INTEGRATION HOST FACTOR, A HISTONE-LIKE ESCHERICHIA-COLI PROTEIN, BINDS TO AT LEAST 4 SITES OF THE DNA FRAGMENT CONTAINING THE RECA GENE

The integration host factor (IHF) is a sequence-specific, histone-like , multifunctional DNA-binding and -bending protein of Escherichia coli . The characterization and functional analysis of this protein has bee n carried out mainly in bacteriophage lambda and other mobile genetic elements. Less is known concerning the role of IHF in E. coli, althoug h it has been implicated in a number of processes in this organism inc luding DNA replication, site-specific recombination, and gene expressi on. In this paper we report data concerning the binding of IHF protein to the recA gene region. IHF binds to at least four sites of the DNA fragment containing the recA gene, as shown by gel mobility shift assa ys. On the basis of the ihf consensus sequences published, we have bee n able to identify two sequences of putative ihf sites (ihf1 and ihf2) into the 1390 bp long sequence containing the recA gene, but only the ihf2 site was able to bind IHF, as measured by gel mobility shift exp eriments. The nonfunctional ihf1 sequence was found to overlap the -35 region of the recA promoter and the functional ihf2 sequence was foun d within the recA gene structure at nt + 780 to +807 (both with three mismatches according to the consensus sequence of K ur et al., 1989). This confirms our earlier results that the IHF-DNA interaction does no t depend on any very rigid sequence, but also on the suitable sequence s of the neighbouring regions, together with the proper DNA conformati on. One ihf binding site was found outside of the recA gene region and was localized between nt -263 and nt -475 (the number are relative to the S(R)' starting point = +1 for the recA gene transcription). The p henomenon that a protein bound at a specific DNA site can influence th e transcription of a gene, hundreds or even thousands of base pairs aw ay, is discussed.