Details of the Researcher

PHOTO

Yoshiyuki Otsubo
Section
Graduate School of Life Sciences
Job title
Associate Professor
Degree

  • 博士(農学) (The University of Tokyo)

Research History 1

  • 2001/04 - 2003/03
    理化学研究所　基礎科学特別研究員

Education 2

  • The University of Tokyo　Graduate School of Agricultural and Life Sciences

    - 2001/03

  • The University of Tokyo　Faculty of Agriculture

    - 1996/03/31

Committee Memberships 3

  • 日本農芸化学会　化学と生物編集委員

    2017/04 - Present

  • ゲノム微生物学会　ニュースレター編集幹事

    2013/04 - Present

  • ゲノム微生物学会　男女共同参画委員

    2013/04 - 2015/03

Professional Memberships 3

  • 日本科学振興協会

    2022/04 - Present

  • 日本ゲノム微生物学会

  • 日本農芸化学会

Research Interests 6

  • ゲノム

  • バイオレメディエーション

  • PCB

  • カタボライト調節

  • 遺伝子発現制御

  • 細菌

Research Areas 2

  • Life sciences / Applied microbiology /

  • Informatics / Software /

Awards 2

  1. 農芸化学奨励賞

    2014/03/27　日本農芸化学会

  2. 日本ゲノム微生物学会研究奨励賞

    2013/03/09　日本ゲノム微生物学会

Papers 116

  1. 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

    DOI： 10.1093/bbb/zbac032 　

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    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.

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

    Yoshiyuki Ohtsubo, Keiichiro Sakai, Yuji Nagata, Masataka Tsuda

    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.

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

    Yoshiyuki Ohtsubo, Haruna Sasaki, Yuji Nagata, Masataka Tsuda

    DNA research : an international journal for rapid publication of reports on genes and genomes　25　(5)　477-487　2018/10/01

    DOI： 10.1093/dnares/dsy018 　

    ISSN： 1340-2838

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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.

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

    Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    SCIENTIFIC REPORTS　7　(1)　6520　2017/07

    DOI： 10.1038/s41598-017-04765-8 　

    ISSN： 2045-2322

  5. 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

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

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

    Proc Natl Acad Sci U S A　112　(46)　14343-14347　2015/11/17

    DOI： 10.1073/pnas.1514326112 　

    ISSN： 0027-8424

  7. Carbon Source Acts as a Deterministic Filter Shaping Microbial Succession and Rare-Abundant Decoupling in Soil Bacterial Communities

    Leonardo Stari, Hiromi Kato, Kouhei Kishida, Yoshiyuki Ohtsubo, Michio Kondoh, Yuji Nagata

    ISME Communications　2026/04/20

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/ismeco/ycag108 　

    eISSN： 2730-6151

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    Abstract The principles governing microbial community assembly and the interplay between deterministic selection and stochasticity remain central debates in ecology. We investigated how chemically diverse carbon sources act as ecological filters shaping soil bacterial communities. Using replicated microcosms amended with distinct substrates (glucose, succinate, naphthalene, phenanthrene, or γ-HCH) or under starvation, we tracked community trajectories via high-frequency 16S rRNA gene sequencing (29 timepoints, triplicate) and quantitative ecological modeling. Null model analysis confirmed the carbon source as the primary deterministic filter, enforcing high reproducibility (homogeneous selection governing ~74% of assembly among replicates) and overriding stochastic effects. Crucially, abundant (>1%) and rare (<0.1%) taxa exhibited decoupled assembly mechanisms. While abundant taxa were driven largely by dispersal limitation (~59%) and variable selection, the rare biosphere displayed a temporal regime shift. Unlike the immediate response of dominant taxa, rare taxa transitioned from stochastic isolation to strong deterministic selection (surging to ~50%) only during later successional stages. This reframes the rare biosphere as a "latent responder" reservoir recruited by metabolic byproducts rather than the primary substrate. Additionally, time-resolved interaction networks revealed that under severe stress from toxicity or starvation, interactions shifted from competitive exclusion to facilitation (e.g., necromass scavenging). These patterns provide strong empirical support for the Stress Gradient Hypothesis in a microbial context. Collectively, our findings demonstrate how deterministic filtering and stress-mediated cooperation jointly structure ecosystems, providing a high-resolution temporal dataset to further interrogate these fundamental ecological principles.

  8. Symbiosis Islands of Bradyrhizobium Determine Relationships with Host Legumes Lespedeza cuneata and Glycine max.

    Yuki Konno, Iori Imamura, Tomoyuki Nemoto, Masaya Kajiwara, Yoshiyuki Ohtsubo, Manabu Itakura, Tomoko Sakai, Hisayuki Mitsui, Kiwamu Minamisawa, Masayuki Sugawara

    Microbes and environments　41　(1)　2026

    DOI： 10.1264/jsme2.ME25072 　

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    Symbiotic N2-fixing bradyrhizobia nodulate various leguminous plants and possess a large symbiosis island (SI) encoding symbiotic functions in their genomes. We obtained 30 rhizobial isolates from root nodules of the tribe Desmodieae of native leguminous plants in northern Japan. Based on their 16S rRNA gene sequences, most isolates (24/30=80%) phylogenetically belonged to Bradyrhizobium. Two isolates (LCT1 and LCT2) from Lespedeza cuneata were placed phylogenetically with Bradyrhizobium diazoefficiens USDA110T, a well-studied soybean (Glycine max [L.] Merr.) symbiont. Genomic comparisons revealed different SIs in the Met-tRNA and Val-tRNA genes on the respective genomes. In contrast, core genomic regions outside the SI regions showed strong collinearity between strains LCT2 and USDA110. Phenotypically, LCT2 formed N2-fixing root nodules on L. cuneata, an original host plant, but not on soybean, whereas USDA110 formed N2-fixing root nodules on soybean, but not on L. cuneata. Therefore, the SI variants were expected to contain the genes responsible for this host specificity. Genes relevant to the type III secretion system (T3SS) showed less homology between LCT2 and USDA110 than nod genes encoding Nod factor biosynthesis. Host plant inoculations with T3SS mutants suggested the involvement of T3SS effectors in differential host specificity. Therefore, the acquisition of distinct SI variants may confer strong host specificity through symbiotic interactions between Bradyrhizobium and host legumes. We discuss the possible pathway of symbiotic bradyrhizobial evolution and its application to the mitigation of greenhouse gas emissions.

  9. Directional Colony Growth of Cupriavidus toward Sphingomonads.

    Hiromi Kato, Shoko Hirano, Chiaki Haga, Sayaka Sakogawa, Yoshiyuki Ohtsubo, Yuji Nagata

    Microbes and environments　41　(2)　2026

    DOI： 10.1264/jsme2.ME25087 　

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    Bacterial communities often originate from physical encounters between distinct species on solid surfaces; however, the mechanisms underlying these initial interactions remain unclear. The γ-hexachlorocyclohexane (γ-HCH; a toxic recalcitrant insecticide)-degrading consortium includes the surface-motile bacterium Cupriavidus sp. strain TKC and the γ-HCH-degrading Sphingobium sp. strain TKS. During a co-culture on R2A agar, TKC colonies exhibited directional colony growth (DCG), characterized by asymmetric expansion toward neighboring TKS colonies. When TKC colonies eventually overgrew TKS colonies, non-motile TKS cells were passively carried along the expanding TKC front, indicating that DCG facilitates the physical association and surface dispersal of Sphingobium cells. DCG activity was also observed against various strains of Sphingobium, Sphingomonas, and Novosphingobium, whereas extremely weak or no DCG activity was observed toward other bacterial groups, including representatives of α-, β-, and γ-proteobacteria as well as actinobacteria. These results indicate that TKC exhibits DCG selectively toward sphingomonads, recognizing taxon-specific cues rather than responding indiscriminately to neighboring colonies. Among the components tested, sphingosine reproducibly triggered DCG in a dose-dependent manner, and the inhibition of sphingolipid biosynthesis in Sphingobium with myriocin markedly suppressed the inducing effect. These results highlight the sphingosine-mediated induction of DCG as a molecular mechanism underlying the initial step in the spatial organization of bacterial communities on solid surfaces.

  10. 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.

  11. Type I partition-related proteins enhance conjugative transfer through transcriptional activation andoriTregion binding International-journal

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

    mBio　16　(9)　e0160025　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.

  12. 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　12　(10)　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.

  13. Transgenic Arabidopsis thaliana plants expressing bacterial γ-hexachlorocyclohexane dehydrochlorinase LinA International-journal

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

    BMC Biotechnology　24　(1)　42-42　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.

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

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

    Scientific Reports　14　(1)　12759-12759　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.

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

    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.

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

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

    Bioscience, biotechnology, and biochemistry　88　(3)　305-315　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.

  17. Degradation of DDT by γ-hexachlorocyclohexane dehydrochlorinase LinA. International-journal

    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.

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

    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.

  19. 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 　

  20. 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 　

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

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

    Bioscience, biotechnology, and biochemistry　86　(6)　800-809　2022/03/17

    DOI： 10.1093/bbb/zbac042 　

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    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 two strains revealed that TA15 shares the same basic genome skeleton 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 with those of UT26. It was inferred that transposition of IS6100 plays 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.

  22. Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade. International-journal

    Yuu Hirose, Yoshiyuki Ohtsubo, Naomi Misawa, Chinatsu Yonekawa, Nobuyoshi Nagao, Yohei Shimura, Takatomo Fujisawa, Yu Kanesaki, Hiroshi Katoh, Mitsunori Katayama, Haruyo Yamaguchi, Hirofumi Yoshikawa, Masahiko Ikeuchi, Toshihiko Eki, Yasukazu Nakamura, Masanobu Kawachi

    DNA research : an international journal for rapid publication of reports on genes and genomes　28　(6)　2021/10/11

    DOI： 10.1093/dnares/dsab024 　

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    Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.

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

    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.

  24. Transcriptome Analysis of Zygotic Induction During Conjugative Transfer of Plasmid RP4 International-journal Peer-reviewed

    Masatoshi Miyakoshi, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    Frontiers in Microbiology　11　1125-1125　2020/06/18

    Publisher: Frontiers Media SA

    DOI： 10.3389/fmicb.2020.01125 　

    eISSN： 1664-302X

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    Conjugative transfer of bacterial plasmid is one of the major mechanisms of horizontal gene transfer, which is mediated by direct contact between donor and recipient cells. Gene expression of a conjugative plasmid is tightly regulated mostly by plasmid-encoded transcriptional regulators, but it remains obscure how differently plasmid genes are expressed in each cell during the conjugation event. Here, we report a comprehensive analysis of gene expression during conjugative transfer of plasmid RP4, which is transferred between isogenic strains of Pseudomonas putida KT2440 at very high frequency. To discriminate the expression changes in the donor and recipient cells, we took advantage of conjugation in the presence of rifampicin (Rif). Within 10 min of mating, we successfully detected transient transcription of plasmid genes in the resultant transconjugant cells. This phenomenon known as zygotic induction is likely attributed to derepression of multiple RP4-encoded repressors. Interestingly, we also observed that the traJIH operon encoding relaxase and its auxiliary proteins were upregulated specifically in the donor cells. Identification of the 5' end of the zygotically induced traJ mRNA confirmed that the transcription start site of traJ was located 24-nt upstream of the nick site in the origin of transfer (oriT) as previously reported. Since the traJ promoter is encoded on the region to be transferred first, the relaxase may be expressed in the donor cell after regeneration of the oriT-flanking region, which in itself is likely to displace the autogenous repressors around oriT. This study provides new insights into the regulation of plasmid transfer processes.

  25. 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.

  26. 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

    Kouhei Kishida, Shouta Nonoyama, Tim Lukas, Shotaro Kawahara, Koji Kudo, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    Applied and environmental microbiology　85　(24)　2019/12/15

    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.

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

    Yuji Nagata, Hiromi Kato, Yoshiyuki Ohtsubo, Masataka Tsuda

    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.

  28. Complete Genome Sequence of Thalassococcus sp. Strain S3, a Marine Roseobacter Clade Member Capable of Degrading Carbazole. International-journal Peer-reviewed

    Felipe Vejarano, Chiho Suzuki-Minakuchi, Yoshiyuki Ohtsubo, Masataka Tsuda, Kazunori Okada, Hideaki Nojiri

    Microbiology resource announcements　8　(28)　e00231-19　2019/07/11

    DOI： 10.1128/MRA.00231-19 　

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    We determined the complete genome sequence of Thalassococcus sp. strain S3, a marine carbazole degrader isolated from Tokyo Bay in Japan that carries genes for aerobic anoxygenic phototrophy. Strain S3 has a 4.7-Mb chromosome that harbors the carbazole-degradative gene cluster and three (96-, 63-, and 46-kb) plasmids.

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

    Natsumi Ogawa, Hiromi Kato, Kouhei Kishida, Eikichi Ichihashi, Taichiro Ishige, Hirofumi Yoshikawa, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    Microbiology (Reading, England)　165　(6)　625-637　2019/06

    DOI： 10.1099/mic.0.000801 　

    ISSN： 1350-0872

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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.

  30. Complete Genome Sequence of an Anaerobic Benzene-Degrading Bacterium, Azoarcus sp. Strain DN11. International-journal Peer-reviewed

    Allan Devanadera, Felipe Vejarano, Yu Zhai, Chiho Suzuki-Minakuchi, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuki Kasai, Yoh Takahata, Kazunori Okada, Hideaki Nojiri

    Microbiology resource announcements　8　(11)　2019/03/14

    DOI： 10.1128/MRA.01699-18 　

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    Here, we present the complete genome sequence of Azoarcus sp. strain DN11, a denitrifying bacterium capable of anaerobic benzene degradation. The DN11 genome is 4,956,835 bp long with a G+C content of 66.3%. Genome analysis suggested the possibility that DN11 utilizes three proposed pathways for anaerobic benzene degradation, namely, methylation, hydroxylation, and carboxylation pathways.

  31. Complete Genome Sequence of Bacillus licheniformis TAB7, a Compost-Deodorizing Strain with Potential for Plant Growth Promotion. International-journal Peer-reviewed

    Enock Mpofu, Felipe Vejarano, Chiho Suzuki-Minakuchi, Yoshiyuki Ohtsubo, Masataka Tsuda, Joydeep Chakraborty, Masatoshi Nakajima, Kazunori Okada, Nobuki Tada, Toshiaki Kimura, Hideaki Nojiri

    Microbiology resource announcements　8　(4)　2019/01

    DOI： 10.1128/MRA.01659-18 　

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    Bacillus licheniformis strain TAB7 degrades short-chain fatty acids responsible for offensive odor in manure and is used as a deodorant in a compost-deodorizing technology. Here, we report the complete genome sequence of strain TAB7, which consists of a 4.37-Mb chromosome and two plasmids (42 kb and 31 kb).

  32. Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5. International-journal Peer-reviewed

    Felipe Vejarano, Chiho Suzuki-Minakuchi, Yoshiyuki Ohtsubo, Masataka Tsuda, Kazunori Okada, Hideaki Nojiri

    Microbiology resource announcements　7　(8)　2018/08

    DOI： 10.1128/MRA.00935-18 　

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    We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium isolated from Tokyo Bay and capable of degrading carbazole. The genome consists of a 3.3-Mb circular chromosome that carries the gene clusters involved in carbazole degradation and biosynthesis of the photosynthetic apparatus of aerobic anoxygenic phototrophic bacteria.

  33. 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

    Kouhei Kishida, Natsumi Ogawa, Eikichi Ichihashi, Hiromi Kato, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    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.

  34. 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)　2017/08

    DOI： 10.1128/AEM.00479-17 　

    ISSN： 0099-2240

    eISSN： 1098-5336

  35. 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

  36. 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

  37. 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

  38. 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

  39. Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755. International-journal Peer-reviewed

    Yuu Hirose, Takatomo Fujisawa, Yoshiyuki Ohtsubo, Mitsunori Katayama, Naomi Misawa, Sachiko Wakazuki, Yohei Shimura, Yasukazu Nakamura, Masanobu Kawachi, Hirofumi Yoshikawa, Toshihiko Eki, Yu Kanesaki

    Genome announcements　4　(2)　2016/03/17

    DOI： 10.1128/genomeA.00090-16 　

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    Cyanobacterial genus Leptolyngbya comprises genetically diverse species, but the availability of their complete genome information is limited. Here, we isolated Leptolyngbya sp. strain NIES-3755 from soil at the Toyohashi University of Technology, Japan. We determined the complete genome sequence of the NIES-3755 strain, which is composed of one chromosome and three plasmids.

  40. Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools. International-journal Peer-reviewed

    Yuu Hirose, Takatomo Fujisawa, Yoshiyuki Ohtsubo, Mitsunori Katayama, Naomi Misawa, Sachiko Wakazuki, Yohei Shimura, Yasukazu Nakamura, Masanobu Kawachi, Hirofumi Yoshikawa, Toshihiko Eki, Yu Kanesaki

    Journal of biotechnology　220　45-6　2016/02/20

    DOI： 10.1016/j.jbiotec.2016.01.011 　

    ISSN： 0168-1656

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    Cyanobacterial phytochrome-class photosensors are recently emerging optogenetic tools. We isolated Fischerella sp. strain NIES-3754 from hotspring at Suwa-shrine, Suwa, Nagano, Japan. We determined complete genome sequence of the NIES-3754 strain, which is composed of one chromosome and two putative replicons (total 5,826,863bp containing no gaps). We identified photosensor genes of 5 phytochromes and 9 cyanobacteriochromes, which will facilitate optogenetics of thermophile.

  41. Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based bioengineering. International-journal Peer-reviewed

    Yuu Hirose, Takatomo Fujisawa, Yoshiyuki Ohtsubo, Mitsunori Katayama, Naomi Misawa, Sachiko Wakazuki, Yohei Shimura, Yasukazu Nakamura, Masanobu Kawachi, Hirofumi Yoshikawa, Toshihiko Eki, Yu Kanesaki

    Journal of biotechnology　218　51-2　2016/01/20

    DOI： 10.1016/j.jbiotec.2015.12.002 　

    ISSN： 0168-1656

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    To explore the diverse photoreceptors of cyanobacteria, we isolated Nostoc sp. strain NIES-3756 from soil at Mimomi-Park, Chiba, Japan, and determined its complete genome sequence. The Genome consists of one chromosome and two plasmids (total 6,987,571 bp containing no gaps). The NIES-3756 strain carries 7 phytochrome and 12 cyanobacteriochrome genes, which will facilitate the studies of phytochrome-based bioengineering.

  42. Complete genome sequence of Rhodovulum sulfidophilum DSM 2351, an extracellular nucleic acid-producing bacterium Peer-reviewed

    Nobuyoshi Nagao, Yuu Hirose, Naomi Misawa, Yoshiyuki Ohtsubo, So Umekage, Yo Kikuchi

    Genome Announcements　3　(2)　e00388-15　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00388-15 　

    ISSN： 2169-8287

  43. Complete genome sequence of cyanobacterium Geminocystis sp. strain NIES-3709, which harbors a phycoerythrin-rich phycobilisome Peer-reviewed

    Yuu Hirose, Mitsunori Katayama, Yoshiyuki Ohtsubo, Naomi Misawa, Erica Iioka, Wataru Suda, Kenshiro Oshima, Mitsumasa Hanaoka, Kan Tanaka, Toshihiko Eki, Masahiko Ikeuchi, Yo Kikuchi, Makoto Ishid, Masahira Hattori

    Genome Announcements　3　(2)　e00385-15　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00385-15 　

    ISSN： 2169-8287

    eISSN： 2169-8287

  44. 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)　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00247-16 　

    ISSN： 2169-8287

  45. 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)　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00246-16 　

    ISSN： 2169-8287

  46. 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)　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00144-16 　

    ISSN： 2169-8287

  47. Complete genome sequence of Algoriphagus sp. strain M8-2, isolated from a brackish lake Peer-reviewed

    Yusuke Muraguchi, Koya Kushimoto, Yoshiyuki Ohtsubo, Tomohiro Suzuki, Hideo Dohra, Kazuhide Kimbara, Masaki Shintani

    Genome Announcements　4　(3)　e00347-16　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00347-16 　

    ISSN： 2169-8287

  48. 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

  49. 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

  50. Complete genome sequences of Sulfurospirillum strains UCH001 and UCH003 isolated from groundwater in Japan Peer-reviewed

    Takamasa Miura, Yoshihito Uchino, Keiko Tsuchikane, Yoshiyuki Ohtsubo, Shoko Ohji, Akira Hosoyama, Masako Ito, Yoh Takahata, Atsushi Yamazoe, Ken-ichiro Suzuki, Nobuyuki Fujita

    Genome Announcements　3　(2)　2016

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00236-15 　

    ISSN： 2169-8287

  51. 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

  52. Properties and biotechnological applications of natural and engineered haloalkane dehalogenases Peer-reviewed

    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

  53. 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

  54. Complete genome sequence of cyanobacterium Geminocystis sp. strain NIES-3708, which performs type II complementary chromatic acclimation Peer-reviewed

    Yuu Hirose, Mitsunori Katayama, Yoshiyuki Ohtsubo, Naomi Misawa, Erica Iioka, Wataru Suda, Kenshiro Oshima, Mitsumasa Hanaoka, Kan Tanaka, Toshihiko Eki, Masahiko Ikeuchi, Yo Kikuchi, Makoto Ishida, Masahira Hattori

    Genome Announcements　3　(3)　e00357-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00357-15 　

    ISSN： 2169-8287

    eISSN： 2169-8287

  55. 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)　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01401-15 　

    ISSN： 2169-8287

  56. 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

  57. 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)　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01399-15 　

    ISSN： 2169-8287

  58. 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)　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01283-15 　

    ISSN： 2169-8287

  59. 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)　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01169-15 　

    ISSN： 2169-8287

  60. 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)　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00782-15 　

    ISSN： 2169-8287

  61. 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

  62. 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　(Pt 5)　883-891　2014/05

    DOI： 10.1099/mic.0.077057-0 　

    ISSN： 1350-0872

    eISSN： 1465-2080

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. Complete genome sequence of a Propionibacterium acnes isolate from a sarcoidosis patient Peer-reviewed

    Kana Minegishi, Chihiro Aikawa, Asuka Furukawa, Takayasu Watanabe, Tsubasa Nakano, Yoshitoshi Ogura, Yoshiyuki Ohtsubo, Ken Kurokawa, Tetsuya Hayashi, Fumito Maruyama, Ichiro Nakagawa, Yoshinobu Eishi

    Genome Announcements　1　(1)　e00016-12　2013

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00016-12 　

    ISSN： 2169-8287

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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　(Pt 5)　1284-1293　2012/05

    DOI： 10.1099/mic.0.057372-0 　

    ISSN： 1350-0872

  77. 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

  78. 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

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

    Kei Inoue, Ryo Miyazaki, Masatoshi Miyakoshi, Yosiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BIOTECHNOLOGY　150　(S1)　S269-S269　2010/11

    DOI： 10.1016/j.jbiotec.2010.09.177 　

    ISSN： 0168-1656

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

    Yoshiyuki Ohtsubo, Shintaro Suzuki, Kaori Onuma, Hiroyuki Goto, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BIOTECHNOLOGY　150　(S1)　S240-S241　2010/11

    DOI： 10.1016/j.jbiotec.2010.09.099 　

    ISSN： 0168-1656

  81. 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

  82. 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

  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. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis Peer-reviewed

    Hikaru Suenaga, Yoshinori Koyama, Masatoshi Miyakoshi, Ryo Miyazaki, Hirokazu Yano, Masahiro Sota, Yoshiyuki Ohtsubo, Masataka Tsuda, Kentaro Miyazaki

    ISME JOURNAL　3　(12)　1335-1348　2009/12

    DOI： 10.1038/ismej.2009.76 　

    ISSN： 1751-7362

    eISSN： 1751-7370

  85. 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 Invited

    大坪 嘉行, 西山 依里, 永田 裕二, 津田 雅孝

    生物工学会誌　87　(9)　434-436　2009

    Publisher:

    ISSN： 0919-3758

  86. 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 　

    ISSN： 1340-2838

    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.

  87. 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

  88. 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

  89. 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

  90. 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　(Pt 6)　1763-1774　2008/06

    DOI： 10.1099/mic.0.2007/015537-0 　

    ISSN： 1350-0872

  91. 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

    Publisher: Japanese Society of Soil Microbiology

    DOI： 10.18946/jssm.62.2_93 　

    ISSN： 0912-2184

  92. 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　2008

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/kagakutoseibutsu.47.35 　

    ISSN： 0453-073X

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

    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

  95. 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

  96. 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

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

    Hirokazu Yano, Christin Garruto, Masahiro Sota, Yoshiyuki Ohtsubo, Yuji Nagata, Gerben J. Zylsra, Peter A. Williams, Masataka Tsuda

    PLASMID　57　(2)　231-231　2007/03

    ISSN： 0147-619X

  98. Exogenous isolation of a plasmid involved in the degradation of gamma-Hexachlorocyclohexane from its contaminated soil.

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

    PLASMID　57　(2)　233-233　2007/03

    ISSN： 0147-619X

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. Strategies for bioremediation of polychlorinated biphenyls Invited Peer-reviewed

    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

  111. The dual functions of biphenyl-degrading ability of Pseudomonas sp KKS102: Energy acquisition and substrate detoxification Peer-reviewed

    M Delawary, Y Ohtsubo, A Ohta

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　67　(9)　1970-1975　2003/09

    DOI： 10.1271/bbb.67.1970 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  112. 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

  113. 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

  114. 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

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

    GENE　256　(1-2)　223-228　2000/10

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

    ISSN： 0378-1119

  115. 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

  116. 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

Show all ︎Show first 5

Misc. 142

  1. ゲノム DNA を鋳型にした サンガーシーケンシング

    大坪嘉行

    日本ゲノム微生物学会 ニュースレター　(24)　2021/12

  2. イルミナシーケンスライブラリー、ハイブリッド型のススメ

    大坪嘉行

    日本ゲノム微生物学会 ニュースレター　(23)　2021/07

  3. 実験技術紹介コーナー(ニュースレター20号)

    大坪嘉行

    日本ゲノム微生物学会 ニュースレター　(20)　2019/12

  4. DNA精製用ミニカラムの作り方

    大坪嘉行

    日本ゲノム微生物学会 ニュースレター　(19)　2019/06

  5. 実験技術紹介コーナー「実験室での消耗品切れを防ぐ方法」

    大坪嘉行

    日本ゲノム微生物学会 ニュースレター　(16)　2017/11

  6. 実験技術紹介コーナー

    佐藤勉, 大坪嘉行

    日本ゲノム微生物学会 ニュースレター　(15)　2017/06

  7. 実験技術紹介コーナー「オートクレーブ後につかう器具乾燥機の整理法」

    本ゲノム微生物学会 ニュースレター　(14)　2016/11

  8. 実験技術紹介コーナー「汚れがこびりついてしまったL字管の洗い方」

    日本ゲノム微生物学会 ニュースレター　(13)　2016/05

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

    ISSN： 2186-7976

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

    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

  24. 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

    岸田なつみ, 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

  25. 単離細菌株を用いた有機塩素系殺虫剤分解細菌コミュニティの構成原理の解明

    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

    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

  26. 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

  27. 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

  28. Why do we need desalting after the Sanger sequence reaction?でどう？

    News Letter of the Society of Genome Microbiology, Japan　(25)　20-21　2022/06

  29. NIESコレクションのシアノバクテリアのゲノム解析

    広瀬侑, 大坪嘉行, 三澤直美, 米川千夏, 長尾信義, 志村遥平, 藤澤貴智, 兼崎友, 加藤浩, 片山光徳, 山口晴代, 吉川博文, 池内昌彦, 浴俊彦, 中村保一, 河地正伸

    日本ゲノム微生物学会年会要旨集　16th (Web)　2022

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 汽水湖からの孔径0.22μmフィルターを通過可能な新奇細菌の分離と解析

    久志本晃弥, 村口雄亮, 佐藤亜里沙, 前島由明, 福田洸平, 大坪嘉行, 道羅英夫, 金原和秀, 金原和秀, 金原和秀, 新谷政己, 新谷政己, 新谷政己

    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　29　2016/06/13

  50. 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

  51. 佐鳴湖から採取された新規微生物の生理活性解析およびゲノム解析

    村口雄亮, 久志本晃弥, 佐藤安里紗, 福田洸平, 大坪嘉行, 鈴木智大, 道羅英夫, 金原和秀, 金原和秀, 金原和秀, 新谷政己, 新谷政己, 新谷政己

    日本農芸化学会大会講演要旨集(Web)　2016　2F122 (WEB ONLY)　2016/03/05

    ISSN： 2186-7976

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. NIESシアノバクテリアの完全ゲノム解析

    広瀬侑, 藤澤貴智, 大坪嘉行, 片山光徳, 三澤直美, 若月幸子, 志村遥平, 中村保一, 河地正伸, 吉川博文, 浴俊彦, 兼崎友

    日本ゲノム微生物学会年会要旨集　10th　2016

  58. プラスミドpCAR1を保持した3宿主における転写開始点の網羅的決定と宿主間比較

    舘はる香, 水口千穂, 高橋裕里香, 大坪嘉行, 津田雅孝, 岡田憲典, 野尻秀昭

    日本農芸化学会大会講演要旨集(Web)　2016　2016

    ISSN： 2186-7976

  59. プラスミドpCAR1上の転写開始点の網羅的決定と宿主間比較

    舘はる香, 水口千穂, 高橋裕里香, 大坪嘉行, 津田雅孝, 岡田憲典, 野尻秀昭

    日本ゲノム微生物学会年会要旨集　10th　2016

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. プラスミドpCAR1上の転写開始点とプロモーター領域の網羅的解析

    舘はる香, 水口(鈴木)千穂, 高橋裕里香, 大坪嘉行, 津田雅孝, 岡田憲典, 野尻秀昭

    日本農芸化学会大会講演要旨集(Web)　2015　2015

    ISSN： 2186-7976

  67. 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 　

  68. Geminocystis属シアノバクテリアに見られる補色応答能の違い

    広瀬侑, 広瀬侑, 片山光徳, 大坪嘉行, 三澤直美, 飯岡恵里香, 須田亙, 大島健志朗, 華岡光正, 田中寛, 浴俊彦, 池内昌彦, 服部正平

    日本ゲノム微生物学会年会要旨集　9th　74　2015

  69. 日本農芸化学会大会学会見聞録

    大坪嘉行, 此木敬一, 榎本 賢, 松沢智彦, 永塚貴弘, 都築 毅, 戸部隆太, 渡部 昭, 小酒井 貴晴, 岡澤敦司

    バイオサイエンスとインダストリー　75　(4)　331-340　2014/07/10

    Publisher: バイオサイエンスインダストリー協会

    More details Close

    ISSN 0914-8981

  70. 学会見聞記 日本農芸化学会大会

    大坪嘉行, 此木敬一, 榎本賢, 後藤知子, 新谷尚弘, 米山裕, 木村ふみ子, 高橋征司, 井上奈穂, 二井勇人

    バイオサイエンスとインダストリー　72　(4)　317-326　2014/07/01

    Publisher: バイオインダストリー協会

    ISSN： 0914-8981

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. 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

  78. 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

  79. 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

  80. P15-6 プラスミドpCAR1上の遺伝子の転写開始点とプロモーター領域の網羅的解析(ポスター発表)

    舘 はる香, 高橋 裕里香, 大坪 嘉行, 津田 雅孝, 水口(鈴木) 千穂, 岡田 憲典, 野尻 秀昭

    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

  81. 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

  82. 2P-029 Genome Sequence of 2,4,6-Trichlorophenol Degrading-Bacterium Ralstonia pickettii and the Gene Analysis

    Hatta Takashi, Iwasaki Tomohiro, Hitsu Tei, Ohotsubo Yoshiyuki

    66　114-114　2014

    Publisher: 日本生物工学会

  83. Mobile catabolic genetic elements in pseudomonads

    Masataka Tsuda, Yoshiyuki Ohtsubo, Hirokazu Yano

    Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve　83-103　2014/01/01

    Publisher: Springer Japan

    DOI： 10.1007/978-4-431-54520-0_5 　

  84. 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 　

  85. 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

  86. 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

  87. 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

  88. 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

  89. 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

  90. 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　(29)　85-85　2013

    Publisher: 日本微生物生態学会

  91. 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

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 自己伝達性プラスミドの接合伝達過程において転写活性化されるプロモーターの解析

    宮腰昌利, 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　4th　2010

  104. Solexaを用いた土壌メタゲノム解析における情報解析~汚染化に伴う菌叢と代謝遺伝子の変動を追う~

    加藤広海, 豊田敦, 大坪嘉行, 丸山史人, 府中玄樹, 遠藤諒, 森宙史, 堂園亜由美, 宮腰昌利, 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　4th　2010

  105. Solexaを用いた土壌メタゲノム解析における情報解析

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

    日本ゲノム微生物学会年会要旨集　4th　2010

  106. ゲノミックアイランド由来ParAホモログによるプラスミド分配阻害

    宮腰昌利, 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　2010　2010

  107. 第二世代シークエンサーを用いた土壌汚染に対する微生物遺伝子プールの変動解析,および汚染物質分解酵素遺伝子の取得

    加藤広海, 豊田敦, 大坪嘉行, 丸山史人, 遠藤諒, 府中玄樹, 森宙史, 堂園亜由美, 宮腰昌利, 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　2010　2010

  108. IncP-9プラスミドNAH7の接合伝達を制御する受容菌染色体支配因子の解析

    井上慧, 宮崎亮, 宮腰昌利, 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　4th　2010

  109. IncP-9プラスミドNAH7の接合伝達を制御する受容菌のリン酸基転移系

    井上慧, 宮崎亮, 宮腰昌利, 大坪嘉行, 永田祐二, 津田雅孝

    日本農芸化学会大会講演要旨集　2010　2010

  110. 芳香族化合物分解系プラスミドの安定的維持を阻害する宿主因子

    宮腰昌利, 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　40th　2010

  111. 受容菌のリン酸基転移系によるナフタレン分解プラスミドNAH7の接合伝達の制御機構の解析

    井上慧, 宮崎亮, 宮腰昌利, 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　40th　2010

  112. 第二世代シークエンサを用いた,土壌汚染に伴う微生物の適応反応の解析

    加藤広海, 森宙史, 豊田敦, 大坪嘉行, 丸山史人, 府中玄樹, 遠藤諒, 堂園亜由美, 宮腰昌利, 永田裕二, 藤山秋佐夫, 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　40th　2010

  113. 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

  114. 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

  115. 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

  116. IncP-7群プラスミドの分配機構による宿主特異性

    宮腰昌利, 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

  117. ナフタレン分解プラスミドNAH7の接合伝達に関与する受容菌側因子の解析

    井上慧, 宮崎亮, 宮腰昌利, 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

  118. 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

  119. 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　(25)　6-6　2009

    Publisher: 日本微生物生態学会

  120. Signature-tagged mutagenesisによるBurkholderia multivorans ATCC17616株の土壌環境生残必須遺伝子の同定

    宮腰昌利, 須藤理絵, 西山依里, 大坪嘉行, 永田裕二, 津田雅孝

    日本農芸化学会大会講演要旨集　2008　2008

  121. 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

  122. 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 　

  123. 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

    Publisher: 秀潤社

  124. 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

  125. 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

  126. 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

  127. 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

  128. 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

  129. 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

  130. 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

  131. IVET法："in vivo"での微生物を知る

    大坪嘉行

    84　(8)　333-333　2006/08

    Publisher: 日本生物工学会

    ISSN： 0919-3758

  132. 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

  133. 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

  134. 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

  135. 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

  136. 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

  137. 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

  138. 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

  139. 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

  140. 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

  141. 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

  142. 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

Show all ︎Show first 5

Books and Other Publications 2

  1. 大学で学べる「科学的素養」 : 科学的素養の明文化～教育研究力向上のために～

    大坪 嘉行

    [Independently published], c2024　2024/07/01

    ISBN: 9798325212314

  2. Causes and Solutions of Science and Technology Decline in Japan

    2022/06

    ISBN: 9798428260090

Presentations 1

  1. 共創:微生物エコシステム構成原理 土壌細菌叢変動とレジームシフト

    第89回日本細菌学会総会　2016/03/23

Industrial Property Rights 1

  1. 二本鎖ＤＮＡ末端の加工方法

    Property Type: Patent

Research Projects 24

  1. 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 学術変革領域研究(A)

    Category: 学術変革領域研究(A)

    Institution: 東北大学

    2021/09/10 - 2026/03/31

  2. 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

  3. 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

  4. 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 Grant-in-Aid for Scientific Research (B)

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

    Institution: Tohoku University

    2022/04/01 - 2025/03/31

  5. 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

  6. 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 Grant-in-Aid for Scientific Research (B)

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

    Institution: Tohoku University

    2019/04/01 - 2022/03/31

  7. 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 Grant-in-Aid for Scientific Research (B)

    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.

  8. 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 Grant-in-Aid for Challenging Exploratory 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.

  9. Understanding of PCB-degrading soil bacterium and development of experimental methods for applied microbiology

    Ohtsubo Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

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

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

    Institution: Tohoku University

    2015/04/01 - 2018/03/31

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    To investigate a PCB degrader Acidovorax sp. KKS102, a method named qTnSeq was developed. We revealed strong 3' tailing activity of a reverse transcriptase, and a series of tailing enhancers. We also optimized an unique reaction named CIS reaction. In the CIS reaction, a single strand DNA with 3' end sequence complementary to the tail is incorporated with concomitant DNA polymerization starting from the 3' tail. We designed and created transposon cassette for qTnSeq, and constructed a Tn mutant library consisting of about 60,000 clones, and we demonstrated the usefulness of the qTnSeq method. In addition, we investigated Acidovorax sp. KKS102 with respect to its catabolite control mechanism and a mobile genetic element that carries PCB-degrading genes.

  10. 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 Grant-in-Aid for Challenging Exploratory 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.

  11. 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 Grant-in-Aid for Scientific Research (B)

    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.

  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 Grant-in-Aid for Scientific Research (B)

    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. 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 Grant-in-Aid for Challenging Exploratory Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2012/04/01 - 2014/03/31

    More details Close

    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.

  14. Studies on features and frequencies of recombination in bacterial evolution

    OHTSUBO Yoshiyuki

    Offer Organization: Japan Society for the Promotion of Science

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

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2011 - 2013

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    To clarify features and frequencies of bacterial recombinational events, two closely related bacterial strains were mixed and incubated in a sterile soil sample. After a long period of incubation cells were recovered on a solid medium, and subjected to illumina sequencing. The illumina sequencing reads were analyzed by developing and using a computational tool named 'ShortReadManager', which is now released at http://www.ige.tohoku.ac.jp/joho/gf/index.php, and I found no evidence that indicates recombination between the two strains. On the other hand, mutated DNA fragment of 16S ribosomal RNA gene was inserted into a genome of a soil bacteria, in which 5 copies of rRNA gene are present. The mutated fragment was expected to be replaced by the wild-type copy. By quantitative PCR analysis, we found a evidence that suggests concerted evolution of multi gene family.

  15. 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 Grant-in-Aid for Scientific Research (B)

    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.

  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 Grant-in-Aid for Scientific Research (B)

    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. 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 Grant-in-Aid for Challenging Exploratory 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

  18. Revealing catabolite-control mechanisms of soil bacteria

    YOSHIYUKI Ohtsubo

    Offer Organization: Japan Society for the Promotion of Science

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

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

    Institution: Tohoku University

    2008 - 2010

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    Mechanisms of the catabolite control were investigated using two soil bacteria. Sensing by the bacteria of the repressive-carbon sources were achieved after the repressive-carbon sources were metabolized. The vidences that PTS systems might play a role in the catabolite control were obtained. It was also found that BphQ-mediated promoter activation required BphP, and the C-terminal domain of BphP had an activity to activate BphQ even in the presence of the repressive carbon sources.

  19. 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 萌芽研究

    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。

  20. 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 Grant-in-Aid for Scientific Research (B)

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

    Institution: Tohoku University

    2006 - 2008

  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 Grant-in-Aid for Scientific Research (B)

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

    Institution: Tohoku University

    2006 - 2008

  22. 環境細菌のカタボライト調節分子メカニズムの解明

    大坪 嘉行

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業 若手研究(B)

    Category: 若手研究(B)

    Institution: 東北大学

    2006 - 2007

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    PCB分解菌であるAcidovorax sp. KKS102株と類縁の土壌細菌であるBurkholderia multivorans ATCC 17616株のカタボライト調節をおこす炭素源について33種類の有機化合物について抑制炭素源となるかどうかについて解析を行った。その結果、抑制炭素源はKKS102株ではモノカルボン酸およびジカルボン酸である一方で、ATCC 17616株ではグルコースおよび関連する糖であることが見いだされた。すなわち二つの株で抑制炭素源となる炭素源が明瞭に異なることを見いだした。またATCC 17616株においてもKKS102株と同様にBphQホモログがカタボライト調節に関与することを見いだした。すなわち基質認識メカニズムが異なるにもかかわらず最終的にはシグナルは相同な因子に伝達されることが推測された。 生育速度が速いことは細胞のエネルギー状態が良好であることと密接に関連していると思われるが、細胞のエネルギー状態が良いことそのこと自体はカタボライト調節を引き起こすシグナルではないことを示唆する結果を得た。また、抑制基質と代謝経路上密接に関連する物質がかならずしも抑制炭素源ではないことがあることから抑制炭素源が抑制炭素源となるには抑制炭素源が細胞の外部に存在することが重要であることが示唆された。 これらと平行してカタボライト調節に関わる遺伝子が類縁菌ゲノムにおいてどのような遺伝子領域に存在するかについて効率よく解析するためのソフトウエアを作成した。

  23. PCB分解土壌細菌のカタボライト調節メカニズムの解明

    大坪 嘉行

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業 若手研究(B)

    Category: 若手研究(B)

    Institution: 東北大学

    2004 - 2005

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    1)Psudomonas sp. KKS102のrDNAの塩基配列を決定したところ、KKS102株はbeta-proteobacteriaであるAcidovorax属に属することが明らかとなった。 2)KKS102のビフェニルPCB分解代謝オペロンのpEプロモーターのカタボライト調節メカニズムの解明を引き続き行った。昨年度までの研究によりカタボライト調節に関与する遺伝子として二成分制御系のセンサーキナーゼ(BphP)およびレスポンスレギュレーター(BphQ)をコードする遺伝子が取得され、その遺伝子破壊株が作製されていた。またpEプロモーターのカタボライト調節はBphQによる転写活性化を各種炭素源が阻害することがその本質であることが明らかにされていたが、どのようにしてBphQの活性が調節されているかについては未解明であった。BphQの転写レベルがコハク酸によって変化しないことがLacZをレポーターとしたアッセイ系により明らかとなったこと、人工的なプロモーター下でbphQを発現させてもカタボライト調節が見られることから、bphQが何らかの転写後制御を受けていることが示唆された。レスポンスレギュレーターはそのおよそ55番目付近に存在するアスパラギン酸のリン酸化によってその活性が制御される例が広く知られている。そこでこの残基(実際は58番目のアスパラギン酸残基)に変異を入れたbphQ遺伝子をbphPQの破壊株に導入した株を作製し解析したところ、通常のカタボライト調節が観察されこのアミノ酸残基がカタボライト調節に関与していることが否定された。以上、pEプロモーターのBphQによるカタボライト調節にはbphQの転写後制御が関わることが示唆されるとともに、BphQが従来知られているレスポンスレギュレーターと異なり、その活性調節にアスパラギン酸55が関与しないことが明らかとなった。

  24. 細菌由来のPCB分解遺伝子群の制御因子の解析および有効なPCB生分解系の構築

    大坪 嘉行

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業 特別研究員奨励費

    Category: 特別研究員奨励費

    Institution: 東京大学

    1998 - 2000

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Works 14

  1. QR-code based Attendance Management System "QR AMS"

    Yoshiyuki Ohtsubo

    2023/03/01 - Present

    Type: Web Service

  2. DNA配列、アミノ酸配列の相互比較描画ソフトウエア「SeqView」

    大坪嘉行

    2021/08/01 - Present

  3. 研究機器共用利用促進システム「DeviceFace」

    大坪嘉行

    2020/04/01 - Present

    Type: Web Service

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    DeviceFaceは、研究機器の共同利用の促進によって研究環境を向上することを目的に作成したウエブシステムです。 当システムにより、お手持ちの研究機器をウエブベースでDeviceFace参加者に公開でき、 また当システムのウエブ使用簿により、どこにどんな機器があり、誰がどれくらい使ったかを「見える化」できます。公開は簡単に取り消せます。 当システムの狙いは、各研究室が機能的に同等な機器を冗長に保有することを防ぐことで予算の効率的使用を可能にすることです。 また同時に、同じ機器の使用者間のコミュニケーションがウエブ使用簿により促進されることで、機器の取り扱い技術が向上することを期待しています。 本システムは研究の現場から研究者の視点で作成しました。おそらく教育研究機関がトップダウンで導入するような既存のシステムとは様々な点で異なった特色あるシステムになっていると思います。 【柔軟性】本システムの主体はそれぞれの研究者です。研究者が自らの意思で手元の機器を公開できます。機器の公開および取り消しは、システム管理者の手を経ることはなく、迅速かつ柔軟に行うことができます。機器の写真も簡単にアップロードすることができます。この柔軟性により、機器の価格によらずどんなものでも公開できます。 【管理タスクの分散】 機器公開者は、情報の更新などの管理権限を委譲することができます。これにより教員など機器管理者が忙しいためにシステムが回らないという事態を防ぐことができます。機器公開および取り消し、情報の更新などは、機器管理者が行うのでシステム管理者の業務はあまりありません。システム管理者がルーチンでしなくてはならないのは、新たに教員となった人の登録と研究グループの更新だけです。 【機器公開者のインセンティブ】機器保有者が機器を公開するインセンティブは、機器の維持管理費の削減です。機器の中には使用せずとも一定の維持コストがかかるものがあります。複数の研究グループが使用するようになればコストを分割できます。DeviceFaceのウエブ使用簿で入力されたデータは集計され、どの研究グループがどれだけ使用したかを容易に把握できるように出力されます。これにより、受益者負担根拠資料を容易に作成できます。インセンティブに対する効果は未知数ですが、公開機器について各ユーザーは「いいね」ボタンを押すことができます。「いいね」情報については、機器の管理者は管理画面より閲覧することができます。 【ウエブ使用簿】使用簿に表示されるQRコード (二次元バーコード)を印刷して機器に貼り付ければ、スマホなどの端末より当該機器のウエブ使用簿に容易にアクセスできます。共通機器の周りには、よく使用簿ノートが置かれていますが、ウエブ使用簿の方がはるかに効率的です。 【ウエブ予約カレンダー】予約カレンダーを利用できます。 【英語環境】日本語と英語を切り替えられます。入力データに3つの半角ビックリマーク(!!!)があると!!!より前の部分が日本語環境で、後ろの部分が英語環境で表示されます。!!!がない場合は全体が表示されます。 【共用化促進のための課題】本システムは機器共用化のために有効に機能するものと思いますが、機器公開に対してインセンティブがより強く働くような仕組み、制度が必要と考えています。例えば、公開者の受益者負担額分の全部または一部を研究機関が肩代わりする、といった制度です。間違えて公開されている機器と同じ機器を購入してしまわないようにチェックする体制も必要かもしれません。

  4. シーケンサーウエブ使用簿システム

    大坪 嘉行

    2018/01 -

    Type: Software

  5. シーケンサー予約システム

    大坪 嘉行

    2018/01 -

    Type: Web Service

  6. シーケンサー由来データの解析ソフトTraceViewer

    2016/01/01 -

    Type: Software

  7. DNA配列の相補鎖を返すエクセル関数comp()

    http://www.ige.tohoku.ac.jp/joho/labhome/tool.html 2012/07/22 -

    Type: Software

  8. DNA配列を翻訳するエクセル関数honyaku()

    http://www.ige.tohoku.ac.jp/joho/labhome/tool.html 2012/07/22 -

    Type: Software

  9. Finishing用ツールAceFileViewer

    http://www.ige.tohoku.ac.jp/joho/gf/index.php 2012/07/20 -

    Type: Software

  10. 次世代シーケンサーデータ解析ツールShortReadManager

    http://www.ige.tohoku.ac.jp/joho/gf/index.php 2012/07/17 -

    Type: Software

  11. Finishing用ツールGenoFinisher

    http://www.ige.tohoku.ac.jp/joho/gf/index.php 2011/07/04 -

    Type: Software

  12. 遺伝子の座標データをもとに描画するエクセルマクロ

    http://www.ige.tohoku.ac.jp/joho/labhome/tool.html 2008/04/08 -

    Type: Software

  13. サーキュラーマップ描画ツールArcWithColor

    http://www.ige.tohoku.ac.jp/joho/gmProject/gmdownloadJP.html 2008/02/21 -

    Type: Software

  14. 比較ゲノム他有用ツールGenomeMatcher

    http://www.ige.tohoku.ac.jp/joho/gmProject/gmhomeJP.html 2007/11/12 -

    Type: Software

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Other 1

  1. 細菌の比較ゲノム解析研究に関する研究

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    不明