Illustration of the different components involved in E. coli transcriptional regulation, transcription and metabolism. (A) Three interconnected networks of cellular organization. Only a subset of the overall network elements is shown for the sake of clarity, i.e. only nodes and edges involved in E. coli central metabolism are depicted. (i) The transcriptional regulatory network (TRN): transcription factors (cyan cubes) control the expression of metabolic genes (gray spheres) either by activation (green links) or repression (red links). (ii) Chromosomal organization: DNA topology is affected globally by supercoiling (see B) and locally by nucleoid associated proteins (see C). (iii) Depiction of E. coli central metabolism (as described in ). Metabolic genes on the chromosome (ii) are connected to reactions (red spheres) according to their gene-protein/enzyme-reaction relationships. (B) Supercoiling energy changes across growth. The early growth phase is governed by high supercoiling, while the later phase is rather associated with low supercoiling. In addition, a wide range of environmental conditions can induce changes in supercoiling energy. In the experiments discussed here, the supercoiling energy has been altered chemically (see Methods), in order to mimic such physiological changes in a controlled fashion. (C) NAPs translate the global superhelical torsion into locally meaningful structures, e.g. loops (FIS) and plectonemes (H-NS).
Sonnenschein et al. BMC Systems Biology 2011 5:40 doi:10.1186/1752-0509-5-40