NMR and plant metabolism

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.

Tribute Roland Douce, 1939-2018

On November 4, 2018, Roland Douce, Professor Emeritus at the University of Grenoble, France, died at the age of 79. In Grenoble, where he spent most of his scientific career, Roland Douce created a world-renowned school of plant science, studying the structure, functions, and interactions of plant organelles involved in photosynthesis, respiration, and photorespiration. His main achievements concern the chemical and functional characterization of chloroplast envelope membranes, the demonstration of the uniqueness of plant mitochondria, and the integration of metabolism within the plant cell, among manifold activities. Roland Douce devoted his whole life to science and research with passion and enthusiasm: he was a true charismatic leader.

Metabolic alterations in conventional and genetically modified soybean plants with GmDREB2A;2 FL and GmDREB2A;2 CA transcription factors during water deficit

Water deficit is one of the main abiotic stress that affects plant growth and productivity. The GmDREB2A;2 (Glyma14g06080) gene is an important transcription factor involved in regulating the plants' responses under water deficit. In previous studies, soybean plants overexpressing full-length (GmDREB2A;2 FL) and constitutively active (GmDREB2A;2 CA) forms of the GmDREB2A;2 gene, presented higher tolerance to water deficit when compared with the conventional cultivar BRS 283. Therefore, identifying the changes in metabolite profile in these tolerant genotypes can contribute to the understanding of the metabolic pathways involved in the tolerance mechanism. In this work, the metabolic changes in roots and leaves of genetically modified (GM) soybean plants subjected to water deficit were elucidated by 1H-NMR spectroscopy. Three events were analyzed, one containing the gene in FL form (GmDREB2A;2 FL) and two presenting its CA form (GmDREB2A;2 CA-1 and GmDREB2A;2 CA-2) and compared with the conventional cultivar BRS 283. The results indicated different responses between leaves and roots for all genotypes. Most of these metabolic variations were related to carbohydrate and amino acid pathways. BRS 283 stood out with higher accumulation of amino acids in leaves under water deficit. The results also showed that the events GmDREB2A;2 FL and GmDREB2A;2 CA-1 presented higher concentrations of β-glucose and fructose in leaves, whereas BRS 283 accumulated more sucrose and pinitol. In roots, the GM events accumulated higher β-glucose, fructose, asparagine and phenylalanine, when compared with the conventional cultivar. These insights can add information on how the transcription factor (TF) DREB2A acts in soybean plants triggering and controlling a network of complex responses to drought.

Metabolomics in Plant Stress Physiology

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

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.

Sensitive, highly resolved, and quantitative (1)H-(13)C NMR data in one go for tracking metabolites in vegetal extracts

The quantification of metabolites is essential for understanding and improving biological systems. With the aim to quantify in one map a complex mixture composed of low concentrated metabolites, a new experiment called the (1)H-(13)C QUIPU HSQC allows improving of both resolution and sensitivity for investigation of vegetal extracts.

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.

Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms

Diatoms are one of the most ecologically successful classes of photosynthetic marine eukaryotes in the contemporary oceans. Over the past 30 million years, they have helped to moderate Earth's climate by absorbing carbon dioxide from the atmosphere, sequestering it via the biological carbon pump and ultimately burying organic carbon in the lithosphere. The proportion of planetary primary production by diatoms in the modern oceans is roughly equivalent to that of terrestrial rainforests. In photosynthesis, the efficient conversion of carbon dioxide into organic matter requires a tight control of the ATP/NADPH ratio which, in other photosynthetic organisms, relies principally on a range of plastid-localized ATP generating processes. Here we show that diatoms regulate ATP/NADPH through extensive energetic exchanges between plastids and mitochondria. This interaction comprises the re-routing of reducing power generated in the plastid towards mitochondria and the import of mitochondrial ATP into the plastid, and is mandatory for optimized carbon fixation and growth. We propose that the process may have contributed to the ecological success of diatoms in the ocean.

Acetate and bicarbonate assimilation and metabolite formation in Chlamydomonas reinhardtii: a 13C-NMR study

Cellular metabolite analyses by ¹³C-NMR showed that C. reinhardtii cells assimilate acetate at a faster rate in heterotrophy than in mixotrophy. While heterotrophic cells produced bicarbonate and CO₂^aq, mixotrophy cells produced bicarbonate alone as predominant metabolite. Experiments with singly ¹³C-labelled acetate (¹³CH₃-COOH or CH₃-¹³COOH) supported that both the ¹³C nuclei give rise to bicarbonate and CO₂^aq. The observed metabolite(s) upon further incubation led to the production of starch and triacylglycerol (TAG) in mixotrophy, whereas in heterotrophy the TAG production was minimal with substantial accumulation of glycerol and starch. Prolonged incubation up to eight days, without the addition of fresh acetate, led to an increased TAG production at the expense of bicarbonate, akin to that of nitrogen-starvation. However, such TAG production was substantially high in mixotrophy as compared to that in heterotrophy. Addition of mitochondrial un-coupler blocked the formation of bicarbonate and CO₂^aq in heterotrophic cells, even though acetate uptake ensued. Addition of PSII-inhibitor to mixotrophic cells resulted in partial conversion of bicarbonate into CO₂^aq, which were found to be in equilibrium. In an independent experiment, we have monitored assimilation of bicarbonate via photoautotrophy and found that the cells indeed produce starch and TAG at a much faster rate as compared to that in mixotrophy and heterotrophy. Further, we noticed that the accumulation of starch is relatively more as compared to TAG. Based on these observations, we suggest that acetate assimilation in C. reinhardtii does not directly lead to TAG formation but via bicarbonate/CO₂^aq pathways. Photoautotrophic mode is found to be the best growth condition for the production of starch and TAG and starch in C. reinhardtii.

Metabolic differentiation of diamondback moth ( Plutella xylostella (L.)) resistance in cabbage ( Brassica oleracea L. ssp. capitata)

The diamondback moth, Plutella xylostella (L.), is a major pest responsible for destroying cabbage and other Brassica vegetable crops. A diamondback moth-resistant cabbage line was studied by comparing its metabolite profiles with those of a susceptible cabbage. Fourier transform infrared spectroscopy analysis revealed that carbohydrates, aromatic compounds, and amides were the major factors that distinguished the resistant and susceptible genotypes. Gas chromatography-time-of-flight mass spectrometry profiled 46 metabolites, including 19 amino acids, 15 organic acids, 8 sugars, 3 sugar alcohols, and 1 amine in two genotypes and F1 hybrid cabbages. The levels of glycolic acid, quinic acid, inositol, fumaric acid, glyceric acid, trehalose, shikimic acid, and aspartic acid were found to be very significantly different between the resistant and susceptible genotypes with a P value of <0.0001. These results will provide a foundation for further studies on diamondback moth resistance in cabbage breeding and for the development of other herbivore-resistant crops.

Phenotypic approaches to drought in cassava: review

Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.

The need for agriculture phenotyping: "moving from genotype to phenotype"

Increase in the world population has called for the increased demand for agricultural productivity. Traditional methods to augment crop and animal production are facing exacerbating pressures in keeping up with population growth. This challenge has in turn led to the transformational change in the use of biotechnology tools to meet increased productivity for both plant and animal systems. Although many challenges exist, the use of proteomic techniques to understand agricultural problems is steadily increasing. This review discusses the impact of genomics, proteomics, metabolomics and phenotypes on plant, animal and bacterial systems to achieve global food security and safety and we highlight examples of intra and extra mural research work that is currently being done to increase agricultural productivity.

BIOLOGICAL SIGNIFICANCE

This review focuses on the global demand for increased agricultural productivity arising from population growth and how we can address this challenge using biotechnology. With a population well above seven billion humans, in a very unbalanced nutritional state (20% overweight, 20% risking starvation) drastic measures have to be taken at the political, infrastructure and scientific levels. While we cannot influence politics, it is our duty as scientists to see what can be done to feed humanity. Hence we highlight the transformational change in the use of biotechnology tools over traditional methods to increase agricultural productivity (plant and animal). Specifically, this review deals at length on how a three-pronged attack, namely combined genomics, proteomics and metabolomics, can help to ensure global food security and safety. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Metabolite adjustments in drought tolerant and sensitive soybean genotypes in response to water stress

Soybean (Glycine max L.) is an important source of protein for human and animal nutrition, as well as a major source of vegetable oil. The soybean crop requires adequate water all through its growth period to attain its yield potential, and the lack of soil moisture at critical stages of growth profoundly impacts the productivity. In this study, utilizing (1)H NMR-based metabolite analysis combined with the physiological studies we assessed the effects of short-term water stress on overall growth, nitrogen fixation, ureide and proline dynamics, as well as metabolic changes in drought tolerant (NA5009RG) and sensitive (DM50048) genotypes of soybean in order to elucidate metabolite adjustments in relation to the physiological responses in the nitrogen-fixing plants towards water limitation. The results of our analysis demonstrated critical differences in physiological responses between these two genotypes, and identified the metabolic pathways that are affected by short-term water limitation in soybean plants. Metabolic changes in response to drought conditions highlighted pools of metabolites that play a role in the adjustment of metabolism and physiology of the soybean varieties to meet drought effects.

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.

The perinatal transition of the circulating metabolome in a nonhuman primate

INTRODUCTION

The fetal-to-neonatal transition is one of the most complex processes in biological existence; much is unknown about this transition on the molecular and biochemical level. Based on growing metabolomics literature, we hypothesize that metabolomic analysis will reveal the key biochemical intermediates that change during the birth transition.

RESULTS

Using two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC-TOFMS), we identified 100 metabolites that changed during this transition. Of these 100 metabolites, 23 demonstrated significant change during the first 72 h. Of note, four intermediates of the tricarboxylic acid (TCA) cycle were identified (α-ketoglutaric acid, fumaric acid, malic acid, and succinyl-CoA), demonstrating a consistent rate of rise during the study. This may signify the transition of the neonate from a hypoxic in utero environment to an oxygen-rich environment. Important signaling molecules were also identified, including myo-inositol and glutamic acid.

DISCUSSION

GC × GC-TOFMS was able to identify important metabolites associated with metabolism and signaling. These data can be used as a baseline for normal birth transition, which may aid in future perinatal research investigations.

METHODS

Late-preterm Macaca nemestrina were delivered by hysterotomy, with plasma drawn from the cord blood and after birth at eight additional time points to 72 h of age.

Analysis of the compartmentalized metabolome - a validation of the non-aqueous fractionation technique

With the development of high-throughput metabolic technologies, a plethora of primary and secondary compounds have been detected in the plant cell. However, there are still major gaps in our understanding of the plant metabolome. This is especially true with regards to the compartmental localization of these identified metabolites. Non-aqueous fractionation (NAF) is a powerful technique for the determination of subcellular metabolite distributions in eukaryotic cells, and it has become the method of choice to analyze the distribution of a large number of metabolites concurrently. However, the NAF technique produces a continuous gradient of metabolite distributions, not discrete assignments. Resolution of these distributions requires computational analyses based on marker molecules to resolve compartmental localizations. In this article we focus on expanding the computational analysis of data derived from NAF. Along with an experimental workflow, we describe the critical steps in NAF experiments and how computational approaches can aid in assessing the quality and robustness of the derived data. For this, we have developed and provide a new version (v1.2) of the BestFit command line tool for calculation and evaluation of subcellular metabolite distributions. Furthermore, using both simulated and experimental data we show the influence on estimated subcellular distributions by modulating important parameters, such as the number of fractions taken or which marker molecule is selected. Finally, we discuss caveats and benefits of NAF analysis in the context of the compartmentalized metabolome.

Distinguishing transgenic from non-transgenic Arabidopsis plants by (1)H NMR-based metabolic fingerprinting

We have recently reported the construction of an nuclear magnetic resonance (NMR)-based metabonomics study platform, Automics. To examine the application of Automics in transgenic plants, we performed metabolic fingerprinting analysis, i.e., (1)H NMR spectroscopy and multivariate analysis, on wild-type and transgenic Arabidopsis. We found that it was possible to distinguish wild-type from four transgenic plants by PLS-DA following application of orthogonal signal correction (OSC). Scores plot following OSC clearly demonstrates significant variation between the transgenic and non-transgenic groups, suggesting that the metabolic changes among wild-type and transgenic lines are possibly associated with transgenic event. We also found that the major contributing metabolites were some specific amino acids (i.e., threonine and alanine), which could correspond to the insertion of the selective marker BAR gene in the transgenic plants. Our data suggests that NMR-based metabonomics is an efficient method to distinguish fingerprinting difference between wild-type and transgenic plants, and can potentially be applied in the bio-safety assessment of transgenic plants.

Rapid vacuolar sequestration: the horseweed glyphosate resistance mechanism

BACKGROUND

Glyphosate-resistant (GR) weed species are now found with increasing frequency and threaten the critically important glyphosate weed-management system [corrected].

RESULTS

The reported (31)P NMR experiments on glyphosate-sensitive (S) and glyphosate-resistant (R) horseweed, Conyza canadensis (L.) Cronq., show significantly more accumulation of glyphosate within the R biotype vacuole.

CONCLUSIONS

Selective sequestration of glyphosate into the vacuole confers the observed horseweed resistance to glyphosate. This observation represents the first clear evidence for the glyphosate resistance mechanism in C. canadensis.

Kinetic metabolic modelling for the control of plant cells cytoplasmic phosphate

A previously developed kinetic metabolic model for plant metabolism was used in a context of identification and control of intracellular phosphate (Pi) dynamics. Experimental data from batch flask cultures of Eschscholtiza californica cells was used to calibrate the model parameters for the slow dynamics (growth, nutrition, anabolic pathways, etc.). Perturbation experiments were performed using a perfusion small-scale bioreactor monitored by in vivo(31)P NMR. Parameter identification for Pi metabolism was done by measuring the cells dynamic response to different inputs for extracellular Pi (two pulse-response experiments and a step-response experiment). The calibrated model can describe Pi translocation between the cellular pools (vacuole and cytoplasm). The effect of intracellular Pi management on ATP/ADP and phosphomonoesters concentrations is also described by the model. The calibrated model is then used to develop a control strategy on the cytoplasmic Pi pool. From the identification of the systems dynamics, a proportional-integral controller was designed and tuned. The closed-loop control was implemented in the small-scale NMR bioreactor and experimental results were in accordance with model predictions. Thus, the calibrated model is able to predict cellular behaviour for phosphate metabolism and it was demonstrated that it is possible to control the intracellular level of cytoplasmic Pi in plant cells.

Multidrug and toxic compound extrusion-type transporters implicated in vacuolar sequestration of nicotine in tobacco roots

Nicotine is a major alkaloid accumulating in the vacuole of tobacco (Nicotiana tabacum), but the transporters involved in the vacuolar sequestration are not known. We here report that tobacco genes (NtMATE1 and NtMATE2) encoding transporters of the multidrug and toxic compound extrusion (MATE) family are coordinately regulated with structural genes for nicotine biosynthesis in the root, with respect to spatial expression patterns, regulation by NIC regulatory loci, and induction by methyl jasmonate. Subcellular fractionation, immunogold electron microscopy, and expression of a green fluorescent protein fusion protein all suggested that these transporters are localized to the vacuolar membrane. Reduced expression of the transporters rendered tobacco plants more sensitive to the application of nicotine. In contrast, overexpression of NtMATE1 in cultured tobacco cells induced strong acidification of the cytoplasm after jasmonate elicitation or after the addition of nicotine under nonelicited conditions. Expression of NtMATE1 in yeast (Saccharomyces cerevisiae) cells compromised the accumulation of exogenously supplied nicotine into the yeast cells. The results imply that these MATE-type proteins transport tobacco alkaloids from the cytosol into the vacuole in exchange for protons in alkaloid-synthesizing root cells.

Quantitative analysis of anionic metabolites for Catharanthus roseus by capillary electrophoresis using sulfonated capillary coupled with electrospray ionization-tandem mass spectrometry

This paper describes a practical method to quantify anionic metabolites using contemporary capillary electrophoresis-electrospray ionization-tandem mass spectrometry (CE-ESI-MS/MS). The use of sulfonated capillary permitted a simultaneous analysis of sugar phosphates, organic acids, nucleotides and coenzyme A compounds with only one CE condition. This capillary also improved the repeatability and sensitivity. MS/MS with multiple reaction monitoring (MRM) detection was utilized to achieve significant selectivity and sensitivity. Under optimized CE-ESI-MS/MS system, the detection limits of 53 metabolites at signal-to-noise ratio of 3 were between 0.040 and 8.8 mumol/l. The relative standard deviations (RSDs) for the majority anionic metabolites were better than 0.5% for migration times, and better than 10.0% for peak areas (n=6). Matrix effects by contaminants in sample solution in CE-ESI-MS/MS analysis were removed dramatically by the sample preparation method with liquid-liquid fractionation and ultrafiltration procedure. Furthermore, the developed method was successfully applied to determine anionic metabolites in a cultured cell of Catharanthus roseus. Accumulation of some metabolites including shikimate, malate, and sedoheptulose 7-phosphate by elicitation of methyl jasmonate was observed. The result would show shikimate, tricarboxylic acid and pentose phosphate pathways were activated. Our method will be useful for detailed analysis of primary metabolism dynamics.

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.

Metabolic processes sustaining the reviviscence of lichen Xanthoria elegans (Link) in high mountain environments

To survive in high mountain environments lichens must adapt themselves to alternating periods of desiccation and hydration. Respiration and photosynthesis of the foliaceous lichen, Xanthoria elegans, in the dehydrated state were below the threshold of CO2-detection by infrared gas analysis. Following hydration, respiration totally recovered within seconds and photosynthesis within minutes. In order to identify metabolic processes that may contribute to the quick and efficient reactivation of lichen physiological processes, we analysed the metabolite profile of lichen thalli step by step during hydration/dehydration cycles, using 31P- and 13C-NMR. It appeared that the recovery of respiration was prepared during dehydration by the accumulation of a reserve of gluconate 6-P (glcn-6-P) and by the preservation of nucleotide pools, whereas glycolytic and photosynthetic intermediates like glucose 6-P and ribulose 1,5-diphosphate were absent. The large pools of polyols present in both X. elegans photo- and mycobiont are likely to contribute to the protection of cell constituents like nucleotides, proteins, and membrane lipids, and to preserve the integrity of intracellular structures during desiccation. Our data indicate that glcn-6-P accumulated due to activation of the oxidative pentose phosphate pathway, in response to a need for reducing power (NADPH) during the dehydration-triggered down-regulation of cell metabolism. On the contrary, glcn-6-P was metabolised immediately after hydration, supplying respiration with substrates during the replenishment of pools of glycolytic and photosynthetic intermediates. Finally, the high net photosynthetic activity of wet X. elegans thalli at low temperature may help this alpine lichen to take advantage of brief hydration opportunities such as ice melting, thus favouring its growth in harsh high mountain climates.

Analytical aspects of plant metabolite profiling platforms: current standings and future aims

Over the past years, metabolic profiling has been established as a comprehensive systems biology tool. Mass spectrometry or NMR spectroscopy-based technology platforms combined with unsupervised or supervised multivariate statistical methodologies allow a deep insight into the complex metabolite patterns of plant-derived samples. Within this review, we provide a thorough introduction to the analytical hard- and software requirements of metabolic profiling platforms. Methodological limitations are addressed, and the metabolic profiling workflow is exemplified by summarizing recent applications ranging from model systems to more applied topics.

From exogenous to endogenous: the inevitable imprint of mass spectrometry in metabolomics

Mass spectrometry (MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its utility derives from its wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing mass spectrometry for metabolomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, we will discuss the techniques involved in this exciting area and the current and future applications of this field.

A comparative study of water distribution, free radical production and activation of antioxidative metabolism in germinating pea seeds

The aim of this study was to investigate whether there is a relationship between hydration of the embryo axes and cotyledons and the resumption of the oxidative metabolism in both organs of germinating seeds of pea (Pisum sativum L. cv. Piast). Nuclear magnetic resonance ((1)H-NMR) spectroscopy and imaging were used to study temporal and spatial water uptake and distribution in pea seeds. The observations revealed that water penetrates into the seed through the hilum, micropyle and embryo axes, and cotyledons hydrate to different extents. Thus, inhomogeneous water distribution may influence the resumption of oxidative metabolism. Electron paramagnetic resonance (EPR) measurements showed that seed germination was accompanied by the generation of free radicals with g(1) and g(2) values of 2.0032 and 2.0052, respectively. The values of spectroscopic splitting coefficients suggest that they are quinone radicals. The highest content of free radicals was observed in embryo axes immediately after emergence of the radicle. Glutathione content decreased during the entire germination period in both embryo axes and cotyledons. A different profile was observed for ascorbate, with significant increases in embryo axes, coinciding with radicle protrusion. Electrophoretic analysis showed that superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), ascorbate peroxidase (APX, EC 1.11.1.11), dehydroascorbate reductase (DHAR, EC 1.8.5.1) and glutathione reductase (GR, EC 1.6.4.2) were present in dry seeds and were activated later during germination, especially in embryo axes. The presence of all antioxidative enzymes as well as low molecular antioxidants in dry seeds allowed the antioxidative machinery to be active as soon as the enzymes were reactivated by seed imbibition. The observed changes in free radical levels, antioxidant contents and enzymatic activities in embryo axes and cotyledons appear to be more closely related to metabolic and developmental processes associated with preparation for germination, and do not correspond directly to the hydration of the tissues.

Rapid analysis of organic acids in plant extracts by capillary electrophoresis with indirect UV detection

A fast, reliable capillary zone electrophoresis (CZE) method with indirect UV detection was optimized and validated to determine the main organic acids contained in plants. Citric, malic, succinic, oxalic, formic, fumaric, acetic acids, and phosphate were quantified. A rapid separation while keeping a good resolution was obtained by optimizing capillary length, separation voltage, electrolyte composition, and pH. Analyses were performed in a 30 cm uncoated fused-silica capillary (length to the detector window) in the co-electroosmotic mode with reversed electroosmotic flow and anodic detection using a -30 kV separation voltage. The pH 9.0 electrolyte contained 3 x 10(-4)mol/L tetradecyltrimethylammonium and 10(-2)mol/L trimellitate. Separation with baseline return was achieved in 100 s. Linearity, detection limits, repeatability, reproducibility, and recoveries were evaluated. Mean precision values of 0.2 and 3.4% for migration times and time-corrected peak areas, respectively, enabled accurate identification and quantification whether in standard solutions or in samples. Such performances were perfectly adapted to high-throughput routine determinations of organic acids in research or industry. Organic acids were assayed in different plant tissues and cells, including sycamore, arabidopsis, buttercup, and pea. Citrate and malate were the most abundant in all plants tested with concentrations reaching 18.9 and 22.3 micromol/g fresh matter, respectively. Cadmium effect on pea leaves metabolism was also assessed.

The expanding role of mass spectrometry in metabolite profiling and characterization

Mass spectrometry has a strong history in drug-metabolite analysis and has recently emerged as the foremost technology in endogenous metabolite research. The advantages of mass spectrometry include a wide dynamic range, the ability to observe a diverse number of molecular species, and reproducible quantitative analysis. These attributes are important in addressing the issue of metabolite profiling, as the dynamic range easily exceeds nine orders of magnitude in biofluids, and the diversity of species ranges from simple amino acids to lipids to complex carbohydrates. The goals of the application of mass spectrometry range from basic biochemistry to clinical biomarker discovery with challenges in generating a comprehensive profile, data analysis, and structurally characterizing physiologically important metabolites. The precedent for this work has already been set in neonatal screening, as blood samples from millions of neonates are tested routinely by mass spectrometry as a diagnostic tool for inborn errors of metabolism. In this review, we will discuss the background from which contemporary metabolite research emerged, the techniques involved in this exciting area, and the current and future applications of this field.

Development of a small-scale bioreactor: application to in vivo NMR measurement

A perfused bioreactor allowing in vivo NMR measurement was developed and validated for Eschscholtzia californica cells. The bioreactor was made of a 10-mm NMR tube. NMR measurement of the signal-to-noise ratio was optimized using a sedimented compact bed of cells that were retained in the bioreactor by a supporting filter. Liquid medium flow through the cell bed was characterized from a mass balance on oxygen and a dispersive hydrodynamic model. Cell bed oxygen demand for 4 h perfusion required a minimal medium flow rate of 0.8 mL/min. Residence time distribution assays at 0.8-2.6 mL/min suggest that the cells are subjected to a uniform nutrient environment along the cell bed. Cell integrity was maintained for all culture conditions since the release of intracellular esterases was not significant even after 4 h of perfusion. In vivo NMR was performed for (31)P NMR and the spectrum can be recorded after only 10 min of spectral accumulation (500 scans) with peaks identified as G-6P, F-6P, cytoplasmic Pi, vacuolar Pi, ATP(gamma) and ADP(beta), ATP(alpha) and ADP(alpha), NADP and NDPG, NDPG and ATP(beta). Cell viability was shown to be maintained as (31)P chemical shifts were constant with time for all the identified nuclei, thus suggesting constant intracellular pH.

Viewpoint: Carbon isotope effect predictions for enzymes involved in the primary carbon metabolism of plant leaves

Carbon isotope effects of enzymes involved in primary carbon metabolism are key parameters in our understanding of plant metabolism. Nevertheless, some of them are poorly known because of the lack of in vitro experimental data on purified enzymes. Some studies have focused on theoretical predictions of isotope effects. Here we show how quantum chemical calculations can be adapted for calculation of isotope effects for the Rubisco-catalysed carboxylation and oxygenation reactions and the citrate synthase reaction. The intrinsic isotope effect of the carboxylation by Rubisco appears to be much smaller than previously thought, being close to the overall isotope effect of the reaction that is, between 25 and 30 per mil. The same applies to the enzyme citrate synthase, that catalyses the first step of the Krebs cycle, with an isotope effect of around 23 per mil. Combined with the isotope effects of equilibrium reactions calculated with β-factors, the Krebs cycle then has an overall isotope effect that depletes organic acids in ¹³C.

NMR analysis of plant nitrogen metabolism

The analysis of primary and secondary nitrogen metabolism in plants by nuclear magnetic resonance (NMR) spectroscopy is comprehensively reviewed. NMR is a versatile analytical tool, and the combined use of (1)H, (2)H, (13)C, (14)N and (15)N NMR allows detailed investigation of the acquisition, assimilation and metabolism of nitrogen. The analysis of tissue extracts can be complemented by the in vivo NMR analysis of functioning tissues and cell suspensions, and by the application of solid state NMR techniques. Moreover stable isotope labelling with (2)H-, (13)C- and (15)N-labelled precursors provides direct insight into specific pathways, with the option of both time-course and steady state analysis increasing the potential value of the approach. The scope of the NMR method, and its contribution to studies of plant nitrogen metabolism, are illustrated with a wide range of examples. These include studies of the GS/GOGAT pathway of ammonium assimilation, investigations of the metabolism of glutamate, glycine and other amino acids, and applications to tropane alkaloid metabolism. The continuing development of the NMR technique, together with potential applications in the emerging fields of metabolomics and metabolic flux analysis, leads to the conclusion that NMR will play an increasingly valuable role in the analysis of plant nitrogen metabolism.

Effect of drought and rewatering on the metabolism of Lupinus albus organs

Alterations in the metabolism of Lupinus albus organs that result from and subsequently follow a period of severe water deficit (WD) are described. By means of 13C-nuclear magnetic resonance (NMR), changes in the major metabolites were monitored in several plant organs (leaflets and petiole, roots, stem stele and cortex). During the stress, most of the leaves were lost and the stem functioned as a storage repository of sugars (glucose and sucrose) and amino acids (asparagine and proline). Upon rewatering, lupin plants rapidly re-established the relative water content (RWC) and produced new leaves. However, at the metabolic level, the events seem to be more complex, since proline (a stress related metabolite) disappeared rapidly while sugars and asparagine reached the initial pattern more slowly, particularly in the stem.

Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection

The study of the metabolomics of primary metabolites using conventional chemical analyses requires a high-throughput method. Chemical derivatizations are a prerequisite for gas-chromatographic separation, and a large sample quantity is needed for liquid-chromatographic separation and nuclear magnetic resonance detection systems. Recently, we have developed a capillary electrophoresis-mass spectrometry (CE-MS) technology that can simultaneously quantify a large number of primary metabolites, using only a small quantity of samples, and without any chemical derivatizations. Parallel use of a capillary electrophoresis-diode array detector (CE-DAD) system further enables almost all water-soluble intracellular metabolites to be analyzed. We demonstrate, with rice leaves, a simple and rapid method of sample preparation for CE analysis; using this method, we have successfully measured the levels of 88 main metabolites involved in glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, photorespiration, and amino acid biosynthesis.

Metabolite profiling in plant biology: platforms and destinations

Optimal use of genome sequences and gene-expression resources requires powerful phenotyping platforms, including those for systematic analysis of metabolite composition. The most used technologies for metabolite profiling, including mass spectral, nuclear magnetic resonance and enzyme-based approaches, have various advantages and disadvantages, and problems can arise with reliability and the interpretation of the huge datasets produced. These techniques will be useful for answering important biological questions in the future.

Gene expression of the NO3- transporter NRT1.1 and the nitrate reductase NIA1 is repressed in Arabidopsis roots by NO2-, the product of NO3- reduction

NRT1.1 and NIA1 genes, which encode a nitrate (NO3-) transporter and the minor isoform of NO3- reductase (NR), respectively, are overexpressed in roots of NR-deficient mutants of Arabidopsis grown on nutrient solution containing NO3- and reduced N. The overexpression is found only in mutants with reduced NIA2 activity, and disruption of the NIA1 gene alone has no effect on NRT1.1 expression. Because the up-regulation of NRT1.1 and NIA1 is observed in N-sufficient NR mutant plants, it cannot be related to a release of the general feedback repression exerted by the N status of the plant. Our data do not support the hypothesis of overinduction of these genes by an increased concentration of NO3- in tissues. Furthermore, although a control by external pH might contribute to the regulation of NRT1.1, changes in external pH due to lack of NR activity cannot alone explain the up-regulation of both genes. The stimulation of NRT1.1 and NIA1 in NR mutants in these conditions suggests that NR activity is able to repress directly the expression of both genes independently of the availability of reduced N metabolites in wild-type plants. Accordingly, nitrite (NO2-) strongly represses NRT1.1 and NIA1 transcript accumulation in the roots. This effect is rapid, specific, and reversible. Furthermore, transport studies on plants exposed to NO2- show that down-regulation of the NRT1.1 gene is associated with a decrease in NO3- influx. These results indicate that feedback regulation of genes of NO3- assimilation relies not only on the repression exerted by reduced N metabolites, such as NH4+ or amino acids, but may also involve the action of NO2- as a regulatory signal.

Cold- and light-induced changes of metabolite and antioxidant levels in two high mountain plant species Soldanella alpina and Ranunculus glacialis and a lowland species Pisum sativum

Leaves of the two cold-acclimated alpine plant species Ranunculus glacialis and Soldanella alpina and, for comparison, of the non-acclimated lowland species Pisum sativum were illuminated with high light intensity at low temperature. The light- and cold-induced changes of antioxidants and of the major carbon and phosphate metabolites were analysed to examine which metabolic pathways might be limiting in non-acclimated pea leaves and whether alpine plants are able to circumvent such limitation. During illumination at low temperature pea leaves accumulated high quantities of sucrose, glucose-6-phosphate, fructose-6-phosphate, mannose-6-phosphate and phosphoglycerate (PGA) whereas ATP/ADP-ratios decreased. Although the PGA content also increased in leaves of R. glacialis the other metabolites did not accumulate and ATP/ADP-ratios remained fairly constant in either alpine species. These data indicate a inorganic phosphate (Pi)-limitation in the chloroplasts of pea leaves but not in the alpine species. However, the total phosphate pool and the percentage of free Pi were highest in pea and did not change during illumination in cold. In contrast, free Pi contents declined markedly in R. glacialis leaves, suggesting that Pi is available for metabolism in this species. In S. alpina leaves contents of ascorbate and glutathione doubled in light and cold, while the contents of sugars did not increase. Obviously, S. alpina leaves can use assimilated carbon for ascorbate synthesis, rather than for the synthesis of sugars. A high capacity for ascorbate synthesis might prevent the accumulation of mannose-6-phosphate and Pi-limitation.

Plant metabolomics: large-scale phytochemistry in the functional genomics era

Metabolomics or the large-scale phytochemical analysis of plants is reviewed in relation to functional genomics and systems biology. A historical account of the introduction and evolution of metabolite profiling into today's modern comprehensive metabolomics approach is provided. Many of the technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry are surveyed. The critical role of bioinformatics and various methods of data visualization are summarized and the future role of metabolomics in plant science assessed.

Reversibility of cold- and light-stress tolerance and accompanying changes of metabolite and antioxidant levels in the two high mountain plant species Soldanella alpina and Ranunculus glacialis

Two high mountain plants Soldanella alpina (L.) and Ranunculus glacialis (L.) were transferred from their natural environment to two different growth conditions (22 degrees C and 6 degrees C) at low elevation in order to investigate the possibility of de-acclimation to light and cold and the importance of antioxidants and metabolite levels. The results were compared with the lowland crop plant Pisum sativum (L.) as a control. Leaves of R. glacialis grown for 3 weeks at 22 degrees C were more sensitive to light-stress (defined as damage to photosynthesis, reduction of catalase activity (EC 1.11.1.6) and bleaching of chlorophyll) than leaves collected in high mountains or grown at 6 degrees C. Light-stress tolerance of S. alpina leaves was not markedly changed. Therefore, acclimation is reversible in R. glacialis leaves, but constitutive or long-lasting in S. alpina leaves. The different growth conditions induced significant changes in non-photochemical fluorescence quenching (qN) and the contents of antioxidants and xanthophyll cycle pigments. These changes did not correlate with light-stress tolerance, questioning their role for light- and cold-acclimation of both alpine species. However, ascorbate contents remained very high in leaves of S. alpina under all growth conditions (12-19% of total soluble carbon). In cold-acclimated leaves of R. glacialis, malate represented one of the most abundant compounds of total soluble carbon (22%). Malate contents declined significantly in de-acclimated leaves, suggesting a possible involvement of malate, or malate metabolism, in light-stress tolerance. Leaves of the lowland plant P. sativum were more sensitive to light-stress than the alpine species, and contained only low amounts of malate and ascorbate.

Vibrational, 1H-NMR spectroscopic, and thermal characterization of gladiolus root exudates in relation to Fusarium oxysporum f. sp. gladioli resistance

Fourier transform Raman (FT Raman) and IR (FTIR) and (1)H-NMR spectroscopies coupled with differential scanning calorimetry (DSC) were applied to the characterization of root exudates from two cultivars of gladiolus (Spic Span and White Prosperity) with different degrees of resistance and susceptibility to Fusarium oxysporum gladioli, the main pathogen of gladiolus. This work was aimed at correlating the composition of root exudates with the varietal resistance to the pathogen. Spectroscopic analysis showed that White Prosperity root exudate differs from Spic Span root exudate by a higher relative amount of the aromatic-phenolic and sugarlike components and a lower relative amount of carbonylic and aliphatic compounds. DSC analysis confirmed the spectroscopic results and showed that White Prosperity root exudate is characterized by an aromatic component that is present in a higher amount than in the Spic Span root exudate. The results are discussed in relation to the spore germination tests showing that White Prosperity, which is characterized by a remarkable resistance toward F. oxysporum gladioli, exudes substances having a negative influence on microconidial germination of the pathogen; root exudates from Spic Span, one of the most susceptible cultivars to F. oxysporum gladioli, proved to have no effect. White Prosperity's ability to inhibit conidial germination of F. oxysporum gladioli can be mainly related to the presence of a higher relative amount of aromatic-phenolic compounds.

Synthesis and 31P NMR characterization of new low toxic highly sensitive pH probes designed for in vivo acidic pH studies

With the aim to provide sensitive 31P NMR probes of intra- and extracellular pH gradients that may reach cellular acidic compartments in biological systems, new alpha-aminophosphonates were designed to meet basic requirements such as a low pK(a)s and a great chemical difference (Deltadelta(ab)) between the limiting 31P NMR chemical shifts in acidic (delta(a)) and basic (delta(b)) media. A series of six phosphorylated pyrrolidines and linear aminophosphonates were synthesized using aminophosphorylation reactions and were screened for cytotoxicity on cultured Müller cells. Among the compounds not being toxic under these conditions, three molecules were selected since they displayed the best in vitro (in several phosphate buffers and in a cytosol-like solution) properties as 31P NMR acidic pH markers, that is 3, 5 and 9, having the pK(a) values of 3.63, 5.89 and 5.66, respectively. The Deltadelta(ab) values of these pH markers were at least 3 times larger than that of standard 31P NMR probes, with a low sensitivity to ionic strength changes. From these data, it was proposed that 3, 5 and 9 could be used as reporting probes of subtle proton movements in acidic compartments, an area that still remains poorly investigated using non invasive 31P NMR methods.