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

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          Abstract

          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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          MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

          MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.
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            Not just a circle: flux modes in the plant TCA cycle.

            The tricarboxylic acid (TCA) cycle is one of the iconic pathways in metabolism. The cycle is commonly thought of in terms of energy metabolism, being responsible for the oxidation of respiratory substrates to drive ATP synthesis. However, the reactions of carboxylic acid metabolism are embedded in a larger metabolic network and the conventional TCA cycle is only one way in which the component reactions can be organised. Recent evidence from labelling studies and metabolic network models suggest that the organisation of carboxylic acid metabolism in plants is highly dependent on the metabolic and physiological demands of the cell. Thus, alternative, non-cyclic flux modes occur in leaves in the light, in some developing oilseeds, and under specific physiological circumstances such as anoxia. 2010 Elsevier Ltd. All rights reserved.
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              Allocating Resources to Reproduction and Defense

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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                09 July 2019
                2019
                : 10
                : 836
                Affiliations
                [1] 1UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, INRA, Université de Bordeaux , Bordeaux, France
                [2] 2UMR 1287 EGFV, INRA, Bordeaux Sciences Agro, Université de Bordeaux , Bordeaux, France
                [3] 3Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, IBVM, Centre INRA de Bordeaux , Bordeaux, France
                Author notes

                Edited by: Alberto Battistelli, Italian National Research Council (CNR), Italy

                Reviewed by: Luca Mazzoni, Marche Polytechnic University, Italy; Filomena Nazzaro, Italian National Research Council (CNR), Italy

                *Correspondence: Annick Moing, annick.moing@ 123456inra.fr

                This article was submitted to Plant Metabolism and Chemodiversity, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2019.00836
                6632546
                31354750
                d7394edb-ae48-4f75-8c44-a2e4a5f4d1b8
                Copyright © 2019 Roch, Dai, Gomès, Bernillon, Wang, Gibon and Moing.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 05 October 2018
                : 12 June 2019
                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 167, Pages: 16, Words: 0
                Funding
                Funded by: Agence Nationale de la Recherche 10.13039/501100001665
                Categories
                Plant Science
                Review

                Plant science & Botany
                amino acids,cross-species,fleshy fruit,inter-species,metabolism regulation,organic acids,primary metabolism,sugars

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