The protein interactome ofEscherichia colicarbohydrate metabolism

Abstract Carbohydrate metabolism is strictly regulated by multiple mechanisms to meet cellular needs (i.e. energy production). Several mechanisms modulate the amount and activity of metabolic enzymes. Here, we investigate how carbohydrate metabolism (CHM) in E. coli is regulated by their interaction properties with other proteins and their quantities. We computationally analyze 378 protein-enzyme interactions (PEIs) potentially involved in carbohydrate metabolism. We identified 20 enzymes and 19 interactors that occur at stoichiometries that are highly likely to affect CHM and 174 interactions that are possibly conserved across thousands of bacteria. These PPIs are predicted to be of global importance, including pathogens. Author summary In systems biology, “big” data are used to reconstruct biological networks which are then investigated in detail to uncover their functional dynamics. Understanding functional dynamics finally helps in identifying biomarkers in the big networks. We apply this concept to the biological network which is a crosstalk of protein-protein interaction network and carbohydrate metabolic pathway in Escherichia coli K-12. We investigate if proteins regulate enzymes when they bind them and we predict that protein-enzyme interactions (PEIs) regulate carbohydrate metabolism in E. coli .