Course of Protochlamydia type III secretion system activity during the developmental cycle. Course of Protochlamydia type III secretion system activity during the developmental cycle. This model is based on the observation that structural components of the type III secretion system and its (putative) effectors are expressed at different time points during the developmental cycle (Fig. S4). This suggests a scenario in which novel, fully assembled, and thus functional secretion systems occur only late in the developmental cycle, and type III secretion reaches its full capacity and highest activity during early stages of the infection. The indicated polarity of the active type III secretion system has been shown for C. trachomatis (54), but it is unclear whether this is also true for P. amoebophila, as the symbionts reside within single-cell inclusions. The color code for type III secretion components and effectors (nomenclature according to Hueck [105]) refers to the respective temporal gene expression classes (Fig. 2 and Fig. S4). Circles inside the cells represent chaperones. Differentially expressed components/effectors are labeled with asterisks; PEX1 and PEX2 refer to members of the expanded effector gene families in Protochlamydia (33); pc0309 is an ortholog of the putative chaperone encoded by CT274 (106). inc, inclusion membrane; hcm, host cell membrane; im, inner membrane; om, outer membrane. Lena König et al. mSystems 2017; doi:10.1128/mSystems.00202-16