The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains

Abstract

Treponema pallidum subspecies pallidum is the causative agent of syphilis, a chronic, multistage, systemic infection that remains a major global health concern. The molecular mechanisms underlying T. pallidum pathogenesis are incompletely understood, partially due to the phylogenetic divergence of T. pallidum. One aspect of T. pallidum that differentiates it from conventional Gram-negative bacteria, and is believed to play an important role in pathogenesis, is its unusual cell envelope ultrastructure; in particular, the T. pallidum peptidoglycan layer is chemically distinct, thinner and more distal to the outer membrane. Established functional roles for peptidoglycan include contributing to the structural integrity of the cell envelope and stabilization of the flagellar motor complex, which are typically mediated by the OmpA domain-containing family of proteins. To gain insight into the molecular mechanisms that govern peptidoglycan binding and cell envelope biogenesis in T. pallidum we report here the structural characterization of the putative OmpA-like domain-containing protein, Tp0624. Analysis of the 1.70 Å resolution Tp0624 crystal structure reveals a multi-modular architecture comprised of three distinct domains including a C-terminal divergent OmpA-like domain, which we show is unable to bind the conventional peptidoglycan component diaminopimelic acid, and a previously uncharacterized tandem domain unit. Intriguingly, bioinformatic analysis indicates that the three domains together are found in all orthologs from pathogenic treponemes, but are not observed together in genera outside Treponema. These findings provide the first structural insight into a multi-modular treponemal protein containing an OmpA-like domain and its potential role in peptidoglycan coordination and stabilization of the T. pallidum cell envelope.

Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel

“…1 However, only recently, a protein with an extremely deep knot has been deposited in the KnotProt database. Tp0624 (PDB code 5JIR) 14 is a three-domain protein, with the central domain knotted, making it the deepest knotted protein known to date 15 with the knot tails exceeding 120 residues (Figure 1). Because of its structure, the protein motivates a fundamental question of how can such proteins fold?…”

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

“…Eight stranded β-barrels also contribute to bacterial virulence by virtue of their ECLs (78). As an example, Ail of Yersinia pestis binds to negatively charged extracellular matrix (ECM) components via its positively charged ECLs (83).The T. pallidum Nichols genome encodes two proteins (TP0624 and TP0292) withOmpA-like domains containing peptidoglycan recognition motifs; neither, however, contains a β-barrel domain(91)(92)(93). The genome does encode four single-domain 8-stranded β-barrels (TP0126, TP0479, TP0698, and TP0733).…”

The hypothetical periplasmic protein PA1624 fromPseudomonas aeruginosafolds into a unique two-domain structure

“…3a). The closest homolog of the C-terminal domain is a building block of Tp0624 from Treponema pallidum (Z-score 8.3; PDB entry 5jir; Parker et al, 2016), which aligns with a C r.m.s.d. of 2.8 Å over 78 residues, displaying a sequence identity of 15% (Figs.…”