title: An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato.
abstract: 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.
authors.affiliation: INRA, université de Bordeaux, biologie du fruit, UMR 619, 33883 Villenave d'Ornon, France.
authors.forename: Virginie
authors.initials: V
authors.lastname: Garcia
authors.forename: Rebecca
authors.initials: R
authors.lastname: Stevens
authors.forename: Laurent
authors.initials: L
authors.lastname: Gil
authors.forename: Louise
authors.initials: L
authors.lastname: Gilbert
authors.forename: Noé
authors.initials: N
authors.lastname: Gest
authors.forename: Johann
authors.initials: J
authors.lastname: Petit
authors.forename: Mireille
authors.initials: M
authors.lastname: Faurobert
authors.forename: Mickael
authors.initials: M
authors.lastname: Maucourt
authors.forename: Catherine
authors.initials: C
authors.lastname: Deborde
authors.forename: Annick
authors.initials: A
authors.lastname: Moing
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Poessel
authors.forename: Daniel
authors.initials: D
authors.lastname: Jacob
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Bouchet
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Giraudel
authors.forename: Barbara
authors.initials: B
authors.lastname: Gouble
authors.forename: David
authors.initials: D
authors.lastname: Page
authors.forename: Moftah
authors.initials: M
authors.lastname: Alhagdow
authors.forename: Capucine
authors.initials: C
authors.lastname: Massot
authors.forename: Hélène
authors.initials: H
authors.lastname: Gautier
authors.forename: Martine
authors.initials: M
authors.lastname: Lemaire-Chamley
authors.forename: Antoine
authors.initials: A
authors.lastname: de Daruvar
authors.forename: Dominique
authors.initials: D
authors.lastname: Rolin
authors.forename: Bjoern
authors.initials: B
authors.lastname: Usadel
authors.forename: Marc
authors.initials: M
authors.lastname: Lahaye
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse
authors.forename: Pierre
authors.initials: P
authors.lastname: Baldet
authors.forename: Christophe
authors.initials: C
authors.lastname: Rothan
mesh_terms: D000704:Analysis of Variance; D001204:Ascorbate Oxidase / Q000235:genetics / Q000378:metabolism; D001205:Ascorbic Acid / Q000378:metabolism*; D002238:Carbohydrate Epimerases / Q000235:genetics / Q000378:metabolism; D005638:Fruit / Q000254:growth & development*; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D023281:Genomics / Q000379:methods*; D018551:Solanum lycopersicum / Q000235:genetics / Q000254:growth & development* / Q000528:radiation effects; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D009247:NADH, NADPH Oxidoreductases / Q000235:genetics / Q000378:metabolism; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000235:genetics / Q000378:metabolism; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D020543:Proteome; D018511:Systems Integration
chemical_list: D010940:Plant Proteins; D020543:Proteome; D001204:Ascorbate Oxidase; D044925:Oxidoreductases Acting on CH-CH Group Donors; C093910:galactonolactone dehydrogenase; D009247:NADH, NADPH Oxidoreductases; C023927:monodehydroascorbate reductase (NADH); D002238:Carbohydrate Epimerases; C019192:GDPmannose 3,5-epimerase; D001205:Ascorbic Acid