Proteomics and Metabolomics of Arabidopsis Responses to Glucosinolate Perturbation.

To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using RNA interference (RNAi) in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes. We have implemented two dimensional difference gel electrophoresis (2D-DIGE) and isobaric tag for relative and absolute quantification (iTRAQ) proteomics approaches, and gas chromatography mass spectrometry (GC-MS), liquid chromatography (LC)-MS and multiple reaction monitoring (MRM)-MS metabolomics approaches to identify proteins and metabolites, correlate changes in response to glucosinolate perturbation and to characterize pathway nodes and edges related to glucosinolate metabolism. Proteins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides and hormones. The metabolomics data were correlated with the proteomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate metabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced crop quality and defense.