• Journal of Applied Biological Chemistry
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• v.53 no.2
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• pp.71-76
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• 2010

A gene encoding the mannanase of Bacillus licheniformis WL-12, which had been isolated from Korean soybean paste, was cloned into Escherichia coli and nucleotide sequence of the mannanase gene was subsequently determined. The mannanase gene consisted of 1,080 nucleotides encoding a polypeptide of 360 amino acid residues. The deduced amino acid sequence was identical to that of putative mannanase from B. liceniformis DSM13 belonging to GH family 26. The mannanase was partially purified from cell-free extract of the recombinant Escherichia coli carrying a WL-12 mannanase gene by ammonium sulfate fractionation and DEAE-Sepharose column chromatography. Optimal conditions for the partially purified enzyme occurred at pH 6.0 and $65^{\circ}C$. The enzyme showed higher activity on locust bean gum (LBG) galactomannan and konjac glucomannan than on guar gum galactomannan. The predominant products resulting from the mannanase hydrolysis were mannose, mannobiose and mannotriose for LBG or mannooligosaccharides. The enzyme could hydrolyze mannooligosaccharides larger than mannobiose.

• Applied Biological Chemistry
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• v.48 no.4
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• pp.311-314
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• 2005

Approximately twelve hundred strains of Actonomycetes isolated from domestic soli were tested for their ability to produce extracellular phytase. Of all these isolates a strain, YB-26, that had the highest potential for phytase activity was chosen. The nucleotide sequence of 16S rDNA of the isolate YB-26 showed the highest similarity to that of strains beloning to genus Streptomyces. The partially purified extracellular phytase was obtained from the culture filtrate of Streptomyces sp. YB-26 grown on GSM broth by ammonium sulfate precipitation (15-70%), DEAE-Sepharose column and Q-Sepharose column chromatography. The partially purified enzyme showed the maximum activity for hydrolysis of phyate at $60^{\circ}C$ and pH 7.0, and retained 90% of its maximum activity at the range of pH $6.0{\sim}8.0$. It was thermolabile and its thermostability did not increase in the presence of calcium chloride.

• Journal of Microbiology and Biotechnology
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• v.15 no.5
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• pp.1125-1129
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• 2005

Cloning of a 6.6-kb BamHI digested chromosomal DNA from S. griseus IFO13350 revealed the presence of an additional gene encoding a novel trypsin-like enzyme, named SprU. The SprU protein shows a high homology ($79\%$ identity, $88\%$ similarity) with the SGT protease, which has been reported as a bacterial trypsin in the same strain. The amino acid sequence deduced from the nucleotide sequence of the sprU gene suggests that SprU is produced as a precursor consisting of an amino-terminal presequence (29 amino acid residues), prosequence (4 residues), and mature trypsin consisting of 222 amino acids with a molecular weight of 22.94 kDa and a calculated pI of 4.13. The serine, histidine, and aspartic acid residues composing the catalytic triad of typical serine proteases are also well conserved. When the trypsin activity of the SprU was spectrophotometrically measured by the enzymatic hydrolysis of the artificial chromogenic substrate, N-${alpha}$-benzoyl-DL-arginine-p-nitroanilide, the S. lividans transformant with pWHM3-U gave 3 times higher activity than that of control. When the same recombinant plasmid was introduced into S. griseus, however, the gene dosage effect was not so significant, as in the cases of other genes encoding serine proteases, such as sprA, sprB, and sprD. Although two trypsins, SprU and SGT, have a high degree of homology, the pI values, the gene dosage effect in S. griseus, and the gene arrangement adjacent to the two genes are very different, suggesting that the biochemical and biological function of the SprU might be quite different from that of the SGT.

• Microbiology and Biotechnology Letters
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• v.40 no.4
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• pp.296-302
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• 2012

A bacterial strain was isolated from soybean paste fermented in a Korean Buddhist temple as a producer of the extracellular thermostable ${\alpha}$-amylase. The isolate YB-1234 has been identified as Bacillus licheniformis on the basis of its 16S rDNA sequence, morphology and biochemical properties. A gene encoding the thermostable ${\alpha}$-amylase of B. licheniformis YB-1234 was cloned into Escherichia coli and its nucleotide sequence was determined. The deduced amino acid sequence of ${\alpha}$-amylase was very highly homologous to those of the thermostable ${\alpha}$-amylases of B. licheniformis belonging to the glycosyl hydrolase family 13. The ${\alpha}$-amylase produced by recombinant E. coli carrying the ${\alpha}$-amylase gene exhibited maximal activity at pH 6.0, identical to ${\alpha}$-amylase in the culture filtrate of B. licheniformis, while the temperature profile was somewhat different between the two. Particularly, ${\alpha}$-amylase produced from B. lcheniformis is much more thermostable than that from recombinant E. coli. The predominant products resulting from the ${\alpha}$-amylase hydrolysis were glucose, maltose and maltotriose for maltotetraose and maltohexaose.

• Journal of Microbiology and Biotechnology
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• v.20 no.9
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• pp.1283-1287
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• 2010

In eukaryotes, eRF3 participates in translation termination and belongs to the superfamily of GTPases. In this work, the dissociation constants for nucleosides bound to Euplotes octocarinatus eRF3 in the presence and absence of eRF1a were determined using fluorescence spectra methods. Furthermore, a GTP hydrolyzing assay of eRF3 was carried out using an HPLC method, and the kinetic parameters for GTP hydrolysis by eRF3 were determined. Consistent with data from humans, the results showed that eRF1a promoted the binding of GTP to eRF3 and the GTP hydrolyzing activity of eRF3. However, in contrast to the lack of GTP binding in the absence of eRF1 in human eRF3, the E. octocarinatus eRF3 was able to bind GTP by itself. The nucleotide binding affinity of the E. octocarinatus eRF3 also differed from the human data. A structure model and amino acid sequence alignment of potential G domains indicated that these differences may be due to valine 317 and glutamate 452 displacing the conserved glycine and lysine involved in GTP binding.

• Journal of Microbiology and Biotechnology
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• v.9 no.4
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• pp.457-463
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• 1999

The physical map of bacteriophage $\PhiFC1$ DNA was constructed with the restriction endonucleases SalI, BamHI, EcoRI, XbaI, and AvaI. The 40.5-kb DNA restriction map is shown to be circularly permuted representing the headful packaging mechanism of the phage. The DNA restriction fragments containing the packaging initiation site(pac) was localized on the restriction map and the nucleotide sequences of the region were analyzed. Four open reading frames (ORFs), following one another with the same orientation, were found at the region. The 2nd ORF (ORF-ts) has significant amino acid sequence homologies to the previously known terminase small subunits of other bacteriophages. The putative terminase small subunit gene has a presumptive NTP-hydrolysis motif and a helix-turn-helix motif. The cleavage site for the first round of packaging was found to be located at the coding sequence of the putative terminase small subunit gene. The fourth ORF, even if partially sequenced, has a good amino acid sequence homology to the portal vertex proteins of other bacteriophages representing the evolutionarily conserved arrangements of genes near the pac site of this bacteriophage, $\PhiFC1$.

• Microbiology and Biotechnology Letters
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• v.39 no.3
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• pp.252-258
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• 2011

A bacterial strain capable of hydrolyzing xylan and locust bean gum (LBG) was isolated from farm soil by enrichment culture using mixture of palm kernel meal (PKM) and wheat bran as carbon source. Nucleotide sequence of 16S rDNA amplified from the isolate YB-1107 showed high similarity with those of genus Cellulosimicrobium strains. Xylanase productivity was increased when the Cellulosimicrobium sp. YB-1107 was grown in the presence of wheat bran or oat spelt xylan, while mannanase productivity was increased drastically when grown in the presence of PKM or LBG. Particularly, maximum mannanase and xylanase activities were obtained in the culture filtrate of media containing 0.7% PKM or 1% wheat bran, respectively. Both enzyme activities were produced at stationary growth phase. Mannanase from the culture filtrate showed the highest activity at $55^{\circ}C$ and pH 6.5. Xylanase activity was optimal at $65^{\circ}C$ and pH 5.5. The predominant products resulting from the mannanase or xylanase hydrolysis were oligosaccharides for LBG or xylan, respectively. In addition, the enzymes could hydrolyze wheat bran and rice bran into oligosaccharides.

• BMB Reports
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• v.28 no.6
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• pp.509-514
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• 1995

A putative secondary structure of the mRNA for the human hepatitis B virus (HBV) X gene is proposed based on not only chemical and enzymatic determination of its single- and double-stranded regions but also selection by the computer program MFOLD for energy minimum conformation under the constraints that the experimentally determined nucleotides were forced or prohibited to base pair. An RNA of 536 nucleotides including the 461-nucleotide HBV X mRNA sequence was synthesized in vitro by the phage T7 RNA polymerase transcription. The thermally renatured transcripts were subjected to chemical modifications with dimethylsulfate and kethoxal and enzymatic hydrolysis with single strand-specific RNase T1 and double strand-specific RNase V1, separately. The sites of modification and cleavage were detected by reverse transcriptase extension of 4 different primers. Many nucleotides could be assigned with high confidence, twenty in double-stranded and thirty-seven in Single-stranded regions. These nucleotides were forced and prohibited, respectively, to base pair in running the recursive RNA folding program MFOLD. The results suggest that 6 different regions (5 within X mRNA) of 14~23 nucleotides are Single-stranded. This putative structure provides a good working model and suggests potential target sites for antisense and ribozyme inhibitors and hybridization probes for the HBV X mRNA.

• Molecules and Cells
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• v.43 no.3
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• pp.286-297
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• 2020

Mammalian patatin-like phospholipase domain containing proteins (PNPLAs) play critical roles in triglyceride hydrolysis, phospholipids metabolism, and lipid droplet (LD) homeostasis. PNPLA7 is a lysophosphatidylcholine hydrolase anchored on the endoplasmic reticulum which associates with LDs through its catalytic region (PNPLA7-C) in response to increased cyclic nucleotide levels. However, the interaction of PNPLA7 with LDs through its catalytic region is unknown. Herein, we demonstrate that PNPLA7-C localizes to the mature LDs ex vivo and also colocalizes with pre-existing LDs. Localization of PNPLA7-C with LDs induces LDs clustering via non-enzymatic intermolecular associations, while PNPLA7 alone does not induce LD clustering. Residues 742-1016 contains four putative transmembrane domains which act as a LD targeting motif and are required for the localization of PNPLA7-C to LDs. Furthermore, the N-terminal flanking region of the LD targeting motif, residues 681-741, contributes to the LD targeting, whereas the C-terminal flanking region (1169-1326) has an anti-LD targeting effect. Interestingly, the LD targeting motif does not exhibit lysophosphatidylcholine hydrolase activity even though it associates with LDs phospholipid membranes. These findings characterize the specific functional domains of PNPLA7 mediating subcellular positioning and interactions with LDs, as wells as providing critical insights into the structure of this evolutionarily conserved phospholipid-metabolizing enzyme family.

• Microbiology and Biotechnology Letters
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• v.42 no.2
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• pp.99-105
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• 2014

A Bacillus strain capable of hydrolyzing locust bean gum was isolated as a producer of extracellular mannanase by way of an enrichment culture in an acidic medium from homemade soybean pastes. The isolate YB-1401 showed a biochemical identity of 61.1% with Brevibacillus laterosporus, while the nucleotide sequence of its 16S rDNA had the highest similarity with that of Bacillus amyloliquefaciens. The mannanase productivity of the Bacillus sp. YB-1401 was drastically increased by mannans. Particularly, maximum mannanase productivity was reached at approximately 265 U/ml in LB medium supplemented with konjac glucomannan (4.0%). The mannanase was the most active at $55^{\circ}C$ and pH 5.5. Mannanase activity was completely maintained after pre-incubation at pH 3.5 to 11.0 for 1 h. The predominant products resulting from the mannanase hydrolysis were mannobiose and mannotriose for LBG, guar gum or mannooligosaccharides. A small amount of mannose was also detected in the hydrolyzates.