Lm. Hales et al., DETERMINING THE DNA-SEQUENCE ELEMENTS REQUIRED FOR BINDING INTEGRATION HOST FACTOR TO 2 DIFFERENT TARGET SITES, Journal of bacteriology, 176(10), 1994, pp. 2999-3006
Binding sites for the Escherichia coli protein integration host factor
(IHF) include a set of conserved bases that can be summarized by the
consensus sequence WATCAANNNNTTR (W is dA or dT, R is dA or dG, and N
is any nucleotide). However, additional 5'-proximal bases, whose commo
n feature is a high dA+dT content, are also thought to be required for
binding at some sites. We examine the relative contribution of these
two sequence elements to IHF binding to the H' and H1 sites in attP of
bacteriophage lambda by using the bacteriophage P22-based challenge-p
hage system. IHF was unable to act as a repressor in the challenge-pha
ge assay at H' sites containing the core consensus element but lacking
the dA+dT-rich element. This indicates that both elements are require
d for IHF to bind to the H' site. In contrast, the core consensus dete
rminant alone is sufficient for IHF binding to the H1 site, which lack
s an upstream dA+dT-rich region. Fifty mutants that decreased or elimi
nated IHF binding to the H1 site were isolated. Sequence analysis show
ed changes in the bases in the core consensus element only, further in
dicating that this determinant is sufficient for IHF binding to the H1
site. We found that placement of a dA+dT-rich element upstream of the
H1 core consensus element significantly increased the affinity, sugge
sting that the presence of a dA+dT-rich element enhances IHF binding.