In plant metabolic engineering, it is secondary metabolism, responsible for better crop physiology & production of neutraceuticals, that has been the primary focus so far. In the upcoming era of Biorefineries, however, plants are likely to be used at a much larger scale for the production of bio-fuels, polymers and even industrial chemicals. For these applications, it is the primary metabolism of plants that will be of interest for identification of potential metabolic engineering targets. Unlike, however, in most prokaryotes and in some cases even in mammalian cells, basic metabolic knowledge is still unavailable in the context of plants. This concerns knowledge of primary metabolic pathway stoichiometry, potential activity of parallel metabolic pathways, which have long ago been unraveled in bacterial systems, and regulatory mechanisms governing plant primary metabolism. Coupling these current limitations with the transient physiological conditions of whole plant studies, it becomes apparent that the application of the available computational and experimental metabolic engineering toolbox for in silico models and in vivo metabolic flux analysis, respectively, could prove indeed quite cumbersome in the context of plant systems. In this case, the post-genomic high-throughput experimental techniques and the multivariate statistical and systems engineering/biology analysis toolbox can be used to increase our understanding of plant physiology.

In this context, we systematically perturbed the Arabidopsis thaliana liquid culture system by applying (1) Elevated CO₂ stress, (2) Osmotic (NaCl) stress, (3) Sugar (trehalose) signal, and (4) Hormone (Ethylene) signal, individually, and stress (1) in combination with stresses (2)-(4). The short-term response of the biological system to this plethora of perturbations was monitored in a high-throughput way at the metabolic level by harvesting plants at different time points throughout the first 30h period after the initiation of the perturbation and measuring their polar metabolomic profile using Gas Chromatography-Mass Spectrometry (GC-MS). It has to be underlined that this is among (if not the first) currently reported studies of plant physiology that concerns metabolic fingerprinting of dynamic plant response to such an extensive number of individual and simultaneously applied perturbations. In the context of plant physiology, this study has provided a vast amount of data that allow for a comprehensive understanding of the primary metabolism regulation. Particularly, the role of CO₂, the primary source of carbon in plants, was elucidated in great extent since it was the common stress among all combined perturbations. Apart from contributing, however, significantly in plant physiology research, the present work materializes also an extensive metabolomic study that demonstrates the importance of metabolomics in deciphering metabolic regulation networks even in highly complex eukaryotic systems.

This work is funded by US NSF (QSB-0331312)