Determination of the genome sequence of Porphyromonas glnglvalls strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. glnglvalls

Mariko Naito, Hideki Hirakawa, Atsushi Yamashita, Naoya Ohara, Mikio Shoji, Hideharu Yukitake, Keisuke Nakeyama, Hidehiro Toh, Fuminobu Yoshimura, Satoru Kuhara, Masahira Hattori, Tetsuya Hayashi, Koji Nakayama

Research output: Contribution to journalArticle

154 Citations (Scopus)

Abstract

The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MYTiPgRS (MITE of P gingivalis with Repeating Sequences).

Original languageEnglish
Pages (from-to)215-225
Number of pages11
JournalDNA Research
Volume15
Issue number4
DOIs
Publication statusPublished - 2008
Externally publishedYes

Fingerprint

Porphyromonas
Porphyromonas gingivalis
Sequence Analysis
Genome
DNA Transposable Elements
Gram-Negative Anaerobic Bacteria
Inverted Repeat Sequences
Interspersed Repetitive Sequences
Chronic Periodontitis
Subcutaneous Tissue
Operon
Transfer RNA
Abscess
Genes
Proteins

Keywords

  • Conjugative transposon
  • Genome rearrangement
  • MITE
  • Porpnyromonas gingivalis
  • Whole genome sequence

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Determination of the genome sequence of Porphyromonas glnglvalls strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. glnglvalls. / Naito, Mariko; Hirakawa, Hideki; Yamashita, Atsushi; Ohara, Naoya; Shoji, Mikio; Yukitake, Hideharu; Nakeyama, Keisuke; Toh, Hidehiro; Yoshimura, Fuminobu; Kuhara, Satoru; Hattori, Masahira; Hayashi, Tetsuya; Nakayama, Koji.

In: DNA Research, Vol. 15, No. 4, 2008, p. 215-225.

Research output: Contribution to journalArticle

Naito, M, Hirakawa, H, Yamashita, A, Ohara, N, Shoji, M, Yukitake, H, Nakeyama, K, Toh, H, Yoshimura, F, Kuhara, S, Hattori, M, Hayashi, T & Nakayama, K 2008, 'Determination of the genome sequence of Porphyromonas glnglvalls strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. glnglvalls', DNA Research, vol. 15, no. 4, pp. 215-225. https://doi.org/10.1093/dnares/dsn013
Naito, Mariko ; Hirakawa, Hideki ; Yamashita, Atsushi ; Ohara, Naoya ; Shoji, Mikio ; Yukitake, Hideharu ; Nakeyama, Keisuke ; Toh, Hidehiro ; Yoshimura, Fuminobu ; Kuhara, Satoru ; Hattori, Masahira ; Hayashi, Tetsuya ; Nakayama, Koji. / Determination of the genome sequence of Porphyromonas glnglvalls strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. glnglvalls. In: DNA Research. 2008 ; Vol. 15, No. 4. pp. 215-225.
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AU - Hirakawa, Hideki

AU - Yamashita, Atsushi

AU - Ohara, Naoya

AU - Shoji, Mikio

AU - Yukitake, Hideharu

AU - Nakeyama, Keisuke

AU - Toh, Hidehiro

AU - Yoshimura, Fuminobu

AU - Kuhara, Satoru

AU - Hattori, Masahira

AU - Hayashi, Tetsuya

AU - Nakayama, Koji

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N2 - The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MYTiPgRS (MITE of P gingivalis with Repeating Sequences).

AB - The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MYTiPgRS (MITE of P gingivalis with Repeating Sequences).

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