Biasing switching outcomes in the Escherichia coli fim site-specific recombination system through DNA supercoiling and nucleoid-associated proteins

Abstract

Type 1 fimbriae are typically expressed in nutrient poor environments and facilitate colonization through attachment when the bacterium can no longer support a motile lifestyle that demands a high metabolic flux. They play a key role in the colonization of various host tissues by E. coli and in biofilm formation on abiotic surfaces such as catheters. The expression of type 1 fimbriae is phase variable and controlled by the site-specific inversion of a DNA segment (fimS), which contains the promoter for the structural components of type 1 fimbriae. In bacteria growing in mid-exponential phase at 37°C in LB broth, the FimB protein inverts the fimS element from the on phase to the off phase and back again at approximately equal rates. However, when novobiocin is used to inhibit DNA gyrase activity, allowing DNA to become more relaxed, the FimB-catalyzed fimS inversion reaction adopts a pronounced bias in favour of the on orientation. Previously, the leucine-responsive regulatory protein (LRP) was identified as playing a role in determining the directionality in this reaction. Specifically, the LRP protein is required to maintain the fmS element in the on orientation and it does this by binding to the LRP-1 and LRP-2 sites within fimS. In the present study, the IHF protein bound to the IHF-1 site was identified as a second recombination directionality factor (RDF) that is required to maintain fimS in the on orientation when gyrase activity is inhibited. The location of the IHF-1 binding site in the non-inverting chromosomal DNA immediately adjacent to IRL explains the differential interaction of IHF with LRP bound within fimS because all three sites are only juxtaposed when the switch is in the phase-on orientation.