Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution

Abstract

Background: Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14, Chicago), four T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), one T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPeC) were tested for the presence of positively selected genes.

Methodology/principal findings: A total of 1068 orthologous genes annotated in all 11 genomes were tested for the presence of positively selected genes using both site and branch-site models with CODEML (PAML package). Subsequent analyses with sequences obtained from 62 treponemal draft genomes were used for the identification of positively selected amino acid positions. Synthetic biotinylated peptides were designed to cover positively selected protein regions and these peptides were tested for reactivity with the patient's syphilis sera. Altogether, 22 positively selected genes were identified in the TP genomes and TPA sets of positively selected genes differed from TPE genes. While genetic variability among TPA strains was predominantly present in a number of genetic loci, genetic variability within TPE and TEN strains was distributed more equally along the chromosome. Several syphilitic sera were shown to react with some peptides derived from the protein sequences evolving under positive selection.

Conclusions/significance: The syphilis-, yaws-, and bejel-causing strains differed relative to sets of positively selected genes. Most of the positively selected chromosomal loci were identified among the TPA treponemes. The local accumulation of genetic variability suggests that the diversification of TPA strains took place predominantly in a limited number of genomic regions compared to the more dispersed genetic diversity differentiating TPE and TEN strains. The identification of positively selected sites in tpr genes and genes encoding outer membrane proteins suggests their role during infection of human and animal hosts. The driving force for adaptive evolution at these loci thus appears to be the host immune response as supported by observed reactivity of syphilitic sera with some peptides derived from protein sequences showing adaptive evolution.

Fig 1. The algorithm used for identification of positively selected genes.

The original search for positively selected genes started with identification of gene orthologs with 3 or more nucleotide differences leading to nonsynonymous amino acid replacements. The original search was performed on a set of 11 complete treponemal genomes listed in Table 1. Subsequently, orthologous gene sequences extracted from published treponemal draft genomes were used and the Cuniculi A orthologs were removed due to frequent sequential diversity and due to lack of pathogenicity of TPeC to humans. Orthologs from draft genomes were used when available and positively selected genes were analyzed within treponemal subspecies using branch-site PAML model analysis.

Fig 2. Positively selected genes as well as positively selected genes with previously identified recombination event that were identified within particular subspecies.

Genes identified as recombinant in a particular treponemal subspecies are shown in bold. Positively selected genes with no evidence of recombination are shown in regular version. Positively selected genes identified between subspecies of treponemes, but not within any of them, are not shown. Note that positively selected genes occur mostly within the TPA and the recombinant genes are within the TEN genomes. The TP0548 and TP0865 genes were found to be positively selected within TPA and also within TPE subspecies.