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

Reversible inversion of the DNA element fimS is responsible for the phase variable expression of type 1 fimbriae in Escherichia coli. The FimB tyrosine integrase site‐specific recombinase inverts fimS in the on‐to‐off and off‐to‐on directions with approximately equal efficiencies. However, when DNA supercoiling is relaxed, fimS adopts predominantly the on orientation. This orientational bias is known to require binding of the nucleoid‐associated protein LRP within fimS. Here we show that binding of the IHF protein to a site immediately adjacent to fimS is also required for phase‐on orientational bias. In the absence of both LRP and IHF binding, fimS adopts the off orientation and the H‐NS protein is required to maintain this alternative orientational bias. Thus, fimS has three Recombination Directionality Factors, H‐NS, IHF and LRP. The relevant H‐NS binding site straddles the left inverted repeat in phase‐off fimS and this site is disrupted when fimS inverts to the on orientation. The inversion of fimS 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.