Analysis of bacteriophage Qβ genome evolution in an experimental coevolution system

• Project/Area Number: 21770255
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Evolutionary biology
• Research Institution: Hirosaki University
• Principal Investigator: KASHIWAGI Akiko 弘前大学, 農学生命科学部, 准教授 (40362652)
• Project Period (FY): 2009 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2010: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2009: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: 共進化 / 実験進化 / Qβファージ / 大腸菌 / バクテリオファージQβ

Research Abstract

How does evolution affect changes in parasite genome sequences? To elucidate the effects of coevolution, we constructed an experimental coevolution system and sole parasite evolution system consisting of Escherichia coli and the lytic RNA bacteriophage Qβ (Qβ phage). We passaged Qβ phage in both systems for approximately 170 phage generations. Comparison of sequential (time-dependent) changes in the Qβ phage genome sequence in both evolution systems revealed that the coevolution system showed about 3.4-fold higher fixation rate.

Research Products

• [Journal Article] PLoS ONE (2011)
  • Author(s): Kazufumi Hosoda, Shingo Suzuki, Yoshinori Yamauchi, Yasunori Shiroguchi, Akiko Kashiwagi, Naoaki Ono, Kotaro Mori, Tetsuya Yomo
  • Journal Title: issue 2 Volume: volume 6
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Kumiko Kihara, Kotaro Mori, Shingo Suzuki, Kazufumi Hosoda, Akito Yamada, Shin'ichi Matsuyama, Akiko Kashiwagi, Tetsuya Yomo
  • Journal Title: Bio Systems Volume: vol.13 Pages: 342-347
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Kotaro Mori, Akiko Kashiwagi, Tetsuya Yomo
  • Journal Title: The Journal of Eukaryotic Microbiology Volume: vol.58(1) Pages: 37-42
  • Peer Reviewed
• [Journal Article] Single-cell Isolation and Cloning of Tetrahymena thermophila Cells with a Fluorescence-activated Cell Sorter (2011)
  • Author(s): Mori, K., Kashiwagi, A., Yomo, T.
  • Journal Title: The Journal of Eukaryotie Microbiology Volume: 58 Pages: 37-42
  • Peer Reviewed
• [Journal Article] Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli (2011)
  • Author(s): Kihara, K., Mori, K., Suzuki, S., Hosoda, K., Yamada, A., Matsuyama, S., Kashiwagi, A., Yomo, T.
  • Journal Title: BioSystems Volume: 13 Pages: 342-347
  • Peer Reviewed
• [Journal Article] Cooperative adaptation to establishment of a synthetic bacterial mutualism (2011)
  • Author(s): Hosoda, K, Suzuki, S., Yamauchi, Y., Shiroguchi, Y., Kashiwagi, A., Ono, N., Mori, K., Yomo, T.
  • Journal Title: PLoS ONE Volume: 6
  • Peer Reviewed
• [Journal Article] (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 Volume: vol.6(10)
  • Peer Reviewed
• [Journal Article] Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution (2010)
  • Author(s): Kishimoto, T., Iijima, L., Tatsumi, M., Ono, N., Oyake, A., Hashimoto, T., Matsuo, M., Okubo, M., Suzuki, S., Mori, K., Kashiwagi, A., Furusawa, C, Ying, BW, Yomo, T.
  • Journal Title: PLoS Genetics Volume: 6
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Saburo Tsuru, Junya Ichinose, Akiko Kashiwagi, Bei-Wen Ying, Kunihiko Kaneko, Tetsuya Yomo
  • Journal Title: Physical Biology Volume: vol.6
  • Peer Reviewed
• [Journal Article] Noisy growth rate of cell size fluctuate protein concentration in bacteria (2009)
  • Author(s): Saburo Tsuru, Junya Ichinose, Akiko Kashiwagi, Bei-Wen Ying, Kunihiko Kaneko, Tetsuya Yomo
  • Journal Title: Pysical Biology Vol.6
  • Peer Reviewed
• [Presentation] On-going analysis of experimental coevolution system with E.coli and RNA bacteriophage Qβ (2010)
  • Author(s): Akiko Kashiwagi
  • Organizer: RCCSB (Research Center for Complex Systems Biology) symposium on cellular biophysics
  • Place of Presentation: 東京都東京大学
  • Year and Date: 2010-12-08
• [Presentation] 実験室内進化系を用いたRNAウイルスの共進化過程解析系の構築と解析 (2010)
  • Author(s): 柏木明子、四方哲也
  • Organizer: 第62回日本生物工学会
  • Place of Presentation: ワールドコンベンションセンターサミット フェニックス・シーガイア・リゾート(宮崎県山崎町浜山)
  • Year and Date: 2010-10-28
• [Presentation] 実験室内共進化系でのバクテリオファージQβのゲノム進化 (2010)
  • Author(s): 柏木明子、四方哲也
  • Organizer: 日本遺伝学会第82回大会
  • Place of Presentation: 札幌市北海道大学
  • Year and Date: 2010-09-20
• [Presentation] 大腸菌とバクテリオファージQβを用いた実験室内共培養系における寄生者の宿主特異性の変化 (2010)
  • Author(s): 柏木明子、四方哲也
  • Organizer: 第12回日本進化学会大会
  • Place of Presentation: 東京都東京工業大学
  • Year and Date: 2010-08-03
• [Presentation] 2種類の大腸菌株による人工栄養共生系の実験進化 (2010)
  • Author(s): 浅尾晃央、細田一史、森光太郎、柏木明子、山内義教、城口泰典、鈴木真吾、四方哲也
  • Organizer: 日本生態学会第57回大会
  • Place of Presentation: 東京大学
  • Year and Date: 2010-03-17
• [Presentation] テトラヒメナと大腸菌の人工共生系における個体群動態 (2010)
  • Author(s): 末吉眞人、松本佑介、森光太郎、柏木明子、細田一史、四方哲也
  • Organizer: 日本生態学会第57回大会
  • Place of Presentation: 東京大学
  • Year and Date: 2010-03-17
• [Presentation] ワールドコンベンションセンターサミット (2010)
  • Author(s): 柏木明子、四方哲也
  • Organizer: 第62回日本生物工学会
  • Place of Presentation: フェニックス・シーガイア・リゾート(宮崎県山崎町浜山)
• [Presentation] 日本遺伝学会第82回大会 (2010)
  • Author(s): 柏木明子、四方哲也
  • Organizer: 日本遺伝学会
  • Place of Presentation: 北海道大学(札幌市)
• [Presentation] 第12回日本進化学会大会 (2010)
  • Author(s): 柏木明子、四方哲也
  • Place of Presentation: 東京工業大学大岡山キャンパス
• [Presentation] Construction of Escherichia coil Gene Expression Level Perturbation Collection (2009)
  • Author(s): Akiko Kashiwagi, Takahiro Sakurai, Saburo Tsuru, Bei-Wen Ying, Kotaro Mori, Tetsuya Yomo
  • Organizer: APBioChEC'09
  • Place of Presentation: 神戸国際会議場
  • Year and Date: 2009-11-24
• [Presentation] Stochastic gene expression induced population selection promotes adaptation to nutrient depletion (2009)
  • Author(s): 津留三良、インベイウェン、森光太郎、潮田純弥、柏木明子、四方哲也
  • Organizer: 日本生物物理学会
  • Place of Presentation: 徳島文理大学
  • Year and Date: 2009-10-30
• [Presentation] Cooperative and adaptive phenotypic plasticity observed in a synthetic mutualism composed of two auxotrophs of Escherichia coli (2009)
  • Author(s): 細田一史、森光太郎、柏木明子、鈴木真吾、四方哲也
  • Organizer: 日本生物物理学会
  • Place of Presentation: 徳島文理大学
  • Year and Date: 2009-10-30
• [Presentation] 2種の大腸菌変異株による人工栄養共生系で観察される適応的表現型変化 (2009)
  • Author(s): 細田一史、鈴木真吾、柏木明子、森光太郎、山内義教、城口泰典、四方哲也
  • Organizer: 第25回個体群生態学会
  • Place of Presentation: 同志社大学
  • Year and Date: 2009-10-17
• [Presentation] アミノ酸枯渇に対する適応的な遺伝子発現 (2009)
  • Author(s): 津留三良、インベイウェン、森光太郎、潮田純弥、柏木明子、四方哲也
  • Organizer: 「細胞を創る」研究会2.0
  • Place of Presentation: 東京大学
  • Year and Date: 2009-10-01
• [Presentation] Adaptive response of a Gene Network to Environmental Changes by Fitness-induced Attractor Selection (2009)
  • Author(s): 柏木明子
  • Organizer: International Symposium on COMPLEX SYSTEMS BIOLOGY
  • Place of Presentation: 東京大学
  • Year and Date: 2009-09-29
• [Presentation] Analysis of adaptive gene expression to nutrient depletion out of native regulatory mechanisms (2009)
  • Author(s): 津留三良、インベイウェン、森光太郎、潮田純弥、柏木明子、四方哲也
  • Organizer: International Symposium on COMPLEX SYSTEMS BIOLOGY
  • Place of Presentation: 東京大学
  • Year and Date: 2009-09-29
• [Presentation] Adaptive phenotypic change in a synthetic ecosystem composed of two strains of Escherichia coil (2009)
  • Author(s): 細田一史、城口泰典、山内義教、森光太郎、鈴木真吾、柏木明子、四方哲也
  • Organizer: International Symposium on COMPLEX SYSTEMS BIOLOGY
  • Place of Presentation: 東京大学
  • Year and Date: 2009-09-29
• [Presentation] 大腸菌の人工相利共生系で観察される協力的表現型変化 (2009)
  • Author(s): 細田一史、森光太郎、鈴木真吾、柏木明子、四方哲也
  • Organizer: 第19回日本数理生物学会大会
  • Place of Presentation: 東京大学
  • Year and Date: 2009-09-09
• [Presentation] 大腸菌と溶菌性RNAバクテリオファージQβの実験室内共培養系における個体群動態とRNAバクテリオファージ集団のゲノム塩基配列変化 (2009)
  • Author(s): 柏木明子、四方哲也
  • Organizer: 日本進化学会
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-09-03
• [Presentation] 栄養枯渇に対する適応応答における遺伝子発現の多様性の役割 (2009)
  • Author(s): 津留三良、インベイウェン、森光太郎、潮田純弥、柏木明子、四方哲也
  • Organizer: 日本進化学会
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-09-03
• [Presentation] 第11回日本進化学会大会(札幌大会) (2009)
  • Author(s): 柏木明子、四方哲也
  • Place of Presentation: 北海道大学高等教育機能開発総合センター
• [Presentation] APBioChEC’09 (2009)
  • Author(s): Akiko Kashiwagi, Takahiro Sakurai, Saburo Tsuru, Bei-Wen Ying, Kotaro Mori, Tetsuya Yomo
  • Place of Presentation: Kobe, JAPAN
• [Presentation] International Symposium on COMPLEX SYSTEMS BIOLOGY (2009)
  • Author(s): Akiko Kashiwagi
  • Place of Presentation: The University of Tokyo, Hongo Campus
• [Remarks]
  • URL: http://nature.cc.hirosaki-u.ac.jp/kohou2/public/oyo/a.kashiwagi/index.htm
• [Remarks]
  • URL: http://nature.cc.hirosaki-u.ac.jp/kohou2/public/oyo/a.kashiwagi/index.htm