Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.
Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.
复制标题
三个treponema pallidum ssp的全基因组序列。 Pertenue菌株：小于基因组序列的0.2％的YAW和梅毒treponemes差异。
DOI：
10.1371/journal.pntd.0001471
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发表时间：
2012-01
影响因子：
3.8
通讯作者：
Smajs D
中科院分区：
文献类型：
--
作者：
Cejková 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
雅司病密螺旋体，梅毒螺旋体ssp.梅毒螺旋体（Treponema pallidum ssp.）苍白球（TPA）。雅司病和梅毒都是根据流行病学特征、临床症状和相应病原体的几种遗传特征来区分的。为了精确定义TPA和TPE之间的遗传差异，使用下一代测序技术确定了三种TPE菌株（Samoa D，CDC-2，Gauthier）的高质量全基因组序列。将TPE基因组序列与TPA菌株（Nichols、DAL-1、SS 14、芝加哥）的四个基因组进行比较。基因组结构在所有三种TPE菌株中是相同的，具有相似的长度范围在1，139，330 bp和1，139，744 bp之间。与四个TPA基因组相比，没有发现主要的基因组重排。TPA和TPE亚种之间的全基因组核苷酸差异（dA）分别是TPA和TPE菌株之间观察到的核苷酸多样性（π）的4.7和4.8倍，对应于TPA和TPE基因组之间99.8%的同一性。一组97个（9.9%）TPE基因编码的蛋白质含有两个或更多个氨基酸置换或其他主要序列变化。TPE趋异基因主要来自编码潜在毒力因子的基因和编码功能未知蛋白的基因。假设的基因，具有遗传差异，始终发现TPE和TPA菌株之间的候选人梅毒螺旋体毒力因子。根据阳性选择预测了17个TPE基因，其中11个编码预测的输出蛋白或膜蛋白，表明它们可能与细胞表面相关。TPE和TPA菌株之间的序列变化以及对单个菌株特异性的变化代表了亚种和菌株特异性分子诊断的合适靶标。梅毒螺旋体亚种梅毒螺旋体（Treponema pallidum ssp.）梅毒（TPA）引起梅毒。雅司病和梅毒都是根据流行病学特征和临床症状来区分的。两种密螺旋体都不能在宿主生物体外繁殖，这排除了用于研究可培养病原体的标准分子生物学技术的使用。在这项研究中，我们确定了TPE菌株的高质量全基因组序列，并将其与已知的T。苍白球亚种苍白球菌株基因组结构在所有三种TPE菌株中以及TPA和TPE菌株之间是相同的。TPE基因组长度在1，139，330 bp和1，139，744 bp之间。TPA和TPE基因组之间的总体序列同一性为99.8%，表明这两种病原体非常密切相关。一组34个TPE基因（3.5%）编码的蛋白质含有6个或更多的氨基酸替换或其他主要序列的变化。这些基因更经常属于预测的毒力和未知功能的基因组，这表明它们参与了雅司病和梅毒之间的感染差异。
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. 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 (dA) 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. 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. 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.
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影响因子：
4.2
作者：
Coil DA;Vandersmissen L;Ginevra C;Jarraud S;Lammertyn E;Anné J
通讯作者：
Anné J
影响因子：
6.4
作者：
Cameron, CE;Lukehart, SA;Van Voorhis, WC
通讯作者：
Van Voorhis, WC
影响因子：
3.1
作者：
Cox, David L.;Luthra, Amit;Radolf, Justin D.
通讯作者：
Radolf, Justin D.
影响因子：
6.4
作者：
Centurion-Lara, A;Castro, C;Lukehart, SA
通讯作者：
Lukehart, SA
影响因子：
3.1
作者：
Citti, C;Kim, MF;Wise, KS
通讯作者：
Wise, KS