• Korean Journal of Microbiology
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• v.37 no.1
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• pp.37-41
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• 2001

Two linear plasmid-like DNAs, 10.2 kb and 7.2 kb were found in the mitochondria of P. ostreatus. They have covalently linked 5'-terminal proteins in both ends. Two continuous fragments of 4.7 kb and 2.3 kb from 7.2 kb DNA were cloned and sequenced. Two long open reading frames (ORF1; 2982 bp, 993 a.a and ORF2; 2703 bp, 900 a.a) and one short open reading frame(ORF3; 771 bp, 256 a.a) were found in the 7.2 kb plasmid. The putative ORF1 and ORF2 have conserved motifs of DNA polymerases and RNA polymerases, respectively, while the ORF3 has homologous regions with phosphatase from Plasmodium, and also with adhesine from Mycoplasma.

• Korean Journal of Microbiology
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• v.41 no.4
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• pp.255-261
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• 2005

A 6.7kb DNA fragment containing the sprT gene encoding Streptomyces griseus trypsin (SGT) was cloned from Streptomyces griseus ATCC 10137, and the complete nucleotide sequence was determined. Nucleotide sequence and deduced amino acid or the EcoRI-HindIII fragment revealed the presence or the six complete ORFs containing the sprT gene and one incomplete ORF, which were named ORF1, SGT, ORF2, ORF3, ORF4, ORF5, and ORF6, respectively. ORF1 has homology with the oxidoreductases from several organisms. ORF2 and ORF3 show similarity with unknown proteins and transcription regulator that belongs to the ArsR family, respectively. ORF4 and ORF5 show homology with the peptidoglycan bound protein with LPXTG motif from Listeria monocytogenes and the membrane protein with transmembrane helix from several organisms, respectively. The last ORF, ORF6, shows homology with the lipoprotein from Streptomyces avermitilis.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.105-111
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• 2009

Norovirus (NV) with a variety of genotypes, a member of the family Caliciviridae, causes acute nonbacterial gastroenteritis in humans. We determined the nucleotide sequence of three open reading frames (ORFs) of a NV Korean strain and characterized the genetic relationship with others. The Korean strain designated Hu/NLV/Gunpo/2006/KO was isolated from the stool specimen of a 2-year-old female suffering from gastroenteritis. By performing reverse transcription and PCR amplification, three overlapping cDNAs were synthesized and used for direct sequencing. We found that like other NVs, this strain contains three ORFs: ORF1, 5,100 bp; ORF2, 1,647 bp; ORF3, 765 bp. Of 35 NVs, ORF1 had a level of genetic diversity lower than ORF2 and ORF3, of which the C-termini of the ORF2 and ORF3 showed a relatively high degree of genetic diversity. Phylogenetic analyses indicated that the Korean strain belonged to genogroup II, with Saitama U1, Gifu'96, Mc37, and Vietnam 026 being formed a single genetic cluster. The nucleotide sequence information of three ORFs of a NV Korean isolate will be useful not only for the development of a diagnostic tool and understanding of genetic relationship, but also provide important basic information for the functional analysis of their gene products.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.260-266
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• 2002

In this study, chromosomal DNA fragment related to the regulation of phenol metabolism in Ralstonia eutropha JMP 134 was cloned and sequenced. The result has shown that two open reading frames (ORF1 and ORF2) exist on this regulatory region. ORF1, which initiates from 454 bp downstream of the stop codon of the phenol hydroxylase genes, was found to be composed of 501 amino acids. ORF2, whose start codon is overlapped with the stop codon of ORFl, was found to contain 232 amino acids. The comparison of amino acid sequences with other proteins has revealed that ORF1 belongs to the family of NtrC transcriptional activator, whereas ORF2 shares high homology with the family of GntR protein, which is known to be a negative regulator. ORF1 and ORF2 were designated as a putative positive regulator, phlR2 and a negative regulator phlA, respectively. Possible regulatory mechanisms of phenol metabolism in this strain was discussed.

• Microbiology and Biotechnology Letters
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• v.34 no.1
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• pp.15-22
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• 2006

A 4,971 bp chromosomal DNA fragment containing the pqrA, paraquat resistance gene, was cloned from Ochrobactrum anthropi JW-2, and the complete nucleotide sequence was determined. Nucleotide and deduced amino acid sequences of the fragment revealed the presence of 4 complete ORFs (orf2, pqrA, orf3, orf4) and two incomplete ORFs(orf1, orf5). Orf1, pqrA, orf4 and orf5 exists at the direct strand but orf2 and orf3 exists at the reverse complementary strand. Orf1 which of incomplete sequences without start codon shares homology with ATP binding region of the response regulator receiver. Orf2 shares high homology with members of the tetR family of transcriptional repressor which have a helix-turn-helix (H-T-H) motif. Therefore, the orf2 is predicted as a transcriptional repressor of pqrA and is designated as pqrR2. Orf3 shares high homology with the members of the lysR family acting as a transcriptional activator which have both of a H-T-H motif at the N-terminal region and substrate binding domain at the C-terminal region. Therefore, the orf3 is predicted as a transcriptional activator of pqrA and is designated as pqrR1. Orf4 shows homology with the periplasmic substrate-binding protein of amino acid ABC transporter. Orf5 which of incomplete sequences without stop codon revealed the homology with the permeases protein of amino acid ABC transporter.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.749-754
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• 2000

PCR primers were designed based on consensus sequences of dTDP-D-glucose 4,6-dehydratase, one of the enzymes involved in the biosynthesis of deoxysugar. The PCR product (360 bp) was obtained from Thermus caldophilus GK24. Colony hybridization was carried out to the cosmid library constructed from T. caldophilus GK24 genomic DNA by the PCR product DNA fragment. We isolated a cosmid clone (pSMTC-1) that was subcloned to call pKCB series plasmid (BamHI fragments), partially sequenced and analyzed. pKCB80 (4.2 kb-BamHI DNA fragment) of them showed ORFs that was orfA, orfB, orfC and orfD. The orfABCD gene cluster is the deosysugar biosynthetic gene ; orfA (glucose-1-phosphate thymidylytransferase), orfB (dTDP-D-glucose 4,6-dehydratase), orfC (dTDP-4-keto-L-rhamnose reductase) and orfD (dTDP-4-keto-6-deoxy-D-glucose 3,5-epimerase). The gene cluster that was related in biosynthesis of dTDP-L-rhamnose was also identified by computer analysis, and we proposed that the biosynthetic pathway of deoxysugar analyzed from DNA sequencing of pKCB80 is from D-glucose-1-phosphate, dTDP-D-glucose, dTDP-4-keto-6-deoxy-D-glucose via dTDP-4-keto-L-rhamnose to dTDP-L-rhamnose.

• Korean Journal of Plant Resources
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• v.16 no.1
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• pp.82-88
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• 2003

Genomic RNA sequence of a tobamovirus infecting Eutrema wasabi plant(TMV-W) was determined. The RNA is composed 6,298 nucleotide and contains four OREs encoding the protein of 180KD(OREI), 130KD(ORE2),30KD(ORF3) and 18KD(coat protein, ORF4). ORE4, ORF 3, ORF 2 and ORF 1 are overlaped by 130, 20 and 40 nucleotides, and the overapping region can be folded into a stable hairpin styucture. This includes the 3'non-coding region of 238 nucleotides, coat protein gene(537 nucleotides,179 amino acid), 30KD movement protein gene(825 nucleotides, 275 amino acid), 13(IKD protein gene(1,896 nucleotides, 632 amino acid) and 180KD protein gene(2,958 nucleotides, 986 amino acid). The genomic RNA sequence was compared with homologous regions of eleven other tobamoviruses. TMV-WTE was similar to TMV-WSF(98.6%) in nucleotide sequence.

• Journal of Life Science
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• v.22 no.8
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• pp.1009-1017
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• 2012

The orf282 gene of Rhodobacter sphaeroides is located between the ccoNOQP operon encoding $cbb_3$ terminal oxidase and the fnrL gene encoding an anaerobic activator, FnrL. Its function remains unknown. In an attempt to reveal the function of the orf282 gene, we disrupted the gene by deleting a portion of the orf282 gene and constructed an orf282-knockout mutant. Two FnrL binding sites were found to be located upstream of orf282, and it was demonstrated that orf282 is positively regulated by FnrL. The orf282 gene is not involved in the regulation of spectral complex formation. The $cbb_3$ oxidase activity detected in the orf282 mutant was comparable to that in the wild-type sample, indicating that the orf282 gene is not involved in the regulation of the ccoNOQP operon and the biosynthesis of the cbb3 cytochrome c oxidase. The elevated promoter activity of the nifH and nifA genes, which are the structural genes of nitrogenase and its regulator, respectively, in the orf282 mutant, suggests that the orf282 gene product acts as a negative effector for nifH and nifA expression.

• Journal of Plant Biotechnology
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• v.38 no.1
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• pp.87-93
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• 2011

S-Adenosylmethionine decarboxylase (SAMDC; EC 4.1.4.50), a key enzyme for polyamines biosynthesis, was tightly regulated for homeostatic levels. Carnation SAMDC gene (CSDC9) has an small upstream open reading frame (uORF) of 54 amino acids in 5'-leader sequence. To explore the functional mechanism of uORFs in controlling translation, we used a GUS reporter gene driven with the 35S promoter and uORF region of SAMDC gene for making transgenic tobacco plants. In our experiment, there were a translational inhibition of its downstream GUS ORF by SAMDC uORF sequence or SAMDC uORF protein. Expecially, translational inhibition was most effective in point-mutated construct, in which the start codon was changed. Therefore, this results suggested the ribosomal stalling might be involved in this translational inhibitory process. The frame shift in amino acid sequence of SAMDC uORF with start codon and stop codon resulted in a moderate increasing in GUS activity, suggesting the native amino acid sequence was important for a function as a translational inhibitor. Also, we showed that the production of GUS protein was significantly inhibited in the presence of the small uORF using histochemical analysis of GUS expression in seedlings and tobacco flowers. Importantly, the small uORF sequence induced a real peptide of 5.7 kDa, which was provided the presence of SAMDC uORF peptide band using an in vitro transcription/translation system. The peptide product of uORF might interact with other components of translational machinery as well as polyamines, which was resulted from that polyamine treatment was inhibited GUS protein band in SDS-PAGE experiment.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2007.04a
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• pp.43-47
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• 2007

많은 생물학적 데이터베이스와 도구들이 네트워크 상에서 이용 가능하다. 데이터베이스와 도구를 효과적으로 활용하면, 비용을 줄이면서 우수한 품질의 분석결과를 얻을 수 있다. 이 논문에서는 서열분석시 관련된 서열을 자동으로 수집하여, 아미노산 서열로 변환하는 도구에서 대해서 소개한다. 개발된 도구는 필요한 서열을 주어진 질의를 기반으로 하나의 DNA 서열 정보와 관련된 서열을 검색하도록 하고, 분석자가 관심 있는 항목을 쉽게 선택하게 하여, 이것을 아미노산 서열로 번역하고, 찾은 ORF를 기반으로 유사한 것을 추천하고, 번역된 ORF 서열과 어울리는 관련된 모든 정보를 검색하는 분석 과정을 자동화한 것이다.