Research Topics
| Y NagataSummaryAffiliation: Tohoku University Country: Japan Publications
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Detail Information
Publications
GenomeMatcher: a graphical user interface for DNA sequence comparisonYoshiyuki Ohtsubo
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai, Japan
BMC Bioinformatics 9:376. 2008..The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed...- Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinAY Nagata
Graduate School of Life Sciences, Tohoku University, Sendai, Japan
Proteins 45:471-7. 2001..The results suggest that LinA and scytalone dehydratase evolved from a common ancestor. LinA may have evolved from an enzyme showing a dehydratase activity... - Degradation of beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26Yuji Nagata
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Appl Environ Microbiol 71:2183-5. 2005..We demonstrate here that the haloalkane dehalogenase LinB, reported earlier to mediate the second step in the degradation of gamma-HCH in Sphingomonas paucimobilis UT26, metabolizes beta-HCH to produce 2,3,4,5,6-pentachlorocyclohexanol... - Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616Yuji Nagata
Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
J Biosci Bioeng 99:603-10. 2005..Pulsed-field gel electrophoresis and Southern blot analyses indicated that both the dnaA and dnaK gene regions exist as single copies on the 3.4 Mb chromosome... - Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26Yuji Nagata
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
FEMS Microbiol Lett 256:112-8. 2006..The linF gene encoding maleylacetate reductase was located on Chr II. These results indicated that the genes for the complete gamma-hexachlorocyclohexane degradation are dispersed on the three large replicons of UT26... - Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradationRyo Miyazaki
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Appl Environ Microbiol 72:6923-33. 2006..To the best of our knowledge, this is the first detailed report of a plasmid involved in gamma-HCH degradation... - [Metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]Yuji Nagata
Tanpakushitsu Kakusan Koso 50:1511-8. 2005 - Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basisYuji Nagata
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai, 980 8577, Japan
Appl Microbiol Biotechnol 76:741-52. 2007.... - Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinBYuji Nagata
Department of Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980 8577, Japan
Appl Environ Microbiol 69:2349-55. 2003..The sixfold mutant, which was supposed to have the active site of Rv2579, exhibited haloalkane dehalogenase activity with the haloalkanes tested, confirming that Rv2579 is a member of the haloalkane dehalogenase protein family... - Complete genome sequence of the representative ?-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26Yuji Nagata
Department of Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
J Bacteriol 192:5852-3. 2010..Here, we report the complete genome sequence of UT26, which consists of two chromosomes and three plasmids. The 15 lin genes involved in ?-HCH degradation are dispersed on the two chromosomes and one of the three plasmids... - Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal ?-hexachlorocyclohexane-degrading bacteriumYuji Nagata
Graduate School of Life Sciences, Tohoku University, Japan
Enzyme Microb Technol 49:499-508. 2011..These facts strongly suggest that IS6100 plays important roles both in the dissemination of the specific lin genes and in the genome rearrangements... - Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205Michihiro Ito
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Arch Microbiol 188:313-25. 2007..This cluster is identical to the one located on the exogenously isolated plasmid pLB1, suggesting that MI1205 had recruited the linB genes by a horizontal transfer event... - Distribution and organization of auxotrophic genes on the multichromosomal genome of Burkholderia multivorans ATCC 17616Harunobu Komatsu
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980 8577, Japan
J Bacteriol 185:3333-43. 2003..The present findings also indicated that the 2.5-Mb chromosome carried various auxotrophic genes with no structural or functional counterparts on the remaining two chromosomes... - Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNAGenki Fuchu
Department of Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
Appl Microbiol Biotechnol 79:627-32. 2008.... - 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 elementsHirokazu Yano
Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980 8577, Japan
J Mol Biol 369:11-26. 2007.... - Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approachesAkira Ono
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Appl Microbiol Biotechnol 74:501-10. 2007.... - Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transferRyo Miyazaki
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
J Bacteriol 190:6281-9. 2008.... - Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmidsHirokazu Yano
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
J Bacteriol 192:4337-47. 2010.... - High-temperature-induced transposition of insertion elements in burkholderia multivorans ATCC 17616Yoshiyuki Ohtsubo
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Appl Environ Microbiol 71:1822-8. 2005..The efficient experimental protocol developed in this study will be useful in quantitatively and simultaneously investigating various IS elements, as well as in capturing novel functional mobile elements from a wide variety of bacteria... - Identification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp. KKS102Yoshiyuki Ohtsubo
Department of Environmental Life Sciences, Graduate School of Life Sciences, 2 1 1 Katahira, Sendai 980 8577, Japan
Mol Microbiol 60:1563-75. 2006..The genes highly similar to bphQ were found from several beta-proteobacteria, such as Burkholderia cenocepacia J2315, B. multivorans ATCC17616, B. xenovorans LB400 and Ralstonia solanacearum RS1085... - Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26Ryo Endo
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
J Bacteriol 187:847-53. 2005..Our previous and present results indicate that UT26 (i) has two gene clusters for degradation of chlorinated aromatic compounds via hydroquinone-type intermediates and (ii) uses at least parts of both clusters for gamma-HCH utilization... - Strategies for bioremediation of polychlorinated biphenylsYoshiyuki Ohtsubo
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai, 980 8577, Japan
Appl Microbiol Biotechnol 65:250-8. 2004..In this mini-review, we briefly summarize these strategies and provide potentially useful knowledge for the further improvement of the bacterial breakdown of PCBs... - Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificitiesYukari Sato
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Appl Environ Microbiol 71:4372-9. 2005..The dehalogenase activity of resting cells and Northern blot analyses both revealed that the dmlA and dbjA genes were expressed under normal culture conditions in MAFF303099 and USDA110 strain cells, respectively... - Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivoransSatoshi Yuhara
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Microbiology 154:1763-74. 2008..Nine of the 13 regions were presumed to be involved in the acquisition and utilization of iron... - Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26Ryo Endo
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
J Bacteriol 189:3712-20. 2007..This study clearly demonstrated that a cellular factor besides catabolic enzymes and transcriptional regulators is essential for utilization of xenobiotic compounds in bacterial cells... - Growth inhibition by metabolites of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26Ryo Endo
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
Biosci Biotechnol Biochem 70:1029-32. 2006..Because only 2,5-DCP accumulated during gamma-HCH degradation, 2,5-DCP is thought to be a main compound for growth inhibition... - Site-specific recombination system encoded by toluene catabolic transposon Tn4651Hiroyuki Genka
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
J Bacteriol 184:4757-66. 2002..Site-specific mutagenesis of the conserved tyrosine residue in TnpS led to the loss of both the resolution and the integration activities, indicating that such a residue took part in both types of recombination... - Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110Yukari Sato
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:294-6. 2007..5%(w/v) PEG 4000, 0.2 M calcium acetate and 0.1 M Tris-HCl pH 7.7-8.0. The space group of the DbjA crystal is P2(1)2(1)2, with unit-cell parameters a = 212.9, b = 117.8, c = 55.8 A. The crystal diffracts to 1.75 A resolution... - Catalytic mechanism of the maloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26Zbynek Prokop
National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
J Biol Chem 278:45094-100. 2003.... - Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibitionAaron J Oakley
Department of Pharmacology Crystallography Centre, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
Biochemistry 41:4847-55. 2002..These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking... - Cloning and characterization of linR, involved in regulation of the downstream pathway for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26Keisuke Miyauchi
Department of Biotechnology, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
Appl Environ Microbiol 68:1803-7. 2002..These results indicated that the linR gene is directly involved in the inducible expression of the linD and linE genes... - Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombinationYoshiyuki Ohtsubo
Department of Biotechnology, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
Appl Environ Microbiol 69:146-53. 2003..This strategy removes the rate-limiting factor associated with transcription and has the potential to improve the degradation activity of a wide variety of microorganisms involved in biodegradation... - Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substratesVictor A Streltsov
Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
Biochemistry 42:10104-12. 2003..This also leads to slight contraction of the whole complex structures. The flexibility detected by crystallographic analysis is in remarkable agreement with flexibility observed by molecular dynamic simulations... - Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastorisTakashi Nakamura
Loschmidt Laboratories, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic
Protein Expr Purif 46:85-91. 2006..Our results show that LinB can be extracellularly expressed in eukaryotic cell and glycosylation had no effect on activity, protein fold and thermal stability of LinB... - Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenasesAndrea Jesenská
Loschmidt Laboratories, Masaryk University, Kamenice 5 A4, 625 00 Brno, Czech Republic
Appl Environ Microbiol 71:6736-45. 2005..The evolution and distribution of haloalkane dehalogenases among mycobacteria is discussed... - Functional analysis of unique class II insertion sequence IS1071Masahiro Sota
Department of Biological Sciences, 222 Life Sciences North, University of Idaho, Moscow, ID 83844 3051, USA
Appl Environ Microbiol 72:291-7. 2006.... - Identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26Keisuke Miyauchi
Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
Biosci Biotechnol Biochem 69:216-9. 2005..The IS, named ISsp1, existed as multi copies in UT26, and its transposition appeared to be activated during the process of Tn5-mutagenesis. It was found that transposon mutagenesis can cause endogenous mutations... - Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residuesAaron J Oakley
Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
Biochemistry 43:870-8. 2004..The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB... - Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomicsYoshikazu Shimoda
Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
DNA Res 15:297-308. 2008..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... - The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: reaction mechanism and molecular evolutionMartina Pavlova
Loschmidt Laboratories, Masaryk University, Brno, Czech Republic
J Struct Biol 157:384-92. 2007..A two-step reaction mechanism was proposed for DhmA. Evolution of different types of catalytic pentads and molecular adaptation towards the synthetic substrate 1,2-dichloroethane within the protein family is discussed... - Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetryMarta Monincová
Loschmidt Laboratories, Masaryk University, Kamenice 5 A4, 625 00 Brno, Czech Republic
Appl Environ Microbiol 73:2005-8. 2007..Detection of these activities is becoming increasingly important for engineering novel biocatalysts using the scaffolds of proteins with promiscuous activities... - Employment of the human estrogen receptor beta ligand-binding domain and co-activator SRC1 nuclear receptor-binding domain for the construction of a yeast two-hybrid detection system for endocrine disruptersHaeng-Seog Lee
Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
J Biochem (Tokyo) 131:399-405. 2002....