Metabolic and transcriptional response to cofactor perturbations in Escherichia coli

Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli.

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Holm AK, Blank LM, Oldiges M, Schmid A, Solem C, Jensen PR, Vemuri GN