The IHF proteins of Rhodobacter capsulatus and Pseudomonas aeruginosa

Abstract

The binding properties of the two IHF consensus sequences present in the promoter region of the hydrogenase structural operon, hupSL, of Rhodobacter capsulatus were studied by gel retardation assays using the heterodimeric IHF-like proteins isolated from R capsulatus, from Pseudomonas aeruginosa and from Escherichia coli. The three IHF proteins bound preferentially to the IHF consensus proximal to hupS. The three-dimensional structure of R capsulatus IHF was modeled using a computer-based amino acid replacement strategy and the known coordinates of crystallized HU protein (HBS) from Bacillus stearothermophilus. Double-stranded DNA and the interaction of IHF and DNA were then modeled using the molecular modeling package Quanta 3.3, and taking into account foot-printing data obtained with IHF-DNA complexes and the fact that the replacement of Arg8 by Cys8 in the α subunit, the product of himA, renders R capsulatus IHF ineffective in the activation of hydrogenase synthesis. In this model, IHF is shown to interact with DNA bent by 140°, and Arg8 of HimA capable of interacting with the phosphate-ribose backbone of DNA in the flanking region of the IHF binding site.