Transcriptional regulatory systems play a central role in coordinating bacterial responses to diverse stimuli. These systems can be studied in progressive stages: from input signals to the final output. At the input stage, transcription factors (TFs) can be classified by their activation from endogenous or exogenous stimuli; in Escherichia coli, up to three-quarters of regulators are estimated to respond directly to extracellular signals through phosphorylation and small-molecule binding. At the processing stage, the signals feed into a densely connected network. The endogenous regulators form most of the connections between TFs and, by dynamically rewiring interactions, they coordinate and distribute the appropriate responses for distinct cellular conditions. At the output stage, network motifs (which are specific patterns of interconnections within a small group of TFs and target genes) determine the precise temporal programme of gene expression changes. Eventually, these components of the regulatory system could be assembled to describe complex bacterial behaviour at the level of whole organisms.