Search for peptide-biosynthetic genes using hydroxy amino acid tracers

• Project/Area Number: 24688010
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Applied microbiology
• Research Institution: Kyoto 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: ¥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.

Research Products

• [Journal Article] Multi-Enzymatic Synthesis of Optically Pure β-Hydroxy α-Amino Acids (2015)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Trehalose accumulation enhances tolerance of Saccharomyces cerevisiae to acetic acid (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Characteristics and biotechnology applications of aliphatic amino acid hydroxylases belonging to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily (2014)
  • 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
  • Peer Reviewed
• [Journal Article] Characterization of a novel l-amino acid oxidase with protein oxidizing activity from Penicillium steckii AIU 027 (2014)
  • 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
  • Peer Reviewed
• [Journal Article] Production of a pharmaceutical intermediate via biohydroxylation using whole cells of Rhodococcus rubropertinctus N82 (2014)
  • 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
  • Peer Reviewed
• [Journal Article] The Case for an Early Biological Origin of DNA (2014)
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Breeding of a Cyclic Imide-Assimilating Bacterium, <i>Pseudomonas putida</i> s52, for High Efficiency Production of Pyruvate (2013)
  • 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
  • Peer Reviewed
• [Journal Article] Enzymatic synthesis of chiral amino acid sulfoxides by Fe(II)/α-ketoglutarate-dependent dioxygenase (2013)
  • 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
  • Peer Reviewed
• [Journal Article] Characterization and application of a l-specific amino acid oxidase from Rhodococcus sp. AIU LAB-3 (2013)
  • 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
  • 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
  • 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 biocatalyst (2013)
  • 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
  • Peer Reviewed
• [Journal Article] A novel 1-isoleucine-4' -dioxygenase and 1-isoleucine dihydroxylation cascade in Pantoea ananatis (2013)
  • 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)
  • 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
  • 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
• [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
• [Presentation] Cyclic amino acid hydroxylases found in filamentous fungi (2014)
  • 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
• [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
• [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）
• [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）
• [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）
  • 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
• [Presentation] Bioconversion of amino acids with whole-cell biocatalysts (2013)
  • 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）
  • Invited
• [Presentation] Microbial Fe(II)/α-ketoglutarate-dependent dioxygenases for valuable amino acid productions (2013)
  • Author(s): M. Hibi
  • Organizer: Biotrans 2013
  • Place of Presentation: Manchester, UK
  • Invited
• [Presentation] Asymmetric monooxygenation of amino acids by Fe(II)/α-ketoglutarate-dependent dioxygenases (2013)
  • Author(s): M. Hibi, S. Shimizu, S. Takahashi, J. Ogawa
  • Organizer: The 17th Japanese-German Workshop on Enzyme Technology
  • Place of Presentation: Hamburg, Germany
  • Invited
• [Presentation] Microbial Fe (II) /α-ketoglutarate-dependent dioxygenases for valuable amino acid productions (2012)
  • 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
• [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
• [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