• BMB Reports
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• v.28 no.2
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• pp.143-148
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• 1995

In E. coli, chromosomal DNA associated with proteins is condensed into an organized structure known as nucleoid. Using a nitrocellulose filter binding assay to identify proteins forming nucleoid, a 21 kDa protein was purified from E. coli. The molecular weight of the purified protein was 21 kDa on SDS-polyactylamide gel electrophoresis and 24 kDa on gel permeation chromatography. A molecular weight of 21 kDa on SDS-polyacrylamide gel electrophoresis is unique among known proteins which are believed to be involved in the formation of nucleoid in E. coli. The 21 kDa protein nonspecifically binds to both double-stranded and single-stranded DNA. Sedimentation in a sucrose gradient revealed that the protein induced significant condensation of both supercoiled plasmid DNA and linear bacteriophage $\lambda$ DNA On the basis of quantitative Western-blot analysis, approximately 40,000 molecules of the protein were estimated to exist in an E. coli. The biochemical properties and cellular abundance of the 21 kDa protein suggest that this protein participates in the formation of nucleoid in E. coli.

• Journal of Microbiology
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• v.40 no.4
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• pp.319-326
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• 2002

Cellular DNA in prokaryotes is organized in nucleic acid-protein self-assemblies referred to as the nucleoid. The physical forces responsible for its stability inside the poor solvent properties of the cytoplasm and their functional implications are not understood. Studies on the organisation and functioning of the cytosol of cells largely rely on experimental protocols performed in highly dilute solutions using biochemically purified molecules, which is not a reliable substitute for the situation existing in vivo. Our current research interest is focused on the characterization of biological and physical forces determining the compaction and phase separation of DNA in Escherichia coli cytoplasm. We have emphasized the effect of excluded volume in solutions with high macromolecular concentrations (macromolecular crowding) upon self-association patterns of reactions. The prokaryotic cytosol was simulated by addition of inert polymer polyethylene glycol (PEG) (average molecular weight 20000), as an agent which afterwards facilitates the self-association of macromolecules. Fluorescence microscopy was used for direct visualization of nucleoids in intact cells, after staining with DAPI (4',6-diamidino-2-phenylindole dihydrochloride). Addition of the crowding agent PEG 20,000, in increasing concentrations generated progressively enhanced nucleoid compaction, the effect being stronger in the presence of 0.2 M NaCl and 5 mM MgCl$\_$2/. Under these conditions, the nucleoids were compacted to volumes of around 2 ㎛$\^$3/ or comparable sizes with that of living cells.

• The Journal of the Korean Society for Microbiology
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• v.11 no.1
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• pp.1-11
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• 1976

An electron microscopic study has been made of the effects of change of cell structure of Escherichia coli treated with several disinfectants. The alterations observed as follows: 1. Nucleoid, cytoplasm which contain ribosomes and cell wall appeared to be composed of a parallel triple. layered membrane can observed in control Escherichia coli. 2. The nuclear material was no longer demonstrable in its normal sites. The cytoplasm lost its granularity, became homogeneous and disruption of cell wall were observed by the treatment with 70% ethyl alcohol and 3% $H_2O_2$. 3. Aggregation of ribosomes and condensation of nuclear material were also observed by the treatment of 5% lysol solution and 1% dodecyl-diamino-ethyl-glycin-hydrochloride. 4. In autoclaved group, the each layer of cell wall was separated and destroyed in some sites where cytoplasm was extracted.

• Proceedings of the Botanical Society of Korea Conference
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• 1999.07a
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• pp.51-56
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• 1999

Plastids, which are organelles unique to plant cells, bear their own genome that is organized into DNA-protein complexes (nucleoids). Regulation of gene expression in the plastid has been extensively investigated because this organelle plays an important role in photosynthesis. Few attempts, however, have been made to characterize the regulation of plastid gene expression at the chromosomal structure, using plastid nucleoids. In this report, we summarize the recent progress in the characterization of DNA-binding proteins in plastids, with special emphasis on CND41, a DNA binding protein, which we recently identified in the choloroplast nucleoids from photomixotrophically cultured tobacco cells. CND41 is a protein of 502 amino acids which consisted of a transit peptide of 120 amino acids and a mature protein of 382 amino acids. The N-terminal of the 'mature' protein has lysine-rich region which is essential for DNA-binding. CNA41 also showed significant identities to some aspartyl proteases. Protease activity of purified CND41 has been recently confirmed and characterized. On the other hand, characterization of accumulation of CND41 both in wild type and transgenic tobacco with reduced amount of CND41 suggests that CND41 is a negative regulator in chloroplast gene expression. Further investigation indicated that gene expression of CND41 is cell-specifically and developmentally regulated as well as sugar-induced expression. The reduction of CND41 expression in transgenic tobacco also brought the stunted plant growth due to the reduced cell length in stem. GA3 treatment on apical meristem reversed the dwarf phenotype in the transformants. Effects of CND41 expression on GA biosynthesis will be discussed.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1290-1296
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• 2020

Recently, it was reported that entire mammalian mtDNA genomes could be transplanted into the mitochondrial networks of yeast, where they were accurately and stably maintained without rearrangement as intact genomes. Here, it was found that engineered mtDNA genomes could be readily transferred to and steadily maintained in the mitochondria of genetically modified yeast expressing the mouse mitochondrial transcription factor A (Tfam), one of the mitochondrial nucleoid proteins. The transferred mtDNA genomes were stably retained in the Tfam-expressing yeast cells for many generations. These results indicated that the engineered mouse mtDNA genomes introduced in yeast mitochondria could be relocated into the mitochondria of other cells and that the transferred genomes could be maintained within a mitochondrial environment that is highly amenable to mimicry of the biological conditions in mammalian mitochondria.

• Journal of Microbiology and Biotechnology
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• v.30 no.6
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• pp.830-838
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• 2020

The histone-like nucleoid structuring protein (H-NS) is an abundant global regulator of environmentally controlled gene expression. Herein, we demonstrate that H-NS represses the expression of LeuO, the master regulator of the cyclic(Phe-Pro)-dependent signaling pathway, by directly binding to the upstream region of the gene. H-NS binds to a long stretched region (more than 160-bp long), which overlaps with binding sites for ToxR and LeuO. A high quantity of H-NS outcompetes ToxR for binding to the cis-acting element of leuO. However, our footprinting analyses suggests that the binding of H-NS is relatively weaker than LeuO or ToxR at the same molarity. Considering that the DNA nucleotide sequences of the upstream regions of leuO genes are highly conserved among various Vibrio, such patterns as those found in V. vulnificus would be a common feature in the regulation of leuO gene expression in Vibrionaceae. Taken together, these results suggest that, in species belonging to Vibrionaceae, H-NS regulates the expression of leuO as a basal stopper when cFP-ToxR mediated signaling is absent.

• Biomedical Science Letters
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• v.24 no.4
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• pp.292-304
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• 2018

Microbes is becoming increasingly forensic possibility as a consequence of advances in massive parallel sequencing (MPS) and bioinformatics. Human DNA typing is the best identifier, but it is not always possible to extract a full DNA profile namely its degradation and low copy number, and it may have limitations for identical twins. To overcome these unsatisfactory limitations, forensic potential for bacteria found in evidence could be used to differentiate individuals. Prokaryotic cells have a cell wall that better protects the bacterial nucleoid compared to the cell membrane of eukaryotic cells. Humans have an extremely diverse microbiome that may prove useful in determining human identity and may even be possible to link the microbes to the person responsible for them. Microbial composition within the human microbiome varies across individuals. Therefore, MPS of human microbiome could be used to identify biological samples from the different individuals, specifically for twins and other cases where standard DNA typing doses not provide satisfactory results due to degradation of human DNA. Microbial forensics is a new discipline combining forensic science and microbiology, which can not to replace current STR analysis methods used for human identification but to be complementary. Among the fields of microbial forensics, this paper will briefly describe information on the current status of microbiome research such as metagenomic code, salivary microbiome, pubic hair microbiome, microbes as indicators of body fluids, soils microbes as forensic indicator, and review microbial forensics as the feasibility of microbiome-based human identification.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1024-1032
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• 2008

Efficient expression of the Salmonella Typhimurium tdc ABCDEG operon involved in the degradation of L-serine and L-threonine requires TdcA, the transcriptional activator of the tdc operon. We found that the tdcA gene was transiently activated when the bacterial growth condition was changed from aerobic to anaerobic, but this was not observed if Salmonella was grown anaerobically from the beginning of the culture. Expression kinetics of six tdc genes after anaerobic shock demonstrated by a real-time PCR assay showed that the tdc CDEG genes were not induced in the tdcA mutant but tdcB maintained its inducibility by anaerobic shock even in the absence of tdcA, suggesting that an additional unknown transcriptional regulation may be working for the tdcB expression. We also investigated the effects of nucleoid-associated proteins by primer extension analysis and found that H-NS repressed tdcA under anaerobic shock conditions, and fis mutation delayed the peak expression time of the tdc operon. DNA microarray analysis of genes regulated by TdcA revealed that the genes involved in N-acetylmannosamine, maltose, and propanediol utilization were significantly induced in a tdcA mutant. These findings suggest that Tdc enzymes may playa pivotal role in energy metabolism under a sudden change of oxygen tension.

• Journal of the Korean Chemical Society
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• v.13 no.4
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• pp.355-364
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• 1969

Cross-hybridizations between DNA of two pseudomonads and a xanthomonad suggested that the three DNA types had a considerable section in common. The existence of this common part was proved by hybridization of preselected DNA, i.e. DNA resulting from a previous hybridization between any one set of two DNA types, with the third type. It was thus shown that about 50% of the DNA of the three organisms was similar. This common part was isolated in pure state and its % (G+C) was found to be indentical to the overall base composition of the native DNA. The evolutionary drift in % (G+C) could thus not be detected. The total molecular weight of the chromosornal DNA/bacterial nucleoid was determined to be 2.4 ${\times} 10^9$daltons. It can therefore be estimated that the common putida-fluorescenspelargonii DNA part consists of some 2,000 cistrons. P. putida and P. fluorescens share an additional 1,300 cistrons, and all xanthomonads share at least an additional 1,000 cistrons.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.4
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• pp.625-636
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• 2011

Cold-adapted bacteria survive in extremely cold temperature conditions and exhibit various mechanisms of adaptation to sustain their regular metabolic functions. These adaptations include several physiological and metabolic changes that assist growth in a myriad of ways. Successfully sensing of the drop in temperature in these bacteria is followed by responses which include changes in the outer cell membrane to changes in the central nucleoid of the cell. Their survival is facilitated through many ways such as synthesis of cryoprotectants, cold acclimation proteins, cold shock proteins, RNA degradosomes, Antifreeze proteins and ice nucleators. Agricultural productivity in cereals and legumes under low temperature is influenced by several cold adopted bacteria including Pseudomonas, Acinetobacter, Burkholderia, Exiguobacterium, Pantoea, Rahnella, Rhodococcus and Serratia. They use plant growth promotion mechanisms including production of IAA, HCN, and ACC deaminase, phosphate solublization and biocontrol against plant pathogens such as Alternaria, Fusarium, Sclerotium, Rhizoctonia and Pythium.