Binding sites for bacteriophage HP1 integrase on its DNA substrates

The temperate phage HP1 integrates its genome into the chromosome of Haemophilus influenzae by site-specific recombination between host and phage DNA segments, the attachment sites. This reaction is promoted by the HP1-encoded integrase. The interactions of HP1 integrase with its DNA substrates have been characterized by DNase I footprinting. Two classes of binding sites were identified. At sites of type I, integrase binding almost completely eliminated cleavage by DNase I; type I sites shared the consensus sequence 5'-AGGGATTTWW. At type II sites, integrase binding produced alternating regions of protection from and enhancement of cleavage, suggesting that binding at these sites distorted the DNA. The consensus sequence for type II sites was 5'-ACTGGCGRTW. Each binding site contained two copies of the relevant consensus. The host attachment site (attB) contains an inverted pair of type I consensus sequences surrounding the strand exchange points. The phage attachment site (attP) includes six binding sites, three of type I and three of type II, distributed along its 500 nucleotide pairs. All type I sites contain two consensus motifs arranged as inverted repeats. One of these surrounds the strand exchange points in this substrate, one is located internally, and the third coincides with the right boundary of the attP sequence. One type II site, consisting of an inverted repeat of two type II consensus motifs, coincides with the left boundary of the attP sequence. The other two type II sites contain directly repeated pairs of the consensus and are internally located.