Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• The Fis protein is a highly abundant DNA-binding protein in E. coli and S. typhimurium.
• Fis regulates crucial cellular processes like DNA recombination, transcription, and replication.
• Fis binds to specific DNA sites with low primary sequence similarity.

Purpose of the Study:

• To investigate the structural variability of Fis-DNA complexes.
• To understand how Fis interacts with DNA flanking recognition sites.
• To develop new models for Fis-DNA complex structures.

Main Methods:

• Analysis of DNA scission using Fis conjugates with 1,10-phenanthroline-copper.
• Comparative gel electrophoresis to assess DNA structures.
• Integration of experimental data with the known crystal structure of Fis.

Main Results:

• Fis-DNA complexes exhibit significant structural variability, with DNA curvatures ranging from 50 to over 90 degrees.
• Differential wrapping of DNA flanking Fis binding sites determines overall complex curvature.
• DNA bending within core Fis recognition regions is relatively consistent.
• Flanking DNA contacts involve electrostatic interactions (Arg 71) and hydrogen bonds (Asn 73), influencing binding kinetics.

Conclusions:

• Fis-DNA complex structures are highly adaptable, primarily due to variable flanking DNA interactions.
• Specific amino acid residues outside the helix-turn-helix motif mediate crucial flanking DNA contacts.
• New models incorporating flanking DNA variability enhance understanding of Fis-DNA complex formation and regulation.