Borrelia burgdorferi PlzA is a cyclic-di-GMP dependent DNA- and RNA-binding protein

The PilZ domain-containing protein, PlzA, is the only cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here we report that PlzA can bind DNA and RNA, and that nucleic acid binding requires c-di-GMP. In studies with the promoter and 5’ UTR of the glycerol catabolism operon, glpFKD, the affinity of PlzA for nucleic acids increased as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. PlzA is a dual-domain protein consisting of a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle dictate PlzA regulatory targets and functions.