Characterization of the roles of NikR, a nickel-responsive pleiotropic autoregulator of Helicobacter pylori

Mol Microbiol. 2003 Aug;49(4):947-63. doi: 10.1046/j.1365-2958.2003.03621.x.


The Helicobacter pylori genome contains a gene (hp1338 or nikR) that encodes a nickel-dependent regulator that is homologous to the Escherichia coli nickel-responsive regulator, NikR. The H. pylori nikR product acts as a pleiotropic metal-dependent regulator. We constructed a non-polar isogenic mutant deleted for the nikR gene. NikR was essential for the survival of H. pylori in the presence of high nickel and cobalt ion concentrations in vitro. We screened a DNA macroarray for genes that were differentially expressed in parental and nikR-deficient H. pylori strains grown in the presence of excess nickel. We found that H. pylori NikR mediates the expression of nickel-activated and -repressed genes. In the presence of excess nickel, NikR activated the transcription of ureA-ureB (hp72-73), nixA (hp1077 ), copA2 (hp1072), hpn (hp1427 ) and hpn-like (hp1432) genes and repressed the expression of genes encoding proteins involved in ferric iron uptake and storage [pfr (hp0653), fur (hp1027 ), frpB4 (hp1512), exbB/exbD (hp1339-1340), ceuE (hp1561)], motility [cheV (hp616), flaA (hp0601), flaB (hp0115 )], stress responses [hrcA-grpE-dnaK (hp111-110-109)] and encoding outer-membrane proteins [omp11(hp0472), omp31 (hp1469), omp32 (hp1501)]. Slot blot DNA/RNA hybridization experiments using RNA from three independent bacterial cultures confirmed the transcriptome data for 10 selected genes. The results of gel shift experiments using purified native NikR, beta-galactosidase assays with the region between nikR and the exbB/exbD divergent operon, and the study of exbB gene expression using a gentamicin/apramycin reporter gene in H. pylori indicated that NikR is an autorepressor that binds to this intergenic region and also controls the expression of the exbB/exbD/tonB operon, which provides energy for ferric iron uptake. Thus, as previously suggested for Fur in H. pylori, NikR appears to be a global regulator of the metabolism of some divalent cations within a highly complex regulated network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Chromosomes, Bacterial
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial*
  • Genetic Vectors
  • Helicobacter pylori / genetics*
  • Helicobacter pylori / metabolism*
  • Molecular Sequence Data
  • Nickel / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Open Reading Frames
  • Operon
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*


  • Escherichia coli Proteins
  • ExbB protein, E coli
  • NikR protein, E coli
  • Recombinant Proteins
  • Repressor Proteins
  • Nickel