Integration host factor (IHF) binds to many sites in the A + T-rich b2 region of phage lambda DNA

Computer analysis of almost the entire b2 region of lambda phage (nt 22346-27475) revealed 23 consensus-like ihf sites, with eleven pointing in one direction and twelve in the opposite direction [27 bp; Kur et al., Gene 81 (1989) 1-15]. To confirm the significance of this finding experimentally, the region was subdivided into 21 fragments and examined for integration host factor (IHF) binding by gel retardation and a variety of footprinting methods. Out of 21 fragments examined 13 were found to be retarded on gels in the presence of IHF and to contain one to three ihf sites each. All sites which differ by up to 2 bp from our 27-bp consensus ihf sequence can bind IHF in vitro. However, three of the computer-predicted sites overlap with sites of opposite orientation; therefore we could not determine at the present time which of the two antiparallel sequences binds IHF. We have compared the predictive values of various kinds of consensus sequences and show that our 27-bp consensus ihf sequence agrees best with the experimental data. It was demonstrated by Kur et al. [Virology 168 (1989) 236-244] that the IHF protein represses transcription from promoters located close to the right terminus of the b2 region, within the phage lambda attachment site. We discuss the possibility that some of the IHF-binding sites could be instrumental in repressing in vivo transcription from the A + T-rich b2 region during the lambda prophage state [Rosenvold et al., Virology 107 (1980) 476-487].