Frontiers in Microbiology (Sep 2022)

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

  • Nicole A. P. Lieberman,
  • Thaddeus D. Armstrong,
  • Benjamin Chung,
  • Daniel Pfalmer,
  • Christopher M. Hennelly,
  • Austin Haynes,
  • Emily Romeis,
  • Qian-Qiu Wang,
  • Qian-Qiu Wang,
  • Rui-Li Zhang,
  • Cai-Xia Kou,
  • Cai-Xia Kou,
  • Giulia Ciccarese,
  • Ivano Dal Conte,
  • Marco Cusini,
  • Francesco Drago,
  • Shu-ichi Nakayama,
  • Kenichi Lee,
  • Makoto Ohnishi,
  • Kelika A. Konda,
  • Kelika A. Konda,
  • Silver K. Vargas,
  • Silver K. Vargas,
  • Maria Eguiluz,
  • Carlos F. Caceres,
  • Jeffrey D. Klausner,
  • Oriol Mitja,
  • Oriol Mitja,
  • Anne Rompalo,
  • Fiona Mulcahy,
  • Edward W. Hook,
  • Edward W. Hook,
  • Edward W. Hook,
  • Irving F. Hoffman,
  • Irving F. Hoffman,
  • Mitch M. Matoga,
  • Mitch M. Matoga,
  • Heping Zheng,
  • Heping Zheng,
  • Bin Yang,
  • Bin Yang,
  • Eduardo Lopez-Medina,
  • Eduardo Lopez-Medina,
  • Lady G. Ramirez,
  • Lady G. Ramirez,
  • Justin D. Radolf,
  • Justin D. Radolf,
  • Justin D. Radolf,
  • Justin D. Radolf,
  • Justin D. Radolf,
  • Kelly L. Hawley,
  • Kelly L. Hawley,
  • Kelly L. Hawley,
  • Kelly L. Hawley,
  • Juan C. Salazar,
  • Juan C. Salazar,
  • Juan C. Salazar,
  • Sheila A. Lukehart,
  • Sheila A. Lukehart,
  • Arlene C. Seña,
  • Jonathan B. Parr,
  • Lorenzo Giacani,
  • Lorenzo Giacani,
  • Alexander L. Greninger,
  • Alexander L. Greninger

DOI
https://doi.org/10.3389/fmicb.2022.1007056
Journal volume & issue
Vol. 13

Abstract

Read online

Sequencing of most Treponema pallidum genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). 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 tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 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 arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp 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 T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.

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