DNA relaxation‐dependent phase biasing of the <i>fim</i> genetic switch in <i>Escherichia coli</i> depends on the interplay of H‐NS, IHF and LRP

<jats:title>Summary</jats:title><jats:p>Reversible inversion of the DNA element <jats:italic>fimS</jats:italic> is responsible for the phase variable expression of type 1 fimbriae in <jats:italic>Escherichia coli</jats:italic>. The FimB tyrosine integrase site‐specific recombinase inverts <jats:italic>fimS</jats:italic> in the on‐to‐off and off‐to‐on directions with approximately equal efficiencies. However, when DNA supercoiling is relaxed, <jats:italic>fimS</jats:italic> adopts predominantly the on orientation. This orientational bias is known to require binding of the nucleoid‐associated protein LRP within <jats:italic>fimS</jats:italic>. Here we show that binding of the IHF protein to a site immediately adjacent to <jats:italic>fimS</jats:italic> is also required for phase‐on orientational bias. In the absence of both LRP and IHF binding, <jats:italic>fimS</jats:italic> adopts the off orientation and the H‐NS protein is required to maintain this alternative orientational bias. Thus, <jats:italic>fimS</jats:italic> has three Recombination Directionality Factors, H‐NS, IHF and LRP. The relevant H‐NS binding site straddles the left inverted repeat in phase‐off <jats:italic>fimS</jats:italic> and this site is disrupted when <jats:italic>fimS</jats:italic> inverts to the on orientation. The inversion of <jats:italic>fimS</jats:italic> with the associated creation and removal of an H‐NS binding site required for DNA inversion biasing represents a novel mechanism for modulating the interaction of H‐NS with a DNA target and for influencing a site‐specific recombination reaction.</jats:p>