Genome analysis of Treponema pallidum subsp. pallidum and subsp. pertenue strains: most of the genetic differences are localized in six regions

Abstract

The genomes of eight treponemes including T. p. pallidum strains (Nichols, SS14, DAL-1 and Mexico A), T. p. pertenue strains (Samoa D, CDC-2 and Gauthier), and the Fribourg-Blanc isolate, were amplified in 133 overlapping amplicons, and the restriction patterns of these fragments were compared. The approximate sizes of the genomes investigated based on this whole genome fingerprinting (WGF) analysis ranged from 1139.3-1140.4 kb, with the estimated genome sequence identity of 99.57-99.98% in the homologous genome regions. Restriction target site analysis, detecting the presence of 1773 individual restriction sites found in the reference Nichols genome, revealed a high genome structure similarity of all strains. The unclassified simian Fribourg-Blanc isolate was more closely related to T. p. pertenue than to T. p. pallidum strains. Most of the genetic differences between T. p. pallidum and T. p. pertenue strains were accumulated in six genomic regions. These genome differences likely contribute to the observed differences in pathogenicity between T. p. pallidum and T. p. pertenue strains. These regions of sequence divergence could be used for the molecular detection and discrimination of syphilis and yaws strains.

Figure 1. An unrooted tree showing the phypogenetic relationship of investigated genomes.

An unrooted tree (Tree View) constructed from the binary RTS data illustrating the relatedness of individual genomes. In addition, we incorporated also RTS data for T. paraluiscuniculi strain Cuniculi A that were taken from the previously published work of Strouhal et al. . Bar scale represents 0.01 restriction target site substitutions per tested RTS. T. p. pallidum strains causing syphilis are shown in bold.

Figure 2. A schematic representation of genome changes found in T. p. pallidum, T. p. pertenue strains and Fribourg-Blanc isolate.

A A schematic representation of indels found in all T. p. pertenue strains and the Fribourg-Blanc isolate but not found in any of the investigated T. p. pallidum strains (see also Table 3). Please note that TP0132 gene was not annotated in pertenue and Fribourg-Blanc strains. B Identified variable genomic regions in most of the investigated strains and isolates (see also Table 2). For more detailed structure of TP0126–TP0127 region see Figure 3, for details on TP0433–TP0434 locus, see . C Indels specific for individual strains and isolates (see also Table 4). T. p. pallidum strains causing syphilis are shown in bold. Deletions are shown as vertical lines, insertions as lines with black triangles.

Figure 3. A schematic representation of the chromosomal region between TP0126 and TP0127.

The newly annotated genes and the previously described gene conversion donor sites for the tprK variable (V) sequences in the intergenic region between genes TP0126 and TP0127 are shown for each strain tested. T. p. pallidum strains causing syphilis are shown in bold.

Figure 4. The unrooted trees constructed from sequences of genes showing major differences in strain clustering.

A An unrooted tree constructed from the binary RTS data without Cuniculi A data. Bar scale represents 0.01 restriction target site substitutions per RTS. The unrooted trees constructed from sequences of 4 treponemal genes including TP0131, TP0136, TP0548, and TP1031 are shown in panel B, C, D, and E, respectively. Bar scale represents 0.01 nucleotide substitutions per site. Bootstrap values based on 1,000 replications are shown next to branches. T. p. pallidum strains causing syphilis are shown in bold.