Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution of Treponema pallidum subsp. pallidum , the Syphilis Spirochete

Abstract

In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum, the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC, tprD, and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used T. pallidum 0548 (tp0548) genotyping and tp0558 sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in T. pallidum subsp. pallidum reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of T. pallidum repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive T. pallidum subsp. pallidum OMP diversity and that genetic exchange contributes to the evolutionary biology of T. pallidum subsp. pallidum. They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development.

Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens

“…The prediction of treponemal protein structures is quite limited due to the lack of the protein homologues. However, a protein structure for tpr C was predicted by Centurion-Lara et al (2013) and more recently by Kumar et al (2018). The recombinant regions identified in the new tpr C3 and tpr C4 alleles found in this study (Supplementary Figure S2) correspond to the identified extracellular loops (L3, L4, L5) of the β-barrel outer membrane protein which were predicted to serve as B-cells epitopes 2 (Kumar et al, 2018; Figure 6).…”

“…However, a protein structure for tpr C was predicted by Centurion-Lara et al (2013) and more recently by Kumar et al (2018). The recombinant regions identified in the new tpr C3 and tpr C4 alleles found in this study (Supplementary Figure S2) correspond to the identified extracellular loops (L3, L4, L5) of the β-barrel outer membrane protein which were predicted to serve as B-cells epitopes 2 (Kumar et al, 2018; Figure 6). Moreover, the newly predicted 3D structures of proteins TP0858 and TP0865 (Figure 6) revealed that the observed recombination-driven diversity almost strictly corresponds to the residues located at the host-pathogen interface.…”

Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis

“…In marked contrast to the OMs of Gram-negative bacteria, the T. pallidum OM is fragile, poorly antigenic, lacks lipopolysaccharide, and has a remarkably low density of integral OMPs [4,16,18,19]. In recent years, great progress has been made in characterizing syphilis spirochete's repertoire of rare, β-barrel-forming OMPs [16,[93][94][95]. The preponderance of T. pallidum-specific antibodies generated during human infection are directed against lipoproteins, not integral OMPs [3,21,23,24].…”

“…pallidum OM is fragile, poorly antigenic, lacks lipopolysaccharide, and has a remarkably low density of integral OMPs [ 4 , 16 , 18 , 19 ]. In recent years, great progress has been made in characterizing syphilis spirochete’s repertoire of rare, β-barrel-forming OMPs [ 16 , 93 – 95 ]. The preponderance of T .…”

Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection

“…The coding change seen between the two isolates here (T260A) mapped to the POTRA3 domain. While the impact of amino acid substitutions in the TP0326 β-barrel on immunoreactivity has been studied [44,45], further work is required to understand the impact of the amino acid substitution observed in our isolates.…”