Horizontal transfer of bacterial genes for degradation of environmental pollutants

2008 Fiscal Year Final Research Report

• Project/Area Number: 18380189
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Boundary agriculture
• Research Institution: Tohoku University
• Principal Investigator: TSUDA Masataka Tohoku University, 大学院・生命科学研究科, 教授 (90172022)
• Co-Investigator(Kenkyū-buntansha): NAGATA Yuji 東北大学, 大学院・生命科学研究科, 准教授 (30237531) ; OHTSUBO Yoshiyuki 東北大学, 大学院・生命科学研究科, 助教 (40342761)
• Project Period (FY): 2006 – 2008
• Keywords: 環境浄化 / 環境細菌 / 可動性遺伝因子 / 遺伝子水平伝播 / プラスミド / ゲノミックアイランド

Research Abstract

各種汚染物質の分解者である環境細菌は、新規環境汚染物質化合物に対する分解能を極めて短時間で獲得するが、このような汚染環境への適応・進化に、分解酵素遺伝子群を担うプラスミドやゲノミックアイランドなどの可動性遺伝因子の種を超えた水平伝播が関与する。本研究では、これら可動性遺伝因子の水平伝播の分子機構、水平伝播能を制御する生物的要因、そして水平伝播可能な受容菌株宿主域規定要因を明らかにした。

Research Products

• [Journal Article] 環境細菌ゲノムの構造と可塑性 -難分解性化合物分解の総合職と専門職の場合-. (2009)
  • Author(s): 大坪嘉行, 永田裕二, 津田雅孝
  • Journal Title: 化学と生物 47 Pages: 35-42
• [Journal Article] Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics (2008)
  • Author(s): Shimoda, Y., H. Mitsui, H. Kamimatsuse, K. Minamisawa, E. Nishiyama, Y. Ohtsubo, Y. Nagata, M. Tsuda, S. Shinpo, A. Watanabe, M. Kohara, M. Yamada, Y. Nakamura, S. Tabata,and S. Sato
  • Journal Title: DNA Res 15 Pages: 297-308
  • Peer Reviewed
• [Journal Article] 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, 西山依里, 宮腰昌利, 湯原悟志, 永田裕二, 大坪嘉行
  • Journal Title: 土と微生物 62 Pages: 93-97
  • Peer Reviewed
• [Journal Article] Revised nomenclature for transposable genetic elements (2008)
  • Author(s): Roberts, A. P., M. Chandler, P. Courvalin, G. Guedon, P. Mullany, T. Pembroke, J. I. Rood, C. J. Smith, A. O. Summers, M. Tsuda, and D. E. Berg
  • Journal Title: Plasmid 60 Pages: 167-173
  • Peer Reviewed
• [Journal Article] Characterization of the traD operon of naphthalene-catabolic plasmid NAH7 (2008)
  • Author(s): Miyazaki, R., Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Journal Title: a host-range modifier in conjugative transfer. J. Bacteriol 190 Pages: 6281-6289
  • Peer Reviewed
• [Journal Article] GenomeMatcher : a graphical user interface for DNA sequence comparison (2008)
  • Author(s): Ohtsubo, Y., W. Ikeda-Ohtsubo, Y. Nagata, and M. Tsuda
  • Journal Title: BMC Bioinformatics 9 Pages: 376
  • Peer Reviewed
• [Journal Article] Insertion sequence-based cassette PCR : cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA (2008)
  • Author(s): Fuchu, G., Y. Ohtsubo, M. Ito, R. Miyazaki, A. Ono, Y. Nagata, and M. Tsuda
  • Journal Title: Appl. Microbiol. Biotechnol 79 Pages: 627-632
  • Peer Reviewed
• [Journal Article] Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans (2008)
  • Author(s): Yuhara, S., H. Komatsu, H. Goto, Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Journal Title: Microbiology 154 Pages: 1763-1774
  • Peer Reviewed
• [Journal Article] 土壌生態系での環境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
  • Journal Title: 極限環境微生物学会誌 6 Pages: 59-62
  • Peer Reviewed
• [Journal Article] 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
  • Journal Title: J. Environ. Biotechnol. 7 Pages: 75-78
  • Peer Reviewed
• [Journal Article] Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp (2007)
  • Author(s): Ito, M., Z. Prokop, M. Klvana, Y. Ohtsubo, M. Tsuda, J. Damborsky, and Y. Nagata
  • Journal Title: Arch. Microbiol 188 Pages: 313-325
  • Peer Reviewed
• [Journal Article] Aerobic degradation of lindane(γ-hexachlorocyclohexane)in bacteria and its biochemical and molecular basis (2007)
  • Author(s): Nagata, Y., R. Endo, M. Ito, Y. Ohtsubo, and M. Tsuda
  • Journal Title: Appl. Microbiol. Biotechnol 74 Pages: 741-752
  • Peer Reviewed
• [Journal Article] 自然環境で実際に機能する微生物遺伝子の遺伝学的手法による検索と解析 (2007)
  • Author(s): 津田雅孝, 西山依里, 永田裕二, 大坪嘉行
  • Journal Title: 化学と生物 45 Pages: 557-563
  • Peer Reviewed
• [Journal Article] Identification and characterization of genes encoding a putative ABC-type transporter essential for the utilization of γ-hexachlorocyclohexane in Sphingobium japonicum UT26 (2007)
  • Author(s): Endo, R., Y. Ohtsubo, M. Tsuda, and Y. Nagata
  • Journal Title: J. Bacteriol. 189 Pages: 3712-3720
  • Peer Reviewed
• [Journal Article] G. J. Zylstra, P. A. Williams, and M. Tsuda : Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements (2007)
  • Author(s): Yano, H., C. E. Garruto, M. Sota, Y. Ohtsubo, Y. Nagata
  • Journal Title: J. Mol. Biol. 369 Pages: 11-26
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110 (2007)
  • Author(s): Sato, Y., R. Natsume, M. Tsuda, J. Damborsky, Y. Nagata, and T. Senda
  • Journal Title: Acta Cryst. F63 Pages: 294-296
  • Peer Reviewed
• [Journal Article] Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids (2007)
  • Author(s): Sota, M., M. Tsuda, H. Yano, L. J. Forney, and E. M.Top
  • Journal Title: J. Bacteriol. 189 Pages: 3091-3098
  • Peer Reviewed
• [Journal Article] The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85 : reaction mechanism and molecular evolution (2007)
  • Author(s): Pavlova, M., M. Klvana, A. Jesenska, Z. Prokop, H. Konecna, T. Sato, M. Tsuda, Y. Nagata, and J. Damborsky
  • Journal Title: J. Struct. Biol 157 Pages: 384-392
  • Peer Reviewed
• [Journal Article] Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl (2007)
  • Author(s): Ono, A., R. Miyazaki, M. Sota, Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Journal Title: Microbiol. Biotechnol 74 Pages: 501-510
  • Peer Reviewed
• [Journal Article] Global gene expression in Bradyrhizobium japonicum cultured with vanillin, vanillate (2006)
  • Author(s): Ito, N., M. Itakura, S. Eda, K. Saeki, H. Oomori, T. Yokoyama, T. Kaneko, S. Tabata, T. Oowada, S. Tajima, T. Uchiumi, E. Masai, M. Tsuda, H. Mitsui, and K. Minamisawa
  • Journal Title: 4-hydroxybenzoate, and protocatechuate. Microbes Environ 21 Pages: 240-250
  • Peer Reviewed
• [Journal Article] ハロアルカンデハロゲナーゼの構造と機能 (2006)
  • Author(s): 永田裕二, 津田雅孝
  • Journal Title: J. Environ. Biotechnol. 6 Pages: 87-92
  • Peer Reviewed
• [Journal Article] Complete nucleotide sequence of an exogenously isolated plasmid pLB1 involved in the degradation of γ-hexachlorocyclohexane (2006)
  • Author(s): Miyazaki, R. Y. Sato, M. Ito, Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Journal Title: Appl. Environ. Microbiol 72 Pages: 6923-6933
  • Peer Reviewed
• [Journal Article] 環境汚染物質を分解する酵素遺伝子の土壌からの直接的取得と解析 (2006)
  • Author(s): 小野玲, 宮崎亮, 永田裕二, 津田雅孝
  • Journal Title: バイオインダストリ- 23 Pages: 44-49
  • Peer Reviewed
• [Journal Article] Comparative analysis of argK-tox clusters and their flanking regions in phaseolotoxin-producing Pseudomonas syringae pathovars (2006)
  • Author(s): Genka, H., T. Baba, M. Tsuda, S. Kanaya, H. Mori, T. Yoshida, M. Tsujimoto-Noguchi, K. Tsuchiya, amd H. Sawada
  • Journal Title: J. Mol. Evol. 63 Pages: 401-414
  • Peer Reviewed
• [Journal Article] Identification of a response regulator gene for catabolite control from a PCB-degrading β-proteobacteria, Acidovorax sp (2006)
  • Author(s): Ohtsubo, Y., H. Goto, Y. Nagata, T. Kudo, and M. Tsuda
  • Journal Title: 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., H. Yano, A. Ono, R. Miyazaki, H. Ishii, H. Genka, E. M. Top, and M. Tsuda
  • Journal Title: J. Bacteriol 188 Pages: 4057-4067
  • Peer Reviewed
• [Journal Article] Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1 that carries carbazole/dioxin degradative genes (2006)
  • Author(s): Shintani, M., H. Yano, H. Habe, T. Omori, H. Yamane, M. Tsuda, and H. Nojiri
  • Journal Title: Appl. Environ. Microbiol 72 Pages: 3206-3216
  • Peer Reviewed
• [Journal Article] Growth inhibition by metabolites of γ-hexachlorocyclohexane in Sphingobium japonicum UT26 (2006)
  • Author(s): Endo, R., Y. Ohtsubo, M. Tsuda, and Y. Nagata
  • Journal Title: Biosci. Biotechnol. Biochem 70 Pages: 1029-1032
  • Peer Reviewed
• [Presentation] Adaptation and evolution of bacteria in natural environments (2008)
  • Author(s): Nagata,Y., Y. Ohtsubo, and M. Tsuda
  • Organizer: Memorial Symposium of the 24th International Prize for Biology -Ecology for the Changing World
  • Place of Presentation: Sendai
  • Year and Date: 20081210-11
• [Presentation] Reconstruction of transcription networks by the conjugative transfer of IncP plasmids. (2008)
  • Author(s): Miyakoshi, M., H. Nojiri, Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Organizer: International Plasmid Biology Conference 2008
  • Place of Presentation: Gdansk, Poland
  • Year and Date: 20080830-0905
• [Presentation] Characterization of plasmids from gamma-hexachlorocyclohexane-degrading bacterium Sphingomonas sp (2008)
  • Author(s): Tabata, M, R. Endo, Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Organizer: MM-1. International Plasmid Biology Conference 2008
  • Place of Presentation: Gdansk, Poland
  • Year and Date: 20080830-0905
• [Presentation] Characterization of the traD operon in IncP-9 plasmid NAH7 : a host-range modifier in conjugative transfer (2008)
  • Author(s): Miyazaki, R., Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Organizer: International Plasmid Biology Conference 2008
  • Place of Presentation: Gdansk, Poland
  • Year and Date: 20080830-0905
• [Presentation] 分子遺伝学的手法による細菌の土壌環境適応戦略の解明 (2008)
  • Author(s): 大坪嘉行, 西山衣里, 宮腰昌利, 永田裕二, 津田雅孝
  • Organizer: 2008年度日本生物工学会大会シンポジウム
  • Place of Presentation: 仙台
  • Year and Date: 20080827-29
• [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: 第59回日本土壌微生物学会2008年度大会シンポジウム
  • Place of Presentation: 静岡
  • Year and Date: 20080613-14
• [Presentation] A. P. Roberts, M. Chandler, P. Courvalin, G. Guedon, P. Mullany, T. Pembroke, J. I. Rood, C. J. Smith, A. O. Summers, and D. E. Berg (2008)
  • Author(s): 津田雅孝
  • Organizer: 原核生物由来の可動性遺伝因子の命名法. 第3回日本ゲノム微生物学会総会
  • Place of Presentation: 東京
  • Year and Date: 20080305-07
• [Presentation] Molecular genetic approaches for elucidating adaptive strategies of bacteria in soil (2008)
  • Author(s): Nagata, Y., Y. Ohtsubo, and M. Tsuda
  • Organizer: ISSM satellite symposium "Environmental genomics"
  • Place of Presentation: Tokyo
  • Year and Date: 2008-11-15
• [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シンポジウム
  • Place of Presentation: 東広島
  • Year and Date: 20070925-27
• [Presentation] 培養非依存的手法による土壌環境からの環境汚染物質分解酵素遺伝子の取得 (2007)
  • Author(s): 永田裕二, 小野玲, 宮崎亮, 府中玄樹, 大坪嘉行, 津田雅孝
  • Organizer: 日本微生物生態学会第23回大会シンポジウム.
  • Place of Presentation: 松山
  • Year and Date: 20070915-18
• [Presentation] 環境での微生物ゲノム情報発現 (2007)
  • Author(s): 津田雅孝
  • Organizer: 2007年度日本農芸化学会中四国・西日本支部合同大会シンポジウム
  • Place of Presentation: 山口
  • Year and Date: 20070914-15
• [Presentation] Characterization of the traD gene cluster involved in the conjugative transfer of naphthalene-catabolic plasmid NAH7 (2007)
  • Author(s): Miyazaki, R., Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Organizer: ASM Conference on Pseudomonas 2007
  • Place of Presentation: Seattle, Washington, USA.
  • Year and Date: 20070826-30
• [Presentation] Functional screening of genes for aromatic ring-hydroxylating oxygenases from soil metagenomic libraries (2007)
  • Author(s): Ono, A., Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Organizer: Metagenomics2007
  • Place of Presentation: San Diego, California, USA
  • Year and Date: 20070711-13
• [Presentation] Haloalkane dehalogenases possess two different structural bases for their enantioselectivity (2007)
  • Author(s): Prokop, Z., Y. Sato, T. Mozga, P. Jerabek, R. Natsume, J. Florian, M. Tsuda, Y. Nagata, T. Senda, and J. Damborsky
  • Organizer: BIOTRANS 2007 - 8th International Symposium on Biocatalysis and Biotransformations
  • Place of Presentation: Oviedo, Spain
  • Year and Date: 20070708-13
• [Presentation] 生態系での細菌ゲノム情報発現 -遺伝学的手法を用いた発現遺伝子群の探索- (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] Genetic organization of IncP-7 TOL plasmid pWW53 and the movement of its residing transposons (2006)
  • Author(s): Yano, H., C. Garruto, M. Sota, Y. Ohtsubo, Y. Nagata, P. A. Williams, G. J. Zylsra, and M. Tsuda
  • Organizer: Plasmid Biology
  • Place of Presentation: South Lake Tahoe, California, USA
  • Year and Date: 20060923-27
• [Presentation] Exogenous isolation of a plasmid involved in the degradation of γ-hexachlorocyclohexane from its contaminated soil (2006)
  • Author(s): Miyazaki, R., Y. Sato, M. Ito, Y. Ohtsubo, Y. Nagata, and M. Tsuda
  • Organizer: Plasmid Biology 2006
  • Place of Presentation: South Lake Tahoe, California, USA
  • Year and Date: 20060923-27
• [Presentation] Genomic and functional analysis of catabolic plasmids and transposons (2006)
  • Author(s): Sota, M., E. M. Top, and M. Tsuda
  • Organizer: Plasmid Biology
  • Place of Presentation: South Lake Tahoe, California, USA
  • Year and Date: 20060923-27
• [Presentation] Direct isolation of genes and a plasmid for the degradation of γ-hexachlorocyclohexane from contaminated soil (2006)
  • Author(s): Nagata, Y., M. Ito, R. Miyazaki, G. Fuchu, Y. Ohtsubo, and M. Tsuda
  • Organizer: International Symposium on Environmental Biotechnology
  • Place of Presentation: Leipzig, Germany
  • Year and Date: 20060709-13
• [Presentation] Novel ABC-type transporter genes essential for the γ-hexachlorocyclohexane utilization in Sphingobium japonicum UT26 (2006)
  • Author(s): Endo, R., Y. Ohtsubo, M. Tsuda, and Y. Nagata
  • Organizer: International Symposium on Environmental Biotechnology
  • Place of Presentation: Leipzig, Germany
  • Year and Date: 20060709-13
• [Presentation] Conjugal transfer of PCB/biphenyl degradation genes in Acidovorax sp. KKS102 (2006)
  • Author(s): Ohtsubo, Y., S. Atobe, Y. Nagata, and M. Tsuda
  • Organizer: International Symposium on Environmental Biotechnology
  • Place of Presentation: Leipzig, Germany
  • Year and Date: 20060709-13
• [Book] 微生物の事典 (2008)
  • Author(s): 津田雅孝, メタゲノム(渡邉信, 西村和子, 内山裕夫, 奥田徹, 加来久敏, 広木幹也編)
  • Total Pages: 661-663
  • Publisher: 朝倉書店
• [Book] Bacterial class II catabolic transposons In : K. Yoshiki and M. Aoki (eds), "DNA Transposable Elements Research" (2008)
  • Author(s): Sota, M., H. Yano, and M. Tsuda
  • Total Pages: 23-67
  • Publisher: Nova Science Publishers, Inc., New York, U.S.A
• [Book] 難培養性細菌も研究対象とするメタゲノム解「バイオフィルムの基礎と制御 : 特性・解析事例から形成防止・有効利用まで」 (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] 土壌環境細菌の比較ゲノム「比較ゲノム学から読み解く生命システム-基本概念から最新ゲノム情報まで-」(藤山秋佐夫監修) (2007)
  • Author(s): 津田雅孝, 永田裕二, 大坪嘉行
  • Total Pages: 166-172
  • Publisher: 秀潤社
• [Remarks] DNA配列比較ソフトウェアGenomeMatcherの開発と公開
  • URL: http://www.ige.tohoku.ac.jp/joho/gmProject/gmhomeJP.html