• Plant Resources
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• v.1 no.2
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• pp.92-97
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• 1998

An isolate of barley yellow mosaic virus(BaYMV-HN) obtained from Haenam, Korea was compared with two BaYMV strains. BaYMV-Ⅱ-1 from Japan and BaYMV-G from Germany. The sequence of the 3'-terminal 3817nucleotides[excluding the poly (A) tail] of RNA 1 of BaYMV-HN was determined to start within a long open reading frame coding for a part of the NIa-VPg polymerase(26 amino acids). NIa-Pro polymerase (343 amino acids), NIb polymerase(528 amino acids) and the entire capsid protein(297 amino acids), which is followed by a noncoding region(NCR) of 235 nucelotides. In the partial ORFs, BaYMV-HN shows higher sequence homology with BaYMV-Ⅱ-1(99.5%) than BaYMV-G(92.7%). The 3' non-coding regions of BaYMV-HN(235nt) shows higher nucleotide sequence homology with BaYMV-G(235nt)(99.6%) than BaYMV-Ⅱ-1(231nt)(97.0%). The 3' NIa-Pro protein sequence of BaYMV-HN shows higher amino acid sequence homology with BaYMV-Ⅱ-1(95.0%) than BaYMV-G(93.6%), but, NIb protein sequence of BaYMV-HN shows same all amino acid sequence. The capsid protein sequence of BaYMV-HN(297aa) shows same with BaYMV-Ⅱ-1, and shows higher nucleotide sequence homology with BaYMV-UK (from United Kingdom)(97.3%) than BaYMV-G(96.9%) and G2(96.9%). Difference of capsid protein amino acid were 0-9 between the Japan, United Kingdom and Germany and were 2-6 between all Korean isolates. Many of the amino acid differences are located in the N-terminal regions of the capsid proteins from 1 to 74 amino acid positions.

• Journal of Plant Biotechnology
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• v.3 no.3
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• pp.131-134
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• 2001

In $\lambda$-Zap II vector system, a cDNA library was constructed for the developing secondary xylem mRNA from hybrid poplar, Populus nigra x maximowiczii. A cDNA clone of 1.5 kb in size, pOMTB1.4 encoding a lignin-bispecific O-methyltransferase was screened by plaque hybridization using a probe of 540 bp cDNA amplified by polymerase chain reaction from the cDNA library and identified by nucleotide sequencing. Its nucleotide sequence contains one open reading frame of 366 amino acids. The deduced amino acid sequence in comparison with that of Populus tremuloides showed the differences of 9 amino acids and revealed 85-99% homology among alfalfa, poplar and aspen.

• Fisheries and Aquatic Sciences
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• v.4 no.4
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• pp.192-196
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• 2001

Proopiomelanocortin (POMC) plays an essential role in the disease resistance system and is the precursor protein of biologically active peptides such as adrenocorticotropin (ACTH), $\alpha-melanocyte-stimulating$ hormone $(\alpha- MSH)$, $(\beta-melanocyte-stimulation hormone\;(\beta- MSH)$ and $\beta-endorphin$. We have isolated and sequenced two different forms of POMC cDNA, POMC-I and POMC-II, from a pituitary cDNA library of flounder. POMC-I cDNA consisted of 956 bp corresponding to deduced amino acids of 216 residues and POMC-II cDNA was 982 bp in length corresponding to 194 amino acids, respectively. The results of deduced amino acids analysis of the clones showed high sequence homology with previously reported POMCs amino acid sequences from various species. The homology between flounder POMC-I and -II is$57\%$ identity. We also constructed a phylogenetic tree based on POMC amino acid sequences.

• Korean Journal of Veterinary Research
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• v.47 no.2
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• pp.169-174
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• 2007

To provide information for the molecular pathogenesis and antigenic structures of Korean isolates of porcine epidemic diarrhea virus (PEDV), the small membrane (sM) protein gene of Chinju99 strain, which was previously isolated from piglets suffering from severe diarrhea was characterized and further analyzed with other PEDV strains. The sM gene of Chinju99 generated by reverse transcription and polymerase chain reaction had a single open reading frame with 231 bases consisting of 24.2% adenine, 18.6% cytosine, 18.1% guanine and 39.0% thymine nucleotides. Nucleotide sequence of the gene revealed 97.8% homology to those of Belgian strain CV777 and British strain Br1/87, and 97.0% to Chinese strain LZC. The gene encoded a protein with 76 amino acids, and putative amino acid sequence of the gene revealed 98.7% homology to those of CV777 and Br1/87, and 96.1% to LZC. The amino acids of Chinju99 sM gene consisted of mostly hydrophobic residues, and there were one potential N-myristylation site and one potential threonine (T)-linked phosphorylation site recognized. Also, there was a transmembrane region with 46 amino acids, and Chinju99 was more close to CV777 and Br1/87 than to LZC in phylogenetic analysis on the sM amino acid sequences.

• BMB Reports
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• v.37 no.4
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• pp.429-438
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• 2004

Complementary DNAs encoding $\alpha$-amylases (Amyl I, Amyl III) and glucoamylase (GA I) were cloned from Aspergillus awamori KT-11 and their nucleotide sequences were determined. The sequence of Amyl III that was a raw starch digesting $\alpha$-amylase was found to consist of a 1,902 bp open reading frame encoding 634 amino acids. The signal peptide of the enzyme was composed of 21 amino acids. On the other hand, the sequence of Amyl I, which cannot act on raw starch, consisted of a 1,500 bp ORF encoding 499 amino acids. The signal peptide of the enzyme was composed of 21 amino acids. The sequence of GA I consisted of a 1,920 bp ORF that encoded 639 amino acids. The signal peptide was composed of 24 amino acids. The amino acid sequence of Amyl III from the N-terminus to the amino acid number 499 showed 63.3% homology with Amyl I. However, the amino acid sequence from the amino acid number 501 to C-terminus, including the raw-starch-affinity site and the TS region rich in threonine and serine, showed 66.9% homology with GA I.

• 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 Microbiology and Biotechnology
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• v.3 no.4
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• pp.224-231
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• 1993

The nucleotide sequence of the xylanase gene (xynY) from alkalophilic Bacillus sp. YC-335 was determined and analyzed. An open reading frame of 1, 062 base pairs for xynY gene was observed and encoded for a protein of 354 amino acids with a molecular weight of 38, 915. S1 nuclease mapping showed that the transcription initiation sites of the xynY gene were different in Bacillus sp. YC-335 and Escherichia coli HB101 (pYS55). S1 mapping also showed that -10 region of the xynY gene recognized by RNA polymerases of E. coli and Bacillus sp. YC-335 were TACAGT and TATGAT , respectively. A ribosome binding site sequence with the free energy of -17.0 Kcal/mol was observed 9 base pairs upstream from the unusual initiation codon, TTG. The proposed signal sequence consisted of 27 amino acids, 2 of which were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YC-335 xylanase showed more than 50% homology with xylanases from B. pumilus, B. subtilis, and B. circulans.

• Korean Journal of Veterinary Research
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• v.46 no.4
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• pp.355-361
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• 2006

Porcine epidemic diarrhea virus (PEDV) strain Chinju99, which was previously isolated from piglets suffering from severe diarrhea was used to characterize the membrane (M) protein gene to establish the molecular information, and the results will be useful in elucidating concepts related to molecular pathogenesis and antigenic structures of PEDV isolates. The Chinju99 M gene generated by reverse transcription and polymerase chain reaction (RT-PCR) consisted of 681 bases containing 22.3% adenine, 22.3% cytosine, 23.1% guanine and 32.3% thymine nucleotides, and the GC content was 45.4%. It had some nucleotide mismatches from M gene of other PEDV strains, such as CV777, Br1/87, KPEDV-9, JMe2, JS2004-2 and LJB-03 with 97-99% nucleotide sequence homology to these strains. Also, it encoded a protein of 226 amino acids, which had some mismatches from those of CV777, Br1/87, KPEDV-9, JMe2, JS20004-2 and LJB-03, as the amino acid sequence homology showed a 97-98% to these strains. The Chinju99 had a very close relationship to the Japanese strain JMe2 for the nucleotide and amino acid sequences of the M gene. The amino acids predicted from Chinju99 M gene consisted of mostly hydrophobic residues and contained three potential sites for asparagine (N)-linked glycosylation, two serine (S)-linked phosphorylation sites by protein kinase C, and two S- or threonine (T)-linked phosphorylation sites by casein kinase II.

• Korean Journal of Plant Tissue Culture
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• v.26 no.1
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• pp.41-47
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• 1999

Phenylalanine ammonia-lyase (PAL; EC 4, 3, 1, 5) genomic clones were isolated from tomato(Lycopersicon esculentum L.) genomic DNA libraries using tomato PAL5 cDNA sequences as probes. The nucleotide sequences of tPAL1, tPAL4 and tPAL5 were compared. tPAL5 contains an open reading frame encoding a polypeptide of 722 amino acids, interrupted by a 710 bp intron in the codon for the amino acid 139. tPAL1 encodes a polypeptide of 249 amino acids which is much shorter than tPAL5 gene due to a premature stop codon and does not contain an intron. tPAL4 encodes a polypeptide of 357 amino acids, interrupted by a 305 bp intron in the codon for the amino acid 138. Premature stop codons observed in tPAL1 and tPAL4 gene produce a short polypeptide rather than a normal polypeptide (722 aa). tPALl shows 87.2% homology with tPAL4 and 85.3% homology with tPAL5 gene whereas tPAL4 showes 91.4% homology with tPAL5 at nucleotide level. In general, phylogenetic analysis showed that genes isolated from tomato, potato, and sweet potato were belong to the same group and another dicot plants such as parsley, bean, soybean, pea and alfalfa formed another group. PAL genes isolated from rice and yeast showed very low homology with other PAL genes and formed the other group.

• Journal of Microbiology and Biotechnology
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• v.3 no.3
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• pp.139-145
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• 1993

The nucleotide sequence of the xylanase gene (xynS) from alkali-tolerant Bacillus sp. YA.14 was determined and analyzed. A 639 base pairs open reading frame for xynS gene was observed and encoded for a protein of 213 amino acids with a molecular weight of 23, 339. S1 nuclease mapping showed that the transcription initiation site of the xynS gene did not exist in the cloned DNA. Ribosome binding site sequence with the free energy of -18.8 Kcal/mol was observed 8 base pairs upstream from the initiation codon, ATG. The proposed signal sequence consisted of 28 amino acids, of which 3 were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YA-14 xylanase showed 48% homology with Bacillus sp. YC-335 xylanase and 96% homology with xylanases from B. subtilis and B. circulans.