Evaluation of the DNA Binding Tendencies of the Transition State Regulator AbrB

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Abstract
Global transition state regulator proteins represent one of the most diverse classes of prokaryotic transcription factors. One such transition state regulator, AbrB from Bacillus subtilis, is known to bind more than 60 gene targets yet displays specificity within this target set by binding each promoter with a different affinity. Microelectrospray ionization mass spectrometry (μESI-MS), circular dichroism, fluorescence, UV spectroscopy, and molecular modeling were used to elucidate differences among AbrB, DNA, and AbrB−DNA complexes. μESI-MS analysis of AbrB confirmed its stable macromolecular state as being tetrameric and verified the same stoichiometric state in complex with DNA targets. μESI-MS, circular dichroism, and fluorescence provided relative binding affinities for AbrB−DNA interactions in a qualitative manner. UV spectroscopy was used in a quantitative manner to determine solution phase dissociation constants for AbrB−DNA complexes. General DNA structural parameters for all known natural AbrB binding sequences were also studied and significant similarities in topological constraints (stretch, opening, and propeller twist) were observed. It is likely that these parameters contribute to the differential binding proclivities of AbrB. In addition to providing an improved understanding of transition state regulator−DNA binding properties and structural tendencies of target promoters, this comprehensive and corroborative spectroscopic study endorses the use of μESI-MS for rapidly ascertaining qualitative binding trends in noncovalent systems in a high-throughput manner.