We'd like to understand how you use our websites in order to improve them. Register your interest. Treponema pallidum strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant woman in the secondary stage of syphilis. Here we describe the 1,, bp long genome of T.
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We'd like to understand how you use our websites in order to improve them. Register your interest. Treponema pallidum strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant woman in the secondary stage of syphilis.
Here we describe the 1,, bp long genome of T. In rabbits, strain DAL-1 replicated better than the T. The comparison of the complete DAL-1 genome sequence with the Nichols sequence revealed a list of genetic differences that are potentially responsible for the increased rabbit virulence of the DAL-1 strain.
Treponema pallidum is an uncultivable human pathogen causing the sexually transmitted disease, syphilis. Until now, three syphilis causing strains of T. The data indicates that pathogenic treponemes are extremely closely related and small genetic changes can result in profound changes in pathogenesis and host range [ 6 ]. The accumulation of genomic data provides new insights into the pathogenesis of treponemal diseases and into the evolution of pathogenic treponemes and brings new opportunities for molecular diagnostics of syphilis [ 6 ].
In rabbits, the DAL-1 strain replicated better than the Nichols strain [ 1 , 7 ]. Therefore, the genome sequencing of the DAL-1 strain and its comparison with the Nichols sequence should reveal a list of genetic differences that are potentially responsible for increased rabbit virulence of the DAL-1 strain. Treponema pallidum , previously known as Spirochaeta pallida [ 8 ], is an etiologic agent of syphilis.
Based on DNA hybridization studies [ 9 ], Treponema pallidum and yaws [ 10 ] causing Treponema pertenue were found to be genetically indistinguishable. The genus Treponema belongs to the family Spirochaetaceae see Table 1.
Genetic relatedness of T. The bar scale represents the number of nucleotide substitutions per 1 nt site. The tree was generated using tree-builder, which is available from the Ribosomal Database project [ 28 ], using the Weighbor weighted neighbor-joining algorithm [ 29 ] and the Jukes-Cantor distance correction [ 30 ]. A Spirochaeta zuelzerae type strain was used as the out-group.
This movement is powered by endoflagella located in the periplasmic space. The cell wall is composed of a cytoplasmic membrane, a thin peptidoglycan layer, a periplasmic space with endoflagella, and an outer membrane [ 31 ]. Cultivation in tissue cultures resulted in approximately fold multiplication [ 32 , 33 ]. Stable propagation of T. As a consequence of its small genome, T. Most essential macromolecules are taken up from the host by a number of transport proteins with broad substrate specificity.
In total, genes of T. Susceptibility of T. No skin lesions were detected following injections of penicillin G: 0. Unlike penicillin, macrolide regimens have a risk of treatment failure due to chromosomally encoded resistance in T. This organism was selected for sequencing on the basis of its increased virulence in rabbits compared to the Nichols strain [ 1 ]. The details of the project are summarized in Table 2.
Strain DAL-1 was grown in rabbit testis, treponemes were extracted and purified from testicular tissue using Hypaque gradient centrifugation [ 1 , 39 ]. Chromosomal DNA was prepared as described previously [ 1 ].
Pyrosequencing reads , raw reads of total read length 51,, bp showing sequence similarity to the Nichols genome sequence [ 1 ] were assembled using the Newbler assembler version 1. Gaps between contigs were closed using Sanger sequencing. The PCR products were sequenced using amplification and, when required, internal primers.
The resulting complete genome sequence of strain DAL-1 was considered to be a draft sequence. Additional Illumina sequencing was applied to improve genome sequencing accuracy and the complete DAL-1 genome sequence was compiled from these data. A total of 2,, raw Illumina reads total length of ,, bp were assembled, using the Velvet 0.
Out of these contigs, showed sequence similarities to the T. Each DAL-1 region not sequenced by Illumina and containing differences from the Nichols genome was resequenced using the Sanger method. In addition, all other discrepancies between the complete DAL-1 genome sequence and the Nichols genome sequence were resolved using Sanger sequencing of both DAL-1 and Nichols strains.
Altogether, 15 errors were identified in the 1, kb Illumina resequenced region, indicating that the complete DAL-1 genome sequence contained 1 error per 73 kbp. Therefore, the final, corrected, strain DAL-1 genome sequence has an error rate less than 10 These coordinates were adapted and recalculated. Newly predicted genes were identified using the GeneMark and Glimmer programs.
In most cases, the original locus tag values of annotated genes were preserved in the DAL-1 orthologs. Newly predicted genes in the DAL-1 genome were named according to the preceding gene with a letter suffix e. The genome consists of a single circular DNA chromosome, 1,, bp in length. Out of the 1, predicted genes, 1, genes were protein-coding. A set of 54 genes coded for RNA and 9 were identified as pseudogenes. The majority of the protein-coding genes Graphical circular map of the T.
However, the tpr K gene was found variable within the DAL-1 strain and therefore the reported 4 nt changes do not refer to the variable tpr K region [ 43 ]. Tpr proteins are known virulence factors in treponemes [ 43 — 48 ] and the changes in the primary sequence of the protein may be of importance in increased DAL-1 rabbit virulence. In addition to the changes in the above mentioned genes, additional 31 nt changes were found throughout the genome 6 single nucleotide deletions, 3 single nucleotide insertions, 16 single nucleotide substitutions, one 2-nt deletion and one 4-nt deletion.
All the indels with exception of the 4-nt deletion were found to be located in the G or C homopolymers. Since G homopolymers, of variable length, affected gene expression rates of tpr genes [ 49 ], these differences may change the gene expression pattern in the DAL-1 genome. All of the above listed genes and all the changes in the intergenic regions potentially affecting gene expression rates should be considered as potential reason for the observed increased virulence in rabbits.
Complete genome sequence of Treponema pallidum , the syphilis spirochete. Science ; — Complete genome sequence of Treponema pallidum ssp pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol ; 8 Complete genome sequence and annotation of the Treponema pallidum subsp.
J Bacteriol ; — Whole Genome Sequences of Three Treponema pallidum ssp. Complete genome sequence of Treponema paraluiscuniculi , strain Cuniculi A: The loss of infectivity to humans is associated with genome decay. Genetic diversity in Treponema pallidum : Implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Infect Genet Evol ; 12 — Identification of Treponema pallidum in amniotic fluid and fetal blood from pregnancies complicated by congenital syphilis.
Obstet Gynecol ; 78 — Schaudin FR, Hoffmann E. Arb K Gesund ; 22 — Google Scholar. Genetic relationship between Treponema pallidum and Treponema pertenue , two noncultivable human pathogens. Castellani A. Further observations on parangi Yaws. BMJ ; 2 — The minimum information about a genome sequence MIGS specification.
Nat Biotechnol ; 26 — The Road Map to the Manual. Draft taxonomic outline of the Bacteroidetes , Planctomycetes, Chlamydiae, Spirochaetes , Fibrobacteres, Fusobacteria, Acidobacteria , Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively.
Opinion Int J Syst Evol Microbiol ; 55 — Buchanan RE. The Primary Subdivisions of the Schizomycetes. J Bacteriol ; 2 — Approved Lists of Bacterial Names. Int J Syst Bacteriol ; 30 — Swellengrebel NH. Ann Inst Pasteur Paris ; 21 — Schaudinn F. Zur Kenntnis der Spirochaete pallida. Dtsch Med Wochenschr ; 31 Smibert RM. Genus III. Treponema Schaudinn ,
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Complete Genome Sequence of Treponema Pallidum, the Syphilis Spirochete
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Complete genome sequence of Treponema pallidum, the syphilis spirochete.
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Complete genome sequence of Treponema pallidum, the syphilis spirochete
Metrics details. Syphilis spirochete Treponema pallidum ssp. Increasing rates of new syphilis cases per year have been observed recently. The genome of the SS14 strain was sequenced to high accuracy by an oligonucleotide array strategy requiring hybridization to only three arrays Comparative Genome Sequencing, CGS. Gaps in the resulting sequence were filled with targeted dideoxy-terminators DDT sequencing and the sequence was confirmed by whole genome fingerprinting WGF.
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