectored diseases entails complex interactions among pathogens, hosts and vectors. Chemistry plays a key role in these interactions; yet, little work has addressed the chemical ecology of insect-vectored diseases, especially in plant pathosystems. Recently, we documented effects of Cucumber mosaic virus (CMV) on the phenotype of its host (Cucurbita pepo) that influence plant-aphid interactions and appear conducive to the non-persistent transmission of this virus. CMV reduces host-plant quality for aphids, causing rapid vector dispersal. Nevertheless, aphids are attracted to the elevated volatile emissions of CMV-infected plants. Here, we show that CMV infection (1) disrupts levels of carbohydrates and amino acids in leaf tissue (where aphids initially probe plants and acquire virions) and in the phloem (where long-term feeding occurs) in ways that reduce plant quality for aphids; (2) causes constitutive up-regulation of salicylic acid; (3) alters herbivore-induced jasmonic acid biosynthesis as well as the sensitivity of downstream defences to jasmonic acid; and (4) elevates ethylene emissions and free fatty acid precursors of volatiles. These findings are consistent with previously documented patterns of aphid performance and behaviour and provide a foundation for further exploration of the genetic mechanisms responsible for these effects and the evolutionary processes that shape them.

Metal species involved in long distance metal transport in plants

The mechanisms plants use to transport metals from roots to shoots are not completely understood. It has long been proposed that organic molecules participate in metal translocation within the plant. However, until recently the identity of the complexes involved in the long-distance transport of metals could only be inferred by using indirect methods, such as analyzing separately the concentrations of metals and putative ligands and then using in silico chemical speciation software to predict metal species. Molecular biology approaches also have provided a breadth of information about putative metal ligands and metal complexes occurring in plant fluids. The new advances in analytical techniques based on mass spectrometry and the increased use of synchrotron X-ray spectroscopy have allowed for the identification of some metal-ligand species in plant fluids such as the xylem and phloem saps. Also, some proteins present in plant fluids can bind metals and a few studies have explored this possibility. This study reviews the analytical challenges researchers have to face to understand long-distance metal transport in plants as well as the recent advances in the identification of the ligand and metal-ligand complexes in plant fluids.

Source-to-sink transport of sugar and regulation by environmental factors

Source-to-sink transport of sugar is one of the major determinants of plant growth and relies on the efficient and controlled distribution of sucrose (and some other sugars such as raffinose and polyols) across plant organs through the phloem. However, sugar transport through the phloem can be affected by many environmental factors that alter source/sink relationships. In this paper, we summarize current knowledge about the phloem transport mechanisms and review the effects of several abiotic (water and salt stress, mineral deficiency, CO2, light, temperature, air, and soil pollutants) and biotic (mutualistic and pathogenic microbes, viruses, aphids, and parasitic plants) factors. Concerning abiotic constraints, alteration of the distribution of sugar among sinks is often reported, with some sinks as roots favored in case of mineral deficiency. Many of these constraints impair the transport function of the phloem but the exact mechanisms are far from being completely known. Phloem integrity can be disrupted (e.g., by callose deposition) and under certain conditions, phloem transport is affected, earlier than photosynthesis. Photosynthesis inhibition could result from the increase in sugar concentration due to phloem transport decrease. Biotic interactions (aphids, fungi, viruses…) also affect crop plant productivity. Recent breakthroughs have identified some of the sugar transporters involved in these interactions on the host and pathogen sides. The different data are discussed in relation to the phloem transport pathways. When possible, the link with current knowledge on the pathways at the molecular level will be highlighted.

Protein profile of Lupinus texensis phloem sap exudates: searching for Fe- and Zn-containing proteins

The aim of this study was to obtain a comprehensive overview of the phloem sap protein profile of Lupinus texensis, with a special focus on proteins binding Fe and Zn. L. texensis was chosen as model plant given the simplicity to obtain exudates from sieve elements. Protein profiling by 2DE revealed 249 spots, and 54 of them were unambiguously identified by MALDI-MS and ESI-MS/MS. The largest number of identified protein species belongs to protein modification/turnover and general metabolism (19-21%), followed by redox homeostasis (9%) and defense and cell structural components (7%). This protein profile is similar to that reported in other plant species, suggesting that the phloem sap proteome is quite conserved. Staining of 2DE gels for Fe-containing proteins and affinity chromatography experiments revealed the presence of two low molecular weight Fe-binding proteins in phloem sap: a metallothionein-like protein type 2B identified in the Fe-affinity chromatography, and a second protein identified with both Fe staining methods. This protein species had a molecular weight of 13.5 kDa, a pI of 5.6 and 51% homology to a phloem-specific protein from Medicago truncatula. Zinc affinity chromatography revealed four Zn-binding proteins in phloem sap, one belonging to the dehydrin family and three Zn finger proteins.

Metabolic acclimation to excess light intensity in Chlamydomonas reinhardtii

There are several well-described acclimation responses to excess light in green algae but the effect on metabolism has not been thoroughly investigated. This study examines the metabolic changes during photoacclimation to high-light (HL) stress in Chlamydomonas reinhardtii using nuclear magnetic resonance and mass spectrometry. Using principal component analysis, a clear metabolic response to HL intensity was observed on global metabolite pools, with major changes in the levels of amino acids and related nitrogen metabolites. Amino acid pools increased during short-term photoacclimation, but were especially prominent in HL-acclimated cultures. Unexpectedly, we observed an increase in mitochondrial metabolism through downstream photorespiratory pathways. The expression of two genes encoding key enzymes in the photorespiratory pathway, glycolate dehydrogenase and malate synthase, were highly responsive to the HL stress. We propose that this pathway contributes to metabolite pools involved in nitrogen assimilation and may play a direct role in photoacclimation. Our results suggest that primary and secondary metabolism is highly pliable and plays a critical role in coping with the energetic imbalance during HL exposure and a necessary adjustment to support an increased growth rate that is an effective energy sink for the excess reducing power generated during HL stress.

Investigation of in vivo metabolic profile of Abelmoschus Manihot based on pattern recognition analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Abelmoschus manihot (L.) Medik. var. manihot is one of the most commonly used Chinese medicines and has played an important role in treating chronic glomerulonephritis and diabetic nephropathy.

AIM OF THE STUDY

Metabolites identification of traditional Chinese medicine (TCM) is a complex and time-consuming process due to the complicity of TCM and subsequent large number of detected ions. In this paper, UPLC-MS combined with pattern recognition analysis approach were used to simplify and quicken the identification of the metabolites of Abelmoschus Manihot.

MATERIALS AND METHODS

Rat urine samples were collected before (as control sample) and after Abelmoschus Manihot administration. Pattern recognition analysis method was used to differentiate components between Abelmoschus Manihot-treated group and its controlled comparison. These components could be considered as Abelmoschus Manihot-related metabolites in vivo.

RESULTS

LC-MS based metabolomics could be an advanced tool to help us find metabolites with regards to its capacity of processing large datasets, differentiating and classifying of sample groups, as well as its indiscriminative nature of biomarker and metabolite identification. Using this method, seven metabolites were identified, which are flavonoid aglycone glucuronidation, sulfatation, and methylation metabolites.

CONCLUSION

Our results showed that UPLC-MS based- pattern recognition analysis approach can be used to quickly identify Abelmoschus Manihot related metabolites in biological fluids. Furthermore, this work demonstrates the potential application of combining the UPLC-MS approach with the metabolomics approach in identifying the metabolites of TCM.

Heavy traffic in the fast lane: long-distance signalling by macromolecules

The two major vascular conduits in plants, the xylem and phloem, theoretically provide opportunities for the long-distance translocation of almost any type of water-borne molecule. This review focuses on the signalling functions conveyed by the movement of macromolecules. Here, a signal is defined as the communication of information from source to destination, where it modifies development, physiology or defence through altered gene expression or by direct influences on other cellular processes. Xylem and phloem sap both contain diverse classes of proteins; in addition, phloem contains many full-length and small RNA species. Only a few of these mobile molecules have proven functions in signalling. The transduction of signals typically depends on connection to appropriate signalling pathways. Incoming protein signals require specific detection systems, generally via receptors. Mobile RNAs require either the translation or presence of a homologous target. Given that phloem sieve elements are enucleate and lack translation machinery, RNA function requires subsequent unloading at least into adjacent companion cells. The binding of RNA by proteins in ribonucleoprotein complexes enables the translocation of some signals, with evidence for both sequence-specific and size-specific binding. Several examples of long-distance macromolecular signalling are highlighted, including the FT protein signal which regulates flowering time and other developmental switches.

Sampling and analysis of phloem sap

The transport tubes of the phloem are essential for higher plants. They not only provide the route for the distribution of assimilates produced during photosynthesis from source to sink organs but also (re-) distribute mineral nutrients. Additionally, the phloem is essential for sending information between distant plant organs and steering developmental and defense processes. For example, flowering and tuberization time are controlled by phloem-mobile signals and important defense reactions on the whole plant level, like systemic acquired resistance or systemic gene silencing, are spread through the phloem. In addition, recent results demonstrate that also the allocation of mineral nutrients is coordinated by phloem mobile signaling molecules. However, in many studies the important analysis of phloem sap is neglected, probably because the content of sieve tubes is not easy to access. This chapter will describe the current methods for sampling and analysis of phloem sap in order to encourage researchers to include the analysis of this crucial compartment in their relevant studies.

Interaction of xylem and phloem during exudation and wound occlusion in Cucurbita maxima

Collection of cucurbit exudates from cut petioles has been a powerful tool for gaining knowledge on phloem sap composition without full notion of the complex exudation mechanism. Only few publications explicitly mentioned that exudates were collected from the basal side of the cut, which exudes more copiously than the apical side. This is surprising since only exudation from the apical side is supposedly driven by phloem pressure gradients. Composition of carbohydrates and pH values at both wounding sides are equal, whereas protein concentration is higher at the basal side. Apparently, exudation is far more complex than just the delivery of phloem sap. Xylem involvement is indicated by lower protein concentrations after elimination of root pressure. Moreover, dye was sucked into xylem vessels owing to relaxation of negative pressure after cutting. The lateral water efflux from the vessels increases turgor of surrounding cells including sieve elements. Simultaneously, detached parietal proteins (PP1/PP2) induce occlusion of sieve plates and cover wound surface. If root pressure is strong enough, pure xylem sap can be collected after removal of the occlusion plug at the wound surface. The present findings provide a mechanism of sap exudation in Cucurbita maxima, in which the contribution of xylem water is integrated.

A novel approach to transforming a non-targeted metabolic profiling method to a pseudo-targeted method using the retention time locking gas chromatography/mass spectrometry-selected ions monitoring

Non-targeted metabolic profiling is the most widely used method for metabolomics. In this paper, a novel approach was established to transform a non-targeted metabolic profiling method to a pseudo-targeted method using the retention time locking gas chromatography/mass spectrometry-selected ion monitoring (RTL-GC/MS-SIM). To achieve this transformation, an algorithm based on the automated mass spectral deconvolution and identification system (AMDIS), GC/MS raw data and a bi-Gaussian chromatographic peak model was developed. The established GC/MS-SIM method was compared with GC/MS-full scan (the total ion current and extracted ion current, TIC and EIC) methods, it was found that for a typical tobacco leaf extract, 93% components had their relative standard deviations (RSDs) of relative peak areas less than 20% by the SIM method, while 88% by the EIC method and 81% by the TIC method. 47.3% components had their linear correlation coefficient higher than 0.99, compared with 5.0% by the EIC and 6.2% by TIC methods. Multivariate analysis showed the pooled quality control samples clustered more tightly using the developed method than using GC/MS-full scan methods, indicating a better data quality. With the analysis of the variance of the tobacco samples from three different planting regions, 167 differential components (p<0.05) were screened out using the RTL-GC/MS-SIM method, but 151 and 131 by the EIC and TIC methods, respectively. The results show that the developed method not only has a higher sensitivity, better linearity and data quality, but also does not need complicated peak alignment among different samples. It is especially suitable for the screening of differential components in the metabolic profiling investigation.

Microbial metabolomics

Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “omics” platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology.

Diurnal changes in assimilate concentrations and fluxes in the phloem of castor bean (Ricinus communis L.) and tansy (Tanacetum vulgare L.)

Reports about diurnal changes of assimilates in phloem sap are controversial. We determined the diurnal changes of sucrose and amino acid concentrations and fluxes in exudates from cut aphid stylets on tansy leaves (Tanacetum vulgare), and sucrose, amino acid and K(+) concentrations and fluxes in bleeding sap of castor bean pedicel (Ricinus communis). Approximately half of the tansy sieve tubes exhibited a diurnal cycle of sucrose concentrations and fluxes in phloem sap. Data from many tansy plants indicated an increased sucrose flux in the phloem during daytime in case of low N-nutrition, not at high N-nutrition. The sucrose concentration in phloem sap of young Ricinus plants changed marginally between day and night, whereas the sucrose flux increased 1.5-fold during daytime (but not in old Ricinus plants). The amino acid concentrations and fluxes in tansy sieve tubes exhibited a similar diurnal cycle as the sucrose concentrations and fluxes, including their dependence on N-nutrition. The amino acid fluxes, but not the concentrations, in phloem sap of Ricinus were higher at daytime. The sucrose/amino acid ratio showed no diurnal cycle neither in tansy nor in Ricinus. The K(+)-concentrations in phloem sap of Ricinus, but not the K(+) fluxes, decreased slightly during daytime and the sucrose/K(+)-ratio increased. In conclusion, a diurnal cycle was observed in sucrose, amino acid and K(+) fluxes, but not necessarily in concentrations of these assimilates. Because of the large variations between different sieve tubes and different plants, the nutrient delivery to sink tissues is not homeostatic over time.

Soluble and filamentous proteins in Arabidopsis sieve elements

Phloem sieve elements are highly differentiated cells involved in the long-distance transport of photoassimilates. These cells contain both aggregated phloem-proteins (P-proteins) and soluble proteins, which are also translocated by mass flow. We used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to carry out a proteomic survey of the phloem exudate of Arabidopsis thaliana, collected by the ethylenediaminetetraacetic acid (EDTA)-facilitated method. We identified 287 proteins, a large proportion of which were enzymes involved in the metabolic precursor generation and amino acid synthesis, suggesting that sieve tubes display high levels of metabolic activity. RNA-binding proteins, defence proteins and lectins were also found. No putative P-proteins were detected in the EDTA-exudate fraction, indicating a lack of long-distance translocation of such proteins in Arabidopsis. In parallel, we investigated the organization of P-proteins, by high-resolution transmission electron microscopy, and the localization of the phloem lectin PP2, a putative P-protein component, by immunolocalization with antibodies against PP2-A1. Transmission electron microscopy observations of P-proteins revealed bundles of filaments resembling strings of beads. PP2-A1 was found weakly associated with these structures in the sieve elements and bound to plastids. These observations suggest that PP2-A1 is anchored to P-proteins and organelles rather than being a structural component of P-proteins.

Large interclone differences in melezitose secretion in the facultatively ant-tended black bean aphid Aphis fabae

Many aphids are known to engage in a trophic mutualism with ants, whereby the aphids secrete sugary-rich honeydew which is collected by the ants for food, and the ants, in exchange, protect the aphids against natural enemies. Previous results, however, suggest that the production of some of the honeydew sugars, such as the ant-attractant trisaccharide melezitose, may induce an indirect cost to the aphids. This led us to believe that large differences in the nature of the secreted honeydew might exist, due to some clones capitalizing more or less on their mutualistic interaction with ants, or due to some "cheater" clones foregoing the production of particular sugars, instead taking advantage of the ant-attracting effect of other non sugar-deficient clones, co-occurring on the same plant. Here we present data on clonal variation in the composition of honeydew of the black bean aphid Aphis fabae which confirm this prediction. In particular, our results show that there was large interclone variation in the amount of glucose, melezitose and total sugar produced. The variation in the production of melezitose, however, showed particularly large differences, with 54% (7 out of 13) of the clones screened being virtually deficient for the production of this sugar, irrespective of whether the aphid colonies were ant-tended or not. The consequences of this finding in the context of the evolution and maintenance of the ant-aphid mutualism, as well as the adaptive benefits of oligosaccharide synthesis in aphids and other insects are discussed.

Urinary metabolite markers of precocious puberty

The incidence of precocious puberty (PP, the appearance of signs of pubertal development at an abnormally early age), is rapidly rising, concurrent with changes of diet, lifestyles, and social environment. The current diagnostic methods are based on a hormone (gonadotropin-releasing hormone) stimulation test, which is costly, time-consuming, and uncomfortable for patients. The lack of molecular biomarkers to support simple laboratory tests, such as a blood or urine test, has been a long standing bottleneck in the clinical diagnosis and evaluation of PP. Here we report a metabolomic study using an ultra performance liquid chromatography-quadrupole time of flight mass spectrometry and gas chromatography-time of flight mass spectrometry. Urine metabolites from 163 individuals were profiled, and the metabolic alterations were analyzed after treatment of central precocious puberty (CPP) with triptorelin depot. A panel of biomarkers selected from >70 differentially expressed urinary metabolites by receiver operating characteristic and logistic regression analysis provided excellent predictive power with high sensitivity and specificity for PP. The altered metabolic profile of the PP patients was characterized by three major perturbed metabolic pathways: catecholamine, serotonin metabolism, and tricarboxylic acid cycle, presumably resulting from activation of the sympathetic nervous system and the hypothalamic-pituitary-gonadal axis. Treatment with triptorelin depot was able to normalize these three altered pathways. Additionally, significant changes in the urine levels of 4-hydroxyphenylacetic acid, 5-hydroxyindoleacetic acid, indoleacetic acid, 5-hydroxytryptophan, and 5-hydroxykynurenamine in the CPP group suggest that the development of CPP condition may involve an alteration in symbiotic gut microbial composition.

Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives

Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites relevant to a specific phenotypic characteristic can be identified. However, the reliability of the analytical data is a prerequisite for correct biological interpretation in metabolomics analysis. In this review the challenges in quantitative metabolomics analysis with regards to analytical as well as data preprocessing steps are discussed. Recommendations are given on how to optimize and validate comprehensive silylation-based methods from sample extraction and derivatization up to data preprocessing and how to perform quality control during metabolomics studies. The current state of method validation and data preprocessing methods used in published literature are discussed and a perspective on the future research necessary to obtain accurate quantitative data from comprehensive GC-MS data is provided.

Accelerating analysis for metabolomics, drugs and their metabolites in biological samples using multidimensional gas chromatography

Gas chromatography (GC) with mass spectrometry (MS) is one of the great enabling analytical tools available to the chemical and biochemical analyst for the measurement of volatile and semi-volatile compounds. From the analysis result, it is possible to assess progress in chemical reactions, to monitor environmental pollutants in a wide range of soil, water or air samples, to determine if an athlete or horse trainer has contravened doping laws, or if crude oil has migrated through subsurface rock to a reservoir. Each of these scenarios and samples has an associated implementation method for GC-MS. However, few samples and the associated interpretation of data is as complex or important as biochemical sample analysis for trace drugs or metabolites. Improving the analysis in both the GC and MS domains is a continual search for better separation, selectivity and sensitivity. Multidimensional methods are playing important roles in providing quality data to address the needs of analysts.

Gas chromatography-mass spectrometric method for metabolic profiling of tobacco leaves

A gas chromatography-mass spectrometric method was developed for profiling of tobacco leaves. The differentiation among tobacco leaves planted in two different regions was investigated. Prior to analysis, the extraction solvent formulation was optimized and a combination of water, methanol and acetonitrile with a volume ratio of 3:1:1 was found to be optimal. The reproducibility of the method was satisfactory. Kendall tau-b rank correlation coefficients were equal to 1 (p<0.05) for 82% of the resolved peaks (up to 95% of the overall peak areas), indicating the good response correlation. Forty-four compounds including 9 saccharides, 9 alcohols, 9 amino acids, 16 organic acids and phosphoric acid were identified based on standard compounds. The method was successfully applied for profiling of tobacco leaves from Zimbabwe and Yunnan of China. Our result revealed that levels of saccharides and their derivatives including xylose, ribose, fructose, glucose, turanose, xylitol and glyceric acid were more abundant while sucrose, glucitol and D-gluconic acid were less abundant in tobacco leaves from Yunnan as compared to those from Zimbabwe. Amino acids such as L-alanine, L-tyrosine and L-threonine were found to be richer in Zimbabwe tobacco than in Yunnan tobacco.

Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics

• Variations in tissue development and spatial composition have a major impact on the nutritional and organoleptic qualities of ripe fleshy fruit, including melon (Cucumis melo). To gain a deeper insight into the mechanisms involved in these changes, we identified key metabolites for rational food quality design. • The metabolome, volatiles and mineral elements were profiled employing an unprecedented range of complementary analytical technologies. Fruits were followed at a number of time points during the final ripening process and tissues were collected across the fruit flesh from rind to seed cavity. Approximately 2000 metabolite signatures and 15 mineral elements were determined in an assessment of temporal and spatial melon fruit development. • This study design enabled the identification of: coregulated hubs (including aspartic acid, 2-isopropylmalic acid, β-carotene, phytoene and dihydropseudoionone) in metabolic association networks; global patterns of coordinated compositional changes; and links of primary and secondary metabolism to key mineral and volatile fruit complements. • The results reveal the extent of metabolic interactions relevant to ripe fruit quality and thus have enabled the identification of essential candidate metabolites for the high-throughput screening of melon breeding populations for targeted breeding programmes aimed at nutrition and flavour improvement.