微生物遺伝研究室
Laboratory of Microbial Genetics and Genomics
東北大学大学院生命科学研究科分子化学生物学専攻

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原著論文・総説・著書

2019年

Kishida K, Nonoyama S, Lukas T, Kawahara S, Kudo K, Nagata Y, Ohtsubo Y, Tsuda M. Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK, Whose Homologs Are Conserved in Various MPF(T)-Type Plasmids. Appl Environ Microbiol. 2019 Nov 27;85(24). pii: e01850-19. doi: 10.1128/AEM.01850-19.

Ohtsubo Y, Sakai K, Nagata Y, Tsuda M. Properties and efficient scrap-and-build repairing of mechanically sheared 3' DNA ends. Commun Biol. 2019 Nov 8;2:409. doi: 10.1038/s42003-019-0660-7.

Nagata Y, Kato H, Ohtsubo Y, Tsuda M. Lessons from the genomes of lindane-degrading sphingomonads. Environ Microbiol Rep. 2019 Oct;11(5):630-644. doi: 10.1111/1758-2229.12762.

Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Okada K, Nojiri H. Complete Genome Sequence of Thalassococcus sp. Strain S3, a Marine Roseobacter Clade Member Capable of Degrading Carbazole. Microbiol Resour Announc. 2019 Jul 11;8(28). pii: e00231-19. doi: 10.1128/MRA.00231-19.

Ogawa N, Kato H, Kishida K, Ichihashi E, Ishige T, Yoshikawa H, Nagata Y, Ohtsubo Y, Tsuda M. Suppression of substrate inhibition in phenanthrene-degrading Mycobacterium by co-cultivation with a non-degrading Burkholderia strain. Microbiology. 2019 Jun;165(6):625-637. doi: 10.1099/mic.0.000801.

Ohtsubo Y, Yamashita Y, Hagiwara K, Ideta SI, Tanaka K, Yukawa R, Horiba K, Kumigashira H, Miyamoto K, Okuda T, Hirano W, Iga F, Kimura SI. Non-trivial surface states of samarium hexaboride at the (111) surface. Nat Commun. 2019 May 24;10(1):2298. doi: 10.1038/s41467-019-10353-3.

Devanadera A, Vejarano F, Zhai Y, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Kasai Y, Takahata Y, Okada K, Nojiri H. Complete Genome Sequence of an Anaerobic Benzene-Degrading Bacterium, Azoarcus sp. Strain DN11. Microbiol Resour Announc. 2019 Mar 14;8(11). pii: e01699-18. doi: 10.1128/MRA.01699-18.

Mpofu E, Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Chakraborty J, Nakajima M, Okada K, Tada N, Kimura T, Nojiri H. Complete Genome Sequence of Bacillus licheniformis TAB7, a Compost-Deodorizing Strain with Potential for Plant Growth Promotion. Microbiol Resour Announc. 2019 Jan 24;8(4). pii: e01659-18. doi: 10.1128/MRA.01659-18.

2018年

Ohtsubo Y, Sasaki H, Nagata Y, Tsuda M. 2018. Optimization of single strand DNA incorporation reaction by Moloney murine leukaemia virus reverse transcriptase. DNA Research 25(5):477-487.

Kishida K, Ogawa N, Ichihashi E, Kato H, Nagata Y, Ohtsubo Y, Tsuda M. 2018. Establishment of plasmid vector and allelic exchange mutagenesis systems in a mycobacterial strain that is able to degrade polycyclic aromatic hydrocarbon. Biosci. Biotechnol. Biochem. 82(7):1169-1171.

Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Okada K, Nojiri H. 2018. Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5. Microbiol Resour Announc. 7(8)

2017年

加藤広海, 津田雅孝. 土壌細菌叢メタゲノムの時間的変動 生体の科学 68:160-164

加藤広海, 津田雅孝. 土壌細菌叢の化学的撹乱に対するロバスト性 - 経時的な土壌メタゲノム解析からみえてきたこと 化学と生物 55:446-447

津田雅孝. 有害化合物汚染土壌の微生物集団による分解・浄化に向けた基盤研究: 分解菌と共存する非分解菌の役割の解明 IFO Res Commun 31:47-56

Sato T, Nonoyama S, Kimura A, Nagata Y, Ohtsubo Y, Tsuda M. 2017. The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616. Appl Environ Microbiol 83(16). e00479-17

Ohtsubo Y, Nagata Y, Tsuda M. 2017. Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase. Scientific Reports 7(1):6520

Sugawara M, Tsukui T, Kaneko T, Ohtsubo Y, Sato S, Nagata Y, Tsuda M, Mitsui H, Minamisawa K. 2017. Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen-Fixing Soybean Symbiont. Genome Announc. 2017 5(9). e01743-16.

Ohtsubo Y, Nagata Y, Tsuda M. 2017. Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase. Scientific Reports 7, 41769

Kishida K, Inoue K, Ohtsubo Y, Nagata Y, Tsuda M. 2016. Host range of the conjugative transfer system of IncP-9 naphthalene-catabolic plasmid NAH7 and characterization of its oriT region and relaxase. Appl Environ Microbiol 83:1e02359-16

2016年

Minami T, Ohtsubo Y, Anda M, Nagata Y, Tsuda M, Mitsui H, Sugawara M, Minamisawa K. 2016. Complete genome sequence of Methylobacterium sp. strain AMS5, an isolate from a soybean stem. Genome Announcements 4:e00144-00116.

Tabata M, Ohhata S, Nikawadori Y, Sato T, Kishida K, Ohtsubo Y, Tsuda M, Nagata Y. 2016. Complete genome sequence of a γ-hexachlorocyclohexane-degrading bacterium, Sphingobium sp. strain MI1205. Genome Announcements 4:e00246-00219.

Tabata M, Ohhata S, Kawasumi T, Nikawadori Y, Kishida K, Sato T, Ohtsubo Y, Tsuda M, Nagata Y. 2016. Complete genome sequence of a γ-hexachlorocyclohexane degrader, Sphingobium sp. strain TKS, Isolated from a γ-hexachlorocyclohexane-degrading microbial community. Genome Announcements 4:e00247-00216.

Ohtsubo Y, Nonoyama S, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. 2016. Complete genome sequence of Sphingopyxis macrogoltabida strain 203N (NBRC 111659), a polyethylene glycol degrader. Genome Announcements 4:e00529-00516.

Ohtsubo Y, Nonoyama S, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. 2016. Complete genome sequence of Sphingopyxis terrae strain 203-1 (NBRC 111660), a polyethylene glycol degrader. Genome Announcements 4:e00530-00516.

Ohtsubo Y, Nonoyama S, Ogawa N, Kato H, Nagata Y, Tsuda M. 2016. Complete genome sequence of Burkholderia caribensis Bcrs1W (NBRC110739), a strain co-residing with phenanthrene degrader Mycobacterium sp. EPa45. Journal of Biotechnology 228:67-68.

Nanasato Y, Namiki S, Oshima M, Moriuchi R, Konagaya K-i, Seike N, Otani T, Nagata Y, Tsuda M, Tabei Y. 2016. Biodegradation of γ-hexachlorocyclohexane by transgenic hairy root cultures of Cucurbita moschata that accumulate recombinant bacterial LinA. Plant Cell Reports 35:1963-1974.

Tabata M, Ohhata S, Nikawadori Y, Kishida K, Sato T, Kawasumi T, Kato H, Ohtsubo Y, Tsuda M, Nagata Y. 2016. Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide. DNA Research 23:581-599.

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., Kanesaki, Y., Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools. Journal of biotechnology 220, 45-46.

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., Kanesaki, Y., Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755. Genome announcements 4:e00090-16

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., Kanesaki, Y., Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based bioengineering. Journal of biotechnology 218, 51-52.

Muraguchi, Y., Kushimoto, K., Ohtsubo, Y., Suzuki, T., Dohra, H., Kimbara, K., Shintani, M., (2016) Complete Genome Sequence of Algoriphagus sp. Strain M8-2, Isolated from a Brackish Lake. Genome announcements 4:e00347-16

加藤広海, 津田雅孝. 2016. 土壌細菌叢のメタ16S・ショットガンメタゲノム解析, p 107-114. In 服部正平 (ed), メタゲノム解析・実験プロトコール - ヒト常在細菌叢から環境メタゲノムまでサンプル調製と解析のコツ-. 羊土社, 東京.

2015年

Nagayama H, Sugawara T, Endo R, Ono A, Kato H, Ohtsubo Y, Nagata Y, Tsuda M. 2015. Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts. Applied Microbiology and Biotechnology 99: 4453-4470.

Kato H, Ogawa N, Ohtsubo Y, Oshima K, Toyoda A, Mori H, Nagata Y, Kurokawa K, Hattori M, Fujiyama A, Tsuda M. 2015. Complete genome sequence of a phenanthrene degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), isolated from a phenanthrene-degrading consortium. Genome Announcements 3: e00782-15.

Ohtsubo Y, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. 2015. Complete genome sequence of polyvinyl alcohol-degrading strain Sphingopyxis sp. 113P3 (NBRC 111507). Genome Announcements 3: e01169-15.

Nagata Y, Ohtsubo Y, Tsuda M. 2015. Properties and biotechnological applications of natural and engineered haloalkane dehalogenases. Applied Microbiology and Biotechnology 99: 9865-9881.

加藤広海, 小川なつみ, 津田雅孝. 2015. メタゲノム情報を基盤とした土壌細菌コミュニティの解析. 日本微生物生態学会誌 30: 57-64.

Ohtsubo Y, Moriya A, Kato H, Ogawa N, Nagata Y, Tsuda M. 2015. Complete genome sequence of a phenanthrene degrader, Burkholderia sp. HB-1 (NBRC 110738). Genome Announcements 3: e01283-15.

Ohtsubo Y, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. 2015. Complete genome sequence of polypropylene glycol- and polyethylene glycol-degrading Sphingopyxis macrogoltabida strain EY-1. Genome Announcements 3: e01399-015.

Ohtsubo Y, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. 2015. Complete genome sequence of a polypropylene glycol-degrading strain, Microbacterium sp. No. 7. Genome Announcements 3: e01400-15.

Ohtsubo Y, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. 2015. Complete genome sequence of Sphingopyxis macrogoltabida type strain NBRC 15033, originally isolated as a polyethylene glycol degrader. Genome Announcements 3: e01401-15.

Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2015. Biodegradation of organochlorine pesticides, In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, 4th Edition. pp 5.1.2-1-5.1.2-30. ASM Press, Washington, D.C.

Anda M, Ohtsubo Y, Okubo T, Sugawara M, Nagata Y, Tsuda M, Minamisawa K, Mitsui H. 2015. Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome. Proceedings of the National Academy of Sciences 112: 14343-14347.

Kato H, Mori H, Maruyama F, Toyoda A, Oshima K, Endo R, Fuchu G, Miyakoshi M, Dozono A, Ohtsubo Y, Nagata Y, Hattori M, Fujiyama A, Kurokawa K, Tsuda M. 2015. Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Research 22: 413-424.

2014 年

Moriuchi, R., H. Tanaka, Y. Nikawadori, M. Ishitsuka, M. Ito, Y. Ohtsubo, M. Tsuda, J. Damborsky, Z. Prokop, and Y. Nagata: Stepwise enhancement of catalytic performance of haloalkane dehalogenase LinB towards β-hexachlorocyclohexane. AMB Express 4:72 (2014)

Nagata, Y., J. Senbongi, Y. Ishibashi, R. Sudo, M. Miyakoshi, Y. Ohtsubo, and M. Tsuda: Identification of Burkholderia multivorans ATCC 17616 genetic determinants for fitness in soil by using signature-tagged mutagenesis. Microbiology 160: 883-891 (2014)

Mori, H., F. Maruyama, H. Kato, A. Toyoda, A. Dozono, Y. Ohtsubo, Y. Nagata, A. Fujiyama, M. Tsuda, and K. Kurokawa: Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes. DNA Research 21: 217-227 (2014)

Ohtsubo, Y., K. Kishida, T. Sato, M. Tabata, T. Kawasumi, Y. Ogura, T. Hayashi, M. Tsuda, and Y. Nagata: Complete genome sequence of Pseudomonas sp.strain TKP isolated from a γ-hexachlorocyclohexane-degrading mixed culture. Genome Announcements  2: e01241-13 (2014)

Shintani, M., Y. Ohtsubo, K. Fukuda, A. Hosoyama, S. Ohji, A. Yamazoe, N. Fujita, Y. Nagata, M. Tsuda, T. Hatta, and K. Kimbara: Complete genome sequence of the thermophilic PCB degrader Geobacillus sp. JF8 (NBRC 109937). Genome Announcements 2: e01213-13 (2014)

Ohtsubo, Y., T. Sato, K. Kishida, M. Tabata, Y. Ogura, T. Hayashi, M. Tsuda, and Y. Nagata:
Complete genome sequence of Pseudomonas aeruginosa MTB-1 isolated from a microbial community enriched by the technical formulation of hexachlorocyclohexane. Genome Announcements  2: e01130-13 (2014)

Chaloupkova R, Prudnikova T, Rezacova P, Prokop Z, Koudelakova T, Daniel L, Brezovsky J, Ikeda-Ohtsubo W, Sato Y, Kuty M, Nagata Y, Smatanova IK, Damborsky J: Structural and functional analysis of novel haloalkane dehalogenase with two halide-binding sites. Acta Crystallographica Section D D70: 1884-1897 (2014)

Nagata, Y., M. Tabata, S. Ohhata, and M. Tsuda: Appearance and evolution of γ-hexachlorocyclohexane-degrading bacteria. In: Nojiri, H., M. Tsuda, M. Fukuda, and Y. Kamagata (eds), Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve. Springer, Tokyo. pp. 19-41 (2014)

Tsuda, M., Y. Ohtsubo, and H. Yano: Mobile catabolic genetic elements in pseudomonads. In: Nojiri, H., M. Tsuda, M. Fukuda, and Y. Kamagata (eds), Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve. Springer, Tokyo. pp. 83-103 (2014)

Ohtsubo, Y., E. Nishiyama, Y. Ishibashi, Y. Nagata, and M. Tsuda: Strategies to reveal genomic function in natural soil systems. In: Nojiri, H., M. Tsuda, M. Fukuda, and Y. Kamagata (eds), Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve. Springer, Tokyo. pp. 279-291 (2014)

2013 年

Ohtsubo, Y., N. Fujita, Y. Nagata, M. Tsuda, T. Iwasaki, and T. Hatta: Complete genome sequence of Ralstonia pickettii DTP0602, a 2,4,6-trichrolophenol degrader. Genome Announcements 1: e00903-13 (2013)

Tabata, M., Y. Ohtsubo, S. Ohhata, M. Tsuda, and Y. Nagata: Complete genome sequence of the γ-hexachlorocyclohexane-degrading bacterium Sphingomonas sp. strain MM-1. Genome Announcements 1: e00247-13 (2013)

Okai, M., J. Ohtsuka, L. Imai, T. Mase, R. Moriuchi, M. Tsuda, K. Nagata, Y. Nagata, and M. Tanokura: Crystal structure and site-directed mutagenesis analyses of haloalkane dehalogenase LinB from Sphingobium sp. MI1205. J. Bacteriol. 195: 2642-2651 (2013)

Inoue, K., R. Miyazaki, Y. Ohtsubo, Y. Nagata, and M. Tsuda: Inhibitory effect of Pseudomonas putida nitrogen-related phosphotransferase system on conjugative transfer of IncP-9 plasmid from Escherichia coli. FEMS Microbiol. Lett. 345: 102-109 (2013)

永山浩史, 菅原智詞, 遠藤諒, 加藤広海, 大坪嘉行, 永田裕二, 津田雅孝: 機能相補による芳香族化合物複合汚染土壌からの新規分解酵素遺伝子の探索. J. Environ. Biotechnol. 13: 51-55 (2013)

石田聖二, 黒川紘子, 富松裕, 加藤広海, 山崎誠和, 河田雅圭: 生態適応科学とは - 克服から適応へ -. 生態適応科学 - 自然のしくみを活かし、持続可能な未来を拓く(東北大学生態適応グローバルCOE編, 日経BP社) pp. 8-13 (2013)

黒川紘子, 佐々木雄大, 牧野能士, 加藤広海: 生態系の適応力. 生態適応科学 - 自然のしくみを活かし, 持続可能な未来を拓く (東北大学生態適応グローバルCOE編, 日経BP社) pp. 16-54 (2013)

Matsushima, R., R. Watanabe, M. Tsuda, and T. Suzuki: Analysis of extracellular alginate lyase (alyA) expression and its regulatory region in a marine bacterial strain, Pseudoalteromonas atlantica AR06, using a gfp gene reporter system. Marine Biotechnol. 15: 349-356 (2013)

Minegishi, K., C. Aikawa, A. Furukawa, R. Watanabe, T. Nakano, Y. Ogura, Y. Ohtsubo, K. Kurokawa, T. Hayashi, F. Maruyama, I. Nakagawa, and Y. Eishi: Complete genome sequence of a Propionibacterium acnes isolate from a Sarcoidosis patient. Genome Announcements1: e00016-12 (2013)

Ogawa, T., K. Noguchi, M. Saito, Y. Nagahata, H. Kato, A. Ohtaki, H. Nakayama, N. Dohmae, Y. Matsushita, M. Odaka, M. Yohda, H. Nyunoya, and Y. Katayama: Carbonyl sulfide hydrolase from Thiobacillus thioparus strain THI115 Is one of the b-carbonic anhydrase family enzymes. J. Amer. Chem. Soci. 135: 3818–3825 (2013)

Yano, H., H. Genka, Y. Ohtsubo, Y. Nagata, E. M. Top, and M. Tsuda: Cointegrate-resolution of toluene-catabolic transposon Tn4651: determination of crossover site and the segment required for full resolution activity. Plasmid 69: 24-35 (2013)

2012 年

Miyakoshi, M., M. Shintani, K. Inoue, T. Terabayashi, F. Sai, M. Ohkuma, H. Nojiri, Y. Nagata, and M. Tsuda: ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids. Environ. Microbiol. 14: 2946-2959 (2012)

Ohtsubo, Y., Y. Ishibashi, H. Naganawa, S. Hirokawa, S. Atobe, Y. Nagata, and M. Tsuda: Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. KKS102 located on integrative and conjugative element. J, Bacteriol. 184: 4237-4248 (2012)

Kimura, A., S. Yuhara, Y. Ohtsubo, Y. Nagata, and M. Tsuda: Suppression of pleiotrophic phenotypes of Burkholderia multivorans fur mutant by oxyR mutation. Microbiology 158: 1284-1293 (2012)

Nishiyama, E., Y. Ohtsubo, Y. Yamamoto, Y. Nagata, and M. Tsuda: Pivotal role of anthranilate dioxygenase genes in the adaptation of Burkholderia multivorans ATCC 17616 in soil. FEMS Microbiol. Lett. 330: 46-55 (2012)

Ito, M., A. Ono, Y. Ohtsubo, M. Tsuda, and Y. Nagata: Cloning of γ-hexachlorocyclohexane dehydrochlorinase gene with its flanking regions from soil by activity-based screening techniques. Euro. J. Soil Biol. 52: 16-19 (2012)

Ohtsubo, Y., F. Maruyama, H. Mitsui, Y. Nagata, and M. Tsuda: Complete genome sequence of Acidovorax sp. KKS102, a polychlorinated biphenyl-degrading strain: J. Bacteriol. 194: 6970-6971 (2012)

Kato, H., Y, Igarashi, Y, Dokiya, and Y, Katayama: Vertical distribution of carbonyl sulfide at Mt. Fuji, Japan. Water, Air, & Soil Pollution. 223: 159-167 (2012)

Mase, T., H. Yabuki, M. Okai, J. Ohtsuka, F. L. Imai, Y. Nagata, and M. Tanokura: Crystallization and preliminary X-ray analysis of the haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58. Acta Crystallographica Section F F68: 652-654 (2012)

2011 年

Hasan, K., A. Fortova, T. Koudelakova, R. Chaloupkova, M. Ishitsuka, Y. Nagata, J. Damborsky, and Z. Prokop: Biochemical characteristics of the novel haloalkane dehalogenase DatA isolated from the plant pathogen Agrobacterium tumefaciens C58. Appl. Environ. Microbiol. 77: 1881-1884 (2011)

T. Prudnikova, R. Chaloupkova, Y. Sato, Y. Nagata, O. Degtjarik, M. Kuty, P. Rezacova, J. Damborsky, and I. K. Smatanova: Development of a crystallization protocol for the DbeA1 variant of novel haloalkane dehalogenase from Bradyrhizobium elikani USDA94. Crystal Growth & Design 11: 516-519 (2011)

Chaloupkova, R., Z. Prokop, Y. Sato, Y. Nagata, and J. Damborsky: Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bardyrhizobium japonicum USDA110: the effect of pH and temperature. FEBS J. 278: 2728-2738 (2011)

Nagata, Y., S. Natsui, R. Endo, Y. Ohtsubo, N. Ichikawa, A. Ankai, A. Oguchi, S. Fukui, N. Fujita, and M. Tsuda: Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal gamma-hexachlorocyclohexane-degrading bacterium. Enzyme Microb. Technol. 49: 499-508 (2011)

Tabata, M., R. Endo, M. Ito, Y. Ohtsubo, A. Kumar, M. Tsuda, and Y. Nagata: The lin genes for gamma-hexachlorocyclohexane degradation in Sphingomonas sp. MM-1 proved to be dispersed across multiple plasmids. Biosci. Biotechnol. Biochem. 75: 466-472 (2011)

佐藤優花里,夏目亮, Zbynek Prokop, Jan Brezovsky, Radka Chaloupkova, Jiri Damborsky, 永田裕二, 千田俊哉: ハロアルカン脱ハロゲン酵素DbjAの鏡像異性体選択性機構の解明, 日本結晶学会誌 53: 124-129 (2011)

2010 年

Nagata, Y., Y. Ohtsubo, R. Endo, N. Ichikawa, A. Ankai, A. Oguchi, S. Fukui, N. Fujita, and M. Tsuda: Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26. J. Bacteriol. 192: 5852-5853 (2010)

Okai, M., K. Kubota, M. Fukuda, Y. Nagata, K. Nagata, and M. Tanokura: Crystal structure of γ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26. J. Mol. Biol. 403: 260-269 (2010)

Yano, H., M. Miyakoshi, K. Ohshima, M. Tabata, Y. Nagata, M. Hattori, and M. Tsuda: Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J. Bacteriol. 192: 4337-4347 (2010)

Prokop, Z., Y. Sato, J. Brezovsky, T. Mozga, R. Chalooupkova, T. Koudelakova, P. Jerabek, V. Stepankova, R. Natsume, J. G.E. van Leeuwen, D. B. Janssen, J. Florian, Y. Nagata, T. Senda, and J. Damborsky: Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering. Angewandte Chemie. 16: 6111-6115 (2010)

Matsushima, R., H. Danno, M. Uchida, K. Ishihara, T. Suzuki, M. Kaneniwa, Y. Ohtsubo, Y. Nagata, and M. Tsuda: Analysis of extracellular alginate lyase and its gene from a marine bacterial strain, Pseudoalteromonas atlantica AR06. Appl Microbiol Biotechnol. 86: 567-576 (2010)

Nishiyama, E., Y. Ohtsubo, Y. Nagata, and M. Tsuda: Identification of Burkholderia multivorans ATCC 17616 genes induced in soil environment by in vivo expression technology. Environ. Microbiol. 12: 2539-2558 (2010)

永田裕二, 津田雅孝: 環境汚染物質分解細菌のメタゲノミクス.「難培養性微生物研究の最新技術II」(大熊盛也, 工藤俊章編集) シーエムシー出版 pp 211-219 (2010)

永田裕二, 津田雅孝: 脱ハロゲン酵素.「酵素利用技術体系」エヌ・ティー・エス社 pp 939-948 (2010)

大坪嘉行, 大坪和香子, 永田裕二, 津田雅孝: ゲノム解析ソフトウエアGenomeMatcher. 化学と生物 48: 313-319 (2010)

加藤広海, 大坪嘉行, 永田裕二, 津田雅孝: 芳香族化合物による土壌撹乱における微生物遺伝子プールの変動. J. Environ. Biotechnol. 10: 63-70 (2010)

2009 年

Suenaga, H., Y. Koyama, M. Miyakoshi, R. Miyazaki, H. Yano, M. Sota, Y. Ohtsubo, M. Tsuda and K. Miyazaki: Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 3: 1335-1348 (2009)

大坪嘉行、西山依里、永田裕二、津田雅孝: 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 生物工学会誌 87: 434-436 (2009)

Miyakoshi, M., H. Nishida, M. Shintani, H. Yamane, and H. Nojiri: High-resolution mapping of plasmid transcriptomes in different host bacteria. BMC Genomics 10: 12 (2009)

大坪嘉行, 永田裕二, 津田雅孝: 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-. 化学と生物 47: 35-42 (2009)

永田裕二、津田雅孝: 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」松永是、竹山春子編集 シーエムシー出版. pp. 166-178(2009)

Okai, M, K. Kubota, M. Fukuda, Y. Nagata, K. Nagata, and M. Tanokura: Crystallization and preliminary X-ray analysis of γ-hexachlorocyclohexane dehydrochlorinasae LinA from Sphingobium japonicum UT26. Acta Crystallographica Section F 65: 822-824 (2009)

Pavlova, M., M. Klvana, Z. Prokop, R. Chaloupkova, P. Banas, M. Otyepka, R. C. Wade, M. Tsuda, Y. Nagata, and J. Damborsky: Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology 5: 727-733 (2009)

Prudnikova, T., T. Mozga, P. Rezacova, R. Chaloupkova, Y. Sato, Y. Nagata, J. Brynda, M. Kuty, J. Damborsky, and I. K. Smatanova: Crystallization and preliminary X-ray analysis of a novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94. Acta Crystallographica Section F 65: 353-356 (2009)

2008年

永田裕二, 津田雅孝: 難培養性細菌も研究対象とするメタゲノム解析. 「バイオフィルムの基礎と制御」(エヌ・ティー・エス社)pp. 103-111 (2008)

S. Yuhara, H. Komatsu, H. Goto, Y. Ohtsubo, Y. Nagata, and M. Tsuda: Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans. Microbiology 154: 1763-1774 (2008)

G. Fuchu, Y. Ohtsubo, M. Ito, R. Miyazaki, A. Ono, Y. Nagata, and M. Tsuda: Insertion sequence-based cassette PCR: cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA. Appl. Microbiol. Biotechnol. 79: 627-632 (2008)

M. Sota, H. Yano, and M. Tsuda: Bacterial class II catabolic transposons. In: K. Yoshiki and M. Aoki (eds), “DNA Transposable Elements Research” pp. 23-67. Nova Science Publishers, Inc. New York. (2008)

Y. Ohtsubo, W. Ikeda-Ohtsubo, Y. Nagata and M. Tsuda: GenomeMatcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics 9: 376 (2008)

津田雅孝: メタゲノム.「微生物の事典」(朝倉書店) pp. 661-663 (2008)

R. Miyazaki, Y. Ohtsubo, Y. Nagata and M. Tsuda: Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer. J. Bacteriol. 190: 6281-6289 (2008)

A. P. Roberts, M. Chandler, P. Courvalin, G. Guédon, P. Mullany, T. Pembroke, J. I. Rood, C. J. Smith, A. O. Summers, M. Tsuda, and D. E. Berg: Revised nomenclature for transposable genetic elements. Plasmid 60: 167-173 (2008)

津田雅孝, 西山依里, 宮腰昌利, 湯原悟志, 永田裕二, 大坪嘉行: 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. 土と微生物. 62: 93-97 (2008)

Y. Shimoda, 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: Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics. DNA Res. 15: 297-308. (2008)

永田裕二: 土壌環境での細菌の生き様を探る. 日本生物工学会誌 86: 549 (2008)

2007年

Y. Nagata, R, Endo, M. Ito, Y. Ohtsubo, and M. Tsuda: Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. App. Microbiol. Biotechnol. 76: 741-752 (2007)

M. Miyakoshi, M. Shintani, T. Terabayashi, S. Kai, H. Yamane, and H. Nojiri: Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J. Bacteriol. 189: 6849-6860. (2007)

M. Sota, E. M. Top, and M. Tsuda: Genomic and functional analysis of catabolic plasmids and transposons. Plasmid 57: 228 (2007)

M. Ito, Z. Prokop, M. Klvana, Y. Ohtsubo, M. Tsuda, J. Damborsky, Y. Nagata: Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205. Arch Microbiol. 188: 313-325 (2007)

H. Yano, C. Garruto, M. Sota, Y. Ohtsubo, Y. Nagata, P. A. Williams, G. J. Zylsra, and M. Tsuda: Genetic organization of IncP-7 TOL plasmid pWW53 and the movement of its residing transposons. Plasmid 57: 231 (2007)

R. Miyazaki, Y. Sato, M. Ito, Y. Ohtsubo, Y. Nagata, and M. Tsuda: Exogenous isolation of a plasmid involved in the degradation of γ-hexachlorocyclohexane from its contaminated soil. Plasmid 57: 233 (2007)

M. Monincova, Z. Prokop, J. Vevodova, Y. Nagata, and J. Damborsky: Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-ray crystallography and microcalorimetry. Appl. Envirom. Microbiol. 73: 2005-2008 (2007)

M. Sota, M. Tsuda, H. Yano, L. J. Forney, and E. M. Top: Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. J. Bacteriol. 189: 3091-3098 (2007)

Y. Sato, R. Natsume, M. Tsuda, J. Damborsky, Y. Nagata and T. Senda: Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110. Acta Cryst Section F F63 :294-296 (2007)

H. Yano, C. E Garruto, M. Sota, Y. Ohtsubo, Y. Nagata, 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. J. Mol. Biol. 369: 11-26 (2007)

R. Endo, Y. Ohtsubo, M. Tsuda, and Y. Nagata: Identification and characterization of genes encoding a putative ABC-type transporter essential for the utilization of γ-Hexachlorocyclohexane in Sphingobium japonicum UT26. J. Bacterol. 189: 3712-3720 (2007)

A Ono, R Miyazaki, M Sota, Y Ohtsubo, Y Nagata, M Tsuda: Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol. 74: 501-510. (2007)

Pavlova M, Klvana M, Jesenska A, Prokop Z, Konecna H, Sato T, Tsuda M, Nagata Y, Damborsky J. : The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: Reaction mechanism and molecular evolution. J Struct Biol. 157: 384-392(2007)

津田雅孝, 西山依里, 永田裕二, 大坪嘉行: 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, 化学と生物, 45: 557-563 (2007)

野尻秀昭,宮腰昌利,新谷政己,西田洋巳: プラスミドは環境中でどのように振る舞うのか. 化学と生物, 45: 635-643 (2007)

津田雅孝, 永田裕二, 大坪嘉行: 土壌環境細菌の比較ゲノム. 細胞工学別冊「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-」(秀潤社) (藤山秋佐夫監修) pp. 166-172 (2007)

津田雅孝, 西山依里, 宮腰昌利, 永田裕二, 大坪嘉行: 土壌生態系での環境細菌ゲノム情報発現, 極限環境微生物学会誌 6: 59-62 (2007)

津田雅孝, 小野玲, 宮崎亮, 府中玄樹, 永田裕二: 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. J. Environ. Biotechnol. 7: 75-78 (2007)

2006年

R. Miyazaki, Y. Sato, M. Ito, Y. Ohtsubo, Y. Nagata, M. Tsuda: Complete Nucleotide Sequence of an Exogenously Isolated Plasmid pLB1 Involved in the Degradation of {gamma}-Hexachlorocyclohexane. Appl Environ Microbiol. 72: 6923-6933 (2006)

Y. Ohtsubo, H. Goto, Y. Nagata, T. Kudo, and M. Tsuda: Identification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp. KKS102. Mol. Microbiol. 60: 1563-75 (2006)

M. Sota, H. Yano, A. Ono, R. Miyazaki, H. Ishii, H. Genka, E. M. Top, and M. Tsuda: Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J. Bacteriol. 188: 4057-4067 (2006)

M. Shintani, H. Yano, H. Habe, T. Omori, H. Yamane, M. Tsuda, and H. Nojiri: Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation. Appl Environ Microbiol. 72: 3206-16 (2006)

R. Endo, Y. Ohtsubo, M. Tsuda, and Y. Nagata: Growth inhibition by metabolites of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26. Biosci. Biotechnol. Biochem. 70: 109-1032 (2006)

M. Sota, H. Yano, Y. Nagata, Y. Ohtsubo, H. Genka, H. Anbutsu, H. Kawasaki, and M. Tsuda: Functional analysis of unique class II insertion sequence IS1071. Appl. Environ. Microbiol. 72: 291-297 (2006)

Y. Nagata, M. Kamakura, R. Endo, R. Miyazaki, Y. Ohtsubo, and M. Tsuda: Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. FEMS Microbiol. Lett. 256: 112-118 (2006)

N. Ito, 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: Global gene expression in Bradyrhizobium japonicum cultured with vanillin, vanillate, 4-hydroxybenzoate, and protocatechuate. Microbes Environ. 21: 240-250 (2006)

H. Genka, T. Baba, M. Tsuda, S. Kanaya, H. Mori, T. Yoshida, M. Tsujimoto-Noguchi, K. Tsuchiya, and H. Sawada: Comparative analysis of argK-tox clusters and their flanking regions in phaseolotoxin-producing Pseudomonas syringae pathovars. J. Mol. Evol. 63: 401-414 (2006)

永田裕二, 津田雅孝: ハロアルカンデハロゲナーゼの構造と機能. J. Environ. Biotechnol. 6: 87-92 (2006)

小野玲, 宮崎亮, 永田裕二, 津田雅孝: 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. バイオインダストリー 23: 44-46 (2006)

永田裕二: メタゲノムは宝の山か? 生物工学会誌 84: 73-73 (2006)

大坪嘉行: IVET法: “in vivo”での微生物を知る. 生物工学会誌 84: 333-333 (2006)

伊藤通浩: 数アミノ酸置換による酵素進化. 日本微生物生態学会誌 21: 60-61 (2006)

2005年

M. Tsuda, H. Yano, H. Genka, S. Wakase, and M. Sota: Structure and rearrangement of a Pseudomonas IncP-7 plasmid carrying toluene catabolic transposons. Plasmid 53: 96. (2005)

Y. Nagata, M. Matsuda, H. Komatsu, Y. Imura, H. Sawada, Y. Ohtsubo, M. Tsuda: Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616. J. Biosci. Bioeng. 99: 603-610. (2005)

Y. Sato, M. Monincova, R. Chaloupkov, Z. Prokop, Y. Ohtsubo, K. Minamisawa, M. Tsuda, J. Damborsky and Y. Nagata: Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities. Appl. Environ. Microbiol. 71: 4372-4379. (2005)

K. Miyauchi, M. Fukuda, M. Takagi, M. Tsuda, and Y. Nagata: Identification of insertion sequence from gamma-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26. Biosci. Biotech. Biochem. 69: 216-219 (2005)

Y. Nagata, Z. Prokop, Y. Sato, P. Jerabek, A. Kumar, Y. Ohtsubo, M. Tsuda, and J. Damborsky: Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Appl. Environ. Microbiol. 71: 2183-2185. (2005)

Y. Ohtsubo, H. Genka, H. Komatsu, Y. Nagata, and M. Tsuda: High-temperature-induced transposition of IS elements in Burkholderia multivorans ATCC 17616. Appl. Environ. Microbiol. 71: 1822-1828. (2005)

R. Endo, M. Kamakura, K. Miyauchi, M. Fukuda, Y. Ohtsubo, M. Tsuda, and Y. Nagata: Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26. J. Bacteriol. 187: 847-853. (2005)

M. Shintani, H. Habe, H. Yamane, T. Omori, M. Tsuda, and H. Nojiri: Characterization of plasmid pCAR1 and pCAR2 carrying carbazole-degradative car operon. Plasmid 53: 45 (2005)

M. Shintani, H. Habe, M. Tsuda, T. Omori, H. Yamane, and H. Nojiri: Recipient range of IncP-7 conjugative plasmid pCAR2 from Pseudomonas putida HS01 is broader than from other Pseudomonas strains. Biotechnol. Lett. 27: 1847-1853 (2005)

津田雅孝: 環境微生物コミュニティのゲノム解析. 蛋白質核酸酵素 50: 2182-2183 (2005)

津田雅孝, 曽田匡洋: 環境浄化能をつかさどる可動性遺伝因子. 蛋白質 核酸 酵素 50: 1527-1534. (2005)

野尻秀昭, 津田雅孝: 環境汚染物質分解細菌の機能進化-特集にあたって. 蛋白質核酸酵素 50: 1505-1510 (2005)

永田裕二, 津田雅孝: 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-. 蛋白質 核酸 酵素 50: 1511-1518. (2005)

永田裕二, 津田雅孝: 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. 化学と生物 43: 33-42 (2005)

2004年

Y. Ohtsubo, T. Kudo, M. Tsuda, and Y. Nagata: Strategies for bioremediation of polychlorinated biphenyls. Appl. Microbiol. Biotechnol. 65: 250-258. (2004)

A. J. Oakley, M. Klvana, M. Otyepka, Y. Nagata, M. C. Wilce, and J. Damborsky: Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95Å resolution: dynamics of catalytic residues. Biochemistry 43: 870-878. (2004)

津田雅孝, 小松春伸, 大坪嘉行, 永田裕二: 環境細菌ゲノムと環境DNA. J. Environ. Biotechnol. 3: 69-78. (2004)

2003年

Y. Nagata, Z. Prokop, S. Marvanova, J. Sykorova, M. Monincova, M. Tsuda, and J. Damborsky: Re-construction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB. Appl. Environ. Microbiol. 60: 349-2355. (2003)

H. Komatsu, Y. Imura, A. Ohori, Y. Nagata, and M. Tsuda: Distribution and organization of auxotrophic genes on the multichromosomal genome of Burkholderia multivorans ATCC17616. J. Bacteriol. 185: 3333-3343. (2003)

M. Sota, H. Kawasaki, and M. Tsuda: Structure of haloacetate-catabolic IncP-1 plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon. J. Bacteriol. 185: 6741-6745. (2003)

R. Chaloupkova, J. Sykorova, Z. Prokop, A. Jesenska, M. Monincova, M. Pavlova, M. Tsuda, Y. Nagata, and J. Damborsky: Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel. J. Biol. Chem. 278: 52622-52628. (2003)

Y. Ohtsubo, M. Shimura, M. Delawary, K. Kimbara, M. Takagi, T. Kudo, A. Ohta, and Y. Nagata: Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombination. Appl. Environ. Microbiol. 69: 146-153. (2003)

2002年

H. Sawada, S. Kanaya, M. Tsuda, F. Suzuki, K. Azegami, and N. Saitou: Phylogenomic study of the OCTase genes in Pseudomonas syringae pathovars: horizontal transfer of argK-tox cluster and the evolutionary history of OCTase genes on their genomes. J. Mol. Evol. 54: 437-457. (2002)

M. Sota, M. Endo, K. Nitta, H. Kawasaki, and M. Tsuda: Characterization of a class II defective transposon carrying two haloacetate dehalogenase genes from Delftia acidovorans plasmid pUO1. Appl. Environ. Microbiol. 68: 2307-2315. (2002)

H. Genka, Y. Nagata, and M. Tsuda: Site-specific recombination system encoded by toluene catabolic transposon Tn4651. J. Bacteriol. 184: 4757-4766. (2002)

M. Bohac, Y. Nagata, Z. Prokop, M. Prokop, M. Monincova, M. Tsuda, J. Koca, and J. Damborsky: Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis. Biochemistry. 41: 14272-14280. (2002)

K. Miyauchi, H.-S. Lee, M. Fukuda, M. Takagi, and Y. Nagata: Cloning and characterization of linR, involved in regulation of downstream pathway for -HCH degradation in Sphingomonas paucimobilis UT26. Appl. Environ. Microbiol. 68: 1803-1807. (2002)

永田裕二, 遠藤銀朗: 微生物による環境修復・環境浄化, p.17-58 In 羽柴輝良 (ed.), 人に役立つ微生物のはなし (くらしの中の化学と生物. 学会出版センター, 東京 (2002)

永田裕二: 有機塩素系農薬による汚染浄化のための環境バイオテクノロジー. J. Environ. Biotechnol. 2: 25-38. (2002)

2001年

T. Shigematsu, J. Fukushima, M. Oyama, M. Tsuda, S. Kawamoto, and K. Okuda: Iron-mediated regulation of alkaline proteinase production in Pseudomonas aeruginosa. Microbiol. Immunol. 45: 579-590. (2001)

M. Tsuda and H. Genka: Identification and characterization of Tn4656, a novel class II transposon carrying a set of toluene-degrading genes from TOL plasmid pWW53. J. Bacteriol. 183: 6215-6224. (2001)

Y. Nagata, K. Mori, M. Takagi, A. G. Murzin, and J. Damborsky: Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA. Proteins: Structure, Function, and Genetics 45: 471-477. (2001)

L. Trantirek, K. Hynkova, Y. Nagata, A. G. Murzin, A. Ansorgova, V. Sklenar, and J. Damborsky: Reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase LinA. J. Biol. Chem. 276: 7734-7740. (2001)

Y. Ohtsubo, M. Delawary, K. Kimbara, M. Takagi, A. Ohta, and Y. Nagata: BphS, a key transcriptional regulator of bph genes involved in PCB/biphenyl degradation in Pseudomonas sp. KKS102. J. Biol. Chem. 276: 36146-36154. (2001)

永田裕二: 残留性農薬の分解系酵素遺伝子群とその動態. In: IGEシリーズ29: 遺伝情報のダイナミズムとその分子機構. 東北大学遺伝生態研究センター, pp. 3-16. (2001)

津田雅孝, 源河浩之: 難分解性芳香族炭水化物分解遺伝子群を担うトランスポゾン. In: IGEシリーズ 29: 遺伝情報のダイナミズムとその分子機構. 東北大学遺伝生態研究センター, pp. 25-37 (2001)

大坪嘉行, 永田裕二: 遺伝子操作土壌細菌を利用したPCB分解技術の開発. エコインダストリー 6: 44-53. (2001)

2000年

J.-K. Akada, M. Shirai, H. Takeuchi, M. Tsuda, and T. Nakazawa: Identification of the urease operon in Helicobacter pylori and its control by mRNA decay in response to pH. Mol. Microbiol. 36: 1071-1084. (2000)

J. Marek, J. Vevodova, I. K. Smatanova, Y. Nagata, L. A. Svensson, J. Newman, M. Takagi, and J. Damborsky: Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39: 14082-14086. (2000)

Y. Ohtsubo, Y. Nagata, K. Kimbara, M. Takagi, and A. Ohta: Expression of the bph genes involved in biphenyl/PCB degradation in Pseudomonas sp. KKS102 induced by the biphenyl degradation intermediate, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. Gene 256: 223-228. (2000)

永田裕二: 環境を汚染する有機塩素系農薬 gamma-hexachlorocyclohexaneの微生物代謝系の解明. 日本農芸化学会誌 74: 1247-1257. (2000)

永田裕二: 可能性を秘めた細菌におけるペリプラズム酵素系 -新しく見出されたSec非依存的新規分泌経路-. 化学と生物 38: 214-216. (2000)

1999年

M. Tsuda, H.-M. Tan, A. Nishi, and K. Furukawa: Mobile catabolic genes in bacteria. J. Biosci. Bioeng. 87: 401-410. (1999)

T. Mizote, M. Tsuda, D. D. S. Smith, H. Nakayama and T. Nakazawa: Cloning and characterization of the thiD/J gene of Escherichia coli encoding a thiamin-synthesizing bifunctional enzyme, hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. Microbiology 145: 495-501. (1999)

Y. Nagata, K. Miyauchi, and M. Takagi: Complete analysis of genes and enzymes for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. J. Indust. Microbiol. Biotechnol. 23: 380-390. (1999)

K. Miyauchi, Y. Adachi, Y. Nagata, and M. Takagi: Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in the degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis. J. Bacteriol. 181: 6712-6719. (1999)

Y. Nagata, K. Hynkova, J. Damborsky, and M. Takagi: Construction and characterization of histidine-tagged haloalkane dehalogenase (LinB) of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26. Protein Expression and Purification. 17: 299-304. (1999)

Y. Ohtsubo, K. Miyauchi, K. Kanda, T. Hatta, H. Kiyohara, T. Senda, Y. Nagata, Y. Mitsui, and M. Takagi: PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase. FEBS Lett. 459: 395-398. (1999)

Y. Nagata, A. Futamura, K. Miyauchi, and M. Takagi: Two different types of dehalogenase, LinA and LinB, which are involved in the gamma-HCH degradation in Sphingomonas paucimobilis UT26, are localized in periplasmic space without molecular processing. J. Bacteriol. 181: 5409-5413. (1999)

K. Hynkova, Y. Nagata, M. Takagi, and J. Damborsky: Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. FEBS Lett. 446: 177-181. (1999)

1998年

M. Tsuda: Use of a transposon-encoded site-specific resolution system for construction of large and defined deletion mutations in bacterial chromosome. Gene 207: 33-41. (1998)

N. Gotoh, H. Tsujimoto, M. Tsuda, K. Okamoto, A. Nomura, T. Wada, M. Nakahashi, and T. Nishino: Characterization of the MexC-MexD-OprJ multidrug efflux system in delta(mexA-mexB-oprM) mutants of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 42: 1938-1943. (1998)

N. Gotoh, H. Tsujimoto, A. Nomura, K. Okamoto, M. Tsuda, and T. Nishino: Functional replacement of OprJ by OprM in the MexCD-OprJ multidrug efflux system of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 165: 21-27. (1998)

H. Takeuchi, M. Shirai, J.-K. Akada, M. Tsuda, and T. Nakazawa: Nucleotide sequence and characterization of cdrA, a cell division-related gene of Helicobacter pylori. J. Bacteriol. 180: 5263-5268. (1998)

K. Miyauchi, S.-K. Suh, Y. Nagata, and M. Takagi: Cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane by Sphingomonas paucimobilis. J. Bacteriol. 180: 1354-1359. (1998)

永田裕二, 金原和秀, 高木正道: PCBを分解する微生物 -環境汚染物質処理技術への応用をめざして-. 現代化学 46-52. (1998)