Evolution of symbiotic system in deep-sea Calyptogena clams

• Project/Area Number: 24570252
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Evolutionary biology
• Research Institution: Japan Agency for Marine-Earth Science and Technology
• Principal Investigator: YOSHIDA Takao 独立行政法人海洋研究開発機構, 海洋生物多様性研究分野, 主任技術研究員 (60399566)
• Co-Investigator(Renkei-kenkyūsha): TAKAKI Yoshihiro 独立行政法人海洋研究開発機構, 深海・地殻内生物圏研究分野, 主任技術研究員 (10399561) ; SHIMAMURA Shigeru 独立行政法人海洋研究開発機構, 深海・地殻内生物圏研究分野, 技術主事 (40416003)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2012: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
• Keywords: 共生 / 共進化 / ゲノム解析 / 比較ゲノム / ゲノム縮小 / ゲノム縮小進化

Outline of Final Research Achievements

The objective of this study is to elucidate the coevolution between host animals and their intracellular bacteria (symbiont), and detailed process of reductive genome evolution in intracellular symbiont by using deep-sea Calyptogena clam-symbiont symbiosis as a model. Some hosts and symbiont showed the obscure patterns of coevolution by the phylogenetic tree analysis. We also found that the genome size of their symbionts were approximately 1.5-fold larger than that of previously reported symbionts. These data suggested that reductive genome evolution in Calyptogen symbiont genomes is still in an earlier stage than that in the previously reported symbiont genomes.

Research Products

• [Journal Article] Cysteine dioxygenase and cysteine sulfinate decarboxylase genes of the deep-sea mussel Bathymodiolus septemdierum: possible involvement in hypotaurine synthesis and adaptation to hydrogen sulfide (2015)
  • Author(s): Nagasaki, T., Hongo, Y., Koito, Y., Nakamura-Kusakabe, I., Shimamura, S., Takaki, Y., Yoshida, T., Maruyama, T., and Inoue, K.
  • Journal Title: Amino Acids Volume: 47 Issue: 3 Pages: 571-578
  • DOI: 10.1007/s00726-014-1891-z
  • Peer Reviewed / Open Access
• [Journal Article] The structure of a deoxygenated 400 kDa hemoglobin reveals ternary and quaternary structural changes of giant hemoglobins (2014)
  • Author(s): Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., and Miki, K.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. Volume: 70 Issue: 7 Pages: 1823-1831
  • DOI: 10.1107/s1399004714008475
  • Peer Reviewed
• [Journal Article] Enhanced Translocation and Growth of <i>Rhodococcus erythropolis</i> PR4 in the Alkane Phase of Aqueous-Alkane Two Phase Cultures Were Mediated by GroEL2 Overexpression (2014)
  • Author(s): H. Takihara, J. Ogihara, T. Yoshida, S. Okuda, M. Nakajima, N. Iwabuchi, M. Sunairi.
  • Journal Title: Microbes and Environments Volume: 29 Issue: 4 Pages: 346-352
  • DOI: 10.1264/jsme2.ME13158
  • NAID: 130004693791
  • ISSN: 1342-6311, 1347-4405
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Sensing deep extreme environments: the receptor cell types, brain centers, and multi-layer neural packaging of hydrothermal vent endemic worms (2014)
  • Author(s): Shigeno, S., Ogura, A., Mori, T., Toyohara, H., Yoshida, T., Tsuchida, S., and Fujikura, K.
  • Journal Title: Frontiers in Zoology Volume: 11 Pages: 82-82
  • Peer Reviewed / Open Access
• [Journal Article] Exclusive localization of carbonic anhydrase in bacteriocytes of the deep-sea clam Calyptogena okutanii with thioautotrophic symbiotic bacteria. (2013)
  • Author(s): Yuki Hongo, Yoshimitsu Nakamura, Shigeru Shimamura, Yoshihiro Takaki, Katsuyuki Uematsu, Takashi Toyofuku, Hisako Hirayama, Ken Takai, Masatoshi Nakazawa, Tadashi Maruyama, Takao Yoshida
  • Journal Title: The Journal of Experimental Biology Volume: 216 Pages: 4403-4414
  • DOI: 10.1242/jeb.092809
  • Peer Reviewed
• [Journal Article] 化学合成生態系における動物と化学合成細菌との共生 (2013)
  • Author(s): 高木善弘・吉田尊雄
  • Journal Title: 生物の科学 遺伝 Volume: 67 Pages: 482-489
• [Presentation] 深海化学合成系における新しい環境適応戦略 ～シチヨウシンカイヒバリガイ共生菌ゲノムから～ (2014)
  • Author(s): 生田 哲朗、高木 善弘、丸山 正、吉田 尊雄
  • Organizer: 日本進化学会第16回大会
  • Place of Presentation: 高槻現代劇場（大阪府・高槻市）
  • Year and Date: 2014-08-21 – 2014-08-24
  • Invited
• [Presentation] 深海性二枚貝に細胞内共生する化学合成細菌のゲノム進化 (2014)
  • Author(s): 吉田 尊雄，高木 善弘，島村 繁，丸山 正
  • Organizer: 第17回微生物アカデミー研究集会
  • Place of Presentation: 北里大学（神奈川県・相模原市）
  • Year and Date: 2014-08-21
• [Presentation] 深海性二枚貝シロウリガイ類における化学合成共生細菌の宿主転換の可能性 (2014)
  • Author(s): Genki Ozawa, Takashi Kaneko, Shigeru Shimamura, Yoshihiro Takaki, Takeshi Koshiishi, Chiaki Kato, Tadashi Maruyama, Takao Yoshida
  • Organizer: 日本地球惑星科学連合2014年大会
  • Place of Presentation: パシフィコ横浜（神奈川県・横浜市）
  • Year and Date: 2014-04-28 – 2014-05-02
  • Invited
• [Presentation] Cospeciation of deep-sea Calyptogena clams and chemoautotrophic bacteria (2013)
  • Author(s): Genki Ozawa, Takashi Kaneko, Shigeru Shimamura,Yoshihiro Takaki, Shin-ichi Yokobori, Takeshi Koshiishi, Chiaki Kato, Tadashi Maruyama, Takao Yoshida
  • Organizer: 5th International Symposium on Chemosynthesis-Based Ecosystems
  • Place of Presentation: Victoria Conference Centre, Victoria, Canada
• [Presentation] Heterogeneous subpopulations of thioautotrophic intracellular symbiont in a deep-sea mussel, Bathymodiolus septemdierum, and their patchy distribution in the host gill. (2013)
  • Author(s): Tetsuro Ikuta, Yoshihiro Takaki, Shigeru Shimamura, Tadashi Maruyama, Takao Yoshida
  • Organizer: 5th International Symposium on Chemosynthesis-Based Ecosystems
  • Place of Presentation: Victoria Conference Centre, Victoria, Canada
• [Presentation] The genomes of intracellur symbionts in deep-sea Calyptogena clams are still in an early phase of reductive genome evolution. (2013)
  • Author(s): Takao Yoshida, Yoshihiro Takaki, Shigeru Shimamura, Yukiko Nagai, Miwako Tsuda, Masatoshi Tsukahara, Maiko Nezuo, Makiko Shimoji, Kuniko Teruya, Morimi Teruya, Tadashi Maruyama
  • Organizer: 5th International Symposium on Chemosynthesis-Based Ecosystems
  • Place of Presentation: Victoria Conference Centre, Victoria, Canada
• [Presentation] The characterization and localization of carbonic anhydrase in symbiotic deep-sea clam Calyptogena okutanii. (2012)
  • Author(s): Yuki Hongo, Yoshimitsu Nakamura, Shigeru Shimamura, Yoshihiro Takaki, Katsuyuki Uematsu, Takashi Toyofuku, Hisako Hirayama, Ken Takai, Masatoshi Nakazawa, Tadashi Maruyama, Takao Yoshida
  • Organizer: Advances in genomics of (Deep-sea) chemoautotrophic symbioses
  • Place of Presentation: Roscoff, France
• [Presentation] ミトコンドリアゲノムから見た深海性二枚貝シロウリガイ類の系統関係および共生細菌との共進化について (2012)
  • Author(s): 小澤元希、島村繁、高木善弘、丸山正、吉田尊雄
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場
• [Presentation] シマイシロウリガイの鰓と卵巣における共生菌の硫黄酸化系遺伝子及び二酸化炭素固定遺伝子の発現の局在解析 (2012)
  • Author(s): 野村洋輔、生田哲朗、中村欽光、丸山正、吉田尊雄
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場