Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli

► Gene regulatory networks include indirect interactions between enzymes and genes. ► We investigate to which extent indirect interactions influence the network dynamics. ► We develop qualitative models of the network controlling carbon assimilation in Escherichia coli. ► The network dynamics is significantly different with and without indirect interactions. ► Only models with indirect interactions can reproduce the available experimental data.