title: Phylogenetic comparison of the known Chlamydia trachomatis sigma(66) promoters across to Chlamydia pneumoniae and Chlamydia caviae identifies seven poorly conserved promoters.
abstract: We used four different phylogenetic footprinting programs and the six chlamydial species with publicly available whole genome sequences to analyze the 12 known sigma(66) 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 sigma(70) promoters. Therefore, these promoters are similar to the promoters of C. trachomatis ltuA and ltuB, as they are sigma(70)-like. Given the fact that 7 out of the 22 known sigma(66) 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.
authors: Institute of Health and Biomedical Innovation, Queensland University of Technology, Corner Musk Avenue and Blamey Street, Kelvin Grove, Brisbane, Queensland 4059, Australia.
authors: Brian
authors: B
authors: Grech
authors: Sarah
authors: S
authors: Mathews
authors: Peter
authors: P
authors: Timms
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D002689:Chlamydia / Q000145:classification / Q000235:genetics*; D017124:Conserved Sequence; D018983:DNA Footprinting; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D012808:Sigma Factor / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D012808:Sigma Factor; C096461:sigma 66 factor, Chlamydia; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases