• Microbiology and Biotechnology Letters
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• v.26 no.1
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• pp.23-33
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• 1998

The entire sequence of a 4,214,810 bp genome of the Bacillus subtilis 168 has been determined by an international project, and the completion has been announced on July 19, 1997. For the sequencing project an international consortium was established and 25 European, 7 Japanese laboratories, 2 biotechnology companies, and our laboratory participated in the project. Within this framework we determined the complete nucleotide sequence of a 53,289 bp fragment upstream of the odhA gene (181 $^{\circ}$) of the B. subtilis 168 chromosome. On the basis of the published DNA sequences of the B. subtilis sspC and odhA genes, we obtained genomic fragments by plasmid rescue and long-range PCR. The sequenced fragment contains 56 putative open reading frames (designated yojA-yolI and 9 known genes (sspC, cge cluster, orfE5, orfRMl and odhA), in which we found many interesting features. In addition, the entire nucleotide sequence of a 53,289 bp region enabled us to revise the current genetic map of this region.

• Journal of agriculture & life science
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• v.52 no.6
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• pp.27-36
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• 2018

Recently, the demand for new cultivar of oriental mustard(Brassica juncea) is increased as the consumption of oriental mustard has increased dramatically in the market due to Kimchi is attracting the world's attention. However, absence of seed supply system can cause many problems including inbreeding depression due to self seed production, deterioration of the seed purity and heterogeneity of commercial seed. To establish the $F_1$ variety breeding system of oriental mustard, pure line and inbred lines were screened from inbreeding genetic resources. Male-sterile line was also selected from breeding combinations for the quality improvement of mustard. The combining ability from(Indojasai ${\times}$ Goheungdamyang) combinations and isolation line of(MS910 ${\times}$ Japan red mustard 8 ${\times}$ Ganghwa mustard 9) was highest, thus these lines were selected as parental lines. PCR(Polymerase Chain Reaction) and gene sequence analysis revealed that the genes related to CMS(orf263, orf220, and orf288) were distributed in mitochondria. The isolated lines from this study also showed good performance in yield test and farmhouse prove test.

• The Plant Pathology Journal
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• v.26 no.2
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• pp.130-138
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• 2010

Orchid fleck virus (OFV) is an unassigned plant virus in the family Rhabdoviridae. OFV was isolated from Cymbidium sp. showing oval necrotic lesions on their leaves in Korea, and designated as OFV-NHHS1. The complete nucleotide sequence of the RNA1 (6,413 nt) (GenBank accession no. AB516442) and RNA2 (6,001 nt) (GenBank accession no. AB516441) was determined in this study. RNA1 and RNA2 contained five and one ORF respectively. RNA1 encodes nucleocapsid (N) of 49 kDa, ORF2 of 26 kDa, ORF3 of 38 kDa, ORF4 of 20 kDa and glycoprotein (G) of 61 kDa proteins, whereas RNA2 encodes a single polymerase of 212 kDa. OFV-NHHS1 shared extremely high similarity of 98.6-100% and 98.9-99.6% in nucleotidle and amino acid sequences with a Japanese isolate, OFV-so, respectively. However, the N, G and L of OFV-NHHS1 revealed 6.9-19.3%, 7.3-12.0%, and 13.4-26.6% identities to those of 29 Rhabdoviruses, respectively. To survey the infection rate of OFV in commercial orchids in Korea, 51 Cymbidium sp., 10 Phalaenopsis sp., 22 Oncidium sp. and 21 Dendrobium sp. plants that showed typical viral symptoms were collected. RT-PCR with specific primers for detection of Cymbidium mosaic virus (CymMV), ORSV and OFV showed high infection rate by ORSV alone and double infection by ORSV and CymMV. One of the orchids tested was infected with OFV. This is the first report of the complete nucleotide sequences of OFV isolated in Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.24 no.1
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• pp.23-27
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• 2012

Porcine circovirus type 2 (PCV2) is a single-stranded circular DNA virus associated with Postweaning multisystemic wasting syndrome (PMWS), which is considered to be an important infectious swine viral disease. PCV2 capsid protein encoded by ORF2 is a structural protein and expected as the high immunogenicity protein. In this study, we generated recombinant baculovirus containing ORF2 of PCV2 and analyzed the optimal conditions for the production of capsid protein in insect cell. Production and status of recombinant capsid protein in insect cell were confirmed by SDS-PAGE and Western blot analysis using His tag antibody and anti-PCV2 serum. The yield of recombinant capsid protein was high like as shown visible on SDS-PAGE. Optimal multiplicity of infection (MOI) and infection time of recombinant virus were determined as 5 MOI and 4 days, respectively. ORF2 is known to have N-linked glycosylation site, but we couldn't detect the glycosylation of recombinant protein in insect cells.

• International Journal of Industrial Entomology and Biomaterials
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• v.30 no.2
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• pp.50-57
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• 2015

Porcine circovirus type 2 (PCV2) is an important infectious swine virus causing postweaning multisystemic wasting syndrome (PMWS). PCV2 capsid protein, encoded by ORF2 has type-specific epitopes, is very immunogenic, and is associated with the induction of neutralizing antibodies. For the efficient production of capsid protein, recombinant Autographa californica nucleopolyhedroviruses were generated to express ORF2 fused with two forms of a partial polyhedrin. Recombinant capsid protein was produced successfully with the partial polyhedrin fusion form and the yield was high, as was shown by SDS-PAGE. Production of recombinant capsid proteins in insect cells was confirmed by Western blot analysis using anti-His monoclonal antibody, anti-ORF2 monoclonal antibody, and anti-PCV2 porcine serum. Fusion expression with amino acids 19 to 110 of the polyhedrin increased the production of recombinant capsid protein, but fusion with amino acids 32 to 85 did not. Additionally, PCV2 capsid protein is a glycoprotein; however, the glycosylation of recombinant protein was not observed. The results of an Enzyme-linked immunosorbent assay (ELISA) showed that recombinant capsid proteins could be utilized as antigens for fast, large-scale diagnosis of PCV2-infected pigs. Our results suggest that the fusion expression of partial polyhedrin is able to increase the production of recombinant PCV2 capsid protein in insect cells.

• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.873-879
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• 2005

Red sea bream iridovirus (RSIV) obtained from infected rock bream was propagated by Bluegill fry-2 (BF-2) cell culture. The virus titer was determined as $10^{5.5}\;TCID_{50}/ml$ on confluent BF-2 cell monolayers. The integrin binding site of ORF 055L of infectious spleen and kidney necrosis virus (ISKNV) was selected for the construction of a primer to obtain the RSIV ORF 055L gene. The genes were amplified using RSIV gene lyzate by PCR. The homologies of the ORF 055L sequence of RSIV with ISKNV and rock bream iridovirus (RBIV) were approximately $96\%$ and $100\%$, respectively. DNA vaccine was constructed by cloning the ORF 055L of RSN into pcDNA 3.1 (+), containing a cytomegalovirus (CMV) promoter. For antibody production, pcDNA-055 DNA vaccine was injected to BALB/c mice. The production of antibodies against pcDNA-055 DNA vaccine was confirmed by the Western blot analysis. The antibodies produced by the pcDNA-055 DNA vaccine showed efficacy to neutralize the RSIV in the neutralization test in BF-2 cell culture.

• Genomics & Informatics
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• v.19 no.4
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• pp.47.1-47.12
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• 2021

Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.

• Research in Plant Disease
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• v.12 no.3
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• pp.213-220
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• 2006

In year 2003, a soybean(Glycine max) sample showing severe dwarfing symptom was collected from a farmers' field in Cheongsong in Korea. The results from the diagnosis of the sample by RT-PCR revealed that it was infected by Soybean dwarf virus(SbDV), SbDV-L81. This study could be the first report of the occurrence of the virus in Korea. To further characterize the virus, the partial nucleotide sequence of the genomic RNA of SbDV-L81 was determined by RT-PCR using species-specific primers. The sequences were analyzed and subsequently compared to previously characterized strains of SbDV based on the pattern of symptom expression and vector specificities. The intergenic region between ORF 2 and 3 and the coding regions of ORF 2, 3 and 4 were relatively similar to those of dwarfing strains(SbDV-DS and DP) rather than those of yellowing strains(SbDV-YS and YP). Likewise, the result from the analysis of 5'-half of the coding region of ORF5 indicated that SbDV-L81 was closely related to strains(SbDV-YP and DP) transmitted by Acyrthosiphon pisum. These data from the natural symptom and the comparisons of five regions of nucleotide sequences of SbDV suggested that SbDV-L81 might be closely related SbDV-DP.

• Archives of Pharmacal Research
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• v.22 no.6
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• pp.542-548
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• 1999

The UL47 gene (b 60390-b 60388) located in the unique long region of the human cytomegalovirus (HCMV) AD169 strain genome was analyzed RNA mapping. Northern blot analysis showed that the UL47 gene was expressed at late times after infection (72 h postinfection). The 9.7-kb transcript was expressed in the infected cells but not in phosphonoformate-treated cells at 72 hpi, indicating that the UL47 gene was only expressed at late times after infection. To map the 5'-end and 3'-end of UL47 transcripts, primer at late times after infection. To map the 5'-end and 3'-end of UL47 transcripts, primer extension and RNase protection analysis were performed. Primer extension analysis revealed that the transcription initiation site of UL47 was located in 27 bp downstream (b 60323) of the TATA box motif. The sizes of UL47 ORF (approximately 2.9-kb) and UL48 ORF (approximately 6.7-kb) deduced from computer sequence analysis suggest that the expressed 9.7-kb transcript of UL47 uses the 3'-end polyadenylation signal of Ul48. The result of RNase protection determined that the 3'-end of UL47 RNA utilized the 3'-end polyadenylation signal of UL48, which is located in HCMV genome b 70082.

• Journal of Microbiology
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• v.38 no.4
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• pp.230-238
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• 2000

Class III chitin synthases in filamentous fungi are important for hyphal growth and differentiation of several filamentous fungi. A genomic clone containing the full gene encoding Chs4, a class III chitin synthase in Penicillium chrysogenum, was cloned by PCR screening and colony hybridization from the genomic library. Nucleotide sequence analysis and transcript mapping of chs4 revealed an open reading frame (ORF) that consisted of 5 exons and 4 introns and encoded a putative protein of 915 amino acids. Nucleotide sequence analysis of the 5'flanking region of the ORF revealed a potential TATA box and several binding sites for transcription activators. The putative transcription initiation site at -716 position was identified by primer extension and the expression of the chs4 during the vegetative growth was confirmed by Northern blot analysis. Amino acid sequence analysis of the Chs4 revealed at least 5 transmembrane helices and several sites for past-transnational modifications. Comparison of the amino acid sequence of Chs4 with those of other fungi showed a close relationship between P chrysogenum and genus Aspergillus.