• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1809-1813
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• 2006

A gene corresponding to 4-${\alpha}$-glucanotransferase (${\alpha}GTase$) was cloned from the thermophilic bacterium Thermus brockianus. The nucleotide sequence analysis showed that the ${\alpha}GTase$ gene is composed of 1,503 nucleotides and encodes a polypeptide that is 500 amino acids long with a calculated molecular mass of 57,221 Da. The deduced amino acid sequences of Thermus brockianus ${\alpha}GTase$ (TBGT) exhibited a high level of similarity to the amino acid sequence of ${\alpha}GTase$ of Thermus thermophilus (86%), but low level of homology to that of E. coli (26%). The TBGT gene was overexpressed in E. coli BL21, and the corresponding recombinant enzyme was efficiently purified by Ni-NTA affinity chromatography. The enzymatic characteristics revealed that optimal pH and temperature were pH 6 and $70^{\circ}C$, respectively. Most interestingly, TBGT reacted with small oligosaccharides, especially maltotriose, to form various maltooligosaccharides by using its disproportionation activity.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.157-167
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• 2000

A thermostable chitosanase gene from the isolated strain, Bacillus sp. CK4, was cloned, and its complete DNA sequence was determined. The thermostable chitosanase gene was composed of an 822-bp open reading frame which encodes a protein of 242 amino acids and a signal peptide corresponding to a 30 kDa enzyme in size. The deduced amino acid sequence of the chitosanase from Bacillus sp. CK4 exhibits 76.6%, 15.3%, and 14.2% similarities to those from Bacillus subtilis, Bacillus ehemensis, and Bacillus circulans, respectively. C-terminal homology analysis shows that Bacillus sp. CK4 belongs to the Cluster III group with Bacillus subtilis. The size of the gene was similar to that of a mesophile, Bacillus subtilis showing a higher preference for codons ending in G or C. The functional importance of a conserved region in a novel chitosanase from Bacillus sp. CK4 was investigated. Each of the three carboxylic amino acid residues were changed to E50D/Q, E62D/Q, and D66N/E by site-directed mutagenesis. The D66N/E mutants enzymes had remarkably decreased kinetic parameters such as $V_{max}$ and k$\sub$cat/, indicating that the Asp-66 residue was essential for catalysis. The thermostable chitosanase contains three cysteine residues at position 49, 72, and 211. Titration of the Cys residues with DTNB showed that none of them were involved in disulfide bond. The C49S and C72S mutant enzymes were as stable to thermal inactivation and denaturating agents as the wild-type enzyme. However the half-life of the C211S mutant enzyme was less than 60 min at 80$^{\circ}C$, while that of the wild type enzyme was about 90 min. Moreover, the residual activity of C211S was substantially decreased by 8 M urea, and fully lost catalytic activity by 40% ethanol. These results show that the substitution of Cys with Ser at position 211 seems to affect the conformational stability of the chitosanase.

• BMB Reports
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• v.38 no.5
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• pp.571-576
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• 2005

Cytokines are proteins produced by many different cells of the immune system and play a significant role in initiating and regulating the inflammatory process. In this research, an important cytokine, interleukin-10 (IL-10) gene, has been identified and characterized from zebrafish (Danio rerio) genome database. Zebrafish IL-10 is located within a 2690 bp fragment and contains five exons and four introns, sharing the same organization with mammalian IL-10 genes. An open reading frame of 543 bp was found to encode a putative 180 amino acid protein with a signal peptide of 22 amino acids, which shares 29.7-80.9% homology with amino acid sequences of other known IL-10. The signature motif of IL-10 is also conserved in zebrafish IL-10. The predicted transcript was finally confirmed by sequencing of cDNA clones. Multi-tissue reverse transcriptase PCR (RT-PCR) was performed to examine the tissue distribution and expression regulation of this gene in seven organs of normal and lipopolysaccharide (LPS) stimulation zebrafish. The results demonstrated that this gene was expressed slightly in normal kidney, gill and gut, no expression was detected in other four tissues. The expression was clearly upregulated after LPS stimulation. Using the ideal zebrafish model, further study of IL-10 characterization and function may provide insight on the understanding of the innate immune system.

• Journal of Plant Biotechnology
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• v.30 no.2
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• pp.135-141
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• 2003

Peroxiredoxin(Pix) are large family of peroxidases that reduce alkyl hydroperoxides and hydrogen peroxide. A cDNA clone (referred to as swPrxl) encoding Pix was from a sweetpotato cDNA library constructed from suspension-sultured cells, and its expression was investigated in terms of stress. The swPrxl contained an open reading frame (ORF) encoding mature protein of 193 amino acids with calculated molecular mass of 20.8kDa. The predicted amino acid sequence of swPrxl has two conserved cysteines that are essential resicues for the reduction of peroxides. It showed high amino acid sequence homology ot PixIIF of Arabidopsis (77%) and putative Prx of rice(72%). RNA gel-blot analysis showed that swPrxl gene was expressed dominantly in leave among intact tissues, and also highly detect in suspension-cultured cells. Interestingly, the level of swPrxl transcripts was almost the same regardless of the growth stage in suspension culture. Furthermore, the transcription level of swPrxl gene was not significantly changed in response to various stress treatments such as wounding, extreme temperature and stress-related chemicals RT-PCR analyses.

• Journal of fish pathology
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• v.22 no.2
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• pp.137-146
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• 2009

The black rockfish Sebastes schlegelii neutrophil cytosolic factor components p47 phox (phagocyte oxidase) cDNA was cloned. The sequence of the cDNA showed that rockfish p47 phox cDNA consisted of 1,952 bp contained open reading frame encoding predicted polypeptide of 420 amino acids. Additionally analysis of the p47 phox amino acid sequence showed two potential SH3 domains. The functional domains are highly conserved in many animals, though the sequence of the components of the black rockfish showed low homology with that of mammals. The deduced amino acid sequence of the black rockfish p47 phox was similar to those of the carp (60.4%), zebrafish (59,2%), rainbow trout (68.5%), xenopus (55.2%), mouse (54.2%), rabbit (54.5%), rat (53.7%), and chicken (50.9%). The expression of the rockfish p47 phox molecule was induced in peripheral blood leukocytes (PBLs) from 1 to 12 h following LPS stimulation, with a peak at 6 h after the stimulation, and which increased at 1, 3, and 12 h after treated with Poly I:C compared with the control. The rockfish p47 phox gene was expressed in various tissues of healthy fish. The level of p47 phox expression was high in the PBLs, kidney and spleen.

• Journal of Plant Biotechnology
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• v.47 no.4
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• pp.316-323
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• 2020

This study aimed to evaluate the potential allergenicity and oral toxicity of the phosphinothricin acetyltransferase (PAT) protein expressed in Zoysia japonica, a herbicide-tolerant genetically modified (GM) zoysiagrass. In silico analysis of PAT showed no similarities with any known allergenic or toxic proteins, with <35% amino acid sequence homology with known allergens across a length of 80 amino acids and no continuous eight amino acid identity with known allergens. The PAT protein expressed in Z. japonica degraded very rapidly in the simulated gastric fluid in the presence of pepsin, and, no glycosylation of PAT was observed. The oral toxicity test revealed no mortality or toxic effect in mice following PAT administration at 4,000 mg/kg body weight. Our findings indicate that the PAT protein expressed in Zoysia japonica does not exhibit allergenic or toxic properties.

• Journal of Microbiology and Biotechnology
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• v.12 no.5
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• pp.729-734
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• 2002

Radiorespirometric analysis revealed that Pseudomonas sp. strain KKI isolated from a soil contaminated with petroleum hydrocarbons was able to catabolize polycyclic aromatic hydrocarbons such as phenanthrene and naphthalene. The rate and extent of phenanthrene mineralization was markedly enhanced when the cells were pregrown on either naphthalene or phenanthrene, compared to the cells grown on universal carbon sources (i.e., TSA medium). Deduced amino acid sequence of the Rieske-type iron-sulfur center of a putative phenanthrene dioxygenase (PhnAl) obtained from the strain KKI shared significant homology with DxnAl (dioxin dioxygenase) from Spingomonas sp. RW1, BphA1b (biphenyl dioxygenase) from Spingomonas aromaticivorans F199, and PhnAc (phenanthrene diokygenase) from Burkholderia sp. RP007 or Alcaligenes faecalis AFK2. Northern hybridization using the dioxygenase gene fragment cloned from KKI showed that the expression of the putative phn dioxygenase gene reached the highest level in cells grown in the minimal medium containing phenanthrene and $KNO_3$, and the expression of the phn gene was repressed in cells grown with glucose. In addition to the metabolic change, phospholipid ester-linked fatty acids (PLFA) analysis revealed that the total cellular fatty acid composition of KKI was significantly changed in response to phenanthrene. Fatty acids such as 14:0, 16:0 3OH, 17:0 cyclo, 18:1$\omega$7c, 19:0 cyclo increased in phenanthrene-exposed cells, while fatty acids such as 10:0 3OH, 12:0, 12:0 2OH, 12:0 3OH, 16:1$\omega$7c, 15:0 iso 2OH, 16:0, 18:1$\omega$6c, 18:0 decreased.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2001.11a
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• pp.102-102
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• 2001

Taurine (2-ethaneaminosulfonic acid) is one of the major intracellular ${\beta}$ -amino acids in mammals and is required for a number of biological processes including membrane stabilization, osmoregulation, antioxidation, detoxification, modulation of calcium flux and neurornodulation. The taurine transporter (TAUT) which contains 12 hydrophobic membrane-spanning domains has been cloned from dog kidney, rat brain, mouse brain, human thyroid, placenta and retina. In this study, The TAUT cDNA from the human intestinal epithelial cell, HT-29 was cloned and sequenced. Reverse-transcription polymerase chain reaction (RT-PCR) was performed to amplify partial cDNA encoding human intestinal TAUT. The coding region of the PCR product was 732 bp long. The primers were designed to encode highly conserved amino acid sequences near the transmembrane domains III (IPYFIFLF) and Ⅵ (KYKYNSYR) both in human and mouse. The TAUT cDNA amplified was ligated into the pGEX 4T-1 expression vector. The resulting sequence of human intestinal TAUT cDNA (Accession number of NCBI Genebank is AF346763) was identical to the sequences of the TAUTs previously determined in the human placenta and retina except 3 base pairs from that of the reported human thyroid. TAUT specific antibodies were generated to use them as biological tools in the studies of the biological role of TAUT. Peptides of 149-162 amino acid residue (14 amino acids) of the TAUT were synthesized. The synthetic peptide used in this study was LFQSFQKELPWAHC. This region was chosen not only to avoid putative glycosylation sites but also to exclude regions of known homology with GABA transporters in the extracellular hydrophilic domains. The synthetic peptide, TAUT-1 was conjugated with carrier protein, kehole lympet hemocyanin (KLH) to use as an antigen. When used for immunization on a rabbit to produce polyclonal antiserum, the conjugates elicited high -titered specific anti-TAUT-1 antibodies, which reacted well with the ovalbumin (OVA) conjugated peptides in ELISA. The KLH-conjugated peptide was also used as immunizing antigen in BALB/c mice to produce TAUT specific monoclonal antibodies. From the culture supernatant of the hybridoma, the specificity of anti-TAUT-1 monoclonal antibodies was confirmed by ELISA. Further applications of more tools in TAUT expression analysis will be performed such as western blotting and flow cytometry.

• Journal of the Korea Organic Resources Recycling Association
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• v.23 no.1
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• pp.70-81
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• 2015

Helicases are known to be a proteins that use the chemical energy of NTP binding and hydrolyze to separate the complementary strands of double-stranded nucleic acids to single-stranded nucleic acids. They participate in various cellular metabolism in many organisms. DEAD-box proteins are ATP-dependent RNA helicase that participate in all biochemical steps involving RNA. DEAD-box3 (DDX3) gene is belonging to the DEAD-box family and plays an important role in germ cell development in many organisms including not only vertebrate, but also invertebrate during asexual and sexual reproduction and participates in stem cell differentiation during regeneration. In this study, in order to identify and characterize DDX3 gene in the earthworm, Perionyx excavatus having a powerful regeneration capacity, total RNA was isolated from adult head containing clitellum. Full length of DDX3 gene from P. excavatus, Pe-DDX3, was identified by RT-PCR using the total RNA from head as a template. Pe-DDX3 encoded a putative protein of 607 amino acids and it also has the nine conserved motifs of DEAD-box family, which is characteristic of DEAD-box protein family. It was confirmed that Pe-DDX3 has the nine conserved motifs by the comparison of entire amino acids sequence of Pe-DDX3 with other species of different taxa. Phylogenetic analysis revealed that Pe-DDX3 belongs to a DDX3 (PL10) subgroup of DEAD-box protein family. And it displayed a high homology with PL10a, b from P. dumerilii.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.277-285
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• 2009

The nucleotide sequence of the Paenibacillus curdlanolyticus B-6 xyn10A gene, encoding a xylanase Xyn10A, consists of 3,828 nucleotides encoding a protein of 1,276 amino acids with a predicted molecular mass of 142,726 Da. Sequence analysis indicated that Xyn10A is a multidomain enzyme comprising nine domains in the following order: three family 22 carbohydrate-binding modules (CBMs), a family 10 catalytic domain of glycosyl hydrolases (xylanase), a family 9 CBM, a glycine-rich region, and three surface layer homology (SLH) domains. Xyn10A was purified from a recombinant Escherichia coli by a single step of affinity purification on cellulose. It could effectively hydrolyze agricultural wastes and pure insoluble xylans, especially low substituted insoluble xylan. The hydrolysis products were a series of short-chain xylooligosaccharides, indicating that the purified enzyme was an endo-$\beta$-1,4-xylanase. Xyn10A bound to various insoluble polysaccharides including Avicel, $\alpha$-cellulose, insoluble birchwood and oat spelt xylans, chitin, and starches, and the cell wall fragments of P. curdlanolyticus B-6, indicating that both the CBM and the SLH domains are fully functioning in the Xyn10A. Removal of the CBMs from Xyn10A strongly reduced the ability of plant cell wall hydrolysis. These results suggested that the CBMs of Xyn10A play an important role in the hydrolysis of plant cell walls.