Study of bacterial pathogenicity evolution by whole genome sequence comparison

• Project/Area Number: 24790412
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bacteriology (including Mycology)
• Research Institution: The University of Tokyo
• Principal Investigator: FURUTA Yoshikazu 東京大学, 新領域創成科学研究科, 特任助教 (40613667)
• Project Period (FY): 2012-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2013: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: ゲノム比較解析 / ピロリ菌 / 次世代シークエンサー / ゲノム再編 / de novo assembly / Mate-pairライブラリ / ゲノム進化

Research Abstract

We developed a method to sequence a whole genome sequence of Helicobacter pylori in high fidelity and high speed manner by utilizing next generation sequencing technology. We adopted this method to 30 strains of East Asian H. pylori strains and confirmed the following East Asian specific characters: (i) duplication of outer membrane protein coding gene oipA, (ii) inactivation of molybdenum related protein coding genes, (iii) 6 positions for genome inversion.

Research Products

• [Journal Article] Chromosome painting in silico in a bacterial species reveals fine population structure (2013)
  • Author(s): Koji Yahara, Ynshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
  • Journal Title: Molecular Biology and Evolution Volume: 30(6) Issue: 6 Pages: 1454-64
  • DOI: 10.1093/molbev/mst055
  • Peer Reviewed / Open Access
• [Journal Article] Large variations in bacterial ribosomal RNA genes. (2012)
  • Author(s): K Lim, Y Furuta, I Kobayashi
  • Journal Title: Mol. Biol. Evol Volume: 29(10) Issue: 10 Pages: 2937-2948
  • DOI: 10.1093/molbev/mss101
  • Peer Reviewed
• [Journal Article] Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species (2012)
  • Author(s): K Yahara, et al., I Kobayashi
  • Journal Title: Genome Biol. Evol Volume: 4(5) Issue: 5 Pages: 628-640
  • DOI: 10.1093/gbe/evs043
  • Peer Reviewed
• [Journal Article] Movement of DNAsequence recognition domains between non-orthologous proteins (2012)
  • Author(s): Y Furuta, I Kobayashi
  • Journal Title: Nucleic AcidsRes Volume: 40(18) Issue: 18 Pages: 9218-9232
  • DOI: 10.1093/nar/gks681
  • Peer Reviewed
• [Journal Article] Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution. (2012)
  • Author(s): Yoshikazu Furuta, Ichizo Kobayashi
  • Journal Title: Mobile Genetic Elements Volume: 2(6) Issue: 6 Pages: 292-296
  • DOI: 10.4161/mge.23371
  • Peer Reviewed
• [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure (2014)
  • Author(s): Koji Yahara, Yoshikazu Furuta, Masahira Hattori, Ichizo Kobayashi
  • Organizer: 第87回日本細菌学会総会
  • Place of Presentation: タワーホール船堀、東京都
  • Year and Date: 2014-03-26
• [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure (2014)
  • Author(s): Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
  • Organizer: 第8回日本ゲノム微生物学会年会
  • Place of Presentation: 東京農業大学、東京都
  • Year and Date: 2014-03-07
• [Presentation] 種内集団構造のインシリコ染色体ペインティングによる解明 (2013)
  • Author(s): 矢原耕史、古田芳一、大島健志朗、吉田優、東健、服部正平、内山郁夫、小林一三
  • Organizer: 日本遺伝学会第85回大会
  • Place of Presentation: 慶應義塾大学、神奈川県
  • Year and Date: 2013-09-21
• [Presentation] 種内集団構造のインシリコ染色体ペインティングによる解明 (2013)
  • Author(s): 矢原耕史、古田芳一、大島健志朗、吉田優、東健、服部正平、内山郁夫、小林一三
  • Organizer: 日本進化学会第15回大会
  • Place of Presentation: 茨城大学、茨城県
  • Year and Date: 2013-08-29
• [Presentation] 種内集団構造のインシリコ染色体ペインティングによる解明 (2013)
  • Author(s): 矢原耕史、古田芳一、大島健志朗、吉田優、東健、服部正平、内山郁夫、小林一三
  • Organizer: 日本進化学会第15回大会
  • Place of Presentation: 筑波大学、茨城県
• [Presentation] 種内集団構造のインシリコ染色体ペインティングによる解明 (2013)
  • Author(s): 矢原耕史、古田芳一、大島健志朗、吉田優、東健、服部正平、内山郁夫、小林一三
  • Organizer: 日本遺伝学会第85回大会
  • Place of Presentation: 慶応義塾大学、神奈川県
• [Presentation] DNA配列認識ドメインの非オーソロガス遺伝子間の移動 (2013)
  • Author(s): 古田芳一、小林一三
  • Organizer: 第86回日本細菌学会総会
  • Place of Presentation: 幕張メッセ、千葉県
• [Presentation] DNA配列認識ドメインの非オーソロガス遺伝子間の移動 (2013)
  • Author(s): 古田芳一、小林一三
  • Organizer: 第7回日本ゲノム微生物学会年会
  • Place of Presentation: 長浜バイオ大学、滋賀県
• [Presentation] Epigenome evolution―Two mechanisms in alteration of DNA sequence recognition domains in restriction-modification systems. (2012)
  • Author(s): Yoshikazu Furuta, Ichizo Kobayashi
  • Organizer: Bacteria, Archaea & Phages
  • Place of Presentation: Cold Spring Harbor, New York, US
• [Presentation] DNA配列認識ドメインの非オーソロガス遺伝子間の移動 (2012)
  • Author(s): 古田芳一、小林一三
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: マリンメッセ福岡、福岡県
• [Presentation] ピロリ菌CagA発がんタンパクのDNA組換えによる進化 (2012)
  • Author(s): 古田芳一、小林一三
  • Organizer: 第18回日本ヘリコバクター学会学術集会
  • Place of Presentation: 岡山コンベンションセンター、岡山県
• [Book] Bacterial Integrative Mobile Genetic Elements (2013)
  • Author(s): Yoshikazu Furuta, Ichizo Kobayashi.
  • Total Pages: 336
  • Publisher: Restriction-modification systems as mobile epigenetic elements.