Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83

Abstract

The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron and B. fragilis. Outside of the CFB phyla the most similar genome to P. gingivalis is that of Chlorobium tepidum, supporting the previous phylogenetic studies that indicated that the Chlorobia and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that P. gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.

FIG. 1.

Circular representation of the P. gingivalis genome. The outer circle shows the predicted coding regions on the plus strand color-coded by role categories as follows: violet, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups, and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; light gray, energy metabolism; magenta, fatty acid and phospholipid metabolism; pink, protein synthesis and fate; orange, purines, pyrimidines, nucleosides, and nucleotides; olive, regulatory functions and signal transduction; dark green, transcription; teal, transport and binding proteins; gray, unknown function; salmon, other categories; blue, hypothetical proteins. The second circle shows the predicted coding regions on the minus strand. The third circle presents the χ² analysis of atypical nucleotide composition; χ² values of >600 are indicated in red. The fourth circle shows the %G+C. The fifth circle shows atypical nucleotide composition (GC skew). The sixth circle shows the IS elements, indicated by color as follows: orange, ISPg1; light green, ISPg2; magenta, ISPg3; cyan, ISPg4; brown, ISPg5; gold, ISPg6; blue-green, ISPg7; pink, ISPg8; and violet, ISPg9; salmon, ISPg10; olive, ISPg11. The seventh circle shows MITE239 (magenta), MITE700 (cyan), and MITE464 (black). The eighth circle shows Tn4555 (blue), CTn (red), and other transposable elements (green). The ninth circle shows tRNA (green), rRNA (black), and sRNA (red).

FIG.2.

Overview of metabolism and transport in P. gingivalis. Primary substrates for energy metabolism are capitalized and underlined. End products of fermentation are highlighted by yellow boxes. Transporters are grouped by substrate specificity and indicated by color as follows: inorganic cations (green), inorganic anions (magenta), organic nutrients (yellow), and drug efflux and other (black). Arrows indicate direction of transport for substrates (and coupling ions, where appropriate).