Fig. 6
The roles of the OD and RD at the frdA and narG promoter regions. NarL is represented by a cartoon figure: the OD is depicted by a yellow circle; the linker region is in red, with the α5-α6 loop shown as a squiggle and helix α6 as a cylinder; the RD is shown as a blue irregular octagon with phosphorylation represented by a “P”. For simplicity, only preferred binding sites or regions are designated at each promoter, which are not drawn to scale. The transcription start site is indicated by an arrow. (a) The frdA promoter. Top panel: wild-type, phosphorylated, NarL binds to the frdA promoter region, leading to gene repression in a nitrate responsive manner. Bottom panel: NarLC (which may include helix α6) is also able to repress frdA gene expression, but does so in a constitutive manner. The ODs are shown to dimerize at the 7-2-7 (−4/+6) binding region near the transcription start site. (b) The narG promoter. Top panel: wild-type, phosphorylated, NarL binds the essential −89 and −195 regions of the narG promoter to activate gene expression. The RD is presumed to dimerize and may also engage in other protein-protein interactions that are not depicted in the diagram. Bottom panel: NarLC (which may include helix α6) cannot activate the narG promoter due to improper binding at the −195 region. Therefore narG operon expression remains low or non-activated in the absence of a phosphorylated RD