• Journal of Microbiology and Biotechnology
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• 제12권1호
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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.

• 한국잠사곤충학회지
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• 제42권2호
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• pp.126-141
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• 2000

A major step towards understanding of the genetic basis of an organism is the complete sequence determination of all genes in target genome. The nucleotide sequence encoded in the genome contains the information that specifies the amino acid sequence of every protein and functional RNA molecule. In principle, it will be possible to identify every protein resposible for the structure and function of the body of the target organism. The pattern of expression in different cell types will specify where and when each protein is used. The amino acid sequence of the proteins encoded by each gene will be derived from the conceptional translation of the nucleotide sequence. Comparison of these sequences with those of known proteins, whose sequences are sorted in database, will suggest an approximate function for many proteins. This mini review describes the development of new sequencing methods and the optimization of sequencing strategies for whole genome, various cDNA and genomic analysis.

• 미생물학회지
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• 제26권3호
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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.

• Journal of Microbiology
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• 제33권3호
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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.

• 대한수의학회지
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• 제43권3호
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• pp.439-448
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• 2003

The VP2 gene of infectious bursal disease virus (IBDV) Chinju which was previously detected in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered vaccines and diagnostic reagents against IBDV. The nucleotide sequence of the entire Chinju VP2 gene consisted of 1,356 bases long encoding 452 amino acids in a single open reading frame (ORF). It consisted of 368 adenine (27.1%), 363 cytosine (26.8%), 339 guanine (25.0%) and 286 thymine (21.1%) residues. The predicted $M_r$ of the Chinju VP2 protein was 48 kDa, and the protein contained 13 phosphorylation sites by protein kinase C, casein kinase II or tyrosine kinase, whereas 3 asparagine-linked glycosylation sites were recognized. The nucleotide sequence of Chinju VP2 ORF had a very close phylogenetic relationship with 98-99% homology to that of the very virulent IBDVs (vvIBDVs) HK46, OKYM, D6948, UK661, UPM97/61 and BD3/99. Also, the Chinju VP2 protein revealed a very close phylogenetic relationship with 99-100% homology to that of these vvIBDVs. The Chinju VP2 protein had 100% amino acid identity in the variable region of residues 206-360 with that of the D6948, HK46, OKYM and UK661, as well as 100% identity in two hypervariable regions of residues 212-224 and 314-324 with those of the D6948, HK46, OKYM, UK661, UPM97/61 and BD3/99. The amino acid sequence of the chinju VP2 protein contained a serine-rich heptapeptide of SWSASGS as in these vvIBDVs.

• 한국정보과학회논문지:데이타베이스
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• 제32권1호
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• pp.24-42
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• 2005

유전체 서열을 포함하는 생물정보는 지속적으로 변화하며 이질적이고 다양하다는 특성을 갖는다. 이러한 생물 정보의 특성을 반영한 관리시스템이 요구되지만 현재 대부분의 기존 생물정보 데이타베이스는 생물 데이타에 대한 저장소로만 이용된다. 따라서 이 논문에서는 생물학 연구실 수준에서 시퀀싱 실험을 통해 생산되거나 다양한 공개용 데이타베이스로부터 수집된 염기 서열 데이타를 파일 포맷 변환, 편집, 저장 및 검색을 수행하는 서열정보관리 시스템을 제시한다. 이질적인 서열 포맷간의 파일 변환을 위하여 XML기반 BSML을 공통 포맷으로 이용한다. 서열 저장관리에서는 동일한 DNA 조각에 대한 서열 구성의 변경정보를 저장하기 위해 서열 버전을 정의하고 능동 트리거 규칙을 이용하여 변경 정보 검출 및 생성 방법을 보여준다. 트리거 기능을 이용하여 서열의 변경 정보를 자동적으로 데이타베이스에서 저장관리 할 수 있음을 보이고 성능을 평가하였다.

• 미생물학회지
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• 제42권1호
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• pp.67-72
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• 2006

클로닝된 Bacillus circulans ATCC21367 유래 cellulolytic xylanase 유전자(bglBC2)의 염기서열을 결정 분석하였다. 본 유전자는 1,224 bp의 407개 아미노산을 암호하는 open reading frame (ORF)으로 구성되어 있었으며 염기서열로부터 산출된 유전자의 분자량은 45 kDa으로 효소의 SDS-PAGE로부터 측정된 분자량과 일치하였다. ATG 개시 코돈의 9bp 위쪽에 Shine-Dalgarno (SD) 서열로 추정되는 5'-AAAGGAG-3' 서열이 확인되었고 그 상단에 promoter로 추정되는 -35 서열(TTTACA)과 -10 서열(TATACT)이 위치하고 있었으며, 이는 B. subtilis promoter consensus sequence와 유사하였다. 한편, 이 효소의 아미노산 서열은 이미 보고된 B. circulans KSM-N257의 alkaline $endo-\beta-1,4-glucanase$와는 97%, B. circulans WL-12의 $endo-\beta-1,3-1,4-glucanase$와는 75%, Bacillus sp. KSM-330의 $endo-\beta-1,4-glucanase$ (cellulase)와는 45%의 유사성을 나타내었다. 또한 bglBCS 염기서 열의 정보를 GenBank에 등록하였으며 등록번호는 Ar269256이다.

• Archives of Pharmacal Research
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• 제23권2호
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• pp.187-195
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• 2000

Nucleotide sequence extending 2,3-dihydroxybiphenyl 1,2-dioxygenase gene (pcbC) and 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase gene (pcbD) of Pseudomonas sp. DJ-12 was previously analyzed and the two genes were present in the order of pcbD-pcbC preceded by a promoter from Pseudomonas sp. DJ-12. In this study, a 3.8-kb nucleotide sequence located downstream of the pcbC gene was analyzed to have three open reading frames (ORFs) that are designated as orf1, pcbE and orf2 genes. All of the ORFs were preceded by each ribosome-binding sequence of 5-GGAXA-3 (X=G or A). However, no promoter-like sequence and transcription terminator sequence were found in the analyzed region, downstream of pcbC gene. Therefore, the gene cluster appeared to be present in the order of pcbD-pcbC-orf1-pcbE-orf2 as an operon, which is unique organization characterized so far in biphenyl- and PCB-degrading bacteria. The orf1 gene was composed of 1,224 base pairs which can encode a polypeptide of molecular weight 44,950 containing 405 amino acid residues. A deduced amino acid sequence of the orf1 gene product exhibited 21-33％ identity with those of indole dioxygenase and phenol hydroxylase components. The pcbE gene was composed of 783 base pairs encoding 2-hydroxypenta-2,4-dienoate hydratase involved in the 4-chlorobiphenyl catabolism. The orf2 gene was composed of 1,017 base pairs encoding a polypeptide of molecular weight 37,378 containing 338 amino acid residues. A deduced amino acid sequence of the orf2 gene product exhibited 31％ identity with that of a nitrilotriacetate monooxygenase component.

• 미생물학회지
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• 제27권3호
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• pp.194-200
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• 1989

S. aureus에서 분리된 plasmid pSBK203 상의 CAT 유전자 염기서열을 결정하였으며 유발성 발현현상이 확인되었다. 염기서열 결과에 의해 예측된 단백질의 아미노산 서열 분석결고 pC221-CAT 와는 78%의 가장 높은 상동성을 나타냈으며 pC194-CAT와는 55%, 그람음성균 유래의 CAT 중 하나인 Tn9-CATdhkss 38%의 상동성을 각각 보여주고 있었다.

• The Plant Pathology Journal
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• 제16권1호
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• pp.43-47
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• 2000

Citrus tristeza virus (CTV) is the causal agent of one of the most important diseases of citrus. Recently, CTV has been detected in Cheju Island by ELISA. The coat protein (CP) gene of CTV isolated form Cheju Island was cloned by RT-PCR and the nucleotide was analyzed in this study. Citrus leaves were collected from trees showing decline symptoms from various region of Cheju Island in the summer of 1998 and 1999. The CP gene open reading frame is composed of 670 nucleotides and encodes a polypeptide of 223 amono acids. Sequence analysis the CP gene revealed that two CTV strains present in Cheju Island. Viruses collected form Sogwipo area and Cheju City area in 1999 ahowed 91-93% nucleotide sequence homology with CTV T36 strain. Viruses collected form Cheju City area in 1999 and Sogwipo City in 1998 showed 94-98% nucleotide sequence homology with CTV SY568 strain. A efficient viral RNA extraction methods was developed by modifying procedure for animal virus RNA purification methods and PCR product was detected form one tenth of RNA purified from as small as 45 mg fresh or frozen tissue.