Integrating metabolism and regulation
One of the challenges in predicting metabolic flow in a cell is the interplay between biochemical reactions and enzyme regulation (both at the level of transcription and at the level of small-molecule binding, e.g. allostery). We are approaching this challenge at different levels of description, starting from basic kinetics of individual reactions, up to genome scale integration of regulatory and metabolic knowledge. For example, we have recently performed high-throughput mRNA expression measurements in the bacterium Shewanella oneidensis MR-1 (whose versatile respiratory functions make it a key candidate for bioremediation and bioenergy applications), and implemented dynamic flux balance models that incorporates regulatory data and metabolite measurements.