High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny

Abstract

Sequencing of most <i>Treponema pallidum</i> genomes excludes repeat regions in <i>tp0470</i> and the <i>tp0433</i> gene, encoding the acidic repeat protein (<i>arp</i>). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence <i>tp0470</i> and <i>arp</i> genes from 212 clinical samples collected from ten countries on six continents. Both <i>tp0470</i> and <i>arp</i> repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of <i>tp0470</i> repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat <i>arp</i> sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many <i>arp</i> sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same <i>arp</i> repeat length, this was not always the case. Structural modeling of TP0470 suggested that the eight residue repeats form an extended α-helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged β-sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in <i>T. pallidum</i> cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.