• Title/Summary/Keyword: nucleotide sequence homology

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Cloning of the Adenosine Deaminase Gene from Pseudomonas iodinum IFO 3558

  • Jo, Young-Bae;Baik, Hyung-Suk;Bae, Kyung-Mi;Jun, Hong-Ki
    • 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.

Nucleotide Sequence Homology in Rotaviruses (Rotaviruses의 염기배열 유사성 측정)

  • ;Spendlove, Rex S.;Barnett, Bill B
    • Korean Journal of Microbiology
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    • v.26 no.3
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    • pp.155-161
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    • 1988
  • Nucleotide sequence homology between bovine, simian, and porcine rotavirus was determined by the RNA:RNA hybridization technique. Single stranded RNA, prepared in vitro with EDTA activated endogeneous viral RNA polymerase, was hhbridized with tritium labeled bovine rotavirus genomic RNA. The heteroduplex RNA was treated with single stranded RNA specific ribonucleases and the RNase resistant hybrid RNA was precipitated, and collected by filtration on a filter paper. Seventy four percent RNA sequence homology between bovine and simian rotavirus and 8 percent RNA sequence homology between bovine and porcine rotavirus was confirmed by hybridization between tritium labeled single stranded RNA and viral genomic RNA.

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Genetic Characteristics of Porcine Epidemic Diarrhea Virus Isolated in Korea (돼지 유행성 설사 바이러스 국내분리주의 유전학적 특성 규명)

  • Chi, Yong-zhe;Kwon, Hyuk-moo;Jeong, Hyun-kyu;Han, Jeong-hee
    • Korean Journal of Veterinary Research
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    • v.43 no.2
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    • pp.219-230
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    • 2003
  • Porcine epidemic diarrhea virus(PED), a member of Coronaviridea, is the etiological agent of enteropathogenic diarrhea in swine. The purpose of this study was to investigate genetic characteristic of PEDV isolated in Korea. Nucleocapsid(N) gene and membrane (M) gene of recent Korean PEDV strains isolated in 2001 were amplified, cloned, sequenced and analyzed. N gene of seven Korean PEDV field isolates bad 94.5% to 99.4% nucleotide and 92.4% to 99.4% amino acid sequence homology each other. Nucleotide and amino acid sequences of Korean field PEDVs were different from published foreign PEDVs, showing 95.1% to 98.0% nucleotide and 93.5% to 97.6% amino acid sequence homology. By phylogenetic tree analysis on based nucleotide sequences, PEDVs were clustered into four groups. By phylogenetic tree analysis based on amino acid sequences. PEDVs were clustered into five groups. M gene of our Korean PEDV field isolates had 99.6% to 100% nucleotide and 98.7% to 100% amino acid sequence homology each other. Nuclotide and amino acid sequences of Korean field PEDVs were different from published foreign PEDVs, showing 98.5% to 98.8% nucleotide and 97.3% to 97.8% amino acid sequence homology. By phylogenetic tree analysis based on nucleotide and amino acid sequences, PEDVs were clustered into two groups which were Korean PEDV isolate group and foreign PEDV isolate group.

Cloning and nucleotide sequence analysis of VP7 genes of bovine rotaviruses isolated in Korea (국내에서 분리된 소 로타바이러스의 VP7 유전자 크로닝 및 염기서열 분석)

  • Kang, Shien-young;Jeon, Seong-jin;Chang, Kyeong-ok;Park, Yong-ha;Kim, Won-yong
    • Korean Journal of Veterinary Research
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    • v.37 no.2
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    • pp.367-374
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    • 1997
  • Bovine rotaviruses(A, 288, 55086 strains) isolated from fecal samples in Korea were propagated onto MA104 cells and were confirmed tentatively as G6, G8, and G10, respectively, by RFLP analysis. Full-length VP7 gene of these isolates was amplified by reverse transcriptase polymerase chain reaction(RT-PCR) using VP7 specific primers and cloned into TA vector. Nucleotide and deduced amino acid sequences of VP7 genes of the isolates were determined and compared with those of bovine rotavirus reference strains(NCDV; G6, UK; G6, Cody I-801; G8 and B223; G10). A, 288 and 55086 isolates showed high degree of nucleotide sequence homology with NCDV and UK(93% and 94%), Cody I-801(86%) and B223(97%), respectively, However, they showed 71~74% of nucleotide sequence homlogy with bovine rotavirus reference strains which belong to different serotypes. From the results of deduced amino acid sequence homology analysis, three isolates showed 94~96% of homology with the same serotype reference strains but 80~84% of homology with the different serotype reference strains. Three bovine rotavirus isolates, A, 288 and 55086 strains, were confirmed as G6, G8, and G10, respectively, by nucleotide and deduced amino acid sequence analysis.

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Sequence Analysis of NS4 Region of HCV Isolated from Korean Patient

  • Paik, Sang-Hoon;Lee, Young-Ik;Kim, Won-Bae;Yang, Jai-Myung
    • Journal of Microbiology
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    • v.33 no.3
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    • pp.260-266
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    • 1995
  • Hepatitis C virus (HCV) has been considered as a mojor causative agent of post-transfusion related non-A, non-B hepatitis. In this study, the cDNA sequence of NS4 region of HCV (HCV-S) obtained from a Korean patient's plasms was determined. Comparative nucleotide sequence analysis between to type II. 67.2% homology to type III, and 66.4% homology to type IV. The putative amino acid sequence homologies to types I, II, III, and IV were 82.8-84.7%, 92.5-95.1%. 72.5, and 71.1%, respectively. This data strongly suggests that HCV-S should be classified as type II. Significant similarities of hydrophobicity profiles and putative transmembranous domains were found in HCV-S and four major prototypes, indicating that the protein structure is similar in spite of the heterogeneities of intertype homologies at the level of the psrimary nucleotide and amino acid sequences.

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Nucleotide Sequence Analysis of the RNA-dependent RNA Polymerase Gene of Infectious Pancreatic Necrosis Virus DRT Strain

  • Lee, Hyung-Hoan;Chung, Hye-Kyung;Lee, Seong-Hun
    • Journal of Microbiology and Biotechnology
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    • v.4 no.4
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    • pp.264-269
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    • 1994
  • To determine the nucleotide sequence of the ds RNA segment B containing the RNA dependent RNA polymerase (RdRp) gene of the DRT strain of infectious pancreatic necrosis virus (lPNV), the cDNA of the ds RNA segment B of the DRT strain of IPNV was synthesized using the reverse transcriptase (RT)-polymerase chain reaction (PCR) and its cDNA nucleotide sequence was determined. The DRT segment B was 2, 783 bp long and contained only a single long open reading frame (ORF) of 2, 535 bp in length. This ORF nucleotides encoded the VPl protein, the putative RdRp of IPNV. The VPl protein comsisted of 845 amino acids. The molecular weight of the RdRp, as deduced from the nucleotide sequence, is 94, 426. The nucleotide sequence of the ORF of the DRT showed 89.7% homology to the Jasper strain, but 80.8% to the Sp strain. The amino acid sequence of the ORF of the DRT sho.wed 97.6% homology to the Jasper strain, but 88.7% to the Sp strain. The conserved GTP-binding motif was detected in VPl protein.

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Cloning and sequencing of p33 in a Korean isolate of Theileria sergenti (러시아범안열원충(Theileria sergenti) 국내 분리주의 33 kDa piroplasm protein 유전자 크로닝 및 염기서열)

  • Gang, Seung-Won;Choe, Eun-Jin;Gwon, Chang-Hui
    • Parasites, Hosts and Diseases
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    • v.35 no.2
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    • pp.105-110
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    • 1997
  • The gene encoding the 33 kDa piroplasm surface protein of Theileria sergenti isolated in Korea was cloned and the nucleotide sequence was determined by dideoxy chaill termination method. The cloned gene corresponds to 869 bps encoding an open reading frame of 283 amino acids. Comparison of the sequence between Korean and .Tapanese isolates showed 99.4% homology rate in the nucleotide sequence and 98.9% homology rate in the amino acid sequence.

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Amino Acid Sequence Homology of Hybrid Poplar O-methyltransferuse Involved in Lignin Biosynthesis

  • Park, Young-Goo;Sul, Ill-Whan;Shin, Dong-Ill;Park, Jang-Won;Park, Hee-Sung
    • 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.

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Identification and Comparison of the Nucleotide Sequence of 16S-23S rRNA Gene Intergenic Small SR(Spacer Region) of Lactobacillus rhamnosus ATCC 53103 with Those of L. casei, L. acidophilus and L. helveticus

  • Byun, J.R.;Yoon, Y.H.
    • Asian-Australasian Journal of Animal Sciences
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    • v.16 no.12
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    • pp.1816-1821
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    • 2003
  • Reliable PCR based identification of lactobacilli has been described utilizing the sequence of 16S-23S rRNA intergenic spacer region. Those sequence comparisons showed a high degree of difference in homology among the strains of L. rhamnosus, L. casei, L. acidophilus and L. helveticus whose 16S-23S rRNA intergenic small SR's sizes were 222 bp, 222 bp, 206 bp and 216 bp respectively. The sequence of 16S-23S rRNA intergenic spacer region of L. rhamnosus ATCC 53103 revealed the close relatedness to those of L. casei strains by the homology ranges from 95.4% to 97.2%. 16S-23S rRNA intergenic spacer region nucleotide sequence of L. acidophilus showed some distant relatedness with L. rhamnosus ATCC 53103 with the homology ranges from 40.3% to 41.8% and that with L. helveticus was shown to be 30% of homology, which exists at the most distant phylogenetic relatedness. The identification of species and strain of lactobacilli was possible on the basis of these results. The common sequences among the 17 strains were CTAAGGAA located in the initiating position of the DNA and some discrepancies were found between the same strains based on these results.

Cloning and Sequenece Analysis of the hpa D Gene Responsible for Homoprotocatechuate 2, 3-Dioxgenae from Pseudomonas sp. DJ-12

  • Lee, Sang-Maha;Chae, Jong-Chan;Kim, Young-Soo;Kim, Chi-Kyung
    • Journal of Microbiology
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    • v.39 no.4
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    • pp.334-337
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    • 2001
  • The degradative pathway of homoprotocatechuate (HPC) is the bacterial routhe wherby 3,4-dihydrox-yphenylactic acid is catabolized to pyruvate and succinate by a series of sequential reactions . The HPC is catalzed by homoprotocatechuate 2, 3-dioxygenase(HPC-2,3O) to from 5-carboxymethy1-2-hydroxy-muco semialdehyde. In this study, the hha D gene encoding. HPC, 2, 3O was Cloned from the chromo-somal DNA of Pseudomonas sp. DJ-12 and its nucleotide sequence was analyzed. The open reding frame of hpaD gene was found to be composed of 864 nucleotide pairs and to encode a poypetide with 287 amino acide residues. The deduced amino acid sequence of the HPC-2,3O from Pseudomonas. sp. DJ-12 exhibited 60~64% homology with those of the corresponding enzymes from E. coli. Salmonella enterica, and Klebsiella pneumoniae.

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