In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12.

The narL gene product is a nitrate-responsive activator and repressor of anaerobic respiratory gene expression. Mutational studies and sequence comparisons have suggested that NarL protein binding sites contain heptameric sequences related to the consensus, TACYNMT (where Y = C or T, M = A or C, and N = any nucleotide). There are four NarL heptamers in the -105 region of the fdnGHI (formate dehydrogenase-N) operon, and mutational analysis supports the role of these heptamers in nitrate induction. To examine NarL-DNA interactions, we purified the NarL protein as a maltose binding protein (MBP) fusion protein (MBP-NarL). A constitutive mutant form with a single substitution (V88A) in the amino-terminal (response regulator) region was used. The MBP-NarL (V88A) protein protected all four heptamers in the fdnG operon control region from DNase I cleavage. Identical footprints were observed with NarL (V88A) protein that had been proteolytically cleaved free from the MBP domain. Binding of MBP-NarL (V88A) protein to the four heptamers in the -105 region of the fdnG operon appeared to be cooperative, and occupancy of the central heptamers was necessary for occupancy of the flanking heptamers. In addition to the V88A substitution, a low molecular weight phosphodonor, such as acetyl phosphate, was required for observable footprints. This indicates that phosphorylation of the NarL protein enhances its affinity for its multiple DNA targets in the fdnG operon, perhaps by increasing protein-protein interactions rather than protein-DNA interactions. We also performed footprinting studies at the narGHJI (nitrate reductase), narK (nitrite efflux), and frdABCD (fumarate reductase) operon control regions. Extensive areas of each control region were protected from DNase I attack by phosphorylated MBP-NarL (V88A) protein. The narG operon control region was protected from positions -50 to -110, and, at higher protein concentrations, also around position -200. Mutational analysis indicates that the NarL heptamer centered at position -89, in addition to the previously-identified -200 region, is involved in nitrate induction. Comparisons of the four operon control regions studied indicate that the NarL heptamers are arranged with diverse orientations and spacing.