Figure 1

A one-step cascade in bacteria. This simple circuit is made of two transcription units: the upper expresses a repressor that, in the absence of chemicals, binds the promoter along the second transcription unit and suppresses the synthesis of a reporter (fluorescent) protein. When chemicals enter the cell, they bind and inactivate the repressors, switching on cell fluorescence. The role of pools as interfaces either between transcription units or between the cell and the environment is apparent. Simple straight lines here represent a mere exchange of molecules; the one ending with a circle symbolizes translation; the one with an orthogonal segment stands for repression; the one with an open arrow induction (see Additional file 1 for an outline of all the symbols used throughout this paper). FaPS means Factors Per Second and it is the flux associated with repressors from one to another transcription unit; SiPS–the flux of chemicals into the cell–stands for Signals Per Second. RNAPS–RNA Per Second–is the acronym for the flux of small RNAs, the only signal carrier not present in this circuit.