Borrelia burgdorferi DnaA and the nucleoid-associated protein EbfC coordinate expression of the dnaX-ebfC operon

Borrelia burgdorferi, the spirochete agent of Lyme disease, has evolved within a consistent infectious cycle between tick and vertebrate hosts. The transmission of the pathogen from tick to vertebrate is characterized by rapid replication and a change in the outer surface protein profile. EbfC, a highly conserved nucleoid-associated protein, binds throughout the borrelial genome affecting expression of many genes, including the Erp outer surface proteins. In B. burgdorferi, like many other bacterial species, ebfC is co-transcribed with dnaX, an essential component of the DNA polymerase III holoenzyme, which facilitates chromosomal replication. The expression of the dnaX-ebfC operon is tied to the spirochetes replication rate, but the underlying mechanism for this connection was unknown. In this work, we provide evidence that the expression of dnaX-ebfC is controlled by direct interactions of DnaA, the chromosomal replication initiator, and EbfC at the unusually long dnaX-ebfC 5 UTR region. Both proteins bind to the 5 UTR DNA, with EbfC also binding to the RNA. The DNA binding of DnaA to this region was similarly impacted by ATP/ADP. In vitro studies characterized DnaA as an activator of dnaX-ebfC and EbfC as an anti-activator. We further found evidence that DnaA may regulate other genes essential for replication. IMPORTANCEThe dual-life cycle of Borrelia burgdorferi, the causative agent of Lyme disease, is characterized by periods of rapid and slowed replication. The expression patterns of many of the spirochetes virulence factors are impacted by these changes in replication rates. The connection between replication and virulence can be understood at the dnaX-ebfC operon. DnaX is a component of the DNA polymerase III holoenzyme that facilitates replication. EbfC is a nucleoid-associated protein that regulates the infection-associated outer surface Erp proteins, as well as other transcripts. The expression of dnaX-ebfC is tied to replication rate, which we demonstrate is mediated by DnaA, the master chromosomal initiator protein and transcription factor, and EbfC.