Fig. 10

Representative regulatory models of the LysR-type TF family in Gammaproteobacteria revealed by PProCoM analyses. a A typical architecture of the regulatory regions of these TFs is the presence of three IR sequences, represented by blue (IR1), green (IR2) and red (IR3) boxes. Some regulatory systems, such as those of our first analysis group, GcvA and MetR, lack the third IR element. b Because the sequence affinities of IR1 and IR3 (observed as sequence conservation of the motifs) are greater than the one for IR2, in the absence of the inducer, the TF of the system only binds to the IR1 and IR3 sites. The positions of IR1 and IR3 are critical for the transcriptional repression of divergent systems. IR1 overlaps the TF promoter, while IR3 overlaps the TF and the TG promoters. c In the presence of the system inducer, the TF dimer can bind cooperatively to a less conserved and less affine IR in the system, i.e., IR2. A remarkable characteristic of several regulatory systems in this family is that IR2 partially overlaps IR3; therefore, a first consequence of the binding of the TF to IR2 is the steric displacement of the TF that was bound to IR3, resulting in TG transcription repression. In addition to this de-repression effect, a second effect of the binding of the TF to IR2 is direct transcriptional activation of the TG due to the position of IR2 immediately upstream of the -35 promoter box of the TG, where the TF interacts with the RNAP. Figure modified from [57]