The Intricate Workings of a Bacterial Epigenetic Switch

Abstract

Bacteria have developed epigenetic mechanisms to control the reversible Off-to-On switching of cell surface structures such as pyelonephritis-associated pili (PAP). The pap pili switch is primarily controlled by the global regulator leucine-responsive regulatory protein (Lrp), the local regulator Papl, and DNA adenine methylase (Dam). There are two sets of binding sites for Lrp in the pap regulatory region: promoter proximal sites 1,2,3 and promoter distal sites 4,5,6. The pilin promoter proximal (GATC^prox) and distal (GATC^dist) targets for Dam are located within Lrp binding sites 2 and 5, respectively. In the Off state, Lrp binds cooperatively to sites 1,2,3 overlapping the papBA pilin promoter, shutting off pilin transcription, and blocking methylation of GATC^prox. Binding of Lrp at sites 1,2,3, together with methylation of GATC^dist, reduces the affinity of Lrp for sites 4,5,6, preventing simultaneous binding of Lrp at sites 4,5,6 upstream. Switching to the phase On state requires the environmentally regulated Papl co-regulator, which increases the affinity of Lrp for sites 5 and 2. Papl binds specifically to Lrp-pap DNA complexes via binding with Lrp as well as contact with DNA sequences within pap sites 5 and 2. Directionality in switching from Off to On appears to be due to methylation of GATC^prox, which prevents formation of the Papl-Lrp-pap site 2 ternary complex. A switch model is presented in which DNA replication is proposed to play a critical role by generating a hemimethylated GATC^dist site and displacing Lrp from sites 1,2,3. This facilitates methylation of GATC^prox and binding of Papl-Lrp to sites 4,5,6, with subsequent activation of pap transcription. The first gene product of the pap operon, PapB, positively regulates papl transcription, resulting in a positive feedback loop that helps maintain the On state. The pap switch is environmentally regulated by a number of factors including the CpxAR two-component regulatory system, the Histone-like nucleoid structuring protein H-NS, and cAMP-Catabolite Gene Activator Protein (CAP), which all involve binding of regulatory binding proteins to pap DNA sequences with subsequent alteration of Papl and Lrp binding. The Pap switch mechanism, with interesting variations, is conserved among a number of enteric bacteria, controlling expression of many unrelated pili-adhesin complexes.