Mechanisms underlying target specificity changes of DNA methyltransferase, and its application to epigenome breeding

• Project/Area Number: 25850049
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Applied microbiology
• Research Institution: The University of Tokyo
• Principal Investigator: Yano Hirokazu 東京大学, 新領域創成科学研究科, 特任助教 (20646773)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2013: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
• Keywords: エピゲノム / トランスクリプトーム / DNAメチル化 / ピロリ菌 / メチローム / 制限修飾系 / 酸化ストレス / エピジェネティクス

Outline of Final Research Achievements

We obtained basic knowledge that contributes to ‘epigenome breeding’ wherein we manipulate bacterial phenotypes using transcriptome-modulation capability of DNA methyltransferases. We demonstrated that a Type II DNA methyltranferase in a H.pylori strain contributes to adaptive phenotypes through gene regulation. Furthermore we found that it is possible to modulate transcriptome of E. coli by introducing sequence-specific DNA methyltransferase genes to E. coli.

Research Products

• [Journal Article] Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities (2015)
  • Author(s): Masaki Fukuyo, Toshiaki Nakano, Yingbiao Zhang, Yoshikazu Furuta, Ken Ishikawa, Miki Watanabe-Matsui, Hirokazu Yano, Takeshi Hamakawa, Hiroshi Ide, Ichizo Kobayashi
  • Journal Title: Nucleic Acids Research Volume: Vol. 43, No. 5 Issue: 5 Pages: 2841-2852
  • DOI: 10.1093/nar/gkv116
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Draft Genome Sequence of Pseudomonas moraviensis R28-S (2014)
  • Author(s): Samuel S. Hunter, Hirokazu Yano, Wesley Loftie-Eaton, Julie Hughes, Leen De Gelder, Pieter Stragier, Paul De Vos, Matthew L. Settles, and Eva M. Top
  • Journal Title: Genome Announcement Volume: 2 Issue: 1
  • DOI: 10.1128/genomea.00035-14
  • Peer Reviewed / Open Access
• [Journal Article] Diverse broad-host-range plasmids from freshwater carry few accessory genes (2013)
  • Author(s): Brown C.J., Sen D., Yano H., Bauer M.L., Rogers L.M., Van der Auwera G.A., and Top E.M.
  • Journal Title: Applied and Environmental Microbiology Volume: 79 Issue: 24 Pages: 76847695-76847695
  • DOI: 10.1128/aem.02252-13
  • Peer Reviewed
• [Journal Article] Diversification of host range within the IncP-1 plasmid group (2013)
  • Author(s): Yano, H., Rogers, L.M., Molly K., Heuer, H., Smalla, K., Brown C.J., and Top E.M.
  • Journal Title: Microbiology Volume: 159 Issue: Pt_11 Pages: 23032315-23032315
  • DOI: 10.1099/mic.0.068387-0
  • Peer Reviewed
• [Presentation] Network of DNA methyltransferase behind the adaptive phenotype in Helicobacteri pylori (2015)
  • Author(s): Hirokazu Yano, Zobaidul M. Alam, Emiko Rimbara, Yoshikazu Furuta, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: Gordon Research Seminar, Microbial Population Biology
  • Place of Presentation: Andover, NH, USA
  • Year and Date: 2015-07-18
  • Int'l Joint Research
• [Presentation] 特定のエピゲノム状態がピロリ菌ストレス耐性を支配する (2015)
  • Author(s): 矢野大和、Zobaidu M. Alam、林原絵美子、古田芳一、鈴木穰、菅野純夫、柴山恵吾、小林一三
  • Organizer: 第21回 ヘリコバクター学会
  • Place of Presentation: 神戸ポートピアホテル
  • Year and Date: 2015-06-26
• [Presentation] 特定のエピゲノム状態がピロリ菌ストレス耐性を支配する (2015)
  • Author(s): 矢野大和、Zobaidu M. Alam、林原絵美子、古田芳一、鈴木穰、菅野純夫、柴山恵吾、小林一三
  • Organizer: 日本ゲノム微生物学会
  • Place of Presentation: 神戸大学六甲第２キャンパス
  • Year and Date: 2015-03-06 – 2015-03-08
• [Presentation] Plasmid-host adapatation through fitness cost ameriolation of a plasmid replication protein (2014)
  • Author(s): Hirokazu Yano, Ktarznya Wegrzyn, Wesley Loftie-Eaton, Igor Konieczny, Eva M. Top
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2014-11-27
• [Presentation] 複製開始タンパク質のフィットネスコストの改善を伴うプラスミドの宿主適応 (2014)
  • Author(s): 矢野大和，Eva M Top
  • Organizer: ゲノム微生物学会 若手の会
  • Place of Presentation: ろうきん研修所富士センター
  • Year and Date: 2014-09-27 – 2014-09-28
• [Presentation] Diverse broad-host-range plasmids from freshwater carry few accessory genes (2014)
  • Author(s): Celeste Brown, Diya Sen, Hirokazu Yano, Matthew Bauer, Linda Rogers, Geraldine Van der Auwera, Eva Top
  • Organizer: 日本ゲノム微生物学会
  • Place of Presentation: 東京農業大学 世田谷キャンパス
• [Presentation] Diversification of host range within the IncP-1 plasmid group
  • Author(s): Hirokazu Yano, Linda Rogers, Molly Knox, Heuer Holger, Kornelia Smalla, Celeste Brown C, and Eva Top
  • Organizer: 日本分子生物学会
  • Place of Presentation: 神戸国際会議場 神戸国際展示場
• [Remarks] Hirokazu Yano
  • URL: https://sites.google.com/site/hymyresearch/
• [Remarks] Hirokazu Yano
  • URL: https://sites.google.com/site/hymyresearch/