Analysis of cyanobacterial chromatic acclimation by next-generation sequencing technology

• Project/Area Number: 25830130
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Genome biology
• Research Institution: Toyohashi University of Technology
• Principal Investigator: HIROSE Yuu 豊橋技術科学大学, 工学(系)研究科(研究院), 助教 (30616230)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2013: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
• Keywords: ゲノム / 光合成 / シアノバクテリア / フィトクロム / シアノバクテリオクロム / フィコビリソーム / 次世代シークエンサー / 補色順化 / フィコシアニン / フィコエリスリン

Outline of Final Research Achievements

Certain cyanobacteria species modulate their photosynthetic antenna proteins, phycocyanin and phycoerythrin, which is a phenomenon called complementary chromatic acclimation (CCA). Recent studies of typical CCA-capable cyanobacteria species suggest the diversity of green and red light-regulated gene set during CCA. In this project, I performed (1) establishment of efficient analysis pipeline of cyanobacterial genomes, (2) de novo genome sequencing of CCA-capable cyanobacteria species, and (3) RNA-Seq and spectral analysis of several cyanobacteria performing unique CCA. These results will facilitate the understanding of the molecular basis of CCA and also many other researches of the cyanobacterial genomes.

Research Products

• [Journal Article] Complete genome sequence of cyanobacterium Geminocystis sp. NIES-3708, which performs type II complementary chromatic acclimation (2015)
  • Author(s): Yuu Hirose, Mitsunori Katayama, Yoshiyuki Ohtsubo, Naomi Misawa, Erica Iioka, Wataru Suda, Kenshiro Oshima, Mitsumasa Hanaoka, Kan Tanaka, Toshihiko Eki, Masahiko Ikeuchi, Yo Kikuchi, Makoto Ishida, and Masahira Hattori
  • Journal Title: Genome Announcement Volume: 3 Issue: 3 Pages: 1-2
  • DOI: 10.1128/genomea.00357-15
  • Peer Reviewed / Open Access
• [Journal Article] Complete genome sequence of cyanobacterium Geminocystis sp. NIES-3709 that harbors phycoerythrin-rich phycobilisome (2015)
  • Author(s): Yuu Hirose, Mitsunori Katayama, Yoshiyuki Ohtsubo, Naomi Misawa, Erica Iioka, Wataru Suda, Kenshiro Oshima, Mitsumasa Hanaoka, Kan Tanaka, Toshihiko Eki, Masahiko Ikeuchi, Yo Kikuchi, Makoto Ishida, and Masahira Hattori
  • Journal Title: Genome Announcement Volume: 3 Issue: 2 Pages: 1-2
  • DOI: 10.1128/genomea.00385-15
  • Peer Reviewed / Open Access
• [Journal Article] Complete Genome Sequence of Rhodovulum sulfidophilum DSM 2351, an Extracellular Nucleic Acid-Producing Bacterium (2015)
  • Author(s): Nagao N, Hirose Y, Misawa N, Ohtsubo Y, Umekage S, Kikuchi Y.
  • Journal Title: Genome Annoucements Volume: 3(2) e00388-15 Issue: 2 Pages: 1-2
  • DOI: 10.1128/genomea.00388-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Loss of cytochrome C_m stimulates cyanobacterial heterotrophic growth in the dark (2015)
  • Author(s): Hiraide, Y., Oshima, K., Fujisawa, T., Uesaka, K., Hirose, Y., Tsujimoto, R., Yamamoto, H., Okamoto, S., Nakamura, Y., Terauchi, K., Omata, T., Ihara, K., Hattori, M. and Fujita, Y.
  • Journal Title: Plant and Cell Physiology Volume: 57 Issue: 2 Pages: 334-345
  • DOI: 10.1093/pcp/pcu165
  • Peer Reviewed / Open Access
• [Journal Article] Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1 (2014)
  • Author(s): Kurata A, Hirose Y, Misawa N, Hurunaka K, Kishimoto N.
  • Journal Title: Genome Annoucements Volume: 2(5) e01051-14 Issue: 5 Pages: 1-2
  • DOI: 10.1128/genomea.01051-14
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Complete Genome Sequence of Enterococcus mundtii QU 25, an Efficient L-(+)-Lactic Acid-Producing Bacterium. (2014)
  • Author(s): Shiwa Y., Yanase H., Hirose Y., Satomi S., Araya-Kojima T., Watanabe S., Zendo T., Chibazakura T., Shimizu-Kadota M., Yoshikawa H., Sonomoto K.
  • Journal Title: DNA Research Volume: in press Issue: 4 Pages: 369-77
  • DOI: 10.1093/dnares/dsu003
  • Peer Reviewed / Open Access
• [Journal Article] Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle (2013)
  • Author(s): Hirose, Y.
  • Journal Title: Proc. Natl. Acad. Sci. U S A Volume: 110 Issue: 13 Pages: 4974-79
  • DOI: 10.1073/pnas.1302909110
  • Peer Reviewed
• [Journal Article] Primary photodynamics of the green/red-absorbing photoswitching regulator of the chromatic adaptation E domain from Fremyella diplosiphon (2013)
  • Author(s): Gottlieb
  • Journal Title: Biochemistry Volume: 52 Issue: 46 Pages: 8198-8208
  • DOI: 10.1021/bi400946q
  • Peer Reviewed
• [Presentation] Geminocystis属シアノバクテリアに見られる補色応答能の違い (2015)
  • Author(s): 広瀬侑、片山光徳、大坪嘉行、三澤直美、飯岡恵里香、須田亙、大島健志朗、華岡光正、田中寛、浴俊彦、池内昌彦、服部正平
  • Organizer: 第9回日本ゲノム微生物学会年会
  • Place of Presentation: 神戸大学（六甲第二キャンパス）
  • Year and Date: 2015-03-06 – 2015-03-08
• [Presentation] Analysis of light color response of cyanobacteria using next generation sequencer (2014)
  • Author(s): Y. Hirose, N. Misawa, S. Wakazuki, E. Sakai and T. Eki
  • Organizer: IRAGO conference 2015
  • Place of Presentation: 産業技術総合研究所（茨城県つくば市）
  • Year and Date: 2014-11-06 – 2014-11-07
• [Presentation] Miseqを用いたシアノバクテリアの光色応答の解析 (2014)
  • Author(s): 広瀬 侑, 三澤 直美
  • Organizer: 第8回 日本ゲノム微生物学会年会
  • Place of Presentation: 東京農業大学
• [Presentation] モデルシアノバクテリアNostoc punctiformeを用いた光色応答の解析 (2014)
  • Author(s): 広瀬 侑, 三澤 直美
  • Organizer: 第55回日本植物生理学会年会
  • Place of Presentation: 富山大学
• [Presentation] NGS時代におけるラン藻ゲノムの協調的解析 (2013)
  • Author(s): 広瀬 侑
  • Organizer: ラン藻の分子生物学2013
  • Place of Presentation: かずさDNA研究所
• [Book] 藻類オイル生産技術研究の最前線 (2013)
  • Author(s): 広瀬侑、池内昌彦
  • Total Pages: 7
  • Publisher: NTS出版