The DNA relaxation-dependent OFF-to-ON biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein.

The structural genes expressing type 1 fimbriae in alternate between expressed (phase ON) and non-expressed (phase OFF) states due to inversion of the 314 bp genetic switch. The FimB tyrosine integrase inverts by site-specific recombination, alternately connecting and disconnecting the operon encoding the fimbrial subunit protein and its associated secretion and adhesin factors, to and from its transcriptional promoter within . Site-specific recombination by the FimB recombinase becomes biased towards phase ON as DNA supercoiling is relaxed, a condition that occurs when bacteria approach the stationary phase of the growth cycle. This effect can be mimicked in exponential phase cultures by inhibiting the negative DNA supercoiling activity of DNA gyrase. We report that this bias towards phase ON depends on the presence of the Fis nucleoid-associated protein. We mapped the Fis binding to a site within the invertible switch by DNase I footprinting. Disruption of this binding site by base substitution mutagenesis abolishes both Fis binding and the ability of the mutated switch to sustain its phase ON bias when DNA is relaxed, even in bacteria that produce the Fis protein. In addition, the Fis binding site overlaps one of the sites used by the Lrp protein, a known directionality determinant of inversion that also contributes to phase ON bias. The Fis–Lrp relationship at is reminiscent of that between Fis and Xis when promoting DNA relaxation-dependent excision of bacteriophage λ from the chromosome. However, unlike the co-binding mechanism used by Fis and Xis at λ , the Fis–Lrp relationship at involves competitive binding. We discuss these findings in the context of the link between inversion biasing and the physiological state of the bacterium.