• Journal of Microbiology and Biotechnology
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• v.17 no.12
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• pp.2056-2060
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• 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
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• v.18 no.2
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• pp.167-176
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• 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.

• Korean Journal of Microbiology
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• v.40 no.2
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• pp.172-177
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• 2004

Photosynthetic bacteria, Rhodospirillum rubrum, have been reported to change their metabolic patterns depend-ing on the light condition. The genetic approach for such a metabolic change is one of main subject in pho-tosynthetic bacteria. It has been reported that the extrachromosomal plasmid might be related to this metabolic regulation. In this study, we have determined the partial sequences of R. rubrum plasmid pKYl with HindIII fragments and the predicted pKYl ORFs and physical map. We found the 8 putative proteins related to the genetic recombination of bacterium, which is reported to the alternative gene expression. Our results suggest that the genes located in pKYl are possibly involved in the metabolic switch according to the photocondition.

• Korean journal of applied entomology
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• v.24 no.1 s.62
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• pp.45-50
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• 1985

The use of a modified procedure for the isolation of extrachromosomal DNA of low to high molecular weight, followed by agarose gel electrophoresis of the crude lysates, provided a simple screening procedure for detecting plasmids ranging in molecular weights from approximately 1 to more than 135 megadaltons from serovars of Bacillus thuringiensis. The procedure provides for a relatively large-volume stable lysate for isolation of plasmids for restriction endonuclease mapping and cloning procedures. The method was used for screening of plasm ids in 6 differenentially effective serovars of B. thuringiensis toxic to dipteran and lepidopteran insects. Relatively large plasmid DNAs of masses above 50 megadaltons (Mdal) were isolated from all of the serovars examined using this technique. The number of extrachromosomal DNAs detected in serovars of B. thuringiensis was 8 for israelensis, 10 for kurstaki, 13 for aizawai, 2 for dendrolimus, 1 for finitimus, and 6 for yunnanensis. Smaller plasmid DNAs were isolated in four of the six serovars that ranged in mass down to approximately 2 Mdal.

• Genomics & Informatics
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• v.14 no.1
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• pp.29-33
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• 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
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• v.55 no.12
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• pp.587-594
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• 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
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• v.10 no.5
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• pp.432-443
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• 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
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• v.40 no.3
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• pp.245-247
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• 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.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.167-170
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• 2019

Pantoea intestinalis SRCM103226, isolated from edible insect mealworm overproduces zeaxanthin as a main carotenoid. The complete genome of P. intestinalis SRCM103226 was sequenced using the Pacific Biosciences (PacBio) RS II platform. The genome of P. intestinalis SRCM103226 comprises a 4,784,919 bp circular chromosome (53.41% G+C content), and is devoid of any extrachromosomal plasmids. Annotation using the RAST server reveals 4,332 coding sequences and 107 RNAs (22 rRNA genes, 85 tRNA genes). Genome annotation analysis revealed that it has five genes involved in the carotenoid pathway. The genome information provides fundamental knowledge for comparative genomics studies of the zeaxanthin pathway.

• Journal of Microbiology and Biotechnology
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• v.10 no.3
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• pp.405-409
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• 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.