As a case study, Arabidopsis thaliana liquid cultures grown for 12 days under constant light and temperature were subjected to perturbations of (1) CO2 level in their growth environment (2) Osmotic stress through addition of NaCl and (3) Trehalose (sugar) signal. Full genome cDNA microarrays (printed in TIGR) were used for dynamic gene expression profiling of the system subjected to the applied perturbations. According to the experimental design it was possible to study the dynamic effect of (a) large number of perturbations applied to the same system (b) combined perturbations and (c) comparison of the combined perturbation with the corresponding individual perturbations. Comparisons revealed individual perturbations are insufficient to predict not a good predictor of the combined response and the part of the regulatory networks that are conserved between the individual and combined responses depends on the system and stresses applied. Gene regulatory networks that are conserved over all the stress responses have biological implications in the context of metabolic pathways, chromosomal location and cellular compartmentalization.
This analysis has not only provided significant information about the physiology of plant in general and A. thaliana in particular, but has also generated a large experimental data set of a highly complex eukaryotic system under systematically applied multiple perturbations. As such it is expected to greatly contribute in enhancing the currently available experimental database and in advancing the systems biology computational and experimental toolbox.