Exploring the possibilities of genome recombination

• Project/Area Number: 22655053
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Single-year Grants
• Research Field: Chemistry related to living body
• Research Institution: Kyoto University
• Principal Investigator: ATOMI Haruyuki 京都大学, 大学院・工学研究科, 教授 (90243047)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥3,420,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥420,000); Fiscal Year 2011: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2010: ¥1,600,000 (Direct Cost: ¥1,600,000)
• Keywords: 遺伝子組換え / 超好熱菌 / メタゲノム / ゲノム組換え / 合成生物学 / 始原菌 / Thermococcus kodakaraensis / ゲノム

Research Abstract

Focusing on the high transformation efficiency of the hyperthermophilic archaeon Thermococcus kodakarensis, we explored the possibilities of performing wide-scale DNA recombination. Mutant strains displaying uracil or tryptophan auxotrophy were used as host cells, and selection was based on their prototrophy. We were able to obtain prototrophs using the genomic DNA of wild-type T. kodakarensis. By inserting a small DNA fragment from the DNA donor beforehand, we were able to obtain transformants using genomic DNA from other hyperthermophiles.

Research Products

• [Journal Article] Model organisms for genetics in the domain Archaea (2011)
  • Author(s): Leigh, J. A., Albers, S. V., Atomi, H., Allers, T.
  • Journal Title: FEMS Microbiology Reviews Volume: 35(4) Pages: 577-608
  • Peer Reviewed
• [Journal Article] Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group (2011)
  • Author(s): Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee G-J, Hattori M, Kanai A, Atomi H, Takai K, Takami H
  • Journal Title: Nucleic Acids Research Volume: 39 Pages: 3204-3223
  • Peer Reviewed
• [Journal Article] His tone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon The rmococcus kodakarensis (2011)
  • Author(s): Maruyama, H., Shin, M., Oda, T., Matsumi, R., Ohniwa, R. L., Itoh, T., Shirahige, K., Imanaka, T., Atomi, H., Yoshimura, S. H., Takeyasu, K
  • Journal Title: Molecular Biology of the Cell Volume: 22(3) Pages: 386-398
  • Peer Reviewed
• [Journal Article] Model organisms for genetics in the domain Archaea : methanogens, halophiles, Thermococcales and Sulfolobales (2011)
  • Author(s): Leigh JA, Albers SV, Atomi H, Allers T
  • Journal Title: FEMS Microbiol Rev. Volume: 35 Issue: 4 Pages: 577-608
  • DOI: 10.1111/j.1574-6976.2011.00265.x
  • Peer Reviewed
• [Journal Article] Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. (2011)
  • Author(s): Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee G-J, Hattori M, Kanai A, Atomi H, Takai K, Takami H.
  • Journal Title: Nucleic Acids Research
  • Peer Reviewed
• [Journal Article] For mate-driven growth coupled with hydrogen production (2010)
  • Author(s): Kim, Y. J., Lee, H. S., Kim, E. S., Bae, S. S., Lim, J. K., Matsumi, R., Lebedinsky, A. V., Sokolova, T. G., Kozhevnikova, D. A., Cha, S. S., Kim, S. J., Kwon, K. K., Imanaka, T., Atomi, H., Bonch-Osmolovskaya, E. A., Lee, J. H., Kang, S. G
  • Journal Title: Nature Volume: 497(7313) Pages: 352-355
  • Peer Reviewed
• [Journal Article] Formate-driven growth coupled with H2 production. (2010)
  • Author(s): Kim YJ, Lee HS, Kim ES, Bae SS, Lim JK, Matsumi R., Lebedinsky AV, Sokolova TG, Kozhevnikova DA, Cha SS, Kim SJ, Kwon KK, Imanaka T, Atomi H, Bonch-Osmolovskaya EA, Lee JH, Kang SG.
  • Journal Title: Nature Volume: 467 Pages: 352-355
  • Peer Reviewed
• [Journal Article] Microbial inorganic carbon fixation. (2010)
  • Author(s): Sato, T., Atomi, H.
  • Journal Title: Encyclopedia of Life Sciences
  • Peer Reviewed
• [Presentation] 超好熱菌Thermococcus kodakarensisの有するウイルス様領域に関する研究 (2011)
  • Author(s): 田頭健太, 松原正晃, 福田青郎, 金井保, 跡見晴幸, 今中忠行
  • Organizer: 日本アーキア研究会第24回講演会
  • Place of Presentation: 慶應義塾大学鶴岡キャンパス
  • Year and Date: 2011-09-03
• [Presentation] 超好熱菌Thermococcus kodakarensisにおけるペントース代謝経路の改変 (2011)
  • Author(s): 松原正晃, 福田青郎, 石井浩子, 松宮芳樹, 跡見晴幸, 今中忠行
  • Organizer: 日本アーキア研究会第24回講演会
  • Place of Presentation: 慶應義塾大学鶴岡キャンパス
  • Year and Date: 2011-09-03
• [Presentation] Identification and characterization of novel enzymes from Thermococcus kodakarensis (2011)
  • Author(s): Atomi, H
  • Organizer: Workshop of Archaea Research Association
  • Place of Presentation: Jeju, Korea
  • Year and Date: 2011-05-10
• [Presentation] Novel enzyme discovery and metabolic engineering in hyperthermophiles (2010)
  • Author(s): Haruyuki Atomi
  • Organizer: Second Japan-Argentina Workshop
  • Place of Presentation: 総評会館、東京
  • Year and Date: 2010-11-09
• [Presentation] 超好熱菌を宿主とした細胞工学の試み (2010)
  • Author(s): 跡見晴幸
  • Organizer: 第5回産業用酵素シンポジウム
  • Place of Presentation: 長浜バイオ大学
  • Year and Date: 2010-11-06
• [Presentation] Novel enzymes and pathways in hyperthermophilic archaea. Gordon Research Conference : Biocatalysis (2010)
  • Author(s): Haruyuki Atomi
  • Organizer: Bryant University
  • Place of Presentation: RI, USA
  • Year and Date: 2010-07-13
• [Presentation] Novel enzymes and pathways in hyperthermophilic archaea (2010)
  • Author(s): 跡見晴幸
  • Organizer: Gordon Research Conference : Biocatalysis
  • Place of Presentation: Bryant大学、米国
  • Year and Date: 2010-07-13
• [Book] Genomics of thermophilic bacteria and archaea (2012)
  • Author(s): Sato, T, Atomi, H
  • Publisher: Springer(in press)
• [Remarks]
  • URL: http://www.sbchem.kyoto-u.ac.jp/atomi-lab/