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Studies on mechanisms of biosynthesis of biomolecules via amino-group carrier protein and expansion of structural diversity of secondary metabolites

Research Project

Project/Area Number 17H06168
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Research Field Applied microbiology
Research InstitutionThe University of Tokyo

Principal Investigator

Nishiyama Makoto  東京大学, 大学院農学生命科学研究科(農学部), 教授 (00208240)

Co-Investigator(Kenkyū-buntansha) 富田 武郎  東京大学, 大学院農学生命科学研究科(農学部), 特任准教授 (50447364)
Project Period (FY) 2017-05-31 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥208,910,000 (Direct Cost: ¥160,700,000、Indirect Cost: ¥48,210,000)
Fiscal Year 2021: ¥30,810,000 (Direct Cost: ¥23,700,000、Indirect Cost: ¥7,110,000)
Fiscal Year 2020: ¥29,640,000 (Direct Cost: ¥22,800,000、Indirect Cost: ¥6,840,000)
Fiscal Year 2019: ¥31,460,000 (Direct Cost: ¥24,200,000、Indirect Cost: ¥7,260,000)
Fiscal Year 2018: ¥51,480,000 (Direct Cost: ¥39,600,000、Indirect Cost: ¥11,880,000)
Fiscal Year 2017: ¥65,520,000 (Direct Cost: ¥50,400,000、Indirect Cost: ¥15,120,000)
Keywords微生物 / 放線菌 / 生合成 / 二次代謝 / 構造生物学 / キャリアタンパク質 / 生物活性物質 / アミノ基キャリアタンパク質 / アミノ酸 / 二次代謝産物 / 構造解析 / マレイマイシン / 結晶構造解析
Outline of Final Research Achievements

Amino-group carrier protein (AmCP) is a newly found protein that carries (a) substrate(s) bound to its C-terminus via an amino group to enzymes in the primary and secondary metabolite biosynthesis. In this project, we tried to determine the three-dimensional structures of biosynthetic enzymes involved in secondary metabolite biosynthesis in Actinomycetes to elucidate the mechanism for the AmCP recognition and expansion of the structural diversity of natural compounds via the AmCP system. Through this project, we discovered and elucidated several new and unique mechanisms.

Academic Significance and Societal Importance of the Research Achievements

AmCPは、微生物の塩基性アミノ酸生合成だけでなく、二次代謝産物の生合成においても重要な機能を果たす。本研究により、AmCPを介して生合成される化合物の多くは新規非タンパク質性アミノ酸であり、それらが様々な生物活性物質へと組み込まれることが分かった。これらは、これまでの生物活性物質の探索で見落とされてきた天然化合物群であり、新規反応を含む多様な生合成システムの解析により、天然化合物の多様性創出機構の解明に貢献した。

Assessment Rating
Verification Result (Rating)

A-

Assessment Rating
Result (Rating)

A: Progress in the research is steadily towards the initial goal. Expected research results are expected.

Report

(11 results)
  • 2022 Research Progress Assessment (Verification Result) ( PDF )
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report   Abstract(Research Progress Assessment) ( PDF )   Research Progress Assessment (Result) ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Abstract ( PDF )   Comments on the Screening Results ( PDF )   Annual Research Report
  • Research Products

    (49 results)

All 2022 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (1 results) Journal Article (11 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Acknowledgement Compliant: 1 results) Presentation (36 results) (of which Int'l Joint Research: 9 results,  Invited: 11 results) Remarks (1 results)

  • [Int'l Joint Research] フライブルグ大学(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius2021

    • Author(s)
      Suzuki, T., Tomita, T., Hirayama, K., Suzuki, M., Kuzuyama, T., and Nishiyama M.
    • Journal Title

      FEBS Journal

      Volume: 288 Issue: 6 Pages: 1975-1988

    • DOI

      10.1111/febs.15527

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reconstitution of a Highly Reducing Type II PKS System Reveals 6π-Electrocyclization Is Required for o-Dialkylbenzene Biosynthesis2021

    • Author(s)
      Zhang J, Yuzawa S, Thong WL, Shinada T, Nishiyama M, Kuzuyama T.
    • Journal Title

      J Am Chem Soc

      Volume: 143 Issue: 7 Pages: 2962-2969

    • DOI

      10.1021/jacs.0c13378

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genome-mining of amino group carrier protein-mediated machinery led to the discovery of an unprecedented hydrazine-forming enzyme in bacteria.2020

    • Author(s)
      松田研一,西山 真
    • Journal Title

      生化学

      Volume: 92 Issue: 1 Pages: 130-135

    • DOI

      10.14952/SEIKAGAKU.2020.920130

    • NAID

      40022176215

    • ISSN
      0037-1017
    • Year and Date
      2020-02-25
    • Related Report
      2019 Annual Research Report
  • [Journal Article] Guanidyl modification of the 1-azabicyclo[3.1.0]hexane ring in ficellomycin essential for its biological activity2020

    • Author(s)
      Kurosawa, S., Matsuda, K., Hasebe, F., Shiraishi, T., Shin-ya, K., Kuzuyama, T., and Nishiyama, M.
    • Journal Title

      Organic and Biomolecular Chemistry

      Volume: 15 Issue: 27 Pages: 5137-5144

    • DOI

      10.1039/d0ob00339e

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria2020

    • Author(s)
      Kei Sakaki, Keita Ohishi, Tetsu Shimizu, Ikki Kobayashi, Naoki Mori, Kenichi Matsuda, Takeo Tomita, Hidenori Watanabe, Kan Tanaka, Tomohisa Kuzuyama and Makoto Nishiyama
    • Journal Title

      Nature Chem. Biol.

      Volume: 16 Issue: 4 Pages: 415-422

    • DOI

      10.1038/s41589-019-0461-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biochemical characterization of archaeal homocitrate synthase from Sulfolobus acidocaldarius2019

    • Author(s)
      Suzuki, T., Akiyama, N., Ayako, Y., Tomita, T., Lassak, K., Haurat, M. F., Okada, T., Takahashi, K., Albers, S.-V., Kuzuyama, T., and Nishiyama, M.
    • Journal Title

      FEBS Letters

      Volume: 594 Issue: 1 Pages: 126-134

    • DOI

      10.1002/1873-3468.13550

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] An ornithine ω-aminotransferase required for growth in the absence of exogenous proline in the archaeon Thermococcus kodakarensis2018

    • Author(s)
      Zheng Ren-Chao、Hachisuka Shin-ichi、Tomita Hiroya、Imanaka Tadayuki、Zheng Yu-Guo、Nishiyama Makoto、Atomi Haruyuki
    • Journal Title

      Journal of Biological Chemistry

      Volume: 293 Issue: 10 Pages: 3625-3636

    • DOI

      10.1074/jbc.ra117.001222

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discovery of Unprecedented Hydrazine-Forming Machinery in Bacteria2018

    • Author(s)
      Matsuda Kenichi、Tomita Takeo、Shin-ya Kazuo、Wakimoto Toshiyuki、Kuzuyama Tomohisa、Nishiyama Makoto
    • Journal Title

      Journal of the American Chemical Society

      Volume: 140 Issue: 29 Pages: 9083-9086

    • DOI

      10.1021/jacs.8b05354

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nobel stand-alone RAM-domain mediated catalytic control of anthranilate phosphoribosyltransferase in tryptophan biosynthesis in Thermus thermophilus2017

    • Author(s)
      T. Kubota, H. Matsushita, T. Tomita, S. Kosono, M. Yoshida, T. Kuzuyama, M. Nishiyama
    • Journal Title

      Extremophiles

      Volume: 1 Issue: 1 Pages: 73-83

    • DOI

      10.1042/bcj20160699

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Genome mining of amino group carrier protein-mediated machinery: discovery and biosynthetic characterization of a natural product with unique hydrazone unit2017

    • Author(s)
      K. Matsuda, F. Hasebe, Y. Shiwa, Y. Kanesaki, T. Tomita, H. Yoshikawa, K. Shin-ya, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      ACS Chemical Biology

      Volume: 12 Issue: 1 Pages: 124-131

    • DOI

      10.1021/acschembio.6b00818

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW2017

    • Author(s)
      S. Fujita, F. Hasebe, S.-H. Cho, T. Tomita, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 491 Issue: 2 Pages: 409-415

    • DOI

      10.1016/j.bbrc.2017.07.088

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Presentation] 放線菌由来1-azabicyclo[3.1.0]hexane環含有化合物におけるアジリジン環合成機構の解明2022

    • Author(s)
      黒澤菫、長谷部文人、岡村仁則、吉田彩子、富田武郎、滝川浩郷、古園さおり、西山真
    • Organizer
      2022年度日本農芸化学会 京都大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] マレイマイシン類生合成経路の解析2022

    • Author(s)
      曽根祐輔、Muhammad Prima PUTRA、松田研一、古園さおり、西山真
    • Organizer
      2022年度日本農芸化学会 京都大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 放線菌においてAmCPを介して生産される新規天然化合物の探索と同定2022

    • Author(s)
      宮永寛哉、曽根祐輔、古園さおり、西山真
    • Organizer
      2022年度日本農芸化学会 京都大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilusのリジン生合成におけるタンパク質間相互作用に関する研究2022

    • Author(s)
      森田裕太郎、叶思言、吉田彩子、古園さおり、西山真
    • Organizer
      2022年度日本農芸化学会 京都大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilusのリジン生合成におけるLysVの機能解析2021

    • Author(s)
      森田裕太郎、叶思言、吉田彩子、古園さおり、西山真
    • Organizer
      2021年極限環境生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Streptomyces lydicusにおけるAmCPを介して生合成される新規化合物の探索2021

    • Author(s)
      林勇太、曽根祐輔、吉田彩子、古園さおり、西山真
    • Organizer
      2021年度(第35回)日本放線菌学会大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] AmCPを介して生合成される新規二次代謝産物の探索2021

    • Author(s)
      宮永寛哉、曽根祐輔、吉田彩子、古園さおり、西山真
    • Organizer
      生合成若手シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] Type II AmCPを介した二次代謝産物の生合成2021

    • Author(s)
      曽根祐輔、Muhammad Prima Putra、松田 研一、古園さおり、西山真
    • Organizer
      生合成若手シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] 超好熱性アーキアにおけるリジン・アルギニン生合成2021

    • Author(s)
      西山真
    • Organizer
      日本農芸化学会 2021年度大会 シンポジウム
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] type II AmCPを介して生合成される新規アミノ酸の同定及び生合成に関する研究2021

    • Author(s)
      曽根 祐輔、Muhammad Prima PUTRA、松田 研一、古園 さおり、西山 真
    • Organizer
      日本農芸化学会 2021年度大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Studies on the biosynthetic machinery in secondary metabolism of Streptomyces to form 1-azabicyclo[3.1.0]hexane ring via aziridine ring2021

    • Author(s)
      Sumire KUROSAWA, Kenichi MATSUDA, Fumihito HASEBE, Takeo TOMITA, Tomohisa KUZUYAMA, Saori KOSONO, Makoto NISHIYAMA
    • Organizer
      日本農芸化学会 2021年度大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 放線菌の生産する抗細菌化合物Ficelomycinの生合成機構2020

    • Author(s)
      西山真
    • Organizer
      ビタミンB研究協議会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 放線菌の生産するアザビシクロ環含有化合物vazabitide A生合成におけるアジリジン環合成経路に関する研究2020

    • Author(s)
      黒澤 菫、松田 研一、長谷部 文人、富田 武郎、葛山 智久、西山 真
    • Organizer
      日本農芸化学会 2020年度大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Serratia sp. ATCC 39006におけるアミノ基キャリアタンパク質を介した生合成についての研究2020

    • Author(s)
      平島 佑樹、曽根 祐輔、菊池 恒志郎、富田 武郎、葛山 智久、古園 さおり、西山 真
    • Organizer
      日本農芸化学会 2020年度大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] typeII AmCPを介して生合成されるマレイマイシン類の生合成機構に関する研究2020

    • Author(s)
      曽根 祐輔、Muhammad Prima PUTRA、松田 研一、葛山 智久、古園 さおり、西山 真
    • Organizer
      日本農芸化学会 2020年度大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 微生物は未知の物質変換系の宝庫である2019

    • Author(s)
      西山 真
    • Organizer
      福井県立大学 福井バイオインキュベーションセンター設立5周年記念 特別講演会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Biosynthesis and modification of azabicyclo ring-containing compounds2019

    • Author(s)
      Makoto Nishiyama
    • Organizer
      2nd China-Japan Symposium on Natural Product Biosynthesis
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] アザビシクロ環含有ジペプチドficellomycinの生合成機構に関する研究2019

    • Author(s)
      黒澤菫、松田研一、長谷部文人、富田武郎、葛山智久、西山真
    • Organizer
      2019年度日本農芸化学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 超好熱・好酸性古細菌Sulfolobus acidocaldarius由来のホモクエン酸合成酵素の構造・機能解析2019

    • Author(s)
      鈴木智大、富田武郎、葛山智久、西山真
    • Organizer
      2019年度日本農芸化学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Maleimycin Biosynthesis is mediated by Type II Amino-group Carrier Protein in Streptomyces sp.2019

    • Author(s)
      Muhammad Prima Putra, Kenichi Matsuda, Takeo Tomita, Kazuo Shin-ya, Tomohisa Kuzuyama, Makoto Nishiyama
    • Organizer
      2019年度日本農芸化学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Amino group carrier protein, a new platform in primary and secondary metabolite biosynthesis2018

    • Author(s)
      Makoto Nishiyama
    • Organizer
      2nd EFB-AFOB Joint Symposium on Applied Biocatalysis
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Amino-group carrier protein-mediated biosynthesi of primary and secondary metabolites2018

    • Author(s)
      Makoto Nishiyama
    • Organizer
      2018 Sino-Japan Symposium on Biocatalysis and Biotransformation
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ヒドラジンを生合成する酵素システムの発見2018

    • Author(s)
      西山真
    • Organizer
      第453回ビタミンB研究協議会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Amino-group carrier protein, a new key machinery contributing to expansion of structural diversity of secondary metabolite2018

    • Author(s)
      Makoto Nishiyama
    • Organizer
      1st Japanese-German Symposium on Biosynthesis and Function of Natural Products
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Discovery of unprecedented lysine biosynthesis using a carrier protein in Thermus thermophilus2018

    • Author(s)
      Makoto Nishiyama
    • Organizer
      International Workshop on 50th anniversary of Thermus thermophilus discovery
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 放線菌の生産するアザビシクロ環含有化合物の生合成機構に関する研究2018

    • Author(s)
      黒澤菫、西山真
    • Organizer
      第9回醗酵学フォーラム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 微生物における生合成機能の多様性2018

    • Author(s)
      西山 真
    • Organizer
      第32回 バイオテクノロジー懇談会(応用微生物・分子細胞性物学研究奨励会)
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] ficellomycin生合成におけるアザビシクロ環の修飾機構に関する研究2018

    • Author(s)
      黒澤 菫、松田 研一、長谷部 文人、富田 武郎、葛山 智久、西山 真
    • Organizer
      日本農芸化学会2018年度大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 超好熱・好酸性古細菌Sulfolobus acidocaldariusのホモクエン酸合成酵素の構造・機能及びフィードバック阻害機構の解析2018

    • Author(s)
      鈴木 智大、富田 武郎、葛山 智久、西山 真
    • Organizer
      日本農芸化学会2018年度大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Studies on Secondary Metabolic Pathway Mediated by Type II Amino-group Carrier Protein in Streptomyces sp.2018

    • Author(s)
      M. Prima PUTRA , K. Matsuda, T. Tomita, K. Shin-ya, T. Kuzuyama, M. Nishiyama
    • Organizer
      日本農芸化学会2018年度大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Secondary metabolite biosynthesis mediated by amino-group carrier protein in Streptomyces2017

    • Author(s)
      Makoto Nishiyama
    • Organizer
      9th US-Japan Seminar on the Biosynthesis of Natural Products
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Secondary metabolite biosynthesis mediated by amino-group carrier protein in Streptomyces2017

    • Author(s)
      Makoto Nishiyama
    • Organizer
      Joint Symposium on Microbial Biotechnology
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Amino-group carrier protein mediated amino acid biosynthesis2017

    • Author(s)
      Makoto Nishiyama
    • Organizer
      The 19th Japanese-German Workshop on Enzyme Technology
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] atural compound biosynthesis mediated by amino-group carrier protein: discovery of novel N-N bond forming enzyme system2017

    • Author(s)
      Makoto Nishiyama
    • Organizer
      New Trends in Enzyme and Microbial Science in the Translational Biology Era
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 放線菌におけるアミノ基キャリアタンパク質を介して生合成される非タンパク性アミノ酸の修飾機構に関する研究2017

    • Author(s)
      黒澤菫, 松田研一, 長谷部文人, 葛山智久, 西山真
    • Organizer
      日本放線菌学会2017年度大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Studies on secondary metabolic pathway mediated by type II amino-group carrier protein (AmCP)in Streptomyces sp.2017

    • Author(s)
      M. Prima Putra,K. Naito, K. Matsuda, T. Tomita, K. Shin-ya, T. Kuzuyama, M. Nishiyama
    • Organizer
      日本放線菌学会2017年度大会
    • Related Report
      2017 Annual Research Report
  • [Remarks] 東京大学生物生産工学研究センター 細胞機能工学研究室

    • URL

      http://park.itc.u-tokyo.ac.jp/biotec-res-ctr/saiboukinou/

    • Related Report
      2019 Annual Research Report

URL: 

Published: 2017-06-01   Modified: 2023-10-16  

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