An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato

C R Biol. 2009 Nov;332(11):1007-21. doi: 10.1016/j.crvi.2009.09.013. Epub 2009 Oct 24.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Analysis of Variance
  • Ascorbate Oxidase / genetics
  • Ascorbate Oxidase / metabolism
  • Ascorbic Acid / metabolism*
  • Carbohydrate Epimerases / genetics
  • Carbohydrate Epimerases / metabolism
  • Fruit / growth & development*
  • Gene Expression Profiling
  • Gene Knockdown Techniques
  • Genomics / methods*
  • Lycopersicon esculentum / genetics
  • Lycopersicon esculentum / growth & development*
  • Lycopersicon esculentum / radiation effects
  • Metabolic Networks and Pathways
  • Metabolome
  • NADH, NADPH Oxidoreductases / genetics
  • NADH, NADPH Oxidoreductases / metabolism
  • Oxidoreductases Acting on CH-CH Group Donors / genetics
  • Oxidoreductases Acting on CH-CH Group Donors / metabolism
  • Phenotype
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Plants, Genetically Modified
  • Proteome
  • Systems Integration

Substances

  • Plant Proteins
  • Proteome
  • Ascorbate Oxidase
  • Oxidoreductases Acting on CH-CH Group Donors
  • galactonolactone dehydrogenase
  • NADH, NADPH Oxidoreductases
  • monodehydroascorbate reductase (NADH)
  • Carbohydrate Epimerases
  • GDPmannose 3,5-epimerase
  • Ascorbic Acid