Curation Information

High-affinity Ni2+ binding selectively promotes binding of Helicobacter pylori NikR to its target urease promoter.;Zambelli B, Danielli A, Romagnoli S, Neyroz P, Ciurli S, Scarlato V;Journal of molecular biology 2008 Nov 28; 383(5):1129-43 [18790698]
NikR [O25896, view regulon]
Reported TF sp.
Helicobacter pylori
Reported site sp.
Helicobacter pylori
Created by
Matthew Coveyou
Curation notes
No specific genome listed in publication. Reference genome selected based on BLAST and CollecTF matches.

Experimental Process

The well-defined HpNikR target urease operator OPureA was selected to investigate the effects of alternative cations on HpNikR-DNA binding. EMSA demonstrated strong binding in the presence of Ni2+ without secondary cations, demonstrating Ni2+ to be sufficient for HpNikR-OPureA binding. DNAse I footprinting further determined Ni2+ to be necessary for binding in the absence of other divalent cations. Parallel footprinting with Zn2+, Co2+, Mg2+, and Ca2+ showed they were capable of promoting HpNikR-DNA binding only to a lesser extent. Isothermal titration calorimetry indicated Mg2+ and Ca2+ effected binding only through “a nonspecific cation effect,” and only in great concentrations. Zn2+ promoted binding most strongly (after Ni2+), with Co2+ interacting with HpNikR in a manner analogous to Zn2+ but to greatly reduced effect. Fluorescence spectroscopy indicated Ni2+, not Zn2+, selectively drives “a conformational rearrangement of HpNikR.” Repeated EMSAs and ITC experiments confirmed Ni2+ alone induces high affinity DNA binding by HpNikR.

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
... ... HP0073 ureB
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - activator tetramer