Abstract
<jats:p>Diverse vacuolar architectures present unique signaling challenges for intracellular bacteria, yet whether distinct niches share host requirements remains unclear. Because host kinases coordinate these complex cellular responses, we performed a comparative chemical-genetic screen of Coxiella burnetii, Chlamydia trachomatis, and Salmonella enterica. The screen revealed that C. burnetii is uniquely dependent on host kinase pathways. Deconvolution of these inhibitor profiles identified the bone morphogenetic protein (BMP) type I receptor, ALK2, as a critical regulatory checkpoint. While C. burnetii activates ALK2-mediated phospho-SMAD1/5/9 signaling to support replication, C. trachomatis actively suppresses this cascade. Mechanistically, ALK2 functions upstream of TFEB nuclear translocation and LAMP1 recruitment, driving the lysosomal biogenesis required to sustain the phagolysosome-like niche of C. burnetii while disrupting the non-lysosomal inclusion of C. trachomatis. Consequently, targeting ALK2 switches replication outcomes, demonstrating how distinct niches implement opposing strategies to exploit a single host signaling node.</jats:p>