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Study of genome of pesticide-degrading bacteria as a representative of environmental bacterium

Research Project

Project/Area Number 16580050
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied microbiology
Research InstitutionTohoku University

Principal Investigator

NAGATA Yuji  Tohoku University, Graduate School of Life Sciences, Associate Professor, 大学院・生命科学研究科, 助教授 (30237531)

Co-Investigator(Kenkyū-buntansha) TSUDA Masataka  Tohoku University, Graduate School of Life Sciences, Professor, 大学院・生命科学研究科, 教授 (90172022)
Project Period (FY) 2004 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥3,800,000 (Direct Cost: ¥3,800,000)
Fiscal Year 2005: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 2004: ¥2,700,000 (Direct Cost: ¥2,700,000)
Keywordsenvironmental pollutant / hexachlorocyclohexane / sphingomonads / genome / horizontal gene transfer / transconjugative plasmid / chlorinated pesticide / adaptation / 水平伝達 / Sphingomonas
Research Abstract

Mechanism for adaptation of environmental bacteria is of great interest. Sphingobium japonicum (formerly Sphingomonas paucimobilis) UT26 utilizes the important insecticide gamma-hexachlorocyclohexane (HCH) as a sole source of carbon and energy. In this study it was demonstrated that the UT26 genome consists three large circular replicons of 3.6 Mb, 670 kb, and 185 kb. The 3.6 Mb and the 670 kb replicons had one and two copies, respectively, of the 16S ribosomal RNA gene, and these replicons were designated as chromosomes (Chr) I and II, respectively. Chr I was indicated to be a main chromosome carrying the dnaA gene. The first three lin genes, linA to linC, for conversion of gamma-HCH to 2, 5-dichlorohydroquinone, were dispersed on Chr I. The 185 kb plasmid, pCHQ1, carried the linRED operon for the conversion of 2,5-dichlorohydroquinone to maleylacetate and was conjugatively transferred to another sphingomonad strain. The linF gene encoding maleylacetate reductase was located on Chr II. These results indicated that the genes for the complete gamma-HCH degradation are dispersed on the three large replicons of UT26. An endogenous insertion sequence of UT26, ISsp1, was identified, which may be involved in the rearrangement of the UT26 genome. Furthermore, it was revealed that metabolites of gamma-HCH had toxic effect on UT26, and a ABC-type transporter which was essential for the utilization of gamma-HCH in UT26 was identified. These results demonstrated the importance of factors except the catalyzing enzymes for the gamma-HCH assimilation in UT26.

Report

(3 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • Research Products

    (47 results)

All 2006 2005 2004

All Journal Article (47 results)

  • [Journal Article] Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris2006

    • Author(s)
      Nakamura, T. et al.
    • Journal Title

      Protein Expression and Purification 46

      Pages: 85-91

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Functional analysis of unique class II insertion sequence IS10712006

    • Author(s)
      Sota, M. et al.
    • Journal Title

      Appl. Envirn. Microbiol. 72

      Pages: 291-297

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT262006

    • Author(s)
      Nagata, Y. et al.
    • Journal Title

      FEMS Microbiol. Lett. 256

      Pages: 112-118

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Growth inhibition by metabolites of γ-hexachlorocyclohexane in Sphingobium japonicum UT262006

    • Author(s)
      Endo, R. et al.
    • Journal Title

      Biosci. Biotechnol. Biochem. 70

      Pages: 1029-1032

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] メタゲノムは宝の山か?(バイオミディア)2006

    • Author(s)
      永田裕二
    • Journal Title

      日本生物工学会誌 84・2

      Pages: 73-73

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris.2006

    • Author(s)
      Nakamura, T., M.Zamocky, Z.Zdrahal, R.Chaloupkova, M.Monincova, Z.Prokop, Y.Nagata, J.Damborsky
    • Journal Title

      Protein Expression and Purification 46

      Pages: 85-91

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Functional analysis of unique class II insertion sequence IS1071.2006

    • Author(s)
      Sota, T., H.Yano, Y.Nagata, Y.Ohtsubo, H.Genka, H.Anbutsu, H.Kawasaki, M.Tsuda
    • Journal Title

      Appl.Environ.Microbiol. 72

      Pages: 291-297

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26.2006

    • Author(s)
      Nagata, Y., M.Kamakura, R.Endo, R.Miyazaki, Y.Ohtsubo, M.Tsuda
    • Journal Title

      FEMS Microbiol.Lett. 256

      Pages: 112-118

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Growth inhibition by metabolites of γ-hexachlorocyclohexane in Sphingobium japonicum UT26.2006

    • Author(s)
      Endo, R., Y.Ohtsubo, M.Tsuda, Y.Nagata
    • Journal Title

      Biosci.Biotechnol.Biochem. 70

      Pages: 1029-1032

    • NAID

      10018532907

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Is metagenome treasure island?2006

    • Author(s)
      Y.Nagata
    • Journal Title

      Seibutsu-Kogaku Kaishi(in Japanese) 84(2)

      Pages: 73-73

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT262006

    • Author(s)
      Nagata, Y. et al.
    • Journal Title

      FEMS Microbiol.Lett. in press

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Identification of insertion sequence from a γ-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT262005

    • Author(s)
      Miyauchi, K. et al.
    • Journal Title

      Biosci. Biotechnol. Biochem. 69

      Pages: 216-219

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Identification and characterization of genes involved in the downstream degradation pathway of γ-hexachlorocyclohexane in Sphingomonas paucimobilis UT262005

    • Author(s)
      Endo, R. et al.
    • Journal Title

      J. Bacteriol. 187

      Pages: 847-853

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT262005

    • Author(s)
      Nagata, Y. et al.
    • Journal Title

      Appl. Envirn. Microbiol. 71

      Pages: 2183-2185

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Two Rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities2005

    • Author(s)
      Sato, Y. et al.
    • Journal Title

      Appl. Envirn. Microbiol. 71

      Pages: 4372-4379

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 176162005

    • Author(s)
      Nagata, Y. et al.
    • Journal Title

      J. Biosci. Bioeng. 99

      Pages: 603-610

    • NAID

      110002695708

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Mycobacterial haloalkane dehalogenases : cloning, biochemical properties and distribution2005

    • Author(s)
      Jesenska, A. et al.
    • Journal Title

      Appl. Envirn. Microbiol. 71

      Pages: 6736-6745

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Mycobacterial haloalkane dehalogenases : cloning, biochemical properties and distribution2005

    • Author(s)
      永田裕二, 津田雅孝
    • Journal Title

      化学と生物 43

      Pages: 33-42

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] High-temperature-induced transposition of IS elements in Burkholderia multivorans ATCC17616.2005

    • Author(s)
      Ohtsubo, Y. et al.
    • Journal Title

      Appl. Environ. Microbiol. 71

      Pages: 1822-1828

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.2005

    • Author(s)
      Kmunicek, J. et al.
    • Journal Title

      Biochemistry 44

      Pages: 3390-2401

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 有機塩素系殺虫剤分解細菌の出現-代謝系の構築と酵素の機能2005

    • Author(s)
      永田裕二, 津田雅孝
    • Journal Title

      蛋白質核酸酵素 50・12

      Pages: 1511-1518

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Identification of insertion sequence from a γ-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26.2005

    • Author(s)
      Miyauchi, K., M.Fukuda, M.Tsuda, M.Takagi, Y.Nagata
    • Journal Title

      Biosci.Biotechnol.Biochem. 69

      Pages: 216-219

    • NAID

      130000030576

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Identification and characterization of genes involved in the downstream degradation pathway of γ-hexachlorocyclohexane in Sphingomonas paucimobilis UT26.2005

    • Author(s)
      Endo, R., M.Kamakura, K.Miyauchi, M.Fukuda, Y.Ohtsubo, M.Tsuda, Y.Nagata
    • Journal Title

      J.Bacteriol. 187

      Pages: 847-853

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.2005

    • Author(s)
      Nagata, Y., Z.Prokop, Y.Sato, P.Jerabek, A.Kumar, Y.Ohtsubo, M.Tsuda, J.Damborsky
    • Journal Title

      Appl.Environ.Microbiol. 71

      Pages: 2183-2185

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] High-temperature-induced transposition of IS elements in Burkholderia multivorans ATCC 17616.2005

    • Author(s)
      Ohtsubo, Y., H.Genka, H.Komatsu, Y.Nagata, M.Tsuda
    • Journal Title

      Appl.Environ.Microbiol. 71

      Pages: 1822-1828

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.2005

    • Author(s)
      Kmunicek, J., K.Hynkova, T.Jedlicka, Y.Nagata, A.Negri, F.Gago, R.C.Wade, J.Damborsky
    • Journal Title

      Biochemistry 44

      Pages: 3390-3401

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Two Rhizobial strains, Mesorhizobium loci MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities.2005

    • Author(s)
      Sato, Y., M.Monincova, R.Chaloupkova, Z.Prokop, Y.Ohtsubo, K.Minamisawa, M.Tsuda, J.Damborsky, Y.Nagata
    • Journal Title

      Appl.Environ.Microbiol. 71

      Pages: 4372-4379

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616.2005

    • Author(s)
      Nagata, Y., M.Matsuda, H.Komatsu, Y.Imura, H.Sawada, Y.Ohtsubo, M.Tsuda
    • Journal Title

      J.Biosci.Bioeng. 99

      Pages: 603-610

    • NAID

      110002695708

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Mycobacterial haloalkane dehalogenases : cloning, biochemical properties and distribution.2005

    • Author(s)
      Jesenska, A., M.Pavlova, M.Strouhal, R.Chaloupkova, I.Tesinska, M.Monincova, Z.Prokop, M.Bartos, I.Pavlik, I.Rychlik, P.Mobius, Y.Nagata, J.Damborsky
    • Journal Title

      Appl.Environ.Microbiol. 71

      Pages: 6736-6745

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Access to novel genes for the degradation of environmental pollutants by metagenomic approaches.2005

    • Author(s)
      Nagata, Y., M.Tsuda
    • Journal Title

      Kagaku-to-Seibutsu(in Japanese) 43

      Pages: 33-42

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, γ-hexachlorocyclohexane.2005

    • Author(s)
      Nagata, Y., M.Tsuda
    • Journal Title

      Protein, Nucleic Acid, and Enzyme(in Japanese) 50(12)

      Pages: 1511-1518

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT262005

    • Author(s)
      Nagata, Y. et al.
    • Journal Title

      Appl.Envirn.Microbiol 71

      Pages: 2183-2185

    • Related Report
      2005 Annual Research Report
  • [Journal Article] High-temperature-induced transposition of IS elements in Burkholderia multivorans ATCC 176162005

    • Author(s)
      Ohtsubo, Y. et al.
    • Journal Title

      Appl.Envirn.Microbiol 71

      Pages: 1822-1828

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Two Rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium _japonicum USDA 110, encode haloalkane2005

    • Author(s)
      Sato, Y. et al.
    • Journal Title

      Appl.Envirn.Microbiol 71

      Pages: 4372-4379

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 176162005

    • Author(s)
      Nagata, Y. et al.
    • Journal Title

      J.Biosci.Bioeng 99

      Pages: 603-610

    • NAID

      110002695708

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Identification of insertion sequence from a γ-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT262005

    • Author(s)
      Miyauchi, K.et al.
    • Journal Title

      Biosci.Biotechnol.Biochem. 69

      Pages: 216-219

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Identification and characterization of genes involved in the downstream degradation pathway of γ-hexachlorocyclohexane in Sphingomonas paucimobilis UT262005

    • Author(s)
      Endo, R.et al.
    • Journal Title

      J.Bacteriology 187

      Pages: 847-853

    • Related Report
      2004 Annual Research Report
  • [Journal Article] メタゲノム的発想に基づいた新規環境汚染物質分解酵素遺伝子へのアプローチ2005

    • Author(s)
      永田裕二, 津田雅孝
    • Journal Title

      化学と生物 43

      Pages: 33-42

    • NAID

      10016570075

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Crystral structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95Å resolution : dynamics of catalytic residues2004

    • Author(s)
      Oakley, A. et al.
    • Journal Title

      Biochemistry 43

      Pages: 870-878

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Strategies for bioremediation of polychlorinated biphenyls2004

    • Author(s)
      Ohtsubo, Y. et al.
    • Journal Title

      Appl. Microbiol. Biotechnol. 65

      Pages: 250-258

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] 環境細菌ゲノムと環境DNA2004

    • Author(s)
      津田雅孝ら
    • Journal Title

      J. Environ. Biotechnol. 3

      Pages: 69-78

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Crystral structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95Å resolution : dynamics of catalytic residues.2004

    • Author(s)
      Oakley, A.J., M.Klvana, M.Otyepka, Y.Nagata, M.C.Wilce, J.Damborsky
    • Journal Title

      Biochemsitry 43

      Pages: 870-878

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Strategies for bioremediation of polychlorinated biphenyls.2004

    • Author(s)
      Ohtsubo, Y., T.Kudo, M.Tsuda, Y.Nagata
    • Journal Title

      Appl.Microbiol.Biotechnol. 65

      Pages: 250-258

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Genome biology of environmental bacteria and environmental DNA.2004

    • Author(s)
      Tsuda, M., H.Komatsu, Y.Ohtsubo, Y.Nagata
    • Journal Title

      J.Environ.Biotechnol.(in Japanese) 3

      Pages: 69-78

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Crystral structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95Å resolution : dynamics of catalytic residues2004

    • Author(s)
      Oakley, A et al.
    • Journal Title

      Biochemsitry 43

      Pages: 870-878

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 環境細菌ゲノムと環境DNA2004

    • Author(s)
      津田雅孝
    • Journal Title

      J.Environ.Biotechnol. 3

      Pages: 69-78

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Strategies for bioremediation of polychlorinated biphenyls2004

    • Author(s)
      Ohtsubo, Y.et al.
    • Journal Title

      Appl.Microbiol.Biotechnol. 65

      Pages: 250-258

    • Related Report
      2004 Annual Research Report

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Published: 2004-04-01   Modified: 2016-04-21  

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