Publications by authors named "Annick Moing"

68 Publications

Putative imbalanced amino acid metabolism in rainbow trout long term fed a plant-based diet as revealed by H-NMR metabolomics.

J Nutr Sci 2021 24;10:e13. Epub 2021 Feb 24.

INRAE, Univ. Pau Pays Adour, UMR Nutrition Metabolism Aquaculture, Centre INRAE Nouvelle Aquitaine Bordeaux, F-64310 Saint Pée-sur-Nivelle, France.

The long-term effect of a plant (P)-based diet was assessed by proton nuclear magnetic resonance (H-NMR) metabolomics in rainbow trout fed a marine fish meal (FM)-fish oil (FO) diet (M), a P-based diet and a control commercial-like diet (C) starting with the first feeding. Growth performances were not heavily altered by long-term feeding on the P-based diet. An H-NMR metabolomic analysis of the feed revealed significantly different soluble chemical compound profiles between the diets. A set of soluble chemical compounds was found to be specific either to the P-based diet or to the M diet. Pterin, a biomarker of plant feedstuffs, was identified both in the P-based diet and in the plasma of fish fed the P-based diet. H-NMR metabolomic analysis on fish plasma and liver and muscle tissues at 6 and 48 h post feeding revealed significantly different profiles between the P-based diet and the M diet, while the C diet showed intermediate results. A higher amino acid content was found in the plasma of fish fed the P-based diet compared with the M diet after 48 h, suggesting either a delayed delivery of the amino acids or a lower amino acid utilisation in the P-based diet. This was associated with an accumulation of essential amino acids and the depletion of glutamine in the muscle, together with an accumulation of choline in the liver. Combined with an anticipated absorption of methionine and lysine supplemented in free form, the present results suggest an imbalanced essential amino acid supply for protein metabolism in the muscle and for specific functions of the liver.
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http://dx.doi.org/10.1017/jns.2021.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8057518PMC
February 2021

Modelling predicts tomatoes can be bigger and sweeter if biophysical factors and transmembrane transports are fine-tuned during fruit development.

New Phytol 2021 05 2;230(4):1489-1502. Epub 2021 Mar 2.

INRAE, Bordeaux Science Agro, EGFV, UMR 1287, Univ. Bordeaux, Villenave d'Ornon, F-33140, France.

The trade-off between yield and quality, a major problem for the production of fleshy fruits, involves fruit expansive growth and sugar metabolism. Here we developed an integrative model by coupling a biophysical model of fleshy fruit growth processes, including water and carbon fluxes and organ expansion, with an enzyme-based kinetic model of sugar metabolism to better understand the interactions between these two processes. The integrative model was initially tested on tomato fruit, a model system for fleshy fruit. The integrative model closely simulated the biomass and major carbon metabolites of tomato fruit developing under optimal or stress conditions. The model also performed robustly when simulating the fruit size and sugar concentrations of different tomato genotypes including wild species. The validated model was used to explore ways of uncoupling the size-sweetness trade-off in fruit. Model-based virtual experiments suggested that larger sweeter tomatoes could be obtained by simultaneously manipulating certain biophysical factors and transmembrane transports. The integrative fleshy fruit model provides a promising tool to facilitate the targeted bioengineering and breeding of tomatoes and other fruits.
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http://dx.doi.org/10.1111/nph.17260DOI Listing
May 2021

Correction to: MRSI vs CEST MRI to understand tomato metabolism in ripening fruit: is there a better contrast?

Anal Bioanal Chem 2021 Mar 27;413(6):1777. Epub 2021 Jan 27.

INRAE, UR QuaPA, 63122, Saint-Genès-Champanelle, France.

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http://dx.doi.org/10.1007/s00216-021-03180-3DOI Listing
March 2021

Metabolite Fruit Profile Is Altered in Response to Source-Sink Imbalance and Can Be Used as an Early Predictor of Fruit Quality in Nectarine.

Front Plant Sci 2020 8;11:604133. Epub 2021 Jan 8.

Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Huechuraba, Chile.

Peaches and nectarines [ (L.) Batsch] are among the most exported fresh fruit from Chile to the Northern Hemisphere. Fruit acceptance by final consumers is defined by quality parameters such as the size, weight, taste, aroma, color, and juiciness of the fruit. In peaches and nectarines, the balance between soluble sugars present in the mesocarp and the predominant organic acids determines the taste. Biomass production and metabolite accumulation by fruits occur during the different developmental stages and depend on photosynthesis and carbon export by source leaves. Carbon supply to fruit can be potentiated through the field practice of thinning (removal of flowers and young fruit), leading to a change in the source-sink balance favoring fruit development. Thinning leads to fruit with increased size, but it is not known how this practice could influence fruit quality in terms of individual metabolite composition. In this work, we analyzed soluble metabolite profiles of nectarine fruit cv "Magique" at different developmental stages and from trees subjected to different thinning treatments. Mesocarp metabolites were analyzed throughout fruit development until harvest during two consecutive harvest seasons. Major polar compounds such as soluble sugars, amino acids, organic acids, and some secondary metabolites were measured by quantitative H-NMR profiling in the first season and GC-MS profiling in the second season. In addition, harvest and ripening quality parameters such as fruit weight, firmness, and acidity were determined. Our results indicated that thinning (i.e., source-sink imbalance) mainly affects fruit metabolic composition at early developmental stages. Metabolomic data revealed that sugar, organic acid, and phenylpropanoid pathway intermediates at early stages of development can be used to segregate fruits impacted by the change in source-sink balance. In conclusion, we suggest that the metabolite profile at early stages of development could be a metabolic predictor of final fruit quality in nectarines.
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http://dx.doi.org/10.3389/fpls.2020.604133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820367PMC
January 2021

Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis.

Plant Cell Environ 2021 May 25;44(5):1504-1521. Epub 2021 Jan 25.

Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine-Bordeaux, INRAE, Univ., Villenave d'Ornon, France.

In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for 2 days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins showed similar variation for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several increasing metabolites or proteins in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding.
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http://dx.doi.org/10.1111/pce.13993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248070PMC
May 2021

MRSI vs CEST MRI to understand tomato metabolism in ripening fruit: is there a better contrast?

Anal Bioanal Chem 2021 Feb 6;413(5):1251-1257. Epub 2021 Jan 6.

INRAE, UR QuaPA, 63122, Saint-Genès-Champanelle, France.

Besides structural information, magnetic resonance imaging (MRI) is crucial to reveal the presence and gradients of metabolites in organs constituted of several tissues. In plant science, such knowledge is key to better understand fruit development and metabolism. Routine methods based on fixation for cytological studies or dissection for metabolite measurements induce biases and plant sample destruction. Magnetic resonance spectroscopy imaging (MSRI) leads to one NMR spectrum per pixel while chemical exchange saturation transfer (CEST) MRI allows mapping metabolites having exchangeable protons. As both methods present different advantages and drawbacks, we compared them to map metabolites in ripe tomato fruits. We demonstrated that MRSI was difficult to interpret due to large spatial chemical shift variations while CEST MRI produced promising image mapping of the main carbohydrates and amino acids. It showed that glucose/fructose was mostly located in the locular tissue, whereas glutamate/glutamine/GABA was found inside the columella.Graphical abstract.
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http://dx.doi.org/10.1007/s00216-020-03101-wDOI Listing
February 2021

Hyperpolarized NMR Metabolomics at Natural C Abundance.

Anal Chem 2020 11 2;92(22):14867-14871. Epub 2020 Nov 2.

Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France.

Metabolomics plays a pivotal role in systems biology, and NMR is a central tool with high precision and exceptional resolution of chemical information. Most NMR metabolomic studies are based on H 1D spectroscopy, severely limited by peak overlap. C NMR benefits from a larger signal dispersion but is barely used in metabolomics due to ca. 6000-fold lower sensitivity. We introduce a new approach, based on hyperpolarized C NMR at natural abundance, that circumvents this limitation. A new untargeted NMR-based metabolomic workflow based on dissolution dynamic nuclear polarization (d-DNP) for the first time enabled hyperpolarized natural abundance C metabolomics. Statistical analysis of resulting hyperpolarized C data distinguishes two groups of plant (tomato) extracts and highlights biomarkers, in full agreement with previous results on the same biological model. We also optimize parameters of the semiautomated d-DNP system suitable for high-throughput studies.
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http://dx.doi.org/10.1021/acs.analchem.0c03510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705890PMC
November 2020

Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth.

J Nutr 2020 09;150(9):2268-2277

INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France.

Background: Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance.

Objective: We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material.

Methods: Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints.

Results: In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80).

Conclusions: These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.
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http://dx.doi.org/10.1093/jn/nxaa206DOI Listing
September 2020

The Tomato Guanylate-Binding Protein SlGBP1 Enables Fruit Tissue Differentiation by Maintaining Endopolyploid Cells in a Non-Proliferative State.

Plant Cell 2020 10 4;32(10):3188-3205. Epub 2020 Aug 4.

Université de Bordeaux, Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie du Fruit et Pathologie, Unité Mixte de Recherche 1332, 33140 Villenave d'Ornon, France.

Cell fate maintenance is an integral part of plant cell differentiation and the production of functional cells, tissues, and organs. Fleshy fruit development is characterized by the accumulation of water and solutes in the enlarging cells of parenchymatous tissues. In tomato (), this process is associated with endoreduplication in mesocarp cells. The mechanisms that preserve this developmental program, once initiated, remain unknown. We show here that analysis of a previously identified tomato ethyl methanesulfonate-induced mutant that exhibits abnormal mesocarp cell differentiation could help elucidate determinants of fruit cell fate maintenance. We identified and validated the causal locus through mapping-by-sequencing and gene editing, respectively, and performed metabolic, cellular, and transcriptomic analyses of the mutant phenotype. The data indicate that disruption of the gene, encoding GUANYLATE BINDING PROTEIN1, induces early termination of endoreduplication followed by late divisions of polyploid mesocarp cells, which consequently acquire the characteristics of young proliferative cells. This study reveals a crucial role of plant GBPs in the control of cell cycle genes, and thus, in cell fate maintenance. We propose that SlGBP1 acts as an inhibitor of cell division, a function conserved with the human hGBP-1 protein.
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http://dx.doi.org/10.1105/tpc.20.00245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7534463PMC
October 2020

Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species.

J Exp Bot 2020 10;71(19):5823-5836

UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France.

Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.
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http://dx.doi.org/10.1093/jxb/eraa302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540837PMC
October 2020

Special Issue on "Fruit Metabolism and Metabolomics".

Metabolites 2020 Jun 3;10(6). Epub 2020 Jun 3.

Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", University of Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain.

Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies.
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http://dx.doi.org/10.3390/metabo10060230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7344593PMC
June 2020

Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species.

Ann Bot 2020 08;126(3):455-470

INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France.

Background And Aims: Sugar concentration is a key determinant of fruit quality. Soluble sugars and starch concentrations in fruits vary greatly from one species to another. The aim of this study was to investigate similarities and differences in sugar accumulation strategies across ten contrasting fruit species using a modelling approach.

Methods: We developed a coarse-grained model of primary metabolism based on the description of the main metabolic and hydraulic processes (synthesis of compounds other than sugar and starch, synthesis and hydrolysis of starch, and water dilution) involved in the accumulation of soluble sugars during fruit development.

Key Results: Statistical analyses based on metabolic rates separated the species into six groups according to the rate of synthesis of compounds other than sugar and starch. Herbaceous species (cucumber, tomato, eggplant, pepper and strawberry) were characterized by a higher synthesis rate than woody species (apple, nectarine, clementine, grape and kiwifruit). Inspection of the dynamics of the processes involved in sugar accumulation revealed that net sugar importation, metabolism and dilution processes were remarkably synchronous in most herbaceous plants, whereas in kiwifruit, apple and nectarine, processes related to starch metabolism were temporally separated from other processes. Strawberry, clementine and grape showed a distinct dynamic compared with all other species.

Conclusions: Overall, these results provide fresh insights into species-specific regulatory strategies and into the role of starch metabolism in the accumulation of soluble sugars in fleshy fruits. In particular, inter-specific differences in development period shape the co-ordination of metabolic processes and affect priorities for carbon allocation across species. The six metabolic groups identified by our analysis do not show a clear separation into climacteric and non-climacteric species, possibly suggesting that the metabolic processes related to sugar concentration are not greatly affected by ethylene-associated events.
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http://dx.doi.org/10.1093/aob/mcaa082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424760PMC
August 2020

Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency.

Plant Physiol 2020 06 15;183(2):501-516. Epub 2020 Apr 15.

Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France

Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.
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http://dx.doi.org/10.1104/pp.19.00842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271774PMC
June 2020

Comparative Metabolomics and Molecular Phylogenetics of Melon (, Cucurbitaceae) Biodiversity.

Metabolites 2020 Mar 24;10(3). Epub 2020 Mar 24.

Newe Ya'ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel.

The broad variability of (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within , we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.
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http://dx.doi.org/10.3390/metabo10030121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143154PMC
March 2020

Integrative Metabolomics for Assessing the Effect of Insect () Protein Extract on Rainbow Trout Metabolism.

Metabolites 2020 Feb 27;10(3). Epub 2020 Feb 27.

INRAE, University Pau & Pays Adour, E2S UPPA, UMR NuMeA Nutrition, Metabolism and Aquaculture, F-64310 Saint Pée sur Nivelle, France.

Nutrition of high trophic species in aquaculture is faced with the development of sustainable plant-based diets. Insects seem particularly promising for supplementing plant-based diets. However, the complex effect of whole insect meal on fish metabolism is not well understood, and even less is known about insect meal extracts. The purpose of this work was to decipher the metabolic utilization of a plant-based diet supplemented with the gradual addition of an insect protein extract (insect hydrolysate at 0%, 5%, 10% and 15%). H-NMR profiling was used to assess metabolites in experimental diets and in fish plasma, liver and muscle. A significant dose-dependent increase in growth and feed efficiency with increasing insect extract amounts was observed. The incremental incorporation of the insect extract in diet had a significant and progressive impact on the profile of dietary soluble compounds and trout metabolome. The metabolites modulated by dietary insect extracts in plasma and tissues were involved in protein and energy metabolism. This was associated with the efficient metabolic use of dietary free amino acids toward protein synthesis through the concomitant supply of balanced free amino acids and energy substrates in muscle. The findings provide new insights into how the dietary food metabolome affects fish metabolism.
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http://dx.doi.org/10.3390/metabo10030083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143670PMC
February 2020

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

Front Plant Sci 2019 9;10:836. Epub 2019 Jul 9.

UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, INRA, Université de Bordeaux, Bordeaux, France.

Although fleshy fruit species are economically important worldwide and crucial for human nutrition, the regulation of their fruit metabolism remains to be described finely. Fruit species differ in the origin of the tissue constituting the flesh, duration of fruit development, coordination of ripening changes (climacteric vs. non-climacteric type) and biochemical composition at ripeness is linked to sweetness and acidity. The main constituents of mature fruit result from different strategies of carbon transport and metabolism. Thus, the timing and nature of phloem loading and unloading can largely differ from one species to another. Furthermore, accumulations and transformations of major soluble sugars, organic acids, amino acids, starch and cell walls are very variable among fruit species. Comparing fruit species therefore appears as a valuable way to get a better understanding of metabolism. On the one hand, the comparison of results of studies about species of different botanical families allows pointing the drivers of sugar or organic acid accumulation but this kind of comparison is often hampered by heterogeneous analysis approaches applied in each study and incomplete dataset. On the other hand, cross-species studies remain rare but have brought new insights into key aspects of primary metabolism regulation. In addition, new tools for multi-species comparisons are currently emerging, including meta-analyses or re-use of shared metabolic or genomic data, and comparative metabolic flux or process-based modeling. All these approaches contribute to the identification of the metabolic factors that influence fruit growth and quality, in order to adjust their levels with breeding or cultural practices, with respect to improving fruit traits.
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http://dx.doi.org/10.3389/fpls.2019.00836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6632546PMC
July 2019

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

Front Plant Sci 2019 15;10:594. Epub 2019 May 15.

UMR1332 BFP, INRA, Univ. Bordeaux, Villenave d'Ornon, France.

Respiration of bulky plant organs such as fleshy fruits depends on oxygen (O) availability and often decreases with O concentration to avoid anoxia, but the relationship between O diffusional resistance and metabolic adjustments remains unclear. Melon fruit ( L.) was used to study relationships between O availability and metabolism in fleshy fruits. Enzyme activities, primary metabolites and O partial pressure were quantified from the periphery to the inner fruit mesocarp, at three stages of development. Hypoxia was gradually established during fruit development, but there was no strong oxygen gradient between the outer- and the inner mesocarp. These trends were confirmed by a mathematical modeling approach combining O diffusion equations and O demand estimates of the mesocarp tissue. A multivariate analysis of metabolites, enzyme activities, O demand and concentration reveals that metabolite gradients and enzyme capacities observed in melon fruits reflect continuous metabolic adjustments thus ensuring a timely maturation of the mesocarp. The present results suggest that the metabolic adjustments, especially the tuning of the capacity of cytochrome c oxidase (COX) to O-availability that occurs during growth development, contribute to optimizing the O-demand and avoiding the establishment of an O gradient within the flesh.
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http://dx.doi.org/10.3389/fpls.2019.00594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6529934PMC
May 2019

NMR-Based Tissular and Developmental Metabolomics of Tomato Fruit.

Metabolites 2019 May 9;9(5). Epub 2019 May 9.

UMR1332 Biologie du Fruit et Pathologie, INRA, University Bordeaux, Centre INRA de Nouvelle Aquitaine-Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d'Ornon, France.

Fruit is a complex organ containing seeds and several interconnected tissues with dedicated roles. However, most biochemical or molecular studies about fleshy fruit development concern the entire fruit, the fruit without seeds, or pericarp only. We studied tomato () fruit at four stages of development (12, 20, 35, and 45 days post-anthesis). We separated the seeds and the other tissues, exocarp, mesocarp, columella with placenta and locular tissue, and analyzed them individually using proton NMR metabolomic profiling for the quantification of major polar metabolites, enzymatic analysis of starch, and LC-DAD analysis of isoprenoids. Pericarp tissue represented about half of the entire fruit mass only. The composition of each fruit tissue changed during fruit development. An ANOVA-PCA highlighted common, and specific metabolite trends between tissues e.g., higher contents of chlorogenate in locular tissue and of starch in columella. Euclidian distances based on compositional data showed proximities within and between tissues. Several metabolic regulations differed between tissues as revealed by the comparison of metabolite networks based on correlations between compounds. This work stressed the role of specific tissues less studied than pericarp but that impact fruit organoleptic quality including its shape and taste, and fruit processing quality.
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http://dx.doi.org/10.3390/metabo9050093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571556PMC
May 2019

Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers.

Metabolomics 2019 03 30;15(4):56. Epub 2019 Mar 30.

UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France.

Introduction: Plant and crop metabolomic analyses may be used to study metabolism across genetic and environmental diversity. Complementary analytical strategies are useful for investigating metabolic changes and searching for biomarkers of response or performance.

Methods And Objectives: The experimental material consisted in eight sunflower lines with two line status, four restorers (R, used as males) and four maintainers (B, corresponding to females) routinely used for sunflower hybrid varietal production, respectively to complement or maintain the cytoplasmic male sterility PET1. These lines were either irrigated at full soil capacity (WW) or submitted to drought stress (DS). Our aim was to combine targeted and non-targeted metabolomics to characterize sunflower leaf composition in order to investigate the effect of line status genotypes and environmental conditions and to find the best and smallest set of biomarkers for line status and stress response using a custom-made process of variables selection.

Results: Five hundred and eighty-eight metabolic variables were measured by using complementary analytical methods such as H-NMR, MS-based profiles and targeted analyses of major metabolites. Based on statistical analyses, a limited number of markers were able to separate WW and DS samples in a more discriminant manner than previously published physiological data. Another metabolic marker set was able to discriminate line status.

Conclusion: This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.
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http://dx.doi.org/10.1007/s11306-019-1515-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441456PMC
March 2019

Characterizing alternative feeds for rainbow trout (O. mykiss) by H NMR metabolomics.

Metabolomics 2018 11 27;14(12):155. Epub 2018 Nov 27.

Bordeaux Metabolome Facility, MetaboHUB, CGFB, Centre INRA de Nouvelle Aquitaine Bordeaux, 33140, Villenave d'Ornon, France.

Introduction: Fish feed formulations are constantly evolving to improve the quality of diets for farmed fish and to ensure the sustainability of the aquaculture sector. Nowadays, insect, microalgae and yeast are feedstuff candidates for new feeds. However, the characterization of aquafeed is still based on proximate and targeted analyses which may not be sufficient to assess feed quality.

Objectives: Our aim was to highlight the soluble compounds that specifically differ between selected plant-based feeds complemented with alternative feedstuffs and discuss their origin and potential for fish nutrition.

Methods: A growth trial was carried out to evaluate growth performances and feed conversion ratios of fish fed plant-based, commercial, insect, spirulina and yeast feeds. H NMR metabolomics profiling of each feed was performed using a CPMG sequence on polar extracts. Spectra were processed, and data were analyzed using multivariate and univariate analyses to compare alternative feeds to a plant-based feed.

Results: Fish fed insect or yeast feed showed the best growth performances associated with the lowest feed conversion ratios compared to plant-based feed. Soluble compound H NMR profiles of insect and spirulina alternative feeds differed significantly from the plant-based one that clustered with yeast feed. In insect and spirulina feeds, specific differences compared to plant-based feed concerned glycerol and 3-hydroxybutyrate, respectively.

Conclusion: This strategy based on compositional differences between plant-based and alternative feeds can be useful for detecting compounds unsuspected until now that could impact fish metabolism.
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http://dx.doi.org/10.1007/s11306-018-1454-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6267160PMC
November 2018

Optimizing 1D H-NMR profiling of plant samples for high throughput analysis: extract preparation, standardization, automation and spectra processing.

Metabolomics 2019 02 26;15(3):28. Epub 2019 Feb 26.

BIOPI - EA 3900, Univ. Picardie Jules Verne, 1, rue des Louvels, 80037, Amiens Cedex, France.

Introduction: Proton nuclear magnetic resonance spectroscopy (H-NMR)-based metabolomic profiling has a range of applications in plant sciences.

Objectives: The aim of the present work is to provide advice for minimizing uncontrolled variability in plant sample preparation before and during NMR metabolomic profiling, taking into account sample composition, including its specificity in terms of pH and paramagnetic ion concentrations, and NMR spectrometer performances.

Methods: An automation of spectrometer preparation routine standardization before NMR acquisition campaign was implemented and tested on three plant sample sets (extracts of durum wheat spikelet, Arabidopsis leaf and root, and flax leaf, root and stem). We performed H-NMR spectroscopy in three different sites on the wheat sample set utilizing instruments from two manufacturers with different probes and magnetic field strengths. The three collections of spectra were processed separately with the NMRProcFlow web tool using intelligent bucketing, and the resulting buckets were subjected to multivariate analysis.

Results: Comparability of large- (Arabidopsis) and medium-size (flax) datasets measured at 600 MHz and from the wheat sample set recorded at the three sites (400, 500 and 600 MHz) was exceptionally good in terms of spectral quality. The coefficient of variation of the full width at half maximum (FWHM) and the signal-to-noise ratio (S/N) of two selected peaks was comprised between 5 and 10% depending on the size of sample set and the spectrometer field. EDTA addition improved citrate and malate resonance patterns for wheat sample sets. A collection of 22 samples of wheat spikelet extracts was used as a proof of concept and showed that the data collected at the three sites on instruments of different field strengths and manufacturers yielded the same discrimination pattern of the biological groups.

Conclusion: Standardization or automation of several steps from extract preparation to data reduction improves data quality for small to large collections of plant samples of different origins.
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http://dx.doi.org/10.1007/s11306-019-1488-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394467PMC
February 2019

Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding.

Metabolomics 2018 09 26;14(10):132. Epub 2018 Sep 26.

UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France.

Introduction: In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context.

Objectives: Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass.

Methods: Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping.

Results: NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance.

Conclusion: After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.
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http://dx.doi.org/10.1007/s11306-018-1427-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208756PMC
September 2018

Characterization of GMO or glyphosate effects on the composition of maize grain and maize-based diet for rat feeding.

Metabolomics 2018 02 17;14(3):36. Epub 2018 Feb 17.

UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France.

Introduction: In addition to classical targeted biochemical analyses, metabolomic analyses seem pertinent to reveal expected as well as unexpected compositional differences between plant genetically modified organisms (GMO) and non-GMO samples. Data previously published in the existing literature led to divergent conclusions on the effect of maize transgenes on grain compositional changes and feeding effects. Therefore, a new study examining field-grown harvested products and feeds derived from them remains useful.

Objectives: Our aim was to use a metabolomics approach to characterize grain and grain-based diet compositional changes for two GMO events, one involving Bacillus thuringiensis toxin to provide insect resistance and the other one conferring herbicide tolerance by detoxification of glyphosate. We also investigated the potential compositional modifications induced by the use of a glyphosate-based herbicide on the transgenic line conferring glyphosate tolerance.

Results: The majority of statistically significant differences in grain composition, evidenced by the use of H-NMR profiling of polar extracts and LC-ESI-QTOF-MS profiling of semi-polar extracts, could be attributed to the combined effect of genotype and environment. In comparison, transgene and glyphosate effects remained limited in grain for the compound families studied. Some but not all compositional changes observed in grain were also detected in grain-based diets formulated for rats.

Conclusion: Only part of the data previously published in the existing literature on maize grains of plants with the same GMO events could be reproduced in our experiment. All spectra have been deposited in a repository freely accessible to the public. Our grain and diet characterization opened the way for an in depth study of the effects of these diets on rat health.
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http://dx.doi.org/10.1007/s11306-018-1329-9DOI Listing
February 2018

The GMO90+ Project: Absence of Evidence for Biologically Meaningful Effects of Genetically Modified Maize-based Diets on Wistar Rats After 6-Months Feeding Comparative Trial.

Toxicol Sci 2019 04;168(2):315-338

INSERM UMR-S1124, Toxicologie Pharmacologie et Signalisation Cellulaire, Université Paris Descartes, USPC, Paris, France.

The GMO90+ project was designed to identify biomarkers of exposure or health effects in Wistar Han RCC rats exposed in their diet to 2 genetically modified plants (GMP) and assess additional information with the use of metabolomic and transcriptomic techniques. Rats were fed for 6-months with 8 maize-based diets at 33% that comprised either MON810 (11% and 33%) or NK603 grains (11% and 33% with or without glyphosate treatment) or their corresponding near-isogenic controls. Extensive chemical and targeted analyses undertaken to assess each diet demonstrated that they could be used for the feeding trial. Rats were necropsied after 3 and 6 months. Based on the Organization for Economic Cooperation and Development test guideline 408, the parameters tested showed a limited number of significant differences in pairwise comparisons, very few concerning GMP versus non-GMP. In such cases, no biological relevance could be established owing to the absence of difference in biologically linked variables, dose-response effects, or clinical disorders. No alteration of the reproduction function and kidney physiology was found. Metabolomics analyses on fluids (blood, urine) were performed after 3, 4.5, and 6 months. Transcriptomics analyses on organs (liver, kidney) were performed after 3 and 6 months. Again, among the significant differences in pairwise comparisons, no GMP effect was observed in contrast to that of maize variety and culture site. Indeed, based on transcriptomic and metabolomic data, we could differentiate MON- to NK-based diets. In conclusion, using this experimental design, no biomarkers of adverse health effect could be attributed to the consumption of GMP diets in comparison with the consumption of their near-isogenic non-GMP controls.
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http://dx.doi.org/10.1093/toxsci/kfy298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432862PMC
April 2019

1H-NMR metabolomic profiling reveals a distinct metabolic recovery response in shoots and roots of temporarily drought-stressed sugar beets.

PLoS One 2018 8;13(5):e0196102. Epub 2018 May 8.

Department of Plant Nutrition, INRES, University of Bonn, Bonn, Germany.

Yield formation in regions with intermittent drought periods depends on the plant's ability to recover after cessation of the stress. The present work assessed differences in metabolic recovery of leaves and roots of drought-stressed sugar beets with high temporal resolution. Plants were subjected to drought for 13 days, and rewatered for 12 days. At one to two-day intervals, plant material was harvested for untargeted 1H-NMR metabolomic profiling, targeted analyses of hexose-phosphates, starch, amino acids, nitrate and proteins, and physiological measurements including relative water content, osmotic potential, electrolyte leakage and malondialdehyde concentrations. Drought triggered changes in primary metabolism, especially increases in amino acids in both organs, but leaves and roots responded with different dynamics to rewatering. After a transient normalization of most metabolites within 8 days, a second accumulation of amino acids in leaves might indicate a stress imprint beneficial in upcoming drought events. Repair mechanisms seemed important during initial recovery and occurred at the expense of growth for at least 12 days. These results indicate that organ specific metabolic recovery responses might be related to distinct functions and concomitant disparate stress levels in above- and belowground organs. With respect to metabolism, recovery was not simply a reversal of the stress responses.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196102PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940195PMC
July 2018

Putting primary metabolism into perspective to obtain better fruits.

Ann Bot 2018 06;122(1):1-21

UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d'Ornon, France.

Background: One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits.

Scope: Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening.

Conclusions: Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.
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http://dx.doi.org/10.1093/aob/mcy057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025238PMC
June 2018

A Systems Biology Study in Tomato Fruit Reveals Correlations between the Ascorbate Pool and Genes Involved in Ribosome Biogenesis, Translation, and the Heat-Shock Response.

Front Plant Sci 2018 14;9:137. Epub 2018 Feb 14.

Institut National de la Recherche Agronomique, Université de Bordeaux, UMR1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France.

Changing the balance between ascorbate, monodehydroascorbate, and dehydroascorbate in plant cells by manipulating the activity of enzymes involved in ascorbate synthesis or recycling of oxidized and reduced forms leads to multiple phenotypes. A systems biology approach including network analysis of the transcriptome, proteome and metabolites of RNAi lines for ascorbate oxidase, monodehydroascorbate reductase and galactonolactone dehydrogenase has been carried out in orange fruit pericarp of tomato (). The transcriptome of the RNAi ascorbate oxidase lines is inversed compared to the monodehydroascorbate reductase and galactonolactone dehydrogenase lines. Differentially expressed genes are involved in ribosome biogenesis and translation. This transcriptome inversion is also seen in response to different stresses in Arabidopsis. The transcriptome response is not well correlated with the proteome which, with the metabolites, are correlated to the activity of the ascorbate redox enzymes-ascorbate oxidase and monodehydroascorbate reductase. Differentially accumulated proteins include metacaspase, protein disulphide isomerase, chaperone DnaK and carbonic anhydrase and the metabolites chlorogenic acid, dehydroascorbate and alanine. The hub genes identified from the network analysis are involved in signaling, the heat-shock response and ribosome biogenesis. The results from this study therefore reveal one or several putative signals from the ascorbate pool which modify the transcriptional response and elements downstream.
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http://dx.doi.org/10.3389/fpls.2018.00137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5817626PMC
February 2018

Mycotoxin Biosynthesis and Central Metabolism Are Two Interlinked Pathways in Fusarium graminearum, as Demonstrated by the Extensive Metabolic Changes Induced by Caffeic Acid Exposure.

Appl Environ Microbiol 2018 04 2;84(8). Epub 2018 Apr 2.

UR1264 MycSA, INRA, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France.

is a major plant pathogen that causes devastating diseases of cereals and produces type B trichothecene (TCTB) mycotoxins in infected grains. A comprehensive understanding of the molecular and biochemical mechanisms underlying the regulation of TCTB biosynthesis is required for improving strategies to control the TCTB contamination of crops and ensuring that these strategies do not favor the production of other toxic metabolites by Elucidation of the association of TCTB biosynthesis with other central and specialized processes was the focus of this study. Combined H nuclear magnetic resonance (H NMR) and liquid chromatography-quadrupole time of flight-mass spectrometry (LC-QTOF-MS) analyses were used to compare the exo- and endometabolomes of grown under toxin-inducing and -repressing caffeic acid conditions. Ninety-five metabolites were putatively or unambiguously identified, including 26 primary and 69 specialized metabolites. Our data demonstrated that the inhibition of TCTB production induced by caffeic acid exposure was associated with significant changes in the secondary and primary metabolism of , although the fungal growth was not affected. The main metabolic changes were an increase in the accumulation of several polyketides, including toxic ones, alterations in the tricarboxylic organic acid cycle, and modifications in the metabolism of several amino acids and sugars. While these findings provide insights into the mechanisms that govern the inhibition of TCTB production by caffeic acid, they also demonstrate the interdependence between the biosynthetic pathway of TCTB and several primary and specialized metabolic pathways. These results provide further evidence of the multifaceted role of TCTB in the life cycle of is a major plant pathogen that causes devastating diseases of cereal crops and produces type B trichothecene (TCTB) mycotoxins in infected grains. The best way to restrict consumer exposure to TCTB is to limit their production before harvest, which requires increasing the knowledge on the mechanisms that regulate their biosynthesis. Using a metabolomics approach, we investigated the interconnection between the TCTB production pathway and several fungal metabolic pathways. We demonstrated that alteration in the TCTB biosynthetic pathway can have a significant impact on other metabolic pathways, including the biosynthesis of toxic polyketides, and vice versa. These findings open new avenues for identifying fungal targets for the design of molecules with antimycotoxin properties and therefore improving sustainable strategies to fight against diseases caused by Our data further demonstrate that analyses should consider all fungal toxic metabolites rather than the targeted family of mycotoxins when assessing the efficacy of control strategies.
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http://dx.doi.org/10.1128/AEM.01705-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5881057PMC
April 2018

Plant metabolism as studied by NMR spectroscopy.

Prog Nucl Magn Reson Spectrosc 2017 11 8;102-103:61-97. Epub 2017 Jun 8.

Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR 6230, CNRS, Université de Nantes, Faculté des Sciences, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris, France. Electronic address:

The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.
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http://dx.doi.org/10.1016/j.pnmrs.2017.05.001DOI Listing
November 2017

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Anal Chem 2018 01 14;90(1):649-656. Epub 2017 Dec 14.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.
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http://dx.doi.org/10.1021/acs.analchem.7b02795DOI Listing
January 2018
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