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8. Modeling Protein Destiny in Developing Fruit

Author

Belouah, Isma, primary, Nazaret, Christine, additional, Pétriacq, Pierre, additional, Prigent, Sylvain, additional, Bénard, Camille, additional, Mengin, Virginie, additional, Blein-Nicolas, Mélisande, additional, Denton, Alisandra K., additional, Balliau, Thierry, additional, Augé, Ségolène, additional, Bouchez, Olivier, additional, Mazat, Jean-Pierre, additional, Stitt, Mark, additional, Usadel, Björn, additional, Zivy, Michel, additional, Beauvoit, Bertrand, additional, Gibon, Yves, additional, and Colombié, Sophie, additional

Published
2019
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9. How to optimize metabolites concentrations and fluxes in a metabolic pathway? Backgrounds and Basics

Author

Nazaret, Christine, Colombié, Sophie, Beauvoit, Bertrand, Dieuaide-Noubhani, Martine, Mazat, Jean-Pierre, Gibon, Yves, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), INRA Grande Ferrade, Institut National de la Recherche Agronomique (INRA), Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), 1074 Institut de Biologie Végétale Moléculaire : actions communes, Institut National de la Recherche Agronomique (INRA)-Santé des plantes et environnement (S.P.E.)-Institut de Biologie Végétale Moléculaire : actions communes (IBVM), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, ANR-15-CE20-0009 FRIMOUSS, S. Schuster, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Nazaret, Christine

Subjects
[MATH] Mathematics [math], [MATH]Mathematics [math], [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract

International audience; The modelling of metabolic pathways is developed here for application to sugar metabolism of tomatoes during fruit expansion. In the now classic calculation of network fluxes, we add concentrations. Under assumptions of steady state and of "minimal effort" as proposed in [1], fluxes and concentrations, respecting constraints of experimental measurements and of thermodynamics, are searched. In order to obtain a well-posed problem, a preliminary mathematical study is in progress.

Published
2016

10. Integrative and predictive biology outside the plant: linking computational tools to fleshy fruit systems

Author

Cabasson, Cecile, Colombie, Sophie, Beauvoit, Bertrand, Nazaret, Christine, Benard, Camille, Dieuaide Noubhani, Martine, Rolin, Dominique, Bernillon, Stéphane, Deborde, Catherine, Jacob, Daniel, Moing, Annick, Maucourt, Mickael, Belouah, Isma, Roch, Léa, Dartigues, Benjamin, Nikolski, Macha, Mazat, Jean-Pierre, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), and ProdInra, Migration

Subjects
Metadata, Fruit development, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Primary metabolism, Metabolic flux modelling, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

11. Flux balance modelling in developing tomato fruit: the respiration climacteric as an emergent property

Author

Colombie, Sophie, Beauvoit, Bertrand, Nazaret, Christine, Bénard, Camille, Cabasson, Cécile, Maucourt, Mickael, Bernillon, Stéphane, Moing, Annick, Dieuaide Noubhani, Martine, Mazat, Jean-Pierre, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux (UB), Centre National de la Recherche Scientifique (CNRS), Réseau Francophone de Métabolomique et Fluxomique (RFMF). FRA., and ProdInra, Migration

Subjects
Based model, Constraint, Flux balance analysis, Respiration climateric, Central metabolism, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Carbon allocation, Environmental stress, Metabolic flux modelling, Tomato fruit development, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

12. Modelling metabolic fluxes during tomato fruit development

Author

Colombie, Sophie, Beauvoit, Bertrand, Nazaret, Christine, Benard, Camille, Dieuaide Noubhani, Martine, Mazat, Jean-Pierre, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Institut Polytechnique de Bordeaux, Université de Bordeaux (UB), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, ProdInra, Archive Ouverte, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
adp glucose pyrophosphorylase, fruit, tomato, adpglucose pyrophosphorylase, tomate, physiologie végétale, sucre, sugar, solanum lycopersicum, peau, développement du fruit, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, métabolisme
Abstract

Modelling metabolic fluxes during tomato fruit development. 12. Solanaceae Conference SOL 2015

Published
2015

13. Modelling fluxes and metabolic network analysis of developing tomato fruits

Author

Colombie, Sophie, Beauvoit, Bertrand, Nazaret, Christine, Dieuaide Noubhani, Martine, Mazat, Jean-Pierre, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux (UB), and ProdInra, Migration

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

14. Chapter 8.3 of Handbook of neurochemistry and molecular neurobiology

Author

MAZAT, Jean-Pierre, AIMAR, Marie, FAUSTIN, Benjamin, LETELLIER, Thierry, MALGAT, Monique, NAZARET, Christine, ROSSIGNOL, Rodrigues, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), ACi MitoScop, Kluwer academic, and Nazaret, Christine

Abstract

chapitre 8.3, vol 5

Published
2006

15. Respiration climacteric in tomato fruits elucidated by constraint‐based modelling

Author

Colombié, Sophie, primary, Beauvoit, Bertrand, additional, Nazaret, Christine, additional, Bénard, Camille, additional, Vercambre, Gilles, additional, Le Gall, Sophie, additional, Biais, Benoit, additional, Cabasson, Cécile, additional, Maucourt, Mickaël, additional, Bernillon, Stéphane, additional, Moing, Annick, additional, Dieuaide‐Noubhani, Martine, additional, Mazat, Jean‐Pierre, additional, and Gibon, Yves, additional

Published
2016
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16. Kinetic modelling of the metabolism and compartmentation of sugars during tomato fruit development

Author

Beauvoit, Bertrand, Colombie, Sophie, Nazaret, Christine, Andrieu, Marie-Hélène, Dieuaide Noubhani, Martine, Biais, Benoit, Mazat, Jean-Pierre, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux Ségalen [Bordeaux 2], and ProdInra, Migration

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

17. The tomato fruit development with a constraint-based model

Author

Colombie, Sophie, Nazaret, Christine, Beauvoit, Bertrand, Solé, Marion, Dieuaide Noubhani, Martine, Biais, Benoit, Mazat, Jean-Pierre, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux Ségalen [Bordeaux 2], and ProdInra, Migration

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

18. Metabolism modeling

Author

Ballet, Pascal, Mazat, Jean-Pierre, Nazaret, Christine, Pérès, S., Laboratoire d'Informatique des Systèmes Complexes (LISYC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne), Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), and Vrit, Catherine

Subjects
ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2006

19. Respiration climacteric in tomato fruits elucidated by constraint-based modelling.

Author

Colombié, Sophie, Beauvoit, Bertrand, Nazaret, Christine, Bénard, Camille, Vercambre, Gilles, Le Gall, Sophie, Biais, Benoit, Cabasson, Cécile, Maucourt, Mickaël, Bernillon, Stéphane, Moing, Annick, Dieuaide‐Noubhani, Martine, Mazat, Jean‐Pierre, and Gibon, Yves

Subjects
TOMATOES, PLANT metabolism, PLANT physiology, RESPIRATION in plants, GAS exchange in plants, PHYSIOLOGY
Abstract

Tomato is a model organism to study the development of fleshy fruit including ripening initiation. Unfortunately, few studies deal with the brief phase of accelerated ripening associated with the respiration climacteric because of practical problems involved in measuring fruit respiration., Because constraint-based modelling allows predicting accurate metabolic fluxes, we investigated the respiration and energy dissipation of fruit pericarp at the breaker stage using a detailed stoichiometric model of the respiratory pathway, including alternative oxidase and uncoupling proteins. Assuming steady-state, a metabolic dataset was transformed into constraints to solve the model on a daily basis throughout tomato fruit development., We detected a peak of CO2 released and an excess of energy dissipated at 40 d post anthesis ( DPA) just before the onset of ripening coinciding with the respiration climacteric. We demonstrated the unbalanced carbon allocation with the sharp slowdown of accumulation (for syntheses and storage) and the beginning of the degradation of starch and cell wall polysaccharides. Experiments with fruits harvested from plants cultivated under stress conditions confirmed the concept., We conclude that modelling with an accurate metabolic dataset is an efficient tool to bypass the difficulty of measuring fruit respiration and to elucidate the underlying mechanisms of ripening. [ABSTRACT FROM AUTHOR]

Published
2017
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20. Modelling central metabolic fluxes by constraint‐based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit

Author

Colombié, Sophie, primary, Nazaret, Christine, additional, Bénard, Camille, additional, Biais, Benoît, additional, Mengin, Virginie, additional, Solé, Marion, additional, Fouillen, Laëtitia, additional, Dieuaide‐Noubhani, Martine, additional, Mazat, Jean‐Pierre, additional, Beauvoit, Bertrand, additional, and Gibon, Yves, additional

Published
2014
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21. Virtual mitochondrion

Author

Mazat, Jean-Pierre, primary, Heiske, Margit, additional, Nazaret, Christine, additional, Ransac, Stéphane, additional, and Klipp, Edda, additional

Published
2012
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23. Modelling the respiratory chain complexes with biothermokinetic equations - The case of complex I

Author

Margit Heiske, Jean-Pierre Mazat, Christine Nazaret, Nazaret, Christine, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), and Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Kinetics, Biophysics, Respiratory chain, Biology, Dynamical system, Biochemistry, Electron Transport, 03 medical and health sciences, chemistry.chemical_compound, Adenosine Triphosphate, 0302 clinical medicine, Complex I, Oxidative phosphorylation, 030304 developmental biology, 0303 health sciences, Electron Transport Complex I, Modeling, Cell Biology, Rate equation, Models, Theoretical, NAD, [SDV] Life Sciences [q-bio], Range (mathematics), Mitochondrial respiratory chain, Order (biology), chemistry, Biological system, Adenosine triphosphate, 030217 neurology & neurosurgery
Abstract

International audience; : The mitochondrial respiratory chain plays a crucial role in energy metabolism and its dysfunction is implicated in a wide range of human diseases. In order to understand the global expression of local mutations in the rate of oxygen consumption or in the production of adenosine triphosphate (ATP) it is useful to have a mathematical model in which the changes in a given respiratory complex are properly modeled. Our aim in this paper is to provide thermodynamics respecting and structurally simple equations to represent the kinetics of each isolated complexes which can, assembled in a dynamical system, also simulate the behavior of the respiratory chain, as a whole, under a large set of different physiological and pathological conditions. On the example of the reduced nicotinamide adenine dinucleotide (NADH)-ubiquinol-oxidoreductase (complex I) we analyze the suitability of different types of rate equations. Based on our kinetic experiments we show that very simple rate laws, as those often used in many respiratory chain models, fail to describe the kinetic behavior when applied to a wide concentration range. This led us to adapt rate equations containing the essential parameters of enzyme kinetic, maximal velocities and Henri-Michaelis-Menten like-constants (KM and KI) to satisfactorily simulate these data.

Published
2014
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24. Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion

Author

Martine Dieuaide-Noubhani, Jean-Pierre Mazat, Antoine Monier, Catherine Chéniclet, Marie-Hélène Andrieu, Sophie Colombié, Benoît Biais, Christine Nazaret, Camille Bénard, Bertrand Beauvoit, Yves Gibon, INRA Grande Ferrade, Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), ANR FRIM, Nazaret, Christine, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
0106 biological sciences, Sucrose, Cell division, [SDV]Life Sciences [q-bio], Plant Science, Vacuole, 01 natural sciences, Fructokinase, Models, Biological, In Brief, 03 medical and health sciences, chemistry.chemical_compound, Solanum lycopersicum, Osmotic Pressure, Glucokinase, 030304 developmental biology, Plant Proteins, 2. Zero hunger, 0303 health sciences, biology, beta-Fructofuranosidase, Biological Transport, Cell Biology, Plants, Genetically Modified, Enzyme assay, [SDV] Life Sciences [q-bio], Kinetics, Invertase, chemistry, Biochemistry, Glucosyltransferases, Fruit, Vacuoles, biology.protein, Sucrose synthase, Carbohydrate Metabolism, Phosphoglucomutase, Carrier Proteins, Cell Division, 010606 plant biology & botany
Abstract

A kinetic model combining enzyme activity measurements and subcellular compartmentation was parameterized to fit the sucrose, hexose, and glucose-6-P contents of pericarp throughout tomato (Solanum lycopersicum) fruit development. The model was further validated using independent data obtained from domesticated and wild tomato species and on transgenic lines. A hierarchical clustering analysis of the calculated fluxes and enzyme capacities together revealed stage-dependent features. Cell division was characterized by a high sucrolytic activity of the vacuole, whereas sucrose cleavage during expansion was sustained by both sucrose synthase and neutral invertase, associated with minimal futile cycling. Most importantly, a tight correlation between flux rate and enzyme capacity was found for fructokinase and PPi-dependent phosphofructokinase during cell division and for sucrose synthase, UDP-glucopyrophosphorylase, and phosphoglucomutase during expansion, thus suggesting an adaptation of enzyme abundance to metabolic needs. In contrast, for most enzymes, flux rates varied irrespectively of enzyme capacities, and most enzymes functioned at

Published
2014
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