Assessment of 1H NMR spectroscopy and multivariate analysis as a technique for metabolite fingerprinting of Arabidopsis thaliana

Ward, Jane L.; Harris, Cassandra; Jw, Lewis; Beale, Michael H.

doi:10.1016/s0031-9422(02)00705-7

Cited by 232 publications

(169 citation statements)

References 15 publications

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“…For example, FT-IR [22] and NMR [37,61] generate global chemical fingerprints with little need for specialised sample preparation [23,24]. However, these methods are less sensitive than FIE-MS [3] and, generally, require a further level of directed analysis to link any differences in wavenumber (FT-IR) or chemical shifts (NMR) to specific chemistry [23].…”

Section: Selection Of Metabolomics Approaches For Characterising Dietmentioning

confidence: 99%

Measurement of dietary exposure: a challenging problem which may be overcome thanks to metabolomics?

et al. 2009

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The diet is an important environmental exposure, and its measurement is an essential component of much health-related research. However, conventional tools for measuring dietary exposure have significant limitations being subject to an unknown degree of misreporting and dependent upon food composition tables to allow estimation of intakes of energy, nutrients and non-nutrient food constituents. In addition, such tools may be inappropriate for use with certain groups of people. As an alternative approach, the recent techniques of metabolite profiling or fingerprinting, which allows simultaneous monitoring of multiple and dynamic components of biological fluids, may provide metabolic signals indicative of food intake. Samples can be analysed through numerous analytical platforms, followed by multivariate data analysis. In humans, metabolomics has been applied successfully in pharmacology, toxicology and medical screening, but nutritional metabolomics is still in its infancy. Biomarkers of a small number of specific foods and nutrients have been developed successfully but less targeted and more high-throughput methods, that do not need prior knowledge of which signals might be discriminatory, and which may allow a more global characterisation of dietary intake, remain to be tested. A proof a principle project (the MEDE Study) is currently underway in our laboratories to test the hypothesis that high-throughput, non-targeted metabolite fingerprinting using flow injection electrospray mass spectrometry can be applied to human biofluids (blood and urine) to characterise dietary exposure in humans.

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Section: Selection Of Metabolomics Approaches For Characterising Dietmentioning

confidence: 99%

Measurement of dietary exposure: a challenging problem which may be overcome thanks to metabolomics?

et al. 2009

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“…As shown below, when applying 1 H high-resolution magic angle spinning NMR spectroscopy ( 1 H HRMAS-NMR), we provide complex metabolic phenotypes (6) or metabotypes (8) suitable for discriminating between C. elegans oxidative stress mutants, which cannot otherwise be distinguished phenotypically (14). In this study, we develop, validate, and apply a strategy using 1 H HRMAS-NMR spectroscopy of whole-model organisms, in this case C. elegans, to reveal the latent phenotypes associated with silent mutations (11) in Metazoans, an approach already developed in yeast and plants using mass spectrometry and liquid-state NMR (15,16). In particular, we investigate subtle metabolic disruptions induced by mutations of oxidative stress enzymes.…”

mentioning

confidence: 99%

Metabotyping of Caenorhabditis elegans reveals latent phenotypes

Blaise

Giacomotto

Elena

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

108

133

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Assigning functions to every gene in a living organism is the next challenge for functional genomics. In fact, 85-90% of the 19,000 genes of the nematode Caenorhabditis elegans genome do not produce any visible phenotype when inactivated, which hampers determining their function, especially when they do not belong to previously characterized gene families. We used 1 H high-resolution magic angle spinning NMR spectroscopy ( 1 H HRMAS-NMR) to reveal the latent phenotype associated to superoxide dismutase (sod-1) and catalase (ctl-1) C. elegans mutations, both involved in the elimination of radical oxidative species. These two silent mutations are significantly discriminated from the wild-type strain and from each other. We identify a metabotype significantly associated with these mutations involving a general reduction of fatty acyl resonances from triglycerides, unsaturated lipids being known targets of free radicals. This work opens up perspectives for the use of 1 H HRMAS-NMR as a molecular phenotyping device for model organisms. Because it is amenable to high throughput and is shown to be highly informative, this approach may rapidly lead to a functional and integrated metabonomic mapping of the C. elegans genome at the systems biology level.functional genomics ͉ metabolic profiling ͉ metabonomics ͉ nuclear magnetic resonance A ssigning functions to every gene in a living organism is the next challenge for functional genomics. However, only a small proportion of genes produce visible phenotypes when inactivated; for example, only 10-15% of the 19,000 genes of the nematode Caenorhabditis elegans produce a visible phenotype (1, 2). For the remaining ones, determining their function is more difficult, especially when they do not belong to previously characterized gene families.For example, oxidative stress is a key, yet subtle, biological process involved in aging, with long-term integration of many slow processes leading to irreversible cellular and molecular damage.Phenotyping plays a critical role in postgenomic sciences. Today, a range of molecular phenotyping tools is available to characterize mutations. Although gene expression and protein profiling are predominantly used (3-5), metabonomic and metabolomic strategies (6, 7) advantageously produce metabolic fingerprints that allow identification of variations in low-molecular-weight compounds in biofluids or organs in response to pathophysiological events (8), drug treatments (9), or genetic polymorphisms (10). It is therefore an attractive hypothesis-free approach for large-scale functional genomics in model organisms (11).Here we capitalize on recent developments in solid-state NMR that allow the acquisition of highly resolved 1 H spectra of metabolites from inhomogeneous materials such as biopsies (12) or food (13). As shown below, when applying 1 H high-resolution magic angle spinning NMR spectroscopy ( 1 H HRMAS-NMR), we provide complex metabolic phenotypes (6) or metabotypes (8) suitable for discriminating between C. elegans oxidative stress mutants, w...

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“…Combined [ 1 H]-NMR and direct infusion electrospray ionization MS (DI-ESI-MS) is a technique that we have developed for rapid metabolite fingerprinting of plant extracts (8,9). When applied to Arabidopsis tissue, the data obtained enable rapid assessment of concentrations and fluctuations of both primary and secondary metabolites.…”

Section: Resultsmentioning

confidence: 99%

Metabolomic analysis ofArabidopsisreveals hemiterpenoid glycosides as products of a nitrate ion-regulated, carbon flux overflow

Ward

Baker

Llewellyn

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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An understanding of the balance between carbon and nitrogen assimilation in plants is key to future bioengineering for a range of applications. Metabolomic analysis of the model plant, Arabidopsis thaliana, using combined NMR-MS revealed the presence of two hemiterpenoid glycosides that accumulated in leaf tissue, to ∼1% dry weight under repeated nitrate-deficient conditions. The formation of these isoprenoids was correlated with leaf nitrate concentrations that could also be assayed in the metabolomic data using a unique flavonoid-nitrate mass spectral adduct. Analysis of leaf and root tissue from plants grown in hydroponics with a variety of root stressors identified the conditions under which the isoprenoid pathway in leaves was diverted to the hemiterpenoids. These compounds were strongly induced by root wounding or oxidative stress and weakly induced by potassium deficiency. Other stresses such as cold, saline, and osmotic stress did not induce the compounds. Replacement of nitrate with ammonia failed to suppress the formation of the hemiterpenoids, indicating that nitrate sensing was a key factor. Feeding of intermediates was used to study aspects of 2-C-methyl-D-erythritol-4-phosphate pathway regulation leading to hemiterpenoid formation. The formation of the hemiterpenoids in leaves was strongly correlated with the induction of the phenylpropanoids scopolin and coniferin in roots of the same plants. These shunts of photosynthetic carbon flow are discussed in terms of overflow mechanisms that have some parallels with isoprene production in tree species.F or centuries mankind has relied on carbon, prehistorically fixed from the atmosphere by plants and algae, as a source of fuel and other materials. This is a dwindling resource and, to develop renewable sources of chemicals, knowledge of the biochemical pathways that link photosynthesis to the accumulation of useful materials will be paramount. Terpenoids (isoprenoids) are examples of carbon-rich products that occur prolifically across the plant kingdom. They are not only end products of chloroplast assimilation of photosynthetic carbon but also, by virtue of the phytyl side chains of chlorophyll, key elements of the machinery of photosynthesis. Some terpenoids are ubiquitous and are classed as primary metabolites (sterols, carotenoids, and phytyl side chains of chlorophyll); others are hormones (gibberellins, abscisic acid, brassinosteroids, and strigolactones). However, the majority of terpenoids, especially those that can accumulate to high levels in plants, are classed as secondary metabolites, although many have roles in chemical ecology. Manipulation of flux through the primary terpenoid pathways and the accumulation of terpenoids via the secondary pathways both have potential for exploitation. Arabidopsis, the model plant, was, until recently, considered to be poorly endowed with terpenoids. For example, this species does not appear to contain oxidized sesqui-and diterpenes, compounds that are widespread in plants (1). There are some 30 terpene synt...

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Assessment of 1H NMR spectroscopy and multivariate analysis as a technique for metabolite fingerprinting of Arabidopsis thaliana

Cited by 232 publications

References 15 publications

Measurement of dietary exposure: a challenging problem which may be overcome thanks to metabolomics?

Measurement of dietary exposure: a challenging problem which may be overcome thanks to metabolomics?

Metabotyping of Caenorhabditis elegans reveals latent phenotypes

Metabolomic analysis ofArabidopsisreveals hemiterpenoid glycosides as products of a nitrate ion-regulated, carbon flux overflow

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