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2009 Fiscal Year Final Research Report

Innovative genomics and metagenomics of environmental bacteria able to degrade organic pollutants

Research Project

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Project/Area Number 17018003
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionTohoku University

Principal Investigator

TSUDA Masataka  Tohoku University, 大学院・生命科学研究科, 教授 (90172022)

Co-Investigator(Kenkyū-buntansha) FUKUDA Masao  長岡技術科学大学, 工学部, 教授 (20134512)
FUJII Takeshi  農業環境技術研究所, 生物生態機能研究領域, 領域長 (00354100)
MINAMISAWA Kiwamu  東北大学, 大学院・生命科学研究科, 教授 (70167667)
OGAWA Naoto  静岡大学, 農学部, 教授 (60354031)
MIYAZAKI Kentaro  産業技術総合研究所, 生物機能工学研究部門, グループ長 (60344123)
Project Period (FY) 2005 – 2009
Keywords細菌 / 土壌 / 環境汚染 / 環境修復 / ゲノム / メタゲノム / 発現制御 / 細菌叢
Research Abstract

Environmental bacteria able to degrade various recalcitrant and xenobiotic compounds play important roles in the removal of organic pollutants. To know the survival and proliferation strategies of such bacteria in their native niche, the genetic loci very important in the survival and specifically induced in the soil environment were identified at the genomic levels using two phylogentically distant strains. Metagenomic analysis was also conducted to clarify the mode how the bacterial population in the soil responded to the exposure of organic pollutants.

  • Research Products

    (53 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (24 results) (of which Peer Reviewed: 24 results) Presentation (17 results) Book (7 results) Remarks (3 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Identification of Burkholderia multivorans ATCC 17616 genes induced in soil environment by in vivo expression technology.2010

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

      Environ. Microbiol (in press)

    • Peer Reviewed
  • [Journal Article] Mutational analysis of the inducer recognition sites of the LysR-type transcriptional regulator TfdT of Burkholderia sp. NK8.2009

    • Author(s)
      Lang, G., Ogawa, N
    • Journal Title

      Appl. Microbiol. Biotechnol 83

      Pages: 1085-1094

    • Peer Reviewed
  • [Journal Article] Functional metagenomics for enzyme discovery: challenges to efficient screening.2009

    • Author(s)
      Uchiyama, T., Miyazaki, K
    • Journal Title

      Curr. Opin. Biotechnol 20

      Pages: 616-622

    • Peer Reviewed
  • [Journal Article] Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis2009

    • Author(s)
      Suenaga, H., 6人, Tsuda, M., Miyazaki, K
    • Journal Title

      ISME J 3

      Pages: 1335-1348

    • Peer Reviewed
  • [Journal Article] The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome2009

    • Author(s)
      Suenaga, H., Mizuta, S., Miyazaki, K
    • Journal Title

      FEMS Microbiol. Ecol 69

      Pages: 472-480

    • Peer Reviewed
  • [Journal Article] An improved method to extract RNA from soil with efficient removal of humic acids.2009

    • Author(s)
      ang, Y., Morimoto, S., Ogawa, N., Oomori, T., Fujii, T
    • Journal Title

      Appl. Microbiol 107

      Pages: 1168-1177

    • Peer Reviewed
  • [Journal Article] Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer.2008

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

      J. Bacteriol 190

      Pages: 6281-6289

    • Peer Reviewed
  • [Journal Article] GenomeMatcher: a graphical user interface for DNA sequence comparison.2008

    • Author(s)
      Ohtsubo, Y., Ikeda-Ohtsubo, W., Nagata Y., Tsuda, M
    • Journal Title

      BMC Bioinformatics 9

      Pages: 376

    • Peer Reviewed
  • [Journal Article] Revised nomenclature for transposable genetic elements.2008

    • Author(s)
      Roberts, A.P., 9人, Tsuda, M., Berg, D. E
    • Journal Title

      Plasmid 60

      Pages: 167-173

    • Peer Reviewed
  • [Journal Article] Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics.2008

    • Author(s)
      Shimoda, Y., 2人, Minamisawa, K., 3人, Tsuda, M., 5人, Tabata, S., Sato, S
    • Journal Title

      DNA Res 15

      Pages: 297-308

    • Peer Reviewed
  • [Journal Article] Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans.2008

    • Author(s)
      Yuhara, S., 4人, Tsuda, M
    • Journal Title

      Microbiology 154

      Pages: 1763-1774

    • Peer Reviewed
  • [Journal Article] Detection of bphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method for RNA preparation from soil.2008

    • Author(s)
      Wang, Y., 4人, T., Ogawa, N., Fukuda, M., Fujii, T
    • Journal Title

      Biosci. Biotechnol. Biochem 72

      Pages: 694-701

    • Peer Reviewed
  • [Journal Article] Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1.2008

    • Author(s)
      Patrauchan, M.A., 4人, Fukuda, M., 2人, Eltis, L. D
    • Journal Title

      J. Bacteriol 190

      Pages: 37-47

    • Peer Reviewed
  • [Journal Article] Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches.2007

    • Author(s)
      Ono, A., 4人, Tsuda, M
    • Journal Title

      App. Microbiol. Biotechnol 74

      Pages: 501-510

    • Peer Reviewed
  • [Journal Article] Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation in a PCB degrader, Rhodococcus sp. strain RHA1.2007

    • Author(s)
      Iwasaki, T., 4人, Fukuda, M
    • Journal Title

      Biosci. Biotechnol. Biochem 71

      Pages: 993-1002

    • Peer Reviewed
  • [Journal Article] Global gene expression in Bradyrhizobium japonicum cultured with vanillin, vanillate, 4-hydroxybenzoate, and protocatechuate.2006

    • Author(s)
      Ito, N., 10人, Tsuda, M., Mitsui, M., Minamisawa, K
    • Journal Title

      Microbes Environ 21

      Pages: 240-250

    • Peer Reviewed
  • [Journal Article] Multiple-subunit genes of the aromatic-ring hydroxylating dioxygenase play an active role in biphenyl and polychlorinated biphenyl degradation in Rhodococcus sp. strain RHA1.2006

    • Author(s)
      Iwasaki, T, Miyauchi, K, Masai, E, Fukuda, M
    • Journal Title

      Appl. Environ. Microbiol 72

      Pages: 5396-5402

    • Peer Reviewed
  • [Journal Article] The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.2006

    • Author(s)
      McLeod, M.P., 24人, Fukuda, M., 2人, Eltis, L. D
    • Journal Title

      Proc. Natl. Acad. Sci. USA 103

      Pages: 15582-15587

    • Peer Reviewed
  • [Journal Article] Identification of a response regulator gene for catabolite control from a PCB-degrading β-proteobacteria.2006

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

      Acidovorax sp. KKS102. Mol. Microbiol 60

      Pages: 1563-1575

    • Peer Reviewed
  • [Journal Article] Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase.2006

    • Author(s)
      Sota, M., 6人, Tsuda, M
    • Journal Title

      J. Bacteriol 188

      Pages: 4057-4067

    • Peer Reviewed
  • [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., 5人, Tsuda, M
    • Journal Title

      J. Biosci. Bioeng 99

      Pages: 603-610

    • Peer Reviewed
  • [Journal Article] High-temperature-induced transposition of IS elements in Burkholderia multivorans ATCC 17616.2005

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

      Appl. Environ. Microbiol 71

      Pages: 1822-1828

    • Peer Reviewed
  • [Journal Article] Two kinds of chlorochatechol 1, 2-dioxygenase from 2, 4-dichlorophenoxyacetate-degrading Sphingomonas sp. strain TFD44.2005

    • Author(s)
      Lang, G., Ogawa, N., Tanaka, Y, Fujii, T., Fulthope, R.R., Fukuda, M., Miyashita, K
    • Journal Title

      Biochem. Biophysi. Res. Comm 332

      Pages: 941-948

    • Peer Reviewed
  • [Journal Article] Analysis of a bacterial community in 3-chlorobenzoate-contaminated soil by PCR-DGGE targeting 16S rDNA and the benzoate 1, 2-dioxygenase gene (benA).2005

    • Author(s)
      Morimoto. S., Togami, K., Ogawa, N., Hasebe, A., Fujii, T
    • Journal Title

      Microbes Environ 20

      Pages: 151-159

    • Peer Reviewed
  • [Presentation] 環境汚染土壌における微生物集団のメタゲノム解析2010

    • Author(s)
      津田雅孝
    • Organizer
      第57回日本生態学会
    • Place of Presentation
      東京
    • Year and Date
      2010-03-15
  • [Presentation] メタゲノム機能解析とその応用研究2009

    • Author(s)
      宮崎健太郎
    • Organizer
      糸状菌分子生物学研究会
    • Place of Presentation
      東京
    • Year and Date
      2009-11-19
  • [Presentation] Bacterial genes specifically induced in soil environment.2009

    • Author(s)
      M. Tsuda, E. Nishiyama, Y. Nagata, Y. Ohtsubo
    • Organizer
      NIAES International Symposium: "Challenges for Agro-Environmental Research in Monsoon Asia"
    • Place of Presentation
      Tsukuba
    • Year and Date
      2009-10-05
  • [Presentation] Molecular genetic approaches for elucidating adaptive strategies of bacteria in soil.2008

    • Author(s)
      Y. Nagata, Y. Ohtsubo, M. Tsuda
    • Organizer
      ISSM satellite symposium "Environmental genomics"
    • Place of Presentation
      Tokyo
    • Year and Date
      2008-11-15
  • [Presentation] 土壌からのRNA抽出と細菌の遺伝子発現解析2008

    • Author(s)
      小川直人, 福田雅夫
    • Organizer
      第60回日本生物工学会大会
    • Place of Presentation
      仙台
    • Year and Date
      2008-08-29
  • [Presentation] Development of degradation pathways for chlorinated organic pollutants.2008

    • Author(s)
      M. Fukuda
    • Organizer
      The 4th International Symposium of Environmental Biotechnology
    • Place of Presentation
      Tainan, Taiwan
    • Year and Date
      2008-08-13
  • [Presentation] PCB分解菌の全ゲノム解明と環境に応答した遺伝子発現の網羅的解析2008

    • Author(s)
      福田雅夫
    • Organizer
      日本土壌微生物学会2008年度大会
    • Place of Presentation
      静岡
    • Year and Date
      2008-06-13
  • [Presentation] ゲノム情報に基づいた植物共生細菌の環境応答と物質循環機能の解明2008

    • Author(s)
      南澤究
    • Organizer
      日本土壌微生物学会2008年度大会
    • Place of Presentation
      静岡
    • Year and Date
      2008-06-13
  • [Presentation] 多重染色体性のBurkholderia multivoransのゲノム構造と土壌でのゲノム情報発現2008

    • Author(s)
      津田雅孝
    • Organizer
      日本土壌微生物学会2008年度大会
    • Place of Presentation
      静岡
    • Year and Date
      2008-06-13
  • [Presentation] メタゲノムを利用したプレタンパク質工学2008

    • Author(s)
      宮崎健太郎
    • Organizer
      日本蛋白質科学会
    • Place of Presentation
      東京
    • Year and Date
      2008-06-12
  • [Presentation] A versatile metabolic system in a Rhodococcus PCB degrader.2008

    • Author(s)
      M. Fukuda
    • Organizer
      The 24th International Symposium on the Frontier of Microbiology: Resources, Environment, and Genome
    • Place of Presentation
      Okayama
    • Year and Date
      2008-01-25
  • [Presentation] 機能発現に基づく環境汚染物質分解酵素遺伝子の生態系からの直接的取得と解析2007

    • Author(s)
      津田雅孝, 小野玲, 宮崎亮, 府中玄樹, 永田裕二
    • Organizer
      第59回日本生物工学会大会
    • Place of Presentation
      東広島
    • Year and Date
      2007-09-25
  • [Presentation] PCB分解菌の芳香族分解遺伝子発現制御と環境応答2007

    • Author(s)
      福田雅夫
    • Organizer
      極限環境微生物学会第8回シンポジウム
    • Place of Presentation
      横浜
    • Year and Date
      2007-07-03
  • [Presentation] 生態系での細菌ゲノム情報発現2007

    • Author(s)
      津田雅孝, 西山依里, 宮腰昌利, 永田裕二, 大坪嘉行
    • Organizer
      極限環境微生物学会第8回シンポジウム
    • Place of Presentation
      横浜
    • Year and Date
      2007-07-03
  • [Presentation] Rhodococcus catabolic genes and enzymes.2006

    • Author(s)
      M. Fukuda
    • Organizer
      BBSRC International Workshop: Developing a Scientific Strategy for Investigating and Exploiting the Biology of Rhodococcus
    • Place of Presentation
      Belfast, UK
    • Year and Date
      2006-09-19
  • [Presentation] 多重染色体をもつ環境細菌のゲノム2005

    • Author(s)
      津田雅孝
    • Organizer
      第7回日本進化学会
    • Place of Presentation
      仙台
    • Year and Date
      2005-08-26
  • [Presentation] Function of duplicated degradation genes in a rhodococcal PCB degrader.2005

    • Author(s)
      M. Fukuda
    • Organizer
      Industrial Microbiology and Biotechnology Meeting 2005
    • Place of Presentation
      Chicago, USA
    • Year and Date
      2005-08-25
  • [Book] 環境汚染物質分解細菌のメタゲノミクス. 「難培養微生物研究の最新技術II」2010

    • Author(s)
      永田裕二, 津田雅孝
    • Total Pages
      211-219
    • Publisher
      シーエムシー出版
  • [Book] カイメン共在細菌メタゲノム中の環境汚染物質分解酵素遺伝子相同配列の解析. 「マリンメタゲノムの有効利用」2009

    • Author(s)
      永田裕二, 津田雅孝
    • Total Pages
      166-178
    • Publisher
      シーエムシー出版
  • [Book] 新規酵素取得のためのメタゲノム利用技術開発. 「マリンメタゲノムの有効利用」2009

    • Author(s)
      宮崎健太郎
    • Total Pages
      55-66
    • Publisher
      シーエムシー出版
  • [Book] Bacterial class II catabolic transposons. In "DNA Transposable Elements Research"2008

    • Author(s)
      Sota, M., Yano, H., Tsuda, M
    • Total Pages
      23-67
    • Publisher
      Nova Science Publishers
  • [Book] 微生物の事典(メタゲノム)2008

    • Author(s)
      津田雅孝
    • Total Pages
      661-663
    • Publisher
      朝倉書店
  • [Book] バイオフィルムの基礎と制御(難培養性細菌も研究対象とするメタゲノム解析)2008

    • Author(s)
      永田裕二, 津田雅孝
    • Total Pages
      103-111
    • Publisher
      エヌ・ティー・エス社
  • [Book] 比較ゲノム学から読み解く生命システム(土壌環境細菌の比較ゲノム)2007

    • Author(s)
      津田雅孝, 永田裕二, 大坪嘉行
    • Total Pages
      166-172
    • Publisher
      秀潤社
  • [Remarks] 比較ゲノム解析ツール: GenomeMatcher

    • URL

      http://www.ige.tohoku.ac.jp/joho/gm/gmhome.html

  • [Remarks] Rhodococcusゲノムデータベース: Rhodococcus Genome Project

    • URL

      http://www.rhodococcus.ca/index.jsp

  • [Remarks] Macroarray analysis page of Bradyrhizobium japonicum

  • [Patent(Industrial Property Rights)] 新規な芳香環水酸化酵素及びその遺伝子2008

    • Inventor(s)
      末永光, 宮崎健太郎
    • Industrial Property Rights Holder
      末永光, 宮崎健太郎
    • Industrial Property Number
      特許権特願2008-214862
    • Filing Date
      2008-08-25
  • [Patent(Industrial Property Rights)] 酵素遺伝子スクリーニング法2008

    • Inventor(s)
      内山拓, 宮崎健太郎
    • Industrial Property Rights Holder
      内山拓, 宮崎健太郎
    • Industrial Property Number
      特許権特願2008-200172
    • Filing Date
      2008-08-01

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Published: 2011-06-18   Modified: 2016-04-21  

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