Borrelia burgdorferi (Bb), the agent of Lyme disease (LD), is maintained in nature within a complex enzootic cycle involving a mammalian reservoir host and a tick vector. To sustain this cycle, Bb must adjust its transcriptome, proteome, and metabolome to arthropod- and mammalian host-derived signals as it shuttles between the two. The Rrp2/RpoN/RpoS pathway has gained widespread recognition as a central player in borrelial gene regulation. Our laboratory has long been at the forefront of efforts to characterize the cohort of genes controlled by RpoS in both the tick and mammal. Unfortunately, we still do not know the entire output of RpoS-RNA polymerase (RNAP) holoenzyme in nature. The present proposal addresses this shortfall by combining state-of-the-art transcriptomic and mutagenesis methodologies to determine where/when individual genes contribute to RpoS's dual-host `mission'. In prior publications, we were instrumental in delineating the temporal boundaries of the RpoS-ON and –OFF states in vivo. In recent years, however, our thinking about this dichotomy has become much more nuanced. We now believe that the contours of the RpoS regulon change profoundly and in host-specific fashion during the RpoS-ON state These results, in concert with studies of the Hk1/Rrp1 pathway, give rise to our central hypothesis--the dynamic nature of the RpoS regulon reflects the confluence of non-RpoS regulatory pathways with mechanisms that govern the ON/OFF states of RpoS and the output of RpoS-RNAP. Along these lines, we now propose that the tick-phase signaling molecule c-di-GMP is crucial to this regulatory cross-talk. Moreover, we and others have found that the c-di-GMP-binding protein PlzA promotes expression of RpoS and, hence, Bb virulence in the mouse, the stage of the enzootic cycle in which the Hk1/Rrp1 pathway is OFF. Our efforts to clarify this bifunctional role of PlzA as a mediator of c-di-GMP signaling in ticks and a c-di-GMP-independent regulator of RpoS in mice takes our field into uncharted territory. Lastly, in years past, our analysis of mammalian host-adapted spirochetes cultivated in dialysis membrane chambers revealed that RpoS not only upregulates genes required for tick transmission and mammalian infection but also represses genes required for colonization and adaptation to the tick. Our recent work suggests that RpoS-RNAP directly represses transcription of tick-phase genes by occluding their σ70 promoters. We will test this `RpoS as repressor' model and explore new data that c-di-GMP antagonizes RpoS-mediated repression in mammalian host-adapted Bb. Our long-term objective is to achieve an integrative understanding of how the Rrp2/RpoN/RpoS pathway fulfills its essential mission--guiding LD spirochetes from tick to mouse and back again. We will accomplish this by defining the contours of the RpoS regulon in ticks and mice (Aim 1); clarifying the convergence of c-di-GMP- and PlzA-dependent signaling with the RpoS pathway (Aim 2); and...