• Journal of Life Science
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• v.9 no.2
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• pp.9-14
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• 1999

Pseudomonas iodinum IFO 3558 adenosine deaminase(ADA) gene was cloned by the polymerase chain reaction and deduced the amino acid sequence of the enzyme. DNA sequence homology of Pseudomonas iodinum IFO 3558 ADA gene was compared to those of E. coli, human and mouse ADA genes. Unambiguous sequence from both strands of pM21 was obtained for the region believed to encode ADA. The sequence included a 804-nucleotide open reading frame, bounded on one end by sense primer and on the other end by two antisense primer. This open reading frame encodes a protein of 268 amino acids having a molecular weight of 29,448. The deduced amino acid sequence shows considerable similarity to those of E. coli, mouse and human ADA. Pseudomonas iodinum IFO 3558 nucleotide sequence shows 98.5% homology with that of the E. coli ADA sequence and 51.7% homology with that of the mouse ADA sequence and 52.5% homology with that of the human ADA sequence. The ADA protein sequence of Pseudomonas iodinum IFO 3558 shows 96.9% homology with that of the E. coli and 40.7% homology with that of the mouse and 41.8% homology with that of the human. The distance between two of the conserved elements, TVHAGE and SL(1)NTDDP has veen exactly conserved at 76 amino acids for all four ADAs. Two of the four conserved sequence elements shared among the four ADAs are also present in the yeast, rat, human (M), and Human(L) AMP deaminase. The SLSTDDP sequence differs only in the conservative substitution of a serine for an asparagine. A conserved cysteine with conserved spacing between these two regions is also found. Thus, sequence analysis of four ADAs and four AMP deaminases revealed the presence of a highly conserved sequence motif, SLN(S)TDDP, a conserved dipeptide, HA, and a conserved cysteine residue.

• Journal of Species Research
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• v.13 no.2
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• pp.127-130
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• 2024

The first complete mitogenome sequence of the Red-tongue Pit Viper (Gloydius ussuriensis) from Korea was characterized using next-generation sequencing. The mitogenome is a circular molecule (17,209 bp) with a typical vertebrate mitogenome arrangement, which consists of 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), two non-coding regions (D-loop), and 13 protein-coding genes (PCGs). The base composition of the mitogenome is 32.7% of A, 27.5% of C, 13.9% of G, and 25.9% of T, with a slight AT bias(58.6%). This phylogenetic analysis infers that G. ussuriensis is in the same group as the Chinese G. ussuriensis (Accession No. KP262412) and is closely related to G. blomhoffi and other species of the genus Gloydius. In our study, the complete mitogenome sequence of Korean G. ussuriensis was characterized and we provided basic genetic information on this species.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.31 no.1 s.49
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• pp.13-16
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• 2005

For the high-throughput-screening system (HTS) of depigmenting agents using a protein chip, effects of oligonucleotide-inhibitor sequence on the binding of Mitf protein to E box of MC1R was investigated. The sequence of oligonucletide-inhibitor affected the binding of the target DNA to Mitf, depending on the location of the sequence variation in the inhibitor nucleotide. The oligonucletide-inhibitor that changed the CATGTG sequence didn't show enough inhibition of the target DNA to Mitf, whereas significant inhibition was observed when the sequence outside the CATGTG was changed. This result indicated that CATCTG is crucial sequence for the binding of Mitf to I-box which initiates the transcription of pigmenting genes.

• Journal of Microbiology and Biotechnology
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• v.8 no.4
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• pp.399-405
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• 1998

From the sequence alignment of various non-ribosomal peptide synthetases, several motifs of highly conserved sequences have been identified within each domain of peptide synthetases. We designed PCR primers based on the highly conserved nucleotide sequences to amplify and isolate a ∼7.2-kb DNA fragment of the Bacillus subtilis 713 which was isolated and reported to produce an antifungal peptide compound. Nucleotide sequence analysis of 4.8 kb of the predicted amino acids revealed significant homology to various peptide synthetases over the whole sequence and also revealed two amino acid-activating domains with highly conserved Core 1 to Core 6 and spacer motif. This suggests that the isolated DNA fragment is part of a peptide synthetase gene for antifungal peptide.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2002.11b
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• pp.54-54
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• 2002

The nucleotide sequence of a Korea isolate of broad bean wilt favavirus from Rehmannia glutinosa Lib., designated BBWV-RE, was determined. Direct amino acid sequencing of the virus coat proteins suggests that a comparison of several favaviruses in terms of nucleotide sequence and amino acid sequences showed that BBWV-2 isolates display high sequence identity. The small coat protein genes of RNA-2 were also determined for three other Japanese isolates(E, L, and 1-2) and two ATCC isolates(PV132 and PV176) of BBWV. the CP sequence suggested distinct evolution lineages. Serotype 2 favaviruses are more prevalent in Asia, Australia and North America, Wheres serotype 1 is more prevalent in europe.(중략)

• Journal of Microbiology and Biotechnology
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• v.24 no.10
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• pp.1301-1307
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• 2014

White-rot fungi of the genus Bjerkandera are cosmopolitan and have shown potential for industrial application and bioremediation. When distinguishing morphological characters are no longer present (e.g., cultures or dried specimen fragments), characterizing true sequences of Bjerkandera is crucial for accurate identification and application of the species. To build a framework for molecular identification of Bjerkandera, we carefully identified specimens of B. adusta and B. fumosa from Korea based on morphological characters, followed by sequencing the internal transcribed spacer region and 28S nuclear ribosomal large subunit. The phylogenetic analysis of Korean Bjerkandera specimens showed clear genetic differentiation between the two species. Using this phylogeny as a framework, we examined the identification accuracy of sequences available in GenBank. Analyses revealed that many Bjerkandera sequences in the database are either misidentified or unidentified. This study provides robust reference sequences for sequence-based identification of Bjerkandera, and further demonstrates the presence and dangers of incorrect sequences in GenBank.

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.172-175
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• 2002

The complete nucleotide sequence of the nahC gene from Pseudomonas fluorescens, the structural gene for 1,2-dihydroxynaphthalene (1,2-DHN) dioxygenase, was determined. The 1,2-DHN dioxygenase is an extradiol ring-cleavage enzyme that cleaves the first ring of 1,2-dihydroxynaphthalene. The amino acid sequence of the dioxygenase deduced from the nucleotide sequence suggested that the holoenzyme consists of eight identical subunits with a molecular weight of approximately 34,200. The amino acid sequence of 1,2-DHN dioxygenase showed more than $90\%$ homology with those of the dioxygenases of other Pseudomonas strains. However, sequence similarity with those of the Sphingomonas species was less than $60\%$. The nahC gene of P. fluorescens was moderately expressed in E. coli NM522, as determined by enzymatic activity.

• Animal cells and systems
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• v.7 no.2
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• pp.133-137
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• 2003

Secreted proteins and membrane proteins play key roles in the formation, differentiation, and maintenance of multicellular organisms. In this study, we undertook to characterize these protein types in the central nervous system of the marine snail Aplysia kurodai using a yeast-based signal sequence trap method. One hundred and three cDNA clones were obtained by screening 300,000 clones from the signal sequence trap cDNA library. Of these, twelve were identical to previously identified Aplysia genes, 19 were related to known proteins in other organisms, and 54 clones were novel. These 54 new genes had high signal peptide scores or were found likely to contain a transmembrane domain sequence. Only 18 of the 103 clones proved to be false positive. The study demonstrates that the signal sequence trap method is an effective tool for Isolating Aplysia genes encoding secreted and membrane proteins.

• Microbiology and Biotechnology Letters
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• v.35 no.4
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• pp.352-356
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• 2007

A Lactobacillus sp. has been isolated from infant feces and characterized according to its physiological properties and identified as Lactobacillus acidophilus KLA1012. A gene coding surface layer protein (SLP) has been cloned and the sequence has been determined. The nucleotide sequence of slpA was 1,338 bp in size and was identical to that of L. acidophilus ATCC 4356 (100%). Amino acid sequence of SLP-A was deduced from the nucleotide sequence and it had signal sequence at N-terminal, consisting of positively charged amino acid mainly lysine. slpA was cloned and heterologously expressed in E. coli M15 and the 45.2 kDa surface-layer protein band was examined by SDS-PAGE and confirmed by Western blotting using polyclonal antibody against L. acidophilus KLA 1012 SLP-A protein.

• Journal of the Korean Data and Information Science Society
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• v.17 no.2
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• pp.569-579
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• 2006

Recently, the amount of genome sequence is increasing rapidly due to advanced computational techniques and experimental tools in the biological area. Sequence comparisons are very useful operations to predict the functions of the genes or proteins. However, it takes too much time to compare long sequence data and there are many research results for fast sequence comparisons. In this paper, we propose a hybrid grid system to improve the performance of the sequence comparisons based on the LanLinux system. Compared with conventional approaches, hybrid grid is easy to construct, maintain, and manage because there is no need to install SWs for every node. As a real experiment, we constructed an orthologous database for 89 prokaryotes just in a week under hybrid grid; note that it requires 33 weeks on a single computer.