• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.63-68
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• 2005

Transcription factors regulate gene expression by binding to gene upstream region. Each transcription factor has the specific binding site in promoter region. So the analysis of gene upstream sequence is necessary for understanding regulatory mechanism of genes, under a plausible idea that assumption that DNA sequence motif profiles are closely related to gene expression behaviors of the corresponding genes. Here, we present an effective approach to the analysis of the relation between gene expression profiles and gene upstream sequences on the basis of kernel canonical correlation analysis (kernel CCA). Kernel CCA is a useful method for finding relationships underlying between two different data sets. In the application to a yeast cell cycle data set, it is shown that gene upstream sequence profile is closely related to gene expression patterns in terms of canonical correlation scores. By the further analysis of the contributing values or weights of sequence motifs in the construction of a pair of sequence motif profiles and expression profiles, we show that the proposed method can identify significant DNA sequence motifs involved with some specific gene expression patterns, including some well known motifs and those putative, in the process of the yeast cell cycle.

• Journal of Photoscience
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• 제12권3호
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• pp.129-133
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• 2005

The psbC gene, encoding the intrinsic chlorophyll-binding protein of CP43, one of the PS core complex polypeptides, was cloned from the Panax ginseng chloroplast, which is composed of 1,422 nucleotides and the overall nucleotide sequence shows more than 84% identity to those of eukaryotic photosynthetic organisms. The predicted topology of CP43, based on hydropathy analysis, includes six membrane-spanning ${\alpha}-helices$ resulting in three lumenal and four stromal loops. The putative translation start codon for the psbC gene is located at 48 nucleotides upstream from the stop codon of the psbD gene whose product is also a component of the PSII reaction center, implying that the promoter of the psbC gene is possibly located in the middle of the structural gene of the psbD gene. Northern blot analysis of the in vivo accumulation of the psbC transcript from the plants grown under the various growth light intensities (5%, 10%, 20%, and 100%) of daylight indicated that the steady-state level of the psbC transcript was not significantly affected by light intensity.

• BMB Reports
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• 제46권2호
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• pp.92-96
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• 2013

The breast cancer susceptibility gene BRCA1 encodes a nuclear protein, which functions as a tumor suppressor and is involved in gene transcription and DNA repair processes. Many families with inherited breast and ovarian cancers have mutations in the BRCA1 gene. However, only a few studies have reported on the mechanism underlying the regulation of BRCA1 expression in humans. In this study, we investigated the transcriptional regulation of BRCA1 in HeLa cells treated with etoposide. We found that three Egr-1-binding sequences (EBSs) were located at -1031, -1005, and -385 within the enhancer region of the BRCA1 gene. Forced expression of Egr-1 stimulated the BRCA1 promoter activity. EMSA data showed that Egr-1 bound directly to the EBS within the BRCA1 gene. Knockdown of Egr-1 through the expression of a small hairpin RNA (shRNA) attenuated etoposide-induced BRCA1 promoter activity. We conclude that Egr-1 targets the BRCA1 gene in HeLa cells exposed to etoposide.

• 한국미생물·생명공학회지
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• 제17권4호
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• pp.334-342
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• 1989

Bacillus stearothermophilus의 cytidine deaminase (cytidine/2'-deoxycytidine aminohydrolase：EC 3.5.4.5)를 코딩하는 cdd 유전자를 E. coli cdd$^-$ 결손변이주를 cloning host로 하여 3-10Kbp의 B. stearothermophilus DNA 단편으로부터 shot gun 법으로 클로닝하였다. 고 복제수 플라스미드 pBR322 의 PstI 부위에 3.0Kb의 B. stearothermophilus DNA 단편을 함유한 pJSC101이 cdd$^+$와 tetracy-line 내성으로서 cloning되었으며, 이어서, 결실 및 subcloning을 연속 수행한 결과 약 1.35kbp의 Eco RI$_1$/PstI$_2$단편이 동일 부위의 pBR322에 삽입된 cdd 양성의 pJSC201을 얻었다. Mini 세포 실험결과, 이 단편에서 합성되는 polypeptide는 약 33 KDa이었기에 이 polypeptide가 cytidine deaminase 로 추정되었다. 또한 이 단편에 함유한 550bp의 EcoRI/AvaI 부분을 lacZ 프로모터 영역에 삽입한 경우 프로모터 활성을 나타내었기에 이 단편의 Eco RI 부위에서 PstI부위로 cdd 유전자가 전사됨을 알 수 있었다. B. subilis와 E. coli에서 발현이 가능한 shuttle vector에 cdd가 함유된 단편을 삽입한 후 이를 양세포에서 동시 발현시켰을 때 B. subtilis에서 발현시킨 경우가 E. coli에서 보다높은 cytidine deaminase 활성을 나타내었으며 이 유전자는 B. subtilis 에서도 E. coli에서와 같이 안정하게 유지됨을 알 수 있었다.

• 제어로봇시스템학회논문지
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• 제12권10호
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• Journal of Microbiology
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• 제42권2호
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• pp.143-146
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• 2004

Vancomycin-resistant Enterococcus faecium (VREFM) is becoming a threatening pathogen. We identified a gene called DD1.5K by differential display-PCR, which was preferentially expressed in the bloodstream isolates of VREFM. Due to its amino acid similarity to transfer complex protein, trsE, and tissue-specific expression, this gene may be involved in virulence of VREFM.

• 한국토양비료학회지
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• 제34권5호
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• pp.333-341
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• 2001

퇴비화 촉진 미생물인 Bacillus subtilis LYH201균주가 분비하는 섬유소 분해효소를 분자생물학적으로 연구한 결과는 다음과 같다. 섬유소를 분해하는 유전자는 유전자은행에 의해 구한 약 5,000개의 clone 중 CMC 배지 상에서 활성을 가지는 clone을 선발하여 bglC(pLYH7-39)로 명명하였다. 섬유소를 분해하는 bglC 유전자는 Pvu II, EcoRI, SspI의 제한효소 site를 가지고 있었으며, BglC는 Clostridium acetobutylicum GUN_CLOAB(P15704)와 57%의 identity와 71%의 homology를 나타내어 상동성이 가장 높았으며, CMC-SDS-PAGE 분석으로 56 kDa의 분자량을 나타냈고, 온도는 $50^{\circ}C$, pH는 7에서 활성이 가장 높았다.

• Journal of Microbiology and Biotechnology
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• 제21권5호
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• pp.515-518
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• 2011

A gene encoding bacillopeptidase F, bpr86-1, was cloned from B. amyloliquefaciens CH86-1 isolated from cheonggukjang. This gene could encode a preproenzyme of 1,431 amino acids. When bpr86-1 was introduced into B. subtilis WB600 via pHY300PLK, an E. coli-Bacillus shuttle vector, the transformant showed fibrinolytic activity. During growth on LB, the fibrinolytic activity of cells increased sharply when they entered the stationary phase. The highest activity (761.4 mU/mg protein) was observed at 96 h of cultivation.

• Journal of Microbiology and Biotechnology
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• 제20권2호
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• pp.370-374
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• 2010

A gene encoding the major secreted fibrinolytic protein of Bacillus amyloliquefaciens CH86-1 was cloned from genomic DNAs. DNA sequencing showed that the gene, aprE86-1, could direct the synthesis of a mature protein 275 amino acids in length after processing. When aprE86-1 was introduced into B. subtilis, a mature 27-kDa protein was produced as expected. The fibrinolytic activity of the B. subtilis transformant (TF) was higher than that of B. amyloliquefaciens CH86-1, showing the possibility of increasing the fibrinolytic activity of Bacillus strains through genetic engineering.

• Preventive Nutrition and Food Science
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• 제2권3호
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• pp.236-240
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• 1997

A crude extract of Smphytum officinale L. (comfrey) was for its ability to inhibit he growth of hepatocellular carcinoma cells and expression of the insulin-like growth factor I (IGF-II) gene. The DNA synthesis of hepatocellular carcinoma cell lines, Hep G2, Hep 3B, and PLC/PRF/5 was inhibited by a crude extract of Smphytum officinale in both a time- and a dose-dependent manners. This plant extract also inhibited expression of the IGF-II gene. Since IGF-II exerts a mitogenic effect on Hep G2 cells, these results suggest that the growth inhibition by Symphytum officinale extract is, in part, mediated through the inhibition of IGF-II gene expression.