• KSBB Journal
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• v.20 no.5 s.94
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• pp.387-391
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• 2005

Totally 16,299 conservative genes, commonly found in 13 thermophilic and hyperthermophilic bacteria, were analyzed. All genes were belong to W 67 COGs (clusters of orthologous groups of proteins). COGs related to protein metabolism were 80 among 167 COGs. Conservative genes were not limited only thermophiles and hyperthermophiles, meaning thermal stability is independent of specific protein. However reverse gyrase was only found in all hyperthermophilic archaebacteria and eubacteria, meaning DNA stability is important in hyperthermophiles. Hyperthermophilic eubacteria and thermophilic archaebacteria had different position between phylogenetic tree of gene content and 165 rRNA gene. Thermophilic archaebacteria hyperthermophilic eubacteria and archaebacteria had similar values by the statistical analysis of distance values with 167 COGs in each organism.

• Journal of Microbiology and Biotechnology
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• v.32 no.5
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• pp.663-671
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• 2022

The saccharification of cellulose and hemicellulose is essential for utilizing lignocellulosic biomass as a biofuel. While cellulose is composed of glucose only, hemicelluloses are composed of diverse sugars such as xylose, arabinose, glucose, and galactose. Sulfolobus acidocaldarius is a good potential candidate for biofuel production using hemicellulose as this archaeon simultaneously utilizes various sugars. However, S. acidocaldarius has to be manipulated because the enzyme that breaks down hemicellulose is not present in this species. Here, we engineered S. acidocaldarius to utilize xylan as a carbon source by introducing xylanase and β-xylosidase. Heterologous expression of β-xylosidase enhanced the organism's degradability and utilization of xylooligosaccharides (XOS), but the mutant still failed to grow when xylan was provided as a carbon source. S. acidocaldarius exhibited the ability to degrade xylan into XOS when xylanase was introduced, but no further degradation proceeded after this sole reaction. Following cell growth and enzyme reaction, S. acidocaldarius successfully utilized xylan in the synergy between xylanase and β-xylosidase.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Microbiology and Biotechnology Letters
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• v.40 no.2
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• pp.104-110
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• 2012

Glycosynthase is an active site nucleophile mutant enzyme, prepared from glycosidase, which is capable of synthesizing oligosaccharide derivatives without the hydrolysis of the product. Thermoacidophilic ${\alpha}$-glucosidase of Thermoplasma acidophilum (AglA) exhibits a transglycosylating activity yielding various glycosides. AglA was converted to glycosynthase by the substitution of the catalytic nucleophile Asp-408 residue into non-nucleophile glycine in order to increase its ability to synthesize various glycosides by transglycosylation. The glycosynthase mutant was purified by Ni-NTA chromatography and its glycoside-synthesizing activity was measured by using an external nucleophile, sodium formate buffer, providing maltose as a donor and p-nitrophenyl-${\alpha}$-D-glucopyranoside ($pNP{\alpha}G$) as an acceptor, respectively. In addition, $pNP{\alpha}G$ was examined for its feasibility to act as both a donor and an acceptor, and products were compared with those of the wildtype enzyme. The mutant enzyme was found to catalyze the formation of a specific product from $pNP{\alpha}G$ with a yield of 42.5% without further hydrolysis, while the wild-type enzyme produced two $pNP{\alpha}G$ products at low yields. The results demonstrate the possibility of satisfactory yields for the reactions in the presence of small amounts of acceptor, and demonstrate that the high activity of the mutant, at pHs below neutrality, was applicable in the transfer of glucose from the natural donor.

• Journal of the Korean Applied Science and Technology
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• v.16 no.3
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• pp.263-271
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• 1999

We checked the presence of phospholipase $A_2(PLA)_2$ which could split the ester bond at the position 2 in the glycerol backbone of glycerophospholipids, in the cells of hyperthermophiles of Pyrococcus horikoshii and Sulfolobus acidocaldarius. The results obtained are as follows; (1). Pyrococcus horikoshii cells were grown in obligate anaerobic conditions at $95^{\circ}C$ and they needed sulfur as energy source instead of oxygen, while Sulfolobus acidocaldarius species grew well in the aerobic medium (pH 2.5) containing yeast and sucrose at $75^{\circ}C$. (2). Pyrococcus horikoshii cells produced phospholipase $A_2$ in the cell culture media although this species did not show lipase activity at least in the pH range of 1.5 ${\sim}$ 3.5. Sulfolobus acidocaldarius cells produced lipase hydrolyzing triacylglycerols such as triolein, but did not split any kind of phospholipids used as substates. (3). The compound of 1-decanoyl-2-(p-nitrophenylglutaryl) phosphatidylcholine was not suitable for a substrate in this experiment, though frequently used as a subtrate for checking presence of phospholipase $A_2$, for its decomposi-tion in this experiment. The L-${\alpha}$-phosphatidylcholine-${\beta}$-[N-7-nitrobenz-2-oxa-1, 3-diazol]aminohexanoyl-${\gamma}$-hexadecanoyl labelled with a fluorescent material, did not show any migration of acyl chains in the molecule during the reaction with phospholipase $A_2$ under a hot condition. (4). Phospholipase $A_2$ in the cells of Pyrococcus horikoshii, showed the optimum activity at $pH6.7{\sim}7.2$ and $95{\sim}105^{\circ}C$, respectively, and was activated by addition of calcium chloride solution. Andthe phospholipase $A_2$ specifically hydrolyzed glycero-phospholipids such as phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine and phosphatidyl inositol, but could not split phospholipid containing ether bonds in the molecule such as DL -${\alpha}$-phosphatidylcholine-${\beta}$-palmitoyl-${\gamma}$-O-hexadecyl, DL-${\alpha}$-phosphati- dylcholine-${\beta}$- oleoyl-${\gamma}$-O-hexadecyl, DL-phosphatidylcholine-dihexadecyl.