• BMB Reports
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• v.34 no.4
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• pp.355-364
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• 2001

Major human Nucleoside diphosphate kinases (NDPKs) exist as hetero-oligomers, consisting of NDPK-A and NDPK-B, rather than homo-oligomer. To investigate their biological function depending on the oligomeric structure in vivo, we characterized the biochemical properties of cellular NDPK. Cellular NDPKs, which are made up of a unique combination of isoforms, were purified from human erythrocyte and placenta. We found that cellular NDPK and recombinant isoforms NDPKs have their own distinct biochemical properties in autophosphorylation, stability toward heat or urea, and DNA binding. Cellular NDPK was found to have unique characteristics rather than the expected additive properties of recombinant isoforms. The mutations in the dimeric interface of NDPK-B (R34G, N69H or K135L) caused defective DNA binding and simultaneously reduced the enzymatic stability These results suggest that the oligomeric interaction could play a major role in the stability of catalytic domain and might be related to the regulation of various cellular functions of NDPK.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.10
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• pp.5037-5042
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• 2012

Background: Tobacco contains agents which generate various potent DNA adducts that can cause gene mutations. Production of DNA adducts may be neutralized by glutathione S transferase (GST) along with other phase I and phase II enzyme systems. The existence of null type of GST among the population increases the susceptibility to various disorders and diseases. The present study focuses on the impact of high tobacco usage and possible null type mutation in GST loci. Methods: Genotypes of GST were detected by multiplex polymerase chain reaction in unrelated 504 volunteers of high tobacco using natives of Gujarat. Allelic frequencies were calculated using Statistical Package for Social Studies-16 software. Hardy Weinberg Equilibrium (HWE) was calculated using Chi square test. Two sided Fisher's significance test was used to compare allelic frequencies of different populations. Results: The frequency of homozygous null genotype of GSTM1 and GSTT1 were 20% (95% CI 16.7-23.9) and 35.5% (95% CI 31.4-39.9) respectively. The GSTM1 and GSTT1 null allele frequency distribution in the Gujarat population was significantly deviating from HWE. GSTT1 null frequency of Gujaratians was significantly higher and different to all reported low tobacco using Indian ethnics, while GSTM1 was not differing significantly. Conclusion: Tobacco usage significantly influences the rate of mutation and frequency of GSTT1 and M1 null types among the habituates. The rate of mutation in GSTT1 loci was an undeviating response to the dose of tobacco usage among the population. This mutational impact of tobacco on GSTT1 postulates the possible gene - environment interaction and selection of null genotype among the subjects to prone them under susceptible status for various cancers and even worst to cure the population with GSTT1 dependent drugs.

• 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.

• Korean Journal of Plant Tissue Culture
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• v.24 no.1
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• pp.1-35
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• 1997

Fertilized egg, by successive cell divisions, differentiates into different tissues and organs with various structures and functions. Different cells and tissues contain different proteins, products of selective gene expression. Not all the genes in any genomes are equally active, temporal and spatial gene expression being the general rule. Present paper attempts to review the tanscriptional mechanisms or the initiations of transcription from several angles. In some of the organisms the genes in the process of transcription or the genes in the inactive state can be seen under the light microscope. Some bands of Drosophila polytene chromosomes may exhibit a swollen or puff appearance under certain conditions. A puff, unfolded or decondensed form of chromomere, represents sets of intense transcriptional activity or RNA synthesis. The heterochromatic X chromosome whose genes remain inactive in the female mammals can be visualized as a dark staining structure called Barr body, Configuration of chromatin differs between transcribed and nontranscribed chromatin. Modification to the chromatin facilitates RNA synthesis. The movement of large polymerase molecule along the DNA would probably be facilitated if some modifications of the chromatin configuration is effected. Methylation of cytosines in CG sequences is associated with inactive genes. Methylation can play a role in determination of mammalian cells during embryogenesis. Demethylation is necessary for the gene to be expressed during development A histone modification that is also known to be correlated with transcriptional capacity of chromatin is acetylation of the lysine residues of the core histones. Chromatin containing a high level of histone acetylation is very sensitive to DNase 1. For the transcription to occur TBP must first bind to the TATA box. Another TF, TF IIB, then binds to the promoter-TBP complex, facilitating the access of RNA polymerase to the transcription initiation site. As recently as eight years ago researchers assumed that histones were irrelevant to the regulation of gene expression. Histones combine with the DNA to form nucleosome of the chromatin. Histones are vital participant in gene regulation. Histone and basal factors compete for access to TATA box. When DNA is exposed to basal factors before histones are introduced, the basal factors assemble on TATA boxes preventing the access of histones, allowing transcription to occur, for transcription to begin, activator protein at the upstream activation sequence or enhancer must interact with the tail of histone H4 at TATA box and cause the histone role particle to dissociate from the TATA box leading to partial breakup of the histone core particle and allowing the basal factors to bind to the TATA box. New concept of genomic flux in contrast to the old concept of static genome has been developed based on the powerful new molecular techniques. Genomic changes such as repetitive DNAs and transposable elements, it is assumed but not yet proved, may affect some of the developmental patterns that characterize particular cells, tissues, organs, and organisms. In the last decade or so remarkable achievement have been made in the researches of the structures and functions of TFs and the specific target sequences located in promoters or enhancers where these TFs bind. TFs have independent domains that bind DNA and that activate transcription. DNA binding domain of TFs serves to bring the protein into the right location. There are many types of DNA binding domains. Common types of motifs can be found that are responsible for binding to DNA. The motifs are usually quite short and comprise only a small part of the protein structure. Steroid receptors have domains for hormone binding, DNA binding, and activating transcription. The zinc finger motif comprises a DNA binding domain. Leucine zipper consist of a stretch of amino acids with a leucine residue in every seventh position Two proteins form a dimer because they interact by means of leucine zippers on similar α-helical domain. This positions their DNA binding basic domains for interaction with the two halves of a DNA sequence with dyad symmetry of TGACTCA, ACTGAGT.

• The Korean Journal of Physiology and Pharmacology
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• v.13 no.6
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• pp.475-482
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• 2009

Rifampicin is a macrocyclic antibiotic which is used extensively for treatment against Mycobacterium tuberculosis and other mycobacterial infections. Recently, a number of studies have focused on the immune-regulatory effects of rifampicin. Therefore, we hypothesized that rifampicin may influence the TLR2 expression in LPS-activated RAW 264.7 cells. In this study, we determined that rifampicin suppresses LPS-induced TLR2 mRNA expression. The down-regulation of TLR2 expression coincided with decreased production of TNF-$\alpha$ Since NF-${\kappa}B$ is a major transcription factor that regulates genes for TLR2 and TNF-$\alpha$, we examined the effect of rifampicin on the LPS-induced NF-${\kappa}B$ activation. Rifampicin inhibited NF-${\kappa}B$ DNA-binding activity in LPS-activated RAW 264.7 cells, while it did not affect IKK$\alpha/\beta$ activity. However, rifampicin slightly inhibited the nuclear translocation of NF-${\kappa}B$ p65. In addition, rifampicin increased physical interaction between pregnane X receptor, a receptor for rifampicin, and NF-${\kappa}B$ p65, suggesting pregnane X receptor interferes with NF-${\kappa}B$ binding to DNA. Taken together, our results demonstrate that rifampicin inhibits LPS-induced TLR2 expression, at least in part, via the suppression of NF-${\kappa}B$ DNA-binding activity in RAW 264.7 cells. Thus, the present results suggest that the rifampicin-mediated inhibition of TLR2 via the suppression of NF-${\kappa}B$ DNA-binding activity may be a novel mechanism of the immune-suppressive effects of rifampicin.

• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.1031-1037
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• 2004

The interaction of chemoattractant receptors and $G{\alpha}_{16}$ was studied to provide the molecular basis to elucidate the interaction of chemoattractant receptors with $G{\alpha}_{16}$ subunit, thereby possibly contributing to finding novel targets for designing new type of G protein antagonists with anti-inflammatory effects. Experiments were performed to characterize the $G{\alpha}_{16}$ subunit domains responsible for efficient coupling to chemoattractant receptors. Thus, a series of chimeric $G{\alpha}_{11}G{\alpha}_{16}$ and $G{\alpha}_{16}G{\alpha}_{11}$ cDNA constructs were expressed, and the ability of chimeric proteins to mediate C5a, IL-8, and fMLP-induced release of inositol phosphate in transfected Cos-7 cells was tested. The results showed that short stretches of residues 154 to residue 167 and from residue 174 to residue 195 of $G{\alpha}_{16}$ contribute to efficient coupling to the C5a receptor. On the other hand, a stretch of amino acid residues 220-240 of $G{\alpha}_{16}$ that is necessary for interacting with C5a receptor did not play any role in the interaction with IL-8 receptor. However, a stretch from residue 155 to residue 195 of $G{\alpha}_{16}$ was found to be crucial for efficient coupling to IL-8 receptor in concert with C-terminal 30 amino acid residues of this ${\alpha}$ subunit. Coupling profiles of a variety of chimeras, composed of $G{\alpha}_{11}G{\alpha}_{16}$ to fMLP receptor indicate that the C-terminal 30 amino acids are most critical for the coupling of $G{\alpha}_{16}$ to fMLP receptor. Taken together, $G{\alpha}_{16}$ subunit recruits multiple and distinctive coupling regions, depending on the type of receptors, to interact.

• The Plant Pathology Journal
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• v.30 no.1
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• pp.58-67
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• 2014

The multifunctional triple gene block protein 1 (TGB1) of the Potexvirus Alternanthera mosaic virus (AltMV) has been reported to have silencing suppressor, cell-to-cell movement, and helicase functions. Yeast two hybrid screening using an Arabidopsis thaliana cDNA library with TGB1 as bait, and co-purification with TGB1 inclusion bodies identified several host proteins which interact with AltMV TGB1. Host protein interactions with TGB1 were confirmed by biomolecular fluorescence complementation, which showed positive TGB1 interaction with mitochondrial ATP synthase delta' chain subunit (ATP synthase delta'), light harvesting chlorophyll-protein complex I subunit A4 (LHCA4), chlorophyll a/b binding protein 1 (LHB1B2), chloroplast-localized IscA-like protein (ATCPISCA), and chloroplast ${\beta}$-ATPase. However, chloroplast ${\beta}$-ATPase interacts only with $TGB1_{L88}$, and not with weak silencing suppressor $TGB1_{L88}$. This selective interaction indicates that chloroplast ${\beta}$-ATPase is not required for AltMV movement and replication; however, TRV silencing of chloroplast ${\beta}$-ATPase in Nicotiana benthamiana induced severe tissue necrosis when plants were infected by AltMV $TGB1_{L88}$ but not AltMV $TGB1_{L88}$, suggesting that ${\beta}$-ATPase selectively responded to $TGB1_{L88}$ to induce defense responses.

• Genes and Genomics
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• v.40 no.12
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• pp.1363-1371
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• 2018

One of the main concerns in biology is extracting sophisticated features from DNA sequence for gene interaction determination, receiving a great deal of researchers' attention. The epigenetic modifications along with their patterns have been intensely recognized as dominant features affecting on gene expression. However, studying sequenced-based features highly correlated to this key element has remained limited. The main objective in this research was to propose a new feature highly correlated to epigenetic modifications capable of classification of genes. In this paper, classification of 34 genes in PPAR signaling pathway associated with muscle fat tissue in human was performed. Using different statistical outlier detection methods, we proposed that 5-mers highly correlated to epigenetic modifications can correctly categorize the genes involved in the same biological pathway or process. Thirty-four genes in PPAR signaling pathway were classified via applying a proposed feature, 5-mers strongly associated to 17 different epigenetic modifications. For this, diverse statistical outlier detection methods were applied to specify the group of thoroughly correlated genes. The results indicated that these 5-mers can appropriately identify correlated genes. In addition, our results corresponded to GeneMania interaction information, leading to support the suggested method. The appealing findings imply that not only epigenetic modifications but also their highly correlated 5-mers can be applied for reconstructing gene regulatory networks as supplementary data as well as other applications like physical interaction, genes prioritization, indicating some sort of data fusion in this analysis.

• Nutrition Research and Practice
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• v.12 no.1
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• pp.61-68
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• 2018

BACKGROUND/OBJECTIVES: This study aimed to test the association between APOA5 3'-UTR variants (rs662799) and cardiometabolic traits in Koreans. SUBJECTS/METHODS: For this study, epidemiological data, Apolipoprotein A5 (APOA5) genotype information, and lymphoblastoid cell line (LCL) biospecimens from a subset of the Ansung-Ansan cohort within the Korean Genome and Epidemiology study (KoGES-ASAS; n = 7,704) as well as epidemiological data along with genomic DNA biospecimens of participants from a subset of the Korea National Health and Nutrition Examination Survey (KNHANES 2011-12; n = 2,235) were obtained. APOA5 mRNA expression was also measured. RESULTS: APOA5 rs662799 genotype distributions in both the KoGES-ASAS and KNHANES groups were 50.6% for TT, 41.3% for TC, and 8.1% for CC, which are similar to those in previous reports. In both groups, minor C allele carriers, particularly subjects with CC homozygosity, had lower high-density lipoprotein (HDL) cholesterol and higher triglyceride levels than TT homozygotes. Linear regression analysis showed that the minor C allele significantly contributed to reduction of circulating HDL cholesterol levels [${\beta}=-2.048$, P < 0.001; ${\beta}=-2.199$, P < 0.001] as well as elevation of circulating triglyceride levels [${\beta}=0.053$, P < 0.001; ${\beta}=0.066$, P < 0.001] in both the KoGES-ASAS and KNHANES groups. In addition, higher expression levels of APOA5 in LCLs of 64 healthy individuals were negatively associated with body mass index (r = -0.277, P = 0.027) and circulating triglyceride level (r = -0.340, P = 0.006) but not significantly correlated with circulating HDL cholesterol level. On the other hand, we observed no significant difference in the mRNA level of APOA5 according to APOA5 rs662799 polymorphisms. CONCLUSIONS: The C allele of APOA5 rs662799 was found to be significantly associated with cardiometabolic traits in a large Korean population from the KoGES-ASAS and KNHANES. The effect of this genotype may be associated with post-transcriptional regulation, which deserves further experimental confirmation.

• Journal of Ginseng Research
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• v.41 no.3
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• pp.330-338
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• 2017

Background: Ginsenoside Rh2 (G-Rh2) is a ginseng saponin that is widely investigated because of its remarkable antitumor activity. However, the molecular mechanism by which (20S) G-Rh2 triggers its functions and how target animals avoid its cytotoxic action remains largely unknown. Methods: Phage display was used to screen the human targets of (20S) G-Rh2. Fluorescence spectroscopy and UV-visible absorption spectroscopy were used to confirm the interaction of candidate target proteins and (20S) G-Rh2. Molecular docking was utilized to calculate the estimated free energy of binding and to structurally visualize their interactions. MTT assay and immunoblotting were used to assess whether human serum albumin (HSA), bovine serum albumin (BSA), and bovine serum can reduce the cytotoxic activity of (20S) G-Rh2 in HepG2 cells. Results: In phage display, (20S) G-Rh2-beads and (20R) G-Rh2-beads were combined with numerous kinds of phages, and a total of 111 different human complementary DNAs (cDNA) were identified, including HSA which had the highest rate. The binding constant and number of binding site in the interaction between (20S)-Rh2 and HSA were $3.5{\times}10^5M^{-1}$ and 1, and those in the interaction between (20S) G-Rh2 and BSA were $1.4{\times}10^5M^{-1}$ and 1. The quenching mechanism is static quenching. HSA, BSA and bovine serum significantly reduced the proapoptotic effect of (20S) G-Rh2. Conclusion: HSA and BSA interact with (20S) G-Rh2. Serum inhibited the activity of (20S) G-Rh2 mainly due to the interaction between (20S) G-Rh2 and serum albumin (SA). This study proposes that HSA may enhance (20S) G-Rh2 water solubility, and thus might be used as nanoparticles in the (20S) G-Rh2 delivery process.