Phylogenetic comparison of the known Chlamydia trachomatis σ66 promoters across to Chlamydia pneumoniae and Chlamydia caviae identifies seven poorly conserved promoters

We used four different phylogenetic footprinting programs and the six chlamydial species with publicly available whole genome sequences to analyze the 12 known σ66 promoters of Chlamydia trachomatis that phylogenetically footprinted negative in our previous paper. The analysis showed that 7 of the 12 promoters were poorly conserved across C. trachomatis, Chlamydia pneumoniae and Chlamydia caviae. Interestingly, the associated gene sets for these seven promoters were homologs and the gene orders were well conserved across these three species. Additional phylogenetic footprinting, across different subsets from that used above, of the six publicly available whole chlamydial genome sequences and transcription initiation site mapping of chlamydial promoters was also performed. This analysis showed that two of the seven poorly conserved promoters, the promoters in the upstream regions of C. caviae ltuA and ltuB, were like Escherichia coli σ70 promoters. Therefore, these promoters are similar to the promoters of C. trachomatis ltuA and ltuB, as they are σ70-like. Given the fact that 7 out of the 22 known σ66 promoters in C. trachomatis are poorly conserved across C. trachomatis, C. pneumoniae and C. caviae, we would like to suggest that many other chlamydial promoters are poorly conserved across these species.