Sequence variability of BamA and FadL candidate vaccinogens suggests divergent evolutionary paths of Treponema pallidum outer membrane proteins

Bettin, E. B.; Aghakhanian, F.; Hennelly, C.; Chen, W.; Davenport, T.; Hackl, S. T.; Grassmann, A. A.; Vargas-Cely, F.; Silva, S.; Garcia-Luna, J. A.; Ramirez, L. G.; Jiang, Y.; Yang, L.-G.; Zheng, h.; Yang, B.; Pospisilova, P.; ?majs, D.; Matoga, M. M.; Hoffman, I.; Lopez-Medina, E.; Nieselt, K.; Moody, M. A.; Sena, A. C.; Salazar, J. C.; Parr, J. B.; Caimano, M. J.; Hawley, K. L.; Radolf, J. D.

doi:10.1101/2025.04.21.649848

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bioRxiv · 10.1101/2025.04.21.649848

Sequence variability of BamA and FadL candidate vaccinogens suggests divergent evolutionary paths of Treponema pallidum outer membrane proteins

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Abstract

Knowledge of Treponema pallidum subspecies pallidum (TPA) outer membrane protein (OMP) sequence variability is essential for understanding spirochete proliferation within endemic populations as well as design of a globally effective syphilis vaccine. Our group has identified extracellular loops (ECLs) of TPA BamA (TP0326) and members of the FadL family (TP0548, TP0856, TP0858, TP0859, and TP0865) as potential components of a multivalent vaccine cocktail. As part of a consortium to explore TPA strain diversity, we mapped the variability of BamA and FadL orthologs in 186 TPA strains from Malawi, China and Colombia onto predicted 3D structures. The 186 genomes fell into eight subclades (five Nichols-, three SS14-lineage) with substantial geographic restriction. Single nucleotide variants accounted for the large majority of proteoforms, with variability notably higher within the Nichols-lineage strains. Most mutations were in regions of the proteins predicted to be extracellular and harboring B cell epitopes. We observed a striking difference in the degree of variability between the six OMPs, suggesting that these proteins are following divergent evolutionary paths. Concatenation of OMP sequences recapitulated the phylogenetic structure of the TPA strains, effectively segregating within clades and largely clustering by subclades. Lastly, we noted that BamA and FadL candidate ECL vaccinogens previously shown to elicit antibodies that kill treponemes during in vitro cultivation are well conserved. Taken as a whole, our study establishes a structural-phylogenetic approach for analyzing the forces shaping the host-pathogen interface in syphilis within endemic populations while informing selection of vaccine targets. IMPORTANCESyphilis remains a major global health concern, reinforcing the need for a safe and effective vaccine. Understanding the variability of TPA OMPs is essential for tracking pathogen evolution and informing vaccine design. Here, we analyzed the variability of six TPA OMPs in 186 strains from Malawi, China, and Colombia, identifying protein-specific evolutionary patterns. Most mutations were localized in extracellular regions and, notably, appeared to correlate with the phylogenetic structure of TPA. Despite OMP heterogeneity, several candidate vaccinogens remained highly conserved, reinforcing their potential as globally effective vaccine targets. Our study establishes a structural-phylogenetic framework for dissecting the forces shaping the host-spirochete interface within endemic populations and provides a foundation for designing a globally effective syphilis vaccine.

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Bettin, E. B., Aghakhanian, F., Hennelly, C., Chen, W., Davenport, T., Hackl, S. T., Grassmann, A. A., Vargas-Cely, F., Silva, S., Garcia-Luna, J. A., Ramirez, L. G., Jiang, Y., Yang, L.-G., Zheng, h., Yang, B., Pospisilova, P., ?majs, D., Matoga, M. M., Hoffman, I., Lopez-Medina, E., Nieselt, K., Moody, M. A., Sena, A. C., Salazar, J. C., Parr, J. B., Caimano, M. J., Hawley, K. L., Radolf, J. D.. 2025-04-23. Sequence variability of BamA and FadL candidate vaccinogens suggests divergent evolutionary paths of Treponema pallidum outer membrane proteins. https://doi.org/10.1101/2025.04.21.649848

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