PROBING PLANT METABOLISM WITH NMR

Visualizing plant intracellular inorganic orthophosphate distribution

Intracellular inorganic orthophosphate (Pi) distribution and homeostasis profoundly affect plant growth and development. However, its distribution patterns remain elusive owing to the lack of efficient cellular Pi imaging methods. Here we develop a rapid colorimetric Pi imaging method, inorganic orthophosphate staining assay (IOSA), that can semi-quantitatively image intracellular Pi with high resolution. We used IOSA to reveal the alteration of cellular Pi distribution caused by Pi starvation or mutations that alter Pi homeostasis in two model plants, rice and Arabidopsis, and found that xylem parenchyma cells and basal node sieve tube element cells play a critical role in Pi homeostasis in rice. We also used IOSA to screen for mutants altered in cellular Pi homeostasis. From this, we have identified a novel cellular Pi distribution regulator, HPA1/PHO1;1, specifically expressed in the companion and xylem parenchyma cells regulating phloem Pi translocation from the leaf tip to the leaf base in rice. Taken together, IOSA provides a powerful method for visualizing cellular Pi distribution and facilitates the analysis of Pi signalling and homeostasis from the level of the cell to the whole plant.

Metabolomics: An Emerging "Omics" Platform for Systems Biology and Its Implications for Huntington Disease Research

Huntington's disease (HD) is a progressive, fatal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. The precise mechanisms of HD progression are poorly understood; however, it is known that there is an expansion of the trinucleotide cytosine-adenine-guanine (CAG) repeat in the Huntingtin gene. Important new strategies are of paramount importance to identify early biomarkers with predictive value for intervening in disease progression at a stage when cellular dysfunction has not progressed irreversibly. Metabolomics is the study of global metabolite profiles in a system (cell, tissue, or organism) under certain conditions and is becoming an essential tool for the systemic characterization of metabolites to provide a snapshot of the functional and pathophysiological states of an organism and support disease diagnosis and biomarker discovery. This review briefly highlights the historical progress of metabolomic methodologies, followed by a more detailed review of the use of metabolomics in HD research to enable a greater understanding of the pathogenesis, its early prediction, and finally the main technical platforms in the field of metabolomics.

Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery

The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.

Determination of phosphorus compounds in plant tissues: from colourimetry to advanced instrumental analytical chemistry

Although the spectrum of effective methods and techniques that allow determination of inorganic or total phosphorus is impressive, more precise analysis of these substances in plant tissues is not a routine or trivial task. The complexity of chemical composition of plant tissues treated as the analytical matrices is thought to be the main cause why there is no one answer, how appropriate phosphorus compounds may be determined qualitatively and quantitatively. Even if more advanced spectrophotometric measurements and classical variants of absorption (FAAS) or emission (ICP-AES/ ICP-OES) spectrometry techniques are used, it is necessary at first to isolate various forms of phosphorus from the matrix, and then to mineralize them prior the determination. Significant progress in such a kind of analytical efforts was brought by implementation of combined methods e.g. ETV-ICP-AES or HR-ETAAS, does allow the isolation of the phosphorus analyte and its detection during a kind of "one step" analytical procedure, directly in plant tissues. Similar benefits, regarding sensitivity of determinations, are obtained when XRF, SIMS or nanoSIMS-more expensive techniques of imaging the presence of phosphorus in biological matrices have been used. Nowadays, obviously being aware of higher limit of detection, nuclear magnetic resonance spectroscopy, especially the ³¹P NMR technique, is thought to be the most universal analytical tool allowing to determine various chemical forms of plant phosphorus qualitatively and quantitatively, at the same time. Although ³¹P NMR provides valuable information about the phosphorus profile of plants, it should be emphasized that each analytical issue related to the determination of phosphorus compounds in plant tissues and organs, requires an individual approach to defined problem.

Lanthanide Metal-Organic Framework-Based Fluorescent Sensor Arrays to Discriminate and Quantify Ingredients of Natural Medicine

The discrimination and quantification of the ingredients from natural medicines are a challenging issue due to their complicated and various structures. Metal-organic frameworks (MOFs) have shown great promise in sensing applications. Here, we report a fluorescent sensor array for rapid identification of some natural compounds using a sensor array composed of four kinds of lanthanide (Eu³⁺ and Tb³⁺) fluorescent MOFs (Ln-MOFs), which have diversified fluorescent responses to 26 active/toxic compounds including 12 saponins, 7 flavonoids, 3 stilbenes, and 4 anthraquinones. The fluorescence of the Ln-MOFs after reaction with the compounds was summarized as datasets and processed by principle component analysis (PCA) and hierarchical cluster analysis (HCA) methods. The corresponding responses of the 4 types of compounds are well separated on 2D/3D PCA score plots and HCA dendrograms. We have also tested typical blind samples by concentration-dependent PCA, and an accuracy of 100% was obtained. In addition, the response mechanisms of the Ln-MOFs to the compounds were also studied. Compared with traditional methods using liquid chromatography-mass spectrometry, the developed fluorescent sensor array provides a more efficient and economic strategy to discriminate various active/toxic ingredients in natural medicine.

Phosphorus homeostasis in Populus alba L. under excess phosphate conditions, assessed by 31P nuclear magnetic resonance spectroscopy and X-ray microfluorescence

The phosphates (Pi) are nowadays recognized as pollutants. We studied the effect of Pi (0.625-12.500 mM KH₂PO₄) in the culture medium on in vitro grown 2-month-old Populus alba trees. The levels of sugar phosphates and vacuolar and cytoplasmic Pi in cell compartments of roots and stems were determined using ³¹P NMR, while tissue-specific micro- and macroelements mapping on stem cross-sections were performed using synchrotron-based X-ray microfluorescence. Plants grown on 0.625 mM Pi (MS/2 medium) showed a survival rate of 70%. With the increase in Pi concentrations up to 6.250 mM, plant growth and survival increased, without changes in total P content per mass or in the levels of cytoplasmic and vacuolar phosphates, in both stems and roots, while the levels of Fe, Cu, Zn, Ca and Mn in stems increased. Further increase in Pi to 9.375 and 12.500 mM in the medium resulted in inhibited growth comparable with plants grown on MS/2, with the increase in total P content per mass up to 50%, in both stems and roots, but with no changes in cytoplasmic and vacuolar phosphates; 12.500 mM Pi affected even plant survival (70%) and thus might be considered as mildly toxic. ³¹P NMR results indicate that the high tolerance of P. alba to increased Pi could result from its ability to maintain an intracellular P homeostasis, despite P accumulation up to 50%, in both stems and roots, indicating P. alba as a promising wood species for dendroremediation.

Tomato roots exhibit in vivo glutamate dehydrogenase aminating capacity in response to excess ammonium supply

In higher plants ammonium (NH₄⁺) assimilation occurs mainly through the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway. Nevertheless, when plants are exposed to stress conditions, such as excess of ammonium, the contribution of alternative routes of ammonium assimilation such as glutamate dehydrogenase (GDH) and asparagine synthetase (AS) activities might serve as detoxification mechanisms. In this work, the in vivo functions of these pathways were studied after supplying an excess of ammonium to tomato (Solanum lycopersicum L. cv. Agora Hybrid F1) roots previously adapted to grow under either nitrate or ammonium nutrition. The short-term incorporation of labelled ammonium (¹⁵NH₄⁺) into the main amino acids was determined by GC-MS in the presence or absence of methionine sulphoximine (MSX) and azaserine (AZA), inhibitors of GS and GOGAT activities, respectively. Tomato roots were able to respond rapidly to excess ammonium by enhancing ammonium assimilation regardless of the previous nutritional regime to which the plant was adapted to grow. The assimilation of ¹⁵NH₄⁺ could take place through pathways other than GS/GOGAT, since the inhibition of GS and GOGAT did not completely impede the incorporation of the labelled nitrogen into major amino acids. The in vivo formation of Asn by AS was shown to be exclusively Gln-dependent since the root was unable to incorporate ¹⁵NH₄⁺ directly into Asn. On the other hand, an in vivo aminating capacity was revealed for GDH, since newly labelled Glu synthesis occurred even when GS and/or GOGAT activities were inhibited. The aminating GDH activity in tomato roots responded to an excess ammonium supply independently of the previous nutritional regime to which the plant had been subjected.

Structural and functional imaging of large and opaque plant specimens

Three- and four-dimensional imaging techniques are a prerequisite for spatially resolving the form-structure-function relationships in plants. However, choosing the right imaging method is a difficult and time-consuming process as the imaging principles, advantages and limitations, as well as the appropriate fields of application first need to be compared. The present study aims to provide an overview of three imaging methods that allow for imaging opaque, large and thick (>5 mm, up to several centimeters), hierarchically organized plant samples that can have complex geometries. We compare light microscopy of serial thin sections followed by 3D reconstruction (LMTS3D) as an optical imaging technique, micro-computed tomography (µ-CT) based on ionizing radiation, and magnetic resonance imaging (MRI) which uses the natural magnetic properties of a sample for image acquisition. We discuss the most important imaging principles, advantages, and limitations, and suggest fields of application for each imaging technique (LMTS, µ-CT, and MRI) with regard to static (at a given time; 3D) and dynamic (at different time points; quasi 4D) structural and functional plant imaging.

In-Vivo NMR Spectroscopy: A Powerful and Complimentary Tool for Understanding Environmental Toxicity

Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning. With in-vivo NMR it is possible to use the same organisms for control and exposure studies (controls are the same organisms prior to exposure inside the NMR). As such individual variability can be reduced while continual data collection over time provides the temporal resolution required to discern complex interconnected response pathways. When multidimensional NMR is combined with isotopic labelling, a wide range of metabolites can be identified in-vivo providing a unique window into the living metabolome that is highly complementary to more traditional metabolomics studies employing extracts, tissues, or biofluids.

Stable isotope compounds - production, detection, and application

Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.

Arbuscular mycorrhiza-specific enzymes FatM and RAM2 fine-tune lipid biosynthesis to promote development of arbuscular mycorrhiza

During arbuscular mycorrhizal symbiosis (AMS), considerable amounts of lipids are generated, modified and moved within the cell to accommodate the fungus in the root, and it has also been suggested that lipids are delivered to the fungus. To determine the mechanisms by which root cells redirect lipid biosynthesis during AMS we analyzed the roles of two lipid biosynthetic enzymes (FatM and RAM2) and an ABC transporter (STR) that are required for symbiosis and conserved uniquely in plants that engage in AMS. Complementation analyses indicated that the biochemical function of FatM overlaps with that of other Fat thioesterases, in particular FatB. The essential role of FatM in AMS was a consequence of timing and magnitude of its expression. Lipid profiles of fatm and ram2 suggested that FatM increases the outflow of 16:0 fatty acids from the plastid, for subsequent use by RAM2 to produce 16:0 β-monoacylglycerol. Thus, during AMS, high-level, specific expression of key lipid biosynthetic enzymes located in the plastid and the endoplasmic reticulum enables the root cell to fine-tune lipid biosynthesis to increase the production of β-monoacylglycerols. We propose a model in which β-monoacylglycerols, or a derivative thereof, are exported out of the root cell across the periarbuscular membrane for ultimate use by the fungus.

Fluxomics links cellular functional analyses to whole-plant phenotyping

Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding.

Performance and Limitations of Phosphate Quantification: Guidelines for Plant Biologists

Phosphate (Pi) is a macronutrient that is essential for plant life. Several regulatory components involved in Pi homeostasis have been identified, revealing a very high complexity at the cellular and subcellular levels. Determining the Pi content in plants is crucial to understanding this regulation, and short real-time(33)Pi uptake imaging experiments have shown Pi movement to be highly dynamic. Furthermore, gene modulation by Pi is finely controlled by localization of this ion at the tissue as well as the cellular and subcellular levels. Deciphering these regulations requires access to and quantification of the Pi pool in the various plant compartments. This review presents the different techniques available to measure, visualize and trace Pi in plants, with a discussion of the future prospects.

Asparagine Metabolic Pathways in Arabidopsis

Inorganic nitrogen in the form of ammonium is assimilated into asparagine via multiple steps involving glutamine synthetase (GS), glutamate synthase (GOGAT), aspartate aminotransferase (AspAT) and asparagine synthetase (AS) in Arabidopsis. The asparagine amide group is liberated by the reaction catalyzed by asparaginase (ASPG) and also the amino group of asparagine is released by asparagine aminotransferase (AsnAT) for use in the biosynthesis of amino acids. Asparagine plays a primary role in nitrogen recycling, storage and transport in developing and germinating seeds, as well as in vegetative and senescence organs. A small multigene family encodes isoenzymes of each step of asparagine metabolism in Arabidopsis, except for asparagine aminotransferase encoded by a single gene. The aim of this study is to highlight the structure of the genes and encoded enzyme proteins involved in asparagine metabolic pathways; the regulation and role of different isogenes; and kinetic and physiological properties of encoded enzymes in different tissues and developmental stages.

Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.

Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

Recent advances in 13C-Metabolic flux analysis (13C-MFA) have increased its capability to accurately resolve fluxes using a genome-scale model with narrow confidence intervals without pre-judging the activity or inactivity of alternate metabolic pathways. However, the necessary precautions, computational challenges, and minimum data requirements for successful analysis remain poorly established. This review aims to establish the necessary guidelines for performing 13C-MFA at the genome-scale for a compartmentalized eukaryotic system such as yeast in terms of model and data requirements, while addressing key issues such as statistical analysis and network complexity. We describe the various approaches used to simplify the genome-scale model in the absence of sufficient experimental flux measurements, the availability and generation of reaction atom mapping information, and the experimental flux and metabolite labeling distribution measurements to ensure statistical validity of the obtained flux distribution. Organism-specific challenges such as the impact of compartmentalization of metabolism, variability of biomass composition, and the cell-cycle dependence of metabolism are discussed. Identification of errors arising from incorrect gene annotation and suggested alternate routes using MFA are also highlighted.

Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future

Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.

Fusarium inhibition by wild populations of the medicinal plant Salvia africana-lutea L. linked to metabolomic profiling

Background

Salvia africana-lutea L., an important medicinal sage used in the Western Cape (South Africa), can be termed a ‘broad-spectrum remedy’ suggesting the presence of a multiplicity of bioactive metabolites. This study aimed at assessing wild S. africana-lutea populations for chemotypic variation and anti-Fusarium properties.

Methods

Samples were collected from four wild growing population sites (Yzerfontein, Silwerstroomstrand, Koeberg and Brackenfell) and one garden growing location in Stellenbosch. Their antifungal activities against Fusarium verticillioides (strains: MRC 826 and MRC 8267) and F. proliferatum (strains: MRC 6908 and MRC 7140) that are aggressive mycotoxigenic phytopathogens were compared using an in vitro microdilution assay. To correlate antifungal activity to chemical profiles, three techniques viz. Gas chromatography-mass spectrometry (GC-MS); Liquid chromatography-mass spectrometry (LC-MS) and ¹H Nuclear Magnetic Resonance (NMR) were employed. Principal Component Analysis (PCA) was applied to the NMR data. The partial least squares-discriminant analysis (PLS-DA) was used to integrate LC-MS and NMR data sets. All statistics were performed with the SIMCA-P + 12.0 software.

Results

The dichloromethane:methanol (1:1; v/v) extracts of the plant species collected from Stellenbosch demonstrated the strongest inhibition of F. verticillioides and F. proliferatum with minimum inhibitory concentration (MIC) values of 0.031 mg ml^-1 and 0.063 mg ml^-1 respectively. GC-MS showed four compounds which were unique to the Stellenbosch extracts. By integrating LC-MS and ¹H NMR analyses, large chemotype differences leading to samples grouping by site when a multivariate analysis was performed, suggested strong plant-environment interactions as factors influencing metabolite composition. Signals distinguishing the Stellenbosch profile were in the aromatic part of the ¹H NMR spectra.

Conclusions

This study shows the potential of chemotypes of Salvia africana-lutea in controlling fungal growth and consequently mycotoxin production. Products for use in the agricultural sector may be developed from such chemotypes.

Isotopomer measurement techniques in metabolic flux analysis I: nuclear magnetic resonance

Two-dimensional [(1)H, (13)C] heteronuclear single quantum correlation (HSQC) spectroscopy nuclear magnetic resonance (NMR) is a comprehensive tool in metabolic flux analysis using (13)C-labeling experiments. NMR is particularly relevant when extensive isotopomer measurements are required, such as for plant cells and tissues, which contain multiple cellular compartments. Several isotope isomers (isotopomers) can be detected and their distribution extracted quantitatively from a single 2-D HSQC NMR spectrum. For example, 2-D HSQC detects the labeling patterns of adjacent carbon atoms and provides the enrichment of individual carbon atoms of the amino acids and glucosyl and mannosyl units present in hydrolysates of glycosylated protein. The HSQC analysis can quantitatively distinguish differences between the glucosyl units in the starch hydrolysate and a protein hydrolysate of plant biomass: this specifies crucial information about compartmentalization in the plant system. The peak structures obtained from the HSQC experiment show multiplet patterns that are directly related to the isotopomer abundances. These abundances have a nonlinear relationship to the fluxes via isotopomer balancing. Fluxes are obtained from the numerical solution of these balances and a stoichiometric model that includes biomass composition data as well as consumption rates of carbohydrate and nitrogen sources. Herein, we describe the methods for the experimental measurements for flux analysis, i.e., determination of the biomass composition (lipid, protein, soluble sugar, and starch) as well as detailed procedures of acid hydrolysis of protein and starch samples and NMR sample preparation, using soybean embryo culture as the model plant system. Techniques to obtain the relative intensity of 16 amino acids and glucosyl units for protein hydrolysate and the glucosyl units of starch hydrolysate of soybean embryos in 2-D HSQC NMR spectra also are provided.

In vivo NMR for ¹³C Metabolic Flux Analysis

The use of in vivo NMR within the framework of Metabolic Flux Analysis in plants is presented. In vivo NMR allows to visualize the active metabolic network, to determine metabolic and isotopic steady state and to measure metabolic fluxes which are not necessarily accessible by isotopic steady state (stationary) Metabolic Flux Analysis. The kinetic data can be used as input for dynamic (nonstationary) Metabolic Flux Analysis. Both 1D and 2D NMR methods are employed.

Assessment of a 1H high-resolution magic angle spinning NMR spectroscopy procedure for free sugars quantification in intact plant tissue

In most plants, sucrose is the primary product of photosynthesis, the transport form of assimilated carbon, and also one of the main factors determining sweetness in fresh fruits. Traditional methods for sugar quantification (mainly sucrose, glucose and fructose) require obtaining crude plant extracts, which sometimes involve substantial sample manipulation, making the process time-consuming and increasing the risk of sample degradation. Here, we describe and validate a fast method to determine sugar content in intact plant tissue by using high-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HR-MAS NMR). The HR-MAS NMR method was used for quantifying sucrose, glucose and fructose in mesocarp tissues from melon fruits (Cucumis melo var. reticulatus and Cucumis melo var. cantalupensis). The resulting sugar content varied among individual melons, ranging from 1.4 to 7.3 g of sucrose, 0.4-2.5 g of glucose; and 0.73-2.83 g of fructose (values per 100 g fw). These values were in agreement with those described in the literature for melon fruit tissue, and no significant differences were found when comparing them with those obtained using the traditional, enzymatic procedure, on melon tissue extracts. The HR-MAS NMR method offers a fast (usually <30 min) and sensitive method for sugar quantification in intact plant tissues, it requires a small amount of tissue (typically 50 mg fw) and avoids the interferences and risks associated with obtaining plant extracts. Furthermore, this method might also allow the quantification of additional metabolites detectable in the plant tissue NMR spectrum.

NMR (¹H) analysis of crude extracts detects light stress in Beta vulgaris and Spinacia oleracea leaves

In highlight stress conditions, the mechanism of non-photochemical quenching (NPQ) of chlorophyll fluorescence is triggered at the chloroplast level. This process allows thermal quenching of the excessive excitation energy and it is strictly related to the efficiency of the xanthophyll cycle. Nowadays, the utilization of the nuclear magnetic resonance (NMR) spectroscopy provides a powerful complementary way for the identification and quantitative analysis of plant metabolites either in vivo or in tissue extracts. Seeing that the oxidative damage caused by light stress in plants and the consequent involvement of pigments are widely studied, NMR spectroscopy can be utilized to compare crude leaf extract at different levels of light stress, allowing an analysis of these compounds. In this paper, the identification of possible relationships between light stress and ¹H NMR signal variations is discussed. The analysis of the ¹H NMR (1D) spectra of two agronomic species (Spinacia oleracea and Beta vulgaris) exposed to different light intensities is presented. In particular, change in carotenoids and xanthophylls signals are analyzed.

High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions

The main goal of metabolomics is the comprehensive qualitative and quantitative analysis of the time- and space-resolved distribution of all metabolites present in a given biological system. Because metabolite structures, in contrast to transcript and protein sequences, are not directly deducible from the genomic DNA sequence, the massive increase in genomic information is only indirectly of use to metabolomics, leaving compound annotation as a key problem to be solved by the available analytical techniques. Furthermore, as metabolites vary widely in both concentration and chemical behavior, there is no single analytical procedure allowing the unbiased and comprehensive structural elucidation and determination of all metabolites present in a given biological system. In this review the different approaches for targeted and non-targeted metabolomics analysis will be described with special emphasis on mass spectrometry-based techniques. Particular attention is given to approaches which can be employed for the annotation of unknown compounds. In the second part, the different experimental approaches aimed at tissue-specific or subcellular analysis of metabolites are discussed including a range of non-mass spectrometry based technologies.

Eukaryotic metabolism: measuring compartment fluxes

Metabolic compartmentation represents a major characteristic of eukaryotic cells. The analysis of compartmented metabolic networks is complicated by separation and parallelization of pathways, intracellular transport, and the need for regulatory systems to mediate communication between interdependent compartments. Metabolic flux analysis (MFA) has the potential to reveal compartmented metabolic events, although it is a challenging task requiring demanding experimental techniques and sophisticated modeling. At present no ready-made solution can be provided to cope with the complexity of compartmented metabolic networks, but new powerful tools are emerging. This review gives an overview of different strategies to approach this issue, focusing on different MFA methods and highlighting the additional information that should be included to improve the outcome of an experiment and associate estimation procedures.

Temporal dynamics of natural product biosynthesis in marine cyanobacteria

Sessile marine organisms are prolific sources of biologically active natural products. However, these compounds are often found in highly variable amounts, with the abiotic and biotic factors governing their production remaining poorly understood. We present an approach that permits monitoring of in vivo natural product production and turnover using mass spectrometry and stable isotope ((15)N) feeding with small cultures of various marine strains of the natural product-rich cyanobacterial genus Lyngbya. This temporal comparison of the amount of in vivo (15)N labeling of nitrogen-containing metabolites represents a direct way to discover and evaluate factors influencing natural product biosynthesis, as well as the timing of specific steps in metabolite assembly, and is a strong complement to more traditional in vitro studies. Relative quantification of (15)N labeling allowed the concurrent measurement of turnover rates of multiple natural products from small amounts of biomass. This technique also afforded the production of the neurotoxic jamaicamides to be more carefully studied, including an assessment of how jamaicamide turnover compares with filament growth rate and primary metabolism and provided new insights into the biosynthetic timing of jamaicamide A bromination. This approach should be valuable in determining how environmental factors affect secondary metabolite production, ultimately yielding insight into the energetic balance among growth, primary production, and secondary metabolism, and thus aid in the development of methods to improve compound yields for biomedical or biotechnological applications.

In vivo nuclear magnetic resonance metabolite profiling in plant seeds

Nuclear magnetic resonance (NMR) spectroscopy has been successfully applied to profile a variety of primary and secondary metabolites in whole intact plant seeds in vivo. The nondestructive nature of NMR spectroscopy allows direct metabolic studies to be performed on the same seed throughout a given physio-logical process or key lifecycle transition, such as dormancy breakage, germination, and early postgerminative growth. Multinuclear NMR is capable of evaluating seed quality by assessing nondestructively nutrient reserves and seed protectants at seed maturity and to further monitor reserve mobilization following germination, which is critical for seedling emergence. In this chapter, we illustrate the use of several in vivo NMR techniques for metabolite profiling in seeds. Importantly, some of these methods have potential for the screening of single seeds or seed populations to identify seedlots with compromised viability either due to developmental problems or as a result of deterioration during prolonged storage.

New monitoring approach for metabolic dynamics in microbial ecosystems using stable-isotope-labeling technologies

We have developed a new approach for monitoring the metabolic dynamics in microbial ecosystems using a combination of DNA fingerprinting and metabolome analysis based on stable-isotope-labeling technologies. Stable-isotope probing of DNA (DNA-SIP) has been used previously for the evaluation of cross-feeding in microbial communities. For the development and validation of our monitoring approach, fecal microbiota were analyzed with stable-isotope-labeled glucose used as the sole carbon source. In order to link the metabolic information and the microbial variability, we performed metabolic-microbial correlation analysis based on nuclear magnetic resonance (NMR) profiles and denaturing gradient gel electrophoresis (DGGE) fingerprints, which successfully identified the glucose-utilizing bacteria and their related extracellular metabolites. Moreover, our approach revealed information regarding the carbon flux, in that the "first" wave of extracellular metabolites secreted by the glucose-utilizing bacteria were incorporated into the "secondary" group of substrate-utilizing bacteria, and that this "secondary" group further produced their own secondary metabolized substrates. Thus, this approach is a powerful tool for monitoring the metabolic dynamics in microbial ecosystems and allows for the tracking of the carbon flux within a microbial community.

An introduction to liquid chromatography-mass spectrometry instrumentation applied in plant metabolomic analyses

Over the past decade the application of non-targeted high-throughput metabolomic analysis within the plant sciences has gained ever increasing interest and has truly established itself as a valuable tool for plant functional genomics and studies of plant biochemical composition. Whilst proton nuclear magnetic resonance ((1)H-NMR) spectroscopy is particularly appropriate for the analysis of bulk metabolites and gas chromatography mass spectrometry (GC-MS) to the analysis of volatile organic compounds (VOC's) and derivatised primary metabolites, liquid chromatography (LC)-MS is highly applicable to the analysis of a wide range of semi-polar compounds including many secondary metabolites of interest to plant researchers and nutritionists. In view of the recent developments in the separation sciences, leading to the advent of ultra high performance liquid chromatography (UHPLC) and MS based technology showing the ever improving resolution of metabolite species and precision of mass measurements (sub-ppm accuracy now being achievable), this review sets out to introduce the background and update the reader upon LC, high performance (HP)LC and UHPLC, as well as the large range of MS instruments that are being applied in current plant metabolomic studies. As well as covering the theory behind modern day LC-MS, the review also discusses the most relevant metabolomics applications for the wide range of MS instruments that are currently being applied to LC.

The metabolic role of the legume endosperm: a noninvasive imaging study

Although essential for normal seed development in the legumes, the metabolic role of the endosperm remains uncertain. We designed noninvasive nuclear magnetic resonance tools for the in vivo study of key metabolites in the transient liquid endosperm of intact pea (Pisum sativum) seeds. The steady-state levels of sucrose, glutamine, and alanine could be monitored and their distribution within the embryo sac visualized. Seed structure was digitalized as a three-dimensional model, providing volume information for distinct seed organs. The nuclear magnetic resonance method, combined with laser microdissection, isotope labeling, in situ hybridization, and electron microscopy, was used to contrast the wild-type endosperm with that of a mutant in which embryo growth is retarded. Expression of sequences encoding amino acid and sucrose transporters was up-regulated earlier in the endosperm than in the embryo, and this activity led to the accumulation of soluble metabolites in the endosperm vacuole. The endosperm provides a temporary source of nutrition, permits space for embryo growth, and acts as a buffer between the maternal organism and its offspring. The concentration of sucrose in the endosperm vacuole is developmentally controlled, while the total amount accumulated depends on the growth of the embryo. The endosperm concentration of glutamine is a limiting factor for protein storage. The properties of the endosperm ensure that the young embryo develops within a homeostatic environment, necessary to sustain embryogenesis. We argue for a degree of metabolite-mediated control exerted by the endosperm on the growth of, and assimilate storage by, the embryo.

Resolving the role of plant glutamate dehydrogenase. I. In vivo real time nuclear magnetic resonance spectroscopy experiments

In higher plants the glutamate dehydrogenase (GDH) enzyme catalyzes the reversible amination of 2-oxoglutarate to form glutamate, using ammonium as a substrate. For a better understanding of the physiological function of GDH either in ammonium assimilation or in the supply of 2-oxoglutarate, we used transgenic tobacco (Nicotiana tabacum L.) plants overexpressing the two genes encoding the enzyme. An in vivo real time (15)N-nuclear magnetic resonance (NMR) spectroscopy approach allowed the demonstration that, when the two GDH genes were overexpressed individually or simultaneously, the transgenic plant leaves did not synthesize glutamate in the presence of ammonium when glutamine synthetase (GS) was inhibited. In contrast we confirmed that the primary function of GDH is to deaminate Glu. When the two GDH unlabeled substrates ammonium and Glu were provided simultaneously with either [(15)N]Glu or (15)NH(4)(+) respectively, we found that the ammonium released from the deamination of Glu was reassimilated by the enzyme GS, suggesting the occurrence of a futile cycle recycling both ammonium and Glu. Taken together, these results strongly suggest that the GDH enzyme, in conjunction with NADH-GOGAT, contributes to the control of leaf Glu homeostasis, an amino acid that plays a central signaling and metabolic role at the interface of the carbon and nitrogen assimilatory pathways. Thus, in vivo NMR spectroscopy appears to be an attractive technique to follow the flux of metabolites in both normal and genetically modified plants.

Use of metabolic control analysis to give quantitative information on control of lipid biosynthesis in the important oil crop, Elaeis guineensis (oilpalm)

* Oil crops are a very important commodity. Although many genes and enzymes involved in lipid accumulation have been identified, much less is known of regulation of the overall process. To address the latter we have applied metabolic control analysis to lipid synthesis in the important crop, oilpalm (Elaeis guineensis). * Top-down metabolic control analysis (TDCA) was applied to callus cultures capable of accumulating appreciable triacylglycerol. The biosynthetic pathway was divided into two blocks, connected by the intermediate acyl-CoAs. Block A comprised enzymes for fatty acid synthesis and Block B comprised enzymes of lipid assembly. * Double manipulation TDCA used diflufenican and bromooctanoate to inhibit Block A and Block B, respectively, giving Block flux control coefficients of 0.61 and 0.39. Monte Carlo simulations provided extra information from previously-reported single manipulation TDCA data, giving Block flux control coefficients of 0.65 and 0.35 for A and B. * These experiments are the first time that double manipulation TDCA has been applied to lipid biosynthesis in any organism. The data show that approaching two-thirds of the total control of carbon flux to lipids in oilpalm cultures lies with the fatty acid synthesis block of reactions. This quantitative information will assist future, informed, genetic manipulation of oilpalm.

Metabolic flux analysis in plants: coping with complexity

Theory and experience in metabolic engineering both show that metabolism operates at the network level. In plants, this complexity is compounded by a high degree of compartmentation and the synthesis of a very wide array of secondary metabolic products. A further challenge to understanding and predicting plant metabolic function is posed by our ignorance about the structure of metabolic networks even in well-studied systems. Metabolic flux analysis (MFA) provides tools to measure and model the functioning of metabolism, and is making significant contributions to coping with their complexity. This review gives an overview of different MFA approaches, the measurements required to implement them and the information they yield. The application of MFA methods to plant systems is then illustrated by several examples from the recent literature. Next, the challenges that plant metabolism poses for MFA are discussed together with ways that these can be addressed. Lastly, new developments in MFA are described that can be expected to improve the range and reliability of plant MFA in the coming years.

Lemna minor L. as a model organism for ecotoxicological studies performing 1H NMR fingerprinting

A validated method applying (1)H NMR fingerprinting for the study of metabolic changes caused in Lemna minor L. by various phytotoxic substances is presented. (1)H NMR spectra of crude extracts from untreated and treated colonies with the herbicides glyphosate, mesotrione, norflurazon, paraquat and the phytotoxin pyrenophorol were subjected to multivariate analyses for detecting differences between groups of treatments. Partial least squares-discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) were carried out in order to discriminate and classify treatments according to the observed changes in the metabolome of the plant. Although the compounds at the concentrations used did not cause macroscopically observable symptoms of phytotoxicity, characteristic metabolic changes were detectable by analyzing (1)H NMR spectra. Analyses results revealed that metabonomics applying (1)H NMR fingerprinting is a potential method for the investigation of toxicological effects of xenobiotics on L. minor, and possibly on other duckweed species, helping in the understanding of such interactions.

In situ investigation of leaf water status by portable unilateral nuclear magnetic resonance

A portable unilateral nuclear magnetic resonance (NMR) instrument was used to detect in field conditions the water status of leaves of herbaceous crops (Zea mays, Phaseolus vulgaris), mesophyllous trees (Populus nigra), and natural Mediterranean vegetation characterized by water-spending shrubs (Cistus incanus) and water-saving sclerophyllous trees (Quercus ilex). A good relationship was observed between NMR signal, leaf relative water content, and leaf transpiration in herbaceous leaves undergoing fast dehydration or slowly developing a drought stress. A relationship was also observed between NMR signal and water potential of Populus leaves during the development of a water stress and when leaves recovered from the stress. In the natural vegetation, the relationship between NMR signal and water status was found in Cistus, the species characterized by high transpiration rates, when measured during a drought stress period and after a rainfall. In the case of the sclerophyllous Quercus, the NMR signal, the relative water content, and the transpiration rate did not change at different leaf water status, possibly because a large amount of water is compartmentalized in cellular structures and macromolecules. The good association between NMR signal and relative water content was lost in leaves exposed for 24 h to dehydration or to an osmotic stress caused by polyethylene glycol feeding. At this time, the transverse relaxation time became longer than in leaves maintained under optimal water conditions, and two indicators of membrane damage, the ion leakage and the emission of products of membrane lipoxygenation [(Z)-3-hexenal, (Z)-3-hexenol, and (E)-2-hexenol], increased. These results taken all together give information on the physiological state of a leaf under a developing stress and show the usefulness of the NMR instrumentation for screening vegetation health and fitness in natural and cultivated conditions. It is concluded that the portable unilateral NMR instrument may be usefully employed in field conditions to monitor nondestructively the water status of plants and to assist agricultural practices, such as irrigation scheduling, to minimize stomatal closure and the consequent limitation to plant production.

Impact of the salt stress on the photosynthetic carbon flux and 13C-label distribution within floridoside and digeneaside in Solieria chordalis

The flux of photosynthetic carbon used in the synthesis of low-molecular weight carbohydrates (digeneaside and floridoside) was investigated by (13)C and (1)H NMR spectroscopy in samples of the red seaweed, Solieria chordalis, incubated at different salinities (22, 34 and 50psu). Carbohydrates were labelled, by pulse-chase, with the stable isotope (13)C from NaH(13)CO(3). In vivo NMR analyses carried out with a cryogenic probe optimised for (13)C detection were performed directly on the living algal tissues to evidence the labelling of the carbohydrates with neither preliminary extraction nor purification step(s). The isotopic enrichment of each compound was determined by high-resolution (1)H and (13)C NMR spectroscopy. These analyses evidenced different orientations of the flux of the photosynthetic carbon in the algae according to the salt stress. At normal and low salinities, the photosynthetic carbon flux was responsible of 70% and 67% of the floridoside synthetized during the pulse period, respectively, whereas it was only of 30% in the thalli exposed to the high salinity, meaning a biosynthesis of high floridoside amount from endogen source leading to the osmotic regulation. Under normal and hyper-osmotic conditions, the stock of floridoside was used for cellular needs during the chase period, whereas it was not under hypo-osmotic conditions. The characterization of isotopomers composition of floridoside and digeneaside and the analysis of adjacent (13)C-labelling gives much more details on the effects of salinity on the metabolic pathways leading to the synthesis or the degradation of these molecules. High turnover of floridoside was evidenced at normal salinity during the chase period and products issued from the degradation of floridoside would not be used for the novo biosynthesis. That suggests that synthesis and degradation of floridoside may be realized in two different cellular compartments. The presence of more numerous (13)C-(13)C blocks in the carbon skeleton of the molecules from the up salt stressed thalli than in those from no salt stressed algae, concomitant with a slower degree of isotopic enrichment of the molecule, provided evidence that the two metabolic pathways (endogen and photosynthetic) may not share the precursor molecules involved in the floridoside synthesis and that these two routes may be totally separate until the constitution of floridoside molecule.

Non-invasive mapping of lipids in plant tissue using magnetic resonance imaging

Plant oil has become an important component in the search for a replacement for non-renewable energy sources, as well as being used for a wide range of industrial purposes, all in addition to its vital importance for human diet. Detailed knowledge of the lipid distribution in plants is fundamental for the understanding of local regulatory networks covering storage metabolism, and for the development of new approaches for plant breeding and transgenic research. We here review a measurement protocol or "tool" based on magnetic resonance imaging (MRI), which allows the non-invasive detection and quantitative visualization of lipid in living plant tissue. The method provides quantitative lipid maps with a resolution close to the cellular level and can be used on a wide range of plants and is applicable at the level of individual tissues, organs, or entire plants during ontogeny. Lipid imaging is designed for both biotechnology and basic science and can be combined with histological, biochemical, and gene expression analysis. Here we present the method as practiced in our group, and discuss unique advantages and limitations of the lipid-imaging tool. Seeds of barley and rapeseed were used as a model for visualization of local oil accumulation at the organ- and tissue-specific scale.

Direct profiling and imaging of plant metabolites in intact tissues by using colloidal graphite-assisted laser desorption ionization mass spectrometry

Laser desorption/ionization (LDI)-based imaging mass spectrometry (MS) has been applied to several biological systems to obtain information about both the identities of the major chemical species and their localization. Colloidal graphite-assisted LDI (GALDI) MS imaging was introduced for the imaging of small molecules such as phospholipids, cerebrosides, oligosaccharides, flavonoids, and other secondary metabolites with high spatial homogeneity due to finely dispersed particles. Mass profiles and images of Arabidopsis thaliana have been recorded directly from various plant surfaces and cross sections. The main targeted metabolites were flavonoids and cuticular waxes, both of which are important in many aspects of functional genomics, proteomics, and metabolomics. The mass spectral profiles revealed tissue-specific accumulation of flavonoids in flowers and petals. In addition, many other location-specific ions were observed. The location and the degree of light-induced accumulation of flavonoids in stem sections were successfully probed by GALDI MS.

Nonuniform distribution of glucosinolates in Arabidopsis thaliana leaves has important consequences for plant defense

The spatial distribution of plant defenses within a leaf may be critical in explaining patterns of herbivory. The generalist lepidopteran larvae, Helicoverpa armigera (the cotton bollworm), avoided the midvein and periphery of Arabidopsis thaliana rosette leaves and fed almost exclusively on the inner lamina. This feeding pattern was attributed to glucosinolates because it was not evident in a myrosinase mutant that lacks the ability to activate glucosinolate defenses by hydrolysis. To measure the spatial distribution of glucosinolates in A. thaliana leaves at a fine scale, we constructed ion intensity maps from MALDI-TOF (matrix assisted laser desorption/ionization-time of flight) mass spectra. The major glucosinolates were found to be more abundant in tissues of the midvein and the periphery of the leaf than the inner lamina, patterns that were validated by HPLC analyses of dissected leaves. In addition, there were differences in the proportions of the three major glucosinolates in different leaf regions. Hence, the distribution of glucosinolates within the leaf appears to control the feeding preference of H. armigera larvae. The preferential allocation of glucosinolates to the periphery may play a key role in the defense of leaves by creating a barrier to the feeding of chewing herbivores that frequently approach leaves from the edge.

Metabolomics of temperature stress

Plants possess inducible tolerance mechanisms that extend the temperature range for survival during acute temperature stress. The inducible mechanisms of cold acclimation and acquired thermotolerance involve highly complex processes. These include perception and signal transduction of non-optimal temperatures or their physical consequences on cellular components that program extensive modification of the transcriptome, proteome, metabolome and composition and physical structure of the cytoplasm, membranes and cell walls. Therefore, a systems biology approach will be necessary to advance the understanding of plant stress responses and tolerance mechanisms. One promise of systems biology is that it will greatly enhance our understanding of individual and collective functions and thereby provide a more holistic view of plant stress responses. Past studies have found that several metabolites that could functionally contribute to induced stress tolerance have been associated with stress responses. Recent metabolite-profiling studies have refocused attention on these and other potentially important components found in the 'temperature-stress metabolome'. These metabolomic studies have demonstrated that active reconfiguration of the metabolome is regulated in part by changes in gene expression initiated by temperature-stress-activated signaling and stress-related transcription factors. One aspect of metabolism that is consistent across all of the temperature-stress metabolomic studies to date is the prominent role of central carbohydrate metabolism, which seems to be a major feature of the reprogramming of the metabolome during temperature stress. Future metabolomic studies of plant temperature-stress responses should reveal additional metabolic pathways that have important functions in temperature-stress tolerance mechanisms.

Metabolic flux analysis in plants: from intelligent design to rational engineering

Metabolic flux analysis (MFA) is a rapidly developing field concerned with the quantification and understanding of metabolism at the systems level. The application of MFA has produced detailed maps of flow through metabolic networks of a range of plant systems. These maps represent detailed metabolic phenotypes, contribute significantly to our understanding of metabolism in plants, and have led to the discovery of new metabolic routes. The presentation of thorough statistical evaluation with current flux maps has set a new standard for the quality of quantitative flux studies. In microbial systems, powerful methods have been developed for the reconstruction of metabolic networks from genomic and transcriptomic data, pathway analysis, and predictive modeling. This review brings together the recent developments in quantitative MFA and predictive modeling. The application of predictive tools to high quality flux maps in particular promises to be important in the rational metabolic engineering of plants.

Quantitative imaging of oil storage in developing crop seeds

In this article, we present a tool which allows the rapid and non-invasive detection and quantitative visualization of lipid in living seeds at a variety of stages using frequency-selected magnetic resonance imaging. The method provides quantitative lipid maps with a resolution close to the cellular level (in-plane 31 microm x 31 microm). The reliability of the method was demonstrated using two contrasting subjects: the barley grain (monocot, 2% oil, highly compartmentalized) and the soybean grain (dicot, 20% oil, economically important oilseed). Steep gradients in local oil storage were defined at the organ- and tissue-specific scales. These gradients were closely coordinated with tissue differentiation and seed maturation, as revealed by electron microscopy and biochemical and gene expression analysis. The method can be used to elucidate similar oil accumulation processes in different tissues/organs, as well as to follow the fate of storage lipids during deposition and subsequent mobilization.

Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing

Methods for accurate and efficient quantification of metabolic fluxes are desirable in plant metabolic engineering and systems biology. Toward this objective, we introduce the application of "bondomers", a computationally efficient and intuitively appealing alternative to the commonly used isotopomer concept, to flux evaluation in plants, by using Catharanthus roseus hairy roots as a model system. We cultured the hairy roots on (5% w/w U-(13)C, 95% w/w naturally abundant) sucrose, and acquired two-dimensional [(13)C, (1)H] and [(1)H, (1)H] NMR spectra of hydrolyzed aqueous extract from the hairy roots. Analysis of these spectra yielded a data set of 116 bondomers of beta-glucans and proteinogenic amino acids from the hairy roots. Fluxes were evaluated from the bondomer data by using comprehensive bondomer balancing. We identified most fluxes in a three-compartmental model of central carbon metabolism with good precision. We observed parallel pentose phosphate pathways in the cytosol and the plastid with significantly different fluxes. The anaplerotic fluxes between phosphoenolpyruvate and oxaloacetate in the cytosol and between malate and pyruvate in the mitochondrion were relatively high (60.1+/-2.5 mol per 100 mol sucrose uptake, or 22.5+/-0.5 mol per 100 mol mitochondrial pyruvate dehydrogenase flux). The development of a comprehensive flux analysis tool for this plant hairy root system is expected to be valuable in assessing the metabolic impact of genetic or environmental changes, and this methodology can be extended to other plant systems.