Energetic methods to study bifunctional biotin operon repressor.

Abstract

Application of a broad range of approaches and techniques to analysis of the functional energetics of the biotin regulatory system has enabled dissection of each of the steps in the assembly of this transcriptional repression complex. Although the molecular details of the interactions are not yet completely understood, the studies described in this article have laid a solid foundation for future studies of the system. The application of kinetic and equilibrium methods to studies of binding of the allosteric effector has allow determination of the kinetic parameters governing the interaction of the protein and ligand. The kinetic parameters have, furthermore, been utilized to calculate the equilibrium parameters associated with the binding. The great advantage of using kinetic methods to study the binding process is the additional information provide about the mechanism of allosteric activation of the protein. Based on the initial observation of a kinetic time course that is consistent with the occurrence of a structural change concomitant with effector binding, additional measurements have been performed that have allowed formulation of a testable hypothesis concerning the nature and location of one locus: the structural change in the three-dimensional structure of BirA. Studies of assembly of the protein indicate the bio-5-AMP is an allosteric activator of dimerization of the protein. The dimerization is, however, weak. These results have been critical in analyzing site-specific DNA binding measurements. Application of the DNase I footprinting technique has allowed formulation of a model for association of holoBirA with bioO. Results of studies of binding of the protein to mutant operator templates, although not yielding the anticipated results, provide further insight into the mechanism of association of the protein and DNA. Two models for binding, the validity of which can be tested via the application of kinetic techniques, have been derived from these measurements. The results of quantitative studies of the biotin regulatory system can be interpreted in the context of the biological function of the system. The biotin holoenzyme ligases are a class of enzymes found across the evolutionary spectrum. Only a subset of these enzymes, including BirA, also function as transcriptional repressors. The tight binding of the allosteric effector may be understood in light of the bifunctional nature of the BirA-bio-5'-AMP complex. It is possible that the unusually high thermodynamic and kinetic stability of the complex ensures that the most probable state of the protein in vivo is the adenylate-bound form. This complex, not the unliganded protein, is active in both enzymatic transfer of biotin and site-specific DNA binding. This ensures that on depletion of the intracellular pool of apoBCCP, BirA-bio-5'-AMP accumulates and binds to bioO to repress transcription of the biotin biosynthesis operon. The intracellular demand for and synthesis of biotin are, consequently, tightly coupled in the system. The dimerization that accompanies adenylate binding to BirA appears to be significant for site-specific binding of the protein to bioO. Functionally, the simultaneous binding of the two monomers to the two operator half-sites, regardless of the kinetic mechanism by which it occurs, ensures coordinate regulation of transcription initiation from both biotin operon promoters. The multifaceted approach utilized in studies of the biotin regulatory system can serve as a model for studies of any complex transcriptional regulatory system. It is critical in elucidating the functional energetics of any of these systems that the assembly first be dissected into the constituent interactions and that each of these interactions be studied in isolation. This is not only critical for understanding the physicochemical properties of each individual contributing interaction, but is also a necessary precursor to studies of thermodynamic linkage in the system. (AB