Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.

TitleWhole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.
Publication TypeJournal Article
Year of Publication2012
AuthorsČejková, D, Zobaníková, M, Chen, L, Pospíšilová, P, Strouhal, M, Qin, X, Mikalová, L, Norris, SJ, Muzny, DM, Gibbs, RA, Fulton, LL, Sodergren, E, Weinstock, GM, Smajs, D
JournalPLoS Negl Trop Dis
Volume6
Issue1
Paginatione1471
Date Published2012 Jan
ISSN1935-2735
KeywordsDNA, Bacterial, Gene Order, Genetic Variation, Genome, Bacterial, Humans, Molecular Sequence Data, Sequence Analysis, DNA, Synteny, Syphilis, Treponema pallidum, Yaws
Abstract

BACKGROUND: The yaws treponemes, Treponema pallidum ssp. pertenue (TPE) strains, are closely related to syphilis causing strains of Treponema pallidum ssp. pallidum (TPA). Both yaws and syphilis are distinguished on the basis of epidemiological characteristics, clinical symptoms, and several genetic signatures of the corresponding causative agents.METHODOLOGY/PRINCIPAL FINDINGS: To precisely define genetic differences between TPA and TPE, high-quality whole genome sequences of three TPE strains (Samoa D, CDC-2, Gauthier) were determined using next-generation sequencing techniques. TPE genome sequences were compared to four genomes of TPA strains (Nichols, DAL-1, SS14, Chicago). The genome structure was identical in all three TPE strains with similar length ranging between 1,139,330 bp and 1,139,744 bp. No major genome rearrangements were found when compared to the four TPA genomes. The whole genome nucleotide divergence (d(A)) between TPA and TPE subspecies was 4.7 and 4.8 times higher than the observed nucleotide diversity (π) among TPA and TPE strains, respectively, corresponding to 99.8% identity between TPA and TPE genomes. A set of 97 (9.9%) TPE genes encoded proteins containing two or more amino acid replacements or other major sequence changes. The TPE divergent genes were mostly from the group encoding potential virulence factors and genes encoding proteins with unknown function.CONCLUSIONS/SIGNIFICANCE: Hypothetical genes, with genetic differences, consistently found between TPE and TPA strains are candidates for syphilitic treponemes virulence factors. Seventeen TPE genes were predicted under positive selection, and eleven of them coded either for predicted exported proteins or membrane proteins suggesting their possible association with the cell surface. Sequence changes between TPE and TPA strains and changes specific to individual strains represent suitable targets for subspecies- and strain-specific molecular diagnostics.

DOI10.1371/journal.pntd.0001471
Alternate JournalPLoS Negl Trop Dis
PubMed ID22292095
PubMed Central IDPMC3265458
Grant ListR01 DA013759 / DA / NIDA NIH HHS / United States
R03 AI69107 / AI / NIAID NIH HHS / United States
R01 AI049252 / AI / NIAID NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
R01 AI49252 / AI / NIAID NIH HHS / United States
R03 AI069107 / AI / NIAID NIH HHS / United States
R01 DE12488 / DE / NIDCR NIH HHS / United States
R01 DE13759 / DE / NIDCR NIH HHS / United States
R01 EY013759 / EY / NEI NIH HHS / United States