Genome Analysis of Treponema pallidum subsp. pallidum and subsp. pertenue Strains: Most of the Genetic Differences Are Localized in Six Regions

The genomes of eight treponemes including T. p. pallidum strains (Nichols, SS14, DAL-1 and Mexico A), T. p. pertenue strains (Samoa D, CDC-2 and Gauthier), and the Fribourg-Blanc isolate, were amplified in 133 overlapping amplicons, and the restriction patterns of these fragments were compared. The approximate sizes of the genomes investigated based on this whole genome fingerprinting (WGF) analysis ranged from 1139.3–1140.4 kb, with the estimated genome sequence identity of 99.57–99.98% in the homologous genome regions. Restriction target site analysis, detecting the presence of 1773 individual restriction sites found in the reference Nichols genome, revealed a high genome structure similarity of all strains. The unclassified simian Fribourg-Blanc isolate was more closely related to T. p. pertenue than to T. p. pallidum strains. Most of the genetic differences between T. p. pallidum and T. p. pertenue strains were accumulated in six genomic regions. These genome differences likely contribute to the observed differences in pathogenicity between T. p. pallidum and T. p. pertenue strains. These regions of sequence divergence could be used for the molecular detection and discrimination of syphilis and yaws strains

Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay

Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies

Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence

Spirochete Treponema pallidum ssp. pertenue (TPE) is the causative agent of yaws while strains of Treponema pallidum ssp. pallidum (TPA) cause syphilis. Both yaws and syphilis are distinguished on the basis of epidemiological characteristics and clinical symptoms. Neither treponeme can reproduce outside the host organism, which precludes the use of standard molecular biology techniques used to study cultivable pathogens. In this study, we determined high quality whole genome sequences of TPE strains and compared them to known genetic information for T. pallidum ssp. pallidum strains. The genome structure was identical in all three TPE strains and also between TPA and TPE strains. The TPE genome length ranged between 1,139,330 bp and 1,139,744 bp. The overall sequence identity between TPA and TPE genomes was 99.8%, indicating that the two pathogens are extremely closely related. A set of 34 TPE genes (3.5%) encoded proteins containing six or more amino acid replacements or other major sequence changes. These genes more often belonged to the group of genes with predicted virulence and unknown functions suggesting their involvement in infection differences between yaws and syphilis

Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry

YesBackground. The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. Methodology/Principal Findings. To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. Conclusions. This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.This work was supported by the grants from the Flanders Research Foundation, SOFI-B Grant to CRK, http://www.fwo.be/, a Public Health Service Grant from the National Institutes of Health to CEC, (grant # AI-051334), https://www.nih.gov/ and a grant from the Grant Agency of the Czech Republic to DS and MS (P302/12/0574, GP14-29596P), https:// gacr.cz/

Distribution of identified errors in the original TPA Nichols and TPA SS14 genome sequences.

<p>Note that the chromosomal positions of identified errors are highly similar in both genomes as a result of the CGS sequencing approach used for sequencing the SS14 genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074319#pone.0074319-Matjkov1" target="_blank">[9]</a>.</p

Unrooted trees constructed from whole genome sequences of TPA strains.

<p>Trees were constructed using the Neighbor-Joining method using the Tamura-Nei genetic distance model and 1,000 bootstrap replicates. The numbers above the branches show bootstrap support and the bar scale represents 0.0001 substitutions per target site. A. A tree constructed from the alignment of genomes from TPA strains Chicago (CP001752.1), DAL-1 (CP003115.1) and Mexico A (CP003064.1) with original versions of whole genome sequences of TPA Nichols (AE000520.1) and SS14 (CP000805.1). B. A tree constructed from alignment of genomes from TPA strains Chicago (CP001752.1), DAL-1 (CP003115.1) and Mexico A (CP003064.1) with the improved whole genome sequences of TPA Nichols-RS (CP004010.2) and SS14-RS (CP004011.1).</p

Effects of error correction on the improved TPA Nichols-RS genome with respect to comparisons with other TPA strains.

<p>The left part of the table shows former number of differences between the original TPA Nichols genome (AE000520.1) and other TPA genomes, the right part of the table shows verified number of differences between the improved TPA Nichols genome (CP004010.2) and other TPA genomes. Numbers in brackets show the percentage of verified differences between the improved TPA Nichols genome and other genomes compared to numbers observed during the comparison of the original Nichols genome and other TPA genomes. Because of high sequence diversities, <i>tprD</i> and <i>tprK</i> were excluded from the analyses.</p><p>sub, substitution; in, insertion; del, deletion.</p

Effects of error correction on the improved TPA SS14-RS genome with respect to other TPA strains.

<p>The left part of the table shows former number of differences between the original TPA SS14 genome (CP000805.1) and other TPA genomes, the right part of the table shows verified number of differences between the improved TPA SS14 genome (CP004011.1) and other TPA genomes. Numbers in brackets show the percentage of verified differences between the improved TPA SS14 genome and other genomes compared to numbers observed during the comparison of the original SS14 genome and other TPA genomes. Because of high sequence diversities, <i>tprD</i> and <i>tprK</i> were excluded from the analyses. Please note that the number of sequence differences between TPA SS14 and Nichols genomes increased after error correction.</p><p>sub, substitution; in, insertion; del, deletion.</p