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In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DMLs). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only a few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here, we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripening- an important developmental process unique to plants. RNAi SlDML2 knockdown results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato.

A detailed study of the diurnal compositional changes was performed in tomato (Solanum lycopersicum cv. Moneymaker) leaves and fruits. Plants were cultivated in a commercial greenhouse under two growth conditions: control and shaded. Expanding fruits and the closest mature leaves were harvested during two different day/night cycles (cloudy or sunny day). High-throughput robotized biochemical phenotyping of major compounds, as well as proton nuclear magnetic resonance and mass spectrometry metabolomic profiling, were used to measure the contents of about 70 metabolites in the leaves and 60 metabolites in the fruits, in parallel with ecophysiological measurements. Metabolite data were processed using multivariate, univariate, or clustering analyses and correlation networks. The shaded carbon-limited plants adjusted their leaf area, decreased their sink carbon demand and showed subtle compositional modifications. For source leaves, several metabolites varied along a diel cycle, including those directly linked to photosynthesis and photorespiration. These metabolites peaked at midday in both conditions and diel cycles as expected. However, transitory carbon storage was limited in tomato leaves. In fruits, fewer metabolites showed diel fluctuations, which were also of lower amplitude. Several organic acids were among the fluctuating metabolites. Diel patterns observed in leaves and especially in fruits differed between the cloudy and sunny days, and between the two conditions. Relationships between compositional changes in leaves and fruits are in agreement with the fact that several metabolic processes of the fruit appeared linked to its momentary supply of sucrose., (© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Cucumis melo fruit is highly valued for its sweet and refreshing flesh, however the flavour and value are also highly influenced by aroma as dictated by volatile organic compounds (VOCs). A simple and robust method of sampling VOCs on polydimethylsiloxane (PDMS) has been developed. Contrasting cultivars of C. melo subspecies melo were investigated at commercial maturity: three cultivars of var. Cantalupensis group Charentais (cv. Cézanne, Escrito, and Dalton) known to exhibit differences in ripening behaviour and shelf-life, as well as one cultivar of var. Cantalupensis group Ha'Ogan (cv. Noy Yisre'el) and one non-climacteric cultivar of var. Inodorus (cv. Tam Dew). The melon cultivar selection was based upon fruits exhibiting clear differences (cv. Noy Yisre'el and Tam Dew) and similarities (cv. Cézanne, Escrito, and Dalton) in flavour. In total, 58 VOCs were detected by thermal desorption (TD)-GC-MS which permitted the discrimination of each cultivar via Principal component analysis (PCA). PCA indicated a reduction in VOCs in the non-climacteric cv. Tam Dew compared to the four Cantalupensis cultivars. Within the group Charentais melons, the differences between the short, mid and long shelf-life cultivars were considerable. ¹H NMR analysis led to the quantification of 12 core amino acids, their levels were 3-10-fold greater in the Charentais melons, although they were reduced in the highly fragrant cv. Cézanne, indicating their role as VOC precursors. This study along with comparisons to more traditional labour intensive solid phase micro-extraction (SPME) GC-MS VOC profiling data has indicated that the high-throughput PDMS method is of great potential for the assessment of melon aroma and quality., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

• Variations in tissue development and spatial composition have a major impact on the nutritional and organoleptic qualities of ripe fleshy fruit, including melon (Cucumis melo). To gain a deeper insight into the mechanisms involved in these changes, we identified key metabolites for rational food quality design. • The metabolome, volatiles and mineral elements were profiled employing an unprecedented range of complementary analytical technologies. Fruits were followed at a number of time points during the final ripening process and tissues were collected across the fruit flesh from rind to seed cavity. Approximately 2000 metabolite signatures and 15 mineral elements were determined in an assessment of temporal and spatial melon fruit development. • This study design enabled the identification of: coregulated hubs (including aspartic acid, 2-isopropylmalic acid, β-carotene, phytoene and dihydropseudoionone) in metabolic association networks; global patterns of coordinated compositional changes; and links of primary and secondary metabolism to key mineral and volatile fruit complements. • The results reveal the extent of metabolic interactions relevant to ripe fruit quality and thus have enabled the identification of essential candidate metabolites for the high-throughput screening of melon breeding populations for targeted breeding programmes aimed at nutrition and flavour improvement., (© 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.)

Polyamines are involved in crucial plant physiological events, but their roles in fruit development remain unclear. We generated transgenic tomato plants that show a 1.5- to 2-fold increase in polyamine content by over-expressing the spermidine synthase gene, which encodes a key enzyme for polyamine biosynthesis. Pericarp-columella and placental tissue from transgenic tomato fruits were subjected to (1)H-nuclear magnetic resonance (NMR) for untargeted metabolic profiling and high-performance liquid chromatography-diode array detection for carotenoid profiling to determine the effects of high levels of polyamine accumulation on tomato fruit metabolism. A principal component analysis of the quantitative (1)H NMR data from immature green to red ripe fruit showed a clear discrimination between developmental stages, especially during ripening. Quantification of 37 metabolites in pericarp-columella and 41 metabolites in placenta tissues revealed distinct metabolic profiles between the wild type and transgenic lines, particularly at the late ripening stages. Notably, the transgenic tomato fruits also showed an increase in carotenoid accumulation, especially in lycopene (1.3- to 2.2-fold), and increased ethylene production (1.2- to 1.6-fold) compared to wild-type fruits. Genes responsible for lycopene biosynthesis, including phytoene synthase, phytoene desaturase, and deoxy-d-xylulose 5-phosphate synthase, were significantly up-regulated in ripe transgenic fruits, whereas genes involved in lycopene degradation, including lycopene-epsilon cyclase and lycopene beta cyclase, were down-regulated in the transgenic fruits compared to the wild type. These results suggest that a high level of accumulation of polyamines in the tomato regulates the steady-state level of transcription of genes responsible for the lycopene metabolic pathway, which results in a higher accumulation of lycopene in the fruit., (Copyright © 2010 Elsevier GmbH. All rights reserved.)

A metabolomics approach using (1)H NMR and GC-MS profiling of primary metabolites and quantification of adenine nucleotides with luciferin bioluminescence was employed to investigate the spatial changes of metabolism in melon fruit. Direct (1)H NMR profiling of juice collected from different locations in the fruit flesh revealed several gradients of metabolites, e.g. sucrose, alanine, valine, GABA or ethanol, with increase in concentrations from the periphery to the center of the fruit. GC-MS profiling of ground samples revealed gradients for metabolites not detected using (1)H NMR, including pyruvic and fumaric acids. The quantification of adenine nucleotides highlighted a strong decrease in both ATP and ADP ratios and the adenylate energy charge from the periphery to the center of the fruit. These concentration patterns are consistent with an increase in ethanol fermentation due to oxygen limitation and were confirmed by observed changes in alanine and GABA concentrations, as well as other markers of hypoxia in plants. Ethanol content in melon fruit can affect organoleptic properties and consumer acceptance. Understanding how and when fermentation occurred can help to manage the culture and limit ethanol production., (Copyright 2009 Elsevier GmbH. All rights reserved.)

Very few reports have studied the interactions between ascorbate and fruit metabolism. In order to get insights into the complex relationships between ascorbate biosynthesis/recycling and other metabolic pathways in the fruit, we undertook a fruit systems biology approach. To this end, we have produced tomato transgenic lines altered in ascorbate content and redox ratio by RNAi-targeting several key enzymes involved in ascorbate biosynthesis (2 enzymes) and recycling (2 enzymes). In the VTC (ViTamin C) Fruit project, we then generated phenotypic and genomic (transcriptome, proteome, metabolome) data from wild type and mutant tomato fruit at two stages of fruit development, and developed or implemented statistical and bioinformatic tools as a web application (named VTC Tool box) necessary to store, analyse and integrate experimental data in tomato. By using Kohonen's self-organizing maps (SOMs) to cluster the biological data, pair-wise Pearson correlation analyses and simultaneous visualization of transcript/protein and metabolites (MapMan), this approach allowed us to uncover major relationships between ascorbate and other metabolic pathways.

A metabolomics approach combining (1)H NMR and gas chromatography-electrospray ionization time-of-flight mass spectrometry (GC-EI-TOFMS) profiling was employed to characterize melon (Cucumis melo L.) fruit. In a first step, quantitative (1)H NMR of polar extracts and principal component analyses (PCA) of the corresponding data highlighted the major metabolites in fruit flesh, including sugars, organic acids, and amino acids. In a second step, the spatial localization of metabolites was investigated using both analytical techniques. Direct (1)H NMR profiling of juice or GC-EI-TOFMS profiling of tissue extracts collected from different locations in the fruit flesh provided information on advantages and drawbacks of each technique for the analysis of a sugar-rich matrix such as fruit. (1)H NMR and GC-EI-TOFMS data sets were compared using independently performed PCA and multiblock hierarchical PCA (HPCA), respectively. In addition a correlation-based multiblock HPCA was used for direct comparison of both analytical data sets. These data analyses revealed several gradients of metabolites in fruit flesh which can be related with differences in metabolism and indicated the suitability of multiblock HPCA for correlation of data from two (or potentially more) metabolomics platforms.

Variations in early fruit development and composition may have major impacts on the taste and the overall quality of ripe tomato (Solanum lycopersicum) fruit. To get insights into the networks involved in these coordinated processes and to identify key regulatory genes, we explored the transcriptional and metabolic changes in expanding tomato fruit tissues using multivariate analysis and gene-metabolite correlation networks. To this end, we demonstrated and took advantage of the existence of clear structural and compositional differences between expanding mesocarp and locular tissue during fruit development (12-35 d postanthesis). Transcriptome and metabolome analyses were carried out with tomato microarrays and analytical methods including proton nuclear magnetic resonance and liquid chromatography-mass spectrometry, respectively. Pairwise comparisons of metabolite contents and gene expression profiles detected up to 37 direct gene-metabolite correlations involving regulatory genes (e.g. the correlations between glutamine, bZIP, and MYB transcription factors). Correlation network analyses revealed the existence of major hub genes correlated with 10 or more regulatory transcripts and embedded in a large regulatory network. This approach proved to be a valuable strategy for identifying specific subsets of genes implicated in key processes of fruit development and metabolism, which are therefore potential targets for genetic improvement of tomato fruit quality.

Here we examined the effects of root hypoxia (1-2% oxygen) on the physiology of the plant and on the biochemical composition of fruits in tomato (Solanum lycopersicum cv. Micro-Tom) plants submitted to gradual root hypoxia at first flower anthesis. Root hypoxia enhanced nitrate absorption with a concomitant release of nitrite and ammonium into the medium, a reduction of leaf photosynthetic activity and chlorophyll content, and an acceleration of fruit maturation, but did not affect final fruit size. Quantitative metabolic profiling of mature pericarp extracts by (1)H NMR showed that levels of major metabolites including sugars, organic acids and amino acids were not modified. However, ammonium concentration increased dramatically in fruit flesh, and ascorbate and lycopene concentrations decreased. Our data indicate that the unfavorable effects of root hypoxia on fruit quality cannot be explained by two of the well-known effects of root hypoxia on the plant, namely a decrease in photosynthesis or an excess in ethylene production, but may instead result from disturbances in the supply of either growth regulators or ammonium, by the roots.

The biochemical composition of grape berries depends on the cultivar genome and is influenced by environmental conditions and growing practices, which vary according to origin and "terroir" (French word accounting for the factors of climate, soil, and cultural practices on grape and wine quality). The components currently measured to determine the potential quality of grapes for wine-making at harvest are sugars, acidity, pH, and total phenolics, referred to as "classic analysis". The aim of this work was to establish metabolic profiles using both conventional physicochemical analyses and 1H NMR spectrometry of the skin and pulp of mature berry extracts in order in four appellations situated in different locations in southern-western France (Bordeaux). Principal component analysis was applied to the physiochemical and 1H NMR data to investigate the variability of the grape composition and to characterize groups of samples. A significant clustering of the metabolic profile of pulps or skins in relation to their terroir was observed. Physicochemical analyses were more discriminant than 1H NMR data, but NMR spectroscopy allowed metabolic finger-printings using identified metabolites and some still nonattributed resonances.

Respiration of bulky plant organs such as fleshy fruits depends on oxygen (O2) availability and often decreases with O2 concentration to avoid anoxia, but the relationship between O2 diffusional resistance and metabolic adjustments remains unclear. Melon fruit (Cucumis melo L.) was used to study relationships between O2 availability and metabolism in fleshy fruits. Enzyme activities, primary metabolites and O2 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 O2 diffusion equations and O2 demand estimates of the mesocarp tissue. A multivariate analysis of metabolites, enzyme activities, O2 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 O2-availability that occurs during growth development, contribute to optimizing the O2-demand and avoiding the establishment of an O2 gradient within the flesh. [ABSTRACT FROM AUTHOR]

In young tomato plants, modifications in mineral composition by short-term cadmium (Cd) treatments have been extensively examined. However, long-term Cd treatments have been fewly investigated, and little information about Cd-stress in fruiting plants is available. In the present work, we examined the changes in mineral nutrients of roots, stems, leaves, flowers, seeds and fruit pericarp of tomato plants submitted to a long-term Cd stress. After a 90-day culture period in hydroponic contaminated environment (0, 20 and 100 μM CdCl 2 ), fruit production was affected by increasing external Cd levels, with the absence of fruit set at 100 μM Cd. Meanwhile, Cd altered the plant mineral contents with an element- and organ-dependent response. At 20 μM, Cd triggered a significant increase in Ca content in roots, mature leaves, flowers and developing fruits. However, at 100 μM Cd, Ca content was reduced in shoots, and enhanced in roots. Cd stress reduced Zn and Cu contents in shoots and increased them in roots. High Cd level led to a significant decrease in K and Mg content in all plant organs. Furthermore, Fe concentration was reduced in roots, stems and leaves but increased in flowers, seeds and red ripe fruits. Our results suggest that tomato plants acclimatize during long-term exposure to 20 μM Cd, while 100 μM Cd results in drastic nutritional perturbations leading to fruit set abortion. [ABSTRACT FROM AUTHOR]