• Journal of Microbiology and Biotechnology
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• v.18 no.4
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• pp.616-623
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• 2008

In spite of an increasing interest in fucoidans as biologically active compounds, no convenient commercial sources with fucoidanase activity are yet available. A marine bacterial strain that showed confluent growth on a minimal medium containing fucoidan, prepared from Korean Undaria pinnatifida sporophylls, as the sole carbon source was isolated and identified based on a 16S rDNA sequence analysis as a strain of Sphingomonas paucimobilis, and named Sphingomonas paucimobilis PF-1. The strain depolymerized fucoidan into more than 7 distinct low-molecular-mass fucose-containing oligosaccharides, ranging from 305 to 3,749 Da. The enzyme activity was shown to be associated with the whole cell, suggesting the possibility of a surface display of the enzyme. However, a whole-cell enzyme preparation neither released the monomer L-fucose from the fucoidan nor hydrolyzed the chromogenic substrate p-nitrophenyl-${\alpha}$-L-fucoside, indicating that the enzyme may be an endo-acting fucoidanase rather than an ${\alpha}$-L-fucosidase. Therefore, this would appear to be the first report on fucoidanolytic activity by a Sphingomonas species and also the first report on the enzymatic degradation of the Korean Undaria pinnatifida sporophyll fucoidan. Moreover, this enzyme activity may be very useful for structural analyses of fucose-containing polysaccharides and the production of bioactive fucooligosaccharides.

• Biomolecules & Therapeutics
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• v.16 no.2
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• pp.100-105
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• 2008

The sphingolipid metabolites act as lipid mediator for cell proliferation and apoptosis in mammalian cells. In bacteria, sphingolipid metabolism remains unknown. The purpose of this study was to investigate whether sphingolipid metabolism is potential target for fumonisin $B_1$($FB_1$) and desipramine in Sphingomonas chungbukensis, Gram-negative bacteria, by comparing the intracellular contents of bacterial sphingolipids with ones of HIT-T15 ${\beta}$-cells, hamster pancreatic cells. The concentrations of ceramide and dihydroceramide were 18.0 ${\pm}$ 12.0 and 0.025 ${\pm}$ 0.018 nmol/mg protein, respectively, in HIT-T15 cells. However, the concentrations of ceramide and dihydroceramide in the bacterial culture were 2.0 ${\pm}$ 1.2 and 10.6 ${\pm}$ 5.5 nmol/mg protein, respectively. $FB_1$ decreased the level of ceramide from 18.0 to 3.8 nmol/mg protein in HIT-T15 ${\beta}$-cells. However, dihydroceramide content in $FB_1$-treated HIT-T15 cells was slightly decreased compared with the control culture. When S. chungbukensis was treated with either $FB_1$ or desipramine, dihydroceramide level was increased by 5- and 4-fold, respectively, compared with the control bacteria. These results indicate that $FB_1$ and desipramine may act as an activator in bacterial sphingolipid biosynthetic pathway, and bacterial sphingolipid metabolism pathway appears to be different from the pathway of mammalian cells.

• Journal of Microbiology and Biotechnology
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• v.14 no.6
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• pp.1134-1141
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• 2004

A bacterial strain capable of hydrolyzing sulfate ester bonds in p-nitrophenyl sulfate and agar was isolated from the Southeast coast of Korea. The isolated strain (AS6330) is aerobic, Gram-negative, rod-shaped, and motile. Octadecanoic acid was the major cellular fatty acid in the isolate. An almost complete 16S rDNA sequence of the isolate was determined and the sequence similarity of the 16S rDNA with those of known Sphingomonas spp. was found to be at most $96.4\%$, implying that the isolate was a new Sphingomonas species. The organism was grown optimally at NaCl concentration of $1.5-3.5\%$. Optimum culture conditions were determined to be $30^{\circ}C$ and pH 7.0 for 48 h fermentation using a laboratory fermentor under constant culture conditions. Partially purified arylsulfatase through Q-Sepharose and phenyl­Sepharose chromatographies catalyzed hydrolysis of sulfate ester bonds in agar, and $97\%$ of sulfates in agar were removed after 4 h reaction at $45^{\circ}C$ and pH 7.0. The arylsulfatase from the isolated bacterium might be useful for the removal of sulfate groups in agar.

• Journal of Microbiology and Biotechnology
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• v.21 no.5
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• pp.494-502
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• 2011

Coenzyme $Q_{10}$ ($CoQ_{10}$) is a widely used supplement in heart diseases treatment or antioxidative dietary. The microbial production of $CoQ_{10}$ was enhanced by addition of solanesol and novel precursors recovered from waste tobacco. The novel precursors were separated by silica gel and identified as ${\alpha}$-linolenic acid (LNA) and butylated hydroxytoluene (BHT) based on the effect on $CoQ_{10}$ production and GC-MS. The effects of novel precursors on $CoQ_{10}$ production by Sphingomonas sp. ZUTE03 were further evaluated in a two-phase conversion system. The precursor's combination of solanesol (70 mg/l) with BHT (30 mg/l) showed the best effect on the improvement of $CoQ_{10}$ yield. A maximal $CoQ_{10}$ productivity (9.5 mg $l^{-1}$ $h^{-1}$) was achieved after 8 h conversion, with a molar conversion rate of 92.6% and 92.4% on BHT and solanesol, respectively. The novel precursors, BHT and LNA in crude extracts from waste tobacco leaves, might become potential candidates for application in the industrial production of $CoQ_{10}$ by microbes.

• KSBB Journal
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• v.21 no.6 s.101
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• pp.428-432
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• 2006

This study investigated the effect of sulfate source on removal efficiency in electrokinetic bioremediation which needs sulfate to degrade contaminants by an applied microorganism. The representative contaminant and the applied microorganism were phenanthrene and Sphingomonas sp. 3Y, respectively. When magnesium sulfate was used, the magnesium ion combined with hydroxyl ion electrically-generated at cathode to cause the decrease of electrolyte pH, and then the microbial activity was inhibited by that. When ammonium sulfate and disodium sulfate were used to solve the pH control problem, the pH values of electrolyte and soil solution were maintained neutrally, and also the high microbial activity was observed. With the former sulfate source, however, ammonium retarded the phenanthrene degradation, and so the removal efficiency decreased to 12.0% rather than 21.8% with magnesium sulfate. On the other hand, the latter improved the removal efficiency to 27.2%. This difference of removal efficiency would be outstanding for an elongated treatment period.

• Journal of Microbiology and Biotechnology
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• v.23 no.4
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• pp.473-482
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• 2013

The desulfurization ability of Sphingomonas subarctica T7b was evaluated using resting and immobilized cells with dibenzothiophene (DBT), alkyl DBTs, and commercial light gas oil (LGO) as the substrates. The resting cells of S. subarctica T7b degraded 239.2 mg of the initial 250 mg of DBT/l (1.36 mM) within 24 h at $27^{\circ}C$, while 127.5 mg of 2-hydroxybiphenyl (2-HBP)/l (0.75 mM) was formed, representing a 55% conversion of the DBT. The DBT desulfurization activity was significantly affected by the aqueous-to-oil phase ratio. In addition, the resting cells of S. subarctica T7b were able to desulfurize alkyl DBTs with long alkyl chains, although the desulfurization rate decreased with an increase in the total carbon number of the alkylated DBTs. LGO with a total sulfur content of 280 mg/l was desulfurized to 152 mg/l after 24 h of reaction. Cells immobilized by entrapment with polyvinyl alcohol (PVA) exhibited a high DBT desulfurization activity, including repeated use for more than 8 batch cycles without loss of biodesulfurization activity. The stability of the immobilized cells was better than that of the resting cells at different initial pHs, higher temperatures, and for DBT biodesulfurization in successive degradation cycles. The immobilized cells were also easily separated from the oil and water phases, giving this method great potential for oil biodesulfurization.

• Bulletin of the Korean Chemical Society
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• v.30 no.6
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• pp.1360-1364
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• 2009

The bacterium Sphingomonas chungbukensis DJ77 produces the extracellular polysaccharide gellan in high yield. Gellan produced by this bacterium is widely used as a gelling agent, and the enzyme UDP-glucose pyrophosphorylase (UGP) is thought to play a key role in the gellan biosynthetic pathway. The UGP gene has been successfully cloned and over-expressed in E. coli. The expressed enzyme was purified with a molecular weight of approximately 32 kDa, as determined by a SDS-polyacrylamide gel, but the enzyme appears as ca. 63 kDa on a native gel, suggesting that the enzyme is present in a homodimer. Kinetic analysis of UDP-glucose for UGP indicates $K_m$ = 1.14 mM and $V_{max}$ = 10.09 mM/min/mg at pH 8.0, which was determined to be the optimal pH for UGP catalytic activity. Amino acid sequence alignment against other bacteria suggests that the UGP contains two conserved domains: An activator binding site and a glucose-1-phosphate binding site. Site-directed mutagenesis of Lys194, located within the glucose-1-phosphate binding site, indicates that substitution of the charge-reversible residue Asp for Lys194 dramatically impairs the UGP activity, supporting the hypothesis that Lys194 plays a critical role in the catalysis.

• Bulletin of the Korean Chemical Society
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• v.30 no.7
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• pp.1547-1552
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• 2009

Sphingomonas chungbukensis DJ77 has the ability to produce large quantities of an extracellular polysaccharide that can be used as a gelling agent in the food and pharmaceutical industries. We identified, cloned and expressed the UDP-glucose dehydrogenase gene of S. chungbukensis DJ77, and characterized the resulting protein. The purified UDP-glucose dehydrogenase (UGDH), which catalyzes the reversible conversion of UDP-glucose to UDPglucuronic acid, formed a homodimer and the mass of the monomer was estimated to be 46 kDa. Kinetic analysis at the optimal pH of 8.5 indicated that the $K_m\;and\;V_{max}$ for UDP-glucose were 0.18 mM and 1.59 mM/min/mg, respectively. Inhibition assays showed that UDP-glucuronic acid strongly inhibits UGDH. Site-directed mutagenesis was performed on Gly9, Gly12 Thr127, Cys264, and Lys267. Substitutions of Cys264 with Ala and of Lys267 with Asp resulted in complete loss of enzymatic activity, suggesting that Cys264 and Lys267 are essential for the catalytic activity of UGDH.

• 한국생물공학회:학술대회논문집
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• 2003.10a
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• pp.775-779
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• 2003

Cultivation environment for effective production of shrimp in shrimp aquaculture, Institute of Marine & Fishery, Soonchunhyang University located at Tae-An, Chung-Nam Province, with the ultimate aim of probiotics development, was monitored. Several environmental factors including dissolved oxygen, water body temperature, pH, salinity, $NH_4-N$, $NO_2-N$, $NO_3-N$, chlorophyll a affecting on the growth of shrimp were examined. Concentrations of $NH_4-N$, $NO_2-N$, and $NO_3-N$ dissolved in water samples were determined to 0.024-0.034 mg/L, 0.03-0.02, and 0.004-0.009 mg/L, respectively. Chlorophyll a content was examined in the range of 0.002-0.118 $ug/m^3$. In order to understand the distribution of different bacteria in water samples collected in shrimp aquaculture, bacteria were isolated and enumerated on the marine agar plates. Total number of bacteria were increased to approximately $6.5\;{\times}\;10^4$. Thirteen predomonant bacteria were isolated and identified. As the results of BIOLOG test of the isolates, these bacteria were identified as Corynebacterium nirilophilus, Clavibacter agropyri, Sphingomonas adhaesiva, Brevundimonas vesicularis, Vibrio parahaemolyticus, Pseudomonas bathycetes, Vibrio tubiashii, Sphingomonas macrogoltabidus, Rhodococcus, rhodochrous, Burkholderia glumae, Corynebacterium urealyticus, Rhodococcus fascians, Psychrobacter immobilis, respectively. Further work will stimulate the elucidation of pathogenicity, corresponding bacteria related to environment and probiotics, providing good information for effective production of shrimp.

• 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.