Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces a aThe GenBank accession numbers for the sequences reported in this paper are indicated in the text.

Abstract

Chlamydiae are major human and animal pathogens. Based on alignments of different protein sequences, a number of conserved indels (insertion/deletions) were identified that appear to be unique and distinctive characteristics of the chlamydial species. The identified signatures include one 16 aa and two single aa inserts in the enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA), a 1 aa insert in protein synthesis elongation factor P (EF-P), a 1 aa insert in the Mg 2M transport protein (MgtE), a 1 aa insert in the carboxyterminal protease and a 1 aa 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. Additionally, a fragment of the murA gene from Waddlia chondrophila and the efp gene from Simkania negevensis, two chlamydia-like species, were also cloned and sequenced. The presence of respective indels in these species provides strong evidence that they are specifically related to the traditional chlamydial species, and that these signatures may be distinctive of the entire Chlamydiales order. A 17 aa 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. The gene for this protein is indicated to have been horizontally transferred from an archaeon to a common ancestor of the chlamydiae. The results also support a lateral transfer of the murA gene between chlamydiae and Streptomyces. The large inserts in these peptidoglycan synthesis related genes in chlamydiae could account for their unusual cell-wall characteristics. These signatures are also potentially useful for screening of the chlamydiae species.

Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification

“…The comparative analyses of these genomes provide a powerful means for identifying novel molecular characteristics that are distinctive to different groups of bacteria (Hatch, 1998;Kalman et al, 1999). In an earlier study, we reported a number of conserved inserts and deletions (indels) in widely distributed proteins that were uniquely shared by Chlamydiaceae species (Griffiths & Gupta, 2002). However, most of these indels were small (1 aa), and for most of them sequence information from other chlamydiae families was not available.…”

“…The cloning and sequencing of these fragments revealed that the indicated signature insert was present in all three species (see Fig. 3), confirming that it is a reliable molecular marker for all chlamydiae.We have previously described a 1 aa insert in EF-P (Griffiths & Gupta, 2002) that is found in all Chlamydiaceae species, including Chlamydophila abortus and Chlamydia suis, which were sequenced in our previous work, as well as Sim. negevensis.…”

Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum

“…The PCRs had a final volume of 10 l, and all primer sets were optimized for Mg 2ϩ concentration (in the range of 1.5 to 4 mM) for each DNA strain tested. PCR amplification was carried out over 30 cycles (15 s at 94°C, 15 s at 55 or 45°C, 1 min at 72°C) with an initial 1-min hot start at 94°C and a final extension step (15 s at 94°C, 15 s at 55°C, 7 min at 72°C) (12). The reaction mix also contained 2% dimethyl sulfoxide, which improves PCR performance by lowering the melting temperature of DNA.…”

“…Deinococcus-Thermus-specific signatures were identified in global multiple sequence alignments by means of visual inspection. Alignments for different proteins were constructed by using the ALIGN PLUS 4 program (Scientific & Educational Software, Durham, N.C.) as described in earlier work (12,14,19). To qualify as a useful group-specific signature, any identified indel was required to be uniquely (or mainly) present in the Deinococcus-Thermus-Meiothermus group of species and to be flanked on both sides by conserved regions to ensure that the observed insertion or deletion was not a result of sequencing errors or alignment artifacts.…”

“…We have described a new approach based on conserved indels (i.e., inserts or deletions) found in different proteins that is helpful in distinguishing the major bacterial phyla and to understand the interrelationships among them (13)(14)(15)17). Recently, a large number of conserved indels (or signature sequences) which provide distinctive molecular markers for the identification of proteobacteria, chlamydiae, and cyanobacteria have been described (12,14,19).…”