2007 Fiscal Year Final Research Report Summary
Structure and function analysis of novel meta-cleavage enzyme for the creation of the enzyme to degrade recalcitrant and environment-polluting compounds
| Project/Area Number |
17380056
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Applied microbiology
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| Research Institution | Shibaura Institute of Technology |
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Principal Investigator |
OMORI Toshio Shibaura Institute of Technology, Engineering graduate course, Professor (20011984)
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| Project Period (FY) |
2005 – 2007
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| Keywords | marine bacteria / meta-cleavage / carbazole / dibenzofuran / recalcitrant compound / x-ray crystallograph |
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| Research Abstract |
Currently, research on the biodegradation of recalcitrant chemicals is mainly concentrated on microorganisms isolated from soils and activated sludge. Studies on marine bacterial genes and enzymes involved in biodegradation of xenobiotics such as carbazole and dioxins are very rare. However, accidents caused by damage to tankers, or the inflow of recalcitrant molecules from rivers, have created pollution in seas that requires environmental remediation.
The concentration of bacteria in the sea is very low, and it is very difficult to culture these bacteria because quantities of trace elements present in the seawater affect the growth of marine bacteria. To overcome of these problems, it is necessary to concentrate the seawater to enable bacterial screening. By manipulating the composition of the isolation medium, we succeeded in isolating organisms from seawater that can degrade carbazole and dibenzofuran. We isolated new bacterial carbazole degraders, classified as Lysobacter sp. strain
… More
s OC6 and OC7, which show very low homology to reported bacteria and probably belong to a new order.
To obtain genes from these marine bacteria that may be involved in the degradation of carbazole, genes from soil bacterial enzymes participating in the degradation of carbazole were used as a probe for Southern hybridization, but no hybridization was achieved. Using the shotgun cloning method, we successfully obtained the genes from marine bacteria that are involved in the degradation of recalcitrant compounds.
The meta-cleavage enzyme involved in the degradation of carbazole and dibenzofuran consists of two subunits, but the three-dimensional (3D) structure of the enzyme is not yet established. However, this information is required to elucidate the 3D structure of the enzymes in order to construct new enzymes that have new substrate specificities and high activity. The meta-cleavage enzyme from Pseudomonas resinovorans CA10, which has two subunits, was purified and crystallized, and the 3D structure was established by the SIRS method. Elucidation of the 3D meta-cleavage enzyme structure of marine bacterial strains is now in progress. These results will be used to construct enzymes with new substrate specificities and activities by comparing the enzymes of terrestrial and marine bacteria. Less
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Research Products
(42 results)
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[Journal Article] Transcriptional regulation of the sulfate-starvation-induced gene sfnA by a o^<54>-dependent activator of Pseudomonas putida2007
Author(s)
Habe, H., Kouzuma, A., Endoh, T., Omori, T., Yamane, H. and Nojiri, H.
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Journal Title
Microbiology 153
Pages: 3091-3098
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] The ptsP gene encoding the PTS family protein EL^<Ntr> is essential for dimethyl sulfone utilization by Pseudomonas putida2007
Author(s)
Kouzuma, A., Endoh, T., T., Omori, Nojiri, H., Yamane, H. and Habe, H.
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Journal Title
Microbiol Lett 275
Pages: 175-181
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Transcriptional regulation of the sulfate-starvation-induced gene sfnA by a am-dependent activator of Pseudomonas putida2007
Author(s)
Habe, H., Kouzuma, A., Endoh, T., Omori, T., Yamane, H., Nojiri, H
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Journal Title
Microbiology 153
Pages: 3091-3098
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] The ptsP gene encoding the PTS family protein EL^<Ntr> is essential for dimethyl sulfone utilization by Pseudomonas putida2007
Author(s)
Kouzuma, A., Endoh, T., T., Omori, Nojiri, H., Yamane, H., Habe, H
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Journal Title
FEMS Microbiol Lett 275
Pages: 175-181
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Detection of a bacterial group within the phylum Chloroflexi and reductive-dehalogenase-homologous genes in pentachlorobenzene-dechlorinating estuarine sediment from the Arakawa River,Japan2006
Author(s)
Santoh, K., Kouzuma, A., Ishizaki, R., Iwata, K., Shimura, M., Hayakawa, T., Hoaki, T., Nojiri, H., Omori, T., Yamane, H. and Habe, H.
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Journal Title
Microbes Environ 21
Pages: 154-162
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Differentiation of carbazole catabolic operons by replacement of the regulated promoter viatransposition of an insertion sequence2006
Author(s)
Miyakoshi, M., Urata, M., Habe, H., Omori, T., Yamane, H. and Nojiri, H.
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Journal Title
Journal of Biological Chemistry 281
Pages: 8450-8457
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Characterization of the replication,maintenance,and transfer features of the Inc P-7 plasmid pCAR1,which carries genes involved in carbazole and dioxin degradation2006
Author(s)
Shintani, M., Yano, H., Habe, H., Omori, T., Yamane, H., Tsuda, M. and Nojiri, H.
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Journal Title
Appl.Environ.Microbiol. 72
Pages: 3206-3216
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Plasmid pCAR3 contains multiple gene sets involved in the conversion of carbazole to anthranilate2006
Author(s)
Urata, M., Uthimura, H., Noguchi, H., Sakaguchi, T., Eto, K., Habe, H., Omori, T., Yamane, H. and Nojiri, H.
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Journal Title
Appl.Environ.Microbiol. 72
Pages: 3198-3205
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Differentiation of carbazole catabolic operons by replacement of the regulated promoter via transposition of an insertion sequence2006
Author(s)
Miyakoshi, M., Urata, M., Habe, H., Omori, T., Yamane, H., Nojiri, H
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Journal Title
Journal of Biological Chemistry 281
Pages: 8450-8457
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Improving the catalytic efficiency of meta-cleavage product hydrolase(CumD) from Pseudomonas fluorescens IPOI2006
Author(s)
So-Young, J., Fushinobu, S. Nojiri, H., Omori, T., Shoun, H., Wakagi, T
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Journal Title
Biochimica et Biophysica Acta 1764
Pages: 1159-1166
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Detection of a bacterial group within the phylum Chloroflexi and reductive-dehalogenase-homologous genes in pentachlorobenzene-dechlorinating estuarine sediment from the Arakawa River, Japan2006
Author(s)
Santoh, K., Kouzuma, A., Ishizaki, R., Iwata, K., Shimura, M., Hayakawa, T., Hoaki, T., Nojiri, H., Omori, T., Yamane, H., Habe, H
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Journal Title
Microbes Environ 21
Pages: 154-162
Description
「研究成果報告書概要(欧文)」より
-
[Journal Article] Characterization of the replication, maintenance, and transfer features of the Inc P-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin2006
Author(s)
Shintani, M., Yano, H., Habe, H., Omori, T., Yamane, H., Tsuda, M., Nojiri, H
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Journal Title
Appl. Environ. Microbiol 72
Pages: 3206-3216
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Plasmid pCAR3 contains multiple gene sets involved in the conversion of carbazole to anthranilate degradation2006
Author(s)
Urata, M., Uthimura, H., Noguchi, H., Sakaguchi, T. Eto, K., Habe, H., Omori, T., Yamane, H., Nojiri, H
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Journal Title
Appl. Environ. Microbiol 72
Pages: 3198-3205
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Expression, purification, and characterization of a meta-cleavage enzyme from a marine bacterium, strain CAR-SF2008
Author(s)
Iwata, K., Nagashima, H., Zulkharnain, A., b., Fuse, H., Omni, T
Organizer
Japan Society for Bioscience, Biotechnology, and Agrochemistry
Place of Presentation
Nagoya
Year and Date
20080300
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Biodegradation of dioxins in contaminated soil by Novosphingobium sp. Strain KA12007
Author(s)
Saiki, Y., Takahasi, M., Kawamoto, Y., Yokota, T., Nojiri, H., Omori, T
Organizer
General Meeting of American Society for Microbiology
Place of Presentation
Canada
Year and Date
20070500
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Expression, purification, and characterization of the meta-cleavage enzymes and the meta-cleavage hydrolase from Sphingomonas sp. KA12007
Author(s)
Zulkharnain, A., b., Akimoto, A., Nagashima, H., Pinyagong, O., Fuse, H., Iwata, Nojiri, H., Omori, T
Organizer
Japan Society for Bioscience, Biotechnology, and Agrochemistry
Place of Presentation
Tokyo
Year and Date
20070300
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Isolation and nucleotide sequences of carbazole catabolic genes from a marine bacterium, strain CAR-SF2007
Author(s)
Zulldiamain. A., b., Akimoto, A., Nagashima, H., Pinyagong, O., Fuse. H., Iwata., K., Nojiri., H., Omori, T
Organizer
Japan Society for Bioscience, Biotechnology, and Agrochemistry
Place of Presentation
Tokyo
Year and Date
20070300
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Isolation and characterization of novel recalcitrant compounds that can be degraded by marine bacteria2007
Author(s)
Maeda, R., Nagashima, H., Fuse, H., Habe, H., Nojiri, H., Omori, T
Organizer
Japan Society for Bioscience, Biotechnology, and Agrochemistry
Place of Presentation
Tokyo
Year and Date
20070300
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Comparison of the characteristics of meta-cleavage enzymes consisting of two subunits that are involved in the degradation of recalcitrant chemicals2006
Author(s)
Zulkhamain, A., b., Kamiya, J., Iwata, K., Habe, H., Nojiri, H., Omori., T
Organizer
Japan Society for Bioscience, Biotechnology, and Agrochemistry
Place of Presentation
Kyoto
Year and Date
20060300
Description
「研究成果報告書概要(欧文)」より
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