Analysis of the BadR regulon in Borrelia burgdorferi

Borrelia burgdorferi, the causative agent of Lyme disease, relies on tightly coordinated gene expression to quickly adapt and survive in the tick vector and mammalian host. BadR, an ROK (repressor, open reading frame, kinase) family transcriptional regulator, binds directly to B. burgdorferi promoter DNA, however, many questions concerning the function of BadR in gene regulation remain unanswered. In particular, there are conflicting reports concerning what genes are regulated by BadR in B. burgdorferi. Furthermore, previous studies have suggested important roles for BadR in unfed ticks, but the BadR regulon has not been defined under such conditions. Additionally, although BadR regulates rpoS expression in a growth phase-dependent manner, it remained unknown whether BadR regulates other genes during different growth phases. To address these questions, we cultivated a B. burgdorferi badR mutant and wild-type strain under various conditions and analyzed the transcriptome using RNA-sequencing. When spirochetes were grown at 37°C and collected at the mid-logarithmic and stationary phase of growth, 211 and 272 genes were differentially expressed in the badR mutant, respectively. A total of 79 genes were differentially expressed when spirochetes were grown at 23°C. Combined, this work supports a role for BadR in global B. burgdorferi gene regulation by modulating expression of different sets of genes at different stages of the enzootic lifecycle. To investigate the genes regulated by BadR in Borrelia burgdorferi, a badR knockout was generated by homologous recombination. The badR mutant and wild-type strains were cultivated in vitro under conditions mimicking the unfed tick and mammalian host. Under mammalian host conditions, cells were collected at two growth phases to determine if BadR regulates genes in a growth-phase dependent manner.