Seshadri, R. et al. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc. Natl Acad. Sci. USA 101, 5646-5651

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 05/2004; 101(15):5646-51. DOI: 10.1073/pnas.0307639101
Source: PubMed


We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.

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    • "A search of the T. denticola 35405 genome sequence (Seshadri et al., 2004) with a consensus S. aureus Lyt- TR recognition sequence did not detect hits with significant identity. In light of the phylogenetic divergence between spirochetes and gram-positive bacteria this is not entirely surprising. "
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    ABSTRACT: Treponema denticola is an oral spirochete and periopathogen that transitions from low abundance in healthy subgingival crevices to high abundance in periodontal pockets. The T. denticola response regulator AtcR harbors the relatively rare, LytTR DNA binding domain. LytTR domain containing response regulators control critical transcriptional responses required for environmental adaptation. Using a multi-step bioinformatics approach, 26 strong lytTR recognition motifs were identified in the genome of T. denticola strain 35405. Electrophoretic mobility shift assays (EMSA) demonstrated that AtcR binds to these recogniation motifs. High specificity-high affinity complexes formed with phosphorylated AtcR. The LytTR recognition sequences were found to exist in three distinct promoter architectures designated as LytTR1, LytTR2 and LytTR3 promoters. LytTR1 and LytTR2 promoters harbor σ(54) binding sites. The functional diversity of the proteins encoded by the putative AtcR regulon suggests that AtcR sits at the top of a regulatory cascade that plays a central role in facilitating T. denticola=s ability to adapt to changing environmental conditions and thrive in periodontal pockets. This article is protected by copyright. All rights reserved.
    Full-text · Article · May 2014 · Molecular Oral Microbiology
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    • "Overgrowth of bacteria from the species T. denticola, Porphyromonas gingivalis, and Tannerella forsythia, often collectively referred to as the “red complex”, is believed to be associated with the clinical progression of periodontitis [7]. The genome sequence of T. denticola strain ATCC 35405 was released in 2004 [8], providing a resource for identifying virulence factors. "
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    ABSTRACT: Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.
    Full-text · Article · Aug 2013 · PLoS ONE
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    • "The phylum Spirochaetes consists of a large group of motile bacteria which are widespread in the environment and are highly prevalent disease causing agents (Seshadri et al., 2004; Paster, 2011a). The members of this phylum share a distinguishing morphological feature, the endoflagella, a special class of flagella that folds back into the cell and remains within the periplasm (Li et al., 2008). "
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    ABSTRACT: The Spirochaetes species cause many important diseases including syphilis and Lyme disease. Except for their containing a distinctive endoflagella, no other molecular or biochemical characteristics are presently known that are specific for either all Spirochaetes or its different families. We report detailed comparative and phylogenomic analyses of protein sequences from Spirochaetes genomes to understand their evolutionary relationships and to identify molecular signatures for this group. These studies have identified 38 conserved signature indels (CSIs) that are specific for either all members of the phylum Spirochaetes or its different main clades. Of these CSIs, a 3 aa insert in the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular marker for this phylum. Seven, six, and five CSIs in different proteins are specific for members of the families Spirochaetaceae, Brachyspiraceae, and Leptospiraceae, respectively. Of the 19 other identified CSIs, 3 are uniquely shared by members of the genera Sphaerochaeta, Spirochaeta, and Treponema, whereas 16 others are specific for the genus Borrelia. A monophyletic grouping of the genera Sphaerochaeta, Spirochaeta, and Treponema distinct from the genus Borrelia is also strongly supported by phylogenetic trees based upon concatenated sequences of 22 conserved proteins. The molecular markers described here provide novel and more definitive means for identification and demarcation of different main groups of Spirochaetes. To accommodate the extensive genetic diversity of the Spirochaetes as revealed by different CSIs and phylogenetic analyses, it is proposed that the four families of this phylum should be elevated to the order level taxonomic ranks (viz. Spirochaetales, Brevinematales ord. nov., Brachyspiriales ord. nov., and Leptospiriales ord. nov.). It is further proposed that the genera Borrelia and Cristispira be transferred to a new family Borreliaceae fam. nov. within the order Spirochaetales.
    Full-text · Article · Jul 2013 · Frontiers in Microbiology
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