Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution of
Treponema pallidum
subsp.
pallidum
, the Syphilis Spirochete
Authors: Kumar Sanjiv , Caimano Melissa J. , Anand Arvind , Dey Abhishek , Hawley Kelly L. , LeDoyt Morgan E. , La Vake Carson J. , Cruz Adriana R. , Ramirez Lady G. , Paštěková Lenka , Bezsonova Irina , Šmajs David , Salazar Juan C. , Radolf Justin D. 
Published: June 2018

In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of
Treponema pallidum
subspecies
pallidum
, the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of
tprC
,
tprD
, and
bamA
in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used
T. pallidum
0548 (
tp0548
) genotyping and
tp0558
sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in
T. pallidum
subsp.
pallidum
reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of
T. pallidum
repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive
T. pallidum
subsp.
pallidum
OMP diversity and that genetic exchange contributes to the evolutionary biology of
T. pallidum
subsp.
pallidum
. They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development.

IMPORTANCE
Despite recent progress characterizing outer membrane proteins (OMPs) of
Treponema pallidum
, little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci,
tprC
,
tprD
, and
bamA
, in
T. pallidum
subsp.
pallidum
isolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations drive
T. pallidum
subsp.
pallidum
OMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance of
T. pallidum
subsp.
pallidum
and frame strategies for vaccine development based upon conserved OMP extracellular loops.