Structure and function of transition metal ions-containing sensor proteins

• Project/Area Number: 17H03093
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bio-related chemistry
• Research Institution: Center for Novel Science Initatives, National Institutes of Natural Sciences
• Principal Investigator: Aono Shigetoshi 大学共同利用機関法人自然科学研究機構(新分野創成センター、アストロバイオロジーセンター、生命創成探究, 生命創成探究センター, 教授 (60183729)
• Project Period (FY): 2017-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000); Fiscal Year 2020: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2019: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2018: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2017: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
• Keywords: 光センサータンパク質 / 水素センサータンパク質 / アデノシルコバラミン / ビタミンB12 / 一酸化炭素 / センサータンパク質 / ヒドロゲナーゼ / 鉄硫黄クラスター / 酸素センサータンパク質 / 光センシング / 水素センシング / 遷移金属イオン / 転写調節因子 / 光センサー / ガス分子センサー

Outline of Final Research Achievements

In this work, I determined the crystal structure of a novel photosensor protein CarH, which uses vitamin B12 (adenosylcobalamin) as a sensor module to elucidate the molecular mechanisms of photo-sensing by CarH. I also determined the crystal structure of HypX, which catalyzes CO biosynthesis for the construction of the sensor module in hydrogen sensor protein, NiFe-type hydrogenase. In the CO biosynthesis by HypX, formyl-CoA is produced as an reaction intermediate through the formyl group-transfer from N10-formyl-THF to coenzyme A.

Academic Significance and Societal Importance of the Research Achievements

これまでに例の無い新規な光センサータンパク質の分子構造を決定し、ビタミンB12（アデノシルコバラミン）が光センサータンパク質中で光応答のためのセンサー素子として機能することを明らかにした。また、水素センサータンパク質中のセンサーモジュールを構築するのに必須要素である一酸化炭素（CO）が、酵素反応により生合成されることを、CO生合成酵素の結晶構造を決定することにより明らかにした。これらの成果は、生物無機化学の新たな研究対象を提供するものであり、研究分野に新たな展開をもたらすことに寄与した。

Research Products

• [Journal Article] Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival (2021)
  • Author(s): Nishinaga Megumi、Sugimoto Hiroshi、Nishitani Yudai、Nagai Seina、Nagatoishi Satoru、Muraki Norifumi、Tosha Takehiko、Tsumoto Kouhei、Aono Shigetoshi、Shiro Yoshitsugu、Sawai Hitomi
  • Journal Title: Communications Biology Volume: 4 Issue: 1 Pages: 467-467
  • DOI: 10.1038/s42003-021-01987-5
  • Peer Reviewed / Open Access
• [Journal Article] Structural Characterization of Y29F Mutant of Thermoglobin from a Hyperthermophilic Bacterium Aquifex aeolicus (2021)
  • Author(s): Muraki Norifumi、Takeda Kouta、Nam Dayeon、Muraki Megumi、Aono Shigetoshi
  • Journal Title: Chemistry Letters Volume: 50 Issue: 4 Pages: 603-606
  • DOI: 10.1246/cl.200879
  • NAID: 130008025746
  • Peer Reviewed / Open Access
• [Journal Article] Use of a Ferritin L134P Mutant for the Facile Conjugation of Prussian Blue in the Apoferritin Cavity (2021)
  • Author(s): Ikenoue Yuta、Tahara Yuhei O.、Miyata Makoto、Nishioka Takanori、Aono Shigetoshi、Nakajima Hiroshi
  • Journal Title: Inorganic Chemistry Volume: 60 Issue: 7 Pages: 4693-4704
  • DOI: 10.1021/acs.inorgchem.0c03660
  • URL: https://ocu-omu.repo.nii.ac.jp/records/2019896
  • Peer Reviewed
• [Journal Article] Structural basis for heme transfer reaction in heme uptake machinery from Corynebacteria (2019)
  • Author(s): Norifumi Muraki, Chihiro Kitatsuji, Yasunomi Okamoto, Takeshi Uchida, Koichiro Ishimori, and Shigetoshi Aono
  • Journal Title: Chem. Commun. Volume: 55 Issue: 92 Pages: 13864-13867
  • DOI: 10.1039/c9cc07369h
  • Peer Reviewed
• [Journal Article] Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase (2019)
  • Author(s): Norifumi Muraki, Kentaro Ishii, Susumu Uchiyama, Satoru G. Itoh, Hisashi Okumura, and Shigetoshi Aono
  • Journal Title: Commun. Biol. Volume: 2 Issue: 1
  • DOI: 10.1038/s42003-019-0631-z
  • Peer Reviewed / Open Access
• [Journal Article] Protein Dynamics of the Sensor Protein HemAT as Probed by Time-Resolved Step-Scan FTIR Spectroscopy (2018)
  • Author(s): Andrea Pavlou, Hideaki Yoshimura, Shigetoshi Aono, and Eftychia Pinakoulaki
  • Journal Title: Biophys. J. Volume: 114 Issue: 3 Pages: 584-591
  • DOI: 10.1016/j.bpj.2017.12.012
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Probing the role of the heme distal and proximal environment in ligand dynamics in the signal transducer protein HemAT by time-resolved step-scan FTIR and resonance Raman spectroscopy (2017)
  • Author(s): Andrea Pavlou, Andreas Loullis, Hideaki Yoshimura, Shigetoshi Aono, and Eftychia Pinakoulaki
  • Journal Title: Biochemistry Volume: 56 Issue: 40 Pages: 5309-5317
  • DOI: 10.1021/acs.biochem.7b00558
  • Peer Reviewed / Int'l Joint Research
• [Presentation] NiFe型ヒドロゲナーゼの活性中心形成に必要なCO生合成反応の分子機構 (2021)
  • Author(s): 青野重利
  • Organizer: 日本農芸化学会大会2021
  • Invited
• [Presentation] 水素代謝酵素の活性中心に必須な一酸化炭素を生合成する分子機構 (2020)
  • Author(s): 村木則文
  • Organizer: 日本農芸化学会中部支部第１８８回例会
  • Invited
• [Presentation] 病原菌の鉄獲得システムで機能するヘムセンサー蛋白質の多機能性とその構造的機序 (2019)
  • Author(s): 西永惠、長井聖奈、村木則文、青野重利、杉本宏、城宜嗣、澤井仁美
  • Organizer: 第19回日本蛋白質科学会年会／第71回日本細胞生物学会大会合同年次大会
• [Presentation] NiFeヒドロゲナーゼの活性中心に必須なCOの生合成を担うHypXの構造基盤 (2019)
  • Author(s): 村木則文、青野重利
  • Organizer: 第19回日本蛋白質科学会年会／第71回日本細胞生物学会大会合同年次大会
• [Presentation] ヒドロゲナーゼ成熟化において一酸化炭素生合成を担うHypXの結晶構造解析 (2019)
  • Author(s): 村木則文、青野重利
  • Organizer: 日本結晶学会年会
• [Presentation] Mechanism of CO biosynthesis for the maturation of [NiFe] hydrogenase revealed by crystal structure of HypX (2019)
  • Author(s): N. Muraki, S. Aono
  • Organizer: 15th International Symposium on Applied Bioinorganic Chemistry
  • Int'l Joint Research
• [Presentation] Structural basis for the assembly of the NiFe-dinuclear active site in [NiFe]-Hydrogenases (2019)
  • Author(s): S. Aono, N. Muraki
  • Organizer: 7th International Symposium on Metallomics
  • Int'l Joint Research
• [Presentation] Structural Characterization of HypX Responsible for CO Biosynthesis in the Maturation of [NiFe]-Hydrogenases (2019)
  • Author(s): S. Aono
  • Organizer: Frontier Bioorganization Forum 2019
  • Int'l Joint Research / Invited
• [Presentation] Structural analysis of HypX responsible for CO production in the maturation of a [NiFe]-hydrogenase (2019)
  • Author(s): N. Muraki, S. Aono
  • Organizer: 19th International Conference on Biological Inorganic Chemistry (ICBIC-19)
  • Int'l Joint Research
• [Presentation] Structural Characterization of HypX Responsible for CO Biosynthesis to assemble the active site of [NiFe]-Hydrogenase (2019)
  • Author(s): S. Aono
  • Organizer: 2019 Korea-Taiwan-Japan Biological Inorganic Chemistry Symposium
  • Int'l Joint Research / Invited
• [Presentation] ヘムセンサータンパク質HrtRによる細胞内ヘム濃度制御の分子機構 (2018)
  • Author(s): 青野重利
  • Organizer: 日本農芸化学会2018年度大会
  • Invited
• [Presentation] 光受容体型転写因子CarHの構造と機能の解明 (2018)
  • Author(s): 村木則文、青野重利
  • Organizer: 第１８回日本蛋白質科学会年会
• [Presentation] Structural basis for heme uptake reaction in Corynebacterium glutamicum (2018)
  • Author(s): 青野重利
  • Organizer: 第５６回日本生物物理学会年会
  • Invited
• [Presentation] Structural insights into the catalytic mechanism of carbon monoxide biosynthesis for the maturation of NiFe-hydrogenases (2018)
  • Author(s): 村木則文、青野重利
  • Organizer: 日本化学会第９９回春季年会
• [Presentation] Structural Basis for Transcriptional Regulation of Heme Homeostasis in Lactococcus lactis (2018)
  • Author(s): Shigetoshi Aono
  • Organizer: 2018 Korea-Taiwan-Japan Bioinorganic Chemistry Symposium
  • Invited
• [Presentation] Structural analyses of the heme uptake machinery in Corynebacterium glutamicum (2018)
  • Author(s): Shigetoshi Aono
  • Organizer: 10th International Conference on Porphyrins and Phthalocyanines
  • Invited
• [Presentation] Regulation of protein function by oxygen binding to heme in the heme-based sensor domain (2018)
  • Author(s): Shigetoshi Aono
  • Organizer: EMBO Workshop, Enzymes, biocatalysis and chemical biology: The new frontiers
• [Presentation] Structure and function of transcriptional regulator adopting heme as a signaling molecule (2018)
  • Author(s): Shigetoshi Aono
  • Organizer: 9th Asian Biological Inorganic Chemistry Conference
  • Invited
• [Presentation] コリネバクテリアのヘム取り込み系の構造と機能 (2017)
  • Author(s): 村木則文、青野重利
  • Organizer: 第１７回日本蛋白質科学会年会
• [Presentation] コリネバクテリアのヘム取込み反応の構造基盤 (2017)
  • Author(s): 青野重利
  • Organizer: 第１７回日本蛋白質科学会年会
  • Invited
• [Presentation] 遷移金属が関与するシグナルセンシングとシグナル伝達 (2017)
  • Author(s): 青野重利
  • Organizer: 第４４回生体分子科学討論会
  • Invited
• [Presentation] コリネバクテリア由来HtaA/HtaBによるヘム認識と輸送の分子基盤 (2017)
  • Author(s): 村木則文、青野重利
  • Organizer: 第１１回バイオ関連化学シンポジウム
• [Presentation] Structural basis for the heme-dependent transcriptional regulation (2017)
  • Author(s): 青野重利
  • Organizer: 第５５回日本生物物理学会年会
  • Invited
• [Presentation] コリネバクテリアによるヘムの獲得に関わるHtaタンパク質の結晶構造 (2017)
  • Author(s): 村木則文、青野重利
  • Organizer: 日本結晶学会年会
• [Presentation] Structural characterization of heme uptake system in Corynebacteria (2017)
  • Author(s): Shigetoshi Aono
  • Organizer: 231st ECS Meeting
  • Invited
• [Presentation] Structure and Function of Heme Transport Proteins in Corynebacterium glutamicum (2017)
  • Author(s): Shigetoshi Aono, Norifumi Muraki
  • Organizer: 8th International Symposium on Metallomics
• [Book] Gas Sensing of Cells (2018)
  • Author(s): Shigetoshi Aono
  • Total Pages: 302
  • Publisher: Royal Society of Chemistry