A5102803885- Microbial bioremediation and biosurfactants
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Structure and Function
- Bacterial Genetics and Biotechnology
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Legume Nitrogen Fixing Symbiosis
- Chemical Reactions and Isotopes
- Enzyme Catalysis and Immobilization
- Protein Structure and Dynamics
- Toxic Organic Pollutants Impact
- Bacteriophages and microbial interactions
- Microbial metabolism and enzyme function
- Wastewater Treatment and Nitrogen Removal
- Environmental remediation with nanomaterials
- Oxidative Organic Chemistry Reactions
- Microbial Fuel Cells and Bioremediation
- Plant Pathogenic Bacteria Studies
- Biofuel production and bioconversion
- Pesticide and Herbicide Environmental Studies
- Electrochemical Analysis and Applications
- Pharmaceutical and Antibiotic Environmental Impacts
- Chemical Synthesis and Reactions
- Amino Acid Enzymes and Metabolism
- Antibiotic Resistance in Bacteria
Tohoku University
2016-2025
Tokushima Bunri University
2022-2024
Miyata Eye Hospital
2020
University of Tsukuba
2016
NHK Spring (Japan)
2015
Hiroshima University
2013
Toshiba (Japan)
2013
The University of Tokyo
1995-2010
National Institute of Technology and Evaluation
2010
Kitami Institute of Technology
2003-2005
The deep sequencing of 16S rRNA genes amplified by universal primers has revolutionized our understanding microbial communities allowing the characterization diversity uncultured majority. However, some also amplify eukaryotic genes, leading to a decrease in efficiency prokaryotic with possible mischaracterization community. In this study, we compared gene sequences from genome-sequenced strains and identified candidates for non-degenerate that could be used amplification genes. 50 were...
The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis needed. We developed GenomeMatcher, a stand-alone package for Mac OS X. GenomeMatcher executes BLAST MUMmer, the detected similarities are displayed in two-dimensional parallel views with similarity values indicated by color. Selection re-computation any subregions easily performed allows flexible in-depth analysis. Furthermore, symbols annotation data along views,...
We report the complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl-degrading isolated from soil sample in Tokyo. The contains single circular 5,196,935-bp chromosome and no plasmids.
The linB gene product (LinB), 1,3,4,6-tetrachloro-1,4-cyclohexadiene halidohydrolase, which is involved in the degradation of gamma-hexachlorocyclohexane Sphingomonas paucimobilis UT26 (Y. Nagata, T. Nariya, R. Ohtomo, M. Fukuda, K. Yano, and Takagi, J. Bacteriol. 175:6403-6410, 1993), was overproduced E. coli purified to homogeneity. molecular mass LinB deduced be 30 kDa by gel filtration chromatography 32 electrophoresis on sodium dodecyl sulfate-polyacrylamide gel, indicating that LiuB a...
In the loop: Engineering of surface loop in haloalkane dehalogenases affects their enantiodiscrimination behavior. The temperature dependence enantioselectivity (lnE versus 1/T) β-bromoalkanes by is reversed (red data points) deletion loop; selectivity switches back when an additional single-point mutation made. This behavior not observed for α-bromoesters. Detailed facts importance to specialist readers are published as "Supporting Information". Such documents peer-reviewed, but copy-edited...
The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in degradation of important environmental pollutant gamma-hexachlorocyclohexane. hydrolyzes a broad range halogenated cyclic and aliphatic compounds. Here, we present 1.58 A crystal structure LinB 2.0 with 1,3-propanediol, product debromination 1,3-dibromopropane, active site enzyme. belongs to alpha/beta hydrolase family contains catalytic triad (Asp108, His272, Glu132) lipase-like topological...
Structural comparison of three different haloalkane dehalogenases suggested that substrate specificity these bacterial enzymes could be significantly influenced by the size and shape their entrance tunnels. The surface residue leucine 177 positioned at tunnel opening dehalogenase from Sphingomonas paucimobilis UT26 was selected for modification based on structural phylogenetic analysis; partially blocks tunnel, it is most variable pocket in dehalogenase-like proteins with nine substitutions...
ABSTRACT Sphingomonas (formerly Pseudomonas ) paucimobilis UT26 utilizes γ-hexachlorocyclohexane (γ-HCH), a halogenated organic insecticide, as sole source of carbon and energy. In previous study, we showed that γ-HCH is degraded to chlorohydroquinone (CHQ) then hydroquinone (HQ), although the rate reaction from CHQ HQ was slow (K. Miyauchi, S. K. Suh, Y. Nagata, M. Takagi, J. Bacteriol. 180:1354–1359, 1998). this cloned characterized gene, designated linE , which located upstream linD...
ABSTRACT Sphingomonas (formerly Pseudomonas ) paucimobilis UT26 utilizes γ-hexachlorocyclohexane (γ-HCH), a halogenated organic insecticide, as sole carbon and energy source. In previous study, we showed that γ-HCH is degraded to 2,5-dichlorohydroquinone (2,5-DCHQ) (Y. Nagata, R. Ohtomo, K. Miyauchi, M. Fukuda, Yano, Takagi, J. Bacteriol. 176:3117–3125, 1994). the present cloned characterized gene, designated linD , directly involved in degradation of 2,5-DCHQ. The gene encodes peptide 343...
Plasmid partitioning and bacterial conjugation are critical processes ensuring plasmid maintenance dissemination, respectively, within populations. Although traditionally regarded as distinct phenomena, these two increasingly recognized interconnected. While ensures inheritance during cell division, its potential influence on conjugative transfer remains poorly understood. A major impediment to understanding their interplay is that partition systems often essential for stability, making it...
Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols by a simple hydrolytic mechanism. Although many bacterial strains possess HLDs or HLD homologues, LinB is the only known be involved in utilization of γ-hexachlorocyclohexane (γ-HCH), man-made chlorinated pesticide. In this study, gain insight into functional evolution toward γ-HCH utilization, linB gene γ-HCH-degrading Sphingobium japonicum strain UT26 was replaced 7 other homologous genes, including 3...
Pseudomonas sp. strain KKS102 is able to degrade biphenyl and polychlorinated biphenyls via the meta-cleavage pathway. We sequenced upstream region of bphA1A2A3BCD (open reading frame 1 [ORF1]) A4 found four ORFs in this region. As deduced amino acid sequences first, second, third are homologous enzymes from CF600 (V. Shingler, J. Powlowski, U. Marklund, Bacteriol. 174:711-724, 1992), these have been named bphE, bphG, bphF, respectively. The fourth ORF (ORF4) showed homology with ORF3...
We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 Å resolution. The data have allowed us to directly observe anisotropic motions catalytic residues. In particular, side-chain nucleophile, Asp108, displays high degree disorder. It has been modeled in two conformations, one similar that observed previously (conformation A) and strained B) approached base (His272). strain conformation B was mainly Cα−Cβ−Cγ angle (126°) deviated by...
Haloalkane dehalogenases are bacterial enzymes capable of carbon-halogen bond cleavage in halogenated compounds. To obtain insights into the mechanism haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB), we studied steady-state and presteady-state kinetics conversion substrates 1-chlorohexane, chlorocyclohexane, bromocyclohexane. The results lead to a proposal minimal kinetic consisting three main steps: (i) substrate binding, (ii) with simultaneous formation an alkyl-enzyme...
ABSTRACT γ-Hexachlorocyclohexane (γ-HCH) is one of several highly chlorinated insecticides that cause serious environmental problems. The cellular proteins a γ-HCH-degrading bacterium, Sphingomonas paucimobilis UT26, were fractionated into periplasmic, cytosolic, and membrane fractions after osmotic shock. Most two different types dehalogenase, LinA (γ-hexachlorocyclohexane dehydrochlorinase) LinB (1,3,4,6-tetrachloro-1,4-cyclohexadiene halidohydrolase), are involved in the early steps γ-HCH...
ABSTRACT Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, have open reading frames (ORFs), mlr5434 blr1087 , respectively, that encode putative haloalkane dehalogenase homologues. The crude extracts Escherichia coli strains expressing showed ability to dehalogenate 18 compounds, indicating these ORFs indeed dehalogenases. Therefore, were referred as dmlA...
Sphingomonas paucimobilis UT26 utilizes gamma-hexachlorocyclohexane (gamma-HCH) as a sole source of carbon and energy. In our previous study, we cloned characterized genes that are involved in the conversion gamma-HCH to maleylacetate (MA) via chlorohydroquinone (CHQ) UT26. this identified an MA reductase gene, designated linF, is essential for utilization A gene named linEb, whose deduced product showed significant identity LinE (53%), was located close linF. novel type ring cleavage...
ABSTRACT β-Hexachlorocyclohexane (β-HCH) is the most recalcitrant among α-, β-, γ-, and δ-isomers of HCH causes serious environmental pollution problems. We demonstrate here that haloalkane dehalogenase LinB, reported earlier to mediate second step in degradation γ-HCH Sphingomonas paucimobilis UT26, metabolizes β-HCH produce 2,3,4,5,6-pentachlorocyclohexanol.