An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato.
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.
Garcia
Virginie
V
INRA, université de Bordeaux, biologie du fruit, UMR 619, 33883 Villenave d'Ornon, France.
Stevens
Rebecca
R
Gil
Laurent
L
Gilbert
Louise
L
Gest
Noé
N
Petit
Johann
J
Faurobert
Mireille
M
Maucourt
Mickael
M
Deborde
Catherine
C
Moing
Annick
A
Poessel
Jean-Luc
JL
Jacob
Daniel
D
Bouchet
Jean-Paul
JP
Giraudel
Jean-Luc
JL
Gouble
Barbara
B
Page
David
D
Alhagdow
Moftah
M
Massot
Capucine
C
Gautier
Hélène
H
Lemaire-Chamley
Martine
M
de Daruvar
Antoine
A
Rolin
Dominique
D
Usadel
Bjoern
B
Lahaye
Marc
M
Causse
Mathilde
M
Baldet
Pierre
P
Rothan
Christophe
C
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
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