• Applied Biological Chemistry
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• v.38 no.2
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• pp.111-117
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• 1995

In Escherichia coli, CRP forms a complex with cAMP and acts as a transcriptional regulator of many genes, including sugar metabolism operons. The E. coli MK2001, which is introduced the altered crp, is functional in the expression of lac, ara and man, in the absence of cAMP. However, the expression of mal gene is fully activated by the addition of cAMP or cGMP. The object of the study is cloning of the sfs (sugar fermentation stimulation) genes, which was involved in regulation of mal gene expression with the altered crp gene, and structural analysis and characterization of the genes at the molecular level. We have cloned 5 different E. coli genes which stimulate the maltose metabolism in a crp, cya::km (MK2001) background. Newly identified genes were designated as sfs. One of the sfs genes (pPC1), located at the 53.2 min map position on the E. coli chromosome, was further analyzed. Expression of the genes, which is involved in maltose metabolism, malQ (amylomaltase), was increased to 5.8-fold in the presence of a plasmid, pAP5, containing the subcloned sfs4 gene. The nucleotide seguence of a common 2,126 bp segment of the pPCM1 was determined and two open reading frames (ORF1 and ORF2) were detected. The ORF1 encodes the sfs4 gene and ORF2 encodes a truncated protein. Potential CRP binding site is located in the upstream of the putative promoter in the regulatory region. Expression of the cloned sfs4 gene was positively regulated by the cAMP-CRP complex.

• Journal of Plant Biotechnology
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• v.48 no.3
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• pp.124-130
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• 2021

Nitrate is an important nutrient and signaling molecule in plants that modulates the expression of many genes and regulates plant growth. In this study, we cover the research status of transcription factors related to the control of gene expression by nitrate signaling in higher plants. Nitrate reductase is a key enzyme in nitrogen assimilation, as it catalyzes the nitrate-to-nitrite reduction process in plants. A variety of factors, including nitrate, light, metabolites, phytohormones, low temperature, and drought, modulate the expression levels of nitrate reductase genes and nitrate reductase activity, which is consistent with the physiological role if. Recently, several transcription factors controlling the expression of nitrate reductase genes have been identified in higher plants. NODULE-INCEPTION-Like Proteins (NLPs) are transcription factors responsible for the nitrate-inducible expression of nitrate reductase genes. Since NLPs also control the nitrate-inducible expression of genes encoding the nitrate transporter, nitrite transporter, and nitrite reductase, the expression levels of nitrate reduction pathway-associated genes are coordinately modulated by NLPs in response to nitrate. Understanding the function of nitrate in plants will be useful to create crops with low nitrogen use.

• Journal of Life Science
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• v.29 no.5
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• pp.514-523
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• 2019

We investigated the gene expression patterns and the mechanisms of action of the apoptotic response by microarray analysis of human keratinocyte HaCaT cells treated with ginsenoside Rb1, a saponin of Panax ginseng C. A. Meyer. Genes related to apoptosis, the G2/M transition of the mitotic cell cycle, cell division, mitotic nuclear division, and intracellular protein transport were 2-fold up-regulated in HaCaT cells treated with the ginsenoside Rb1, whereas genes related to DNA repair, regeneration fission, and extracellular matrix organization were 2-fold down-regulated. Apoptosis signaling may be mediated by FAS and PLA2G4A, and pathway analysis indicated that STAT3 might be an upstream regulator of these genes. The activity of FAS and PLA2G4A was verified by qPCR, which showed that FAS was increased about 2-fold in HaCaT cells treated with $10{\mu}g/ml$ of ginsenoside Rb1 for 24 hr, PLA2G4A was increased about twice after 6 hours, and gene expression was increased more than 2-fold after 24 hr. Knockdown of STAT3 with siRNA decreased FAS expression and increased PLA2G4A expression but only FAS was passed from the upstream regulator STAT3. These results indicate that STAT3, which is an upstream regulator, induces apoptosis via FAS during treatment with ginsenoside Rb1.

• Microbiology and Biotechnology Letters
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• v.50 no.2
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• pp.301-309
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• 2022

Helicobacter pylori (H. pylori) establishes infection in the human gastric mucosa for a long time and causes severe gastric diseases such as peptic ulcer and gastric cancer. When H. pylori is exposed to the antibacterial agents or inhibitors, the expression of pathogenic associated genes could be altered. In this study, we analyzed the transcriptional changes of H. pylori genes induced by zerumbone treatment. RNA expression changes were analyzed using next-generation sequencing (NGS), and then reverse transcription-polymerase chain reaction (RT-PCR) was performed to verify the results. As a result of NGS analysis, a total of 23 out of 1,632 genes were differentially expressed by zerumbone treatment. RT-PCR confirmed that zerumbone treatment regulated the expression level of 14 genes. Among the genes associated with DNA replication, transcription, virulence factors and T4SS components, 10 genes (dnaE, dnaQ, rpoA, rpoD, secA, flgE, flhA, virB5, virB8 and virB9) were significantly down-regulated and 4 genes (flaA, flaB, virB4 and virD4) were up-regulated. The results of our current study imply that zerumbone might be a potential therapeutic agent for H. pylori infection by regulating factors related to various H. pylori pathogenicity.

• Journal of Life Science
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• v.21 no.10
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• pp.1466-1472
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• 2011

We characterized embryo early gene (EEG)-704 promoter of the silkworm Bombyx mori, which is specifically regulated in the development stages. To determine core promoter region, 10 different partial mutant clones were tested by luciferase assay in Sf9 cells. About 1.5 kb promoter shows higher luciferase activity than constitutive promoter (BmA3). Interestingly, EEG-704 shares the same DNA sequences with BmHsp20.8 by the result of BLAST analysis; its expression is also increased under heat shock condition. Development of such promoter inducible, directly or indirectly in the developmental-stage, is very useful in making recombinant proteins in transgenic silkworms.

• Korean Journal of Food Science and Technology
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• v.54 no.4
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• pp.398-402
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• 2022

Black chokeberry (Aronia melanocarpa), a rich source of polyphenols, exerts hypocholesterolemic effects. However, little is known about its effects on the regulation of the hepatic cholesterol metabolism and the underlying mechanisms. In the present study, the effects of polyphenol-rich black chokeberry extract (CBE) on hepatic cholesterol metabolism were investigated by measuring the expression of genes involved in the absorption, de novo synthesis, and efflux of cholesterol in HepG2 cells. There was a significant reduction in the expression levels of genes involved in cholesterol metabolism, the low-density lipoprotein receptor, 3-hydroxy-3-methylglutaryl coenzyme A reductase, and sterol regulatory element-binding protein 2, in CBE-treated HepG2 cells. Meanwhile, CBE increased the expression levels of genes involved in cholesterol and bile acid efflux. The expression levels of mitochondrial fatty acid oxidation genes increased, whereas those of lipogenic genes decreased following CBE treatment. These data suggest that the consumption of black chokeberry may be beneficial for the prevention of hypercholesterolemia.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2007.11a
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• pp.145-148
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• 2007

생명과학분야에서 마이크로어레이 기술은 세포에서의 RNA 발현 프로파일을 관찰할 수 있도록 함으로써 생명현상의 규명 및 약물개발 둥에서 분자수준의 생명현상에 대한 관찰과 분석이 가능 해지고 있다. 마이크로어레이 데이터분석에서는 특정한 처리나 과정에서 현저한 특성을 보이는 유전자를 식별하기 위한 분석뿐만 아니라 유전자 전체인 게놈수준에서의 분석도 이루어진다. 최근 유전자의 발현이 다양한 조절, 신호전달 및 대사경로에 의해서 영향을 받고 있다는 관점에서 게놈수준의 분석에 관심이 증가하고 있다. 약물반응 실험에서는 약물에 대한 게놈수준의 발현 프로파일을 관찰하는 것도 많은 정보를 제공할 수 있다. 약물실험에서는 대조군과 실험군들간에 관심 있는 상대적인 발현특성을 갖는 유전자군을 전체적으로 추출하는 것이 필요한 경우가 있다. 예를 들면 정상군은 두개의 실험군에 대해서 중간청도의 발현정도를 갖는 유전자군을 식별하는 분석을 하는 경우, 생물학적인 데이터의 특성상 절대값을 비교하는 방법으로는 유용한 유전자들을 효과적으로 식별해 낼 수 없다. 이 논문에서는 정상군과 실험군들의 발현정도값의 경향을 판단하기 위해서 각 유전자에 대해서 집단별 대표값을 선정하여 퍼지집합으로 집단의 값의 범위를 결정하고, 이를 이용하여 특정 패턴을 갖는 유전자들을 식별해내는 방법을 제안하고, 실제 데이터를 통해서 실험한 결과를 보인다.

• The Korean Journal of Applied Statistics
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• v.29 no.3
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• pp.437-448
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• 2016

Gene set analysis utilizing biologic information is expected to produce more interpretable results because the occurrence of tumors (or diseases) is believed to be associated with the regulation of related genes. Many methods have been developed to identify statistically significant gene sets across different phenotypes; however, most focus exclusively on either the differential gene expression or the differential correlation structure in the gene set. This research provides a new method that simultaneously considers the differential expression of genes and differential coexpression with multiple genes in the gene set. Application of this NEW method is illustrated with real microarray data example, p53; subsequently, a simulation study compares its type I error rate and power with GSEA, SAMGS, GSCA and GSNCA.

• Development and Reproduction
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• v.3 no.1
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• pp.1-13
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• 1999

It is believed that genetic defects make an important contribution to male infertility. Since spermatogenesis is such a complex process, it seems inevitable that many genes are involved in controlling the entire development of germ cells. Genes for infertility, however, are considered to be only those which are defected in the reproduction ability, but normal in other functions. Microdeletions of the Y chromosome have been observed frequently in infertile males. At least two genes, RBM and DAZ, are known to present in the loci where microdeletions occur frequently. A number of autosomal genes were also considered as candidates of infertility genes, based on phenotypes of knockout mice that were deficient of these genes.

• Microbiology and Biotechnology Letters
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• v.19 no.1
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• pp.37-44
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• 1991

- I aimed to isolate trans-acting factors involved in the basal expression level of eukaryotic genes. One of the yeast histidine biosynthetic gene, HIS5 was taken as a model for this study. HIS5 gene has a substantial basal level in amino acid rich medium and is derepressed if starved for any single amino acid. The derepression is mediated by cis-acting DNA sequences 5'-TGACTC-3' found in 5' non-transcribed region of the gene and trans-acting factors including GCN4 as positive factor and its negative factor GCDI 7, and GCNZ as a negative factor of GCD17. I first investigated the role of these trans-acting factors in HIS5 basal expression level by using HIS5-pH05 fusion in which expression of pH05 gene encoding inorganic phosphate-repressible acid phosphatase (APase) is regulated by HIS5 promoter. Strain with gcn2 or gcn4 mutation showed 3 to 4 fold lower APase activity than wild type. The level of APase activity was similar in gcn2 and gcn4 mutants. Trans-acting factors involved in basal level were identified by isolating 14 mutants showing increased expression of HISSPH05 fusion from gcn4 background. All the mutants carry a single nuclear recessive mutation and fall into four complementation groups, designated as bell (basal expression level), be12, be23 and be14.