SAMPLE COMPANY

業績(原著論文・総説・著書) 2013年〜現在

 

2023 年

Yusuf Habibullah KO, Ito R, Stari L, Kishida K, Ohtsubo Y, Masai E, Fukuda M, Miyauchi K, Nagata Y Degradation of DDT by γ-hexachlorocyclohexane dehydrochlorinase LinA. Biosci. Biotechnol. Biochem. 87: in press (2023)

Kato H, Ohtsubo Y, Hirano S, Masuda S, Shibata A, Shirasu K, Nagata Y Draft genome sequence of Cupriavidus sp. strain TKC, isolated from a γ-hexachlorocyclohexane-degrading community. Microbiology Resource Announcements in press (2023)

Idola D, Mori H, Nagata H, Nonaka L, Yano H Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria. Mobile DNA 14: Article number 7 (2023)

永田裕二、加藤広海、大坪嘉行 土壌微生物による加賀王合成農薬分解のフロンティア 農薬学会誌48(2): 125-131 (2023)

永田裕二 たったひとつの遺伝子の発現でかすみを食べる細菌に バイオミディア 生物工学会誌 第101巻 第10号 (2023)

 

2022 年

Yang D, Kato H, Kawatsu K, Osada Y, Azuma T, Nagata Y, Kondoh M Reconstruction of a Soil Microbial Network Induced by Stress Temperature. Microbiol Spectr. e02748-22 (2022)

Ohtsubo Y, Hirose Y, Nagata Y Algorisms used for in silico finishing of bacterial genomes based on short-read assemblage implemented in GenoFinisher, AceFileViewer, and ShortReadManager. Biosci. Biotechnol. Biochem. 86: 693-703 (2022)

Kato H, Su L, Tanaka A, Katsu H, Ohtsubo Y, Otsuka S, Kenoo K, Nagata Y Genome evolution related to g-hexachlorocyclohexane metabolic function in the soil microbial population. Biosci. Biotechnol. Biochem. 86: 800-809 (2022)

永田裕二、加藤広海、大坪嘉行 従属栄養細菌の極貧影響環境でのCO2依存的な増殖現象 環境バイオテクノロジー学会誌 22 (1): 22 (1): 9-13 (2022)

 

2021 年

Masaki M, Iizuka R, Kato H, Kojima Y, Ogawa T, Yoshida M, Matsushita Y, and Katayama Y Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases. Microbes and Environments 36(2): ME20058 (2021)

Kawamoto Y, Kato H, Nagata Y, and Urabe J Microbial communities developing within bulk sediments under fish carcasses on a tidal flat. PLOS ONE 16(2): e0247220 (2021)

 

2020 年

Kato H, Ogawa T, Ohta H, and Katayama Y Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method. Microbes and environments 35(2): ME19139 (2020)

Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M, Furuta Y, Nishiyama T, Shigenobu S, Hasebe M, Toyoda A, Suzuki Y, Sugano S, Shibayama K, Kobayashi I Networking and specificity-changing DNA methyltransferease in Helicobacter pylori. Frontiers in Microbiology: in press (2020)

Nonoyama S, Kishida K, Sakai K, Nagata Y, Ohtsubo Y, Tsuda M A transcriptional regulator, IscR, of Burkholderia multivorans acts as both repressor and activator for transcription of iron-sulfur cluster-biosynthetic isc operon. Research in Microbiology 171: 319-330 (2020)

Miyakoshi M, Ohtsubo Y, Nagata Y, and Tsuda M Transcriptome analysis of zygotic induction during conjugative transfer of plasmid RP4. Frontiers in Microbiology 11: 1125 (2020)

Marek M, Chaloupkova R, Prudnikova T, Sato Y, Rezacova P, Nagata Y, Smatanova IK, Damborsky J Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal 18: 1352-1362 (2020)

Inaba S, Sakai H, Kato H, Horiuchi T, Yano H, Ohtsubo Y, Tsuda M, Nagata Y Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions. Microbiology 166: 531-545 (2020)

Nagata Y Special Issue: Microbial degradation of xenobiotics. Microorganisms 8: 487 (2020)

永田裕二 従属栄養細菌のCO2依存的な極貧栄養環境適応 バイオサイエンスとインダストリー 78(6) 498-500 (2020)

 

2019 年

Arikawa K, Ichijo T, Nakajima S, Nishiuchi Y, Yano H, Tamaru A, Yoshida S, Maruyama F, Ota A, Nasu M, Starkova DA, Mokrousov I, Narvskaya OV, and Iwamoto T Genetic relatedness of Mycobacterium avium subsp. hominissuis isolates from bathrooms of healthy volunteers, rivers, and soils in Japan with human clinical isolates from different geographical areas. Infect. Genet. Evol. 73: 103923 (2019)

Kishida K, Nonoyama S, Lukas T, Kawahara S, Kudo K, Nagata Y, Ohtsubo Y, Tsuda M Conjugative transfer of IncP-9 catabolic plasmids requires a previously uncharacterized gene, mpfK, whose homologs are conserved in various MPFT-type plasmids. Appl Environ Microbiol 85: e01850-19 (2019)

Yano H, Suzuki, H, Maruyama F, Iwamoto T The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium BMC Genomics 20: 752 (2019)

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

Nagata Y, Kato H, Ohtsubo, Y, Tsuda M Lessons from the genomes of lindane‐degrading sphingomonads. Environ. Microbiol. Rep. 11: 630-644 (2019)

Yano H, Shintani M, Tomita M, Suzuki H, and Oshima T Reconsidering plasmid maintenance factors for computational plasmid design. Comput. Struct. Biotechnol. J. 17: 70-81 (2019)

Nagata Y, Kato H, Ohtsubo, Y, Tsuda M Mobile genetic elements involved in the evolution of bacteria that degrade recalcitrant xenobiotic compounds, Chapter 9. pp 215-244. In Nishida H and Oshima T (ed), DNA Traffic in the Environment. Springer (2019)

 

2018 年

Nonaka L, Yamamoto T, Maruyama F, Hirose Y, Onishi Y, Kobayashi T, Suzuki S, Nomura N, Masuda M, and Yano H Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate. PLoS One 13: e0198613 (2018)

Miyazaki R*, Yano H*, Sentchilo V, and Van der Meer JR Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Scientific Rep. 8: 5550 (2018) *Equal contribution

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

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

Katsuyama Y, Sato Y, Sugai Y, Higashiyama Y, Senda M, Senda T, and Ohnishi Y Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination. The FEBS journal, 285: 1540-1555 (2018)

Ray-Gallet D, Ricketts MD, Sato Y, Gupta K, Boyarchuk E, Senda T, Marmorstein R, Almouzni G Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit. Nat Commun. 9:3103 (2018)

加藤広海、小川なつみ、津田雅孝、永田裕二 汚染物質分解コンソーシアムにおけるキープレイヤーとオーディエンス 環境バイオテクノロジー学会誌 18 (1): 15-20 (2018)

 

2017 年

Sugawara M, Tsukui T, Kaneko T, Ohtsubo Y, Sato S, Nagata Y, Tsuda M, Mitsui H, Minamisawa K Complete genome sequence of Bradyrhizobium diazoefficiens USDA 122, a nitrogen-fixing soybean symbiont. Genome A. 5:e01743-16 (2017)

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

Kishida K, Inoue K, Ohtsubo Y, Nagata Y, Tsuda M Conjugative transfer system of IncP-9 naphthalene-catabolic plasmid NAH7: characterization of its oriT region and relaxase and host range of conjugative system. Appl. Environ. Microbiol. 83: e02359-16 (2017)

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

Sato T, Nonoyama S, Kimura A, Nagata Y, Ohtsubo Y, Tsuda M The small protein HemP is a transcriptional activator for the hemin uptake operon in Burkholderia multivorans ATCC 17616. Appl. Environ. Microbiol. 83: e00479-17 (2017)

Stalder T, Rogers LM, Renfrow C, Yano H, Smith Z. and Top EM Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance. Scientific Rep. 7: 4588 (2017)

Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, and Maruyama F Population structure and local adaptation of MAC lung disease agent Mycobacterium avium subsp. hominissuis. Genome Biol. Evol. 9: 2403-2417 (2017)

T. Ogawa, S. Hattori, K. Kamezaki, H. Kato, N. Yoshida, Y. Katayama Isotopic Fractionation of Sulfur in Carbonyl Sulfide by Carbonyl Sulfide Hydrolase of Thiobacillus thioparus THI115. Microbes and environments 32, (2017), 367-375

 

2016 年

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

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

Ohtsubo Y, Nonoyama S, Nagata Y, Numata M, Tsuchikane, K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. Complete genome sequence of Sphingopyxis terrae strain 203-1 (NBRC 111660), a polyethylene glycol degrader. Genome Announc. 4: e00530-16 (2016)

Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. Biodegradation of organochlorine pesticides. Chapter 5.1.2 p. 1-30. In: Manual of Environmental Microbiology, 4th ed. ASM Press, Washington, DC. (2016)

Ohtsubo Y, Nonoyama S, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. Complete genome sequence of Sphingopyxis macrogoltabida strain 203N (NBRC 111659), a polyethylene glycol degrader. Genome Announc. 4: e00529-16 (2016)

Ohtsubo Y, Nonoyama S, Ogawa N, Kato H, Nagata Y, Tsuda M. Complete genome sequence of Burkholderia caribensis Bcrs1W (NBRC110739), a strain co-residing with phenanthrene degrader Mycobacterium sp. Epa45. J Biotechnol. 228: 67-68 (2016)

Tabata M, Ohhata S, Kawasumi T, Nikawadori Y, Kishida K, Sato T, Ohtsubo Y, Tsuda M, Nagata Y. Complete genome sequence of a γ-hexachlorocyclohexane degrader, Sphingobium sp. strain TKS, which was isolated from a γ-hexachlorocyclohexane-degrading microbial community. Genome Announc. 4: e00247-16 (2016)

Tabata M, Ohhata S, Nikawadori Y, Sato T, Kishida K, Ohtsubo Y, Tsuda M, Nagata Y. Complete genome sequence of a γ-hexachlorocyclohexane-degrading bacterium Sphingobium sp. strain MI1205. Genome Announc. 4: e00246-16 (2016)

Minami T, Ohtsubo Y, Anda M, Nagata Y, Tsuda M, Mitsui H, Sugawara M, Minamisawa K. Complete genome sequence of Methylobacterium sp. strain AMS5, an isolate from a soybean stem. Genome Announc. 4: e00144-16 (2016)

Kamezaki K, Hattori S, Ogawa T, Toyoda S, Kato H, Katayama Y, Yoshida N. Sulfur isotopic fractionation of carbonyl sulfide during degradation by soil bacteria. Environ. Sci. Technol. 50: 3537-44 (2016)

 

2015 年

Anda M, Ohtsubo Y, Okubo T, Sugawara M, Nagata Y, Tsuda M, Minamisawa K, Mitsui H. Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome. Proc Natl Acad Sci USA 112: 14343-14347 (2015)

Nagata Y, Ohtsubo Y, Tsuda M. Properties and biotechnological applications of natural and engineered haloalkane dehagoneases. Appl. Microbiol. Biotechnol. 99:9865-9881 (2015)

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

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

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

Ohtsubo Y, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F. Complete genome sequence of a polypropylene glycol and polyethylene glycol-degrading strain Sphingopyxis macrogoltabida EY-1. Genome Announc. 3: e01399-15 (2015)

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

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

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

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

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

 

2014 年

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

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

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

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

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

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

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

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

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

 

2013 年

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

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

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

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

Hassan K, Gora A, Brezvsky J, Chaloupkova R, Moskalikova H, Fortova A, Nagata Y, Damborsky J, Prokop Z. The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58. FEBS J. 280: 3149-3159 (2013)

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

Yano H, Genka H, Ohtsubo Y, Nagata Y, Top EM, Tsuda M. Coinetgrate-resolution of toluene-catabolic transposon Tn4651. Plasmid 69: 24-35 (2013)

永山浩史, 菅原智詞, 遠藤諒, 加藤広海, 大坪嘉行, 永田裕二, 津田雅孝. 機能相補による芳香族化合物複合汚染土壌からの新規分解酵素遺伝子の探索. J. Environ. Biotechnol. 13: 51-56 (2013)

加藤広海,河田雅圭, 他(共著). 東北大学生態適応グローバルCOE編. 生態適応科学 自然のしくみを活かし、持続可能な未来を拓く.日経BP社. (2013)

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