A systems biology approach to disentangle the direct and indirect effects of global transcription factors on gene expression in Escherichia coli

Abstract

Delineating the pleiotropic effects of global transcriptional factors (TFs) is critical in understanding the system-wide regulatory response in a particular environment. Currently, with the availability of genome-wide TF binding and gene expression data for Escherichia coli, several gene targets can be assigned to the global TFs albeit inconsistently. Here, using a systematic integrated approach with emphasis on metabolism, we characterize and quantify the direct effects as well as the growth-rate mediated indirect effects of global TFs using deletion mutants of FNR, ArcA, and IHF regulators under glucose fermentative condition. Apart from the previous known metabolite-TF interactions, we predicted with high confidence several novel interactions arising from the allosteric effects of the intracellular metabolites. Our combined experimental and compendium level computational analyses revealed the co-expressed genes regulated by these TFs as well as the coordination of the direct and indirect target gene expressions in the context of the economy of intracellular metabolites. Besides, we extended our analysis to combinatorial deletions of these TFs to determine their cross-talk effects as well as conserved patterns of regulatory interactions. Overall, this study leverages the fundamentals of TF-driven regulation which could serve as a better template for deciphering mechanisms underlying complex phenotypes.