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Yoshiyuki Otsubo

Section

Graduate School of Life Sciences

Job title

Associate Professor

Degree

博士（農学）（東京大学）
修士（農学）（東京大学）

researchmap

https://researchmap.jp/read0200797

J-GLOBAL ID

200901009017909830

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

農芸化学奨励賞

2014/03/27　日本農芸化学会
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 127

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

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

2025/01/22
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2025.01.22.634284 　

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ABSTRACT Plasmid partitioning and bacterial conjugation are critical processes ensuring plasmid maintenance and dissemination, respectively, within bacterial populations. Although traditionally regarded as distinct phenomena, these two processes are increasingly recognized as interconnected. While partitioning ensures plasmid inheritance during cell division, its potential influence on conjugative transfer remains poorly understood. A major impediment to understanding their interplay is that partition systems are often essential for plasmid stability, making it difficult to distinguish their direct effects on conjugation. In this study, we addressed this challenge using a mini-conjugative plasmid derived from thePseudomonas putidaNAH7 plasmid. This engineered plasmid, containing all conjugation-related genes, was cloned into anE. coli-compatible vector. Additionally, thepargenes from NAH7 were expressed from a separate plasmid to investigate their roles in conjugative transfer. Our results revealed that thepargene cluster plays a significant role in enhancing the conjugative transfer of the mini-conjugative plasmid. Specifically, ParB, a centromere-binding protein, functions as a transcriptional activator of conjugation-related genes with bindingparS_NAHsite. 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 theparS_NAHsite—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.
Evolution of the Tn4371 ICE family: traR-mediated coordination of cargo gene upregulation and horizontal transfer. International-journal

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

Microbiology spectrum　e0060724　2024/09/12

DOI： 10.1128/spectrum.00607-24 　

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

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

BMC Biotechnology　24　(1)　2024/06/19
Publisher: Springer Science and Business Media LLC
DOI： 10.1186/s12896-024-00867-0 　

eISSN： 1472-6750

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Abstract Background γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degrading bacterial strains are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the low survival rate of the exogenous bacteria. Another strategy for the bioremediation of γ-HCH involves the use of transgenic plants expressing bacterial enzyme for γ-HCH degradation through phytoremediation. Results We generated transgenic Arabidopsis thaliana expressing γ-HCH dehydrochlroninase LinA from bacterium Sphingobium japonicum strain UT26. Among the transgenic Arabidopsis T2 lines, we obtained one line (A5) that expressed and accumulated LinA well. The A5-derived T3 plants showed higher tolerance to γ-HCH than the non-transformant control plants, indicating that γ-HCH is toxic for Arabidopsis thaliana and that this effect is relieved by LinA expression. The crude extract of the A5 plants showed γ-HCH degradation activity, and metabolites of γ-HCH produced by the LinA reaction were detected in the assay solution, indicating that the A5 plants accumulated the active LinA protein. In some A5 lines, the whole plant absorbed and degraded more than 99% of γ-HCH (10 ppm) in the liquid medium within 36 h. Conclusion The transgenic Arabidopsis expressing active LinA absorbed and degraded γ-HCH in the liquid medium, indicating the high potential of LinA-expressing transgenic plants for the phytoremediation of environmental γ-HCH. This study marks a crucial step toward the practical use of transgenic plants for the phytoremediation of POPs.
Increase of secondary metabolites in sweet basil (Ocimum basilicum L.) leaves by exposure to N2O5 with plasma technology

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

Scientific Reports　14　(1)　2024/06/04
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-024-63508-8 　

eISSN： 2045-2322

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Abstract Exposure to N₂O₅ generated by plasma technology activates immunity in Arabidopsis through tryptophan metabolites. However, little is known about the effects of N₂O₅ exposure on other plant species. Sweet basil synthesizes many valuable secondary metabolites in its leaves. Therefore, metabolomic analyses were performed at three different exposure levels [9.7 (Ex1), 19.4 (Ex2) and 29.1 (Ex3) μmol] to assess the effects of N₂O₅ on basil leaves. As a result, cinnamaldehyde and phenolic acids increased with increasing doses. Certain flavonoids, columbianetin, and caryophyllene oxide increased with lower Ex1 exposure, cineole and methyl eugenol increased with moderate Ex2 exposure and l-glutathione GSH also increased with higher Ex3 exposure. Furthermore, gene expression analysis by quantitative RT-PCR showed that certain genes involved in the syntheses of secondary metabolites and jasmonic acid were significantly up-regulated early after N₂O₅ exposure. These results suggest that N₂O₅ exposure increases several valuable secondary metabolites in sweet basil leaves via plant defense responses in a controllable system.
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.
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　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.
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.
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.
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 　
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 　
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　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.
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.
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.
Transcriptome Analysis of Zygotic Induction During Conjugative Transfer of Plasmid RP4 Peer-reviewed

Masatoshi Miyakoshi, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

Frontiers in Microbiology　11　2020/06/18
Publisher: Frontiers Media SA
DOI： 10.3389/fmicb.2020.01125 　

eISSN： 1664-302X
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.
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.
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.
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.
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.
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.
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).
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.
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.
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
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
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
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
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
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.
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.
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Complete Genome Sequence of Acidovorax sp Strain KKS102, a Polychlorinated-Biphenyl Degrader Peer-reviewed

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

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

DOI： 10.1128/JB.01848-12 　

ISSN： 0021-9193
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. Peer-reviewed

Y. Nagata, R, Endo, M. Ito, Y. Ohtsubo, M. Tsuda

App. Microbiol. Biotechnol.　2007/04/01
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
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
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
Complete nucleotide sequence of an exogenously isolated plasmid pLB1 involved in the degradation of g-hexachlorocyclohexane Peer-reviewed

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

Appl. Environ. Microbiol　2006/11

DOI： 10.1128/AEM.01531-06 　
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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Misc. 80

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 　
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
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

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ISSN 0914-8981
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
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
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
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
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
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
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
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
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
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
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
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 　
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 　
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 　
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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Books and Other Publications 2

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
Causes and Solutions of Science and Technology Decline in Japan

2022/06

ISBN: 9798428260090

Presentations 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

二本鎖ＤＮＡ末端の加工方法

Property Type: Patent

Research Projects 23

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
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
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
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
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
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.
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.
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.
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.
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.
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.
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

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

QR-code based Attendance Management System "QR AMS"

Yoshiyuki Ohtsubo

2023/03/01 - Present

Type: Web Service
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
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。
シーケンサーウエブ使用簿システム

大坪嘉行

2018/01 -

Type: Software
シーケンサー予約システム

大坪嘉行

2018/01 -

Type: Web Service
シーケンサー由来データの解析ソフトTraceViewer

2016/01/01 -

Type: Software
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
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
Finishing用ツールAceFileViewer

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

Type: Software
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
Finishing用ツールGenoFinisher

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

Type: Software
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
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
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

細菌の比較ゲノム解析研究に関する研究

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不明