The Environment-Dependent Regulatory Landscape of the E. coli Genome

1 Abstract All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the so-called y-ome) and how they adapt to changing environments via regulation. Here we describe a joint experimental and theoretical dissection of the regulation of a broad array of more than 100 biologically interesting genes in E. coli across 39 diverse environments, enabling us to identify the binding sites and transcription factors that mediate regulatory control. Using a combination of mutagenesis, massively parallel reporter assays, mass spectrometry, and tools from information theory and statistical physics, we go from complete ignorance of a promoter’s environment-dependent regulatory architecture to a quantitative description of its binding sites, candidate transcription factors that bind them where identifiable, and the conditions under which they act. As proof of principle of the biological insights to be gained from such a study, we chose a combination of genes from the y-ome, toxin-antitoxin pairs, and genes hypothesized to be part of regulatory modules; we discovered a host of new insights into their underlying regulatory landscape and resulting biological function. We highlight discoveries for y-ome genes, including transcription start sites and transcription factor binding sites at base-pair resolution, and their dependence on growth conditions. Competing Interest Statement The authors have declared no competing interest. Footnotes The manuscript has been revised to better summarize the results and contains a significant change to the data processing and binding site identification method.