• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.129-131
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• 2006

Through molecular phylogenetic analysis using the nef gene sequences of HIV-l isolated from Korean registered in the NCBI GenBank together with 41 reference strains and 94 foreign isolates, we verified that most (${\sim}80%$) of Korean isolates belonged to subtype B and 78% of subtype B were clustered together exclusively of foreign isolates, and this cluster was named Korean clade subtype B ($K_cB$). Similarity study suggested that the $K_cB$ cluster was more homogeneous than and clearly distinctive from the non-Korean subtype B ($NK_cB$). Comparison of the consensus amino acid sequences of the $K_cB\;or\;NK_cB$ revealed characteristic $K_cB$ signature amino acid pattern comprised of 13 amino acid residues. The $K_cB$ signature amino acid residues were critical in separating the $K_cB$ ftom the $NK_cB$, since substitution of the $NK_cB$ sequences with $K_cB$ signature amino acids relocated them to the Koran clade, and vice versa. Synonymous and nonsynonymous substitution rate study suggested positive selection event for the $K_cB$.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.823-828
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• 2000

The complete nucleotide sequence of hepatitis B virus DNA isolated from Korean patient serum was determined and characterized, and its phylogenetic relation was then investigated. The viral genome was 3,215 base pairs long and included four well known open reading frames (i.e. surface antigens, core antigens, X protein and DNA polymerase). The sequence of the surface antigen showed that the HBV genome under investigation, designated HBV 315, was characteristic of subtype adr. A phylogenetic analysis using the total genome sequence revealed that HBV315 was grouped into genomic group C together with isolates from Japan, China, Thailand, Polynesia, and New Caledonia. The mean percent similarity between HBV315 and other HBV isolates in genomic group C was 97.25%, and that with other genomic groups ranged from 86.16% to 91.25%. The predicted amino acid sequences of HBV315 were compared with two closely related subtype adr isolates, M38636 and D12980. The results showed that the X gene product was identical in the three strains, while there were significant amino acid sequence differences between HBV315 and M38636 in the Pre-S1 and Pre-S2 regions.

• International Journal of Industrial Entomology and Biomaterials
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• v.6 no.1
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• pp.99-102
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• 2003

A cDNA of novel immulectin homologue (BmIML), a C-type lectin, was cloned from the silkworm, Bombyx mori. The immulectin cDNA is an open reading frame of 921 bp encoding 307 amino acid residues. The deduced amino acid sequence from the BmIML cDNA contains two C-type carbohydrate recognition domains (CRDs). The BmIML was most similar (61 % protein sequence identity) to the M. sexta immulectin-1, whereas BmIML showed relatively lower identity to the B. mori lipopolysaccharide-binding protein (25% protein sequence identity). These features of BmIML indicate that BmIML is a novel member of C-type lectin superfamily. Northern blot analysis revealed that the BmIML is specifically expressed in the fat body of B. moli larvae.

• Korean Journal of Microbiology
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• v.42 no.4
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• pp.313-318
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• 2006

A thermophilic bacterium producing the extracellular cellulase was isolated from soybean paste, and the isolate WL-12 has been identified as Bacillus licheniformis on the basis on its 16S rRNA sequence, morphology and biochemical properties. A gene encoding the cellulase of B. licheniformis WL-12 was cloned and its nucleotide sequence was determined. This cellulase gene, designated celA, consisted of 1,551 nucleotides, encoding a polypeptide of 517 amino acid residues. The gene product contained catalytic domain and cellulose binding domain. The deduced amino acid sequence was highly homologous to those of cellulases of B. licheniformis, B. subtilis and B. amytoliquefaciens belonging to the glycosyl hydrolase family 5. When the celA gene was highly expressed using a strong B. subtilis promoter, the extracellular cellulase was produced up to 7.0 units/ml in B. subtilis WB700.

• Journal of Microbiology
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• v.35 no.1
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• pp.40-46
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• 1997

The pWHM220 cosmid with a 24-kb insert cloned from Streptomyces albus ATCC 21838 induces the biosynthesis of a polysther antibiotic similar to salinomycin in Streptomyces invidans. We have analyzed this region by DNA sequencing as well as Southern blot hybridization with type I and type II polyketide synthase (PKS) probes. Surprisingly, we found another set of type II SKS genes only 10-kb from the original PKS genes, salABCDE. The DNA sequence revealed two complete open reading frames (ORFs) named salB2 and salC2, and one partial ORF that does not resemble any known DNA or deduced protein sequence. The salC2 should code for chain length determining factor while the deduced amino acid sequence encoded by salB2 exhibits high similarity to .betha.-ketoacyl synthase from different PKS gene clusters. The highest identity was found for .betha.-keetoacyl synthases from S. argillaceus (MtmP. 59.1% identity), the mithramycin producer and from S. venezuelae ISP5230 (JadA, 52.3% identity), the jadomycin producer. The SalC2 protein clearly resembles its counterparts in order aromatic PKS gene clusters that are believed to influence the length of the polyketide chain. The highest identities observed were to that of S. argillaceus (MtmK, 62.3%) and S. venezuelae ISP 5230 (JadB, 55.1%) proteins, Moreover, the deduced amino acid sequences of the salB2 and salC2 products were 29.0% identical.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.53-53
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• 2003

Calumenin was previously identified as a high affinity Ca$\^$2+/ binding protein in mouse cardiac sarcoplasmic reticulum (SR). For the present study, a 48 kDa skeletal homologue of calumenin was identified by sucrose-density gradient of rabbit skeletal SR membranes, concanavalin A treatment, 2D-gel electrophoresis, $\^$45/Ca$\^$2+/ overlay, Stains-all staining, and MALDI-TOF analysis. We attempted to clone the skeletal calumenin by RT-PCR based on mouse cardiac and human calumenin sequences. The deduced amino acid sequence (315 residues) of the skeletal calumenin showed high identity to mouse cardiac calumenin (90％). As seen in the cardiac calumenin, the deduced sequence contains a 19 amino acid N-terminal signal sequence and a HDEF C-terminal sequence, a putative retrieval signal to ER. Also, the skeletal calumenin contains one N-glycosylation site, three PKC phosphorylation sites, eight casein kinase 2 phosphorylation sites, and 6 EF-hand domains. GST-calumenin showed a conformational change and increased mobility in the presence of Ca$\^$2+/ in SDS-PAGE. Three calumenin interacting proteins (ryanodine receptor 1, glycogen phosphorylase, and phosphofructo kinase) were identified by pull-down assay with GST-calumenin and solubilized SR. All the interactions were Ca$\^$2+/dependent. The present results suggest that calumenin plays an important role in Ca$\^$2+/ homeostasis of muscle cells.

• Biomolecules & Therapeutics
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• v.9 no.2
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• pp.79-87
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• 2001

Heat shock proteins serve as chaperone by preventing the aggregation of denatured proteins and promote survival of pathogens in harsh environments. In this study, heat shock gene encoding a 84-kDa (p84) protein, which is one of the three major heat shock proteins in S. pneumoniae, was cloned and characterized. PCR with a forward primer derived from N-terminal amino acid sequence of the p84 and a reverse primer derived from the conserved second ATP-binding region of Clp family was used for amplification of the gene encoding the p84 and subsequently the PCR product was used for sequence determination. Sequence analysis of the p84 gene demonstrated that it is a member of ClpL. The deduced amino acid sequence of pneumococcal ClpL shows homology with other members of the Clp family, and particularly, even in variable leader region, with bovine Clp-like protein and L. lactis ClpL. S. pneumoniae clpL is the smallest clop member (701 amono acids) containing the two conserved ATP-binding regions, and hydrophilic N-terminal variable region of pneu-mococcal Clp ATPase is much shorter than any known Clp ATPases. Histidine tagged ClpL was overexpressed and purified from E. coli. Immunoblot analysis employing antisera raised against pneumococcus p84 demonstrated no cross-reactivity with Clp analog in Eschericha coli, Staphylococcus aureus and human HeLa cells. Preimmunization of mice with ClpL extended mice life partially but did not protect them from death.

• YAKHAK HOEJI
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• v.43 no.6
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• pp.789-792
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• 1999

The complete nucleotide sequence of pKH4, a small multidrug resistance (smr) plasmid isolated from multidrug resistant Staphylococcus aureus SA5, was determined. Sequence analysis has revealed that pKH4 has two open reading frames for Rep and Smr proteins. The comparison of the amino acid sequence of Smr protein of pKH4 with those of other Smr proteins of various Staphylococcus showed that Smr protein of pKH4 is a new member of the SMR family.

• Journal of Microbiology
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• v.44 no.5
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• pp.515-522
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• 2006

A cDNA library of Ganoderma lucidum has been constructed using a Zap Express cloning vector. A glyceraldehyde-3-phosphate dehydrogenase gene (gpd) was isolated from this library by hybridization of the recombinant phage clones with a gpd-specific gene probe generated by PCR. By comparison of the cDNA and the genomic DNA sequences, it was found that the complete nucleotide sequence encodes a putative polypeptide chain of 338 amino acids interrupted by 6 introns. The predicted amino acid sequence of this gene shows a high degree of sequence similarity to the GPD proteins from yeast and filamentous fungi. The promoter region contains a CT-rich stretch, two CAAT boxes, and a consensus TATA box. The possibility of using the gpd promoter in the construction of new transformation vectors is discussed.

• Proceedings of the Microbiological Society of Korea Conference
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• 1991.04a
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• pp.225-236
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• 1991

The genes encoding the thermostable $\alpha$-amylase and maltogenic amylase from Bacillus lichenciformis were cloned and expressed in E. coli. The recombinant plasmid pTA322 was found to contain a 3.1kb EcoRI genomic DNA fragment of the thermostable $\alpha$-amylase. The cloned $\alpha$-amylase was compared with the B. licheniformis native $\alpha$-amylase. Both $\alpha$-amylase have the same optimal temperature of $70^{\circ}C$ and are stable in the pH range of 6 and 9. The complete nucleotide sequences of the thermostable $\alpha$-amylase gene were determined. It was composed of one open reading rame of 1,536 bp. Start and stop codons are ATG and TAG. From the amino acid sequence deduced from the nucleotide sequence, the cloned thermostable $\alpha$-amylase is composed of 483 amino acid residues and its molecular weight is 55,200 daltons. The content of guanine and cytosine is $47.46mol\%$ and that of third base codon was $53_41mol\%$. The recombinant plasmid, pIJ322 encoding the maltogenic amylase contains a 3.5kb EcoRI-BamHI genomic DNA fragment. The optimal reaction temperature and pH of the maltogenci amylase were $50^{\circ}C$ and 7, respectively. The maltogenic amylase was capable of hydrolysing pullulan, starch and cyclodextrin to produce maltose from starch and panose from pullulan. The maltogenic amylase also showed the transferring activity. The maltogenic amylase gene is composed of one open reading frame of 1,734bp. Start and stop codons are ATG and ATG. At 2bp upstream from start codon, the nucleotide sequence AAAGGGGGAA seems to be the ribosome-binding site(RBS, Shine-Dalgarno sequence). A putative promoter(-35 and-10 regions) was found to be GTTAACA and TGATAAT. From deduced amino acid sequence from the nucleotide srquence, this enzyme was comosed of 578 amino acid residues and its molecular weight was 77,233 daltons. The content of guanine and cytosine was $48.1mol\%$. The new recombinant plasmid, pTMA322 constructed by inserting the thermostable $\alpha$-amylase gene in the EcoRI site of pIJ322 to produce both the thermostable $\alpha$-amylase and the maltogenic amylase were expressed in the E. coli. The two enzymes expressed from E. coli containing pTMA322 was reacted with the $15\%$ starch slurry at $40^{\circ}C$ for 24hours. The distribution of the branched oligosaccharides produced by the single-step process was of the ratio 50 : 50 between small oligosaccharide up DP3 and large oligosaccharide above DP3.