Beyond the Chlamydiaceae

The order Chlamydiales are characterised by an extraordinary diversity of host range and habitats, of which we still know little. A key feature of the Anderson and Everett taxonomy of the Chlamydiales [and one of the reasons why this site supports it] is that it provides a rational place for the Chlamydiales beyond the family Chlamydiaceae. Currently these include the Parachlamydiaceae, Simkaniaceae and the Waddliaceae and may even eventually include a new family Rhabdochlamydiaceae. Leaving aside the taxonomic arguments there are two strong pieces of experimental data:

1. Genomic sequencing. The first genome sequence beyond the Chlamydiaceae, that of  Parachlamydia UWE25 is now complete. From a preliminary presentation at the first Chlamydia BRS meeting in March 2003, roughly 80% of the Parachlamydia genome of 2,429,974 nucleotides, is coding sequence, embodying some 1845 open reading frames. Although at 35% its G+C ratio is substantially lower than the 40 - 42% ratio for the Chlamydiaceae, some 44% of the open reading frames had clear homologues among the Chlamydiaceae including the characteristic CPAF and inclusion proteins. This is strong evidence that this organism belongs in the Chlamydiales but outside the Chlamydiaceae, as it lacks their characteristic MOMP or POMPs.

2. Among comparative alignments of chlamydial gene sequences, Griffiths and Gupta 2002 identified a number of insertion/deletions (indels) that were unique and distinctive of the chlamydial species. These included one 16 amino acid, and two single amino acid inserts in the enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA), one amino acid inserts in protein synthesis elongation factor P (EF-P), in the Mg⁺⁺ transport protein (MgtE) and carboxy-terminal protease and a one amino acid deletion in the tRNA (guanine-N(1)-)-methyltransferase (TrmD) protein. The homologues of these proteins are found in all major groups of bacteria and the observed indels are present in all available chlamydial sequences but not in any other species (except for the large insert in MurA in Streptomyces). The validity of three of these signatures (MurA, EF-P and MgtE) was tested by PCR-amplifying the signature regions from several chlamydial species for which no sequence information was available. All Chlamydiaceae species for which specific fragments could be amplified (Chlamydia suis, Chlamydophila abortus, Chlamydophila psittaci, Chlamydophila felis) contained the expected signatures. A fragment of the murA gene from Waddlia chondrophila and the efp gene from Simkania negevensis were also cloned and sequenced. The presence of these respective indels in these species provided strong evidence that they are indeed specifically related to the traditional species in the Chlamydiaceae, and that these signatures may be distinctive of the entire Chlamydiales order. A 17 amino acid conserved indel was also identified in the cell wall biosynthesis enzyme UDP-N-acetylglucosamine pyrophosphorylase (GlmU), which is shared by all archaeal and chlamydial homologues. This suggests the gene for this protein was horizontally transferred from an archaeon to the chlamydial last common ancestor. The results also supported a lateral transfer of the murA gene between chlamydiae and Streptomyces.  The large inserts in these peptidoglycan synthesis-related genes in chlamydiae might account for their unusual cell-wall characteristics. These signatures are also potentially useful for screening chlamydial species.

[MEW] June 2003

Reference

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