Curation Information

Regulation of high affinity nickel uptake in bacteria. Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites.;Chivers PT, Sauer RT;The Journal of biological chemistry 2000 Jun 30; 275(26):19735-41 [10787413]
NikR [P0A6Z6, view regulon]
Reported TF sp.
E. coli strain BB101
Reported site sp.
E. coli strain BB101
Created by
Matthew Coveyou
Curation notes

Experimental Process

DNAse I footprinting in a previous study identified a putative NikR binding site. EMSA and a second DNAse I footprinting confirmed specific, Ni2+ dependent binding. Dimethylsulfate protection footprinting identified two sites of close contact between the DNA and NikR, termed half-sites, separated by 16 base pairs. Symmetric double mutants were created for each position in the half-sites, along with a single 11-base mutant in the central region. EMSA illustrated affinity differences between mutants, which clarified the precise binding site. Beta-gal assay of the nikABCDE operon promoter in the wild-type demonstrated in vivo repression by NikR.

Transcription Factor Binding Sites


Gene Regulation

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
... ... nikD nikC nikB nikA nikE nikR
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Premethylation interference footprinting (ECO:0005656) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified