Metabolite profiling of mycorrhizal roots of Medicago truncatula

Metabolite profiling of soluble primary and secondary metabolites, as well as cell wall-bound phenolic compounds from roots of barrel medic (Medicago truncatula) was carried out by GC-MS, HPLC and LC-MS. These analyses revealed a number of metabolic characteristics over 56 days of symbiotic interaction with the arbuscular mycorrhizal (AM) fungus Glomus intraradices, when compared to the controls, i.e. nonmycorrhizal roots supplied with low and high amounts of phosphate. During the most active stages of overall root mycorrhization, elevated levels of certain amino acids (Glu, Asp, Asn) were observed accompanied by increases in amounts of some fatty acids (palmitic and oleic acids), indicating a mycorrhiza-specific activation of plastidial metabolism. In addition, some accumulating fungus-specific fatty acids (palmitvaccenic and vaccenic acids) were assigned that may be used as markers of fungal root colonization. Stimulation of the biosynthesis of some constitutive isoflavonoids (daidzein, ononin and malonylononin) occurred, however, only at late stages of root mycorrhization. Increase of the levels of saponins correlated AM-independently with plant growth. Only in AM roots was the accumulation of apocarotenoids (cyclohexenone and mycorradicin derivatives) observed. The structures of the unknown cyclohexenone derivatives were identified by spectroscopic methods as glucosides of blumenol C and 13-hydroxyblumenol C and their corresponding malonyl conjugates. During mycorrhization, the levels of typical cell wall-bound phenolics (e.g. 4-hydroxybenzaldehyde, vanillin, ferulic acid) did not change; however, high amounts of cell wall-bound tyrosol were exclusively detected in AM roots. Principal component analyses of nonpolar primary and secondary metabolites clearly separated AM roots from those of the controls, which was confirmed by an hierarchical cluster analysis. Circular networks of primary nonpolar metabolites showed stronger and more frequent correlations between metabolites in the mycorrhizal roots. The same trend, but to a lesser extent, was observed in nonmycorrhizal roots supplied with high amounts of phosphate. These results indicate a tighter control of primary metabolism in AM roots compared to control plants. Network correlation analyses revealed distinct clusters of amino acids and sugars/aliphatic acids with strong metabolic correlations among one another in all plants analyzed; however, mycorrhizal symbiosis reduced the cluster separation and enlarged the sugar cluster size. The amino acid clusters represent groups of metabolites with strong correlations among one another (cliques) that are differently composed in mycorrhizal and nonmycorrhizal roots. In conclusion, the present work shows for the first time that there are clear differences in development- and symbiosis-dependent primary and secondary metabolism of M. truncatula roots.     

Metabolite profiling of Arabidopsis seedlings in response to exogenous sinalbin and sulfur deficiency

In order to determine how plant uptake of a sulfur-rich secondary metabolite, sinalbin, affects the metabolic profile of sulfur-deficient plants, gas chromatography time-of-flight mass spectrometry (GC-TOF-MS), in combination with liquid chromatography-mass spectrometry (LC-MS), was used to survey the metabolome of Arabidopsis seedlings grown in nutrient media under different sulfur conditions. The growth media had either sufficient inorganic sulfur for normal plant growth or insufficient inorganic sulfur in the presence or absence of supplementation with organic sulfur in the form of sinalbin (p-hydroxybenzylglucosinolate). A total of 90 metabolites were identified by GC-TOF-MS and their levels were compared across the three treatments. Of the identified compounds, 21 showed similar responses in plants that were either sulfur deficient or sinalbin supplemented compared to sulfur-sufficient plants, while 12 metabolites differed in abundance only in sulfur-deficient plants. Twelve metabolites accumulated to higher levels in sinalbin-supplemented than in the sulfur-sufficient plants. Secondary metabolites such as flavonol conjugates, sinapinic acid esters and glucosinolates, were identified by LC-MS and their corresponding mass fragmentation patterns were determined. Under sinalbin-supplemented conditions, sinalbin was taken up by Arabidopsis and contributed to the endogenous formation of glucosinolates. Additionally, levels of flavonol glycosides and sinapinic acid esters increased while levels of flavonol diglycosides with glucose attached to the 3-position were reduced. The exogenously administered sinalbin resulted in inhibition of root and hypocotyl growth and markedly influenced metabolite profiles, compared to control and sulfur-deficient plants. These results indicate that, under sulfur deficient conditions, glucosinolates can be a sulfur source for plants. This investigation defines an opportunity to elucidate the mechanism of glucosinolate degradation in vivo.     

Content of adenosine phosphate compounds in pea roots grown in saline media

The levels of ATP, ADP and AMP, the activity of phosphatases, and the ability for oxidative phosphorylation were studied in roots of pea (Pisum sativum) plants grown in media salinized either with NaCl or Na₂SO₄. In response to salinity, the ATP level in the roots decreased, whereas the ADP level increased slightly. As a result, the ADP:ATP ratio in the tissue increased with increasing salinity in the growth medium. The AMP level in the tissue was not affected by salinity.     

Growth response of Anacystis nidulans to sodium and phosphate availability

The growth response of Anacystis nidulans to sodium and phosphate was studied in batch culture under controlled laboratory conditions. Sodium (range=0–10 mg/l) significantly enhanced growth, most notably, after sodium and phosphate starvation. The magnitude of the increase in growth was dependent on the initial cell density, external concentrations of phosphate, sodium, and potassium, and the nutritional status of the algal inoculum. The increase in ambient sodium levels in many lakes may provide a competitive advantage to some blue-green algae.     

Tracheids in white spruce seedling's long lateral roots in response to nitrogen availability

This study examined how the availability of inorganic nitrogen (N) modified the anatomical characteristics of white spruce (Picea glauca (Moench) Voss) roots related to their hydraulic properties. Seedlings were grown for one growing season in 4 L capacity pots filled with sand under one of three N levels: low (10 ppm), medium (50 ppm) and high (125 ppm). First order lateral roots with intact tips were sampled from dormant seedlings in October. Root segments were collected from 4, 10, and 14 cm distances above the root tip for fixation and sectioning and for maceration. Additional specimens were collected from the 4 and 14 cm distances for maceration and scanning electron microscopy of xylem pits. Root diameter and surface area occupied by the xylem in root cross sections increased basipetally in all treatments but exceptions were found. Higher N-levels significantly increased root diameter and surface area occupied by the xylem. In the two higher N treatments secondary root development was more advanced near the root tip than in the low N treatment. There was a strong positive correlation between root diameter and cross-sectional root area occupied by the xylem (30–50% of the root cross section) but not in portions with little secondary development. Non-conducting space within the xylem occupied 10–13% of its cross-sectional surface. Tracheids of the primary xylem were larger, had larger lumens but thinner cell walls than those of the secondary xylem. Low N treatment seedling tracheids had smaller total cross-sectional area, less lumen, and less cell wall surface area than the two other N treatments. Tracheid diameter means were between 19–20 μm in the high and medium N treatments, and 15.2 μm in the low N treatment. The range was 4.5–51.3 μm. Tracheid length was not significantly affected by N. The average tracheid was about 1000 μm long, and the range was 110–3530 μm. Pit-border diameters ranged between 4.1–20.6 μm (average 10–11 μm) and were not affected by the N treatment. Pit aperture diameters were within 0.62–10.2 μm range (average between 3–4 μm) and were also not significantly affected by the N treatment, although tracheids from the medium N-treatment roots tended to have larger apertures. The pit border diameter equals that of the margo while the aperture size should be similar to that of the torus of the pit membrane. If the capacity for axial water transport in spruce roots is affected by N, it would be by its impact on conduit diameter and, possibly on the pit-membrane pore sizes but not by changes to conduit length and to the size of the pit membrane surface area. This revised version was published online in June 2006 with corrections to the Cover Date.     

Auxin and the response of pea roots to auxin transport inhibitors: morphactin

The auxin transport inhibitor methyl-2-chloro-9-hydroxyfluorene-9-carboxylate (CFM), a morphactin, inhibits negative geotropism, causes cellular swelling, and induces root hair formation in roots of intact Pisum sativum L. seedlings. In excised pea root tips, CFM inhibits elongation more than increase in fresh weight (swell ratio = 1.3 at 20 mum CFM). CFM growth inhibition was expressed in the presence of ethylene. Indoleacetic acid (IAA) prevented the expression of CFM growth inhibition possibly because IAA inhibited the accumulation of CFM into the tissue sections. CFM inhibited the accumulation of IAA and 2,4-dichlorophenoxyacetic acid into excised root tips. Applying Leopold's (1963. Brookhaven Symp. Biol. 16: 218-234) model for polar auxin transport, this result suggests a possible explanation for CFM inhibition of geotropism in pea roots, i.e. disruption of auxin transport by interfering with auxin binding.     

Metabolite profiling: from diagnostics to systems biology

The concept of metabolite profiling has been around for several decades, but only recent technical innovations have allowed metabolite profiling to be carried out on a large scale - with respect to both the number of metabolites measured and the number of experiments carried out. As a result, the power of metabolite profiling as a technology platform for diagnostics, and the research areas of gene-function analysis and systems biology, is now beginning to be fully realized.     

Metabolite profiling as an aid to metabolic engineering in plants

The past decade has seen some impressive successes in the metabolic engineering of biotechnologically important plant pathways. However, plant metabolic engineering currently proceeds more by trial and error than by intelligent system design. A change in philosophy away from studying pathways in isolation and towards studying metabolism as a network is necessary. To support this development, improvements in technologies for metabolic analysis, a wider adoption of metabolite-profiling approaches and significant innovations in data analysis methodologies are required.     

Cytokinins in seedling roots of pea

The natural occurrence of cytokinins existing both in a free form and as a constituent of transfer RNA was examined in serial segments of young seedling roots of pea. Purified ethanol extracts of root apices were resolved into four factors capable of inducing soybean callus tissue proliferation. The most active factor was identified as zeatin or some closely related compound; it produced polyploid divisions and tracheary element differentiation when tested on cultured pea root segments. The terminal 0- to 1-millimeter root tip contained 43 to 44 times more free cytokinin on a fresh weight or a per cell basis than the next 1- to 5-millimeter root segment. Extracts of more proximal segments behind the tip contained no measurable free cytokinin. Acid hydrolysates of transfer RNA exhibited reproducible cytokinin activity. Bioassays revealed that the predominant amounts of free cytokinin and that present in transfer RNA were restricted to the extreme root tip. There was approximately 27 times more free cytokinin than the amount detected in transfer RNA in root apices.     

Diffusion of phosphate to plant roots in soil

Summary Autoradiographs of rape (Brassica napus L.) seedlings growing in a Begbroke Sandy Loam treated to different P levels showed P accumulations near root apices of primary and lateral roots, without corresponding depletion from the adjacent soil, indicating marked translocation.Laterals less than 2 days old did not deplete the soil despite considerable P accumulations in them. Their growth and P uptake were enhanced when the growth of the primary root was checked. The length of root hairs decreased markedly with increasing P supply.The P depletion zones developed in the same way at all points along the primary axis (except for a short length behind the apex). At the highest P level the concentration of exchangeable P at the root surface was lowered by about 30% on day 2, by about 40% on day 4 and rose slowly after day 8.Whereas in P treated soils the depletion from within the root hair cylinder was fairly uniform, in the low P soil there was a continuous decrease in P concentrations toward the root surface, within the root hair zone.Soil Science Laboratory, Department of Agricultural Science, University of Oxford     

Diffusion of phosphate to plant roots in soil

Summary Improved resolution in autoradiography, achieved by the use of the low energy isotope, P³³, as tracer for soil phosphorus, enables the exchangeable phosphorus in a soil block to be measured quantitatively. A technique is described for the autoradiography of the P-depletion zone around the roots growing in soil, from which the P gradients are measured by microdensitometry.The amounts of P taken up by rape (Brassica napus) on a P-treated Begbroke Sandy Loam compared well with that removed from the soil as measured from the autoradiograph of the depletion zone. The P gradient around the roots suggests intense root hair activity; but the zone of depletion extended well beyound the tips of root hairs. The experimentally observed gradient is much closer to the one predicted from diffusion theory considering uniform depletion from within the equivalent root hair cylinder, than to the one obtained assuming the root hairs are inactive.A rapid depletion of up to about 60 per cent of the exchangeable P was observed within the root hair cylinder during the initial 3 days of absorption. The corresponding concentration of P in solution within the cylinder determined from a desorption isotherm, is hence brought down to a low level very rapidly, and is held at or near this level at later periods. The amounts transferred into the root hair cylinder from outside as calculated from a diffusion model were lower than the experimental values. It is suggested that the discrepancy may lie in the calculation of the effective diffusion coefficients for P in the soil from a P-desorption isotherm, owing to difficulties involved in simulating the root environment in the desorption isotherm experimentSoil Science Laboratory, Department of Agricultural Science, University of Oxford     

Diffusion of phosphate to plant roots in soil

Summary A method is described for computing the theoretical distribution of solutes around a root with root hairs. The P concentration profile around the primary root of a rape seedling with root hairs, growing in a low-P soil, showed considerably greater depletions than predicted by this method, using the relationship between P in soil and in solution obtained from a desorption isotherm experiment. This suggests an enhanced release of soil P into solution in the rhizosphere.Soil Science Laboratory, Department of Agricultural Science, University of Oxford     

Metabolite profiling of Alzheimer's disease cerebrospinal fluid

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive loss of cognitive functions. Today the diagnosis of AD relies on clinical evaluations and is only late in the disease. Biomarkers for early detection of the underlying neuropathological changes are still lacking and the biochemical pathways leading to the disease are still not completely understood. The aim of this study was to identify the metabolic changes resulting from the disease phenotype by a thorough and systematic metabolite profiling approach. For this purpose CSF samples from 79 AD patients and 51 healthy controls were analyzed by gas and liquid chromatography-tandem mass spectrometry (GC-MS and LC-MS/MS) in conjunction with univariate and multivariate statistical analyses. In total 343 different analytes have been identified. Significant changes in the metabolite profile of AD patients compared to healthy controls have been identified. Increased cortisol levels seemed to be related to the progression of AD and have been detected in more severe forms of AD. Increased cysteine associated with decreased uridine was the best paired combination to identify light AD (MMSE>22) with specificity and sensitivity above 75%. In this group of patients, sensitivity and specificity above 80% were obtained for several combinations of three to five metabolites, including cortisol and various amino acids, in addition to cysteine and uridine.     

Metabolite profiling for analysis of yeast stress response during very high gravity ethanol fermentations

A laboratory strain and an industrial strain of Saccharomyces cerevisiae were grown at high substrate concentration, so-called very high gravity (VHG) fermentation. Simultaneous saccharification and fermentation (SSF) was applied in a batch process using 280 g/L maltodextrin as carbon source. It was shown that known ethanol and osmotic stress responses such as decreased growth rate, lower viability, higher energy consumption, and intracellular trehalose accumulation occur in VHG SSF for both strains when compared with standard laboratory medium (20 g/L glucose). The laboratory strain was the most affected. GC-MS metabolite profiling was applied for assessing the yeast stress response influence on cellular metabolism. It was found that metabolite profiles originating from different strains and/or fermentation conditions were unique and could be distinguished with the help of multivariate data analysis. Several differences in the metabolic responses to stressing conditions were revealed, particularly the increased energy consumption of stressed cells was also reflected in increased intracellular concentrations of pyruvate and related metabolites.     

Metabolite profiling of Panax notoginseng using UPLC-ESI-MS

The metabolite profiling of different parts of Panax notoginseng was carried out using rapid ultra-performance liquid chromatography-electrospray ionization mass spectrometry (UPLC-ESI-MS) and multivariate statistical analysis. Principal component analysis (PCA) of the UPLC-ESI-MS data showed a clear separation of compositions among the flower buds, roots and rhizomes of P. notoginseng. The saponins accounting for such variations were identified through the corresponding loadings weights and were further verified by accurate mass, tandem mass and retention times of available standard saponins using UPLC quadrupole time-of-flight mass spectrometer (UPLC-QtofMS). Finally, the influential factors of different metabolic phenotypes of P. notoginseng was elucidated. The currently proposed UPLC-ESI-MS/MS analytical method coupled with multivariate statistical analysis can be further utilized to evaluate chemical components obtained from different parts of the plant and/or the plant of different geographical locations, thereby classifying the medicinal plant resources and potentially elucidating the mechanism of inherent phytochemical diversity.     

Metabolite fingerprinting and profiling in plants using NMR

Although less sensitive than mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy provides a powerful complementary technique for the identification and quantitative analysis of plant metabolites either in vivo or in tissue extracts. In one approach, metabolite fingerprinting, multivariate analysis of unassigned 1H NMR spectra is used to compare the overall metabolic composition of wild-type, mutant, and transgenic plant material, and to assess the impact of stress conditions on the plant metabolome. Metabolite fingerprinting by NMR is a fast, convenient, and effective tool for discriminating between groups of related samples and it identifies the most important regions of the spectrum for further analysis. In a second approach, metabolite profiling, the 1H NMR spectra of tissue extracts are assigned, a process that typically identifies 20-40 metabolites in an unfractionated extract. These profiles may also be used to compare groups of samples, and significant differences in metabolite concentrations provide the basis for hypotheses on the underlying causes for the observed segregation of the groups. Both approaches generate a metabolic phenotype for a plant, based on a system-wide but incomplete analysis of the plant metabolome. However, a review of the literature suggests that the emphasis so far has been on the accumulation of analytical data and sample classification, and that the potential of 1H NMR spectroscopy as a tool for probing the operation of metabolic networks, or as a functional genomics tool for identifying gene function, is largely untapped.     

Lactic acid content and formation in pea roots exposed to salinity

Lactic acid content and production, as well as lactic dehydrogenaseactivity were studied in pea root tips grown in media salinatedwith NaCl or Na₂SO₄. Salinity of both types depressed the lacticacid content of the tissue. Lactic dehydrogenase activity linkedto NADH was depressed by high concentrations of NaCl in thegrowth medium, but was stimulated by increasing concentrationsof Na₂SO₄. There was a trace of NADPH linked activity of theenzyme; this activity was not affected by chloride salinitybut was depressed by sulphate salinity. It is not yet clearhow these events are connected with the overall effect of salinityon the carbohydrate metabolism of pea root tips. (Received June 27, 1970; )