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Search for peptide-biosynthetic genes using hydroxy amino acid tracers

Research Project

Project/Area Number 24688010
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Applied microbiology
Research InstitutionKyoto University

Principal Investigator

HIBI Makoto  京都大学, (連合)農学研究科(研究院), 助教 (30432347)

Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥26,910,000 (Direct Cost: ¥20,700,000、Indirect Cost: ¥6,210,000)
Fiscal Year 2014: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000)
Fiscal Year 2013: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2012: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000)
Keywords水酸化アミノ酸 / ペプチド生合成 / アミノ酸変換酵素 / α-ケトグルタル酸依存性ジオキシゲナーゼ / 非リボソームペプチド合成酵素 / 機能性ペプチド
Outline of Final Research Achievements

By the gene cluster analysis method based on amino acid hydroxylase (DO), biosynthetic pathway elucidation of novel peptide molecular species was carried out. A partial peptide biosynthetic pathway was revealed by functional analysis of each constitutive enzyme in non-ribosomal peptide synthesis (NRPS) cluster including a DO gene found in the genome of Burkholderia ambifaria AMMD. Also, novel DOs were found from filamentous fungi to generate hydroxy cyclic amino acids, which often constitute peptides, and were applied to detailed enzymatic characterization analysis. Taking advantage of these results, isotopically labeled hydroxy amino acids were successfully produced by enzyme catalytic processes, and were it possible to trace microbial metabolic intermediates in peptide biosynthesis.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (28 results)

All 2015 2014 2013 2012

All Journal Article (14 results) (of which Peer Reviewed: 14 results,  Acknowledgement Compliant: 1 results,  Open Access: 1 results) Presentation (14 results) (of which Invited: 4 results)

  • [Journal Article] Multi-Enzymatic Synthesis of Optically Pure β-Hydroxy α-Amino Acids2015

    • Author(s)
      M. Hibi, T. Kasahara, T. Kawashima, H. Yajima, S. Kozono, S.V. Smirnov, T. Kodera, M. Sugiyama, S. Shimizu, K. Yokozeki, J. Ogawa
    • Journal Title

      Adv. Synth. Catal.

      Volume: 357 Issue: 4 Pages: 767-774

    • DOI

      10.1002/adsc.201400672

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Trehalose accumulation enhances tolerance of Saccharomyces cerevisiae to acetic acid2015

    • Author(s)
      Yoko Yoshiyama, Koichi Tanaka, Kohei Yoshiyama, Makoto Hibi, Jun Ogawa, and Jun Shima
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 119 Issue: 2 Pages: 172-175

    • DOI

      10.1016/j.jbiosc.2014.06.021

    • NAID

      110009922577

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characteristics and biotechnology applications of aliphatic amino acid hydroxylases belonging to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily2014

    • Author(s)
      Hibi, M., J. Ogawa
    • Journal Title

      Appl. Microbiol. Biotechnol.

      Volume: 98(9) Issue: 9 Pages: 3869-3876

    • DOI

      10.1007/s00253-014-5620-z

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of a novel l-amino acid oxidase with protein oxidizing activity from Penicillium steckii AIU 0272014

    • Author(s)
      K. Isobe, R. Taira, Y. Hoshi, S. Matsuda, M. Yamada, M. Hibi, S. Kishino, J. Ogawa
    • Journal Title

      J. Biosci. Bioeng.

      Volume: 117 Issue: 6 Pages: 690-695

    • DOI

      10.1016/j.jbiosc.2013.11.008

    • NAID

      110009823152

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Production of a pharmaceutical intermediate via biohydroxylation using whole cells of Rhodococcus rubropertinctus N822014

    • Author(s)
      T. Kimura, C. Ishikawa, A. O. Lozada, K. T. Robins, M. Hibi, J. Ogawa
    • Journal Title

      Biosci. Biotechnol. Biochem.

      Volume: 78 Issue: 10 Pages: 1772-1776

    • DOI

      10.1080/09168451.2014.925781

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Case for an Early Biological Origin of DNA2014

    • Author(s)
      Anthony M. Poole, Nobuyuki Horinouchi, Ryan J. Catchpole, Dayong Si, Makoto Hibi, Koichi Tanaka, Jun Ogawa
    • Journal Title

      Journal of Molecular Evolution

      Volume: 79 Issue: 5-6 Pages: 204-212

    • DOI

      10.1007/s00239-014-9656-6

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural optimization of SadA, an Fe(II)- and α-ketoglutarate-dependent dioxygenase targeting biocatalytic synthesis of N-succinyl-L-threo-3,4-dimethoxyphenylserine.2014

    • Author(s)
      Hui-Min Qin, Takuya Miyakawa, Akira Nakamura, Makoto Hibi, Jun Ogawa, Masaru Tanokura
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 450 Issue: 4 Pages: 1458-1461

    • DOI

      10.1016/j.bbrc.2014.07.008

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Breeding of a Cyclic Imide-Assimilating Bacterium, <i>Pseudomonas putida</i> s52, for High Efficiency Production of Pyruvate2013

    • Author(s)
      M. Hibi, N. Horinouchi, W. Tu, C.L. Soong, M. Ito, T. Segawa, X. Mu, T. Hagishita, K. Yokozeki, S. Shimizu, J. Ogawa
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 77 Issue: 8 Pages: 1650-1654

    • DOI

      10.1271/bbb.130182

    • NAID

      10031195812

    • ISSN
      0916-8451, 1347-6947
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enzymatic synthesis of chiral amino acid sulfoxides by Fe(II)/α-ketoglutarate-dependent dioxygenase2013

    • Author(s)
      Hibi, M., T. Kawashima, H. Yajima, S.V. Smirnov, T. Kodera, M. Sugiyama, S. Shimizu, K. Yokozeki , J. Ogawa
    • Journal Title

      Tetrahedron : Asymmetry

      Volume: 24(17) Issue: 17 Pages: 990-994

    • DOI

      10.1016/j.tetasy.2013.07.017

    • NAID

      120005323888

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization and application of a l-specific amino acid oxidase from Rhodococcus sp. AIU LAB-32013

    • Author(s)
      K. Isobe, S. Satou, E. Matsumoto, S. Yoshida, M. Yamada, M. Hibi, J. Ogawa
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 115 Issue: 6 Pages: 613-617

    • DOI

      10.1016/j.jbiosc.2012.12.003

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of a novel N-substituted L-amino acid dioxygenase from Burkholderia ambifaria AMMD.2013

    • Author(s)
      Hui-Min Qin, Takuya Miyakawa, Min Ze Jia, Akira Nakamura, Jun Ohtsuka, You-Lin Xue, Takashi Kawashima, Takuya Kasahara, Makoto Hibi, Jun Ogawa, Masaru Tanokura
    • Journal Title

      PLoS One

      Volume: 8 Issue: 5 Pages: e63996-e63996

    • DOI

      10.1371/journal.pone.0063996

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 1-Leucine 5-hydroxylase of Nostoc punctiforme is a novel type of Fe(II)/α-ketoglutarate-dependent dioxygenase that is useful as a biocatalyst2013

    • Author(s)
      Hibi, M., T. Kawashima, P.M. Sokolov, S.V. Smirnov, T. Kodera, M. Sugiyama, S. Shimizu, K. Yokozeki, J. Ogawa
    • Journal Title

      Appl. Microbiol. Biotechnol.

      Volume: 97(6) Issue: 6 Pages: 2467-2472

    • DOI

      10.1007/s00253-012-4136-7

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A novel 1-isoleucine-4' -dioxygenase and 1-isoleucine dihydroxylation cascade in Pantoea ananatis2013

    • Author(s)
      S. V. Snirnov, P. M. Sokolov, V. A. Kotlyarova, N.N. Sansonova, T. Kodera, I Sugiyama, T. Torii, M. Hibi, S. Shinizu, K. Yokozeki, J. Ogawa
    • Journal Title

      MicrobiologyOpen

      Volume: (印刷中)

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A novel family of bacterial dioxygenases that catalyse the hydroxylation of free L-amino acids. FEMS Microbiol. Lett., 331 (2), 97-104 (2012).2012

    • Author(s)
      Smirnov, S.V.
    • Journal Title

      FEMS Microbiol. Lett.

      Volume: 331 Issue: 2 Pages: 97-104

    • DOI

      10.1111/j.1574-6968.2012.02558.x

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] Rhodococcus rubropertinctusを用いた水酸化反応による医薬中間体の合成2015

    • Author(s)
      石川 千弘, 宗石 和久, 木村 隆利, 日比 慎, 高橋 里美, 小川 順
    • Organizer
      日本農芸化学会2015年度大会
    • Place of Presentation
      岡山大学
    • Year and Date
      2015-03-26 – 2015-03-29
    • Related Report
      2014 Annual Research Report
  • [Presentation] trans-4-ヒドロキシ-L-ピペコリン酸生産プロセスの開発2015

    • Author(s)
      福田 大, 日比 慎, 森 亮輔, 三宅 良磨, 川端 潤, 高橋 里美, 小川 順
    • Organizer
      日本農芸化学会2015年度大会
    • Place of Presentation
      岡山大学
    • Year and Date
      2015-03-26 – 2015-03-29
    • Related Report
      2014 Annual Research Report
  • [Presentation] Cyclic amino acid hydroxylases found in filamentous fungi2014

    • Author(s)
      M. Hibi, R. Mori, R. Miyake, H. Kawabata, S. Takahashi, J. Ogawa
    • Organizer
      Active Enzyme Molecule 2014
    • Place of Presentation
      富山国際会議場
    • Year and Date
      2014-12-17 – 2014-12-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 糸状菌に由来する新規環状アミノ酸水酸化酵素群の機能解析2014

    • Author(s)
      日比 慎, 森 亮輔, 福田 大, 三宅 良磨, 川端 潤, 高橋 里美, 小川 順
    • Organizer
      第66回日本生物工学会大会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-09 – 2014-09-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] 新規環状アミノ酸水酸化酵素の探索と機能解析2014

    • Author(s)
      森 亮輔、日比 慎、三宅 良磨、川端 潤、高橋 里美、小川 順
    • Organizer
      日本農芸化学会2014年度大会
    • Place of Presentation
      明治大学(川崎)
    • Related Report
      2013 Annual Research Report
  • [Presentation] アミノ酸水酸化反応に有用なα-ケトグルタル酸依存性ジオキシゲナーゼの補基質供給系の開発2014

    • Author(s)
      日比 慎、富田 弥生、矢島 紘子、高橋 里美、小川 順
    • Organizer
      日本農芸化学会2014年度大会
    • Place of Presentation
      明治大学(川崎)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 代謝共役型酵素合成プロセスの有用物質生産への展開2014

    • Author(s)
      日比 慎、堀之内 伸行、木村 隆利、小川 順
    • Organizer
      日本農芸化学会2014年度大会
    • Place of Presentation
      明治大学(川崎)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole-eell biocatalystを用いた立体選択的アミノ酸酸素添加反応の検討2013

    • Author(s)
      日比慎, 笠原拓也, 河嶋隆志, 高橋里美, 小川順
    • Organizer
      日本農芸化学会2013年度大会
    • Place of Presentation
      東北人学(宮城県)
    • Year and Date
      2013-03-24
    • Related Report
      2012 Annual Research Report
  • [Presentation] Bioconversion of amino acids with whole-cell biocatalysts2013

    • Author(s)
      M. Hibi, S. Shimizu, S. Takahashi, J. Ogawa
    • Organizer
      Enzyme Engineering XXII
    • Place of Presentation
      富山国際会議場(富山市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Microbial Fe(II)/α-ketoglutarate-dependent dioxygenases for valuable amino acid productions2013

    • Author(s)
      M. Hibi
    • Organizer
      Biotrans 2013
    • Place of Presentation
      Manchester, UK
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Asymmetric monooxygenation of amino acids by Fe(II)/α-ketoglutarate-dependent dioxygenases2013

    • Author(s)
      M. Hibi, S. Shimizu, S. Takahashi, J. Ogawa
    • Organizer
      The 17th Japanese-German Workshop on Enzyme Technology
    • Place of Presentation
      Hamburg, Germany
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Microbial Fe (II) /α-ketoglutarate-dependent dioxygenases for valuable amino acid productions2012

    • Author(s)
      I Hibi, S. Shiaizu, K. Yokozeki, J. Ogawa
    • Organizer
      13th Swiss Japanese Conference on Biotechnology and Bioprocess Engineering
    • Place of Presentation
      Waizenhausen(Switzerland)
    • Year and Date
      2012-11-04
    • Related Report
      2012 Annual Research Report
  • [Presentation] アミノ酸不斉酵素触媒としてのFe (II)/α-ケトグルタル酸依存性ジオキシゲナーゼ2012

    • Author(s)
      日比慎, 清水昌, 横関健三, 小川順
    • Organizer
      酵素工学研究会第68回講演会
    • Place of Presentation
      東京人学(東京都)
    • Year and Date
      2012-10-05
    • Related Report
      2012 Annual Research Report
  • [Presentation] Burkholderia ambifaria AMMD由来N置換アミノ酸β位水酸化酵素の機能解析2012

    • Author(s)
      日比慎, 笠原拓哉, 河嶋隆志, 横関健三, 清水昌, 小川順
    • Organizer
      2012年度日本農芸化学会関西支部大会
    • Place of Presentation
      京都学園大学(京都府)
    • Year and Date
      2012-09-29
    • Related Report
      2012 Annual Research Report

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Published: 2012-04-24   Modified: 2019-07-29  

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