Jm. Hakimi et Jj. Scocca, BINDING-SITES FOR BACTERIOPHAGE-HP1 INTEGRASE ON ITS DNA SUBSTRATES, The Journal of biological chemistry, 269(33), 1994, pp. 21340-21345
The temperate phage HPI integrates its genome into the chromosome of H
aemophilus 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 c
lasses of binding sites were identified. At sites of type I, integrase
binding almost completely eliminated cleavage by DNase I; type I site
s shared the consensus sequence 5'-AGGGATTTWW. At type II sites, integ
rase binding produced alternating regions of protection from and enhan
cement of cleavage, suggesting that binding at these sites distorted t
he DNA. The consensus sequence for type II sites was 5'-ACTGGCGRTW. Ea
ch binding site contained two copies of the relevant consensus. The ho
st attachment site (attB) contains an inverted pair of type I consensu
s sequences surrounding the strand exchange points. The phage attachme
nt site (attP) includes six binding sites, three of type I and three o
f type E, distributed along its 500 nucleotide pairs. All type I sites
contain two consensus motifs arranged as inverted repeats. One of the
se surrounds the strand exchange points in this substrate, one is loca
ted 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 p
airs of the consensus and are internally located.