Details of the Researcher

PHOTO

Yuji Nagata
Section
Graduate School of Life Sciences
Job title
Professor
Degree

  • Ph. D. (The University of Tokyo)

Professional Memberships 6

  • 日本ゲノム微生物学会

  • 環境バイオテクノロジー学会

  • The Japanese Society of Microbial Ecology

  • American Society for Microbiology

  • The Society for Biotechnology, Japan

  • The Society for Bioscience, Biotechnology, and Agrochemistry

︎Show all ︎Show first 5

Research Interests 4

  • genome

  • protein engineering

  • biodegradation

  • Environmental pollutant

Research Areas 1

  • Life sciences / Applied biochemistry /

Awards 4

  1. Siemens Innovation Prize 2014 in Czech Republic

    2015/02　Siemens　Biotechnologies using dehalogenases

  2. 東北大学大学院生命科学研究科内研究奨励賞

    2004/10　東北大学大学院生命科学研究科　環境汚染物質分解に関わる脱ハロゲン酵素遺伝子の自然生態系からの直接的取得と解析

  3. インテリジェント・コスモス奨励賞

    2003/05/15　インテリジェント・コスモス学術振興財団　細菌由来の有機塩素系環境汚染物質分解酵素の蛋白質工学的及び分子生態学的研究

  4. 農芸化学奨励賞

    2000/04　日本農芸化学会　環境を汚染する有機塩素系農薬gamma-HCHの微生物代謝系の解明

Papers 162

  1. Haloalkane dehalogenases other than LinB can contribute to the γ-hexachlorocyclohexane utilization. International-journal

    Nannan Chen, Kouhei Kishida, Leonardo Stari, Ryota Moriuchi, Yoshiyuki Ohtsubo, Jiri Damborsky, Yuji Nagata

    Bioscience, biotechnology, and biochemistry　89　(6)　898-909　2025/05/21

    DOI： 10.1093/bbb/zbaf022 　

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    Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols by a simple hydrolytic mechanism. Although many bacterial strains possess HLDs or HLD homologues, LinB is the only HLD known to be involved in the utilization of γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide. In this study, to gain insight into the functional evolution of HLDs toward γ-HCH utilization, the linB gene in γ-HCH-degrading Sphingobium japonicum strain UT26 was replaced by 7 other HLD or HLD homologous genes, including 3 putative ancestral enzymes. Interestingly, strains carrying genes for DmmA from a marine metagenome or Rluc_anc, an ancestor of Renilla-luciferin 2-monooxygenase and LinB, produced 2,5-dichlorophenol and 2,5-dichlorohydroquinone from γ-HCH, which are indicators of LinB activity, and grew in minimal medium supplied with γ-HCH as a sole carbon source. These results indicated that other HLDs, in addition to LinB, can play roles in the γ-HCH utilization.

  2. Type I partition-related proteins enhance conjugative transfer through transcriptional activation andoriTregion binding

    Kouhei Kishida, Koji Kudo, Ren Kumagai, Wenhao Deng, Leonardo Stari, Natsumi Ogawa-Kishida, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    2025/01/22

    Publisher: Cold Spring Harbor Laboratory

    DOI： 10.1101/2025.01.22.634284 　

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    ABSTRACT Plasmid partitioning and bacterial conjugation are critical processes ensuring plasmid maintenance and dissemination, respectively, within bacterial populations. Although traditionally regarded as distinct phenomena, these two processes are increasingly recognized as interconnected. While partitioning ensures plasmid inheritance during cell division, its potential influence on conjugative transfer remains poorly understood. A major impediment to understanding their interplay is that partition systems are often essential for plasmid stability, making it difficult to distinguish their direct effects on conjugation. In this study, we addressed this challenge using a mini-conjugative plasmid derived from thePseudomonas putidaNAH7 plasmid. This engineered plasmid, containing all conjugation-related genes, was cloned into anE. coli-compatible vector. Additionally, thepargenes from NAH7 were expressed from a separate plasmid to investigate their roles in conjugative transfer. Our results revealed that thepargene cluster plays a significant role in enhancing the conjugative transfer of the mini-conjugative plasmid. Specifically, ParB, a centromere-binding protein, functions as a transcriptional activator of conjugation-related genes with bindingparSNAHsite. In contrast, ParR, a KorA homolog, was not found to enhance transcription directly but binds extensively to theoriTregion. This binding probably facilitates the recruitment or stabilization of the relaxosome, thereby enhancing conjugation efficiency. Together, these findings unveil a previously unappreciated role for partition proteins in stimulating bacterial conjugation, providing new insights into how plasmids coordinate vertical and horizontal dissemination, highlighting that these processes can occur simultaneously within bacterial communities. IMPORTANCE Plasmid partition systems are classified into three types. While some systems have been reported to influence conjugative transfer, this study uncovers a novel mechanism utilized by a Type I system to enhance DNA transfer. Strikingly, repeat sequences perfectly matching theparSNAHsite—bound by ParB to activate downstream conjugative transfer genes—were identified on both plasmids and chromosomes across diverse proteobacterial taxa. Furthermore, many of these repeat sequences were localized near genes involved in conjugative transfer and partitioning, suggesting the presence of a conserved regulatory mechanism mediated by these repeats. This study provides important insights into how plasmid partition systems coordinate both vertical and horizontal dissemination. Such knowledge is essential for understanding and mitigating the spread of antibiotic resistance and other plasmid-encoded traits, and it offers a foundation for developing strategies to manage plasmid-associated genetic exchange.

  3. Evolution of the Tn4371 ICE family: traR-mediated coordination of cargo gene upregulation and horizontal transfer. International-journal

    Satoshi Matsumoto, Kouhei Kishida, Shouta Nonoyama, Keiichiro Sakai, Masataka Tsuda, Yuji Nagata, Yoshiyuki Ohtsubo

    Microbiology spectrum　e0060724　2024/09/12

    DOI： 10.1128/spectrum.00607-24 　

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    ICEKKS102Tn4677 carries a bph operon for the mineralization of polychlorinated biphenyls (PCBs)/biphenyl and belongs to the Tn4371 ICE (integrative and conjugative element) family. In this study, we investigated the role of the traR gene in ICE transfer. The traR gene encodes a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371 family ICEs. The traR belongs to the bph operon, and its overexpression on solid medium resulted in modest upregulation of traG (threefold), marked upregulation of xis (80-fold), enhanced ICE excision and, most notably, ICE transfer frequency. We propose the evolutional roles of traR, which upon insertion to its current position, might have connected the cargo gene activation and ICE transfer. This property of ICE, i.e., undergoing transfer under environmental conditions that lead to cargo gene activation, would instantly confer fitness advantages to bacteria newly acquiring this ICE, thereby resulting in efficient dissemination of the Tn4371 family ICEs.IMPORTANCEOnly ICEKKS102Tn4677 is proven to transfer among the widely disseminating Tn4371 family integrative and conjugative elements (ICEs) from β and γ-proteobacteria. We showed that the traR gene in ICEKKS102Tn4677, which is conserved in the ICE family with fixed location and direction, is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing of traR by an ancestral ICE to the current position established the Tn4371 family of ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371 family of ICEs across bacterial species.

  4. Transgenic Arabidopsis thaliana plants expressing bacterial γ-hexachlorocyclohexane dehydrochlorinase LinA

    Wenhao Deng, Yoshinobu Takada, Yoshihiko Nanasato, Kouhei Kishida, Leonardo Stari, Yoshiyuki Ohtsubo, Yutaka Tabei, Masao Watanabe, Yuji Nagata

    BMC Biotechnology　24　(1)　2024/06/19

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1186/s12896-024-00867-0 　

    eISSN： 1472-6750

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    Abstract Background γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degrading bacterial strains are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the low survival rate of the exogenous bacteria. Another strategy for the bioremediation of γ-HCH involves the use of transgenic plants expressing bacterial enzyme for γ-HCH degradation through phytoremediation. Results We generated transgenic Arabidopsis thaliana expressing γ-HCH dehydrochlroninase LinA from bacterium Sphingobium japonicum strain UT26. Among the transgenic Arabidopsis T2 lines, we obtained one line (A5) that expressed and accumulated LinA well. The A5-derived T3 plants showed higher tolerance to γ-HCH than the non-transformant control plants, indicating that γ-HCH is toxic for Arabidopsis thaliana and that this effect is relieved by LinA expression. The crude extract of the A5 plants showed γ-HCH degradation activity, and metabolites of γ-HCH produced by the LinA reaction were detected in the assay solution, indicating that the A5 plants accumulated the active LinA protein. In some A5 lines, the whole plant absorbed and degraded more than 99% of γ-HCH (10 ppm) in the liquid medium within 36 h. Conclusion The transgenic Arabidopsis expressing active LinA absorbed and degraded γ-HCH in the liquid medium, indicating the high potential of LinA-expressing transgenic plants for the phytoremediation of environmental γ-HCH. This study marks a crucial step toward the practical use of transgenic plants for the phytoremediation of POPs.

  5. Increase of secondary metabolites in sweet basil (Ocimum basilicum L.) leaves by exposure to N2O5 with plasma technology

    Rie Tateishi, Natsumi Ogawa-Kishida, Nobuharu Fujii, Yuji Nagata, Yoshiyuki Ohtsubo, Shota Sasaki, Keisuke Takashima, Toshiro Kaneko, Atsushi Higashitani

    Scientific Reports　14　(1)　2024/06/04

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41598-024-63508-8 　

    eISSN： 2045-2322

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    Abstract Exposure to N2O5 generated by plasma technology activates immunity in Arabidopsis through tryptophan metabolites. However, little is known about the effects of N2O5 exposure on other plant species. Sweet basil synthesizes many valuable secondary metabolites in its leaves. Therefore, metabolomic analyses were performed at three different exposure levels [9.7 (Ex1), 19.4 (Ex2) and 29.1 (Ex3) μmol] to assess the effects of N2O5 on basil leaves. As a result, cinnamaldehyde and phenolic acids increased with increasing doses. Certain flavonoids, columbianetin, and caryophyllene oxide increased with lower Ex1 exposure, cineole and methyl eugenol increased with moderate Ex2 exposure and l-glutathione GSH also increased with higher Ex3 exposure. Furthermore, gene expression analysis by quantitative RT-PCR showed that certain genes involved in the syntheses of secondary metabolites and jasmonic acid were significantly up-regulated early after N2O5 exposure. These results suggest that N2O5 exposure increases several valuable secondary metabolites in sweet basil leaves via plant defense responses in a controllable system.

  6. Clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis by Taq polymerase involves nick-translation. International-journal Peer-reviewed

    Yoshiyuki Ohtsubo, Syoutaro Kawahara, Yuji Nagata

    Scientific reports　14　(1)　2030-2030　2024/01/23

    DOI： 10.1038/s41598-024-52095-3 　

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    The development and characterization of a new enzyme reaction contribute to advancements in modern biotechnology. Here, we report a novel CIS (clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis) reaction catalyzed by Taq polymerase. In the reaction, a single-stranded DNA (ssDNA) with 3' Cs is attached with a preformed 3' G-tail of double-stranded DNA (dsDNA); DNA syntheses starting from both 3' ends result in the incorporation of ssDNA. A 3' G-tail length of 3 nucleotides adequately supports this reaction, indicating that Taq polymerase can clump short Watson-Crick base pairs as short as three pairs and use them to initiate DNA polymerization. The reverse transcriptase from Molony murine leukemia virus catalyzes strand displacement synthesis and produces flapped-end DNA, whereas the reaction by Taq polymerase involves the nick translation. These new reaction properties may be beneficial for the development of new molecular tools applicable in various fields. Apart from its CIS reaction activity, we also report that Taq polymerase has the undesirable characteristic of removing 5' fluorescent labels from dsDNA. This characteristic may have compromised various experiments involving the preparation of fluorescently-labeled dsDNA by PCR for a long time.

  7. Three distinct metabolic phases of PCB/biphenyl degrader Acidovorax sp. KKS102 in nutrient broth. International-journal Peer-reviewed

    Keiichiro Sakai, Kouhei Kishida, Satoshi Matsumoto, Yuji Nagata, Masataka Tsuda, Yoshiyuki Ohtsubo

    Bioscience, biotechnology, and biochemistry　2024/01/08

    DOI： 10.1093/bbb/zbad178 　

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    Acidovorax sp. KKS102 is a beta-proteobacterium capable of degrading polychlorinated biphenyls (PCBs). In this study we examined its growth in liquid nutrient broth supplemented with different carbon sources. KKS102 had at least three distinct metabolic phases designated as metabolic phases 1 to 3, with phase 2 having two sub-phases. For example, succinate, fumarate, and glutamate, known to repress the PCB/biphenyl catabolic operon in KKS102, were utilized in phase 1, while acetate, arabinose, and glycerol in phase 2, and glucose and mannose in phase 3. We also showed that the BphQ response regulator mediating catabolite control in KKS102, whose expression level increased moderately through the growth, plays important roles in carbon metabolism in phases 2 and 3. Our study elucidates the hierarchical growth of KKS102 in nutrient-rich media. This insight is crucial for studies exploiting microbial biodegradation capabilities and advancing studies for catabolite regulation mechanisms.

  8. Degradation of DDT by γ-hexachlorocyclohexane dehydrochlorinase LinA. International-journal Peer-reviewed

    Kafayat Olaide Yusuf Habibullah, Ren Ito, Leonardo Stari, Kouhei Kishida, Yoshiyuki Ohtsubo, Eiji Masai, Masao Fukuda, Keisuke Miyauchi, Yuji Nagata

    Bioscience, biotechnology, and biochemistry　88　(1)　123-130　2023/12/19

    DOI： 10.1093/bbb/zbad141 　

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    1,1,1-Trichloro-2,2-bis(4-chlorophenyl)-ethane (DDT) is the first synthetic insecticide and one of the most widely used pesticides. The use of DDT has been banned, but it remains one of the most notorious environmental pollutants around the world. In this study, we found that γ-hexachlorocyclohexane (γ-HCH) dehydrochlorinase LinA from a γ-HCH-degrading bacterium, Sphingobium japonicum UT26, converts DDT to 1,1-dichloro-2,2-bis(4-chlorophenyl)-ethylene (DDE). Because of the weak DDT degradation activity of LinA, we could not detect such activity in UT26 cells expressing LinA constitutively. However, the linA-deletion mutant of UT26 harboring a plasmid for the expression of LinA, in which LinA was expressed at a higher level than UT26, showed the DDT degradation activity. This outcome highlights the potential for constructing DDT-degrading sphingomonad cells through elevated LinA expression.

  9. Draft genome sequence of Cupriavidus sp. strain TKC, isolated from a γ-hexachlorocyclohexane-degrading community. International-journal Peer-reviewed

    Hiromi Kato, Yoshiyuki Ohtsubo, Shoko Hirano, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Yuji Nagata

    Microbiology resource announcements　12　(12)　e0056723　2023/12/14

    DOI： 10.1128/MRA.00567-23 　

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    Cupriavidus sp. strain TKC was isolated from a microbial community enriched with γ-hexachlorocyclohexane (γ-HCH). This strain did not show γ-HCH-degrading activity but was one of the major members of the community. Here, we present the draft genome sequence of the strain TKC with a size of 7 Mb.

  10. たったひとつの遺伝子の発現でかすみを食べる細菌に Invited Peer-reviewed

    永田裕二

    生物工学会誌　101　(10)　554-554　2023/10

    DOI： 10.34565/seibutsukogaku.101.10_554 　

  11. 土壌微生物による化学合成農薬分解のフロンティア Invited Peer-reviewed

    永田裕二, 加藤広海, 大坪嘉行

    農薬学会誌　48　(2)　125-131　2023/08

    DOI： 10.1584/jpestics.W23-22 　

  12. Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria Peer-reviewed

    Desmila Idola, Hiroshi Mori, Yuji Nagata, Lisa Nonaka, Hirokazu Yano

    Mobile DNA　14　(7)　2023/05

    DOI： 10.1186/s13100-023-00295-5 　

  13. Reconstruction of a Soil Microbial Network Induced by Stress Temperature Peer-reviewed

    Dailin Yang, Hiromi Kato, Kazutaka Kawatsu, Yutaka Osada, Toyohiro Azuma, Yuji Nagata, Michio Kondoh

    Microbiology Spectrum　10　(5)　2022/10/26

    Publisher: American Society for Microbiology

    DOI： 10.1128/spectrum.02748-22 　

    eISSN： 2165-0497

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    By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.

  14. CO2 -dependent High-yield Growth of a Heterotrophic Bacterium under Oligotrophic Conditions Invited Peer-reviewed

    Yuji Nagata, Hiromi Kato, Yoshiyuki Ohtsubo

    Journal of Environmental Biotechnology　22　(1)　9-13　2022/06

    DOI： 10.50963/jenvbio.22.1_9 　

  15. Algorisms used for in silico finishing of bacterial genomes based on short-read assemblage implemented in GenoFinisher, AceFileViewer, and ShortReadManager International-journal Invited Peer-reviewed

    Yoshiyuki Ohtsubo, Yuu Hirose, Yuji Nagata

    Bioscience, Biotechnology, and Biochemistry　86　(6)　693-703　2022/04/14

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/bbb/zbac032 　

    eISSN： 1347-6947

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    ABSTRACT In these days, for bacterial genome sequence determination, ultralong reads with homopolymeric troubles are used in combinations with short reads, resulting in genomic sequences with possible incorrect uniformity of repeat sequences. We have been determining complete bacterial genomic sequences based on NGS short reads and Newbler assemblage by utilizing functions implemented in 3 software GenoFinisher, AceFileViewer, and ShortReadManager without conducting additional experiments for gap closing, proving the concept that NGS short reads enclose enough information to determine complete genome sequences. Although some manual in silico tasks are to be conducted, they will ultimately be solved in a single pipeline. In this review, we describe the tools and implemented ideas that have enabled complete sequence determination solely based on short reads, which would be useful for establishing the basis for the future development of a short-read-based assembler that enables complete and accurate genome sequence determination at a lower cost.

  16. Genome evolution related to γ-hexachlorocyclohexane metabolic function in the soil microbial population International-journal Peer-reviewed

    Hiromi Kato, Lijun Su, Ayami Tanaka, Honami Katsu, Yoshiyuki Ohtsubo, Shigeto Otsuka, Keishi Senoo, Yuji Nagata

    Bioscience, Biotechnology, and Biochemistry　2022/03/17

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/bbb/zbac042 　

    eISSN： 1347-6947

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    ABSTRACT γ-Hexachlorocyclohexane (γ-HCH)-degrading strain, Sphingobium sp. TA15, was newly isolated from an experimental field soil from which the archetypal γ-HCH-degrading strain, S. japonicum UT26, was isolated previously. Comparison of the complete genome sequences of these 2 strains revealed that TA15 shares the same basic genome backbone with UT26, but also has the variable regions that are presumed to have changed either from UT26 or from a putative common ancestor. Organization and localization of lin genes of TA15 were different from those of UT26. It was inferred that transposition of IS6100 had played a crucial role in these genome rearrangements. The accumulation of toxic dead-end products in TA15 was lower than in UT26, suggesting that TA15 utilizes γ-HCH more effectively than UT26. These results suggested that genome evolution related to the γ-HCH metabolic function in the soil microbial population is ongoing.

  17. Microbial communities developing within bulk sediments under fish carcasses on a tidal flat Peer-reviewed

    Yasutake Kawamoto, Hiromi Kato, Yuji Nagata, Jotaro Urabe

    PLOS ONE　16　(2)　e0247220-e0247220　2021/02/25

    Publisher: Public Library of Science (PLoS)

    DOI： 10.1371/journal.pone.0247220 　

    eISSN： 1932-6203

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    Animal carcasses are often brought into tidal flats where they are at the boundary between terrestrial and marine ecosystems. Since these carcasses act as microhabitats with large amounts of energy and nutrients, they likely develop unique bacterial assemblages in the ambient sediment, which in turn may stimulate colonization of other organisms such as protozoans. However, little is known about the microbial assemblages colonized in sediment around animal carcasses in the tidal zone. Herein we examined the bacterial and ciliophoran assemblages developed in association with fish carcasses by incubating the carcasses in the Higashiyachi tidal flat (Sendai, Japan). We collected sediment samples at 2, 9, and 42 days of incubation and analyzed the bacterial and ciliophoran assemblages by 16S and 18S rRNA gene amplicon sequencing. We observed significant differences in the composition and relative abundance of bacterial and ciliophoran operational taxonomic units (OTUs) between the sediments with and without the carcasses. Our analyses suggest that these unique assemblages were created through the direct effects of the carcass and indirect effects through interactions between bacteria and ciliophorans. These results also suggest that animal carcasses developed a temporally unique microbial food web in the sediments close to the carcasses, although it disappeared for several weeks.

  18. A transcriptional regulator, IscR, of Burkholderia multivorans acts as both repressor and activator for transcription of iron-sulfur cluster-biosynthetic isc operon. International-journal Peer-reviewed

    Shouta Nonoyama, Kouhei Kishida, Keiichiro Sakai, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    Research in microbiology　171　(8)　319-330　2020/12

    DOI： 10.1016/j.resmic.2020.06.005 　

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    Bacterial iron-sulfur (Fe-S) clusters are essential cofactors for many metabolic pathways, and Fe-S cluster-containing proteins (Fe-S proteins) regulate the expression of various important genes. However, biosynthesis of such clusters has remained unknown in genus Burkholderia. Here, we clarified that Burkholderia multivorans ATCC 17616 relies on the ISC system for the biosynthesis of Fe-S clusters, and that the biosynthetic genes are organized as an isc operon, whose first gene encodes IscR, a transcriptional regulatory Fe-S protein. Transcription of the isc operon was repressed and activated under iron-rich and -limiting conditions, respectively, and Fur, an iron-responsive global transcriptional regulator, was indicated to indirectly regulate the expression of isc operon. Further analysis using a ΔiscR mutant in combination with a constitutive expression system of IscR and its derivatives indicated transcriptional repression and activation of isc operon by holo- and apo-forms of IscR, respectively, through their binding to the sequences within an isc promoter-containing (Pisc) fragment. Biochemical analysis using the Pisc fragment suggested that the apo-IscR binding sequence differs from the holo-IscR binding sequence. The results obtained in this study revealed a unique regulatory system for the expression of the ATCC 17616 isc operon that has not been observed in other genera.

  19. Transcriptome Analysis of Zygotic Induction During Conjugative Transfer of Plasmid RP4 Peer-reviewed

    Masatoshi Miyakoshi, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    Frontiers in Microbiology　11　2020/06/18

    Publisher: Frontiers Media SA

    DOI： 10.3389/fmicb.2020.01125 　

    eISSN： 1664-302X

  20. Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions. International-journal Peer-reviewed

    Shinnosuke Inaba, Hironori Sakai, Hiromi Kato, Takayuki Horiuchi, Hirokazu Yano, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    Microbiology (Reading, England)　166　(6)　531-545　2020/04/20

    DOI： 10.1099/mic.0.000908 　

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    Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO2-dependent and accompanied with CO2 incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO2-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.

  21. Special Issue: Microbial Degradation of Xenobiotics Invited Peer-reviewed

    Yuji Nagata

    Microorganisms　8　(4)　487-487　2020/03/30

    Publisher: MDPI AG

    DOI： 10.3390/microorganisms8040487 　

    eISSN： 2076-2607

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    Xenobiotics are released into the environment by human activities, and they often cause problems such as environmental pollution, since most such compounds cannot be readily degraded, and have harmful effects on human beings and the natural ecosystem [...]

  22. 従属栄養細菌のCO2依存的な極貧栄養環境適応 Invited Peer-reviewed

    永田裕二

    バイオサイエンスとインダストリー　78　498-500　2020

  23. Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. International-journal Peer-reviewed

    Martin Marek, Radka Chaloupkova, Tatyana Prudnikova, Yukari Sato, Pavlina Rezacova, Yuji Nagata, Ivana Kuta Smatanova, Jiri Damborsky

    Computational and structural biotechnology journal　18　1352-1362　2020

    DOI： 10.1016/j.csbj.2020.05.019 　

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    Engineering enzyme catalytic properties is important for basic research as well as for biotechnological applications. We have previously shown that the reshaping of enzyme access tunnels via the deletion of a short surface loop element may yield a haloalkane dehalogenase variant with markedly modified substrate specificity and enantioselectivity. Here, we conversely probed the effects of surface loop-helix transplantation from one enzyme to another within the enzyme family of haloalkane dehalogenases. Precisely, we transplanted a nine-residue long extension of L9 loop and α4 helix from DbjA into the corresponding site of DbeA. Biophysical characterization showed that this fragment transplantation did not affect the overall protein fold or oligomeric state, but lowered protein stability (ΔTm = -5 to 6 °C). Interestingly, the crystal structure of DbeA mutant revealed the unique structural features of enzyme access tunnels, which are known determinants of catalytic properties for this enzyme family. Biochemical data confirmed that insertion increased activity of DbeA with various halogenated substrates and altered its enantioselectivity with several linear β-bromoalkanes. Our findings support a protein engineering strategy employing surface loop-helix transplantation for construction of novel protein catalysts with modified catalytic properties.

  24. Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK, Whose Homologs Are Conserved in Various MPFT-Type Plasmids. International-journal Peer-reviewed

    Kishida K, Nonoyama S, Lukas T, Kawahara S, Kudo K, Nagata Y, Ohtsubo Y, Tsuda M

    Applied and environmental microbiology　85　(24)　2019/12

    DOI： 10.1128/AEM.01850-19 　

    ISSN： 0099-2240

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    Conjugative transfer of bacterial plasmids to recipient cells is often mediated by type IV secretion machinery. Experimental investigations into the minimal gene sets required for efficient conjugative transfer suggest that such gene sets are variable, depending on plasmids. We have been analyzing the conjugative transfer of Pseudomonas-derived and IncP-9 plasmids, NAH7 and pWW0, whose conjugation systems belong to the MPFT type. Our deletion analysis and synthetic biology analysis in this study showed that these plasmids require previously uncharacterized genes, mpfK (formerly orf34) and its functional homolog, kikA, respectively, for their efficient conjugative transfer. MpfK was localized in periplasm and had four cysteine residues whose intramolecular or intermolecular disulfide bond formation was suggested to be important for efficient conjugative transfer. The mpfK homologs were specifically carried by many MPFT-type plasmids, including non-IncP-9 plasmids, such as R388 and R751. Intriguingly, the mpfK homologs from the two non-IncP-9 plasmids were not required for conjugation of their plasmids, but were able to complement efficiently the transfer defect of the NAH7 mpfK mutant. Our results suggested the importance of the mpfK homologs for conjugative transfer of MPFT-type plasmids.IMPORTANCE IncP-9 plasmids are important mobile genetic elements for the degradation of various aromatic hydrocarbons. Elucidation of conjugative transfer of such plasmids is expected to greatly contribute to our understanding of its role in the bioremediation of polluted environments. The present study mainly focused on the conjugation system of NAH7, a well-studied and naphthalene-catabolic IncP-9 plasmid. Our analysis showed that the NAH7 conjugation system uniquely requires, in addition to the conserved components of the type IV secretion system (T4SS), a previously uncharacterized periplasmic protein, MpfK, for successful conjugation. Our findings collectively revealed a unique type of T4SS-associated conjugation system in the IncP-9 plasmids.

  25. Lessons from the genomes of lindane-degrading sphingomonads. International-journal Invited Peer-reviewed

    Nagata Y, Kato H, Ohtsubo Y, Tsuda M

    Environmental microbiology reports　11　(5)　630-644　2019/10

    DOI： 10.1111/1758-2229.12762 　

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    Bacterial strains capable of degrading man-made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ-hexachlorocyclohexane, γ-HCH, or γ-BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane-degrading sphingomonad strains clearly demonstrated that (i) lindane-degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane-degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic 'gene pool' available to bacteria.

  26. Suppression of substrate inhibition in phenanthrene-degrading Mycobacterium by co-cultivation with a non-degrading Burkholderia strain. International-journal Peer-reviewed

    Ogawa N, Kato H, Kishida K, Ichihashi E, Ishige T, Yoshikawa H, Nagata Y, Ohtsubo Y, Tsuda M

    Microbiology (Reading, England)　165　(5)　625-637　2019/06

    DOI： 10.1099/mic.0.000801 　

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    In natural environments contaminated by recalcitrant organic pollutants, efficient biodegradation of such pollutants has been suggested to occur through the cooperation of different bacterial species. A phenanthrene-degrading bacterial consortium, MixEPa4, from polluted soil was previously shown to include a phenanthrene-degrading strain, Mycobacterium sp. EPa45, and a non-polycyclic aromatic hydrocarbon (PAH)-degrading strain, Burkholderia sp. Bcrs1W. In this study, we show that addition of phenanthrene to rich liquid medium resulted in the transient growth arrest of EPa45 during its degradation of phenanthrene. RNA-sequencing analysis of the growth-arrested cells showed the phenanthrene-dependent induction of genes that were predicted to be involved in the catabolism of this compound, and many other cell systems, such as a ferric iron-uptake, were up-regulated, implying iron deficiency of the cells. This negative effect of phenanthrene became much more apparent when using phenanthrene-containing minimal agar medium; colony formation of EPa45 on such agar was significantly inhibited in the presence of phenanthrene and its intermediate degradation products. However, growth inhibition was suppressed by the co-residence of viable Bcrs1W cells. Various Gram-negative bacterial strains, including the three other strains from MixEPa4, also exhibited varying degrees of suppression of the growth inhibition effect on EPa45, strongly suggesting that this effect is not strain-specific. Growth inhibition of EPa45 was also observed by other PAHs, biphenyl and naphthalene, and these two compounds and phenanthrene also inhibited the growth of another mycobacterial strain, M. vanbaalenii PYR-1, that can use them as carbon sources. These phenomena of growth inhibition were also suppressed by Bcrs1W. Our findings suggest that, in natural environments, various non-PAH-degrading bacterial strains play potentially important roles in the facilitation of PAH degradation by the co-residing mycobacteria.

  27. Properties and efficient scrap-and-build repairing of mechanically sheared 3' DNA ends. International-journal Peer-reviewed

    Ohtsubo Y, Sakai K, Nagata Y, Tsuda M

    Communications biology　2　409-409　2019

    DOI： 10.1038/s42003-019-0660-7 　

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    Repairing of DNA termini is a crucial step in a variety of DNA handling techniques. In this study, we investigated mechanically-sheared DNA 3'-ends (MSD3Es) to establish an efficient repair method. As opposed to the canonical view of DNA terminus generated by sonication, we showed that approximately 47% and 20% of MSD3Es carried a phosphate group and a hydroxyl group, respectively. The others had unidentified abnormal terminal structures. Notably, a fraction of the abnormal 3' termini (about 20% of the total) was not repaired after the removal of 3' phosphates and T4 DNA polymerase (T4DP) treatment. To overcome this limitation, we devised a reaction, in which the 3'- > 5' exonuclease activity of exonuclease III (3'- > 5' exonuclease, insensitive to the 3' phosphate group) was counterbalanced by the 5'- > 3' polymerase activity of T4DP. This combined reaction, termed "SB-repairing" (for scrap-and-build repairing), will serve as a useful tool for the efficient repair of MSD3Es.

  28. Optimization of single strand DNA incorporation reaction by Moloney murine leukemia virus reverse transcriptase International-journal Peer-reviewed

    Y. Ohtsubo, H. Sasaki, Y. Nagata, M. Tsuda

    DNA Research　25　(5)　477-487　2018/10

    DOI： 10.1093/dnares/dsy018 　

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    In this study, we investigated CIS reaction (clamping-mediated incorporation of single-stranded DNA with concomitant DNA syntheses) of Moloney murine leukaemia virus reverse transcriptase (MMLV-RT), and established a set of conditions with which single-stranded DNA is ligated to a G-tailed model substrate DNA at efficiencies close to 100%. Prior to the CIS reaction, a target blunt-end DNA was 3' G-tailed by MMLV-RT in the presence of a tailing enhancer, deoxycytidine. In the CIS reaction, the G-tail reacted with a single-stranded DNA carrying a stretch of Cs on its 3' end (termed as GAO for guide adaptor oligonucleotide), and MMLV-RT performed DNA polymerization, starting from the 3' overhang, using the GAO as a template. We could append a given nucleotide sequence of as long as 72 nucleotides, which would be sufficient for various NGS-sequencing platforms. The high efficiency and the unique features of this MMLV-RT activity that enables the labelling of each DNA molecule with a unique degenerate sequence as a molecular identifier has many potential uses in biotechnology.

  29. Establishment of plasmid vector and allelic exchange mutagenesis systems in a mycobacterial strain that is able to degrade polycyclic aromatic hydrocarbon. International-journal Peer-reviewed

    Kishida K, Ogawa N, Ichihashi E, Kato H, Nagata Y, Ohtsubo Y, Tsuda M

    Bioscience, biotechnology, and biochemistry　82　(7)　1169-1171　2018/07

    DOI： 10.1080/09168451.2018.1445522 　

    ISSN： 0916-8451

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    Plasmid vector and allelic exchange mutagenesis systems were established for the genetic analysis of a phenanthrene-degrading mycobacterial strain, Mycobacterium sp. EPa45. Successful application of these systems revealed the necessity of the EPa45 phdI gene for the degradation of 1-hydroxy-2-naphthoate, which has been proposed to be an intermediate product in the degradation pathway of phenanthrene.

  30. The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616 Peer-reviewed

    Takuya Sato, Shouta Nonoyama, Akane Kimura, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　83　(16)　e00479-17　2017/08

    DOI： 10.1128/AEM.00479-17 　

    ISSN： 0099-2240

    eISSN： 1098-5336

  31. Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    SCIENTIFIC REPORTS　7　6520　2017/07

    DOI： 10.1038/s41598-017-04765-8 　

    ISSN： 2045-2322

  32. Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    SCIENTIFIC REPORTS　7　41769　2017/02

    DOI： 10.1038/srep41769 　

    ISSN： 2045-2322

  33. Host Range of the Conjugative Transfer System of IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Characterization of Its oriT Region and Relaxase Peer-reviewed

    Kouhei Kishida, Kei Inoue, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　83　(1)　e02359-16　2017/01

    DOI： 10.1128/AEM.02359-16 　

    ISSN： 0099-2240

    eISSN： 1098-5336

  34. Complete genome sequence of Bradyrhizobium diazoefficiens USDA 122, a nitrogen-fixing soybean symbiont Peer-reviewed

    Masayuki Sugawara, Takahiro Tsukui, Takakazu Kaneko, Yoshiyuki Ohtsubo, Shusei Sato, Yuji Nagata, Masataka Tsuda, Hisayuki Mitsui, Kiwamu Minamisawa

    Genome Announcements　5　(9)　e01743-16　2017

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01743-16 　

    ISSN： 2169-8287

  35. Comparison of the complete genome sequences of four gamma-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide Peer-reviewed

    Michiro Tabata, Satoshi Ohhata, Yuki Nikawadori, Kouhei Kishida, Takuya Sato, Toru Kawasumi, Hiromi Kato, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    DNA RESEARCH　23　(6)　581-599　2016/12

    DOI： 10.1093/dnares/dsw041 　

    ISSN： 1340-2838

    eISSN： 1756-1663

  36. Biodegradation of gamma-hexachlorocyclohexane by transgenic hairy root cultures of Cucurbita moschata that accumulate recombinant bacterial LinA Peer-reviewed

    Yoshihiko Nanasato, Sayuri Namiki, Masao Oshima, Ryota Moriuchi, Ken-ichi Konagaya, Nobuyasu Seike, Takashi Otani, Yuji Nagata, Masataka Tsuda, Yutaka Tabei

    PLANT CELL REPORTS　35　(9)　1963-1974　2016/09

    DOI： 10.1007/s00299-016-2011-1 　

    ISSN： 0721-7714

    eISSN： 1432-203X

  37. Complete genome sequence of Burkholderia caribensis Bcrs1W (NBRC110739), a strain co-residing with phenanthrene degrader Mycobacterium sp EPa45 Peer-reviewed

    Yoshiyuki Ohtsubo, Shouta Nonoyama, Natsumi Ogawa, Hiromi Kato, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BIOTECHNOLOGY　228　67-68　2016/06

    DOI： 10.1016/j.jbiotec.2016.04.042 　

    ISSN： 0168-1656

    eISSN： 1873-4863

  38. Complete genome sequence of Methylobacterium sp. strain AMS5, an isolate from a soybean stem Peer-reviewed

    Tomoyuki Minami, Yoshiyuki Ohtsubo, Mizue Anda, Yuji Nagata, Masataka Tsuda, Hisayuki Mitsui, Masayuki Sugawara, Kiwamu Minamisawa

    Genome Announcements　4　(2)　e00144-16　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00144-16 　

    ISSN： 2169-8287

  39. Complete genome sequence of a γ-hexachlorocyclohexane-degrading bacterium, Sphingobium sp. strain MI1205 Peer-reviewed

    Michiro Tabata, Satoshi Ohhata, Yuki Nikawadori, Takuya Sato, Kouhei Kishida, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    Genome Announcements　4　(2)　e00246-16　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00246-16 　

    ISSN： 2169-8287

  40. Complete genome sequence of a γ-hexachlorocyclohexane degrader, Sphingobium sp. strain TKS, isolated from a γ-hexachlorocyclohexane-degrading microbial community Peer-reviewed

    Michro Tabata, Satoshi Ohhata, Toru Kawasumi, Yuki Nikawadori, Kouhei Kishida, Takuya Sato, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    Genome Announcements　4　(2)　e00247-16　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00247-16 　

    ISSN： 2169-8287

  41. Complete genome sequence of Sphingopyxis macrogoltabida strain 203N (NBRC 111659), a polyethylene glycol degrader Peer-reviewed

    Yoshiyuki Ohtsubo, Shouta Nonoyama, Yuji Nagata, Mitsuru Numata, Keiko Tsuchikane, Akira Hosoyama, Atsushi Yamazoe, Masataka Tsuda, Nobuyuki Fujita, Fusako Kawai

    Genome Announcements　4　(3)　e00529-16　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00529-16 　

    ISSN： 2169-8287

  42. Complete genome sequence of Sphingopyxis terrae strain 203-1 (NBRC 111660), a polyethylene glycol degrader Peer-reviewed

    Yoshiyuki Ohtsubo, Shouta Nonoyama, Yuji Nagata, Mitsuru Numata, Keiko Tsuchikane, Akira Hosoyama, Atsushi Yamazoe, Masataka Tsuda, Nobuyuki Fujita, Fusako Kawai

    Genome Announcements　4　(3)　e00530-16　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00530-16 　

    ISSN： 2169-8287

  43. Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance Peer-reviewed

    Hiromi Kato, Hiroshi Mori, Fumito Maruyama, Atsushi Toyoda, Kenshiro Oshima, Ryo Endo, Genki Fuchu, Masatoshi Miyakoshi, Ayumi Dozono, Yoshiyuki Ohtsubo, Yuji Nagata, Masahira Hattori, Asao Fujiyama, Ken Kurokawa, Masataka Tsuda

    DNA RESEARCH　22　(6)　413-424　2015/12

    DOI： 10.1093/dnares/dsv023 　

    ISSN： 1340-2838

    eISSN： 1756-1663

  44. Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome Peer-reviewed

    Mizue Anda, Yoshiyuki Ohtsubo, Takashi Okubo, Masayuki Sugawara, Yuji Nagata, Masataka Tsuda, Kiwamu Minamisawa, Hisayuki Mitsui

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　112　(46)　14343-14347　2015/11

    DOI： 10.1073/pnas.1514326112 　

    ISSN： 0027-8424

  45. Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts Peer-reviewed

    Hirofumi Nagayama, Tomonori Sugawara, Ryo Endo, Akira Ono, Hiromi Kato, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　99　(10)　4453-4470　2015/05

    DOI： 10.1007/s00253-014-6322-2 　

    ISSN： 0175-7598

    eISSN： 1432-0614

  46. Complete genome sequence of a phenanthrene degrader, Mycobacterium sp. strain EPa45 (NBRC 110737), isolated from a phenanthrene-degrading consortium Peer-reviewed

    Hiromi Kato, Natsumi Ogawa, Yoshiyuki Ohtsubo, Kenshiro Oshima, Atsushi Toyoda, Hiroshi Mori, Yuji Nagata, Ken Kurokawa, Masahira Hattori, Asao Fujiyama, Masataka Tsuda

    Genome Announcements　3　(4)　e00782-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00782-15 　

    ISSN： 2169-8287

  47. Complete genome sequence of polyvinyl alcoholdegrading strain Sphingopyxis sp. 113P3 (NBRC 111507) Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Mitsuru Numata, Kieko Tsuchikane, Akira Hosoyama, Atsushi Yamazoe, Masataka Tsuda, Nobuyuki Fujita, Fusako Kawai

    Genome Announcements　3　(5)　e01169-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01169-15 　

    ISSN： 2169-8287

  48. Complete genome sequence of a phenanthrene degrader, Burkholderia sp. HB-1 (NBRC 110738) Peer-reviewed

    Yoshiyuki Ohtsubo, Azusa Moriya, Hiromi Kato, Natsumi Ogawa, Yuji Nagata, Masataka Tsuda

    Genome Announcements　3　(6)　e01283　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01283-15 　

    ISSN： 2169-8287

  49. Complete genome sequence of polypropylene glycol- and polyethylene glycol-degrading Sphingopyxis macrogoltabida strain EY-1 Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Mitsuru Numata, Kieko Tsuchikane, Akira Hosoyama, Atsushi Yamazoe, Masataka Tsuda, Nobuyuki Fujita, Fusako Kawai

    Genome Announcements　3　(6)　e01399-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01399-15 　

    ISSN： 2169-8287

  50. Complete genome sequence of a polypropylene glycol-degrading strain, Microbacterium sp. No. 7 Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Mitsuru Numata, Kieko Tsuchikane, Akira Hosoyama, Atsushi Yamazoe, Masataka Tsuda, Nobuyuki Fujita, Fusako Kawai

    Genome Announcements　3　(6)　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01400-15 　

    ISSN： 2169-8287

  51. Complete genome sequence of Sphingopyxis macrogoltabida type strain NBRC 15033, originally isolated as a polyethylene glycol degrader Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Mitsuru Numata, Kieko Tsuchikane, Akira Hosoyama, Atsushi Yamazoe, Masataka Tsuda, Nobuyuki Fujita, Fusako Kawai

    Genome Announcements　3　(6)　e01401-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01401-15 　

    ISSN： 2169-8287

  52. Stepwise enhancement of catalytic performance of haloalkane dehalogenase LinB towards beta-hexachlorocyclohexane Peer-reviewed

    Ryota Moriuchi, Hiroki Tanaka, Yuki Nikawadori, Mayuko Ishitsuka, Michihiro Ito, Yoshiyuki Ohtsubo, Masataka Tsuda, Jiri Damborsky, Zbynek Prokop, Yuji Nagata

    AMB EXPRESS　4　72　2014/09

    DOI： 10.1186/s13568-014-0072-5 　

    ISSN： 2191-0855

  53. Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites Peer-reviewed

    Radka Chaloupkova, Tatyana Prudnikova, Pavlina Rezacova, Zbynek Prokop, Tana Koudelakova, Lukas Daniel, Jan Brezovsky, Wakako Ikeda-Ohtsubo, Yukari Sato, Michal Kuty, Yuji Nagata, Ivana Kuta Smatanova, Jiri Damborsky

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　70　1884-1897　2014/07

    DOI： 10.1107/S1399004714009018 　

    ISSN： 1399-0047

  54. Identification of Burkholderia multivorans ATCC 17616 genetic determinants for fitness in soil by using signature-tagged mutagenesis Peer-reviewed

    Yuji Nagata, Junko Senbongi, Yoko Ishibashi, Rie Sudo, Masatoshi Miyakoshi, Yoshiyuki Ohtsubo, Masataka Tsuda

    MICROBIOLOGY-SGM　160　883-891　2014/05

    DOI： 10.1099/mic.0.077057-0 　

    ISSN： 1350-0872

    eISSN： 1465-2080

  55. 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 Peer-reviewed

    Hiroshi Mori, Fumito Maruyama, Hiromi Kato, Atsushi Toyoda, Ayumi Dozono, Yoshiyuki Ohtsubo, Yuji Nagata, Asao Fujiyama, Masataka Tsuda, Ken Kurokawa

    DNA RESEARCH　21　(2)　217-227　2014/04

    DOI： 10.1093/dnares/dst052 　

    ISSN： 1340-2838

    eISSN： 1756-1663

  56. Complete genome sequence of Pseudomonas aeruginosa MTB-1, isolated from a microbial community enriched by the technical formulation of hexachlorocyclohexane Peer-reviewed

    Yoshiyuki Ohtsubo, Takuya Sato, Kouhei Kishida, Michro Tabata, Yoshitoshi Ogura, Tetsuya Hayashi, Masataka Tsuda, Yuji Nagata

    Genome Announcements　2　(1)　e01130-13　2014

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.e01130-13 　

    ISSN： 2169-8287

  57. Complete genome sequence of the thermophilic polychlorinated biphenyl degrader Geobacillus sp. strain JF8 (NBRC 109937) Peer-reviewed

    Masaki Shintani, Yoshiyuki Ohtsubo, Kohei Fukuda, Akira Hosoyama, Shoko Ohji, Atsushi Yamazoe, Nobuyuki Fujita, Yuji Nagata, Masataka Tsuda, Takashi Hatta, Kazuhide Kimbara

    Genome Announcements　2　(1)　e01213-13　2014

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.e01213-13 　

    ISSN： 2169-8287

  58. Complete genome sequence of Pseudomonas sp. strain TKP, isolated from a γ-hexachlorocyclohexane-degrading mixed culture Peer-reviewed

    Yoshiyuki Ohtsubo, Kouhei Kishida, Takuya Sato, Michiro Tabata, Toru Kawasumi, Yoshitoshi Ogura, Tetsuya Hayashim, Masataka Tsuda, Yuji Nagata

    Genome Announcements　2　(1)　e01241-13　2014

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.e01241-13 　

    ISSN： 2169-8287

  59. Inhibitory effect of Pseudomonas putida nitrogen-related phosphotransferase system on conjugative transfer of IncP-9 plasmid from Escherichia coli Peer-reviewed

    Kei Inoue, Ryo Miyazaki, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    FEMS Microbiology Letters　345　(2)　102-109　2013/08

    DOI： 10.1111/1574-6968.12188 　

    ISSN： 0378-1097 1574-6968

  60. The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacteriumtumefaciens C58 Peer-reviewed

    Khomaini Hasan, Artur Gora, Jan Brezovsky, Radka Chaloupkova, Hana Moskalikova, Andrea Fortova, Yuji Nagata, Jiri Damborsky, Zbynek Prokop

    FEBS JOURNAL　280　(13)　3149-3159　2013/07

    DOI： 10.1111/febs.12238 　

    ISSN： 1742-464X

  61. Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp Strain MI1205 Peer-reviewed

    Masahiko Okai, Jun Ohtsuka, Lica Fabiana Imai, Tomoko Mase, Ryota Moriuchi, Masataka Tsuda, Koji Nagata, Yuji Nagata, Masaru Tanokura

    JOURNAL OF BACTERIOLOGY　195　(11)　2642-2651　2013/06

    DOI： 10.1128/JB.02020-12 　

    ISSN： 0021-9193

    eISSN： 1098-5530

  62. Cointegrate-resolution of toluene-catabolic transposon Tn4651: Determination of crossover site and the segment required for full resolution activity Peer-reviewed

    Hirokazu Yano, Hiroyuki Genka, Yoshiyuki Ohtsubo, Yuji Nagata, Eva M. Top, Masataka Tsuda

    PLASMID　69　(1)　24-35　2013/01

    DOI： 10.1016/j.plasmid.2012.07.004 　

    ISSN： 0147-619X

  63. Complete genome sequence of the γ-hexachlorocyclohexane-degrading bacterium Sphingomonas sp. strain MM-1 Peer-reviewed

    M. Tabata, Y. Ohtsubo, S. Ohhata, M. Tsuda, Y. Nagata

    Genome Announcements　1　(3)　e00247-13　2013

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00247-13 　

    ISSN： 2169-8287

  64. Complete genome sequence of Ralstonia pickettii DTP0602, a 2,4,6-trichlorophenol degrader Peer-reviewed

    Yoshiyuki Ohtsubo, Nobuyuki Fujita, Yuji Nagata, Masataka Tsuda, Tomohiro Iwasaki, Takashi Hatta

    Genome Announcements　1　(6)　e00903-13　2013

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00903-13 　

    ISSN： 2169-8287

  65. Complete Genome Sequence of Acidovorax sp Strain KKS102, a Polychlorinated-Biphenyl Degrader Peer-reviewed

    Yoshiyuki Ohtsubo, Fumito Maruyama, Hisayuki Mitsui, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BACTERIOLOGY　194　(24)　6970-6971　2012/12

    DOI： 10.1128/JB.01848-12 　

    ISSN： 0021-9193

  66. ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids Peer-reviewed

    Masatoshi Miyakoshi, Masaki Shintani, Kei Inoue, Tsuguno Terabayashi, Fumiya Sai, Moriya Ohkuma, Hideaki Nojiri, Yuji Nagata, Masataka Tsuda

    ENVIRONMENTAL MICROBIOLOGY　14　(11)　2946-2959　2012/11

    DOI： 10.1111/j.1462-2920.2012.02861.x 　

    ISSN： 1462-2912

    eISSN： 1462-2920

  67. Cloning of gamma-hexachlorocyclohexane dehydrochlorinase gene with its flanking regions from soil by activity-based screening techniques Peer-reviewed

    Michihiro Ito, Akira Ono, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    EUROPEAN JOURNAL OF SOIL BIOLOGY　52　16-19　2012/09

    DOI： 10.1016/j.ejsobi.2012.05.001 　

    ISSN： 1164-5563

  68. Conjugal Transfer of Polychlorinated Biphenyl/Biphenyl Degradation Genes in Acidovorax sp Strain KKS102, Which Are Located on an Integrative and Conjugative Element Peer-reviewed

    Yoshiyuki Ohtsubo, Yoko Ishibashi, Hideaki Naganawa, Satoshi Hirokawa, Satomi Atobe, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BACTERIOLOGY　194　(16)　4237-4248　2012/08

    DOI： 10.1128/JB.00352-12 　

    ISSN： 0021-9193

  69. Crystallization and preliminary X-ray analysis of the haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 Peer-reviewed

    Tomoko Mase, Hideya Yabuki, Masahiko Okai, Jun Ohtsuka, Fabiana Lica Imai, Yuji Nagata, Masaru Tanokura

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　68　652-654　2012/06

    DOI： 10.1107/S1744309112013942 　

    ISSN： 1744-3091

    eISSN： 2053-230X

  70. Suppression of pleiotropic phenotypes of a Burkholderia multivorans fur mutant by oxyR mutation Peer-reviewed

    Akane Kimura, Satoshi Yuhara, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    MICROBIOLOGY-SGM　158　1284-1293　2012/05

    DOI： 10.1099/mic.0.057372-0 　

    ISSN： 1350-0872

  71. Pivotal role of anthranilate dioxygenase genes in the adaptation of Burkholderia multivorans ATCC 17616 in soil Peer-reviewed

    Eri Nishiyama, Yoshiyuki Ohtsubo, Yasuhiro Yamamoto, Yuji Nagata, Masataka Tsuda

    FEMS MICROBIOLOGY LETTERS　330　(1)　46-55　2012/05

    DOI： 10.1111/j.1574-6968.2012.02532.x 　

    ISSN： 0378-1097

  72. Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal gamma-hexachlorocyclohexane-degrading bacterium Peer-reviewed

    Yuji Nagata, Shunsuke Natsui, Ryo Endo, Yoshiyuki Ohtsubo, Natsuko Ichikawa, Akiho Ankai, Akio Oguchi, Shigehiro Fukui, Nobuyuki Fujita, Masataka Tsuda

    ENZYME AND MICROBIAL TECHNOLOGY　49　(6-7)　499-508　2011/12

    DOI： 10.1016/j.enzmictec.2011.10.005 　

    ISSN： 0141-0229

  73. Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature Peer-reviewed

    Radka Chaloupkova, Zbynek Prokop, Yukari Sato, Yuji Nagata, Jiri Damborsky

    FEBS JOURNAL　278　(15)　2728-2738　2011/08

    DOI： 10.1111/j.1742-4658.2011.08203.x 　

    ISSN： 1742-464X

  74. The lin Genes for gamma-Hexachlorocyclohexane Degradation in Sphingomonas sp MM-1 Proved to Be Dispersed across Multiple Plasmids Peer-reviewed

    Michiro Tabata, Ryo Endo, Michihiro Ito, Yoshiyuki Ohtsubo, Ashwani Kumar, Masataka Tsuda, Yuji Nagata

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　75　(3)　466-472　2011/03

    DOI： 10.1271/bbb.100652 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  75. Biochemical Characteristics of the Novel Haloalkane Dehalogenase DatA, Isolated from the Plant Pathogen Agrobacterium tumefaciens C58 Peer-reviewed

    Khomaini Hasan, Andrea Fortova, Tana Koudelakova, Radka Chaloupkova, Mayuko Ishitsuka, Yuji Nagata, Jiri Damborsky, Zbynek Prokop

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　77　(5)　1881-1884　2011/03

    DOI： 10.1128/AEM.02109-10 　

    ISSN： 0099-2240

  76. Development of a Crystallization Protocol for the DbeA1 Variant of Novel Haloalkane Dehalogenase from Bradyrhizobium elkani USDA94 Peer-reviewed

    T. Prudnikova, R. Chaloupkova, Y. Sato, Y. Nagata, O. Degtjarik, M. Kuty, P. Rezacova, J. Damborsky, I. Kuta Smatanova

    CRYSTAL GROWTH & DESIGN　11　(2)　516-519　2011/02

    DOI： 10.1021/cg1013363 　

    ISSN： 1528-7483

  77. Conjugative transfer of naphthalene-catabolic plasmid NAH7 regulated by nitrogen-related phosphotransferase system of recipient cells Peer-reviewed

    K. Inoue, R. Miyazaki, M. Miyakoshi, Y. Ohtsubo, Y. Nagata, M Tsuda

    Journal of Biotechnology　150　(S1)　269　2010/11

  78. PCB / biphenyl degradation operon repressed by different compounds in Acidovorax sp. KKS102 and Burkholderia multivorans ATCC 17616 Peer-reviewed

    Y. Ohtsubo, S. Suzuki, K. Onuma, H. Goto, Y. Nagata, M Tsuda

    Journal of Biotechnology　150　(S1)　240-241　2010/11

  79. Complete Genome Sequence of the Representative gamma-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum UT26 Peer-reviewed

    Yuji Nagata, Yoshiyuki Ohtsubo, Ryo Endo, Natsuko Ichikawa, Akiho Ankai, Akio Oguchi, Shigehiro Fukui, Nobuyuki Fujita, Masataka Tsuda

    JOURNAL OF BACTERIOLOGY　192　(21)　5852-5853　2010/11

    DOI： 10.1128/JB.00961-10 　

    ISSN： 0021-9193

  80. Crystal Structure of gamma-Hexachlorocyclohexane Dehydrochlorinase LinA from Sphingobium japonicum UT26 Peer-reviewed

    Masahiko Okai, Keiko Kubota, Masao Fukuda, Yuji Nagata, Koji Negata, Masaru Tanokura

    JOURNAL OF MOLECULAR BIOLOGY　403　(2)　260-269　2010/10

    DOI： 10.1016/j.jmb.2010.08.043 　

    ISSN： 0022-2836

  81. Identification of Burkholderia multivorans ATCC 17616 genes induced in soil environment by in vivo expression technology Peer-reviewed

    Eri Nishiyama, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    ENVIRONMENTAL MICROBIOLOGY　12　(9)　2539-2558　2010/09

    DOI： 10.1111/j.1462-2920.2010.02227.x 　

    ISSN： 1462-2912

  82. Complete Nucleotide Sequence of TOL Plasmid pDK1 Provides Evidence for Evolutionary History of IncP-7 Catabolic Plasmids Peer-reviewed

    Hirokazu Yano, Masatoshi Miyakoshi, Kenshiro Ohshima, Michiro Tabata, Yuji Nagata, Masahira Hattori, Masataka Tsuda

    JOURNAL OF BACTERIOLOGY　192　(17)　4337-4347　2010/09

    DOI： 10.1128/JB.00359-10 　

    ISSN： 0021-9193

    eISSN： 1098-5530

  83. Analysis of extracellular alginate lyase and its gene from a marine bacterial strain, Pseudoalteromonas atlantica AR06 Peer-reviewed

    Ryoji Matsushima, Hiroko Danno, Motoharu Uchida, Kenji Ishihara, Toshiyuki Suzuki, Masaki Kaneniwa, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　86　(2)　567-576　2010/03

    DOI： 10.1007/s00253-009-2278-z 　

    ISSN： 0175-7598

  84. Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering Peer-reviewed

    Zbynek Prokop, Yukari Sato, Jan Brezovsky, Tomas Mozga, Radka Chaloupkova, Tana Koudelakova, Petr Jerabek, Veronika Stepankova, Ryo Natsume, Jan G. E. van Leeuwen, Dick B. Janssen, Jan Florian, Yuji Nagata, Toshiya Senda, Jiri Damborsky

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION　49　(35)　6111-6115　2010

    DOI： 10.1002/anie.201001753 　

    ISSN： 1433-7851

  85. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate Peer-reviewed

    Martina Pavlova, Martin Klvana, Zbynek Prokop, Radka Chaloupkova, Pavel Banas, Michal Otyepka, Rebecca C. Wade, Masataka Tsuda, Yuji Nagata, Jiri Damborsky

    NATURE CHEMICAL BIOLOGY　5　(10)　727-733　2009/10

    DOI： 10.1038/nchembio.205 　

    ISSN： 1552-4450

  86. Crystallization and preliminary X-ray analysis of gamma-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26 Peer-reviewed

    Masahiko Okai, Keiko Kubota, Masao Fukuda, Yuji Nagata, Koji Nagata, Masaru Tanokura

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　65　822-824　2009/08

    DOI： 10.1107/S1744309109026645 　

    ISSN： 1744-3091

    eISSN： 2053-230X

  87. Crystallization and preliminary X-ray analysis of a novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94 Peer-reviewed

    Tatyana Prudnikova, Tomas Mozga, Pavlina Rezacova, Radka Chaloupkova, Yukari Sato, Yuji Nagata, Jiri Brynda, Michal Kuty, Jiri Damborsky, Ivana Kuta Smatanova

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　65　353-356　2009/04

    DOI： 10.1107/S1744309109007039 　

    ISSN： 1744-3091

  88. Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics. International-journal Peer-reviewed

    Yoshikazu Shimoda, Hisayuki Mitsui, Hiroko Kamimatsuse, Kiwamu Minamisawa, Eri Nishiyama, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda, Sayaka Shinpo, Akiko Watanabe, Mitsuyo Kohara, Manabu Yamada, Yasukazu Nakamura, Satoshi Tabata, Shusei Sato

    DNA research : an international journal for rapid publication of reports on genes and genomes　15　(5)　297-308　2008/10

    DOI： 10.1093/dnares/dsn017 　

    More details Close

    Rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wide functional studies of the physiological roles of many rhizobial genes. In order to carry out genome-wide phenotypic screenings, we have constructed a large mutant library of the nitrogen-fixing symbiotic bacterium, Mesorhizobium loti, by transposon mutagenesis. Transposon insertion mutants were generated using the signature-tagged mutagenesis (STM) technique and a total of 29,330 independent mutants were obtained. Along with the collection of transposon mutants, we have determined the transposon insertion sites for 7892 clones, and confirmed insertions in 3680 non-redundant M. loti genes (50.5% of the total number of M. loti genes). Transposon insertions were randomly distributed throughout the M. loti genome without any bias toward G+C contents of insertion target sites and transposon plasmids used for the mutagenesis. We also show the utility of STM mutants by examining the specificity of signature tags and test screenings for growth- and nodulation-deficient mutants. This defined mutant library allows for genome-wide forward- and reverse-genetic functional studies of M. loti and will serve as an invaluable resource for researchers to further our understanding of rhizobial biology.

  89. Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer Peer-reviewed

    Ryo Miyazaki, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BACTERIOLOGY　190　(19)　6281-6289　2008/10

    DOI： 10.1128/JB.00709-08 　

    ISSN： 0021-9193

  90. GenomeMatcher: A graphical user interface for DNA sequence comparison Peer-reviewed

    Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda

    BMC BIOINFORMATICS　9　376　2008/09

    DOI： 10.1186/1471-2105-9-376 　

    ISSN： 1471-2105

  91. Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans Peer-reviewed

    Satoshi Yuhara, Harunobu Komatsu, Hiroyuki Goto, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    MICROBIOLOGY-SGM　154　1763-1774　2008/06

    DOI： 10.1099/mic.0.2007/015537-0 　

    ISSN： 1350-0872

  92. Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNA Peer-reviewed

    Genki Fuchu, Yoshiyuki Ohtsubo, Michihiro Ito, Ryo Miyazaki, Akira Ono, Yuji Nagata, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　79　(4)　627-632　2008/06

    DOI： 10.1007/s00253-008-1463-9 　

    ISSN： 0175-7598

  93. Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp MI1205 Peer-reviewed

    Michihiro Ito, Zbynek Prokop, Martin Klvana, Yoshiyuki Otsubo, Masataka Tsuda, Jiri Damborsky, Yuji Nagata

    ARCHIVES OF MICROBIOLOGY　188　(4)　313-325　2007/10

    DOI： 10.1007/s00203-007-0251-8 　

    ISSN： 0302-8933

  94. 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 Peer-reviewed

    Hirokazu Yano, Christine E. Garruto, Masahiro Sota, Yoshiyuki Ohtsubo, Yuji Nagata, Gerben J. Zylstra, Peter A. Williams, Masataka Tsuda

    JOURNAL OF MOLECULAR BIOLOGY　369　(1)　11-26　2007/05

    DOI： 10.1016/j.jmb.2007.02.098 　

    ISSN： 0022-2836

  95. Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26 Peer-reviewed

    Ryo Endo, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    JOURNAL OF BACTERIOLOGY　189　(10)　3712-3720　2007/05

    DOI： 10.1128/JB.01883-06 　

    ISSN： 0021-9193

    eISSN： 1098-5530

  96. Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110

    Yukari Sato, Ryo Natsume, Masataka Tsuda, Jiri Damborsky, Yuji Nagata, Toshiya Senda

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS　63　294-296　2007/04

    DOI： 10.1107/S1744309107008652 　

    ISSN： 1744-3091

  97. Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-ray crystallography and microcalorimetry Peer-reviewed

    Marta Monincova, Zbynek Prokop, Jitka Vevodova, Yuji Nagata, Jiri Damborsky

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　73　(6)　2005-2008　2007/03

    DOI： 10.1128/AEM.02416-06 　

    ISSN： 0099-2240

  98. Genetic organization of IncP-7 TOL plasmid pWW53 and the movement of its residing transposons

    H. Yano, C. Garruto, M. Sota, Y. Ohtsubo, Y. Nagata, P. A. Williams, G. J. Zylsra, M. Tsuda

    Plasmid　57　(2)　231-231　2007/02

  99. Exogenous isolation of a plasmid involved in the degradation of γ-hexachlorocyclohexane from its contaminated soil

    R. Miyazaki, Y. Sato, M. Ito, Y. Ohtsubo, Y. Nagata, M. Tsuda

    Plasmid　57　(2)　233-233　2007/02

  100. The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: Reaction mechanism and molecular evolution Peer-reviewed

    Martina Pavlova, Martin Klvana, Andrea Jesenska, Zbynek Prokop, Hana Konecna, Takashi Sato, Masataka Tsuda, Yujj Nagata, Jiri Damborsky

    JOURNAL OF STRUCTURAL BIOLOGY　157　(2)　384-392　2007/02

    DOI： 10.1016/j.jsb.2006.09.004 　

    ISSN： 1047-8477

  101. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches Peer-reviewed

    Akira Ono, Ryo Miyazaki, Masahiro Sota, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　74　(2)　501-510　2007/02

    DOI： 10.1007/s00253-006-0671-4 　

    ISSN： 0175-7598

  102. Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation Peer-reviewed

    Ryo Miyazaki, Yukari Sato, Michihiro Ito, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　72　(11)　6923-6933　2006/11

    DOI： 10.1128/AEM.01531-06 　

    ISSN： 0099-2240

  103. Identification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp KKS102 Peer-reviewed

    Y Ohtsubo, H Goto, Y Nagata, T Kudo, M Tsuda

    MOLECULAR MICROBIOLOGY　60　(6)　1563-1575　2006/06

    DOI： 10.1111/j.1365-2958.2006.05197.x 　

    ISSN： 0950-382X

  104. Growth inhibition by metabolites of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26 Peer-reviewed

    R Endo, Y Ohtsubo, M Tsuda, Y Nagata

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　70　(4)　1029-1032　2006/04

    DOI： 10.1271/bbb.70.1029 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  105. Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris Peer-reviewed

    T Nakamura, M Zamocky, Z Zdrahal, R Chaloupkova, M Monincova, Z Prokop, Y Nagata, J Damborsky

    PROTEIN EXPRESSION AND PURIFICATION　46　(1)　85-91　2006/03

    DOI： 10.1016/j.pep.2005.08.022 　

    ISSN： 1046-5928

    eISSN： 1096-0279

  106. Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26 Peer-reviewed

    Y Nagata, M Kamakura, R Endo, R Miyazaki, Y Ohtsubo, M Tsuda

    FEMS MICROBIOLOGY LETTERS　256　(1)　112-118　2006/03

    DOI： 10.1111/j.1574-6968.2005.00096.x 　

    ISSN： 0378-1097

  107. Functional analysis of unique class II insertion sequence IS1071 Peer-reviewed

    M Sota, H Yano, Y Nagata, Y Ohtsubo, H Genka, H Anbutsu, H Kawasaki, M Tsuda

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　72　(1)　291-297　2006/01

    DOI： 10.1128/AEM.72.1.291-297.2006 　

    ISSN： 0099-2240

  108. Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases Peer-reviewed

    A Jesenska, M Pavlova, M Strouhal, R Chaloupkova, Tesinska, I, M Monincova, Z Prokop, M Bartos, Pavlik, I, Rychlik, I, P Mobius, Y Nagata, J Damborsky

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　71　(11)　6736-6745　2005/11

    DOI： 10.1128/AEM.71.11.6736-6745.2005 　

    ISSN： 0099-2240

  109. [Metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]. Peer-reviewed

    Nagata Y, Tsuda M

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme　50　(12)　1511-1518　2005/10

    ISSN： 0039-9450

  110. Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum, USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities Peer-reviewed

    Y Sato, M Monincova, R Chaloupkova, Z Prokop, Y Ohtsubo, K Minamisawa, M Tsuda, J Damborsky, Y Nagata

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　71　(8)　4372-4379　2005/08

    DOI： 10.1128/AEM.71.8.4372-4379.2005 　

    ISSN： 0099-2240

  111. Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616 Peer-reviewed

    Y Nagata, M Matsuda, H Komatsu, Y Imura, H Sawada, Y Ohtsubo, M Tsuda

    JOURNAL OF BIOSCIENCE AND BIOENGINEERING　99　(6)　603-610　2005/06

    DOI： 10.1263/jbb.99.603 　

    ISSN： 1389-1723

  112. Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 Peer-reviewed

    Y Nagata, Z Prokop, Y Sato, P Jerabek, A Kumar, Y Ohtsubo, M Tsuda, J Damborsky

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　71　(4)　2183-2185　2005/04

    DOI： 10.1128/AEM.71.4.2183-2185.2005 　

    ISSN： 0099-2240

  113. High-temperature-induced transposition of insertion elements in Burkholderia multivorans ATCC 17616 Peer-reviewed

    Y Ohtsubo, H Genka, H Komatsu, Y Nagata, M Tsuda

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　71　(4)　1822-1828　2005/04

    DOI： 10.1128/AEM.71.4.1822-1828.2005 　

    ISSN： 0099-2240

  114. Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 Peer-reviewed

    J Kmunicek, K Hynkova, T Jedlicka, Y Nagata, A Negri, F Gago, RC Wade, J Damborsky

    BIOCHEMISTRY　44　(9)　3390-3401　2005/03

    DOI： 10.1021/bi047912o 　

    ISSN： 0006-2960

  115. Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26 Peer-reviewed

    R Endo, M Kamakura, K Miyauchi, M Fukuda, Y Ohtsubo, M Tsuda, Y Nagata

    JOURNAL OF BACTERIOLOGY　187　(3)　847-853　2005/02

    DOI： 10.1128/JB.187.3.847-853.2005 　

    ISSN： 0021-9193

  116. Identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26 Peer-reviewed

    K Miyauchi, M Fukuda, M Tsuda, M Takagi, Y Nagata

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　69　(1)　216-219　2005/01

    DOI： 10.1271/bbb.69.216 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  117. Genes and enzymes for gamma-hexachlorocyclohexanedegradation in Sphingomonas paucimobilis UT26 Peer-reviewed

    Y. Nagata, K. Miyauchi, M. Tsuda

    International Biodeterioration & Biodegradation　53　(4)　246-246　2004/06

  118. Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 angstrom resolution: Dynamics of catalytic residues Peer-reviewed

    AJ Oakley, M Klvana, M Otyepka, Y Nagata, MCJ Wilce, J Damborsky

    BIOCHEMISTRY　43　(4)　870-878　2004/02

    DOI： 10.1021/bi034748g 　

    ISSN： 0006-2960

  119. Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel Peer-reviewed

    R Chaloupkova, J Sykorova, Z Prokop, A Jesenska, M Monincovaa, M Pavlova, M Tsuda, Y Nagata, J Damborsky

    JOURNAL OF BIOLOGICAL CHEMISTRY　278　(52)　52622-52628　2003/12

    DOI： 10.1074/jbc.M306762200 　

    ISSN： 0021-9258

  120. Catalytic mechanism of the haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 Peer-reviewed

    Z Prokop, M Monincova, R Chaloupkova, M Klvana, Y Nagata, DB Janssen, J Damborsky

    JOURNAL OF BIOLOGICAL CHEMISTRY　278　(46)　45094-45100　2003/11

    DOI： 10.1074/jbc.M307056200 　

    ISSN： 0021-9258

  121. Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates Peer-reviewed

    VA Streltsov, Z Prokop, J Damborsky, Y Nagata, A Oakley, MCJ Wilce

    BIOCHEMISTRY　42　(34)　10104-10112　2003/09

    DOI： 10.1021/bi027280a 　

    ISSN： 0006-2960

  122. Distribution and organization of auxotrophic genes on the multichromosomal genome of Burkholderia multivorans ATCC 17616 Peer-reviewed

    H Komatsu, Y Imura, A Ohori, Y Nagata, M Tsuda

    JOURNAL OF BACTERIOLOGY　185　(11)　3333-3343　2003/06

    DOI： 10.1128/JB.185.11.3333.3343.2003 　

    ISSN： 0021-9193

  123. Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB Peer-reviewed

    Y Nagata, Z Prokop, S Marvanova, J Sykorova, M Monincova, M Tsuda, J Damborsky

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　69　(4)　2349-2355　2003/04

    DOI： 10.1128/AEM.69.4.2349-2355.2003 　

    ISSN： 0099-2240

  124. Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: Promoter implantation by homologous recombination Peer-reviewed

    Y Ohtsubo, M Shimura, M Delawary, K Kimbara, M Takagi, T Kudo, A Ohta, Y Nagata

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　69　(1)　146-153　2003/01

    DOI： 10.1128/AEM.69.1.146-153.2003 　

    ISSN： 0099-2240

  125. Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis Peer-reviewed

    M Bohac, Y Nagata, Z Prokop, M Prokop, M Monincova, M Tsuda, J Koca, J Damborsky

    BIOCHEMISTRY　41　(48)　14272-14280　2002/12

    DOI： 10.1021/bi026427v 　

    ISSN： 0006-2960

  126. Site-specific recombination system encoded by toluene catabolic transposon Tn4651 Peer-reviewed

    H Genka, Y Nagata, M Tsuda

    JOURNAL OF BACTERIOLOGY　184　(17)　4757-4766　2002/09

    DOI： 10.1128/JB.184.17.4757-4766.2002 　

    ISSN： 0021-9193

  127. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: Evidence for product- and water-mediated inhibition Peer-reviewed

    AJ Oakley, Z Prokop, M Bohac, J Kmunicek, T Jedlicka, M Monincova, Kuta-Smatanova, I, Y Nagata, J Damborsky, MCJ Wilce

    BIOCHEMISTRY　41　(15)　4847-4855　2002/04

    DOI： 10.1021/bi015734i 　

    ISSN： 0006-2960

  128. Cloning and characterization of linR, involved in regulation of the downstream pathway for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 Peer-reviewed

    K Miyauchi, HS Lee, M Fukuda, M Takagi, Y Nagata

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　68　(4)　1803-1807　2002/04

    DOI： 10.1128/AEM.68.4.1803-1807.2002 　

    ISSN： 0099-2240

  129. Employment of the human estrogen receptor beta ligand-binding domain and co-activator SRC1 nuclear receptor-binding domain for the construction of a yeast two-hybrid detection system for endocrine disrupters Peer-reviewed

    HS Lee, K Miyauchi, Y Nagata, R Fukuda, S Sasagawa, H Endoh, S Kato, H Horiuchi, M Takagi, A Ohta

    JOURNAL OF BIOCHEMISTRY　131　(3)　399-405　2002/03

    ISSN： 0021-924X

  130. Identification of protein fold and catalytic residues of γhexachlorocyclohexane dehydrochlorinase LinA Peer-reviewed

    Yuji Nagata, Katsuki Mori, Masamichi Takagi, Alexey G. Murzin, Jií Damborsk

    Proteins: Structure, Function and Genetics　45　(4)　471-477　2001/12/01

    DOI： 10.1002/prot.10007 　

    ISSN： 0887-3585

  131. BphS, a key transcriptional regulator of bph genes involved in polychlorinated biphenyl/biphenyl degradation in Pseudomonas sp KKS102 Peer-reviewed

    Y Ohtsubo, M Delawary, K Kimbara, M Takagi, A Ohta, Y Nagata

    JOURNAL OF BIOLOGICAL CHEMISTRY　276　(39)　36146-36154　2001/09

    DOI： 10.1074/jbc.M100302200 　

    ISSN： 0021-9258

  132. Biochemical characterization of broad-specificity enzymes using multivariate experimental design and a colorimetric microplate assay: Characterization of the haloalkane dehalogenase mutants Peer-reviewed

    Soa Marvanová, Yuji Nagata, Michaela Wimmerová, Jana Sýkorová, Kamila Hynková, Jirí Damborský

    Journal of Microbiological Methods　44　(2)　149-157　2001/03/01

    DOI： 10.1016/S0167-7012(00)00250-5 　

    ISSN： 0167-7012

  133. Reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase LinA Peer-reviewed

    L Trantirek, K Hynkova, Y Nagata, A Murzin, A Ansorgova, Sklenar, V, J Damborsky

    JOURNAL OF BIOLOGICAL CHEMISTRY　276　(11)　7734-7740　2001/03

    ISSN： 0021-9258

  134. Structure-specificity relationships for haloalkane dehalogenases Peer-reviewed

    Jiří Damborský, Emiel Rorije, Andrea Jesenská, Yuji Nagata, Gilles Klopman, Willie J. G. M. Peijnenburg

    Environmental Toxicology and Chemistry　20　(12)　2681-2689　2001

    DOI： 10.1002/etc.5620201205 　

    ISSN： 0730-7268

  135. Isolation and characterization of acetoacetyl-CoA thiolase gene essential for n-decane assimilation in yeast Yarrowia lipolytica Peer-reviewed

    Setsu Yamagami, Toshiya Iida, Yuji Nagata, Akinori Ohta, Masamichi Takagi

    Biochemical and Biophysical Research Communications　282　(3)　832-838　2001

    Publisher: Academic Press Inc.

    DOI： 10.1006/bbrc.2001.4653 　

    ISSN： 0006-291X

  136. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 Peer-reviewed

    J. Marek, J. Vevodova, I. K. Smatanova, Y. Nagata, L. A. Svensson, J. Newman, M. Takagi, J. Damborsky

    Biochemistry　39　(46)　14082-14086　2000/11/21

    DOI： 10.1021/bi001539c 　

    ISSN： 0006-2960

  137. Determination of haloalkane dehalogenase activity by capillary zone electrophoresis Peer-reviewed

    Zdeněk Glatz, Mária V. Marini, Michaela Wimmerová, Jiří Damborský, Yuji Nagata

    Journal of Chromatography A　895　(1-2)　219-225　2000/10/20

    DOI： 10.1016/S0021-9673(00)00635-X 　

    ISSN： 0021-9673

  138. 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 Peer-reviewed

    Yoshiyuki Ohtsubo, Yuji Nagata, Kazuhide Kimbara, Masamichi Takagi, Akinori Ohta

    Gene　256　(1-2)　223-228　2000/10/03

    DOI： 10.1016/S0378-1119(00)00349-8 　

    ISSN： 0378-1119

  139. Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis Peer-reviewed

    K Miyauchi, Y Adachi, Y Nagata, M Takagi

    JOURNAL OF BACTERIOLOGY　181　(21)　6712-6719　1999/11

    ISSN： 0021-9193

  140. PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase Peer-reviewed

    Y Ohtsubo, K Miyauchi, K Kanda, T Hatta, H Kiyohara, T Senda, Y Nagata, Y Mitsui, M Takagi

    FEBS LETTERS　459　(3)　395-398　1999/10

    DOI： 10.1016/S0014-5793(99)01305-8 　

    ISSN： 0014-5793

  141. Two different types of dehalogenases, LinA and LinB, involved in gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 are localized in the periplasmic space without molecular processing Peer-reviewed

    Y Nagata, A Futamura, K Miyauchi, M Takagi

    JOURNAL OF BACTERIOLOGY　181　(17)　5409-5413　1999/09

    ISSN： 0021-9193

  142. Crystallization and preliminary X-ray diffraction analysis of haloalkane dehalogenase linB from Sphingomonas paucimobilis UT26 Peer-reviewed

    Ivana Smatanová, Yuji Nagata, L. Anders Svensson, Masamichi Takagi, Jaromír Marek

    Acta Crystallographica Section D: Biological Crystallography　55　(6)　1231-1233　1999/06

    DOI： 10.1107/S090744499900459X 　

    ISSN： 0907-4449

  143. Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 Peer-reviewed

    Kamila Hynková, Yuji Nagata, Masamichi Takagi, Jiří Damborský

    FEBS Letters　446　(1)　177-181　1999/03/05

    DOI： 10.1016/S0014-5793(99)00199-4 　

    ISSN： 0014-5793

  144. Construction and characterization of histidine-tagged haloalkane dehalogenase (LinB) of a new substrate class from a γ-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26 Peer-reviewed

    Yuji Nagata, Kamila Hynková, Jiří Damborský, Masamichi Takagi

    Protein Expression and Purification　17　(2)　299-304　1999

    Publisher: Academic Press Inc.

    DOI： 10.1006/prep.1999.1143 　

    ISSN： 1046-5928

  145. Mechanism-based structure-biodegradability relationships for hydrolytic dehalogenation of chloro-and bromo-alkenes Peer-reviewed

    Damborsky, J, A. Berglund, M. Kuty, A. Ansorgova, Y. Nagata, M. Sjotrom

    Quantitative Structure-Activity Relationships　17　450-458　1998/09

    DOI： 10.1002/(SICI)1521-3838(199810)17:05<450::AID-QSAR450>3.3.CO;2-V 　

  146. Cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane by Sphingomonas paucimobilis Peer-reviewed

    K Miyauchi, SK Suh, Y Nagata, M Takagi

    JOURNAL OF BACTERIOLOGY　180　(6)　1354-1359　1998/03

    ISSN： 0021-9193

  147. Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26 Peer-reviewed

    Y Nagata, K Miyauchi, J Damborsky, K Manova, A Ansorgova, M Takagi

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　63　(9)　3707-3710　1997/09

    ISSN： 0099-2240

  148. Isolation and characterization of Tn5-induced mutants of Sphingomonas paucimobilis defective in 2,5-dichlorohydoquinone degradation Peer-reviewed

    Y Nagata, K Miyauchi, SK Suh, A Futamura, M Takagi

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　60　(4)　689-691　1996/04

    DOI： 10.1271/bbb.60.689 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  149. Genes and enzymes for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 Peer-reviewed

    Y Nagata, M Fukuda, K Miyauchi, M Takagi

    MOLECULAR BIOLOGY OF PSEUDOMONADS　58-70　1996

  150. Pseudomonas fluorescens KKL101, a benzoic acid degrader in a mixed culture that degrades biphenyl and polychlorinated biphenyls Peer-reviewed

    Y Kikuchi, Y Nagata, Y Ohtsubo, T Koana, M Takagi

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　59　(12)　2303-2304　1995/12

    DOI： 10.1271/bbb.59.2303 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  151. Identification of the bphA and bphB Genes of Pseudomonas sp. Strain KKS102 Involved in degradation of biphenyl and polychlorinated biphenyls Peer-reviewed

    Masao Fukuda, Yuji Yasukochi, Yutaka Kikuchi, Yuji Nagata, Kazuhide Kimbara, Hiroyuki Horiuchi, Masamichi Takagi, Keiji Yano

    Biochemical and Biophysical Research Communications　202　(2)　850-856　1994/07/29

    DOI： 10.1006/bbrc.1994.2008 　

    ISSN： 1090-2104 0006-291X

  152. NUCLEOTIDE-SEQUENCE AND FUNCTIONAL-ANALYSIS OF THE META-CLEAVAGE PATHWAY INVOLVED IN BIPHENYL AND POLYCHLORINATED BIPHENYL DEGRADATION IN PSEUDOMONAS SP STRAIN KKS102 Peer-reviewed

    Y KIKUCHI, Y YASUKOCHI, Y NAGATA, M FUKUDA, M TAKAGI

    JOURNAL OF BACTERIOLOGY　176　(14)　4269-4276　1994/07

    ISSN： 0021-9193

  153. CLONING AND SEQUENCING OF A 2,5-DICHLORO-2,5-CYCLOHEXADIENE-1,4-DIOL DEHYDROGENASE GENE INVOLVED IN THE DEGRADATION OF GAMMA-HEXACHLOROCYCLOHEXANE IN PSEUDOMONAS-PAUCIMOBILIS Peer-reviewed

    Y NAGATA, R OHTOMO, K MIYAUCHI, M FUKUDA, K YANO, M TAKAGI

    JOURNAL OF BACTERIOLOGY　176　(11)　3117-3125　1994/06

    ISSN： 0021-9193

  154. IDENTIFICATION OF THE BPHA4 GENE ENCODING FERREDOXIN REDUCTASE INVOLVED IN BIPHENYL AND POLYCHLORINATED BIPHENYL DEGRADATION IN PSEUDOMONAS SP STRAIN KKS102 Peer-reviewed

    Y KIKUCHI, Y NAGATA, M HINATA, K KIMBARA, M FUKUDA, K YANO, M TAKAGI

    JOURNAL OF BACTERIOLOGY　176　(6)　1689-1694　1994/03

    ISSN： 0021-9193

  155. CLONING AND SEQUENCING OF A DEHALOGENASE GENE ENCODING AN ENZYME WITH HYDROLASE ACTIVITY INVOLVED IN THE DEGRADATION OF GAMMA-HEXACHLOROCYCLOHEXANE IN PSEUDOMONAS-PAUCIMOBILIS Peer-reviewed

    Y NAGATA, T NARIYA, R OHTOMO, M FUKUDA, K YANO, M TAKAGI

    JOURNAL OF BACTERIOLOGY　175　(20)　6403-6410　1993/10

    ISSN： 0021-9193

  156. PURIFICATION AND CHARACTERIZATION OF GAMMA-HEXACHLOROCYCLOHEXANE (GAMMA-HCH) DEHYDROCHLORINASE (LINA) FROM PSEUDOMONAS-PAUCIMOBILIS Peer-reviewed

    Y NAGATA, T HATTA, R IMAI, K KIMBARA, M FUKUDA, K YANO, M TAKAGI

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　57　(9)　1582-1583　1993/09

    DOI： 10.1271/bbb.57.1582 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  157. ISOLATION AND CHARACTERIZATION OF TN5-INDUCED MUTANTS OF PSEUDOMONAS-PAUCIMOBILIS UT26 DEFECTIVE IN GAMMA-HEXACHLOROCYCLOHEXANE DEHYDROCHLORINASE (LINA) Peer-reviewed

    Y NAGATA, R IMAI, A SAKAI, M FUKUDA, K YANO, M TAKAGI

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　57　(5)　703-709　1993/05

    DOI： 10.1271/bbb.57.703 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  158. STEREOCHEMICAL ANALYSIS OF GAMMA-HCH DEGRADATION BY PSEUDOMONAS-PAUCIMOBILIS UT26 Peer-reviewed

    S NAGASAWA, R KIKUCHI, Y NAGATA, M TAKAGI, M MATSUO

    CHEMOSPHERE　26　(6)　1187-1201　1993/03

    DOI： 10.1016/0045-6535(93)90205-J 　

    ISSN： 0045-6535

  159. Aerobic mineralization of γ-HCH by Pseudomonas paucimobilis UT26 Peer-reviewed

    Satoru Nagasawa, Ryoichi Kikuchi, Yuji Nagata, Masamichi Takagi, Masatoshi Matsuo

    Chemosphere　26　(9)　1719-1728　1993

    DOI： 10.1016/0045-6535(93)90115-L 　

    ISSN： 0045-6535

  160. ISOLATION AND CHARACTERIZATION OF A DEHYDROCHLORINASE GENE FOR THE DEGRADATION OF GAMMA-HEXACHLOROCYCLOHEXANE IN PSEUDOMONAS-PAUCIMOBILIS Peer-reviewed

    R IMAI, Y NAGATA, M FUKUDA, K YANO, M TAKAGI

    PSEUDOMONAS : MOLECULAR BIOLOGY AND BIOTECHNOLOGY　292-300　1992

  161. MOLECULAR-CLONING OF A PSEUDOMONAS-PAUCIMOBILIS GENE ENCODING A 17-KILODALTON POLYPEPTIDE THAT ELIMINATES HCL MOLECULES FROM GAMMA-HEXACHLOROCYCLOHEXANE Peer-reviewed

    R IMAI, Y NAGATA, M FUKUDA, M TAKAGI, K YANO

    JOURNAL OF BACTERIOLOGY　173　(21)　6811-6819　1991/11

    ISSN： 0021-9193

  162. DEHYDROCHLORINATION OF GAMMA-HEXACHLOROCYCLOHEXANE (GAMMA-BHC) BY GAMMA-BHC-ASSIMILATING PSEUDOMONAS-PAUCIMOBILIS Peer-reviewed

    R IMAI, Y NAGATA, K SENOO, H WADA, M FUKUDA, M TAKAGI, K YANO

    AGRICULTURAL AND BIOLOGICAL CHEMISTRY　53　(7)　2015-2017　1989/07

    DOI： 10.1271/bbb1961.53.2015 　

    ISSN： 0002-1369

Show all ︎Show first 5

Misc. 173

  1. Dynamic spectral decomposition of soil microbial community

    長田穣, STARI Leonardo, 加藤広海, 永田裕二, 大坪嘉行, 近藤倫生

    日本生態学会大会講演要旨(Web)　71st　2024

  2. A role of bacterial membrane phospholipids in conjugation

    熊谷連, 大坪嘉行, 永田裕二, 岸田康平

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  3. Construction and characterization of transgenic Arabidopsis thaliana expressing bacterial enzyme for degradation of organochlorine pesticide γ-HCH

    DENG Wenhao, 高田美信, 岸田康平, 大坪嘉行, 渡辺正夫, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  4. TrbB, conjugative transfer ATPase of type IV secretion system, is involved in the TraR-mediated activation of ICEKKS102Tn4677 excision

    松本哲, 岸田康平, 永田裕二, 大坪嘉行

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  5. Hitchhiking phenomenon in which Paenibacillus sp.NK-L2 transports an organochlorine pesticide-degrading bacterial strain

    松添華子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  6. Substrates of AdhX that causes the high-yield growth under oligotrophic conditions in heterotrophic bacteria

    伊藤蓮, STARI Leonardo, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  7. A mutant of Cupriavidus strain exhibiting thin-colony-expansion phenotype

    平野翔子, XIONG Zhiyu, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  8. capturing experiments of dehalogenase genes for degradation of organochlorine pesticide toward various bacterial communities and isolates

    岡俊璃, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

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  9. Formation of an organochlorine insecticide-degrading bacterial community by Sphingobium-Cupriavidus strains

    XIONG Zhiyu, 平野翔子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  10. Reconstruction of an organochlorine insecticide-degrading bacterial community

    手塚隆博, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  11. Cupriavidus sp.TKC株におけるThin Colony Expansion表現型の機構解明

    平野翔子, XIONG Zhiyu, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本微生物生態学会大会(Web)　37th　2024

  12. 非移動性の環境汚染物質分解細菌株が移動性細菌株により運ばれるヒッチハイク現象

    松添華子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  13. γ-HCH分解性Sphingobium属株と非分解性Cupriavidus属株のコミュニティ形成

    ZHIYU Xiong, 平野翔子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  14. 起源未解明の有機塩素系殺虫剤分解酵素遺伝子を乗せたICEの発見

    岡俊璃, 岸田康平, 大坪嘉行, 永田裕二

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  15. 環境汚染物質分解細菌に対するヘルパー効果の強化:新規な細胞間接着ツールの開発

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    手塚隆博, 加藤広海, 岸田康平, 大坪嘉行, 岸田なつみ, 永田裕二

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  17. Cupriavidus sp.TKC株のThin Colony Expansion表現型に関与する推定Histidine Kinase遺伝子の同定

    平野翔子, ZHIYU Xiong, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  18. 接合伝達を阻害するペプチド創薬のデザインとスクリーニング

    岸田康平, 熊谷連, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2023 (CD-ROM)　2023

  19. 原核生物における新しい可動遺伝因子グループSE(strand-biased circularizing integrative element)の発見

    矢野大和, 矢野大和, IDOLA Desmila, 森宙史, 永田裕二, 野中里佐

    日本遺伝学会大会プログラム・予稿集　95th (CD-ROM)　2023

  20. Temperature-Induced Reconstruction of Soil Microbial Networks

    YANG Dailin, AZUMA Toyohiro, KATO Hiromi, NAGATA Yuji, KONDOH Michio

    日本生態学会大会講演要旨(Web)　69th　2022

  21. Rewired Community Networks of Soil Microbiota Induced by Increased Temperature

    YANG Dailin, AZUMA Toyohiro, KATO Hiromi, NAGATA Yuji, KONDOH Michio

    日本生態学会大会講演要旨(Web)　68th　2021

  22. Analysis of Transcriptional activation involved in iron-sulfur cluster biogenesis operon in Burkholderia multivorans

    野々山翔太, 岸田康平, 酒井啓一郎, 永田裕二, 津田雅孝, 大坪嘉行

    日本農芸化学会大会講演要旨集(Web)　2021　2021

    ISSN： 2186-7976

  23. Analysis of Transcriptional activation involved in iron-sulfur cluster biogenesis operon in Burkholderia multivorans

    野々山翔太, 岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2020　2020

    ISSN： 2186-7976

  24. Discovery of non-conjugative integrative element moving as if an IS element: bacterial new transposon family

    DESMILA Idola, 森宙史, 永田裕二, 野中里佐, 矢野大和

    日本進化学会大会プログラム・講演要旨集(Web)　22nd　2020

  25. 微⽣物はなぜ群れを作るのか？平板培地実験進化系を⽤いたBQHの検証

    仁平賢, 山本 達也, 平野 彰大, 野村 暢彦, 永田 裕二, 矢野 大和

    日本微生物生態学会 第33回大会 プログラム集　2019/09/10

  26. 土壌細菌叢の液体培養系における遷移の動態解析

    東豊浩, 加藤広海, 長田穣, 永田裕二, 近藤倫生

    日本微生物生態学会大会(Web)　33rd　2019

  27. 生態学は生物群集デザインに活用できるか?

    近藤倫生, 東豊浩, 加藤広海, 川津一隆, 長田穣, 永田裕二

    日本生物工学会大会講演要旨集　71st　2019

  28. Mycobacterium sp.EPa45株におけるフェナントレン分解遺伝子群の転写解析

    市橋永吉, 小川なつみ, 加藤広海, 岸田康平, 野々山翔太, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　13th　2019

  29. プラスミドベクターpBBR1MCSの宿主域に関する研究

    岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　13th　2019

  30. Burkholderia属細菌における鉄硫黄クラスター生合成系の転写制御機構の解析

    野々山翔太, 岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2019　2019

    ISSN： 2186-7976

  31. PCB/ビフェニル分解資化遺伝子群を有すICEKKS1024677の水平伝播宿主域の解析

    川原昌太郎, 岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2019　2019

    ISSN： 2186-7976

  32. プラスミドベクターpBBR1MCSの広宿主域性に関する研究

    岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2019　2019

    ISSN： 2186-7976

  33. ナフタレン分解プラスミドNAH7のPartition systemが関与する接合伝達頻度上昇

    久土晃二, 岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　13th　2019

  34. フェナントレン分解Mycobacterium株の遺伝子破壊系構築とビフェニル分解への転写応答

    市橋永吉, 小川なつみ, 岸田康平, 加藤広海, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　12th　2018

  35. IncP-9群プラスミドNAH7の新規な接合伝達必須遺伝子の機能解明

    岸田康平, LUCAS Tim, 野々山翔太, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2018　2018

    ISSN： 2186-7976

  36. ナフタレン分解遺伝子有すプラスミドNAH7の新規接合伝達必須遺伝子の同定

    岸田康平, 野々山翔太, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会東北支部大会プログラム・講演要旨集　153rd　2018

  37. PCB/ビフェニル分解菌Acidovorax sp. KKS102株が有するICEの水平伝播域規定因子の同定

    川原昌太郎, 岸田康平, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　12th　2018

  38. ナフタレン分解プラスミドNAH7の接合伝達に必須な遺伝子セットの同定

    岸田康平, LUCAS Tim, 野々山翔太, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　12th　2018

  39. 難分解性芳香族化合物分解コンソーシアム由来の分解細菌Mycobacteirum sp.EPa45株における生育阻害機構

    小川なつみ, 加藤広海, 岸田康平, 市橋永吉, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2018　2018

    ISSN： 2186-7976

  40. 汚染物質分解コンソーシアムにおけるキープレイヤーとオーディエンス

    加藤広海, 小川なつみ, 津田雅孝, 永田裕二

    環境バイオテクノロジー学会誌　1　(1)　15-20　2018

  41. 接合伝達の鍵酵素relaxaseの金属イオンコファクターの違いによるnick導入塩基配列特異性の変化

    岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    日本ゲノム微生物学会年会要旨集　11th　2017

  42. IncP-9群プラスミドの接合伝達に関わる全遺伝子の同定

    岸田康平, LUKAS Tim, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2017　2017

    ISSN： 2186-7976

  43. Burkholderia multivoransの鉄硫黄クラスター生合成遺伝子群に対する転写因子Fur及びIscRの作用機序

    野々山翔太, 佐藤拓哉, 岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    日本ゲノム微生物学会年会要旨集　11th　2017

  44. IncP-9群プラスミドNAH7の新規接合伝達必須遺伝子の機能解析

    岸田康平, LUCAS Tim, 大坪嘉行, 永田裕二, 津田雅孝

    日本微生物生態学会大会(Web)　2017　2017

  45. 土壌細菌Burkholderia multivoransにおける鉄硫黄クラスター生合成系の転写制御機構の解析

    野々山翔太, 佐藤拓哉, 岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2017　2017

    ISSN： 2186-7976

  46. 土壤における細菌叢の形成・定着過程の長期モニタリング

    加藤広海, 渡来直生, 森宙史, 永田裕二, 黒川顕, 津田雅孝

    環境バイオテクノロジー学会大会プログラム講演要旨集　2016　45　2016/06/13

  47. 土壌微生物のノトバイオロジー

    加藤広海, 森宙史, 永山浩史, 大坪嘉行, 永田裕二, 黒川顕, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2016　4SY07‐3 (WEB ONLY)　2016/03/05

    ISSN： 2186-7976

  48. ナフタレン分解プラスミドNAH7の接合伝達関連機能未知遺伝子群traDEFの解析

    岸田康平, 井上慧, 大坪嘉行, 永田裕二, 津田雅孝

    日本ゲノム微生物学会年会要旨集　10th　2016

  49. Burkholderia multivoransにおける鉄硫黄クラスター合成遺伝子群の転写制御に対するFur及びIscRの作用機作

    野々山翔太, 佐藤拓哉, 岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    日本ゲノム微生物学会年会要旨集　10th　2016

  50. ナフタレン分解プラスミドNAH7の接合伝達関連遺伝子traDEFの解析

    岸田康平, 井上慧, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2016　2016

    ISSN： 2186-7976

  51. Burkholderia multivoransにおける鉄硫黄クラスター合成系遺伝子群の転写制御機構の解析

    野々山翔太, 佐藤拓哉, 岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2016　2016

    ISSN： 2186-7976

  52. ナフタレン分解プラスミドNAH7の接合伝達関連遺伝子の解析

    岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    環境バイオテクノロジー学会大会プログラム講演要旨集　2016　2016

  53. ハロアルカンデハロゲナーゼの細胞内酵素機能進化系の構築

    小山旺, 森内良太, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2016　2016

    ISSN： 2186-7976

  54. 汚染土壌細菌叢の新規環境への定着及び再汚染のメタゲノム解析

    加藤広海, 森宙史, 渡来直生, 永山浩史, 大坪嘉行, 永田裕二, 豊田敦, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　10th　91　2016

  55. 微生物群集動態の原理解明に向けた再現モデルの構築

    渡来直生, 森宙史, 加藤広海, 大坪嘉行, 小椋義俊, 永田裕二, 豊田敦, 藤山秋佐夫, 林哲也, 津田雅孝, 黒川顕

    日本ゲノム微生物学会年会要旨集　10th　90　2016

  56. 再構築された土壌微生物群集の超長期培養

    加藤広海, 渡来直生, 森宙史, 大坪嘉行, 永田裕二, 黒川顕, 黒川顕, 津田雅孝

    日本微生物生態学会大会(Web)　31st　55 (WEB ONLY)　2016

  57. Bacterial Glade with the ribosomal RNA operon on a small plasmid rather than the chromosome

    Mizue Anda, Yoshiyuki Ohtsubo, Takashi Okubo, Masayuki Sugawara, Yuji Nagata, Masataka Tsuda, Kiwamu Minamisawa, Hisayuki Mitsui

    GENES & GENETIC SYSTEMS　90　(6)　376-376　2015/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  58. Properties and biotechnological applications of natural and engineered haloalkane dehalogenases

    Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　99　(23)　9865-9881　2015/12

    DOI： 10.1007/s00253-015-6954-x 　

    ISSN： 0175-7598

    eISSN： 1432-0614

  59. ナフタレン分解プラスミドNAH7の接合伝達宿主域に関する研究

    岸田康平, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2015　2015

    ISSN： 2186-7976

  60. 移植された土壌微生物の定着過程と,その安定性について

    加藤広海, 森宙史, 丸山史人, 永山浩史, 大坪嘉行, 永田裕二, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　9th　2015

  61. Biodegradation of Organochlorine Pesticides

    Nagata Y, Tabata M, Ohtsubo, Y, Tsuda M

    Manual of Environmental Microbiology, 4th Edition　5.1.2-1　2015

    Publisher: ASM Press, Washington, DC

    DOI： 10.1128/9781555818821.ch5.1.2 　

  62. ナフタレン分解プラスミドNAH7のoriTの同定と宿主域の解析

    岸田康平, 井上慧, 宮崎亮, 大坪嘉行, 永田裕二, 津田雅孝

    日本ゲノム微生物学会年会要旨集　8th　2014

  63. IncP-9群NAH7のoriTの同定と接合伝達宿主域に関する研究

    岸田康平, 井上慧, 宮崎亮, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2014　2014

    ISSN： 2186-7976

  64. 土壌微生物の移植メタゲノム

    加藤広海, 森宙史, 丸山史人, 豊田敦, 永山浩史, 大坪嘉行, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　8th　2014

  65. O29-07 フェナントレン分解細菌と共存する非分解優占種細菌の機能解明(口頭発表)

    小川 なつみ, 加藤 広海, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　2014　113-113　2014

    Publisher: 日本微生物生態学会

  66. O11-03 土壌における微生物コミュニティの形成過程について(口頭発表)

    加藤 広海, 森 宙史, 丸山 史人, 永山 浩史, 大坪 嘉行, 永田 裕二, 黒川 顕, 津田 雅孝

    日本微生物生態学会講演要旨集　2014　78-78　2014

    Publisher: 日本微生物生態学会

  67. P15-5 土壌細菌での鉄応答制御因子Furを介した転写調節機構の解明(ポスター発表)

    佐藤 拓哉, 湯原 悟志, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　2014　156-156　2014

    Publisher: 日本微生物生態学会

  68. O33-02 rRNA遺伝子オペロンが9.4kbレプリコンにのみ存在する細菌ゲノムの発見(口頭発表)

    按田 瑞恵, 大坪 嘉行, 大久保 卓, 菅原 雅之, 三井 久幸, 永田 裕二, 津田 雅孝, 南澤 究

    日本微生物生態学会講演要旨集　2014　120-120　2014

    Publisher: 日本微生物生態学会

  69. O33-03 完全ゲノム配列比較に基づいた人為起源有機塩素系殺虫剤γ-HCH分解細菌の出現と進化の考察(口頭発表)

    永田 裕二, 田端 理朗, 大畑 智史, 荷川取 佑記, 大坪 嘉行, 津田 雅孝

    日本微生物生態学会講演要旨集　2014　120-120　2014

    Publisher: 日本微生物生態学会

  70. P22-15 芳香族化合物複合汚染土壌から培養非依存的手法で取得したインディゴ生成活性に関与するコスミドクローンの解析(ポスター発表)

    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

    日本微生物生態学会講演要旨集　2014　217-217　2014

    Publisher: 日本微生物生態学会

  71. P19-16 クラスター化した代謝酵素遺伝子群の導入による有機塩素系殺虫剤gamma-hexachlorocyclohexane資化能を有する新規細菌株の分子育種(ポスター発表)

    荷川取 佑記, 宮崎 亮, 古屋 佑磨, 大畑 智史, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　2014　194-194　2014

    Publisher: 日本微生物生態学会

  72. Appearance and evolution of γ-hexachlorocyclohexane-degrading bacteria

    Yuji Nagata, Michiro Tabata, Satoshi Ohhata, Masataka Tsuda

    Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve　19-41　2014/01/01

    Publisher: Springer Japan

    DOI： 10.1007/978-4-431-54520-0_2 　

  73. Strategies to reveal genomic function in natural soil systems

    Yoshiyuki Ohtsubo, Eri Nishiyama, Yoko Ishibashi, Yuji Nagata, Masataka Tsuda

    Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve　279-291　2014/01/01

    Publisher: Springer Japan

    DOI： 10.1007/978-4-431-54520-0_14 　

  74. IncP-9群プラスミドNAH7の接合伝達開始配列の解析

    岸田康平, 井上慧, 宮崎亮, 大坪嘉行, 永田裕二, 津田雅孝

    日本ゲノム微生物学会年会要旨集　7th　2013

  75. IncP-9群NAH7接合伝達系のoriTを中心とした解析

    岸田康平, 井上慧, 宮崎亮, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2013　2013

    ISSN： 2186-7976

  76. IncP-9群プラスミドNAH7のoriTの同定及び接合伝達関連遺伝子traFの解析

    岸田康平, 井上慧, 宮崎亮, 大坪嘉行, 永田裕二, 津田雅孝

    環境バイオテクノロジー学会大会プログラム講演要旨集　2013　2013

  77. 撹乱に対する土壌微生物のレジリエンス

    加藤広海, 森宙史, 丸山史人, 豊田敦, 堂園亜由美, 大坪嘉行, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　7th　2013

  78. 累積置換変異導入によるハロアルカンデハロゲナーゼLinBのbeta-HCH分解活性の機能進化に関する研究

    永田裕二, 森内良太, 田中裕興, 大坪嘉行, 津田雅孝

    環境バイオテクノロジー学会大会プログラム講演要旨集　2013　2013

  79. OE-005 土壌微生物の他土壌への移植メタゲノミクス(微生物群集構造,口頭発表)

    加藤 広海, 森 宙史, 丸山 史人, 豊田 敦, 大坪 嘉行, 永田 裕二, 藤山 秋佐夫, 黒川 顕, 津田 雅孝

    日本微生物生態学会講演要旨集　29th　(29)　85-85　2013

    Publisher: 日本微生物生態学会

  80. 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検索

    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

    Journal of Environmental Biotechnology　13　(1)　51-56　2013

  81. 芳香族化合物汚染土壌における経時的メタゲノムによって明らかになった土壌微生物の適応反応

    加藤広海, 森宙史, 豊田敦, 大坪嘉行, 丸山史人, 堂園亜由美, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2012　2012

    ISSN： 2186-7976

  82. 細菌由来のβ-ヘキサクロロシクロヘキサン(β-HCH)分解酵素遺伝子linB_MIを導入したカボチャ毛状根のβ-HCH分解能の解析

    七里吉彦, 並木小百合, 森内良太, 清家伸康, 大谷卓, 永田裕二, 津田雅孝, 田部井豊

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集　30th　2012

  83. Sphingobium sp.MI1205株由来のハロアルカンデハロゲナーゼLinB_MIにおけるbeta-HCH分解活性に重要なアミノ酸残基の同定

    森内良太, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2012　2012

    ISSN： 2186-7976

  84. ハロアルカンデハロゲナーセLinBのbeta-HCH分解活性に関する機能進化

    田中裕興, 森内良太, 大坪嘉行, 永田裕二, 津田雅孝

    日本生化学会大会(Web)　85th　2012

  85. Sphingobium sp.MI1205由来ハロアルカンデハロゲナーゼLinBの結晶構造解析

    岡井公彦, 大塚淳, IMAI Fabiana Lica, 間瀬朋子, 森内良太, 永田裕二, 永田宏次, 田之倉優

    日本農芸化学会大会講演要旨集(Web)　2012　2012

    ISSN： 2186-7976

  86. 2Hp08 Genomes and mobile genetic elements of gamma-HCH-degrading bacteria

    Nagata Yuji, Tabata Michiro, Ohhata Satoshi, Ohtsubo Yoshiyuki, Tsuda Masataka

    64　75-75　2012

    Publisher: 日本生物工学会

  87. 4Ca08 Functional analysis of various haloalkane dehalogenase genes derived from bacterial genomes

    Tanaka Hiroki, Ohtsubo Yoshiyuki, Nagata Yuji, Tsuda Masataka

    64　193-193　2012

    Publisher: 日本生物工学会

  88. 4Da02 Mechanism for the oligotrophic mutation of a gamma-HCH-degrading bacterial strain

    Hirano Joe, Ui Hiroki, Ohtsubo Yoshiyuki, Nagata Yuji, Tsuda Masataka

    64　202-202　2012

    Publisher: 日本生物工学会

  89. Sphingobium sp.MI1205株由来のハロアルカンデハロゲナーゼLinB_MIのbeta-HCH分解活性に重要なアミノ酸残基の同定

    森内良太, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集　2011　2011

  90. Sphingobium sp. MI1205株由来のハロアルカンデハロゲナーゼLinB_MI特異的なbeta-HCH分解活性に重要なアミノ酸残基の同定

    森内良太, 大坪嘉行, 永田裕二, 津田雅孝

    環境バイオテクノロジー学会大会プログラム講演要旨集　44th　2011

  91. 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

    佐藤優花里, 夏目亮, Zbynek Prokop, Jan Brezovsky, Radka Chaloupkova, Jiri Damborsky, 永田裕二, 千田俊哉

    日本結晶学会誌　53　(2)　124-129　2011

    Publisher: The Crystallographic Society of Japan

    DOI： 10.5940/jcrsj.53.124 　

    ISSN： 0369-4585

    More details Close

    Enzymes are widely used for the synthesis of pharmaceuticals, agrochemicals, and food additives because they can catalyze high enantioselective transformations. In order to construct selective enzymes by protein engineering, it is important to understand the molecular basis of enzyme-substrate interactions that contribute to enantioselectivity. The haloalkane dehalogenase DbjA showed high enantioselectivity for two racemic mixtures: α-bromoesters and β-bromoalkanes. Thermodynamic analysis, protein crystallography, and computer simulations indicated that DbjA carries two bases for the enantiodiscrimination of each racemic mixture. This study helps us understand the molecular basis of the enantioselectivity and opens up new possibilities for constructing enantiospecific biocatalysts through protein engineering.

  92. Organization and dynamism of gamma-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26 genome

    Yuji Nagata, Shunsuke Natsui, Yoshiyuki Ohtsubo, Natsuko Ichikawa, Akiho Ankai, Akio Oguchi

    JOURNAL OF BIOTECHNOLOGY　150　S46-S46　2010/11

    DOI： 10.1016/j.jbiotec.2010.08.127 　

    ISSN： 0168-1656

  93. Complete Nucleotide Sequence of TOL Plasmid pDK1 Provides Evidence for Evolutionary History of IncP-7 Catabolic Plasmids (vol 192, pg 4337, 2010)

    Hirokazu Yano, Masatoshi Miyakoshi, Kenshiro Ohshima, Michiro Tabata, Yuji Nagata, Masahira Hattori, Masataka Tsuda

    JOURNAL OF BACTERIOLOGY　192　(20)　5558-5558　2010/10

    DOI： 10.1128/JB.00971-10 　

    ISSN： 0021-9193

  94. ゲノム解析ソフトウェアGenomeMatcher

    大坪嘉行, 大坪和香子, 永田裕二, 津田雅孝

    化学と生物　48　(5)　313-319　2010/05

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/kagakutoseibutsu.48.313 　

    ISSN： 0453-073X

  95. 環境汚染物質分解細菌のメタゲノミクス

    永田裕二, 津田雅孝

    難培養微生物研究の最新技術II〜ゲノム解析を中心とした最前線と将来展望〜　2010/04

    Publisher: シーエムシー出版

  96. 脱ハロゲン酵素

    永田裕二, 津田雅孝

    酵素利用技術大系　939-948　2010/04

    Publisher: (株)エヌ・ティー・エス

  97. 0605 GenomeMatcher : GUI tool for genomic analysis

    Ohtsubo Yoshiyuki, Ohtsubo Wakako, Nagata Yuji, Tsuda Masataka

    バイオエンジニアリング講演会講演論文集　2009　(22)　90-90　2010/01/08

    Publisher: 一般社団法人日本機械学会

  98. 1C-12 Pattern and mechanism of fluctuation of soil metagenomes induced by contamination with aromatic hydrocarbons(Oral Session)

    KATO HIROMI, MORI HIROSHI, TOYODA ATUSHI, OHTSUBO YOSHIYUKI, MARUYAMA FUMITO, FUCHU GENKI, ENDO RYO, DOZONO AYUMI, MIYAKOSHI MASATOSHI, NAGATA YUJI, FUJIYAMA ASAO, KUROKAWA KEN, TSUDA MASAKATA

    (26)　81-81　2010

    Publisher: 日本微生物生態学会

  99. 1B-3 Oligotrophic mutants of a gamma-HCH-degrading bacterium Sphingobium japonicum UT26(Oral Session)

    UI HIROKI, SASAKI HIROSHI, TABATA MICHIRO, OHTSUBO YOSHIYUKI, NAGATA YUJI, TSUDA MASATAKA

    (26)　69-69　2010

    Publisher: 日本微生物生態学会

  100. 環境バイオテクノロジー学会シンポジウム「生態機能と環境保全」

    永田裕二

    微生物生態学会誌　25　(2)　77-78　2010

    Publisher: 日本微生物生態学会

    DOI： 10.20709/jsmeja.25.2_77 　

  101. 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

    加藤広海, 大坪嘉行, 永田裕二, 津田雅孝

    環境バイオテクノロジー学会誌　10　(2)　63-70　2010

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

  102. 特集「土壌環境での細菌の生き様を探る」によせて

    永田裕二

    日本生物工学会誌　87　(9)　418-418　2009/09

    Publisher: 日本生物工学会

    ISSN： 0919-3758

  103. 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

    大坪嘉行, 西山依里, 永田裕二, 津田雅孝

    日本生物工学会誌　87　(9)　434-436　2009/09

    Publisher: 日本生物工学会

    ISSN： 0919-3758

  104. 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

    永田裕二, 津田雅孝

    マリンメタゲノムの有効利用　166-178　2009/07

    Publisher: シーエムシー出版

  105. 芳香族化合物による土壌の汚染化に対する土壌細菌集団の応答

    遠藤諒, 府中玄樹, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集　2009　2009

  106. 1A-11 芳香族化合物による土壌撹乱に対する微生物反応のメタゲノム的解析(口頭発表)

    加藤 広海, 府中 玄樹, 遠藤 諒, 大坪 嘉行, 永田 裕二, 森 宙史, 丸山 史人, 豊田 敦, 黒川 顕, 藤山 秋佐夫, 津田 雅孝

    日本微生物生態学会講演要旨集　25th　(25)　6-6　2009

    Publisher: 日本微生物生態学会

  107. 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-

    大坪嘉行, 永田裕二, 津田雅孝

    化学と生物　47　(1)　35-42　2009/01

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/kagakutoseibutsu.47.35 　

    ISSN： 0453-073X

  108. 土壌環境での細菌の生き様を探る（2008年度日本生物工学会大会報告）

    永田裕二

    日本生物工学会誌　86　(11)　549　2008/11

  109. 難培養性細菌も研究対象とするメタゲノム解析

    永田裕二, 津田雅孝

    バイオフィルムの基礎と制御　103-111　2008/02

    Publisher: 株式会社エヌ・ティー・エス

  110. 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

    津田雅孝, 西山依里, 宮腰昌利, 湯原悟志, 永田裕二, 大坪嘉行

    土と微生物　62　(2)　93-97　2008/02

    Publisher: Japanese Society of Soil Microbiology

    DOI： 10.18946/jssm.62.2_93 　

    ISSN： 0912-2184

  111. 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

    津田雅孝, 西山依里, 宮越昌利, 永田裕二, 大坪嘉行

    日本土壌微生物学会講演要旨集　2008　2008

  112. 土壌環境での細菌の生き様を探る(第60回大会シンポジウム報告)

    永田 裕二

    生物工学会誌 : seibutsu-kogaku kaishi　86　(11)　549-549　2008

    Publisher: 日本生物工学会

    ISSN： 0919-3758

  113. 1S5p06 Molecular genetics for revealing lives of soil microorganisms

    Ohtsubo Yoshiyuki, Nishiyama Eri, Miyakoshi Masatoshi, Nagata Yuji, Tsuda Masataka

    20　55-55　2008

    Publisher: 日本生物工学会

  114. 土壌生態系での環境細菌ゲノム情報発現

    津田雅孝, 西山依里, 宮腰昌利, 永田裕二, 大坪嘉行

    極限環境微生物学会誌　6　59-62　2007/12

    DOI： 10.3118/jjse.6.59 　

  115. メタゲノム研究と環境バイオテクノロジー

    永田裕二

    日本生物工学会誌　85　(12)　535-536　2007/12

    Publisher: 日本生物工学会

    ISSN： 0919-3758

  116. 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

    津田雅孝, 小野玲, 宮崎亮, 府中玄樹, 永田裕二

    J. Environ. Biotechnol.　7　(2)　75-78　2007/12

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

  117. 土壌環境細菌の比較ゲノム

    津田雅孝, 永田裕二, 大坪嘉行

    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（細胞工学 別冊）　166-172　2007/10

  118. Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis

    Yuji Nagata, Ryo Endo, Michihiro Ito, Yoshiyuki Ohtsubo, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　76　(4)　741-752　2007/09

    DOI： 10.1007/s00253-007-1066-x 　

    ISSN： 0175-7598

  119. 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

    津田雅孝, 西山依里, 永田裕二, 大坪嘉行

    化学と生物　45　(8)　557-563　2007/08

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/kagakutoseibutsu1962.45.557 　

    ISSN： 0453-073X

  120. 学会見聞記２００７年日本農芸化学会大会

    小林厚志, 永田裕二, 大崎雄介, 白川仁, 仲川清隆, 日出間志寿

    バイオサイエンスとインダストリー　65　(7)　360-363　2007/07/01

    Publisher: （財）バイオインダストリー協会

    ISSN： 0914-8981

  121. 2007年度日本農芸化学会見聞記「環境科学」

    永田裕二

    バイオサイエンスとインダストリー　65　35-35　2007/07

  122. 環境DNA

    永田裕二

    日本生化学会誌　2007/06

  123. PB-96 Signature-tagged mutagenesis法によるBurkholderia multivorans ATCC17616株の土壌環境必須遺伝子の同定(追加,ポスターセッションB,ポスター発表)

    宮腰 昌利, 須藤 理絵, 西山 依里, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(23)　162-162　2007

    Publisher: 日本微生物生態学会

  124. S1-5 Isolation of genes for degradation of environmental pollutants from soil by cultivation-independent techniques(Symposium I Environmental Genomics in Microbial Ecology)

    Nagata Yuji, Ono Akira, Miyazaki Ryo, Fuchu Genki, Ohtsubo Yoshiyuki, Tsuda Masataka

    (23)　175-175　2007

    Publisher: 日本微生物生態学会

  125. PB-98 カイメン共在細菌メタゲノム由来のメタ開裂酵素遺伝子の取得と解析(追加,ポスターセッションB,ポスター発表)

    渡邊 洋平, 小野 玲, 横内 裕子, 竹山 春子, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(23)　163-163　2007

    Publisher: 日本微生物生態学会

  126. PA-31 有機塩素系殺虫剤gamma-HCHによる土壌の試験的汚染化に関する研究(農耕地生態系,ポスターセッションA,ポスター発表)

    府中 玄樹, 小野 玲, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(23)　92-92　2007

    Publisher: 日本微生物生態学会

  127. 3H09-3 Putative haloalkane dehalogenase genes from marine sponge metagenome

    ARAI Yasusuke, ITO Michihiro, YOKOUCHI Hiroko, TAKEYAMA Haruko, OHTSUBO Yoshiyuki, NAGATA Yuji, TUDA Masataka

    19　184-184　2007

    Publisher: 日本生物工学会

  128. 3H09-2 Research of gamma-HCH degradation genes from Sphingomonas sp. MM-1 which is from gamma-HCH contaminated soil in India

    Tabata Michiro, Endo Ryo, Ito Michihiro, Otsubo Yoshiyuki, Nagata Yuji, Tsuda Masataka

    19　184-184　2007

    Publisher: 日本生物工学会

  129. 2S1PM3 Isolation and characterization of functional genes for degradation of environmental pollutants from soil samples by cultivation-independent techniques

    TSUDA Masataka, ONO Akira, MIYAZAKI Ryo, FUCHU Genki, NAGATA Yuji

    19　10-10　2007

    Publisher: 日本生物工学会

  130. 2007年度日本農芸化学会大会（学会見聞記）

    小林厚志, 永田裕二, 大崎雄介, 白川仁, 仲川清隆, 日出間志寿

    バイオサイエンスとインダストリー　65　34-38　2007

  131. Structure-function relationships of haloalkane dehalogenases

    Journal of environmental biotechnology　6　(2)　87-92　2006/12

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

  132. 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

    小野玲, 宮崎亮, 永田裕二, 津田雅孝

    バイオインダストリー　23　(11)　44-49　2006/11/01

    Publisher: シーエムシー出版

    ISSN： 0910-6545

  133. ハロアルカンデハロゲナーゼの構造と機能

    永田裕二, 津田雅孝

    J. Environ. Biotechnol.　6　87-92　2006/11/01

  134. メタゲノムは宝の山か？

    永田裕二

    84　(2)　73-73　2006/02

    Publisher: 日本生物工学会

    ISSN： 0919-3758

  135. PB-17 Several amino acid residues differing among β-HCH dechlorinases have critical effects on their activity profiles toward HCH-related compounds(Bioremediation,Session B,(1)Poster Presentation)

    Ito Michihiro, Otsubo Yoshiyuki, Nagata Yuji, Tsuda Masataka

    (22)　135-135　2006

    Publisher: 日本微生物生態学会

  136. 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-

    永田裕二, 津田雅孝

    蛋白質核酸酵素　50　(12)　1511-1518　2005/10

    Publisher: 共立出版

    ISSN： 0039-9450

  137. B-09 Degradation of β-HCH by a newly isolated bacterium utilizing γ-HCH as a sole carbon and energy source(BIOREMEDIATION,(2) Oral presentation)

    Ito Michihiro, Otsubo Yoshiyuki, Nagata Yuji, Tsuda Masataka

    (21)　229-229　2005

    Publisher: 日本微生物生態学会

  138. 2B13-4 Isolation and characterization of a ABC-type transporter gene which is involved in the gamma-HCH degradation in Sphingomonas paucimobilis UT26

    ENDO Ryo, OHTSUBO Yoshiyuki, NAGATA Yuji, TSUDA Masataka

    17　86-86　2005

    Publisher: 日本生物工学会

  139. 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

    永田裕二, 津田雅孝

    化学と生物　43　(1)　33-42　2005/01

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/kagakutoseibutsu1962.43.33 　

    ISSN： 0453-073X

  140. Strategies for bioremediation of polychlorinated biphenyls

    Y Ohtsubo, T Kudo, M Tsuda, Y Nagata

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　65　(3)　250-258　2004/08

    DOI： 10.1007/s00253-004-1654-y 　

    ISSN： 0175-7598

  141. 環境細菌ゲノムと環境DNA

    津田雅孝, 小松春伸, 大坪嘉行, 永田裕二

    J. Environ. Biotechnol.　3　(2)　69-78　2004/06

  142. B-10 可動性遺伝因子を利用して土壌環境から取得したナフタレン分解酵素遺伝子の解析(遺伝子伝播,口頭発表)

    宮崎 亮, 小野 玲, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(20)　172-172　2004

    Publisher: 日本微生物生態学会

  143. C-39 γ-Hexachlorocyclohexane(γ-HCH)分解菌におけるγ-HCH分解中間代謝産物による生育阻害効果(バイオレメディエーション,口頭発表)

    遠藤 諒, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(20)　241-241　2004

    Publisher: 日本微生物生態学会

  144. S1-2 環境浄化能を司る遺伝子を担う細菌可動遺伝因子のダイナミズム(シンポジウム1 遺伝情報の再編成・水平伝播と環境適応・進化)

    津田 雅孝, 永田 裕二, 大坪 嘉行, 曽田 匡洋

    日本微生物生態学会講演要旨集　(20)　244-244　2004

    Publisher: 日本微生物生態学会

  145. C-38 汚染土壌からのγ-HCH分解酵素遺伝子の取得と解析(バイオレメディエーション,口頭発表)

    伊藤 通浩, 小野 玲, 宮崎 亮, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(20)　240-240　2004

    Publisher: 日本微生物生態学会

  146. 2E15-3 Structure-function relationship of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110

    SATO Yukari, IKEDA Wakako, OHTSUBO Yoshiyuki, NAGATA Yuji, DAMBORSKY JIRI, MINAMISAWA Kiwamu, TSUDA Masataka

    16　171-171　2004

    Publisher: 日本生物工学会

  147. 27-B-12 土壌環境遺伝子資源からの新規脱塩素酵素遺伝子の取得と解析(バイオレメディエーション,一般講演)

    伊藤 通浩, 小野 玲, 源河 浩之, 大坪 嘉行, 永田 裕二, 津田 雅孝

    日本微生物生態学会講演要旨集　(19)　47-47　2003

    Publisher: 日本微生物生態学会

  148. Isolation and characterization of a maleylacetate reductase gene which is involved in the gamma-HCH degradation in Sphingomonas paucimobilis UT26

    Endo Ryo, Nagata Yuji, Tsuda Masataka

    15　202-202　2003

    Publisher: 日本生物工学会

  149. Characterization of haloalkane dehalogenase from Rhizobia

    Sato Yukari, Ikeda Wakako, Nagata Yuji, Minamisawa Kiwamu, Tsuda Masataka

    15　201-201　2003

    Publisher: 日本生物工学会

  150. 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

    永田裕二

    J. Environ. Biotechnol.　2　(1)　25-38　2002/06

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

  151. スフィンゴモナス属細菌の残留性農薬分解系と汚染土壌浄化への応用

    永田裕二, 宮内啓介, 今井亮三, 津田雅孝

    日本農芸化学会大会講演要旨集　2002　362　2002/03/05

  152. 918 Isolation of novel genes for degradation of aromatic hydrocarbon from Soil

    Ono akira, Genka Hiroyuki, Ishii Hidenori, Nagata Yuji, Tsuda Masataka

    14　169-169　2002

    Publisher: 日本生物工学会

  153. 814 Characterization of a haloalkane dehalogenase from Bradyrhizobium japonicum

    Sato Yukari, Nagata Yuji, Minamisawa Kiwamu, Tsuda Masataka

    14　146-146　2002

    Publisher: 日本生物工学会

  154. 遺伝子操作土壌細菌を利用したPCB分解技術の開発

    大坪嘉行, 永田裕二

    エコインダストリー　6　(10)　44-53　2001/10

    Publisher: シ-エムシ-

    ISSN： 1342-3037

  155. 残留性農薬の分解系酵素遺伝子群とその動態

    永田裕二

    遺伝情報のダイナミズムとその分子機構 IGEシリーズ　29　3-16　2001/06

  156. 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 -

    永田裕二

    化学と生物　38　214-216　2000/04

  157. 環境を汚染する有機塩素系農薬γ-HCHの微生物代謝系の解明

    永田 裕二

    日本農芸化学会誌　74　434-437　2000/03/05

    Publisher: 日本農芸化学会

    ISSN： 0002-1407

  158. Study on microbial degradation of organochlorine pesticide, γ-hexachlorocyclohexane, which causes environmental pollution

    Yuji Nagata

    Nippon Nogeikagaku Kaishi　74　(11)　1247-1257　2000

    Publisher: Japan Society for Bioscience Biotechnology and Agrochemistry

    DOI： 10.1271/nogeikagaku1924.74.1247 　

    ISSN： 0002-1407

  159. Complete analysis of genes and enzymes for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26

    Y. Nagata, K. Miyauchi, M. Takagi

    Journal of Industrial Microbiology and Biotechnology　23　(4-5)　380-390　1999

    Publisher: Nature Publishing Group

    DOI： 10.1038/sj.jim.2900736 　

    ISSN： 1367-5435

  160. 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−

    永田裕二, 金原和秀, 高木正道

    現代化学　(323)　46-52　1998/02

    Publisher: 東京化学同人

    ISSN： 0386-961X

  161. Characterrization and utilization of microbiol genes involved in metabolism of environmental compounds

    TAKAGI Masamichi, NAGATA Yuji, HORIUCHI Hiroyuki

    Bioscience & industry　55　(12)　11-16　1997/12/01

    Publisher: バイオインダストリ-協会

    ISSN： 0914-8981

  162. 地球環境中の有機化合物の代謝・循環に関与する微生物から得た有用遺伝子の解析と利用

    高木正道, 永田裕二, 堀内裕之

    バイオサイエンスとインダストリー　55　839-844　1997/06

  163. Function of a linD gene product involved in the degradation of 2,5-dichlorohydroquinone in Sphingomonas paucimobilis UT26.

    宮内啓介, 永田裕二, 高木正道

    日本生物工学会大会講演要旨集　1996　119-119　1996

    Publisher: 日本生物工学会

  164. Degradation pathway of 2-chlorohydroquinone in .GAMMA.-HCH degrader, Sphingomonas paucimobilis UT26.

    永田裕二, 宮内啓介, 高木正道

    日本生物工学会大会講演要旨集　1996　119-119　1996

    Publisher: 日本生物工学会

  165. Analysis of the insecticide .GAMMA.-HCH decomposition involving gene cluster of Sphingomonas paucimobilis and consideration of the acquisition process.

    永田裕二, 宮内啓介, 高木正道

    日本微生物生態学会講演要旨集　11th　97　1995/11

  166. Sphingomonas paucimobilisのγ-HCH分解代謝系酵素群の細胞内局在性の解析 : 微生物

    二村 晶子, 永田 裕二, 宮内 啓介, 高木 正道

    日本農藝化學會誌　69　61-61　1995/07/05

    Publisher: 社団法人日本農芸化学会

    ISSN： 0002-1407

  167. Purification and characterization of dehalogenasae (LinB) involved in the degradation of .GAMMA.-hexachlorocyclohexane in Sphingomonas paucimobilis.

    永田裕二, 宮内啓介, 高木正道

    日本生物工学会大会講演要旨集　1995　223-223　1995

    Publisher: 日本生物工学会

  168. Cloning and Sequencing of a gene involved in the degradation of 2,5-dichlorohydroquinone in Sphingomonas paucimobilis.

    宮内啓介, 永田裕二, 高木正道

    日本生物工学会大会講演要旨集　1995　222-222　1995

    Publisher: 日本生物工学会

  169. Sphingomonas (旧名 Pseudomonas) paucimobilis の殺虫剤 γ-hexachlorocyclohexane (HCH, BHC, lindane) 分解代謝系

    永田裕二

    Pseudomonas 研究会会誌　(3)　18-22　1994/06

  170. Pseudomonas paucimobilisのγ‐BHC分解に関与するdehydrogenase遺伝子の単離と構造解析

    永田裕二, 宮内啓介, 大友量, 高木正道

    日本農芸化学会誌　68　(3)　468　1994/03

    ISSN： 0002-1407

  171. Sequence analysis of transcriptional regulation factor of bph genes in Pseudomonas sp. strain KKS102.

    Kikuchi Yutaka, Miyauchi Keisuke, Koana Takao, Takagi Masamichi

    6　202-202　1994

    Publisher: 日本生物工学会

  172. Isolation and characterization of Tn5-induced mutants of Sphingomonas paucimobilis defective in 2,5-dichlorohydroquinone degradation.

    永田裕二, 宮内啓介, 二村晶子, 高木正道

    日本生物工学会大会講演要旨集　1994　201-201　1994

    Publisher: 日本生物工学会

  173. Cloning and Sequencing of the Genes for γ-BHC Degradation in Pseudomonas paucimobilis

    Nagata Yuji, Ohtomo Ryo, Nariya Tomoki, Fukuda Masao, Yano Keiji, Takagi Msamichi

    日本生物工学会大会講演要旨集　4　23-23　1992

    Publisher: 日本生物工学会

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Books and Other Publications 13

  1. DNA Traffic in the Environment

    Nagata Y, Kato H, Ohtsubo, Y, Tsuda M

    Springer　2019/02

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    Mobile genetic elements involved in the evolution of bacteria that degrade recalcitrant xenobiotic compounds

  2. 酵素利用技術体系

    永田裕二, 津田雅孝

    エヌ・ティー・エス　2010/04/16

  3. 難培養性微生物研究の最新技術II

    永田裕二, 津田雅孝

    シーエムシー出版　2010/04/09

  4. マリンメタゲノムの有効利用

    永田裕二, 津田雅孝

    シーエムシー出版　2009/07/24

  5. バイオフィルムの基礎と制御

    永田裕二, 津田雅孝

    株式会社エヌ・ティー・エス　2008/02/04

  6. 農芸化学の事典

    鈴木昭憲, 荒井綜一編集

    朝倉書店　2003/10

  7. 人に役立つ微生物のはなし（くらしの中の化学と生物８）

    永田裕二, 遠藤銀朗

    学会出版センター　2002/12

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    微生物による環境修復・環境浄化

  8. バイオテクノロジーの流れ-過去から未来へ-

    斉藤日向, 太田隆久, 高木正道

    1996/06

  9. バイオレメディエーションの実際技術

    永田裕二, 高木正道

    シーエムシー, 東京　1996/06

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    微生物による農薬分解技術

  10. Molecular Biology of Pseudomonads

    Nagata, Y, M. Fukuda, K. Miyauchi, M. Takagi

    American Society for Microbiology, Washington, DC　1996/06

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    Genes and Enzymes for γ-Hexachlorocyclohexane Degradation in Sphingomonas paucimobilis UT26

  11. 新遺伝子操作の基礎技術

    太田美智男

    1996/03

  12. 地球を守る小さな生き物たち

    永田裕二

    技報堂出版　1995/06

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    農薬(BHC)を分解する細菌

  13. Pseudomonas；molecular biology and biotechnology

    Imai, R, Y. Nagata, M. Fukuda, K. Yano, M. Takagi

    American Society for Microbiology, Washington, DC　1992/06

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    Isolation and characterization of a dehydrochlorinase gene for the degradation of γ-hexachlorocyclohexane in Pseudomonas paucimobilis

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Presentations 11

  1. 従属栄養細菌の極貧栄養環境での CO 2依存的な増殖現象 Invited

    永田裕二

    日本農芸化学会2021年度大会シンポジウム「細菌の低栄養環境に対する増殖を伴う適応機構」　2021/03/21

  2. 細菌の進化機構の理解と環境浄化への応用 Invited

    永田裕二

    社会にインパクトある研究F-1「生命の奇跡のプロセスに学ぶイノベーション」キックオフシンポジウム　2019/12/22

  3. 環境浄化で活躍する微生物 Invited

    永田裕二

    Visionary 農芸化学100シンポジウム・「微生物と私たちの健康・暮らし・環境 〜世界に誇る日本の微生物研究〜」　2018/12/15

  4. HCH脱塩素反応を触媒するハロアルカンデハロゲナーゼの多様性とバイオレメディエーションへの応用 Invited

    永田 裕二

    第36回農薬環境科学研究会　2018/11/08

  5. 人為起源環境汚染物質分解微生物から進化に迫る Invited

    永田 裕二

    東北大学大学院生命科学研究科改組記念講演会　2018/07/04

  6. 高度難分解性環境汚染物質分解細菌から微生物進化を探る Invited

    永田 裕二

    日本農芸化学会大会シンポジウム「微生物の多様性ーIFO寄付講座10年の歩み」　2018/03/18

  7. Evolution of Bacteria Degrading Highly Recalcitrant Environmental Pollutants Invited

    NAGATA Yuji

    Special seminar at University of Hyderabad　2018/02/20

  8. 環境汚染物質を食べる細菌から微生物進化を探る〜細菌の進化機構の解明と微生物機能開発への応用〜 Invited

    永田 裕二

    日本農芸化学会東北支部シンポジウム「多様な広がりで魅せる微生物研究」　2017/06/24

  9. 人為起源物質分解細菌の進化と微生物機能開発 Invited

    永田 裕二

    東北大学大学院生命科学研究科「微生物進化機能開発」寄附講座開設記念シンポジウム　2016/11/24

  10. Haloalkane dehalogenases in bacteria International-presentation Invited

    NAGATA Yuji

    Pacifichem 2015「Enzymes Essential to Biosphere Health: Bioremediation and Biogeochemical Cycling」　2015/12/19

  11. 環境を汚染する難分解性農薬分解遺伝子群の水平伝播 Invited

    永田 裕二

    日本微生物生態学会第30回大会シンポジウム「環境での遺伝子リスクの醸成：薬剤耐性と病原性の遺伝子伝播」　2015/10/20

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Industrial Property Rights 1

  1. ハロアルカンデハロゲナーゼを使用するイペリットの解毒方法

    プロコプ, ズビーネク, ダンボルスキー, ジリー、オプルスティル, フランティシェク、イェセンスカー, アンドレア、ナガタ, ユウジ

    特許第4793947号

    Property Type: Patent

Research Projects 38

  1. Study on biodegradation of polychlorinated biphenyls Competitive

    1991/06 - Present

  2. Study on Biodegradation of γ-hexachlorocyclohexane Competitive

    1991/06 - Present

  3. 土壌微生物機能発揮の鍵となる群集・メタゲノム構造の特定

    近藤 倫生, 川津 一隆, 永田 裕二, 大坪 嘉行, 加藤 広海

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 学術変革領域研究(A)

    Institution: 東北大学

    2021/09/10 - 2026/03/31

  4. Development of efficient utilization system of unexplored genetic resources using gene acquisition ability of bacteria

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Research (Exploratory)

    Institution: Tohoku University

    2024/06 - 2026/03

  5. Advanced utilization strategies of beneficial bacteria based on the survival and growth mechanisms of bacteria under poor conditions

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2022/04/01 - 2025/03/31

  6. Advanced utilization strategies of beneficial bacteria based on the survival and growth mechanisms of bacteria under poor conditions

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2022/04/01 - 2025/03/31

  7. Approach to the substance of bacterial extracellular genetic information storage device

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory)

    Category: Grant-in-Aid for Challenging Research (Exploratory)

    Institution: Tohoku University

    2022/06/30 - 2024/03/31

  8. Development of practical use of useful bacteria by understanding their behavior in the environment

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2019/04/01 - 2022/03/31

  9. Soil-derived bacterial consortium capable of degrading chemical pollutant: interaction between pollutant-degrader and co-residing non-degraders

    Tsuda Masataka

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2017/04/01 - 2020/03/31

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    Our previous study has indicated that (i) growth of some environmental bacterial strains capable of degrading phenanthrene (a representative chemical pollutant) is drastically inhibited by this compound, and (ii) such inhibition is significantly suppressed by the co-residence of various phenanthrene-non-degrading bacterial strains. Our present comprehensive analysis of such growth inhibition and its suppression phenomena revealed their details and the mechanisms that govern each phenomenon, consequently providing a novel type of interaction between different bacterial species.

  10. Behavior of environmental bacteria in microbial community and oligotrophic growth state

    Nagata Yuji, KATO HIROMI

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2016/04/01 - 2018/03/31

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    We studied on behavior of environmental bacteria in microbial community and oligotrophic growth state by using a bacteria degrading recalcitrant organochlorine insecticide and a microbial community from which the bacterial strain was isolated as models. We showed (i) the importance of non-degrading bacterial strains in the community and (ii) the generality of the phenomenon that environmental bacteria can grow on the solid minimal salt medium without addition of any carbon source accompanying CO2 fixation by expression of the alcohol dehydrogenase gene, and obtained a lot of knowledge leading to the elucidation of the mechanisms of these phenomena. A theoretical foundation for the practical application of bacteria in real environments has been established.

  11. Studies on metabolic pathway involved in oligotrophic growth of heterotrophic bacteria

    Nagata Yuji, TSUDA MASATAKA, OHTSUBO YOSHIYUKI

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2014/04/01 - 2016/03/31

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    An aerobic and heterotrophic bacterium Sphingobium japonicum UT26 shows oligotrophic growth phenotype, i.e., growth on minimal salt medium without the supply of any carbon source accompanying with the CO2-fixation, by the over expression of the adhX gene. Protein product of adhX showed alcohol dehydrogenase activity, and its activity had equilateral correlation with the oligotrophic phenotype. Furthermore, it was strongly suggested that the adhX-dependent oligotrophic phenotype is one of the bacterial fundamental mechanisms for adaptation to oligotrophic conditions.

  12. Behavior of microbial community in the environment polluted by aromatic compound

    Tsuda Masataka, KUROKAWA Ken, NAGATA Yuji, OHTSUBO Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2013/04/01 - 2016/03/31

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    Environmental microbial communities play very important roles in the bioremediation of chemical pollutants. Analysis of a phenanthrene-degrading bacterial consortium in this study showed that such degradation ability of a strain is enhanced by other co-residing and non-degrading strains through two types of mechanisms. Furthermore, transplantation of bacterial community to independent and sterilized environmental samples resulted in very similar time-course changes in the community compositions, indicating the validity of such transplantation to obtain reproducible information on bacterial degradation of chemical pollutants in natural environments.

  13. Mechanisms for acquiring ability to degrade novel compounds in sphingomonads and their applications

    Nagata Yuji, TSUDA MASATAKA, OHTSUBO YOSHIYUKI, Jiri Damborsky, Zbynek Prokop, TANOKURA MASARU, OKAI MASAHIKO

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2013/04/01 - 2016/03/31

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    Studies on degradation of a recalcitrant environmental pollutant, gamma-hexachlorocyclohexane, in sphingomonads revealed that (i) activity of a key enzyme was improved in stepwise manner by the accumulation of single mutations, (ii) sphingomands-specific plasmids and an insertion sequence play significant roles to acquire novel genes, (iii) sphingomonads have genetic background suitable for the degradation of recalcitrant compounds. These important knowledges for the functional evolution of bacteria in the environment can be used for the practical applications in the future.

  14. Studies on oligotrophic mutants of an aerobic heterotrophic bacterium

    NAGATA Yuji, TSUDA Masataka, OHTSUBO Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2012/04/01 - 2014/03/31

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    An aerobic and heterotrophic bacterium Sphingobium japonicum UT26 shows oligotrophic growth phenotype, i.e., growth on minimal salt medium without the supply of any carbon source, by the over expression of the adhX gene. Transposon mutagenesis toward the UT26 variant over-expressing the adhX gene and the subsequent analysis of the mutants demonstrated that the putative acetyl-CoA synthetase, pyruvate/phosphate dikinase, and isocitrate lyase genes are necessary for the oligotrophic phenotype. By combining with the genome information of UT26, it was strongly suggested that glyoxylate cycle accompanying with the CO2-fixation process catalyzed by phosphoenolpyruvate carboxylase is involved in the oligotrophic phenotype of the UT26 variant.

  15. Bacterial genetic determinants that control horizontal transfer of genes for degradation of environmental pollutants

    TSUDA Masataka, NAGATA Yuji

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2011 - 2012

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    Conjugative transfer of bacterial plasmids plays an important role in rapid adaptation and evolution of host cells. However, the factors governing the host range of transfer, i.e., limited transfer to specific recipient strains within a species, remain unclear. In this study, such factors were investigated using the two plasmids encoding the traits for degradation of environmental pollutants, and the mating pair-formation in the conjugation process and a regulatory system for various metabolisms in the recipient cells were found to be involved in restricting the conjugative transfer of the plasmids.

  16. Response of soil microbial community to exposure of environmental pollutants

    TSUDA Masataka, KUROKAWA Ken, NAGATA Yuji, OHTSUBO Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2010 - 2012

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    Soil microbial communities play very important role in the bioremediation of chemical pollutants. To investigate how such a community responded to and degrade the pollutants, time series analysis of the community in an artificially polluted and closed soil system was carried out by metagenomic sequencing of the community in conjunction with the isolation and characterization of the genes and bacterial strains able to degrade the pollutants. Our analysis strongly suggested the crucial catabolic genes and their host genera involved in the bioremediation in the polluted soil.

  17. Studies on molecular mechanisms for functional evolution of bacteria in the environment

    NAGATA Yuji, TSUDA Masataka, OHTSUBO Yoshiyuki, DAMBORSKY Jiri, SENDA Toshiya, TANOKURA Masaru

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2010 - 2012

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    To get insights into the functional evolution of bacteria in the environment, bacteria, which degrade man-made chlorinated pesticide γ-HCH, and dehalogenases, which are key enzymes for the degradation of chlorinated compounds, were analyzed in detail. (1) structure-function relationships of some dehalogenases were revealed and their evolution process was suggested, (2) the process of appearance and evolution of γ-HCH-degrading bacteria was proposed on the basis of the structure and function of their genomes and mobile genetic elements, and (3) the system for verifying evolution process of bacteria in the environment was constructed.

  18. Genomic organization and genomic dynamism of versatile sphingomonads

    NAGATA Yuji, TSUDA Masataka, OHTSUBO Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2010 - 2011

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    gamma-Hexachlorocyclohexane (gamma-HCH)is a completely man-made chlorinated pesticide that has caused serious environmental problems due to its toxicity and long persistence in upland soils. In our previous study, the complete genome sequence of an archetypal gamma-HCH-degrading strain, Sphingobium japonicum UT26, was determined. The ‘specific' lin genes (linA to linE)for the conversion of gamma-HCH to maleylacetate are dispersed on chromosome 1 (linA, linB, and linC)and a plasmid pCHQ1 (linD and linE)in the UT26 genome. IS6100 is often found in close proximity to the ‘specific' lin genes not only in UT26 but also in other gamma-HCH-degrading strains. To get more insights into the appearance and evolution of gamma-HCH-degrading bacteria, the draft genome sequences of three other such strains, Sphingomonas sp. MM-1, Sphingobium sp. TKS, and Sphingobium sp. MI1205 (5), which were isolated at geographically different area with one another, were determined and compared with the complete genome sequences of UT26 and other closely related but non-gamma-HCH-degrading sphingomonad strains. All the former three gamma-HCH-degrading strains also have the ‘specific' lin genes, but the location of such genes on their genomes are different from that on UT26, and for example, MM-1 carries such genes on three plasmids. Furthermore, genome contents and organizations of the four gamma-HCH-degraders are different with one another. These results suggested that these degraders had been created independently by lateral gene transfer of the ‘specific' lin genes. Analysis of flanking regions of 13 copies of IS6100 in UT26 suggested the DNA exchanges between chromosome and plasmids via the IS6100 transposition. Our use of sacB-based IS entrapment technique indeed revealed the transposability of endogenous IS6100 in UT26. These results strongly suggested that IS6100 plays important roles in the dissemination of the ‘specific' lin genes among gamma-HCH-degrading bacteria as well as in their genome rearrangements

  19. 培養非依存的手法を用いた自然生態系からの新規プラスミドの取得とその多様性の解明

    津田 雅孝, 永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 挑戦的萌芽研究

    Institution: 東北大学

    2008 - 2009

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    細菌由来の多種多様な生物機能を支配するプラスミドは、水平伝播能を備えることから、宿主細胞の広範で迅速な環境適応能獲得と進化に極めて大きく貢献する。しかし、未だ培養困難な細菌群が大多数を占める実際の自然生態系に存在するプラスミドに関する系統立てた包括的解析は皆無である。本研究では、宿主細胞の培養を割愛した手法を駆使して、自然生態系から様々な機能を担うプラスミドを網羅的に取得・解析し、また、当該生態系での取得プラスミドの挙動を解析することで、細菌におけるプラスミドの生物学的重要性を包括的に提示することを目的としている。当該年度には、昨年度に宿主細胞の培養を割愛した手法で取得した200kbの多環芳香族化合物分解プラスミドの更なる解析を行い、取得したプラスミドは大腸菌でも複製・維持可能なIncP-9不和合性群伝達性プラスミドであることを明示した。一方、環境汚染物質である複数石油主要成分芳香族系化合物で人工的に汚染化した土壌から経時的に調製したメタゲノムDNA試料の塩基配列を、第2世代シーケンサーを用いて大規模解読した。この結果、汚染物質が効率よく分解されていた時期由来のメタゲノム内には分解酵素遺伝子を担うことが知られていたプラスミド群の複製・分裂装置の遺伝子群と相同性を示す塩基配列の数が、分解酵素遺伝子の数とともに、上昇していた。従って、プラスミド支配の分解酵素遺伝子が汚染物質分解に対して重要な役割を果たしていたことが強く示唆された。

  20. 挿入配列の土壌環境での動態の解明と新規遺伝子獲得への応用

    永田 裕二, 津田 雅孝, 大坪 嘉行

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 萌芽研究

    Institution: 東北大学

    2007 - 2008

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    環境細菌は、変動しやすい様々な環境に適応し生存するために、複雑な遺伝子発現調節機構に加えて、水平伝播による遺伝子の外部からの獲得やゲノム構造の再編成など、よりダイナミックな遺伝子構造の変化を伴う環境適応機構を有していると考えられる。本研究では、難分解性環境汚染物質分解酵素遺伝子の周辺領域に高頻度で検出される可動性のISに注目することにより、(1) これらISの自然環境での分布と動態の把握、(2) 自然環境での機能的遺伝子カセット創出のメカニズムの解明、(3) ISを利用した新規遺伝子取得方法の確立を達成目標とする。前年度までに、有機塩素系農薬gamma-HCH汚染土壌から直接抽出したDNAを鋳型とし、PCRで増幅した2コピーのIS6100で挟まれた領域に高頻度でgamma-HCH分解に関与するlin遺伝子群が存在することを明らかにし、その成果を国際学術誌に発表した。さらに、(i) IS6100は、gamma-HCH汚染土壌由来DNAからはPCRで検出されるが、各種非汚染土壌からは検出されないこと、(ii) PCRでIS6100が検出されない非汚染土壌をgamma-HCHで人工的に汚染させた場合に、IS6100が検出されるようになること、(iii) 同非汚染土壌を各種芳香族化合物で人工的に汚染させた場合には、IS6100が検出されるようにはならないこと、を確認し、土壌環境微生物中で、gamma-HCH汚染特異的にIS6100の増幅が認められることを明らかにした。また、(i) 汚染化土壌中で、2コピーのIS6100で挟まれた領域の塩基配列が汚染化後の日数によって変化し、IS6100が汚染化により動的挙動を示していること、(ii) 汚染化土壌には既知のlin遺伝子群を有さない微弱なgamma-HCH分解菌が出現しているらしいこと、が明らかとなった。

  21. Horizontal transfer of bacterial genes for degradation of environmental pollutants

    TSUDA Masataka, NAGATA Yuji, OHTSUBO Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2006 - 2008

  22. Comprehensive development of bacterial ability for the degradation ofchlorinated environmental pollutants using unexplored genetic sources

    NAGATA Yuji, TSUDA Masataka, OHTSUBO Yoshiyuki, JIRI Damborsky, SENDA Toshiya, TANOKURA Masaru, TAKEYAM Haaruko

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2006 - 2008

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

    NAGATA Yuji, TSUDA Masataka

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2004 - 2005

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    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.

  24. セパシア菌ゲノムの構造と多様化・進化に関する研究

    津田 雅孝, 永田 裕二, 澤田 宏之

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 東北大学

    2004 - 2004

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    ヒトや動植物への病原性、植物病原菌駆除能、環境汚染物質も含む多様な有機化合物資化能をもつセパシア菌ATCC17616株では、ゲノムが3.4Mb,2.5Mb,0.9Mbの3種環状染色体から構成され、生育環境変動により各染色体が大規模な再編成を示す結果、新規形質を容易に獲得する。各染色体の構成原理と構造的動態、そして多様化と染色体進化を司る分子機構の実験的提示をめざし、以下の成果を得た。 1.本株ゲノムのrandom shotgunシーケンシングを約10万リード、冗長度8倍で実施し、53のメージャーコンティグを得た。この中に、基本的生命活動に必須な多くの遺伝子とともに、動植物に対する病原因子の遺伝子、炭素源となりうる各種芳香族化合物分解遺伝子等を見出した。 2.2.5Mbと0.9Mb染色体の複製・分配関連遺伝子領域は、いずれもプラスミド型のrepA-parB-parAという遺伝子構造を持っていた。repA上流とparA下流には、それぞれ各染色体の複製起点並びに分配にシスに働くと想定される特徴的な繰り返し配列が存在していた。 3.高鉄濃度で活性型になる鉄レギュロンの統括的制御因子Furの突然変異体では、活性酸素種への感受性増大の他、最低16種の多様な化合物の分解資化能の消失、活性窒素である亜硝酸イオンへの嫌気条件での感受性の増大を見出した。一方、高鉄濃度で転写量が増大する2種の炭素源分解遺伝子を見出した。また、上記のコンティグのin silico解析から、Furが結合する塩基配列がゲノム上に最低29コピー存在することが示唆された。 4.近隣細菌株由来でカタボライト抑制を受けるビフェニル分解遺伝子プロモーターを用いることで、本ATCC17616株にはガラクトースやブドウ糖によるカタボライト抑制が存在し、本抑制には2成分シグナル伝達系が関与することが示唆された。

  25. 全ゲノム塩基配列情報に基づく根粒菌の共生機構の解明

    南澤 究, 横山 正, 田島 茂行, 佐伯 和彦, 永田 裕二, 大和田 琢二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 東北大学

    2003 - 2003

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    本調査の目的は、根粒菌とマメ科植物の共生機構および生態を根粒菌ポストゲノム解析により明らかにする総合的な戦略を練り、食糧生産および環境保全に資する共生科学を創成することにある。8月12-13日に仙台において、ワークショップ「根粒菌のポストゲノム研究の展開」を開催し、数回の打合せ行い、以下のような項目について調査を行った。 1)モデルマメ科植物分子遺伝解析に対応したミヤコグサ根粒菌の戦略の検討:根粒菌の遺伝子が宿主植物側の共生受容系や防御応答系とどのような相互作用を通じて共生成立に至るのかという点を、モデルマメ科植物ミヤコグサの分子遺伝解析タイアップしながら進行させる必要がある。既に共同研究として論文発表した網羅的な遺伝子発現解析・破壊株の共生特性の解析以外に、CalcofluorやTn-phoA変異などの根粒菌の細胞膜構造、分泌タンパク、多糖生産の変異株が、相互作用機構解明に適したアプローチ方法であると結論された。 2)ダイズ根粒菌のアレイ解析・ライブラリー構築利用の基本戦略の策定:ミヤコグサ根粒菌と同様に整列化コスミッドライブラリーが、品種特異的共生因子の同定に有効であると判断された。また、ミヤコグサ根粒菌で使用したマクロアレイ系のダイズ根粒菌への適用は、クローンの選択・RNA抽出方法などの改善が必要であると考えられた。 3)食糧生産および環境保全への応用:根粒菌ゲノム情報から難分解物質分解系遺伝子、脱窒遺伝子群は、根粒菌接種に環境保全への付加価値をつけ、また機能性遺伝子導入根粒菌による共生環境修復への発展性が期待された。また、グリシンベタインによる浸透圧(塩)耐性、乾燥耐性は、応用研究に有効であると考えられた。野外利用はセルフクローニング系が有望であった。 4)クローン管理およびデータベース構築:データベース構築・公開は大阪大学で、クローン管理は東北大学と東京農工大学で共同で行うこととした。

  26. セパシア菌のゲノム構造とその再編成・多様化・進化に関する研究

    津田 雅孝, 澤田 宏之, 永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 東北大学

    2003 - 2003

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    ヒトや動植物への病原性、植物病原菌駆除能、環境汚染物質も含む多様な有機化合物資化能をもつセパシア菌ATCC17616株では、ゲノムが3.4Mb,2.5Mb,0.9Mbの3種環状染色体から構成され、生育環境変動により各染色体が大規模な再編成を示す結果、新規形質を容易に獲得する。各染色体の構成原理と構造的動態、そして再編成と染色体進化を司る分子機構の実験的提示をめざし、以下の成果を得た。 1.本株ゲノムrandom shotgunシーケンシングの2万リード弱で得られた配列情報に関して、解析を実施しているとともに、類縁菌株には存在しないユニークな遺伝子の検出を行っている。 2.昨年度取得済みの3.4Mb染色体分配関連遺伝子領域に加え、さらに、2.5Mbと0.9Mb染色体の分配関連遺伝子領域を取得した。新規に取得した2領域はいずれもプラスミド型の遺伝子構造を持っていたが、ビブリオ属やブルセラ属細菌の副(第2)染色体との系統学的類縁関係は低かった。 3.高鉄濃度で活性型となる鉄レギュロンの統括的制御因子Furは、チトクロームcオキシダーゼ遺伝子(cox)クラスターとともに、酸素ストレス耐性賦与に関わるMn含有スーパーオキシドジスムターゼをコードする遺伝子sodBの発現を転写レベルで促進することが判明した。また、活性のあるFurタンパク質の精製に成功し、cox並びにsodB遺伝子プロモーター領域への結合を検討している。 4.本菌株ゲノム上に存在する各種可動遺伝因子の転移頻度を定量的に評価する実験系を構築した。本系を用い、様々な環境ストレス存在下での各種挿入配列(IS)の転移頻度度を検討した結果、高温ストレスがこれら、ISの転移頻度を上昇させることを見いだした。

  27. セパシア菌ゲノムを構成する3種染色体の構造とその可塑性に関する研究

    津田 雅孝, 澤田 宏之, 永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 東北大学

    2002 - 2002

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    ヒトや動植物への病原性、植物病原菌駆除能、環境汚染物質も含む多様な有機化合物資化能をもつセパシア菌ATCC17616株では、ゲノムが3.4Mb,2.5Mb,0.9Mbの3種環状染色体から構成され、生育環境変動により各染色体が大規模な再編成を示す結果、新規形質を容易に獲得する。各染色体の構成原理と構造的動態、そして再編成と染色体進化を司る分子機構の実験的提示をめざし、以下の成果を得た。 1.Tn5誘導体挿入突然変異の更なる解析から、窒素代謝レギュロンの統括的転写制御因子遺伝子rpoNとntrCの3.4Mb染色体支配を見出した。また、本染色体にはヒスチジン合成に必要な全his遺伝子クラスターが、そして、2.5Mb染色体のleuCDB近傍にはtrpFBAクラスターが存在していた。これら遺伝子のゲノムでのコピー数は1であった。 2.多くの細菌種とは異なり、3.4Mb染色体上のrpmH-dnaA間には染色体複製開始起点は存在しなかった。両遺伝子と隣接性がなかった3.4Mb染色体分配関連遺伝子領域は通常細菌染色体の当該領域と高い構造的相同性を示すgidA-gidB-parA-parBの構造を有し、parA-parB破壊株の富栄養条件での生育には顕著な欠損はなかった。一方、2.5Mb染色体のparAはプラスミド型の遺伝子構造を持っていた。 3.0.9Mb染色体には、高鉄濃度で転写促進されるチトクロームcオキシダーゼ遺伝子クラスターとともに、ISやIS関連転移酵素遺伝子が50%を占める12kbの領域が存在することが判明した。 4.塩基配列決定と可動遺伝因子捕捉系で同定した10種ISはゲノムで8コピー以下であり、これらISの転移がゲノム再編成に深く関与する可能性は高くなかった。また、ISBmu2とISBmu4はIS5グループ、IS408とISBmu6はIS21グループに属することが判明した。

  28. Isolation and characterization of a novel gene for degradation of environmental pollutants from environmental genetic source

    NAGATA Yuji, TSUDA Masataka

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2001 - 2002

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    It is difficult to isolate a novel gene or enzyme for degradation of environmental pollutants by using the conventional enrichment-culture method. We directly isolated and purified long chain DNA from soil environment, and constructed soil DNA library using cosmid vector. The resultant soil DNA library was introduced into the host strain that could not grow on naphthalene because of its lack of one of genes for naphthalene assimilation. The clones which grew on naphthalene were isolated. The gene that complemented the naphthalene assimilation ability of the strain did not show homology to knwon genes for naphthalene degradation. Furthermore, we constructed strains which could not grow on BHC or haloalkanes becuse of their lack of one of genes for assimilation of BHC or haloalkanes. By using these strains, it is theoretically possible to isolate novel genes for BHC dehydrochlorinase or haloalkane dehalogenase. Introduction of the soil DNA library into these stratns are in progress.

  29. スフィンゴモナス属細菌を用いる環境浄化システム構築基盤

    村田 幸作, 河合 富佐子, 福田 雅夫, 永田 裕二, 五十嵐 泰夫, 室岡 義勝

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 京都大学

    2001 - 2001

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    スフィンゴモナス属細菌は、グラム陰性であるにも関わらず、外膜にリポ多糖(LPS)を持たず、代わりに動物細胞の細胞膜に特有のスフィンゴ糖脂質を含む特徴的な細菌である。そのため、細胞表層は通常の細菌よりも疎水的雰囲気が強く、ダイオキシンなど水不溶性の環境有害物質の強力な分解菌として注目されている。また、この細菌群の細胞表層は巨大な襞分子によって覆われており、環境条件や栄養条件に依存してその襞分子を再編成し、巨大な孔(体腔)を形成する。この体腔は、巨大分子の取り込み口として機能する。このような特徴的な構造と強力な人工物質代謝能を利用することにより、強力な環境浄化・再生能を持っ細菌の育種が考えられる。そこで、スフィンゴモナス属細菌のかかる性質を、構造と機能、並びに自然界での生存形態の観点から詳細に解析し、その環境浄化・再生への適用の可能性を調査・研究した。その結果、本菌群が現在検討されている様々な細菌群よりも並外れた能力を有し、更に機能の向上を図ることによって、実用的な環境浄化・再生細菌の育種が可能であるという見通しを得た。更に、研究班員を動員して、平成13年11月21日、京都において本菌群の構造と機能に関するシンポジウム(産官学合わせて60余名の参加)を開催し、環境有害物質(天然高分子、人工高分子、環境ホルモン、農薬など)の分解能、分解機構、並びに分解に関わる酵素とその遺伝子について詳細な討議を行った。自然環境下でのスフィンゴモナス属細菌の形態形成制御とエコーシステムに関しても討議した。また、スフィンゴモナス属細菌の全ゲノム構造を決定するビッグサイエンスも開始しており、今後、この研究成果を特定研究にまで発展させる基礎と重要性が認識された。これを機に、我が国のスフィンゴモナス属細菌研究者を網羅した環境微生物研究会を正式に発足した。

  30. セパシア菌のゲノム構造とその可塑性に関する研究

    津田 雅孝, 澤田 宏之, 永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究(C)

    Institution: 東北大学

    2001 - 2001

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    ヒトや動植物への病原性、植物病原菌駆除能、環境汚染物質も含む多様な有機化合物資化能をもつセパシア菌ATCC17616株では、ゲノムが3.4Mb,2.5Mb、0.9Mbの3種環状染色体から構成され、生育環境変動により各染色体が大規模な再編成を示す結果、新規形質を容易に獲得する。各染色体の構成原理と構造的動態、そして再編成と染色体進化を司る分子機構の実験的提示をめざし、以下の成果を得た。 1.約40のTn5誘導体挿入栄養要求性突然変異の多くは3.4Mb染色体に分布し、本染色体上のargH, hisCBHAFIE, trpEGDCの詳細構造を示した。また、2.5Mb染色体でのargGとleuADB, lysRAの存在が判明した。鉄レギュロンの統括的転写制御因子遺伝子furは遺伝子破壊が可能で、高鉄濃度でFurは病原因子シデロフォアの産生を負に、細胞に酸素ストレス耐性を賦与する酵素群の発現を正に制御していた。また、これら遺伝子はゲノムでのコピー数が1で、想定機能を有していた。 2.3.4Mb染色体上のrpmH-dnaA-dnaN-gyrBのrpmH-dnaAでのDnaA boxの存在、2.5Mb染色体上でのgrpE-dnaK-dnaJの存在、そして、これら7遺伝子とgroEL, rpoD, recAのゲノムでのコピー数が1であることを示した。また、2種の異なるparAファミリー遺伝子を担うコスミドを取得した。 3.可動遺伝因子捕捉系で取得した5種のISはゲノムで3〜9コピー存在した。1.3kbの新規IS(ISBmu1)はISRso3と80%以上の相同性を示した。 4.0.9Mb染色体へのTn5誘導体挿入は約100の候補株内にはなかった。そこで別法で、本染色体断片を有する複数のコスミドを取得した。本染色体を欠失・除去、他細菌種に接合伝達させる誘導体株作製の最終段階に至った。

  31. セパシア菌ゲノムの分子遺伝学的研究

    津田 雅孝, 永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究(C)

    Institution: 東北大学

    2000 - 2000

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    ヒトや植物への病原性や植物病原菌駆除能、難分解性環境汚染物質も含む多種多様な有機化合物資化能をもつβ-プロテオバクテリアのセパシア菌(Burkholderia cepacia)ATCC17616株では、ゲノムが3.4Mb,2.5Mb,0.9Mbの3種の環状染色体から構成され、生育環境変動により各染色体が大規模で多様な再編成化現象を示す結果、新規形質を容易に獲得する。本菌株染色体の構造と再編成の解明、そして再編成と染色体進化を司る分子機構の実験的提示を本研究ではめざし、以下の成果を得た。 1.PacI,PmeI,SwaI,I-CeuIとPFGE法を用い、3種の染色体の物理地図を決定し、3種の染色体地図上でのrrnオペロンの位置を決めた。 2.PCR法を用いて、dnaA,gyrB,rpoD,dnaK,recA等の基本的生命維持・活動に関与する15種の遺伝子を単離した。dnaAとgyrBは3.4Mb染色体、dnaKは2.5Mb染色体、rpoDは両染色体に存在していた。 3.染色体地図上での挿入部位同定と挿入部位近傍領域の単離が容易なTn5誘導体の染色体挿入ライブラリー約5,000株から、37株の各種栄養要求性突然変異株と40株の鉄獲得・代謝異常突然変異株を取得した。his及びasp突然変異や鉄獲得系突然変異はいずれも3.4Mb染色体に、lys突然変異は2.5Mb染色体に存在したが、met及びtrp遺伝子群は両染色体に支配されていた。 4.既知の5種の挿入配列(IS)をPCR法で取得したが、ゲノムあたりのコピー数はいずれも3〜9と少なかった。一方、遺伝学的捕捉系を用い、可動遺伝因子を多数取得したが、この中には既知のISとともに新規のISが複数見出された。

  32. Study on a novel dehydrochlorinase from BHC-degrading bacterium

    NAGATA Yuji

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    1999 - 2000

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    γ-Hexachlorocyclohexane dehydrochlorinase (LinA) is a unique dehydrochlorinase that has no homologous sequence at the amino acid-sequence level, and for which the evolutionary origin is unknown. We here propose that LinA is a member of a novel structural superfamily of enzymes containing scytalone dehydratase, 3-oxo-Δ5-steroid isomerase, nuclear transport factor-2, and the β-subunit of naphthalene dioxygenase-all known structures with different functions. The three-dimensional structure of LinA is predicted by homology modeling. More than twenty mutants were prepared by site-directed mutagenesis. These mutants were expressed in E.coli, and their activities in crude extract were evaluated. Most of the features of the LinA mutants could be explained on the basis of the present LinA model, indicating its validity. We conclude that LinA catalyses the proton abstraction via the catalytic dyad H73-D25 by the similar mechanism as described for scytalone dehydratase. The results suggest that LinA and scytalone dehydratase evolved from a common ancestor. LinA may have evolved from an enzyme showing a dehydratase activity. Stereochemical analysis of the reaction products formed during conversion of γ-HCH by LinA was investigated by GC-MS, NMR, CD and molecular modeling. LinA requires the presence of a 1, 2-biaxial HCl pair on a substrate molecule. LinA enantiotopologically differentiates two 1, 2-biaxial HCl pairs present on γ-HCH and gives rise to a single PCCH enantiomer 1, 3 (R), 4 (S), 5(S), 6 (R)-PCCH.Furthermore, LinA enantiomerically differentiates 1, 3 (S), 4 (R), 5 (R), 6 (S)-PCCH and 1, 3 (R), 4 (S), 5 (S), 6 (R)-PCCH.The proposed mechanism of enzymatic biotransformation of γ-HCH to 1, 2, 4-TCB by LinA consists of two 1, 2-anti conformationally dependent dehydrochlorinations followed by 1, 4-anti dehydrochlorination.

  33. Mechanism-Based Biodegradability Prediction of Dehalogenase

    OHTA Akinori, NAGATA Yuji, TAKAGI Masamichi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B).

    Institution: The University of Tokyo

    1998 - 1999

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    The deduced amino acid sequence of LinB (1, 3, 4, 6-tetrachloro-1, 4-cyclohexadiene halidohydrolase) showed highest level, of similarity to haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJIO, suggesting that LinB belongs to the family of haloalkane dehalogenase enzymes catalyzing the dehalogenation by hydrolytic mechanism. LinB is believed to belong the family of α/β-hydrolases which employ catalytic triad, i.e. nucleophile-histidine-acid, during the catalytic reaction. At first, the position of the catalytic triad within the sequence of LinB was probed by site-directed mutagenesis. The catalytic triad residues of the haloalkane dehalogenase LinB are proposed to be ?D108, H272, and E132 For further analysis, we determined three dimentional structure of LinB. The purified LinB was crystallized using the hanging-drop vapoul-diffusion method. The crystals diffract to 1.58 angstrom using synchrotron X-ray under cryogenic (100K) conditions. The structure of LinB was solved by molecular replacement with dehalogenase (DhaA) from Rhodococcus.

  34. Studies on location of xenobiotics degradation in the cell of BHC-degrading bacterium.

    NAGATA Yuji

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: The University of Tokyo

    1997 - 1998

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    gamma-Hexachlorocyclohexane (gamma-HCH, BHC, and lindane) is one of several highly chlorinated insecticides that cause serious environmental problems. The cellular proteins of a gamma-HCH-degrading bacterium Sphingomonas paucimobilis UT26 were fractionated into periplasmic, cytosolic and membrane fractions after osmotic shock. Most of activities of LinA, LinB, LinC, LinD, and LinE that are involved in the early steps of gamma-HCH degradation in UT26, were detected in the periplasmic fraction. Antibodies were raised against LinA and LinB.Most of the LinA and LinB protein was detected in the periplasmic fraction and had not undertaken molecular processing. Furthermore, immunoelectron microscopy clearly showed that LinA and LinB are periplasmic proteins. LinA and LinB both lack a typical signal sequence for export, so they may be secreted into the periplasmic space via a hitherto unknown mechanism.

  35. Construction of effective PCB-degradation bioreactor by modification of regulatory system of PCB-degrading bacterium using genetic engineering.

    TAKAGI Masamichi, SHIMURA Minoru, KIMBARA Kazuhide, NAGATA Yuji

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: The University of Tokyo

    1997 - 1998

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    The bph operon of PCB-degraging bacterium, Pseudomonas sp. KKS102 was inducibly expressed by addition of biphenyl. A gene whose deduced amino acid sequence shows similarity to the LysR-type regulator was found just downstream of the bph operon, and named it bphR.The disruption of the bphR gene had no effect on the inducible expression of the bph operon, indicating that the bphR is not a regulator of the bph operon. Four disruptants of bph genes (bphA, bphB, bphC, and bphD) were constructed. The bphA, bphB, and bphC disruptants did not show the inducibility of the bphE gene expression when biphenyl was added. Whlie, the bphD disruptant showed the inducibility. These results indicated that the direct inducer of the bph operon is not biphenyl but meta-cleavage compound which is produced by BphA, BphB, and BphC from biphenyl. Furthermore, cis-element locating just upstream of the bphE gene for a response of biphenyl was identified. In this study, we revealed a novel regulation mechanism of the bph operon in KKS1O2. We consider that our finding will be able to be applied for the modification of the PCB-degrading bioreactor.

  36. 殺虫剤BHC分解に関与する脱塩素酵素群のグラム陰性細菌細胞内局在性に関する研究

    永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 東京大学

    1996 - 1996

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    グラム陰性細菌であるS.paucimobilis UT26のBHC分解に関与する酵素の局在性を検討する第一段階として,まず,同じグラム陰性細菌である大腸菌の細胞内成分の分画法に準じてUT26の細胞内成分をペリプラズム,細胞質,膜の3つの画分に分画し,それぞれの画分のBHC分解関与酵素(LinA,LinB,LinC,LinD,LinE)活性を測定し,その分布を調べた。分画の正当性は,局在性がわかっているphosphatase,glyceroaldehyde 3-phosphate dehydrogenase,pyruvate dehydrogenase等のマーカー酵素の活性を測定するなどして行った。その結果,LinA,LinB,LinDの3種の脱塩素酵素活性の多くは,ペリプラズム画分に,LinC活性は膜画分に,LinE活性は細胞質画分に見出された。さらに,精製したLinA,LinBを用いて,それぞれの抗体を作製し,LinA,LinBのタンパク自体の分布についても検討を加えた結果,両蛋白質の多くはペリプラズム画分に見出された。当初の予定であった免疫電顕法による解析には至らなかったが,LinA,LinBの多くがペリプラズムに局在していることをほぼ示すことが出来た。一方,クローン化したlinA,linB遺伝子を大腸菌に導入し,発現させた際のLinA,LinBの局在性についても検討を加えた結果,大腸菌でもUT26と同様の分布,すなわちペリプラズムへの局在化を示すことが示唆された。 以上,今回の申請研究において,既知のシグナル配列を持たない脱塩素酵素LinA,LinBがペリプラズムに局在化するという現象をほぼ抑えることができた。

  37. 殺虫剤BHC分解に関与するPseudomonas属細菌の新規脱塩素酵素系の解析

    永田 裕二

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 奨励研究(A)

    Institution: 東京大学

    1995 - 1995

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    BHCを好気的に分解資化するという大変ユニークな性質を持つPseudomonas paucimobilis UT26が有する脱塩素酵素反応を触媒する酵素の性質についての解析を行った。まず,BHCから直接脱塩化水素を行うdehydrochlorinase (LinA)と次の段階の加水分解的脱塩素反応を行うhydrolytic dehalogenase (LinB)の相互作用を検討するために,量酵素をコードする遺伝子をタンデムに結合し,tac プロモーターを利用して両遺伝子を大腸菌中で同時に高発現させた。粗酵素抽出液に両酵素の活性が検出されたために,この抽出液から両タンパク質の精製を試みた。硫安分画を行ったところ,両酵素活性性は異なる画分に検出された。すなわち,当初予想された両酵素が複合体を形成し,一連の脱塩素反応を行っている可能性は低いと思われた。そこで,以下は,その酵素学的特徴について解析が不十分である,LinB酵素に的を絞って解析を行った。すなわち,クローン化した遺伝子を用いてLinB蛋白を大腸菌内で大量に生産し、これを硫安分画,疎水クロマト,陰イオン交換クロマト,ゲルろ過の各ステップを経て,SDS-PAGE上で単一のバンドとなるまで精製した。その酵素学的解析を行ったところ,約30-kDの単量体であること,至適pHが8.2であることなどの特徴は,既に酵素学的解析が行われているLinBと推定アミノ酸配列において有意な相同性を示すhaloalkane dehalogenase, DhlAと類似の特徴を示したが,基質特異性においては顕著な違いが観察された。すなわち,DhlAが鎖長の短いhaloalkaneを良い基質とするのに対して,LinBは比較的鎖長の長居haloalkaneを良い基質とした。推定アミノ酸配列の違いと,基質特異性の違いの対応関係はコンピューター解析によって推定されるものとよく一致し,本申請研究において,今後,dehalogenaseの構造・機能相関を明らかにしていくための十分な下地を確立することができた。

  38. Genetic Engineering of Long Chain Dicarboxylic Acid Production in Yeast

    OHTA Akinori, MATSUI Tohru, FURUHASHI Keizo, NAGATA Yuji

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Developmental Scientific Research (B)

    Institution: The University of Tokyo

    1994 - 1995

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    The research plan constituted of following three parts. (1) Construction of new dicarboxylic acid-producing yeast by using genetic engineering system which was developed for n-alkane-assimilating yeast Candida maltosa in our laboratory. (2) Improvement of production efficiency and purity of the dicarboxylic acid by overproducing specific cytochrome P-450. (3) Improvement of dicarboxylic acid production by disruption of acyl-CoA oxidase gene which works in degradation of the product. In 1994, we analyzed various genes encoding cytochromes P-450 in C.maltosa.and attained overproduction of specific cytochrome P-450 by GAL gene promoters. We also analyzed the substrate specificity and catalyzed products of the cytochromes. In 1995, disruption of C.maltosa POX2 gene encoding acyl-CoA oxidase was successfully accomplished. Production of dicarboxylic acid from n-tetradecane by the disrupted strain was subsequently confirmed by the Japan Energy group who had fermentation and detection equipments. We constructed a vector that was stably maintained in C.maltosa and isolated cytochrome P-450 reductase gene, of which overexpression will further improve alkane oxidation by C.maltosa.

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  1. POPsやその候補化合物を分解する微生物酵素・遺伝子の探索と解析

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    環境修復に有効な組換え植物の作製のために、POPs等の有機塩素系化合物を分解する微生物酵素遺伝子を取得する。

  2. 難分解性化合物分解酵素を支配する新規遺伝子の未利用土壌遺伝資源からの取得と解析

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    土壌環境から培養過程を経ずに難分解性物質分解酵素遺伝子を取得する方法を確立し、実際に有害化学物質の除去に有効な酵素遺伝子の取得を試みた。