Sequence variation of rare outer membrane protein β-barrel domains in clinical strains provides insights into the evolution ofTreponema pallidumsubsp.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: May 2018

ABSTRACTIn recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) ofTreponema pallidumsubspeciespallidum(TPA), 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 oftprC,tprD, andbamA, 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 usedtp0548genotyping andtp0558sequences 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 inTPAreference 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. Based upon structural models, non-conservative amino acid substitutions in predicted transmembrane β-strands of 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 driveTPAOMP diversity and that genetic exchange contributes to the evolutionary biology ofTPA. They also set the stage for topology-based analysis of antibody responses against OMPs and help frame strategies for syphilis vaccine development.IMPORTANCEDespite recent progress characterizing outer membrane proteins (OMPs) ofTreponema pallidum(TPA), 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, andbamA,inTPAfrom a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurred predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function also were noted. Our findings suggest that selection pressures exerted by human populations driveTPAOMP 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 ofTPAand frame strategies for vaccine development based upon conserved OMP extracellular loops.