24 25 To detect and respond to the diverse environments they encounter, bacteria often use two-26 component regulatory systems (TCSs) to coordinate essential cellular processes required for 27 survival. In pathogenic Bordetella species, the BvgAS TCS regulates expression of hundreds of 28 genes, including those encoding all known protein virulence factors, and its kinase activity is 29 essential for respiratory infection. Maintenance of BvgS kinase activity in the lower respiratory 30 tract (LRT) depends on the function of another TCS, PlrSR. While the periplasmic venus fly-trap 31 domains of BvgS have been implicated in responding to so-called modulating signals in vitro 32 (nicotinic acid and MgSO 4 ), a role for the cytoplasmic Per-Arnt-Sim (PAS) domain in signal 33 perception has not previously been demonstrated. By comparing B. bronchiseptica strains with 34 mutations in the PAS domain-encoding region of bvgS with wild-type bacteria in vitro and in 35vivo, we found that although the PAS domain is not required to sense modulating signals in 36 vitro, it is required for the inactivation of BvgS that occurs in the absence of PlrS in the LRT of 37 mice, suggesting that the BvgS PAS domain functions as an independent signal perception 38 domain. Our data also indicate that the BvgS PAS domain is important for controlling absolute 39 levels of BvgS kinase activity and the efficiency of the response to modulating signals in vitro. 40Our results indicate that BvgS is capable of integrating sensory inputs from both the periplasm 41 and the cytoplasm to control precise gene expression patterns in diverse environmental 42 conditions. 43 44 Importance 45 46 Despite high rates of vaccination, Pertussis, a severe, highly contagious respiratory disease, 47 caused by the bacterium Bordetella pertussis, has reemerged as a significant health threat. In 48Bordetella pertussis and the closely related species, Bordetella bronchiseptica, activity of the 49 BvgAS two-component regulatory system is critical for colonization of the human respiratory 50 tract and other mammalian hosts, respectively. Here we show that the cytoplasmic PAS domain 51 of BvgS can function as an independent signal perception domain that is capable of integrating 52 environmental signals that influence overall BvgS activity. Our work is significant as it reveals a 53critical, yet previously unrecognized role, for the PAS domain in the BvgAS phosphorelay and 54 provides a greater understanding of virulence regulation in Bordetella. 55 56 Introduction 57