The evolution and regulation of DNA-binding by the nickel-dependent transcription factor NikR

Transition metal homeostasis is critical for all cells to balance cellular metal requirements with metal availability. One common homeostatic mechanism in bacteria is metal-dependent transcriptional regulation. The Ni 2+-dependent transcription factor NikR is a member of the ribbon-helix-helix (RHH) family of DNA-binding proteins and is widespread among bacteria and archea with vastly different nickel physiologies. The goal of this thesis was to better understand basic aspects of cellular transition metal homeostasis by examining the activity and regulatory properties of NikR family members from different bacterial species. One organism that exhibits a prominent and well-defined nickel physiology is Helicobacter pylori, making it an ideal system with which to examine various aspects of metal homeostasis. Genetic studies demonstrated that NikR activation is controlled by a hierarchy of nickel-trafficking in H. pylori, where nickel is preferentially trafficked to the urease assembly pathway. NikR differentially regulates multiple nickel-related genes in response to distinct extracellular nickel concentrations, functioning to coordinate multiple activities important for metal homeostasis. Differential gene regulation resulted from NikR binding to promoters from different genes with a range of affinities and in distinct conformations, due to a flexible N-terminal arm that makes different DNA contacts at two promoters. In addition, the arm expands the specific DNA interactions by NikR as compared to previously characterized RHH transcription factors. Examination of additional previously uncharacterized NikR family members revealed that the N-terminal arm has been adapted differently in some cases but is also critical for DNA-binding affinity and specificity. This structural feature provides a molecular basis for tuning NikR activity to the physiology of the cell. These studies provide insight into how multiple metal-dependent activities in cells are coordinated and controlled in response to fluctuations in environmental metal. Further, they establish a robust experimental system with which to further investigate the molecular details of the evolution of transcriptional regulation, an integral component of metal homeostasis.