DNAse I footprinting identified two putative NikR binding sites in the nikR-exbB intergenic region, one associated with each gene promoter; confirmed previous studies of binding to the ureA promoter; and identified two putative sites on the fur promoter, denoted OpI and OpII. The ureA promoter was aligned with those of four other H. pylori strains, which demonstrated high conservation. Scanning mutagenesis of the ureA site identified key nucleotides, which were then aligned with the putative nikR and exbB sites. Western blot assays were performed on nikR and fur mutants to determine the regulatory effect, if any, of nikR on fur expression. NikR was shown to repress fur expression (though not as dramatically as fur autorepression), and these results were confirmed by primer extension assay. This was judged sufficient to warrant alignment of fur-OpI and OpII with the ureA, nikR, and exbB putative sites.
Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.
|Site sequence||Regulated genes||Gene diagram||Experimental techniques||TF function||TF type|