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InBorrelia burgdorferi(Bb), the alternative sigma factor RpoS plays a central role during Bb's adaptation to ticks and mammals. Previous studies have demonstrated that RpoS is not expressed during the early stages of spirochetal growth or when Bb resides in ticks during the intermolt phase, but the molecular details of these events remain unknown. In the current study, biomagnetic bead separation ofrpoSpromoter-binding proteins, coupled with genetic inactivation, was employed to identify BadR (BB0693) as a negative regulator that controls growth phase-dependent induction ofrpoSandbosRin Bb. WhenbadRwas inactivated, the expression ofrpoSandbosRwas induced only during the early stages of bacterial growth, but not during the stationary growth phase. Recombinant BadR bound to the promoter DNA ofrpoSand the regulatory region upstream ofbosRvia AT-rich TAAAATAT motifs. Mutations in this motif markedly inhibited or abolished rBadR binding. These results suggest that BadR directly influences the expression of bothrpoSandbosRin Bb. This newly recognized role for BadR to fine-tune the activation of the RpoN–RpoS pathway at strategic times in Bb's life cycle potentially represents another layer of gene control over σ54-dependent gene regulation.In Borrelia burgdorferi, RpoS governs the organism's capacity to adapt to tick and mammalian environments. The transcription of rpoS is controlled by σ54, but is also dependent on the two activators Rrp2 and BosR. This article shows that the expression of rpoS and bosR is negatively influenced by BadR in a growth phase- or cell density-dependent manner; BadR binds to the promoter region of rpoS and the regulatory region upstream of bosR via TAAAATAT motifs.