• Bulletin of the Korean Chemical Society
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• v.33 no.6
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• pp.1839-1844
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• 2012

We have investigated binding between wild-type and mutant Heat Shock Factor (HSF) DNA binding domains (DBDs) with 17-bp HSE containing a central 5'-NGAAN-3' element by equilibrium analytical ultracentrifugation using multi-wavelength technique. Our results indicate that R102 plays critical role in HSE recognition and the interactions are characterized by substantial negative changes of enthalpy (${\Delta}H^0_{\theta}=-9.90{\pm}1.13kcal\;mol^{-1}$) and entropy (${\Delta}S^0_{\theta}=-12.46{\pm}3.77cal\;mol^{-1}K^{-1}$) with free energy change, ${\Delta}G^0_{\theta}$ of $-6.15{\pm}0.03kcal\;mol^{-1}$. N105 plays minor role in the HSE interactions with ${\Delta}H^0_{\theta}$ of $-2.54{\pm}1.65kcal\;mol^{-1}$, ${\Delta}S^0_{\theta}$ of $19.28{\pm}5.50cal\;mol^{-1}K^{-1}$ and ${\Delta}G^0_{\theta}$ of $-8.35{\pm}0.05kcal\;mol^{-1}$, which are similar to those observed for wild-type DBD:HSE interactions (${\Delta}H^0_{\theta}=-3.31{\pm}1.86kcal\;mol^{-1}$, ${\Delta}S^0_{\theta}=17.38{\pm}6.20cal\;mol^{-1}K^{-1}$ and ${\Delta}G^0_{\theta}=-8.55{\pm}0.06kcal\;mol^{-1}$) indicating higher entropy contribution for both wild-type and N105A DBD bindings to the HSE.

• Microbiology and Biotechnology Letters
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• v.31 no.2
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• pp.111-116
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• 2003

The xylA gene of Bacillus stearothermophilus No. 236 encoding $\beta$-xylosidase was cloned and sequenced previously. The transcriptional start site of the xylA gene cloned in E. coli was identified to be the guanine (G) by primer extension analysis. This supports that the expression of xylA gene is also directed in the E. coli cells by the previously determined transcription initiation signals, -10 sequence (CATAAT) and -35 sequence (TTGTTA) separated by 12 bp. To increase the expression of $\beta$-xylosidase, firstly the spacer region of xylA promoter was extended from 12 to 17 bp, and then the -10 and -35 elements were converted into their respective consensus sequences. The mutant promoters thus obtained were tested for their activities in both the E. coli and B. subtilis host cells. The change of the length of the spacer region from 12 to 17 bp resulted in a 1.6- and 2.5-fold increase in promoter strength in comparison with the wild type promoter in E. coli and B. subtilis cells, respectively. Also, strength of the promoter with the fourth T to A transversion on its -35 element increased in the transcription level by about 35 times compared with that of wild-type promoter. However, surprisingly the 5' end C-to-T transition of the -10 hexamer showed a 5- to 15-fold reduction in $\beta$-xylosidase activity in both E. coli and B. subtilis. Together, the present data demonstrated that the 5' end nucleotide C of the -10 sequence CATAAT and the fourth nucleotide A of the -35 hexamer are two most critical nucleotides for the promoter activity in the context of the xylA promoter.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.2 no.1
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• pp.77-79
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• 2002

The urea cycle, consisting of a series of six enzymatic reactions, plays key roles to prevent the accumulation of toxic nitrogenous compound and synthesize arginine de novo. Five well characterized diseases have been described, resulting from an enzymatic defect in the biosynthesis of one of the normally expressed enzyme. This presentation will focus on two representative diseases; ornithine transcarbamylase(OTC) deficiency and citrullinemia(argininosuccinate synthetase deficiency). OTC deficiency is one of the most common inborn error of urea cycle, which is inherited in X-linked manner. We identified 17 different mutations in 20 unrelated Korean patients with OTC deficiency; L9X, R26P, R26X, T44I, R92X, G100R, R141Q, G195R, M205T, H214Y, D249G, R277W, F281S, 853 del C, R320X, V323M and 10 bp del at nt. 796-805. These mutations occur at well conserved nucleotide sequences across species or CpG hot spot. The L9X and R26X lead to the disruption of leader sequences, required for directing mitochondrial localization of the OTC precursor. Their phenotypes are severe, and neonatal onset. The G100R, R277W and V323M mutations were uniquely identified in patients with late onset OTC deficiency. The other genotypes are associated with neonatal onset. Out of 20 patients with OTC deficiency, only 6 patients are alive; two were liver transplanted, and normal in growth and development at 2, 4 years after transplantation respectively. Citrullinemia is an autosomal recessive disease, caused by the mutations in the argininosuccinate synthetase(ASS) gene. We identified in 3 major mutations in 11 unrelated Korean patients with citrullinemia; G324S, $IVS6^{-2}$ A to G, and 67 bp ins at nt 1125-1126. Among these, the 67 base pair insertion mutation is novel. The allele frequency of each mutation is; G324S(45%), IVS6-2 A to G(32%), and 67 base pair insertion(14%). All patients are diagnosed at neonatal or infantile age. Interestingly, two patients presented with stroke like episode. Out of 11 patients, 5 patients died. Among 6 patients alive, one patient was successfully liver transplanted.

• Korean Journal of Oriental Medicine
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• v.14 no.3
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• pp.49-56
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• 2008

Glehnia littoralis Fr. Schmidt et Miquel is an important medicinal plants in East Asian countries. This plant species naturally distributed in Korea, Japan, China, and Taiwan, but it is a rare plants living in the coastal dune in Korea. To investigate the genetic variation, genetic diversity and genetic evolutionary relationships of 14 different geographical G. littoralis, ITS sequence and random amplified polymorphic DNA (RAPD) were analyzed. On the basis of ITS sequences, it was clearly showed that the ITS1 and ITS2 sequences among 14 populations are identical regardless of geographical origin excepting 2 bp in pair-wise comparison of ITS1. Furthermore, RAPD results also showed that 14 different geographical G. littoralis produce various polymorphic patterns without critical relationship among neighboring regions. These combined results suggest that the geographical variation and genetic evolution of G. littoralis is stable and provide important information on genetic diversity, and conservation of this rare plant species in situ and ex situ.

• Environmental Mutagens and Carcinogens
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• v.24 no.4
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• pp.171-179
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• 2004

Cytochrome P4503A4(CYP3A4) is the most abundnat CYPs in human liver, comparising approximately 30% of the total liver CYPs contents ans is involbed in the metabolism of more than 60% of currently used therapeutic drugs. The expression of CYP3A4 is induced by a variety of structurally unrelated xonobiotics including the antibiotic rifampicin and endogenous hormones, and might be mediated through steroid and xenobiotic receptor(SXR) system. The molecular mechanisms underlying regulation of CYP3A4 gene expression hae not been understood. In order to gain the insight of the molecular mechanism of CYP3A4 gene expression, study has been undertaken to investigate if the histone deacelylation is involved in the regulation of CYP3A4 gene expression by proximal promoter or not. Also SXR was investigated to see if they were involved in the regulation of CYP3A4 proximal promoter activity. HepG2 or Hena-I cells were transfected with a plasmid containing~1kb of the CYP3A4 proximal promoter region (-863 to +64bp) cloned in front of a reporter gene, luciferase, in the presence or absence of SXR or hER. Transfected cells were treated with CYP3A4 inducers such as rifampicin, PCN and RU 486, or with estradiol, in order to exmine to regulation of CYP3A4 gene expression in the presence or absence of trichostatin A (TSA). In HepG2 cells, CYP3A4 inducers and estradiol increased significantly the luciferase activity by CYP3A4 proximal promoter, only when TSA was co-treated after SXR cotransfection. In the case of Hepa-I cells CYP3A4 inducers and estradiol incressed modestly the luciferase activity when TSA was co-treated, but this increment was not enhanced by SXR cotransfection in contrast to HepG2 cells. Taken together, these results indicated that the inhibition of histone deacetylation was required to SXR-mediated increase in CYP3A4 proximal promoter region when rifampicin, or PCN was treated. Futher a trans-activation by SXR may demand other species-specific transcription factors.

• International Journal of Oncology
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• v.56 no.6
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• pp.1509-1520
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• 2020

The phosphoinositide 3-kinase (PI3K) signaling pathway plays an important role in human cancer as it regulates critical cellular functions, such as survival, proliferation and metabolism. In the present study, a novel PI3Kα inhibitor (HS-146) was synthesized and its anticancer effects on MCF-7, MDA-MB-231, SKBR3 and BT-474 human breast cancer cell lines were confirmed. HS-146 was found to be most effective in inhibiting the proliferation of MCF-7 cells and in inducing cell cycle arrest in the G0/G1 phase by downregulating cyclin D1, cyclin E, cyclin-dependent kinase (Cdk)2 and Cdk4, and upregulating p21Waf1/Cip1 protein levels in this cell line. The induction of apoptosis by HS-146 was confirmed by DAPI staining and western blot analysis. Cell shrinkage and nuclear condensation, which are typical morphological markers of apoptosis, were increased by HS-146 in the MCF-7 cells in a concentration-dependent manner, and HS-146 also increased the protein expression levels of cleaved poly(ADP-ribose) polymerase (PARP) and decreased the protein expression levels of Mcl-1 and caspase-7. In addition, HS-146 effectively decreased the phosphorylation levels of downstream PI3K effectors, such as Akt, mammalian target of rapamycin (mTOR), glycogen synthase kinase 3β (GSK3β), p70S6K1 and eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1). Hypoxia-inducible factor (HIF)-1α and vascular endothelial growth factor (VEGF) expression were also suppressed by HS-146 under hypoxic conditions, and HS-146 inhibited the migration and invasion of MCF-7 cells in a concentration-dependent manner. On the whole, the findings of the present study suggest that HS-146, a novel PI3Kα inhibitor, may be an effective novel therapeutic candidate that suppresses breast cancer proliferation and metastasis by inhibiting the PI3K/Akt/mTOR pathway.

• BMB Reports
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• v.44 no.3
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• pp.147-157
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• 2011

The meiotic process from the primordial stage to zygote in female germ cells is mainly adjusted by post-transcriptional regulation of pre-existing maternal mRNA and post-translational modification of proteins. Several key proteins such as the cell cycle regulator, Cdk1/cyclin B, are post-translationally modified for precise control of meiotic progression. The second messenger (cAMP), kinases (PKA, Akt, MAPK, Aurora A, CaMK II, etc), phosphatases (Cdc25, Cdc14), and other proteins (G-protein coupled receptor, phosphodiesterase) are directly or indirectly involved in this process. Many proteins, such as CPEB, maskin, eIF4E, eIF4G, 4E-BP, and 4E-T, post-transcriptionally regulate mRNA via binding to the cap structure at the 5' end of mRNA or its 3' untranslated region (UTR) to generate a closed-loop structure. The 3' UTR of the transcript is also implicated in post-transcriptional regulation through an association with proteins such as CPEB, CPSF, GLD-2, PARN, and Dazl to modulate poly(A) tail length. RNA interfering is a new regulatory mechanism of the amount of mRNA in the mouse oocyte. This review summarizes information about post-transcriptional and post-translational regulation during mouse oocyte meiotic maturation.

• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

• Korean Journal of Microbiology
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• v.32 no.3
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• pp.198-201
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• 1994

The nucleotide sequence of the cohesive end site (cos) of Lactobacillus casei phage J1 genome was determined. Comparison between the nucleotide sequences of the circular cos and the left end of the linear J1 DNA showed that the nicking sites of the terminase were as follows: 5'- GGTCGGCC$\downarrow$ -3' 3'- $\uparrow$CCAGCCGG -5' The cohesive single-stranded ends of J1 were found to be 3'-protruding and composed of 8 nucleotides. The mol% G + C of the cohesive ends was 87.5. The cos site shows dyad symmetry from -33 to + 25 bp if the 5' terminal nucleotide of the left end of the linear J1 DNA is numbered +1. No homology was found among the cos sites of phages reported so far.

• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1337-1350
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• 2023

Caproic acid is a precursor substance for the synthesis of ethyl caproate, the main flavor substance of nongxiangxing baijiu liquor. In this study, Clostridium butyricum GD1-1, a strain with high caproic acid concentration (3.86 g/l), was isolated from the storage pit mud of nongxiangxing baijiu for sequencing and analysis. The strain's genome was 3,840,048 bp in length with 4,050 open reading frames. In addition, virulence factor annotation analysis showed C. butyricum GD1-1 to be safe at the genetic level. However, the annotation results using the Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server predicted a deficiency in the strain's synthesis of alanine, methionine, and biotin. These results were confirmed by essential nutrient factor validation experiments. Furthermore, the optimized medium conditions for caproic acid concentration by strain GD1-1 were (g/l): glucose 30, NaCl 5, yeast extract 10, peptone 10, beef paste 10, sodium acetate 11, L-cysteine 0.6, biotin 0.004, starch 2, and 2.0% ethanol. The optimized fermentation conditions for caproic acid production by C. butyricum GD1-1 on a single-factor basis were: 5% inoculum volume, 35℃, pH 7, and 90% loading volume. Under optimal conditions, the caproic acid concentration of strain GD1-1 reached 5.42 g/l, which was 1.40 times higher than the initial concentration. C. butyricum GD1-1 could be further used in caproic acid production, NXXB pit mud strengthening and maintenance, and artificial pit mud preparation.