VARIABLE STRUCTURES OF FIS-DNA COMPLEXES DETERMINED BY FLANKING DNA-PROTEIN CONTACTS

The Fis protein from Escherichia coli and Salmonella typhimurium regul ates many diverse reactions including recombination, transcription, an d replication and is one of the most abundant DNA binding proteins pre sent in the cell under certain physiological conditions. As a specific regulator, Fis binds to discrete sites that are poorly related in pri mary sequence. Analysis of DNA scission by a collection of Fis conjuga tes to 1,10-phenanthroline-copper combined with comparative gel electr ophoresis has shown that the structures of Fis-DNA complexes are highl y variable, displaying overall DNA curvatures that range from less tha n or equal to 50 degrees to greater than or equal to 90 degrees. This variability is primarily determined by differential wrapping of flanki ng DNA around Fis. By contrast, DNA bending within the core recognitio n regions appears similar among the binding sites that were analyzed. Flanking DNA contacts by Fis depend on the nucleotide sequence and are mediated by an electrostatic interaction with arginine 71 and a hydro gen bond with asparagine 73, both of which are located outside of the helix-turn-helix DNA binding motif. These contacts strongly influence the kinetics of binding. These data, combined with the crystal structu re of Fis, have enabled us to generate new models for Fis-DNA complexe s that emphasize the variability in DNA structures within the flanking regions. (C) 1996 Academic Press Limited