FIGURE 1 

(A) The type-1 coherent FFL (Mangan and Alon, 2003). In many cases, Y regulates its own production as shown. (B) The SUM-FFL in the flagella class 2 regulation network. X is flhDC, Y is fliA and Z is the fliLMNOPQR operon (termed fliL) and other class 2 operons. In this circuit, the activator X regulates Y, X and Y act additively to activate the output gene Z. The input Sx is the production rate of X (or, more generally, a stimulus that activates X). The input Sy regulates the activity of Y. In the flagella system, Y positively regulates its own production. (C) A more detailed view of the flagella network and the basal-body checkpoint. The flhDC promoter is controlled by several transcription factors responsive to environmental stress and starvation. The class 2 genes encode the structural proteins that make up the basal bodies. FliA is involved in a positive feedback loop called the basal body checkpoint. In this loop, the activity of FliA as a transcription factor is inhibited by binding the protein FlgM (dashed -| sign indicating inhibition). FlgM is exported out of the cell once the first active basal bodies are formed, by a specific transport mechanism that exports FlgM through the basal bodies (dashed inhibition symbol between the basal body and FlgM). Thus, FliA helps activate genes that produce basal bodies, which export the inhibitor FlgM out of the cell, relieving the inhibition of FliA.