Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer

Abstract

Genome sequencing of Chlamydia trachomatis serovar D has identified polymorphic membrane proteins (Pmp) that are a newly recognized protein family unique to the Chlamydiaceae family. Cumulative data suggest that these diverse proteins are expressed on the cell surface and might be immunologically important. We performed phylogenetic analyses and statistical modeling with 18 reference serovars and 1 genovariant of C. trachomatis to examine the evolutionary characteristics and comparative genetics of PmpC and pmpC, the gene that encodes this protein. We also examined 12 recently isolated ocular and urogenital clinical samples, since reference serovars are laboratory adapted and may not represent strains that are presently responsible for human disease. Phylogenetic reconstructions revealed a clear distinction for disease groups, corresponding to levels of tissue specificity and virulence of the organism. Further, the most prevalent serovars, E, F, and Da, formed a distinct clade. According to the results of comparative genetic analyses, these three genital serovars contained two putative insertion sequence (IS)-like elements with 10- and 15-bp direct repeats, respectively, while all other genital serovars contained one IS-like element. Ocular trachoma serovars also contained both insertions. Previously, no IS-like elements have been identified for Chlamydiaceae. Surprisingly, 7 (58%) of 12 clinical isolates revealed pmpC sequences that were identical to the sequences of other serovars, providing clear evidence for a high rate of whole-gene recombination. Recombination and the differential presence of IS-like elements among distinct disease and prevalence groups may contribute to genome plasticity, which may lead to adaptive changes in tissue tropism and pathogenesis over the course of the organism's evolution.

FIG. 1.

Nucleotide sequences of pmpC domains containing the IS-like elements for all C. trachomatis serovars. (A) First IS element (42-nt insertion); (B) second IS element (30-nt insertion). The sequences were aligned with the GenBank sequence for strain D/UW-3 (accession number AE001315). Numbers at the top of the alignments represent the nucleotide positions. The shaded area represents IS elements. Boxes represent DTR sequences. Dots represent sequence homology; dashes represent the absence of nucleotides. These sequence data are available from GenBank under accession numbers AF519747 through AF519765.

FIG. 2.

The distribution of conserved cysteine residues for the 15 C. trachomatis reference serovars within each Pmp is denoted by relative amino acid positions indicated as vertical bars. The numbers of conserved cysteines for PmpC, PmpE, PmpH, and PmpI were 13, 15, 14, and 18, respectively.

FIG. 3.

Phylogenetic reconstruction of nucleotide (A) and amino acid (B) sequences, showing the evolutionary history of pmpC by neighbor-joining tree topologies as determined on the basis of distance estimates made using a Kimura two-parameter model for substitution events. These reconstructions were made on the basis of pmpC sequences of the 18 serovars and the genovariant Ja of C. trachomatis. Branch lengths are proportional to distances between serovars. The values at the nodes are the bootstrap confidence levels, representing the percentages of 1,000 bootstrap resamplings for which the strains to the right were separated from the others.

FIG. 4.

Upper and middle graphs show mean synonymous mutation rates and mean nonsynonymous mutation rates, respectively, for each pmp determined by the method of Nei and Gojobori (p-distance model). Minimum and maximum values represent lower and upper limits of the 95% CI of the estimate, while values plotted at the horizontal bar level represent the mean estimates. The lower graph shows the nonsynonymous- to synonymous-mutation ratio for each pmp determined on the basis of the mean estimates shown in the prior two graphs.

FIG. 5.

Mean p distance within each pmp determined on the basis of the average p distance for all possible pairs of sequences (different serovars) for the same pmp. (A) Minimum and maximum values represent lower and upper limits of the 95% CI of the estimate, while values plotted at horizontal bar level represent the mean estimates. (B) Absolute and percent values for the nucleotide and amino acid mean genetic distance for each pmp. aa, amino acid.

FIG. 6.

Phylogenetic reconstruction of the nucleotide sequences, showing the evolutionary history of pmpC determined on the basis of pmpC sequences of the 18 serovars and the genovariant Ja of C. trachomatis and 12 clinical isolates representing ompA genotypes C, E, F, G, H, I, J, and Ja. Branch lengths are proportional to distances between serovars; bootstrap values are shown at the nodes. In the names of the clinical isolates, the first character represents the ompA genotype and the characters in parentheses represent the serovar(s) to which the pmpC sequence is similar.