• Journal of Microbiology and Biotechnology
• /
• 제17권12호
• /
• pp.2056-2060
• /
• 2007

Transcription factor GATA-3 is the critical transcription factor for Th2 cell differentiation. In spite of its importance in Th2 cell differentiation, the molecular mechanism for its action in Th2 differentiation is poorly understood. Previous studies have suggested that GATA-3 may be involved in the chromatin remodeling in the Th2 cytokine locus. To determine whether GATA-3 exerts its effect on its target sites in the extrachromosomal status, cell transfection assay was performed. In this assay, 800 bp IL4 promoter-luciferase constructs linked with GATA-3 target sites were transfected into the M12 B cell line, D10 mouse Th2 cell lines, and human T lymphoma Jurkat cell lines with or without the GATA-3 expression vector. The GATA-3 effects on its target sites were minimal in the extrachromosomal status, supporting the previous propositions that GATA-3 functions at the chromatin level by remodeling chromatin structure.

• Applied Microscopy
• /
• 제18권2호
• /
• pp.167-176
• /
• 1988

Extrachromosomal circular DNA complexes from erythrocytes and splenocytes isolated from Carassius carassius were examined by mica-press-absorption method. The method was described that released small polydisperse circular DNA molecules in situ from the erythrocytes and the splenocytes and that allows selective observation of the small circular DNA complexes bound to cellular components. The released polydisperse circular DNA complexes were absorbed preferentially on mica in a divalent cation-free medium then processed for electron microscopy. Small circular DNAs showed a heterogeneous size distribution of $2{\sim}10{\mu}m$ with a mean contour length of $4.3{\mu}m$ for the circulating erythrocytes and that of $0.7{\sim}3.6{\mu}m$ with a mean contour of length $2.04{\mu}m$ for the splencytes. Cells contained $100{\sim}300$ copies and $300{\sim}700$ copies obtained from the erythrocytes and the splenocytes, repectively. Possible biological functional implications for size distribution of extrachromosomal circular DNAs are discussed.

• 미생물학회지
• /
• 제40권2호
• /
• pp.172-177
• /
• 2004

광합성 박테리아 Rhodospirillum rubrum은 광원의 조건에 따라 균주 내의 신진대사 양상이 변화된다고 보고 되어 왔다. 이러한 광조건에 의한 신진대사 변환 과정을 담당하는 유전자에 대한 연구는 광합성 박테리아에 관한 주된 과제 중 하나이다. 근래 이러한 광조건에 의한 균주내 변화 과정이 균주가 지니는 extrachromosomal plasmid와 관련이 있음이 보고되었다. 본 연구는 광합성 박테리아 R. rubrum의 extrachromosomal plamid pKYl 을 분리 정제하고 이를 제한효소 HindIII로 단편화 하여 이들 단편의 일부에 대한 염기서열을 분석하고 이들의 기능을 추론하였다. 본 연구를 통하여 plasmid pKY1에 박테리아의 유전적 재조합 (genetic recombination)에 관여하는 단백질에 대한 정보가 위치하고 있음을 유전자 및 아미노산 상동성 조사를 통하여 알 수 있었다.

• 한국응용곤충학회지
• /
• 제24권1호
• /
• pp.45-50
• /
• 1985

Bacillus thuringiensis 변종(變種)들로부터 Extrachromosomal DNA를 추출분리(抽出分離)코저 종래(從來)의 방법(方法)을 보완(補完)하여 적용(適用)한바 분자량(分子量)의 크기가 1 Megadalton에서 135 Megadalton에 이르는 plasmid들을 분리(分離)함에 보다 효과적(效果的)이었고 또 이 plasmid들을 이용(利用), 제한효소(制限酵素)에 의(依)한 유전자배열작성(遺傳子配列作成) 및 gene Cloning을 하는데 비교적(比較的) 안정(安定)된 많은 양(量)의 세포용해물(細胞溶解物)을 얻을 수 있었다. 파리목과 나비목에 각기(各其) 독성(毒性)이 다른 Bacillus thuringiensis 6개(個) 변종(變種)으로부터 plasmid들을 분리(分離)한 결과(結果) 분자량(分子量)이 큰 50 Megadalton 이상(以上)의 plasmid들이 공시(供試) 된 모든 변종(變種)으로부터 추출(抽出)되었으며 이들 plasmid의 수(數)를 보면 israelensis로부터 8개(個) kurstaki로부터 10개(個) $aizawa{\ddot{u}}$로부터 13개(個) dendrolimus로부터 2개(個), finitimus로부터 1개(個) 그리고 yunnanensis로부터 6개(個)가 각각(各各) 검출(檢出)되었다. 공시(供試)된 변종중(變種中) 4개(個)의 변종(變種)으로부터는 2 Megadalton 이하(以下)의 적은 plasmid들도 추출(抽出)되었다.

• Genomics & Informatics
• /
• 제14권1호
• /
• pp.29-33
• /
• 2016

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.

• BMB Reports
• /
• 제55권12호
• /
• pp.587-594
• /
• 2022

A persistent DNA tumor virus infection transforms normal cells into cancer cells by either integrating its genome into host chromosomes or retaining it as an extrachromosomal entity called episome. Viruses have evolved mechanisms for attaching episomes to infected host cell chromatin to efficiently segregate the viral genome during mitosis. It has been reported that viral episome can affect the gene expression of the host chromosomes through interactions between viral episomes and epigenetic regulatory host factors. This mini review summarizes our current knowledge of the tethering sites of viral episomes, such as EBV, KSHV, and HBV, on host chromosomes analyzed by three-dimensional genomic tools.

• Biotechnology and Bioprocess Engineering:BBE
• /
• 제10권5호
• /
• pp.432-443
• /
• 2005

Microarray technology has contributed Significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed for Clostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analyses it is demonstrated that Signal quality is significantly improved by increasing the hybridization volume. possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality. In addition to Q-RT-PCR, array validation was tested by examining the transcriptional program of a mutant (M5) strain lacking the pSOL1 178-gene megaplasmid relative to the wildtype (WT) strain. Under optimal conditions, it is demonstrated that the fraction of false positive genes is 1% when considering differentially expressed genes and 7% when considering all genes with signal above background. To enhance genomic-scale understanding of organismal physiology, using data from these microarrays we estimated that $40{\sim}55%$ of the C. acetobutylicum genome is expressed at any time during batch culture, similar to estimates made for Bacillus subtilis.

• Journal of Microbiology
• /
• 제40권3호
• /
• pp.245-247
• /
• 2002

A genomic DNA library of the fungus Trametes versicolor was constructed in a yeast integration vector which contains the URA3 gene of the budding yeast Saccharomyces cerevisiae and the gene responsible for hygromycin B resistance, and fragments acting as autonomously replicating sequences (ARSes) in the budding yeast were identified from the genomic DNA library. Sixteen recombinant plasmids from the library transformed the budding yeast Saccharomyces cerevisiae to Ura+ at high frequencies. They were maintained stably under selective conditions, but were gradually lost from yeast cells at different rates under nonselective conditions, indicating that they contain eukaryotic origins of DNA replication and exist as extrachromosomal plasmids. Base sequences of four ARS DNAs among the 16 cloned fragments revealed that all or the four contain at least one 11 bp ［(A/T)TTTA(T/C)(A/G)TTT(A/T)］consensus sequence of the budding yeast ARS.

• 미생물학회지
• /
• 제55권2호
• /
• pp.167-170
• /
• 2019

Pantoea intestinalis SRCM103226은 식용곤충 밀웜으로부터 분리하였으며, zeaxanthin을 메인으로 생산하였다. P. intestinalis SRCM103226의 유전체 분석을 실시하여 4,784,919 bp 크기의 염기서열, GC 비율은 53.41%로 나타났으며, 플라스미드는 존재하지 않는다. RAST server를 이용하여 annotation한 결과 4,332개의 코딩유전자, 22개의 rRNA, 85개의 tRNA 유전자가 확인되었다 지놈분석결과 zeaxanthin 생합성회로 5개 유전자를 가지고 있다. 이러한 유전체 정보는 zeaxanthin 생합성 경로의 분자 진화의 비교 유전체학 연구에 대한 기초 정보를 제공한다.

• Journal of Microbiology and Biotechnology
• /
• 제10권3호
• /
• pp.405-409
• /
• 2000

We have studied the genome of an obligately commensal thermophile, Symbiobacterium toebii. The chromosome was extracted from pure cultures of S. toebii recently established. Total DNA of S. toebii was resolved by pulsed-field gel electrophoresis (PFGE) into discrete numbers of fragments by digenstion with the endonuclease SspI, SpeI, XbaI, and HpaI. Estimated sizes of fragments produced by the four enzymes and their sum consistently yielded a total genome size of 2.8 Mb. Because restriction endonucleases NotI and SwaI, recognizing 8 bp, released too many fragments, these enzymes could not be used for the estimation of the genome size. Considering no mobility of undigested genome under PFGE, the genome of S. toebii appears to be circular. The presence of extrachromosomal DNA in S. toebii was excluded by the results of the conventional 1% agarose gel electrophoresis and the field inversion gel electrophoresis of undigested S. toebii DNA.