Y Nagata

Summary

Affiliation: Tohoku University
Country: Japan

Publications

  1. pmc GenomeMatcher: a graphical user interface for DNA sequence comparison
    Yoshiyuki Ohtsubo
    Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai, Japan
    BMC Bioinformatics 9:376. 2008
  2. ncbi request reprint Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA
    Y Nagata
    Graduate School of Life Sciences, Tohoku University, Sendai, Japan
    Proteins 45:471-7. 2001
  3. pmc Degradation of beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26
    Yuji 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
  4. ncbi request reprint Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616
    Yuji Nagata
    Graduate School of Life Sciences, Tohoku University, 2 1 1 Katahira, Sendai 980 8577, Japan
    J Biosci Bioeng 99:603-10. 2005
  5. ncbi request reprint Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26
    Yuji Nagata
    Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
    FEMS Microbiol Lett 256:112-8. 2006
  6. pmc Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation
    Ryo 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
  7. ncbi request reprint [Metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]
    Yuji Nagata
    Tanpakushitsu Kakusan Koso 50:1511-8. 2005
  8. ncbi request reprint Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis
    Yuji 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
  9. pmc Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB
    Yuji Nagata
    Department of Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980 8577, Japan
    Appl Environ Microbiol 69:2349-55. 2003
  10. pmc Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26
    Yuji 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

Collaborators

Detail Information

Publications45

  1. pmc GenomeMatcher: a graphical user interface for DNA sequence comparison
    Yoshiyuki 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...
  2. ncbi request reprint Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA
    Y 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...
  3. pmc Degradation of beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26
    Yuji 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...
  4. ncbi request reprint Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616
    Yuji 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...
  5. ncbi request reprint Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26
    Yuji 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...
  6. pmc Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation
    Ryo 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...
  7. ncbi request reprint [Metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]
    Yuji Nagata
    Tanpakushitsu Kakusan Koso 50:1511-8. 2005
  8. ncbi request reprint Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis
    Yuji 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
    ....
  9. pmc Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB
    Yuji 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...
  10. pmc Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26
    Yuji 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 γ-HCH degradation are dispersed on the two chromosomes and one of the three plasmids...
  11. doi request reprint Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium
    Yuji 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...
  12. ncbi request reprint Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205
    Michihiro 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...
  13. pmc Distribution and organization of auxotrophic genes on the multichromosomal genome of Burkholderia multivorans ATCC 17616
    Harunobu 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...
  14. doi request reprint Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNA
    Genki Fuchu
    Department of Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
    Appl Microbiol Biotechnol 79:627-32. 2008
    ....
  15. ncbi request reprint 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
    Hirokazu Yano
    Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980 8577, Japan
    J Mol Biol 369:11-26. 2007
    ....
  16. ncbi request reprint Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches
    Akira 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
    ....
  17. pmc Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer
    Ryo 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
    ....
  18. pmc Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids
    Hirokazu Yano
    Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
    J Bacteriol 192:4337-47. 2010
    ....
  19. pmc High-temperature-induced transposition of insertion elements in burkholderia multivorans ATCC 17616
    Yoshiyuki 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...
  20. ncbi request reprint Identification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp. KKS102
    Yoshiyuki 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...
  21. pmc Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26
    Ryo 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...
  22. ncbi request reprint Strategies for bioremediation of polychlorinated biphenyls
    Yoshiyuki 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...
  23. pmc Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities
    Yukari 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...
  24. doi request reprint Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans
    Satoshi 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...
  25. pmc Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26
    Ryo 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...
  26. ncbi request reprint Growth inhibition by metabolites of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26
    Ryo 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...
  27. pmc Site-specific recombination system encoded by toluene catabolic transposon Tn4651
    Hiroyuki 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...
  28. pmc Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110
    Yukari 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...
  29. ncbi request reprint Catalytic mechanism of the maloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26
    Zbynek Prokop
    National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
    J Biol Chem 278:45094-100. 2003
    ....
  30. ncbi request reprint Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition
    Aaron 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...
  31. pmc Cloning and characterization of linR, involved in regulation of the downstream pathway for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26
    Keisuke 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...
  32. pmc Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombination
    Yoshiyuki 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...
  33. ncbi request reprint Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates
    Victor 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...
  34. ncbi request reprint Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel
    Radka Chaloupkova
    National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
    J Biol Chem 278:52622-8. 2003
    ..The strategy of using site-directed mutagenesis to modify a specific entrance tunnel residue identified by structural and phylogenetic analyses, rather than combinatorial screening, generated a high percentage of viable mutants...
  35. ncbi request reprint Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris
    Takashi 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...
  36. ncbi request reprint Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26
    Jan Kmunícek
    National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
    Biochemistry 44:3390-401. 2005
    ..The mechanism of molecular adaptation toward a different specificity is discussed on the basis of quantitative comparison of models derived for two protein family members...
  37. pmc Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases
    Andrea 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...
  38. pmc Functional analysis of unique class II insertion sequence IS1071
    Masahiro Sota
    Department of Biological Sciences, 222 Life Sciences North, University of Idaho, Moscow, ID 83844 3051, USA
    Appl Environ Microbiol 72:291-7. 2006
    ....
  39. ncbi request reprint Identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26
    Keisuke 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...
  40. ncbi request reprint Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues
    Aaron 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...
  41. pmc Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics
    Yoshikazu 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...
  42. ncbi request reprint The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: reaction mechanism and molecular evolution
    Martina 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...
  43. pmc Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry
    Marta 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...
  44. ncbi request reprint Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis
    Michal Bohác
    National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
    Biochemistry 41:14272-80. 2002
    ..The differences in the halide stabilizing residues of three haloalkane dehalogenases are discussed in the light of molecular adaptation of these enzymes to their substrates...
  45. ncbi request reprint Employment of the human estrogen receptor beta ligand-binding domain and co-activator SRC1 nuclear receptor-binding domain for the construction of a yeast two-hybrid detection system for endocrine disrupters
    Haeng Seog Lee
    Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    J Biochem 131:399-405. 2002
    ....