Northern blot analysis using a YodB deletion mutant demonstrated negative control of catDE operon expression by YodB. Northern blot experiments were further sued to determine the Cys7 residue is critical in YodB binding. DNase I footprinting localized overlapping CatR/YodB binding sites in the catDE promoter region. Site-directed mutagenesis in conjunction with EMSA confirmed the specificity of the binding regions by showing that as IR sequences were deleted, binding was reduced. MALDI-TOF, Western blot and Northern blot experiments were performed, proving that CatR and YodB do not form a complex. Multiple sequence alignment using the YodB binding sites for catD, yocJ, yodC and spx further characterized the YodB consensus sequence. Repression of yocJ, yodC and spx were previously reported in other papers.
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|