While the bacterium displayed improved biosynthetic qualities as as opposed to Chlamydia species, a related dependency on host derived metabolites was noticed [26]. Intriguingly, no homologs to significant outer membrane proteins and polymorphic membrane proteins have been recognized, suggesting these hugely immunogenic proteins might be Chlamydiaceae loved ones specific. The availability of genome sequences in new people of the Chlamydiales order is important to superior recognize the biology of Chlamydia-related bacteria. As a result, we sequenced the complete genome of W. chondrophila making use of the two 454/Roche and Solexa/ Illumina technologies, also uncovering the existence of a low copy amount plasmid. The genome annotation uncovered quite a few intriguing features introduced right here which we foresee will assist promote and push even further investigation into this fascinating and medically important bacterial order.
The genome of Waddlia chondrophila WSU 86-1044 consists of a circular chromosome MEDChem Express SMT C1100of 291169312 bp with a G+C information of forty three.eight% and a 159593 bp round plasmid with a G+C content of 37.six% (Figure 1 and Table 1). The chromosome sequence shows a typical “V”-inverted condition on a cumulative GC skew plot (Figure S1), permitting the origin and terminus of replication to be located and the assembly accuracy to be confirmed [29,30]. An additional typically utilized marker for the origin of replication is dnaA [31]. Nevertheless, like other Chlamydiales, W. chondrophila encodes two copies of dnaA, none of which is linked to the least of the cumulative GC skew (Figure S1). Employing bioinformatics analyses, a substantial quantity of repetitive sequences (.two hundred bp) were discovered encompassing 4.nine% of the chromosome, a considerably greater proportion than other sequenced Chlamydiales (Figure 1 and Table one). Two sets of rRNAs and 37 tRNA genes had been determined as very well as 1934 protein coding genes, which depict ninety two% of the whole genome. A putative perform or household membership could be inferred for 1243 (sixty five%) of them, whilst 253 (13%) are conserved hypothetical proteins and the remaining 438 (23%) show no similarity to acknowledged proteins (Desk S1 and Figure S2). Of the conserved hypothetical proteins, the key group of 156 proteins is most very similar to hypothetical proteins from the Parachlamydiaceae household. The remainder display greatest BLAST hits in opposition to Eukaryotes (2), Archaea (four), Chlamydiaceae (4) and various other bacterial phyla (87). The comparison of W. chondrophila encoded proteins with these of C. trachomatis and P. amoebophila confirmed the large proportion of family-certain proteins and proteins badly conserved at the amino acid stage inside this remarkably diverse bacterial order (Determine S3). The X-plot representation of conserved genes highlighted tiny collinear locations in between Waddlia and Protochlamydia, even even though quite a few rearrangements happened, altering gene orientation and placement. In contrast, conserved gene order is barely distinguishable between Waddlia and Chlamydia.
The comparison involving the common read depth of the W. chondrophila chromosome (40x) and its plasmid (440x) suggests that the plasmid is present in about 11 copies for every cell. It encodes 22 proteins that largely present no homology to other chlamydial plasmid proteins, with the exception of an integrase that displays fifty four% identity to the plasmid integrase pCpA1_003 of C. psittaci. The Waddlia chromosome includes numerous smaller locations (164 bp) identical to sequences in the plasmid. In addition, 7 chromosomal areas ranging from 57 bp to 849bp that encode overall or partial integrated transposases share among 99% and a hundred% id with the two plasmid transposases (Determine one). Each of these two transposases is strongly comparable to several proteins encoded on the P. amoebophila genome. Last but not least, two adjacent genes were being observed to be built-in into the Waddlia chromosome sharing 88% nucleic acid id to their plasmid counterparts. 1 of the encoded591813 proteins is homologous to MazF, an endoribonuclease of the MazEF module, a single of the most totally studied toxin-antitoxin techniques [32], that may well be included in the secure routine maintenance of the plasmid for the duration of cell division. Typically, mazE encodes a labile antitoxin that stops the lethal influence of the secure toxin encoded by mazF. Although the neighbouring genes of mazF do not demonstrate any sequence similarity to mazE, one particular of them may characterize the needed antitoxin.