Structural Modeling of the Treponema pallidum Outer Membrane Protein Repertoire: a Road Map for Deconvolution of Syphilis Pathogenesis and Development of a Syphilis Vaccine

Abstract

Treponema pallidum, an obligate human pathogen, has an outer membrane (OM) whose physical properties, ultrastructure and composition differ markedly from those of phylogenetically distant Gram-negatives. We developed structural models for the outer membrane protein (OMP) repertoire of T. pallidum Nichols using solved Gram-negative structures, computational tools, and small angle X-ray scattering (SAXS) of selected recombinant periplasmic domains. The T. pallidum ‘OMPeome’ harbors two ‘stand-alone’ proteins (BamA and LptD) involved in OM biogenesis and four paralogous families involved in influx/efflux of small molecules: 8-stranded β-barrels, long-chain fatty acid transporters (FadLs), OM factors (OMFs) for efflux pumps, and T. pallidum repeat proteins (Tprs). BamA (TP0326), the central component of a BAM/TAM hybrid, possesses a highly flexible POTRA1-5 predicted to interact with TamB (TP0325). TP0515, an LptD ortholog, contains a novel, unstructured C-terminal domain that models inside the β-barrel. T. pallidum has four 8-stranded β-barrels, each containing positively charged extracellular loops that could contribute to pathogenesis. Three of five FadL-like orthologs have a novel α-helical, presumptively periplasmic C-terminal extension. SAXS and structural modeling further supported the bipartite membrane topology and tri-domain architecture of full-length members of the Tpr family. T. pallidum’s two efflux pumps presumably extrude noxious small molecules via four co-expressed OMFs with variably charged tunnels. For BamA, LptD and OMFs, we modeled the molecular machines that deliver their substrates into the OM or external milieu. The spirochete’s extended families of OM transporters collectively confer a broad capacity for nutrient uptake. The models also furnish a structural roadmap for vaccine development. Importance The unusual outer membrane (OM) of T. pallidum, the syphilis spirochete, is the ultrastructural basis for its well-recognized capacity for invasiveness, immune evasion, and persistence. In recent years, we have made considerable progress identifying T. pallidum’s repertoire of OMPs. Herein, we developed three-dimensional (3D) models for the T. pallidum Nichols OMPeome using structural modeling, bioinformatics, and solution scattering. The OM contains three families of OMP transporters, an OMP family involved in extrusion of noxious molecules, and two ‘stand alones’ involved in OM biogenesis. This work represents a major advance towards elucidating host-pathogen interactions during syphilis, understanding how T. pallidum, an extreme auxotroph, obtains a wide array of biomolecules from its obligate human host, and developing a vaccine with global efficacy.