BioProject

We investigated the way global gene expression changed in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways with features varying in: carbon influx flow rate; entry points in the metabolic network; modes of transport. More...

We investigated the way global gene expression changed in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways with features varying in: carbon influx flow rate; entry points in the metabolic network; modes of transport. Quantitative coarse-grained expression-pattern analysis demonstrated that the gene expression trend following immediately the reduction of carbon influx flow rate was determined by its initial expression level. Subsequent fine-grained expression-pattern analysis demonstrated that the Crp regulator, associated to a change in growth rate, governed the response of most carbon influx-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or PTS (phosphotransferase system) transported sugars following an idiosyncratic way, with the function of each of these regulators being titrated by the metabolism of the corresponding substrates. This work also allowed us to expand the extent of the gene complement regulated by each regulator with additional genes (27 genes in the Crp regulon, 49 genes in the Cra regulon, 1 gene in the Mlc regulon and 2 genes in Fur regulon) and to elucidate the regulatory functions of each regulator comprehensively. Strikingly, Crp and Cra worked in concert to coordinate central carbon metabolism with amino acids biosynthesis. Together, these results demonstrated the power of physiology-based interperation of global data in revealing regulatory networks of bacteria. Overall design: Examination of the gene expression when E. coli NCM3722 grew in 7 different carbon sources (Ace, G6P, Glc, Gly, Lac, Sor, Suc), as well as its crp- & cyaA- mutant (CY104) grew in Glc. Less...