Regulation of nitrous oxide formation in cell

• Project/Area Number: 26620140
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Bio-related chemistry
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Yoshitsugu Shiro 国立研究開発法人理化学研究所, 放射光科学総合研究センター, 主任研究員 (70183051)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: 一酸化窒素 / 亜酸化窒素 / 脱窒菌 / 嫌気呼吸 / 温室効果ガス / オゾン層破壊物質 / 細胞内タンパク質複合体

Outline of Final Research Achievements

Nitrous oxide (N2O) is not only a green-house gas but also ozone-depleting substance. About 70% of the global emission of N2O is attributable to the anaerobic respiration of denitrification micro-organisms. We aimed to elucidate and to regulate a molecular mechanism of the N2O generation by the micro-organisms. On he basis of the X-ray crystallographic analysis, the functional analysis of some mutants and the molecular dynamic simulation, we proposed that the complex of the NO generation enzyme (nitrite reductase) and NO detoxifying enzyme (nitric oxide reductes) in micro-organism cell is a key player for the N2O generation. We also found four compounds which inhibit the NiR function, and eventually the N2O formation.

Research Products

• [Int'l Joint Research] University of Liverpool(英国)
• [Int'l Joint Research] Stockholm University(スウェーデン)
• [Int'l Joint Research] University of Liverpool(英国)
• [Journal Article] Dynamics of Nitric Oxide Controlled by Protein Complex in Bacterial System (2017)
  • Author(s): E. Terasakaa, K. Yamada, P.-H. Wang, K. Hosokawa, R. Yamagiwa, K. Matsumoto, S. Ishii, T. Mori, K. Yagi, H. Sawai, H. Arai, H. Sugimotoa, Y. Sugitac, Y. Shiroa, T. Tosha
  • Journal Title: Proc. Natl. Acd. SCI. USA Volume: 印刷中
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Crystal structure of bacterial haem importer complex in the inward-facing conformation (2016)
  • Author(s): Naoe, Y., Nakamura, N., Doi, A., Sawabe, M., Nakamura, H., Shiro, Y., Sugimoto, H.
  • Journal Title: Nature Communications Volume: 7 Issue: 1 Pages: 13411-13411
  • DOI: 10.1038/ncomms13411
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A Study of the Dynamics of the Heme Pocket and C-helix in CooA Upon CO Dissociation Using Time-resolved Visible and UV Resonance Raman Spectroscopy (2016)
  • Author(s): Akihiro Otomo, Haruto Ishikawa, Misao Mizuno, Tetsunari Kimura, Minoru Kubo, Yoshitsugu Shiro, Shigetoshi Aono, and Yasuhisa Mizutani
  • Journal Title: J. Phys. Chem. B Volume: 120 Issue: 32 Pages: 7836-7843
  • DOI: 10.1021/acs.jpcb.6b05634
  • Peer Reviewed
• [Journal Article] Regulatory Implications of Structural Changes in Tyr201 of the Oxygen Sensor Protein FixL (2016)
  • Author(s): Takeo Yamawaki, Haruto Ishikawa, Misao Mizuno, Hiro Nakamura, Yoshitsugu Shiro, and Yasuhisa Mizutani
  • Journal Title: Biochemistry Volume: 55 Issue: 29 Pages: 4027-4035
  • DOI: 10.1021/acs.biochem.6b00405
  • Peer Reviewed
• [Journal Article] A Substrate-Binding-State Mimic of H2O2-Dependent Cytochrome P450 Produced by One-point Mutagenesis and Peroxygenation of Non-native Substrates (2016)
  • Author(s): O. Shoji, T. Fujishiro, K. Nishio, Y. Kano, H. Kimoto, S. Chien, H. Onoda, A. Muramatsu, S. Tanaka, A. Hori, H. Sugimoto, Y. Shiro, Y. Watanabe
  • Journal Title: Catal. Sci. Tech. Volume: 6 Issue: 15 Pages: 5806-5811
  • DOI: 10.1039/c6cy00630b
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] A Nearly On-axis Spectroscopic System for Simultaneously Measuring UV-visible Absorption and X-ray Diffraction in the SPring-8 Structural Genomics Beamline (2016)
  • Author(s): M. Sakaguchi, T. Kimura, T. Nishida, T. Tosha, Y. Yamaguchi, S. Yanagisawa, G. Ueno, H. Murakami, H. Ago, M. Yamamoto, T. Ogura, Y. Shiro, M. Kubo
  • Journal Title: J. Synchro. Rad. Volume: 23 Issue: 1 Pages: 334-338
  • DOI: 10.1107/s1600577515018275
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The Initial O2 Inserting Step of Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study (2015)
  • Author(s): R. Makino, E. Obayashi, H. Hori, T. Iizuka, K. Mashima, Y. Shiro, Y. Ishimura
  • Journal Title: Biochemistry Volume: 54 Issue: 23 Pages: 3604-3616
  • DOI: 10.1021/acs.biochem.5b00048
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystal Structure of Response Regulator ChrA in the Heme-Sensing Two-Component System of Corynebacterium diphtheriae (2015)
  • Author(s): A. Doi, H. Nakamura, Y. Shiro, H. Sugimoto
  • Journal Title: Acta Crysll. F Volume: 71 Issue: 8 Pages: 966-971
  • DOI: 10.1107/s2053230x15009838
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Contribution of the Distal Pocket Residue to the Acyl-chain-length Substrate Specificity of (R)-specific Enoyl-CoA Hydratases from Pseudomonas: Site-directed Mutagenesis, Chimeragenesis, X-ray Crystallographic Analysis, and Homology Modeling (2015)
  • Author(s): T. Tsuge, S. Sato, A. Hiroe, K. Ishizuka, H. Kanazawa, Y. Shiro, T. Hisano
  • Journal Title: Appl. Environm. Microbio. Volume: 81 Issue: 23 Pages: 8076-8083
  • DOI: 10.1128/aem.02412-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystal Structure, Exogenous Ligand Binding and Redox Properties of an Engineered Diiron Active Site in a Bacterial Hemerythrin (2014)
  • Author(s): A. Onoda, Y. Okamoto, H. Sugimoto, Y. Takano, S. Hirota, D. Kurtz, Y. Shiro, T. Hayashi
  • Journal Title: Chem. Comm. Volume: 50 Pages: 3421-3423
  • Peer Reviewed
• [Journal Article] Structures of Reduced and Ligand-Bound Nitric Oxide Reductase Provide Insights into Functional Differences in Respiratory Enzymes (2014)
  • Author(s): N. Sato, S. Ishii, H. Sugimoto, T. Hino, Y. Fukumori, Y. Sako, Y. Shiro, T. Tosha
  • Journal Title: PROTEINS: Structure, Function, and Bioinformatics Volume: 82 Pages: 1258-1271
  • Peer Reviewed
• [Journal Article] An in vivo Inhibitory Effect on the Heme Uptake of Pseudomonas aeruginosa by Its Hemophore (HasAp) Carrying Synthetic Metal Complexes (2014)
  • Author(s): C. Shirataki, O. Shoji, M. Terada, S. Ozaki, H. Sugimoto, Y. Shiro, Y. Watanabe
  • Journal Title: Angw. Chem. Int. Ed. Volume: 53 Pages: 2862-2866
  • Peer Reviewed
• [Journal Article] Characterization of Quinol-Dependent Nitric Oxide Reductase from Geobacillus Stearothermophilus: Enzymatic Activity and Active Site Structure (2014)
  • Author(s): E. Terasaka, N. Okada, N. Sato, Y. Sako, Y. Shiro, T. Tosha
  • Journal Title: Biochim. Biophys. Acta - Bioenergetics Volume: 1837 Pages: 1019-1026
  • Peer Reviewed
• [Journal Article] Disulfide Bonds Regulate Binding of Exogenous Ligand to Human Cytoglobin (2014)
  • Author(s): H. Tsujino, T. Yamashita, A. Nose, K. Kukino, H. Sawai, Y. Shiro, T. Uno
  • Journal Title: J. Inor. Biochem. Volume: 135 Pages: 20-27
  • Peer Reviewed
• [Journal Article] Palladium-Nanoparticle-Catalyzed 1,7-Palladium Migration Involving C-H Activation, Followed by Intramolecular Amination: Regioselective Synthesis of N1-Arylbenzotriazoles and an Evaluation of Their Inhibitory Activity Towards Indoleamine 2,3-Dioxygenase (2014)
  • Author(s): K. Takagi, M. Al-Amin, N. Hoshiya, J. Wouters, H. Sugimoto, Y. Shiro, H. Fukuda, S. Shuto, M. Arisawa
  • Journal Title: J. Org. Chem. Volume: 79 Pages: 6366-6371
  • Peer Reviewed
• [Journal Article] Structure-function Analyses of Cytochrome P450revI Involved in Reveromycin A Biosynthesis and Evaluation of the Biological Activity of Its Aubstrate, Reveromycin T (2014)
  • Author(s): S. Takahashi, S. Nagano, T. Nogawa, N. Kanoh, M. Uramoto, M. Kawatani, T. Shimizu, T. Miyazawa, Y. Shiro, H. Osada
  • Journal Title: J. Biol. Chem. Volume: 289 Pages: 32446-32458
  • Peer Reviewed
• [Journal Article] Activation of Wild-type Cytochrome P450BM3 by the Next Generation of Decoy Molecules: Enhanced Hydroxylation of Gaseous Alkanes and Crystallographic Evidence (2014)
  • Author(s): Z. Cong, O. Shoji, C. Kasai, N. Kawakami, H. Sugimoto, Y. Shiro, Y. Watanabe
  • Journal Title: ACS Catalysis Volume: 5 Pages: 150-156
  • Peer Reviewed
• [Presentation] Structural Basis for Molecular Mechanism of Bacterial Nitric Oxide Reductases (2017)
  • Author(s): Shiro, Y.
  • Organizer: IGER Intl. Symp. Physics of Life
  • Place of Presentation: 名大、ES Hall、名古屋
  • Year and Date: 2017-03-25
  • Int'l Joint Research / Invited
• [Presentation] NO Dynamics in Biology: Its Generation and Decomposition (2016)
  • Author(s): Shiro, Y.
  • Organizer: Royal Society Meeting Inorganic Chemistry
  • Place of Presentation: 阪大、銀杏会館、豊中
  • Year and Date: 2016-10-26
  • Int'l Joint Research / Invited
• [Presentation] Damage-free X-ray Crystallographic Analysis of P450nor in the NO Bound Form using SACLA. (2016)
  • Author(s): Kubo, M., Nomura, T., Nishida, T., Tosha, T., Sugimoto, H., Kimura, T., Takano, Y., Yamashita, K., Hirata, K., Ueno, G., Ago, H., Yamamoto, M., Shiro, Y.
  • Organizer: British Biophysical Society 2016 Biennial Meeting
  • Place of Presentation: Liverpool, UK
  • Year and Date: 2016-07-07
  • Invited
• [Presentation] Molecular Mechanism of NO Reduction by Bacterial Nitric Oxide Reductases (2016)
  • Author(s): Shiro, Y.
  • Organizer: ICCP9
  • Place of Presentation: Nanjing, China
  • Year and Date: 2016-06-03
  • Int'l Joint Research / Invited
• [Presentation] Molecular Mechanism of NO Reduction by Bacterial Nitric Oxide Reductases (2016)
  • Author(s): Shiro, Y.
  • Organizer: 229th ECS Meeting
  • Place of Presentation: San Diego, USA
  • Year and Date: 2016-05-29
  • Int'l Joint Research / Invited
• [Presentation] Proton Transfer in Bacterial Nitric Oxide Reductases Coupled with NO Reduction (2015)
  • Author(s): Y. Shiro
  • Organizer: PACIFICHEM2015 The International Chemical Congress of Pacific Basin Societies
  • Place of Presentation: Honolulu, USA
  • Year and Date: 2015-12-15
• [Presentation] Molecular Mechanism of NO Reduction by Bacterial Nitric Oxide Reductases (2015)
  • Author(s): Y. Shiro
  • Organizer: PACIFICHEM2015 The International Chemical Congress of Pacific Basin Societies
  • Place of Presentation: Honolulu, USA
  • Year and Date: 2015-12-15
• [Presentation] Dynamics of Nitric Oxide in Bacterial Cellular System (2015)
  • Author(s): Y. Shiro
  • Organizer: “Cell Biology of Metals” Gordon Research Conference
  • Place of Presentation: West Dover, VT, USA
  • Year and Date: 2015-07-26
  • Int'l Joint Research / Invited
• [Presentation] Molecular Mechanism of NO Decomposition by Nitric Oxide Reductases (2015)
  • Author(s): Y. Shiro
  • Organizer: ICBIC17 17th International Conference of Biological Inorganic Chemistry
  • Place of Presentation: Beijing, China
  • Year and Date: 2015-07-20
  • Int'l Joint Research / Invited
• [Presentation] Generation, Channeling and Decomposition of NO in Bacterial System (2015)
  • Author(s): Shiro, Y.
  • Organizer: “Metals in Biology” Gordon Research Conference
  • Place of Presentation: Ventura, USA
  • Year and Date: 2015-01-25 – 2015-01-30
  • Invited
• [Presentation] これからの生物無機化学 ー金属タンパク質の過去と未来ー (2014)
  • Author(s): 城 宜嗣
  • Organizer: 第87回日本生化学会
  • Place of Presentation: 京都
  • Year and Date: 2014-10-15 – 2014-10-18
  • Invited
• [Presentation] Generation, Propagation and Decomposition of Nitric Oxide in Bacterial Denitrification (2014)
  • Author(s): Shiro, Y.
  • Organizer: 18th European Bioenergetics Conference (EBEC 2014)
  • Place of Presentation: Lisbon, Portugal
  • Year and Date: 2014-07-12 – 2014-07-17
  • Invited
• [Presentation] Bacterial Nitrite Reductase and Nitric Oxide Reductase; NO Generation, Channeling and Decomposition (2014)
  • Author(s): Shiro, Y.
  • Organizer: Eighth International Conference on Porphyrins and Phtalocyanines (ICPP8)
  • Place of Presentation: Istanbul, Turky
  • Year and Date: 2014-06-22 – 2014-06-27
  • Invited
• [Book] Metalloenzymes in Denitrification (2017)
  • Author(s): T. Tosha, Y. Shiro
  • Total Pages: 452
  • Publisher: Royal Society of Chemistry Metallobiology Series
• [Book] 鉄の事典 (2014)
  • Author(s): 藤井 浩、城 宜嗣
  • Total Pages: 820
  • Publisher: 朝倉書店
• [Remarks] 理化学研究所 城生体金属科学研究室
  • URL: http://www.riken.jp/biometal/index.htm
• [Remarks] 兵庫県立大 理学部 細胞制御Ⅱ研究室
  • URL: http://www.sci.u-hyogo.ac.jp/life/regulation/index-j.html
• [Remarks] 兵庫県立大学 理学部 細胞制御Ⅱ研究室
  • URL: http://www.sci.u-hyogo.ac.jp/life/regulation/index-j.html