Metabolomics to define the role of aerobic respiration in the control of plant metabolism

The mitochondrial electron transport chain (mtETC) is a major electron sink in the plant cell and changes in its activity have the potential to influence metabolic reactions throughout the cell. Respiratory inhibition due to oxygen-deprivation is a naturally occurring phenomenon and a major constraint on plant productivity in areas that become flooded or waterlogged. Hence, an understanding of the metabolic effects of respiratory inhibition has implications for not only basic biological understanding but also for agriculture. The emergence of GC/MS based metabolomics technology provides an opportunity to expand our current understanding of the control the respiration has over metabolism. Software for automated GC/MS metabolomics data processing, analysis and databasing was developed in order to efficiently extract biological insights from raw GC/MS data. This software was then used in a series of metabolomics experiments aimed at elucidating the set of interactions that link respiratory processes with the rest of the plant metabolic network. Metabolite levels were monitored in a variety of systems subject to respiration-targeted perturbations. These perturbations included: i) pharmacological inhibitions of mtETC complex I and mtETC complex III in Arabidopsis thaliana cell suspension cultures with classic respiratory inhibitors rotenone and antimycin A, respectively; ii) genetic perturbation of the mitochondrial alternative oxidase (AOX) combined with environmental perturbations; iii) oxygen deprivation during germination of rice; iv) oxygen deprivation of aerobically-germinated rice seedlings; v) supply of air to anaerobically-germinated rice seedlings; and vi) floodinginduced hypoxia of Poplar tree roots. These experiments revealed that changes in respiratory activity lead to widespread changes in metabolite levels in all systems. Moreover, the results demonstrate that the nature of the metabolomic response depends on the point of perturbation of the mtETC,