Integration host factor binds specifically to multiple sites in the ompB promoter of Escherichia coli and inhibits transcription

Escherichia coli integration host factor (IHF) is a DNA-binding protein that participates in gene regulation, site-specific recombination, and other processes in E. coli and some of its bacteriophages and plasmids. In the present study, we showed that IHF is a direct negative effector of the ompB operon of E. coli. Gel retardation experiments and DNase I footprinting studies revealed that IHF binds to three sites in the ompB promoter region. In vitro transcription from ompB promoter fragments was specifically blocked by IHF. In vivo experiments showed that IHF is a negative effector of ompB expression in growing cells. Analysis of IHF binding site mutations strongly suggested that IHF binding in the ompB promoter region is necessary for the negative effects seen in vivo. Integration host factor (IHF) is a sequence-specific DNA-binding protein of Escherichia coli encoded by the himA and hip genes (39). This histonelike protein (10) is involved in a wide variety of processes in a number of bacteriophages and plasmids, including site-specific recombination events, phage packaging and partition, and DNA replication (re-viewed in references 10 and 14). IHF also participates in regulation of gene expression in a number of phages and in E. coli (reviewed in references 10 and 14) and some other gram-negative bacteria (6, 18, 25, 48). Although the exact mechanism of action of this multifunctional protein is not completely understood, IHF has been shown to bend th