• Journal of Life Science
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• v.25 no.2
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• pp.121-129
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• 2015

Alginates are found in marine brown seaweeds and in extracellular biofilms secreted by some bacteria. Previously, we reported an oligoalginate lyase from Sphingomonas sp. MJ-3 (MJ3-Oal) that had an exolytic activity and protein sequence homology with endolytic polymannuronate (polyM) lyase in the N-terminal region. In this study, the MJ3-Oal was tested for both exolytic and endolytic activity by homology modeling using the crystal structure of Alg17c from Saccharophagus degradans 2-40T. The tyrosine residue at the $426^{th}$ position, which possibly formed a hydrogen bond with the substrate, was mutated to phenylalanine. The FPLC profiles showed that MJ3-Oal degraded alginate quickly to monomers as a final product through the oligmers, whereas the Tyr426Phe mutant showed only exolytic alginate lyase activity. $^1H$-NMR spectra also showed that MJ3-Oal degraded the endoglycosidic bond of polyM and polyMG (polymannuronate-guluronate) blocks. These results indicate that oligoalginate lyase from Sphingomonas sp. MJ-3 probably catalyzes the degradation of both exo- and endo-glycosidic bonds of alginate.

• Journal of Microbiology and Biotechnology
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• v.28 no.9
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• pp.1502-1510
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• 2018

Organic solvent-tolerant (OST) enzymes are widely applied in various industries for their activity and stability in organic solvents, for their higher substrate solubility, and for their greater stero-selectivity. However, the criteria for identifying OST enzymes largely remain undefined. In this study, we compared the amino acid composition of 19 OST esterases with that of 19 non OST esterases. OST esterases have increased the ratio of Ala and Arg residues and decreased the ratio of Asn, Ile, Tyr, Lys, and Phe residues. Based on our amino acid composition analysis, we cloned a carboxylesterase (EstSP2) from a psychrophilic bacterium, Sphingomonas glacialis PAMC 26605, and characterized its recombinant protein. EstSP2 is a substrate specific to p-nitrophenyl acetate and hydrolyzed aspirin, with optimal activity at $40^{\circ}C$; at $4^{\circ}C$, the activity is approximately 50% of its maximum. As expected, EstSP2 showed tolerance in up to 40% concentration of polar organic solvents, including dimethyl sulfoxide, methanol, and ethanol. The results of this study suggest that selecting OST esterases based on their amino acid composition could be a novel approach to identifying OST esterases produced from bacterial genomes.

• Korean Journal of Microbiology
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• v.43 no.2
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• pp.83-90
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• 2007

Sphingomonas sp. KS 301, which was isolated from oil contaminated soil, was shown to have five different SODs (SODI, II, III, IV, V) which can be separated by DEAE-Sepharose chromatography, and SOD III was finally purified in this study by ammonium sulfate precipitation, DEAE-Sepharose chromatography, Superose 12 gel filtration and Uno-Q1 ion exchange chromatography. The molecular weight of SOD III was 23 kDa as determined by SDS-PAGE and the apparent molecular weight of the native enzyme was estimated to be approximately 71 kDa by Superose-12 gel filtration chromatography. These data suggest that the purified SOD consists of at least two subunits. The specific activity of the SOD III was higher than Mn type or Fe type SOD of Escherichia coli by 5 fold. To determine the type of SOD III, inhibitory effects of $NaN_{3},\;H_{2}O_{2},\;KCN$ were examined. 10 mM $NaN_{3}$ was able to inhibit 56% of the SOD III activity, which indicates that this SOD is Mn type. The optimum pH of the SOD III was 7.0 and the optimum temperature was $20^{\circ}C$. N-terminal amino acid sequence of purified SOD III was most similar to those of Psudomonase ovalis and Vibrio cholerae among bacteria.

• Korean Journal of Microbiology
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• v.41 no.3
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• pp.195-200
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• 2005

Comamonas sp. strain DJ-12 is a bacterial isolate capable of degrading of 4-chlorobiphenyl (4CB) as a carbon and energy source. The degradation pathway was characterized as being conducted by consecutive reactions of the meta-degradation of 4CB, hydrolytic dechlorination of 4-chlorobenzoate (4CBA), hydroxylation of 4-hydroxybenzoate, and meta-degradation of protocatechuate to product TCA metabolites. The 6.8 kb fragment from the chromosomal DNA of Comamonas sp. strain DJ-12 included the genes encoding for the meta-degradation of PCA; the genes of protocatechuate 4,5-dioxygenase alpha and beta subunits (pmcA and pmcB), 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (pmcC), 2-pyrone-4,6-dicarboxylate hydrolase (pmcD), 4-oxalomesaconate (OMA) hydratase(pmcE), 4-oxalocitramalate (OCM) aldolase (pmcF), and transporter gene (pmcT). They were organized in the order of pmcT-pmcE-pmcF-pmcD-pmcA-pmcB-pmcC. The amino acid sequences deduced from the nucleotide sequences of pmcABCDEFT genes from Comamonas sp. strain DJ-12 exhibited 94 to $98\%$ homologies with those of Comamonas testosteroni BR6020 and Pseudomonas ochraceae NGJ1, but only 52 to $74\%$ with homologies Sphingomonas paucimobilis SYK-6, Sphingomonas sp. LB126, and Arthrobacter keyseri 12B.

• Journal of Microbiology and Biotechnology
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• v.16 no.8
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• pp.1306-1310
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• 2006

Sphingomonas sp. strain SB5 could degrade carbofuran and carbofuran-7-phenol to a hydrolytic product, 2-hydroxy-3-(3-methlypropan-2-o1)phenol, and several red metabolites. However, the chemical structures of the red metabolites have largely remained unidentified. In this study, we identified the structure of one of the red metabolites as 5-(2-hydroxy-2-methyl-propyl)-2,2-dimethyl- 2,3-dihydro-naphtho[2,3-6]furan-4,6,7,9-tetrone by using mass spectrometric and NMR ($^1$H, $^{13}$C) analyses. It is suggested that the red metabolite resulted from condensation of some metabolites in the degradation of 2-hydroxy-3-(3-methlypropan-2-o1)phenol, a hydrolytic product derived from carbofuran. To our knowledge, this is the first paper to report a red metabolite in bacterial degradation of the insecticide carbofuran.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.724-727
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• 2000

A Phenanthrene-degrading bacterium, Strain 1-21 was isolated from oil-contaminated soil. This strain was a Gram-negative, aerobic, and rod-shaped bacterium, and exhibited a 99% sequence similarity of 16S rDNA to that of Sphingomonas subarctica. The major cellular fatty acid was a summed feature 7(18:1 w7c, 18:1 w9t, 18:1 s12t), which is a characteristic of the Sphingomonas species. When 200 and 1,000 ppm of phenanthrene was added as the sole carbon source, Strain 1-21 degraded 98% and 67% after 10 days of incubation, respectively. Futhermore, this strain was also able to utilized naphthalene and fluorene as sole carbon and energy sources.

• Proceedings of the Korean Society of Life Science Conference
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• 2007.10a
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• pp.60.2-60.2
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• 2007

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• Journal of Korean Society on Water Environment
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• v.27 no.3
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• pp.334-341
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• 2011

The free residual chlorine of tap water samples, collected from 266 faucets on the water pipe network in Daegu City, was between 0.1 and 0.79 mg/L. On microorganic tests, general bacteria and the coliform goup were not detected and thus the tap water was turned out to be fit to drink. In particular, samples of which free residual chlorine was 0.1 mg/L and over were cultured in R2A agar media at $25^{\circ}C$ for 7 days, and as a result heterotrophic bacteria were detected in 65.9% of samples; (1). The closer tap water got to the faucet from the stilling basin, the lower residual chlorine concentration became but the more the bacterial count became. And, more bacteria were detected in the R2A agar medium than in the PCA medium. (2). In the case of separated strains, most colonies were reddish or yellowish. 16S rRNA sequence was identified as Methylobacterium sp. and Williamsia sp., and yellow strain was identified as Sphingomonas sp., Sphingobium sp., Novosphingobium sp., Blastomonas sp., Rhodococcus sp. and Microbacterium sp. White strain was identified as Staphylococcus sp. (3). Sterilized tap water in polyethylene bottles was inoculated with separated strain and was left as it was for 2 months. As a result, bio-film was observed in tap water inoculated with Methylobacterium sp. and Sphingomonas sp. It was found that heterotrophic bacteria increased when free residual chlorine was removed from tap water in the water pipe network. Thus, there is a need to determine a base value for heterotrophic bacteria in order to check the cleanliness of tap water in the water pipe network.

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1170-1177
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• 2005

Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to monitor inoculated oil-degrading microorganisms during bioremedial treatability tests. A pair of universal primers, fluorescently labeled 521F and 1392R, was employed to amplify small subunit rDNA in order to simultaneously detect two bacterial strains, Corynebacterium sp. IC10 and Sphingomonas sp. KH3-2, and a yeast strain, Yarrowia lipolytica 180. Digestion of the 5'-end fluorescence/labeled PCR products with HhaI produced specific terminal-restriction fragments (T-RFs) of 185 and 442 bases, corresponding to Corynebacterium sp. IC10 and Y. lipolytica 180, respectively. The enzyme NruI produced a specific T-RF of 338 bases for Sphingomonas sp. KH3-2. The detection limit for oildegrading microorganisms that were inoculated into natural environments was determined to be $0.01\%$ of the total microbial count, regardless of the background environment. When three oil-degrading microorganisms were released into oil-contaminated sand microenvironments, strains IC10 and 180 survived for 35 days after inoculation, whereas strain KH3-2 was detected at 8 days, but not at 35 days. This result implies that T-RFLP could be a useful tool for monitoring the survival and relative abundance of specific microbial strains inoculated into contaminated environments.

• Journal of the Korea Organic Resources Recycling Association
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• v.19 no.4
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• pp.84-89
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• 2011

Cellulose-degrading bacteria were isolated and identified from cocopeat which has a good quality as a bulking agent in composting. Various bacteria from different sourecs of cocopeat were detected on CMC agar media, and these were found to be Burkholderi2a sp., Bacillu subtilis, Sphingomonas sp., Rhodotorula sp. & Pseudomonas sp. etc. Among these, four bacteria were further selected and analyzed for their biochemical characteristics and CMCase activities. CMCase activities of four bacteria, P. aeruginosa, P. stutzeri, B. subtilis, and P. luteola were found to be 83%, 40%, 8%, 6%, respectively, compared with that of the standard strain Cellulomonas sp.