Diversity of s66-Specific Promoters Contributes to Regulation of Developmental Gene Expression in Chlamydia trachomatis

Promoter recognition by the RNA polymerase (RNAP) holoenzyme is a key step in gene regulation. In Chlamydia trachomatis, a medically important obligate intracellular bacterium, sigma(66) allows the RNAP to initiate promoter-specific transcription throughout the chlamydial developmental cycle. Here, we investigated the intrinsic properties of sigma(66)-specific promoters with emphasis on their role in the developmental gene expression of C. trachomatis. First, we examined whether promoters that contain a 5'-T(-15)G(-14)-3' (TG) motif upstream from the -10 element appear more often than others in genes that are preferentially expressed during the early, middle, or late stages of the C. trachomatis developmental cycle. We then determined the critical genetic elements that are required for transcription initiation in vitro. We also assessed the activity of promoters in the presence of Scc4, which can directly interact with sigma(66)RNAP. Finally, we evaluated the promoter-specific dynamics during C. trachomatis infection using a reporter assay. These results reveal that the TG motif is an important determinant in certain early or late promoters. The TG promoters that have the -35 element are recognized by sigma(66)RNAP and Scc4 differently from those lacking the -35 element. Based on these properties, the sigma(66)-specific promoters can fall into three classes. Architectural diversity, behavioral plasticity, and the specific interplays between promoters and the sigma(66)RNAP likely contribute to developmental gene transcription in C. trachomatis.