• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.149-155
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• 1987

Growth and development of a higher plant, or any living organism for that matter, could be defined as an orderly expression of the genome in time and space in close interaction with the environment. During differentiation and development of a tissue or organ a group of genes must be selectively turned on or turned off mainly by trans-acting regulators. In this general concept of regulation of regulation of gene expression, a DNA molecule is recognized at a specific nucleotide sequence by DNA-binding factors. Molecular biology of the regulatory factors such as hormones, and their receptors, target DNA sequences and DNA-binding proteins are well advanced. What is not clearly understood is the molecular basis of the interactions between DNA and binding factors, expecially of the usages of the dyad symmetry of the target DNA sequences and the dimeric nature of the DNA-binding proteins. A unique 3-dimensional structure of DNA has been proposed that may play an important role in the orderly expression of the gene. A foldback intercoil (FBI) DNA configuration which was originally found by electron microscopy among mtDNA molecules from pearl millet has some unique features. The FBI configuration of DNA is believed to be formed when a flexible double helix folds back and interwines in the widened major grooves resulting in a four stranded, intercoil DNA whose thickness is the same as that of double stranded DNA. More recently, the FBI structure of DNA has been also induced in vitro by a novel enzyme which was purified from pearl millet mitochondria. It has been proposed that the FBI DNA could be utillized in intramolecular recombination which leads to inversion or deletion, and in intermolecular recombination which can lead to either site-specific recombination, genetic recombination via single strand invasion, or cross strand recombination. The structure and function of DNA in 3-dimensional aspect is emphasized for better understanding orderly expression of genes during growth and development.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.188-193
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• 2011

As a specific and effective therapeutic genetic material against hepatitis C virus (HCV) multiplication, HCV internal ribosome entry site (IRES)-targeting hammerhead ribozyme which activity is allosterically regulated by HCV regulatory protein, NS5B RNA replicase, was constructed. The allosteric ribozyme was composed of sequence of RNA aptamer to HCV NS5B, communication module sequence which can transfer structural transition for inducing ribozyme activity upon binding NS5B to the aptamer, and sequence of ribozyme targeting +382 nucleotide of HCV IRES. With real-time PCR analysis, the ribozyme was found to efficiently inhibit HCV replicon replication in cells. Of note, the allosteric ribozyme was shown to inhibit HCV replicon replication more efficiently than either HCV genome-targeting ribozyme or NS5B aptamer only. This allosteric ribozyme can be used as a lead genetic agent for the specific and effective suppression of HCV replication.

• BMB Reports
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• v.32 no.1
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• pp.20-24
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• 1999

The first step of the branch pathway in tryptophan biosynthesis is catalyzed by anthranilate synthase, which is subjected to feedback inhibition by the end product of the pathway. The $trpE^{FBR}$ gene from a mutant Escherichia coli strain coding for anthranilate synthase that was insensitive to feedback inhibition by tryptophan has been cloned. To identify the amino acid changes involved in the feedback regulation of anthranilate synthase, the nucleotide sequence of the mutant $trpE^{FBR}$ gene was determined. Sequence analysis of the $trpE^{FBR}$ gene revealed that four bases were changed in the structural gene while alteration was not found in the 5' control region. Among these base changes, only two base substitutions caused the alterations in amino acid sequences. From the results of restriction fragment exchange mapping, the 61st nucleotide, C to A substitution, that changed $Pro^{21}{\rightarrow}Ser$ was identified as the cause of the desensitization to feedback inhibition by tryptophan. Additional feedback-resistant enzymes of the E. coli anthranilate synthases were constructed by site-directed mutagenesis to examine the effect of the $Ser^{40}\;{\rightarrow}\;Arg^{40}$ change found in the $trpE^{FBR}$ gene of Brevibacterium lactofermentum. From the feedback inhibition analysis, the $Pro^{21}{\rightarrow}Ser$ and $Ser^{40}{\rightarrow}Arg$ mutants maintained about 50% and 90% of their maximal activities, respectively, even at the extreme concentration of 10 mM tryptophan. From these results, we suggest that the $Pro^{21}$ and $Ser^{40}$ residues are involved in the tryptophan binding in the E. coli enzyme.

• The Plant Pathology Journal
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• v.17 no.2
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• pp.83-87
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• 2001

Disease resistance in plants is often controlled by gene-for-gene mechanism in which avirulence (avr) gene products encoding by pathogens are specifically recognized, either directly or indirectly by plant disease resistance (R) gene products. Recent studies arising from molecular cloning of a number of R genes from various plant species that confer resistance to different pathogens and corresponding avr genes from various pathogens resulted in the accumulation of a wealth of knowledge on mode of action of gene-for-gene interaction. Specially, members of the NBS-LRR class of R genes encoding proteins containing a nucleotide binding site (NBS) and carboxyl-terminal leucine-rich repeats (LRRs) confer resistance to very different types of phytopathogens, such as bacteria, fungi, oomycetes, viruses, nematodes and aphids. This article reviewed the molecular events that occur up-stream of defense response pathway, specially, bacterial avr gene protein recognition mediated by NBS-LRR type R gene product in plant based on current research results of well studied model plants.

• Journal of Life Science
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• v.15 no.5 s.72
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• pp.734-738
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• 2005

A gene coding for xylanase from alkali-tolerant Bacillus alcalophilus AX2000 was cloned into Escherichia coli $DH5\alpha$ using pUC19. Among 2,000 transformants, one transformant showed clear zone on the detection agar plate containing oat-spells xylan. Its recombinant plasmid, named pXTY99, was found to carry 7.0 kb insert DNA fragment. When the nucleotide sequence of the cloned xylanase gene (xynT) was determined, xynT gene was found to consist of 1,020 base-pair open reading frame coding for a poly-peptide of 340 amino acids with a deduced molecular weight of 40 kDa. The coding sequence was preceded by a putative ribosome binding site, and the transcription initiation signals. The deduced amino acid sequence of xylanase is similar to those of the xylanases from Bacillus sp. Nl37 and B. stearothermophilus 21 with $61\%$ and $59\%$ identical residues, respectively.

• Proceedings of the Microbiological Society of Korea Conference
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• 1991.04a
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• pp.225-236
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• 1991

The genes encoding the thermostable $\alpha$-amylase and maltogenic amylase from Bacillus lichenciformis were cloned and expressed in E. coli. The recombinant plasmid pTA322 was found to contain a 3.1kb EcoRI genomic DNA fragment of the thermostable $\alpha$-amylase. The cloned $\alpha$-amylase was compared with the B. licheniformis native $\alpha$-amylase. Both $\alpha$-amylase have the same optimal temperature of $70^{\circ}C$ and are stable in the pH range of 6 and 9. The complete nucleotide sequences of the thermostable $\alpha$-amylase gene were determined. It was composed of one open reading rame of 1,536 bp. Start and stop codons are ATG and TAG. From the amino acid sequence deduced from the nucleotide sequence, the cloned thermostable $\alpha$-amylase is composed of 483 amino acid residues and its molecular weight is 55,200 daltons. The content of guanine and cytosine is $47.46mol\%$ and that of third base codon was $53_41mol\%$. The recombinant plasmid, pIJ322 encoding the maltogenic amylase contains a 3.5kb EcoRI-BamHI genomic DNA fragment. The optimal reaction temperature and pH of the maltogenci amylase were $50^{\circ}C$ and 7, respectively. The maltogenic amylase was capable of hydrolysing pullulan, starch and cyclodextrin to produce maltose from starch and panose from pullulan. The maltogenic amylase also showed the transferring activity. The maltogenic amylase gene is composed of one open reading frame of 1,734bp. Start and stop codons are ATG and ATG. At 2bp upstream from start codon, the nucleotide sequence AAAGGGGGAA seems to be the ribosome-binding site(RBS, Shine-Dalgarno sequence). A putative promoter(-35 and-10 regions) was found to be GTTAACA and TGATAAT. From deduced amino acid sequence from the nucleotide srquence, this enzyme was comosed of 578 amino acid residues and its molecular weight was 77,233 daltons. The content of guanine and cytosine was $48.1mol\%$. The new recombinant plasmid, pTMA322 constructed by inserting the thermostable $\alpha$-amylase gene in the EcoRI site of pIJ322 to produce both the thermostable $\alpha$-amylase and the maltogenic amylase were expressed in the E. coli. The two enzymes expressed from E. coli containing pTMA322 was reacted with the $15\%$ starch slurry at $40^{\circ}C$ for 24hours. The distribution of the branched oligosaccharides produced by the single-step process was of the ratio 50 : 50 between small oligosaccharide up DP3 and large oligosaccharide above DP3.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.593-598
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• 2004

The arsenical resistance (ars) operon was cloned from a 67-kilobase pair (kb) plasmid, which was previously shown to be responsible for arsenic salts resistance in K. oxytoca D12. When plasmid pAE48, carrying the ars operon, was transformed into E. coli, transformed cells displayed enhanced survival in the presence of 4 mM arsenite, 50 mM arsenate, or 0.4 mM antimonite. The nucleotide sequence of the 5.6-kb fragment encoding arsenical resistance revealed five open reading frames (ORFs), which were predicted to encode polypeptides of 12.8 (arsR), 13.4 (arsD), 62.6 (arsA), 45 (arsB), and 16.7 (arse) kilodaltons (kDa). Each ORF was preceded by a ribosome binding site. A putative promoter-like sequence was identified upstream of arsR, and a possible termination site was found downstream of arsC. When the deduced amino acid sequences of the K. oxytoca Dl2 Ars proteins were compared with the amino acid sequences of the E. coli R773 Ars proteins, a significant amino acid similarity was observed (87.9％ for ArsR, 89.2％ for ArsD, 83.2％ for ArsA, 92.6％ for ArsB, and 91.3％ for ArsC), suggesting an evolutionary relationship of the ars genes of E. coli plasmid R773 and K. oxytoca Dl2.

• Microbiology and Biotechnology Letters
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• v.21 no.1
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• pp.30-35
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• 1993

Clp is a relatively abundant ATP-dependent protease found in E. coli. Its specific activity was proportional to the concentration of the limiting amount of Clp A and an excess amount of Clp P, and vice versa. Clp A has an intrinsic ATPase activity that is stimulated by casein, and contains a second site for binding A TP, in addition to the ATPase site. The modification of sulfhydryl groups in Clp A with reagents which have bulky groups such as N-phenylmaleimide led to nullifying both ATPase and protease activity. The same sites were modified by sulfhydryl reagents. It seems that the sulfhydryl groups of Clp A are not directly involved in catalysis. Since non-hydrolyzable analogs of ATP do not activate Clp, ATP hydrolysis may be essential for the proteolytic activity of Clp protease. Clp A and Clp P did not associate in the absence of nucleotide. The results suggest that the activity of the proteolytic component, Clp P, is regulated by the A TP-dependent cycling of Clp A between the activator form and the non-activator form.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.188-188
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• 2022

Our previous study identified a resistance locus to Phytophthora sojae (isolate 2457) in an interval of 3.8-4.7 Mbp on chromosome 3 via genetic mapping using a 'Daepung'×'Daewon' recombinant inbred population. Since differential gene expression between Daepung (susceptible) and Daewon (resistant) after inoculation of P. sojae is unknown, RNA sequencing was carried out to compare transcriptomic changes between the two genotypes following inoculation with P. sojae isolate 2457. The two varieties were inoculated using hypocotyl inoculation at the VC stage and stem tissue of 1 cm above and below of the inoculated site were sampled at 0, 6, 12 hours after inoculation (hai), respectively. Differentially expressed genes (DEGs) under same cultivar in different time point and Daepung vs. Daewon in same time point were investigated. In comparison of Daepung vs. Daewon at 12 hai, a total of 3,513 DEGs were identified, including two nucleotide-binding site-leucine rich repeat (NBS-LRR) genes (Glyma.03g034800 and Glyma.03g034900) that are located in the previously reported resistance locus on chromosome 3. In addition, 14,966 DEGs were detected between 0 vs. 6 hai, containing one of candidate genes (Glyma.03g035300). This gene was upregulated by up to 4-fold in Daewon and Daepung. Additional results will be further discussed in the presentation. This study will provide valuable information for soybean crop improvement.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.16
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• pp.6505-6510
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• 2014

Objective: This study was conducted to identify whether polymorphic variants of set domain-containing protein 8 (SET8) and tumor protein p53 (TP53) codon 72, either independently or jointly, might be associated with increased risk for cervical cancer. Methods: We genotyped SET8 and TP53 codon 72 polymorphisms of peripheral blood DNA from 114 cervical cancer patients and 200 controls using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct DNA sequencing. Results: The frequency of SET8 CC (odds ratios (OR) = 2.717, 95% CI=1.436-5.141) or TP53 GG (OR=2.168, 95% CI=1.149-4.089) genotype was associated with an increased risk of cervical cancer on comparison with the SET8 TT or TP53 CC genotypes, respectively. In additional, interaction between the SET8 and TP53 polymorphisms increased the risk of cervical cancer in a synergistic manner, with the OR being 9.913 (95% CI=2.028-48.459) for subjects carrying both SET8 CC and TP53 GG genotypes. Conclusion: These data suggest that there are significant associations between the miR-502-binding site SNP in the 3'-UTR of SET8 and the TP53 codon 72 polymorphism with cervical cancer in Chinese, and there is a gene-gene interaction.