• The Journal of Natural Sciences
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• v.14 no.1
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• pp.25-37
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• 2004

T7 RNA polymerase also recognize intrinsic, hairpin-independent termination signal, a conserved 7-base pair sequence (ATCTGTT in the non-template stand) and U-rich sequence downstream of it. These intrinsic, hairpin-independent termination signal were commonly found in PTH and CJ termination sequences. There are two types of mutant T7 RNA polymerases recognizing sensitively(X3, X19, BG8) of insensitively (R173C) the intrinsic termination signals. We determined the T7 transcription activities of these mutants. Compared to wild-type, mutants X4, 19 and BG8 show highly reduced transcription activities (8%, 33%, 34%). On the other hand mutant R173C shows comparable transcription activity of wild-type (112%). Also transcription termination efficiencies at the PTH or CJ termination signals were determined by using mutant RNA polymerases. Temination of mutnats X4, X19 and BG8 are increased compared to wild-type. On the other hadn mutant R173C proceeds through PTH and CJ termination signals.

• International Journal of Industrial Entomology and Biomaterials
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• v.28 no.2
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• pp.71-84
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• 2014

The full-length heat shock protein 88 (HSP88) complementary DNA (cDNA) of Paecilomyces tenuipes Jocheon-1 was obtained by screening the Paecilomyces tenuipes (P. tenuipes) Jocheon-1 Uni-Zap cDNA library and performing 5' RACE polymerase chain reaction (PCR). The P. tenuipes Jocheon-1 HSP88 cDNA contained an open reading frame (ORF) of 2,139-basepair encoding 713 amino acid residues. The deduced amino acid sequence of the P. tenuipe s Jocheon-1 HSP88 cDNA showed 77% identity to Nectria haematococca HSP88 and 45-76% identity to other fungal homologous HSP88s. Phylogenetic analysis and BLAST program analysis confirmed that the deduced amino acid sequences of the P. tenuipes Jocheon-1 HSP88 gene belonged to the ascomycetes group within the fungal clade. The P. tenuipes Jocheon-1 HSP88 also contained the conserved ATPase domain at the N-terminal region. The cDNA encoding P. tenuipes Jocheon-1 HSP88 was expressed as an 88 kilodalton (kDa) polypeptide in baculovirus-infected insect Sf9 cells. Under higher temperature conditions for the growth of the entomopathogenic fungus, mRNA expression of P. tenuipes Jocheon-1 HSP88 was quantified by real time PCR (qPCR). The results showed that heat shock stress induced a higher level of mRNA expression compared to normal growth conditions.

• FLOWER RESEARCH JOURNAL
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• v.18 no.4
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• pp.278-283
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• 2010

This study was conducted to investigate the involvement of flower abnormality and S-adenosyl-L-homocysteine hydrolase (SAHH), which is one of the key enzyme in the maintenance of methylation. Plants exposed to high temperature (HT) and long day (LD) condition from 14-27days after short day (SD) produced abnormal flower, having numbers of ray florets. Numbers of ray florets were increased more than 2 folds by HT of $35/20^{\circ}C$ and LD of 14 hour comparing those of $25/20^{\circ}C$ (12 h/12 h). Full-length cDNA clone of S-adenosyl-L-homocysteine hydrolase (DgSAHH) in spray chrysanthemum 'Lerbin' contained an 1455 bp open reading frame coding for 485 amino acids. It showed highly conserved coding sequences among the different plant species with over 90% homology. DgSAHH expression was decreased in abnormal flower inducing treatment of HT and LD, while DgSAHH transcripts accumulated in flower bud of non abnormality inducing condition. This result implicate that DgSAHH expression is affected by temperature and photoperiod during flower development and suppression of DgSAHH is a one of the cause of abnormal flower under HT and LD condition.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.103-111
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• 2019

DNA methylation is involved in diverse processes in bacteria, including maintenance of genome integrity and regulation of gene expression. CcrM, the DNA methyltransferase conserved in Alphaproteobacterial species, carries out $N^6$-adenine or $N^4$-cytosine methyltransferase activities using S-adenosyl methionine as a co-substrate. Celeribacter marinus IMCC12053 from the Alphaproteobacterial group was isolated from a marine environment. Single molecule real-time sequencing method (SMRT) was used to detect the methylation patterns of C. marinus IMCC12053. Gibbs motif sampler program was used to observe the conversion of adenosine of 5'-GANTC-3' to $N^6$-methyladenosine and conversion of $N^4$-cytosine of 5'-GpC-3' to $N^4$-methylcytosine. Exocyclic DNA methyltransferase from the genome of strain IMCC12053 was chosen using phylogenetic analysis and $N^4$-cytosine methyltransferase was cloned. IPTG inducer was used to confirm the methylation activity of DNA methylase, and cloned into a pQE30 vector using dam-/dcm- E. coli as the expression host. The genomic DNA and the plasmid carrying methylase-encoding sequences were extracted and cleaved with restriction enzymes that were sensitive to methylation, to confirm the methylation activity. These methylases protected the restriction enzyme site once IPTG-induced methylases methylated the chromosome and plasmid, harboring the DNA methylase. In this study, cloned exocyclic DNA methylases were investigated for potential use as a novel type of GpC methylase for molecular biology and epigenetics.

• Korean Journal of Poultry Science
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• v.46 no.3
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• pp.185-191
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• 2019

Nucleoporin 210 (Nup210) is associated with several physiological processes including muscle and neural cell differentiation, autoimmune diseases, and peripheral T cell homeostasis. Chicken Nup210 (chNup210) gene was originally identified as one of the differentially expressed genes (DEGs) in the kidney tissues of chicken. To elucidate the role of Nup210 in metabolic disease of chicken, we studied the molecular characteristics of chNup210 and analyzed its gene expression under the stimulation of Toll-like receptor 3 (TLR3) ligands. The Nup210 genomic DNA and amino acid sequences of various species including fowls, fishes, and mammals were retrieved from the Ensemble database and subjected to bioinformatics analyses. The expression of Nup210 from several chicken tissues was probed through qRT-PCR, and chicken fibroblast DF-1 cell line was used to determine the change in expression of chNup210 after stimulation with TLR3 ligand, polyinosinic-polycytidylic acid (poly (I:C)). The chNup210 gene was highly expressed in chicken lung and spleen tissues. Although highly conserved among the species, chNup210 was evolutionary clustered in the same clade as that of duck compared to other mammals. Furthermore, this study revealed that chNup210 is expressed in TLR3 signaling pathway and provides fundamental information on Nup210 expression in chicken. Future studies that offer insight into the involvement of chNup210 in the chicken innate immune response against viral infection are recommended.

• Journal of Life Science
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• v.27 no.11
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• pp.1331-1339
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• 2017

DNA barcoding is the identification of a species based on the DNA sequence of a fragment of the cytochrome C oxidase subunit I (COI) gene in the mitochondrial genome. It is widely applied to assist with the sustainable development of fishery-product resources and the protection of fish biodiversity. This study attempted to verify horse-head fish (Branchiostegus japonicus) and fake horse-head fish (Branchiostegus albus) species, which are commonly consumed in Korea. For the validation of the two species, a real-time PCR method was developed based on the species' mitochondrial DNA genome. Inter-species variations in mitochondrial DNA were observed in a bioinformatics analysis of the mitochondrial genomic DNA sequences of the two species. Some highly conserved regions and a few other regions were identified in the mitochondrial COI of the species. In order to test whether variations in the sequences were definitive, primers that targeted the varied regions of COI were designed and applied to amplify the DNA using the real-time PCR system. Threshold-cycle (Ct) range results confirmed that the Ct ranges of the real-time PCR were identical to the expected species of origin. Efficiency, specificity and cross-reactivity assays showed statistically significant differences between the average Ct of B. japonicus DNA ($21.85{\pm}3.599$) and the average Ct of B. albus DNA ($33.49{\pm}1.183$) for confirming B. japonicus. The assays also showed statistically significant differences between the average Ct of B. albus DNA ($22.49{\pm}0.908$) and the average Ct of B. japonicus DNA ($33.93{\pm}0.479$) for confirming B. albus. The methodology was validated by using ten commercial samples. The genomic DNA-based molecular technique that used the real-time PCR was a reliable method for the taxonomic classification of animal tissues.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.226-239
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• 2021

Sebastes minor, Sebastes trivittatus, Sebastes owstoni, and Sebastes steindachneri are indigenous fish species inhabiting the central part of the East Sea, Korea. In order to understand the molecular evolution of these four rockfishes, we sequenced the complete mitochondrial genomes (mitogenomes) of S. minor and S. trivittatus. To further analyze the phylogeny of Sebastes species, the mitogenomes of 16 rockfishes were comparatively investigated. The complete mitochondrial DNA (mtDNA) nucleotide sequences of S. minor and S. trivittatus were 16,408 bp and 16,409 bp in length, respectively. A total of 37 genes were found in mtDNA of S. minor and S. trivittatus, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which exhibited similar characters with other Sebastes species in the East Sea, Korea. In addition, we detected a conserved motif "ATGTA" in the control region of the four Sebastes species, but no tandem repeat units. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that control regions were more variable than the concatenated protein-coding genes. As a result of analysing phylogenetic relationships of four Sebastes species by using concatenated nucleotide sequences of 13 protein-coding genes, S. minor, S. trivittatus, S. owstoni and S. steindachneri were clustered into three clades. The phylogenetic tree exhibited that S. minor and S. steindachneri shared a closer relationship, whereas S. trivittatus and S. vulpes formed another distinct clade. Our results contribute to a better understanding of evolutionary patterns of Sebastes species inhabiting the middle East Sea, Korea.

• Applied Biological Chemistry
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• v.38 no.1
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• pp.55-62
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• 1995

To understand the molecular structure of Korean garlic viruses, cDNA cloning of virus genomic RNA was attempted. Virus particles were isolated from virus-infected garlic leaves and a cDNA library was constructed from garlic virus RNA. One of these clones, S81, selected by random sequencing has been identified as a member of potexvirus group other than potyvirus and carlavirus. The clone is 873 bp long contains most of the coat protein (CP) coding region and 3'-noncoding region including poly(A) tail. A putative polyadenylation signal sequence (AAUAAA) and the hexanucleotide motif (ACUUAA), a replicational cis-acting element conserved in the 3'-noncoding region of potexvirus RNAs are noticed. The clone S81 shows about 30-40% identity in both nucleotide and amino acid sequences with CPs of potexviruses. The genome size of the virus was analysed to be 7.46 knt by Northern blot analysis, which was longer than those of other potexviruses. The open reading frame encoding CP was expressed as a fusion protein (S81CP) in Escherichia coli and the recombinant protein was purified by immobilized metal binding affinity chromatography. Polyclonal antibody was raised against S81CP in rabbit to examine the occurrence of garlic potexvirus in Korean garlic plants by immunoblot analysis. Two virus protein bands of Mr 27,000 and 29,000 from garlic leaf extract of various cultivars reacted with the antibody. It was shown that Mr 27,000 band might not be a degradation product of Mr 29,000 band, suggesting that two types of potexvirus different in size of coat protein could exist in Korean garlic plants.

• Journal of Plant Biotechnology
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• v.41 no.3
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• pp.146-158
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• 2014

Camelina sativa that belongs to Brassicaceae family is an emerging oilseed crop. Camelina seeds contain approximately 40% storage oils per seed dry weight, which are useful for human and animal diets and industrial applications. Microsomal delta-12 fatty acid desaturase2 (FAD2) catalyzes the conversion of oleic acid to linoleic acid. The polymorphisms of FAD2 genes are correlated with the levels of oleic acids in seed oils. Microsomal delta-12 fatty acid desaturase2 (FAD2) catalyzes the conversion of oleic acid to linoleic acid. The polymorphisms of FAD2 genes are correlated with the levels of oleic acids in seed oils. In this study, three CsFAD2 genes (CsFAD2-1, CsFAD2-2 and CsFAD2-3.1) were isolated from developing seeds of Camelina sativa (L.) cv. CAME. The nucleotide and deduced amino acid sequences of three CsFAD2 genes were compared with those from dicotyledon and monocotyledon plants including Camelina cultivars Sunesone and SRS933. Three histidine motifs (HECGH, HRRHH, and HVAHH) required for FAD activity and a hydrophobic valine or isoleucine residue, which is a SNP (single nucleotide polymorphism) marker related with enzyme activity are well conserved in three CsFAD2s. The expressions of CsFAD2-1 and CsFAD2-3.1 were ubiquitously detected in various Camelina organs, whereas the CsFAD2-2 transcripts were predominantly detected in flowers and developing seeds. The contents of oleic acids decreased, whereas the amounts of linoleic acid increased in dry seeds of transgenic fad2-2 lines expressing each CsFAD2 gene compared with fad2-2 mutant, indicating that three CsFAD2 genes are functionally active. The isolated CsFAD2 genes might be applicable in metabolic engineering of storage oils with high oleic acids in oilseed crops.