Development of the comprehensive system for useful secondary metabolism and bioconversion of useful compounds

• Project/Area Number: 20310122
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Applied genomics
• Research Institution: Kitasato University
• Principal Investigator: IKEDA Haruo Kitasato University, 大学院・感染制御科学府, 教授 (90159632)
• Co-Investigator(Kenkyū-buntansha): TAKAMATSU Satoshi 日本大学, 薬学部, 准教授 (30236351) ; KOMATSU Mamoru 北里大学, 大学院・感染制御科学府, 助教 (40414057)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000); Fiscal Year 2010: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2009: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000); Fiscal Year 2008: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
• Keywords: 産業微生物ゲノム / 物質生産 / 染色体再構成 / 二次代謝産物 / 放線菌 / 2次代謝産物 / ゲノム / 産業微生物

Research Abstract

Genetic analysis of production process in secondary metabolites reveals their biosynthetic pathways and their regulatory networks for gene expression. These results reflect on not only basic research but also application to the industrial production process. But almost Streptomyces microorganisms that produce valuable secondary metabolites including antibiotics cannot be applied to molecular genetic approaches (DNA transformation, gene targeting and so on). In this study, we have developed a versatile host for the production of exogenous secondary metabolites using efficient heterologous gene expression system. An industrial anthelmintic antibiotic, avermectin, producer S. avermitilis was used as this model and its chromosome has been engineered for heterologous expression of gene cluster for secondary metabolite biosynthesis. The results indicate that the versatile host constructed is useful for the heterologous expression of many gene clusters for secondary metabolite biosynthesis.

Research Products

• [Journal Article] Genome mining in Streptomyces. Elucidation of the role of Baeyer-Villiger monooxygenases and non-heme iron-dependent dehydrogenase/oxygenases in the final steps of the biosynthesis of pentalenolactone and neopentalenolactone. (2011)
  • Author(s): Seo, M-J. Zhu, D. Endo, S. Ikeda, H. Cane, D.E.
  • Journal Title: Biochemistry 50 Pages: 1739-1754
  • Peer Reviewed
• [Journal Article] Genome mining in Streptomyces. Discovery of an unprecedented P450-catalyzed oxidative rearrangement that is the final step in the biosynthesis of pentalenolactone. (2011)
  • Author(s): Zhu, D. Seo, M-J. Ikeda, H. Cane, D.E.
  • Journal Title: J.Am.Chem.Soc. 133 Pages: 2128-2131
  • Peer Reviewed
• [Journal Article] Characterization of a silent sesquiterpenoid biosynthetic pathway in Streptomyces avermitilis controlling epi-isozizaene and albaflavenone biosynthesis and isolation of a new oxidized epi-isozizaene metabolite. (2011)
  • Author(s): Takamatsu, S. Lin, X. Nara, A. Komatsu, M. Cane, D.E. Ikeda, H.
  • Journal Title: Microb.Biotechnol. 4 Pages: 184-191
  • Peer Reviewed
• [Journal Article] Biosynthesis of 2-methylisoborneol in Cyanobacteria. (2011)
  • Author(s): Giglio, S. Chou, W.K.W. Ikeda, H. Cane, D.E. Monis, T.
  • Journal Title: Environ.Sci.Technol. 45 Pages: 992-998
  • Peer Reviewed
• [Journal Article] Pentalenic acid is a shunt metabolite in the biosynthesis of the pentalenolactone family of metabolites : Hydroxylation of 1-deoxypentalenic acid mediated by CYP105D7 (SAV_7469) of Streptomyces avermitilis. (2011)
  • Author(s): Takamatsu, S. Lin, X. Fushinobu, S. Shoun, H, Komatsu, M. Cane, D.E. Ikeda, H.
  • Journal Title: J.Antibiot. 64 Pages: 65-71
  • NAID: 10030637591
  • Peer Reviewed
• [Journal Article] Pentalenic acid is a shunt metabolite in the biosynthesis of the pentalenolactone family of metabolites : Hydroxylation of 1-deoxypentalenic acid mediated by CYP105D7 (SAV_7469) of Streptomyces avermitilis. (2011)
  • Author(s): Takamatsu, S., et al.
  • Journal Title: J.Antibiot. Volume: 64 Pages: 65-71
  • NAID: 10030637591
  • Peer Reviewed
• [Journal Article] Biosynthesis of 2-methylisoborneol in Cyanobacteria. (2011)
  • Author(s): Giglio, S., et al.
  • Journal Title: Environ.Sci.Technol. Volume: 45 Pages: 992-998
  • Peer Reviewed
• [Journal Article] pi-isozizaene and albaflavenone biosynthesis and isolation of a new oxidized epi-isozizaene metabolite. (2011)
  • Author(s): Takamatsu, S., et al.
  • Journal Title: Microb.Biotechnol. Volume: 4 Pages: 184-191
  • Peer Reviewed
• [Journal Article] Genome sequence of Kitasatospora setae NBRC 14216T : An evolutionary snapshot of the family Streptomycetaceae. (2010)
  • Author(s): Ichikawa, N. Oguchi, A. Ikeda, H. Ishikawa, J. Kitani, S. Watanabe, Y. Nakamura, S. Katano, Y. Kishi, E. Sasagawa, M. Ankai, A. Fukui, S. Hashimoto, Y. Kamata, S. Otoguro, M. Nihira, T. Horinouchi, S. Ohnishi, Y. Hayakawa, M. Kuzuyama, T. Arisawa, A. Nomoto, F. Miura, H. Takahashi, Y. Fijita, N.
  • Journal Title: DNA Res. 17 Pages: 393-406
  • Peer Reviewed
• [Journal Article] Regio-and stereospecificity of filipin hydroxylation sites revealed by crystal structure of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis. (2010)
  • Author(s): Lin, X. Fushinobu, S. Takamatsu, S. Wakagi, T, Ikeda, H. Shoun, H.
  • Journal Title: J.Biol.Chem. 285 Pages: 16844-16853
  • Peer Reviewed
• [Journal Article] Genome mining in Streptomyces avermitilis : Cloning and characterization of SAV_76, the synthase for a new sesquiterpene. avermitilol. (2010)
  • Author(s): Chou, W.K.W. Fanizza, I. Uchiyama, T. Komatsu, M. Ikeda, H. Cane, D.E.
  • Journal Title: J.Am.Chem.Soc. 132 Pages: 8850-8851
  • Peer Reviewed
• [Journal Article] Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. (2010)
  • Author(s): Komatsu, M. Uchiyama, Takuma, Cane, D.E. Omura, S. Ikeda, H.
  • Journal Title: Proc.Natl.Acad.Sci.USA. 107 Pages: 2646-2651
  • Peer Reviewed
• [Journal Article] Genome Mining in Streptomyces avermitilis : Cloning and characterization of SAV_76, the synthase for a New sesquiterpene.Avermitilol. (2010)
  • Author(s): Chou, W.K.W., et al.
  • Journal Title: J.Am.Chem.Soc Volume: 132 Pages: 8850-8851
  • Peer Reviewed
• [Journal Article] Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structure of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis. (2010)
  • Author(s): Lin, X., et al.
  • Journal Title: J.Biol.Chem. Volume: 285 Pages: 16844-16853
  • Peer Reviewed
• [Journal Article] Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. (2010)
  • Author(s): Komatsu, M., et al.
  • Journal Title: Proc.Natl.Acad.Sci.USA. Volume: 107 Pages: 2646-2651
  • Peer Reviewed
• [Journal Article] Genome sequence of Kitasatospora setae NBRC 14216^T : An evolutionary snapshot of the family Streptomycetaceae. (2010)
  • Author(s): Ichikawa, N., et al.
  • Journal Title: DNA Res. Volume: 17 Pages: 393-406
  • Peer Reviewed
• [Journal Article] Nocardamin production by Streptomyces avermitilis. (2009)
  • Author(s): Ueki, M. Suzuki, R. Takamatsu, S. Takagi, H. Uramoto, M. Ikeda, H. Osada, H.
  • Journal Title: Actinomycetol 23 Pages: 34-39
  • NAID: 10025872918
  • Peer Reviewed
• [Journal Article] Genomic basis for natural product biosynthetic diversity in the actinomycetes. (2009)
  • Author(s): Nett, M. Ikeda, H. Moore, B.S.
  • Journal Title: Nat.Prod.Rep. 26 Pages: 1362-1384
  • Peer Reviewed
• [Journal Article] Genome mining in Streptomyces avermitilis : A biochemical Baeyer-Villiger reaction and discovery of a new branch of the pentalenolactone family tree. (2009)
  • Author(s): Jiang, J. Tetzlaff, C.N. Takamatsu, S. Iwatsuki, M. Komatsu, M. Ikeda, H. Cane, D.E.
  • Journal Title: Biochemistry 48 Pages: 6431-6440
  • Peer Reviewed
• [Journal Article] The site-specific recombination system of actinophage TG1. (2009)
  • Author(s): Morita, K. Yamamoto, T. Fusada, N. Komatsu, M. Ikeda, H. Hirano, N. Takahashi, H.
  • Journal Title: FEMS Microbiol.Lett. 297 Pages: 234-240
  • Peer Reviewed
• [Journal Article] In vitro characterization of the site-specific recombination system based on actinophage TG1 integrase. (2009)
  • Author(s): Morita, K. Yamamoto, T. Fusada, N. Komatsu, M. Ikeda, H. Hirano, N. Takahashi, H.
  • Journal Title: Mol.Genet.Genome. 282 Pages: 607-616
  • Peer Reviewed
• [Journal Article] Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes. (2009)
  • Author(s): Tanaka, Y. Komatsu, M. Okamoto, S. Tokuyama, S. Kaji, A. Ikeda, H. Ochi, K.
  • Journal Title: Appl.Env.Microbiol. 75 Pages: 4919-4922
  • Peer Reviewed
• [Journal Article] Characterization of a regulatory gene, aveR, for the biosynthesis of avermectin in Streptomyces avermitilis. (2009)
  • Author(s): Kitani, S. Ikeda, H. Sakamoto, T. Noguchi, S. Nihira, T.
  • Journal Title: Appl.Microbiol Biotechnol. 82 Pages: 1089-1096
  • Peer Reviewed
• [Journal Article] Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis : conformational flexibility and histidine ligand state. (2009)
  • Author(s): Lin, X. Fushinobu S. Ikeda H. Wakagi T. Shoun H.
  • Journal Title: J.Bacteriaol. 191 Pages: 1211-1219
  • Peer Reviewed
• [Journal Article] Genomic basis for natural product biosynthetic diversity in the actinomycetes (2009)
  • Author(s): Nett, M.Ikeda, H.Moore, BS
  • Journal Title: Nat.Prod.Rep 26 Pages: 1362-1384
  • Peer Reviewed
• [Journal Article] Genome mining in Streptomyces avermitilis : A biochemical Baeyer-Villiger reaction and discovery of a new branch of the pentalenolactone family tree (2009)
  • Author(s): Jiang, J., et.al.
  • Journal Title: Biochemistry 48 Pages: 6431-6440
  • Peer Reviewed
• [Journal Article] Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes (2009)
  • Author(s): Tanaka Y., et.al.
  • Journal Title: Appl.Env.Microbiol 75 Pages: 4919-4922
  • Peer Reviewed
• [Journal Article] In vitro characterization of the site-specific recombination system based on actinophage TG1 integrase (2009)
  • Author(s): Morita, K., et.al.
  • Journal Title: Mol.Genet.Genome 228 Pages: 607-616
  • Peer Reviewed
• [Journal Article] The site-specific recombination system of actinophageTG1 (2009)
  • Author(s): Morita, K., et.al.
  • Journal Title: FEMS Microbiol.Lett 297 Pages: 234-240
  • Peer Reviewed
• [Journal Article] Characterization of a regulatory gene, aveR, for the biosynthesis of avermectin in Streptomyces avermitilis (2009)
  • Author(s): Kitani, S., et.al.
  • Journal Title: Appl.Microbiol Biotechnol. 82 Pages: 1089-1096
  • Peer Reviewed
• [Journal Article] Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis : conformational flexibility and histidine ligand state (2009)
  • Author(s): Xu, LH., et.al.
  • Journal Title: J.Bacteriaol 191 Pages: 1211-1219
  • Peer Reviewed
• [Journal Article] Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol (2009)
  • Author(s): M. Komatsu, M. Tsuda, S. Omura, H. Oikawa, H. Ikeda
  • Journal Title: Proc. Natl. Acad. Sci. USA. 105 Pages: 7423-7427
  • Peer Reviewed
• [Journal Article] Crystal Structures of Cytochrome P450 105P1 from Streptomyces avermitilis : Conformational Flexibility and Histidine Ligation State (2009)
  • Author(s): L. -H. Xu, S. Fushinobu, H. Ikeda, T. Wakagi, H. Shoun
  • Journal Title: J. Bacteriol. 191 Pages: 1211-1219
  • Peer Reviewed
• [Journal Article] Characterization of a regulatory gene, aveR, for the biosynthesis of avermectin in Streptomyces avermitilis (2009)
  • Author(s): S. Kitani, H. Ikeda, T. Sakamoto, S. Noguchi, T. Nihira
  • Journal Title: Appl. Microbiol. Biotechnol. 82 Pages: 1089-1096
  • Peer Reviewed
• [Journal Article] Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol. (2008)
  • Author(s): Komatsu, M. Tsuda, M. Omura, S. Oikawa, H. Ikeda, H.
  • Journal Title: Proc.Natl.Acad.Sci.USA. 105 Pages: 7422-7427
  • Peer Reviewed
• [Journal Article] Organization of the biosynthetic gene cluster for the polyketide antitumor macrolide, Pladienolide, in Streptomyces platensis Mer-11107. (2008)
  • Author(s): Machida, K. Arisawa, A. Takeda, S. Tsuchida, T. Aritoku, Y. Yoshida, M. Ikeda, H.
  • Journal Title: Biosci.Biotechnol.Biochem. 72 Pages: 2946-2952
  • NAID: 10027534096
  • Peer Reviewed
• [Presentation] Exploring the bacterial terpenome (2010)
  • Author(s): Ikeda, H.
  • Organizer: RIKEN Chemical Biology International Symposium
  • Place of Presentation: Wako, Japan(Invited Symposium)
  • Year and Date: 2010-10-26
• [Presentation] Discovery of new sesquiterpenoid compounds, "Avermitilol" and"Avermitilone" by genome mining of Streptomyces avermitilis (2010)
  • Author(s): Ikeda, H.
  • Organizer: 2010 KSBB Fall Meeting & International Symposium.
  • Place of Presentation: Incheon, Korea(Invited Symposium)
  • Year and Date: 2010-10-08
• [Presentation] Cytochrome P450s are involved in the biosynthesis and shnut metabolism of pentalenolactone family of metabolites in Streptomyces avermitilis. (2010)
  • Author(s): Ikeda, H.
  • Organizer: Actinobacteria and application of their oxidoreductases (Seoul National University, Seoul Development Institute)
  • Place of Presentation: Seoul, Korea(Invited Symposium)
  • Year and Date: 2010-10-07
• [Presentation] 物質生産のためのStreptomyces avermitilisのゲノム改変 (2010)
  • Author(s): 池田治生
  • Organizer: 2010年度日本放線菌学会大会
  • Place of Presentation: 東京
  • Year and Date: 2010-09-02
• [Presentation] Characterization of relA mutant of industrial microorganism Streptomyces avermitilis (2010)
  • Author(s): Komatsu, M.Tanaka, Y.Ochi, K.Ikeda, H.
  • Organizer: 11^<th> International Symposium on the Genetics of Industrial Microorganisms
  • Place of Presentation: Melbourne, Australia
  • Year and Date: 2010-06-30
• [Presentation] Optimized Streptomyces host for the heterologous expression of secondary metabolism. (2010)
  • Author(s): Ikeda H., Komatsu M., Uchiyama T.
  • Organizer: 11^<th> International Symposium on the Genetics of Industrial Microorganisms.
  • Place of Presentation: Melbourone, Australia
  • Year and Date: 2010-06-29
• [Presentation] Waking up bacterial sleeping genes: a new method to elicit bacterial capabilities. (2010)
  • Author(s): Ochi K., Tanaka Y., Komatsu M., Hosaka H., Ikeda H.
  • Organizer: 11^<th> International Symposium on the Genetics of Industrial Microorganisms.
  • Place of Presentation: Melbourone, Australia
  • Year and Date: 2010-06-29
• [Presentation] Characterization of relA mutant of industrial microorganism Streptomyces avermitilis. (2010)
  • Author(s): Komatsu M., Tanaka Y., Ochi K., Ikeda H.
  • Organizer: 11^<th> International Symposium on the Genetics of Industrial Microorganisms.
  • Place of Presentation: Melbourone, Australia
  • Year and Date: 2010-06-29
• [Presentation] Optimized Streptomyces host for the heterologous expression of secondary metabolism. (2010)
  • Author(s): Ikeda, H.Komatsu, M.Uchiyama, T.
  • Organizer: 11^<th> International Symposium on the Genetics of Industrial Microorganisms
  • Place of Presentation: Melbourne, Australia(Invited Symposium)
  • Year and Date: 2010-06-29
• [Presentation] Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism (2010)
  • Author(s): Haruo Ikeda
  • Organizer: 5^<th> Japan-Korea Chemical Biology symposium
  • Place of Presentation: Busan, Korea
  • Year and Date: 2010-01-27
• [Presentation] A versatile host for secondary metabolite production and its regulatiry analysis (2009)
  • Author(s): Haruo Ikeda
  • Organizer: 15^<th> International Symposium on the Biology of Actinomycetes
  • Place of Presentation: Shanghai, China
  • Year and Date: 2009-08-21
• [Presentation] Minimization of Streptomyces avermitilis genome for use as metabolic machinery (2009)
  • Author(s): Haruo Ikeda
  • Organizer: 2009 Seoul Conference in Actinomycetes
  • Place of Presentation: Seoul, Korea
  • Year and Date: 2009-08-18
• [Presentation] 異なったストレプトマイシン耐性変異(rsmGおよびrpsL)導入による放線菌の抗生物質生産性の増強放線菌由来フラボヘモグロビンパラログに関する研究Streptomyces avermitilis SUKAlにおける4-ヒドロキシ酪酸の発酵生産の構築16員環マクロライドBafilomycinの生合成遺伝子群の解析16員環マクロライドbafIlomycInの側鎖生合成遺伝子の解析産業利用放線菌を宿主としたァミノグリコシド抗生物質の生産ァクテノアァージTGIの産生するSer型インテグテーゼによる部位特異的組み換え機構の解析アクテノァァージTGIインテグラーゼの部位特異的組み換えに関わる配列要素の解析 (2009)
  • Author(s): 1. 田中幸徳, 小松護, 岡本晋, 徳山真治, 池田治生, 越智幸三2. 加藤慶一, 池田宗一郎, 吉本明弘, 黒木進吾, 矢嶋俊介, 池田治生, 大澤貫寿, 祥雲弘文3. 信殿正光, 春日和, 志村洋一郎, 古澤結子, 田母神繁, 小林正之, 池田治生, 小嶋郁夫4. 奈良綾子, 沼田淳, 小松護, 高松智, 葛山智久, 池田治生5. 沼田淳, 奈良綾子, 小松護, 池田治生, 葛山智久, 西山真6. 小松護, 高野英晃, 春日和, 高松智, 上田賢志, 小嶋郁夫, 池田治生T. 森田健太郎, 山本智之, 房田直記, 小松護, 池田治生, 平野展孝, 高橋秀夫8. 山本智之, 森田健太郎, 房田直記, 小松護, 池田治生, 平野展孝, 高橋秀夫
  • Organizer: 日本農芸化学会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2009-03-29
• [Presentation] 16員環マクロライドBafilomycinの生合成遺伝子群の解析Streptomyces avermitilisにおけるオートレギュレータ制御系についてストレプトマイシン弱耐性変異rmsG導入によるStreptomyces属の二次代謝能の変化微生物ゲノムデーターベースからの異臭物質(2-methylisoborneol)生合成遺伝子の同定 (2008)
  • Author(s): 1. 奈良綾子, 小松護, 高橋洋子, 藤田信之, 池田治生2. 宮本聖子, 木谷茂, 池田治生, 仁平卓也3. 田中幸徳, 岡本晋, 小松護, 徳山真治, 池田治生, 越智幸三4. 小松護, 津田宗哉, 大村智, 及川英秋, 池田治生
  • Organizer: 日本放線菌学会
  • Place of Presentation: フルーツパーク富士屋ホテル
  • Year and Date: 2008-07-10
• [Presentation] Comparative Analysis of Biosynthetic Gene Clusters for Anthelmintic Macrocyclic Lactones (2008)
  • Author(s): Haruo Ikeda
  • Organizer: 7^<th> US-Japan Seminar on the Biosynthesis of Natural Products
  • Place of Presentation: La JoIIa, California, U.S.A.
  • Year and Date: 2008-06-23
• [Remarks] ホームページ
  • URL: http://avermitilis.ls.kitasato-u.ac.jp/
• [Remarks]
  • URL: http://avermitilis.ls.kitasato-u.ac.jp/
• [Remarks]
  • URL: http://avermitilis.ls.kitasato-u.ac.jp/
• [Remarks]
  • URL: http://avermitilis.ls.kitasato-u.ac.jp