The RNA polymerase of Chlamydia trachomatis has a flexible sequence requirement at the -10 and -35 boxes of its promoters.

Mutated variants of the predicted promoter of the countertranscript of the Chlamydia trachomatis plasmid were tested by in vitro transcription with chlamydial extract. A 3-bp deletion within the -10 region of the putative promoter caused the RNA polymerase to initiate transcription 3 bases downstream. Many single mutations in the -10 and -35 regions did not alter promoter function. However, some multiple mutations in both hexamers rendered the promoter inefficient or ineffective. Taken together, these results indicate that (i) the sequence requirement for chlamydial promoters differs from that for Escherichia coli and (ii) chlamydial RNA polymerase can tolerate considerably more variation at the -10 and -35 regions. These results are paradoxical considering the homology between C. trachomatis sigma 66 and E. coli sigma 70.