A systems oriented approach towards compartmentalized metabolic networks, their dynamics and interconnections

The eukaryotic cell comprises a large number of subcellular compartments and organelles. While theses compartments are physically and biochemically distinct, a tight inter- and intra-compartmental process regulation in relation to external as well as internal stimuli is essential for the metabolic functionality of the eukaryotic cell.

Knowledge about the subcellular localization of metabolites is also crucial regarding their functional implication as some molecules might act also as signals within organelles or triggers signalling between compartments. To gain a comprehensive insight into the compartmental metabolite localization and their dynamic changes we employ, in close collaboration with Dr. Stephan Krueger and Dr. Patrick Giavalisco, the non-aqueous fractionation (NAF) method in conjunction with orthogonal analytical methodologies. Our primary goals are:

to better understand how subcellular metabolic networks are interconnected and regulated, and
to functionally elucidate how environmental cues are integrated into cellular and subcellular metabolic responses assisting in the adjustments of the systems performance.

For this purpose we have developed and optimized the down-stream data analyses using a novel and improved BestFit software tool, which among other features also enables the statistical assessment and the validation of the estimated subcellular distributions. Furthermore, we started to work on marker-free based approaches to obtain a better assignment of metabolites into known but also yet undesignated subcellular compartments.