Investigating the Intersection of Nickel and pH in Helicobacter pylori through the HpNikR

Helicobacter pylori is a pathogenic bacterium that colonizes the human stomach. To survive its acidic environment, H. pylori synthesizes large quantities of the nickel-containing urease enzyme, which hydrolyzes urea into ammonia to neutralize the local environment of the cell. The importance of nickel to the survival of H. pylori is counterbalanced by the cytotoxicity of nickel, and the nickel-responsive HpNikR transcription factor helps maintain this balance by regulating a variety of genes in H. pylori in response to elevated nickel concentrations. Previous evidence also suggested that HpNikR can also bind DNA in a pH-responsive manner, but the biological relevance of this observation was unclear. In this work, the nickel-responsive regulon of HpNikR was probed, and two novel targets of nickel-dependent repression by HpNikR in vivo were identified. The pH-responsiveness of HpNikR was also explored, and cytosolic pH measurements confirm that the cytoplasm of H. pylori becomes sufficiently acidic to trigger pH-dependent DNA binding by HpNikR when the bacteria are exposed to pH 2 conditions. This drop in cytosolic pH allows HpNikR to regulate several genes in the acid adaptation pathway in a pH-dependent manner, including ureA and amiE. Biochemical characterization of an isogenic H. pylori ΔnikR strain revealed that HpNikR is important for the survival of H. pylori undergoing severe acidic shock, and that the loss of viability in the ΔnikR strain is not because of over-acidification of the cytoplasm. The network of gene regulation in H. pylori is very complex, and understanding the role that HpNikR plays during acidic shock is critical to elucidating how this bacterium survives the harsh environment of the human stomach. Understanding how H. pylori survives in the stomach can facilitate new treatment strategies and reveal how this pathogen has evolved to colonize its unique biological niche.