Genome Network Analysis in thermo-tolerant evolution of Escherichia coli

2010 Fiscal Year Final Research Report

• Project/Area Number: 20370092
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Evolutionary biology
• Research Institution: Osaka University
• Principal Investigator: YOMO Tetsuya Osaka University, 大学院・情報科学研究科, 教授 (00222399)
• Co-Investigator(Kenkyū-buntansha): KISHIMOTO Toshihiko 東邦大学, 理学部, 准教授 (90339200)
• Project Period (FY): 2008 – 2010
• Keywords: トランスクリプトーム解析 / プロテオーム解析 / 耐熱化機構 / 大腸菌

Research Abstract

For elucidation of the mechanism of evolution, we have developed thermo-tolerant E. coli and analyzed mutation of genome DNA, gene expression (transcriptome), and protein expression and thermo-stability (proteome) of several strains of E. coli through thermo-tolerant evolution process. Whole-genome sequence analysis revealed the transition from positive to neutral in mutation fixation, accompanied with a considerable escalation of spontaneous substitution rate in the late fitness recovery phase. Moreover, transcriptome analysis revealed transition from increase to convergence in fluctuation of gene expression, and proteome analysis revealed that no remarkable change in thermo-stability of expressed proteins.

Research Products

• [Journal Article] Transition frpositive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution. (2010)
  • Author(s): Toshihiko Kishimoto, Leo Iijima, Makoto Tatsumi, Naoaki Ono, Ayana Oyake, Tomomi Hashimoto, Moe Matsuo, Masato Okubo, Shingo Suzuki, Kotaro Mori, Akiko Kashiwagi, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo
  • Journal Title: PLoS Genetics. 6巻10 Pages: e1001164
  • Peer Reviewed
• [Journal Article] Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress. (2010)
  • Author(s): Takaaki Horinouchi, Kuniyasu Tamaoka, Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu
  • Journal Title: BMC Genomics. 11巻579 Pages: e579
  • Peer Reviewed
• [Journal Article] Quantifying epistatic interactions among the components constituting the protein translation system. (2009)
  • Author(s): Matsuura, T., Kazuta, Y., Aita, T., Adachi, J., Yomo, T.
  • Journal Title: Molecular Systems Biology 5巻297
  • Peer Reviewed
• [Journal Article] How selection affects phenotypic fluctuation. (2009)
  • Author(s): Ito, Y., Toyota, H., Kaneko, K., Yomo, T.
  • Journal Title: Molecular Systems Biology 5巻264
  • Peer Reviewed
• [Presentation] Genome-wide mutation and transcriptional reorganization in the thermal adaptive Escherichia coli from laboratory evolution (2010)
  • Author(s): Bei-Wen Ying, Kazuki Kitahara, Leo Ijima, Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Tetsuya Yomo
  • Organizer: BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会合同大会)
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2010-12-07
• [Presentation] Construction of high temperature genetic engineering system for thermo-tolerant E. coli (2010)
  • Author(s): Toshihiko Kishimoto, Saeko Shimada, Ayana Oyake, Tomomi Hashimoto, Tetsuya Yomo
  • Organizer: BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会合同大会)
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2010-12-07
• [Presentation] 複雑システムとしての生物の進化 (2010)
  • Author(s): 四方哲也
  • Organizer: 理研ASI細胞システムコロキウムシリーズI「理論生物学」鈴木梅太郎記念ホール
  • Place of Presentation: 理化学研究所和光キャンパス
  • Year and Date: 2010-12-03
• [Presentation] 細胞の個性と環境応答 (2010)
  • Author(s): 四方哲也
  • Organizer: JSME26(第26回日本微生物生態学大会)
  • Place of Presentation: 筑波大学
  • Year and Date: 2010-11-26
• [Presentation] 長期実験室内進化からみた大腸菌の変異と発現の変遷 (2010)
  • Author(s): 應〓文、北原和樹、飯島玲生、小野直亮、古澤力、鈴木真吾、岸本利彦、四方哲也
  • Organizer: 第12回日本進化学会大会
  • Place of Presentation: 東京工業大学大岡山キャンパス
  • Year and Date: 2010-08-03
• [Presentation] Biological Noise Induced Gene Production in Bacteria-a Universal Principle in the Adaptive Response to Starvation (2010)
  • Author(s): Bei-Wen Ying, Saburo Tsuru, Yuki Matsumoto, Yoshihiro Shimizu, Yoichiro Ito, Tetsuya Yomo
  • Organizer: ibio2010, Dalian Municipal Party Committee Hotel
  • Place of Presentation: China
  • Year and Date: 2010-07-25
• [Presentation] Constructive approach to proto-cellular life. (2010)
  • Author(s): 四方哲也
  • Organizer: UK-Japan Workshop on Synthetic Biology
  • Place of Presentation: British Embassy, Tokyo
  • Year and Date: 2010-01-21
• [Presentation] 大腸菌高温適応進化過程における細胞間相互作用の増殖速度への影響 (2009)
  • Author(s): 小宅綾菜、橋本智美、青柳美穂、岸本利彦、四方哲也
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2009-12-12
• [Presentation] Genome-wide analysis of thermal adaptive Escherichia coli from laboratory evolution. (2009)
  • Author(s): インベイウェン、北原和樹、飯島玲王、小野直亮、鈴木真吾、岸本利彦、古澤力、四方哲也
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2009-12-10
• [Presentation] Phenotypic fluctuation induced biological adaptation. (2009)
  • Author(s): Bei -Wen Ying, Yoichiro Ito, Yoshihiro Shimizu, Yuki Matsumoto, Junya Ichinose, Saburo Tsuru, Tetsuya Yomo
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: 徳島文理大学
  • Year and Date: 2009-10-30
• [Presentation] 大腸菌ゲノムの高温適応進化 (2009)
  • Author(s): 四方哲也
  • Organizer: 「細胞を創る」研究会2.0
  • Place of Presentation: 東京大学鉄門記念講堂
  • Year and Date: 2009-10-03
• [Presentation] Phenotypic fluctuation in experimental evolution. (2009)
  • Author(s): 四方哲也
  • Organizer: International Symposium on Complex System Biology
  • Place of Presentation: The University of Tokyo, Japan
  • Year and Date: 2009-09-30
• [Presentation] How Darwinian selection affects phenotypic fluctuation. (2009)
  • Author(s): 四方哲也
  • Organizer: 13th Evolutionary Biology Meeting at Marseilles
  • Place of Presentation: Marseilles, France
  • Year and Date: 2009-09-25
• [Presentation] 遺伝子発現揺らぎを用いた適応応答 (2009)
  • Author(s): 四方哲也
  • Organizer: 日本遺伝学会第81回大会
  • Place of Presentation: 信州大学
  • Year and Date: 2009-09-17
• [Presentation] 実験室内進化させた高温適応大腸菌のゲノムワイド解析 (2009)
  • Author(s): 應〓文、北原和樹、飯島玲生、小野直亮、鈴木真吾、岸本利彦、古澤力、四方哲也
  • Organizer: 第11回日本進化学会大会
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-09-04
• [Presentation] Constructive approach to proto-cellular life. (2009)
  • Author(s): 四方哲也
  • Organizer: Workshop OQOL'09 : Open Questions on the Origins of Life 2009
  • Place of Presentation: San Sebastian, Spain
  • Year and Date: 2009-05-21
• [Presentation] 耐熱性を進化させた大腸菌のゲノム変異の解析 (2008)
  • Author(s): 飯島玲生、小野直亮、鈴木真吾、岸本利彦、辰巳誠、森光太郎、インベイウェン、古澤力、四方哲也
  • Organizer: 第81回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2008-12-10
• [Presentation] Cellular fluctuation in protein concentration and its role on adaptive response (2008)
  • Author(s): Yomo, T., Tsuru, S., Ichinose, J., Kaneko, K., Ying, B.W.
  • Organizer: The 9th International Conference on Systems Biology.
  • Place of Presentation: Goteborg, Sweden
  • Year and Date: 2008-08-25
• [Presentation] 大腸菌を使った耐熱化実験進化系の中で出現した相互作用を中心とした現象の解析 (2008)
  • Author(s): 岸本利彦、四方哲也
  • Organizer: 第10回日本進化学会大会
  • Place of Presentation: 東京大学駒場キャンパス
  • Year and Date: 2008-08-23