Go to the main menu
Skip to content
Go to bottom
REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
> Journal Vol & Issue
The Korean Journal of Microbiology
Journal Basic Information
Journal DOI :
The Microbiological Society of Korea
Editor in Chief :
Volume & Issues
Volume 43, Issue 4 - Dec 2007
Volume 43, Issue 3 - Sep 2007
Volume 43, Issue 2 - Jun 2007
Volume 43, Issue 1 - Mar 2007
Selecting the target year
Expression of Endogenous Retroviruses and Disease
Lee, Jae-Yeong ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 237~242
One of the chief characteristics of the retrovirus life cycle is the appearance of provirus caused by integration of viral genome into the host cell genome, and its delivery stably to the next generation as a part of host germ line. This stable form is called endogenous retrovirus (ERV) and expressed by exogenous or endogenous factors. HERVs and MuERVs are present in humans and mice correspondingly, and their expressions frequently cause diseases. Several diseases such as cancer, autoimmunity and neurological disorders are related with HERVs. Therefore, various strategies should be established for the development of effective therapies for the suffering patients.
Stability of Human Centromeric Alphoid DNA Repeat during Propagation in Recombination-Deficient Yeast Strains
Kim, Kwang-Sup ; Shin, Young-Sun ; Lee, Sang-Yeop ; Ahn, Eun-Kyung ; Do, Eun-Ju ; Park, In-Ho ; Leem, Sun-Hee ; SunWoo, Yang-Il ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 243~249
The centromere is a highly differentiated structure of the chromosome that fulfills a multitude of essential mitotic and meiotic functions. Alphoid DNA (
-satellite) is the most abundant family of repeated DNA found at the centromere of all human chromosomes, and chromosomes of primates in general. The most important parts in the development of Human Artificial Chromosomes (HACs), are the isolation and maintenance of stability of centromeric region. For isolation of this region, we could use the targeting hook with alphoid DNA repeat and cloned by Transformation-Associated Recombination (TAR) cloning technique in yeast Saccharomyces cerevisiae. The method includes rolling-circle amplification (RCA) of repeats in vitro to 5 kb-length and elongation of the RCA products by homologous recombination in yeast. Four types of
of centromeric DNA repeat arrays (2, 4, 5, 6 mer) are used to examine the stability of repeats in homologous recombination mutant strains (rad51, rad52, and rad54). Following the transformation into wild type, rad51 and rad54 mutant strains, there were frequent changes in inserted size. A rad52 mutant strain showed extremely low transformation frequency, but increased stability of centromeric DNA repeat arrays at least 3 times higher than other strains. Based on these results, the incidence of large mutations could be reduced using a rad52 mutant strain in maintenance of centromeric DNA repeat arrays. This genetic method may use more general application in the maintenance of tandem repeats in construction of HAC.
Characterization of Single Stranded DNA-Dependent ATPase Activities of Deinococcus radiodurans RecA Protein
Kim, Jong-Il ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 250~255
The RecA protein of Deinococcus radiodurans is essential for the extreme radiation resistance of this organism. The central steps involved in recombinational DNA repair require DNA-dependent ATP hydrolysis by recA protein. Key feature of RecA protein-mediated activities is the interactions with ssDNA and dsDNA. The ssDNA is the site where RecA protein filament formation nucleates and where initiation of DNA strand exchange takes place. The effect of sequence heterogeneity of ssDNA was examined in this experiment. The rate of homopolymeric synthetic ssDNA-dependent ATP hydrolysis was constant or nearly so over a broader range of pHs. For poly(dT)-dependent ATP or dATP hydrolysis, rates were generally faster, with a broader optimum between pH 7.0 and 8.0. Activities of RecA protein were affected by the ionic environment. The ATPase activity was shown to have different sensitivity to anionic species. The presence of glutamate seemed to slimulate the hydrolytic activity. Dr RecA protein was shown to require
ion greater than 2 mM for binding to etheno ssDNA and the binding stoichiometry of 3 nucleotide for RecA protein monomer.
Characteristics of Vibrio vulnificus Isolated in Incheon
Oh, Bo-Young ; Kim, Jung-Hee ; Gong, Young-Woo ; JeGal, Seung ; Kim, Hye-Yeung ; Lee, Mi-Yeon ; Hwang, Kyoung-Wha ; Koh, Yeon-Ja ; Lee, Jae-Mann ; Go, Jong-Myoung ; Kim, Yong-Hee ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 256~263
We performed the biochemical characteristics, molecular epidemiologocal analysis, and drug susceptibility test on V. vulnificus isolated from environmental sources in Incheon. For this study, 233 strains were isolated from seawater, sediment, shellfish. V. vulnificus isolates were divided into 15 biochemical groups, which were positive for ONPG and Amygdalin test. Among the 209 strains, 206 (98.6%) strains and 110 (52.6%) strains revealed positive for vvhA and viuB gene, and the viuB gene detection rates of V. vulnificus from seawater, shellfish and sediment were 48%, 48.5% and 61.6%, respectively. From disc diffusion test on 175 isolates, most of strains were sensitive to Imipenem (100.0%), Sulfamethoxazole/trimethoprim (98.9%), Tetracycline, Ciprofloxacin (98.3%), Ampicillin/sulbactam (97.1%), Ohloramphenicol (96.6%), Cefepime (94.9%) and Ceftriaxone (94.8%), multi-drug resistance rates was 31.5% of seawater, 34.4% of sediment and 29.2% of shellfish. PFGE was performed on 233 V. vulnificus isolates with the objective of investigating the extent of genetic diversity of these isolates in our region. We could find that at least 126 different PFGE patterns were generated according by 90% of similarity and 13 clusters by 58% of similarity. The major cluster was type I (44.6%) during the most of the year, and type J was frequent pattern in June and October. There were 9 distinct PFGE types in July, 8 types in August, 7 types in June, 6 types in September, 5 types in October 3 types in May and 1 type in March.
Ultra-Rapid Two-Step Real-Time PCR for the Detection of Human Immunodeficiency Virus (HIV)
Lee, Dong-Woo ; Kim, Eul-Hwan ; Yoo, Mi-Sun ; Kim, Il-Uk ; Yoon, Byoung-Su ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 264~272
For the detection of human immunodeficiency virus (HIV), ultra-rapid real-time PCR methods were developed. The target DNA sequences were used 495 bp HIV-1-specific env gene (gi_1184090) and 294 bp HIV-2-specific env gene (gi_1332355). Ultra-rapid real-time PCR was peformed by
(Samsung, Korea) using microchip-based,
of reaction volume with extremely short running time in only 2 steps (denaturation, annealing/extension) in each cycle of PCR. Total reaction for 30 cycled ultra-rapid PCR detection including melting temperature analysis was completed in 7 min and 30 sec. The HIV-1-specific 117 bp-long or HIV-2-spe-cific 119 bp-long PCR products were successfully amplified from the minimum of template,
copies of each euv gene using 30 cycled two-steps ultra-rapid PCR. This kind of ultra-rapid real-time PCR method would be useful not only for the rapid-detection of HIV, but also rapid-detection of other pathogens.
Biodegradation of Phenanthrene by Transformant Trametes versicolor MrP1
Choi, Yun-Seong ; Choi, Hyoung-Tae ; Song, Hong-Gyu ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 273~278
As a model compound of PAHs (polycyclic aromatic hydrocarbons) phenanthrene has been regarded as a toxic material, mutagen and carcinogen in various animals. Biodegradation conditions of phenanthrene such as pH, temperature, shaking speed, stabilizer and cofactor of degrading enzymes were investigated with Trametes versicolor and its transformant T. versicolor MrP1 in YMG medium, minimal medium and soil microcosm. T. versicolor MrP1 can overexpress mrp gene encoding Mn-repressed peroxidase that is involved in fungal degradation. Biodegradations of phenanthrene by T. versicolor and T. versicolor MrP1 were optimally performed in conditions of weak-acid (pH 6.0),
, shaken culture and medium containing 5 mM veratryl alcohol or tryptophan. In these optimal conditions, biodegradation of phenanthrene by T. versicolor MrP1 is 31% higher than that of wild type strain in a minimal medium for 20 days. Biodegradation of phenanthrene by T. versicolor MrP1 was also higher than that of wild type in soil microcosm. T. versicolor MrP1 can be a excellent candidate for the bioremediation of PAHs contaminated environments.
Growth Promotion of Tomato Seedlings by Applicaion of Bacillus sp. Isolated from Rhizosphere
Lee, Kang-Hyeong ; Song, Hong-Gyu ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 279~284
Two bacterial strains isolated from soil (Bacillus subtilis strains: PS2 and RFO41) were evaluated to determine their promoting effect on the growth of tomato seedling under axonic and pot conditions. The production of phytohormone, such as indole-3-acetic acid, indole-3-butyric acid, gibberellin and zeatin by these two strains was investigated as possible mechanisms for plant growth stimulation. Both PS2 and RFO41 were shown to produce various phytohormones, and. the production of phytohormones was stimulated by the addition of peptone-rich brain heart broth medium. In addition, these bacteria exhibited high levels of phosphatase activity, which ranged from 2.18 to
. PS2 and RFO41 were applied to the pot test for growth of tomato seed with phosphate. Root and shoot lengths of germinated tomato after 15 days were 45.5% and 36.5% longer than that of control in RFO41 treated samples, respectively. Baciller sp. PS2 and RFO41 may have a potential for biofertilizer in the agriculture.
Classification of Viruses Based on the Amino Acid Sequences of Viral Polymerases
Nam, Ji-Hyun ; Lee, Dong-Hun ; Lee, Keon-Myung ; Lee, Chan-Hee ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 285~291
According to the Baltimore Scheme, viruses are classified into 6 main classes based on their replication and coding strategies. Except for some small DNA viruses, most viruses code for their own polymerases: DNA-dependent DNA, RNA-dependent RNA and RNA-dependent DNA polymerases, all of which contain 4 common motifs. We undertook a phylogenetic study to establish the relationship between the Baltimore Scheme and viral polymerases. Amino acid sequence data sets of viral polymerases were taken from NCBI GenBank, and a multiple alignment was performed with CLUSTAL X program. Phylogenetic trees of viral polymerases constructed from the distance matrices were generally consistent with Baltimore Scheme with some minor exceptions. Interestingly, negative RNA viruses (Class V) could be further divided into 2 subgroups with segmented and non-segmented genomes. Thus, Baltimore Scheme for viral taxonomy could be supported by phylogenetic analysis based on the amino acid sequences of viral polymerases.
Immune Enhancing Effects of Intracellular and Extracellular Polysaccharides Extracted from Mycelial Cultivate of Agaricus blazei Murill
Kim, Moo-Sung ; Cho, Hong-Bum ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 292~297
This study was performed to compare in vitro immune enhancing effects of polysaccharides extracted from cultivated mycelia of Agaricus blazei Murill. Carbohydrate contents of semi-purified polysaccharides were 85.6% and 95.3%, while
-glucan conents were 67.9% and 88.1% for intracellular and extracellular polysaccharide, respectively. Samples were adjusted to the same in their carbohydrate contents before efficacy tests. Both intracellular and extracellular polysaccharide increased nitric oxide (NO) synthesis of macrophage RAW 264.7 in dose dependent manner, and the maximum increase rate was 53.9 and 53.1% in intracellular and extraceltular polysaccharide, respectively. The polysaccharides also increased synthesis of cytokines such as interleukin (IL)-
, IL-6 and tumor necrosis factor (TNF)-
in RAW 264.7. For all the 3 cytokines, the increase rate of synthesis was much higher in extracellular polysaccharide compared to intracellular polysaccharide, especially at low concentration. Both polysaccarides increased the proliferation of splenocytes in vitro, intracellular polysaccharide showed increase in dose dependent manner while extraceltular polysaccharide showed increase untill medium concentration (
). They did not show direct cytotoxicity against cancer cells such as B16F0 melanoma. As results, it was regarded that the both intracellular and extracellular polysaccharide from A. blazei showed immune enhancing effects in vitro, but the activity is higher in extracellular polysaccharide compared to intracellular polysaccharide.
Antithrombotic Activities of Cheongkookjang and Cheongkookjang Fermented with Green Tea or Mugwort
Lee, Kyung-Ae ; Jang, Jeong-Oak ; Yoon, Hye-Kyung ; Kim, Moo-Sung ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 298~303
Antithrombotic activities of water extract of cheongkookjang and cheongkookjang fermented with green tea or mugwort were evaluated on some antithrombosis related activities in vitro and thrombotic death inhibition in vivo. Cheongkookjang made of white soybean (Glycine max) or black small soybean (Rhynchosia nulubilis) showed potent antioxidative activities. Addition of green tea or mugwort during cheongkookjang fermentation increased the antioxidative activity, cheongkookjang with green tea showed more drastic increase compared with cheongkookjang with mugwort. Nitrite scavenging effects of the cheongkookjang extracts were prominent but the addition of green tea or mugwort seldom increased the scavenging effects. All the cheongkookjang extracts showed strong inhibitory activities on platelet aggregation. The inhibitory activities of cheongkookjang were increased considerably by addition of green tea or mugwort even with low concentration. Plasmin unit as fibrinolytic activity was not affected considerably by addition of green tea. Addition of mugwort decreased the activity transiently at low concentration (
) but increased again slowly at higher concentration (
). In vitro thrombotic death inhibition test, the antithrombotic activity of cheongkookjang made of black small bean with green tea was higher by about 1.5 times compared to that without green tea. As results, cheongkookjang might inhibit antithrombosis not only by fibrinolytic action but also by inhibition of platelet aggregation and antioxidative action. The addition of functional materials such as green tea or mugwort could increase the antithrombotic function, even at low concentration.
Production of 5-Aminolevulinic Acid (ALA) by Bacillus cereus 1-1
Ahn, Kyung-Joon ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 304~310
Bacillus cereus 1-1 strain produced 2 mM of ALA in the aerobic dark condition without any inhibitor like levulinic acid. The optimum culture conditions for the ALA production were that preculture and main culture were continued for 18 hr in TCY medium, and 16 mM of organic acids like acetic acid were added at the late log phase when the pH was 6.8. And the addition of 0.3% glucose was effective at the beginning of the main culture. ALA production was continued for more than 8 hr by the addition of glutamic acid instead of acetic acid, and was inhibited by addition of
gabaculine seriously. These results confirmed that B. cereus 1-1 strain produced ALA through C-5 pathway.
Isolation and Characterization of A Thiodiglycol-Degrading Cupravidus sp.
Park, Jong-Deok ; Kim, Jee-Cheon ; Yoon, Ki-Hong ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 311~316
A Gram-negative bacterium capable of degrading thiodiglycol (TDG), main hydrolysis product of sulfur mustard, was isolated from ginseng field in enrichment medium supplemented with TDG as carbon source. The isolate, WS-32, grew optimally at
and pH 6.0-8.0. It was found to be similar to the genus Cupriavi연 on the basis of 165 rRNA sequence, while its biochemical properties were highly homologous to Alcaligenes faecalis. The cell growth of WS-32 strain was slightly inhibited on LB broth by TDG, but the maximum level of its growth was maintained stably in the presence of TDG. After incubation of inoculated LB medium or uninoculated LB medium containing TDG for 2 days, TDG amount of the culture filtrate was analyzed to decrease noticeably by HPLC. TDG and alcohols were also oxidized by cell-free extract of the isolate with maximum activities at pH 8.0 and
A Base-Calling Error Detection Program for Use in Microbial Genome Projects
Lee, Dae-Sang ; Park, Kie-Jung ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 317~320
In this paper, we have developed base-calling error detection program and algorithm which show the list of the genes or sequences that are suspected to contain base-calling errors. Those programs detect dubious bases in a few aspects in the process of microbial genome project. The first module detects base-calling error from the Phrap file by using contig assembly information. The second module analyzes frame shift mutation if it is originated from real mutation or artifact. Finally, in the case that there is control microbial genome annotation information, the third module extracts and shows the candidate base-calling error list by comparative genome analysis method.
Serological Analysis of the Antigenicity during Cultivation of Streptomyces Strains
Kim, Jae-Heon ; Jo, Sung-Kee ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 321~324
The changes in antigenicity during cultivation of streptomycetes were determined by immunodiffusion assay and indirect ELISA. New precipitin lines in immunodiffusion assay began to appear in the growth period of the soluble pigment production and became thickened thereafter. The increase in the antigenicity was also confirmed by ELISA. The antigenic development was relatively weak for S. lavendulae and S. viridochromogenes while that was strong for S. lavendulae and S. viridochromogenes. The results indicated that Streptomyces strains, even though not proved for some strains, changed the compositions of cell envelope during submerged growth and this could be estimated quantitatively by serological method.
Identification and Functional Analysis of Escherichia coli RNase E Mutants
Shin, Eun-Kyoung ; Go, Ha-Young ; Kim, Young-Min ; Ju, Se-Jin ; Lee, Kang-Seok ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 325~330
RNase E is an essential Escherichia coli endoribonuclease that plays a major role in the decay and processing of a large fraction of RNAs in the cell and expression of N-terminal domain consisted of 1-498 amino acids (N-Rne) is sufficient to support normal cellular growth. By utilizing these properties of RNase E, we developed a genetic system to screen for amino acid substitutions in the catalytic domain of the protein (N-Rne) that lead to various phenotypes. Using this system, we identified three kinds of mutants. A mutant N-Rne containing amino acid substitution in the S1 domain (I6T) of the protein was not able to support survival of E. coli cells, and another mutant N-Rne with amino acid substitution at the position 488 (R488C) in the small domain enabled N-Rne to have an elevated ribonucleolytic activity, while amino acid substitution in the DNase I domain (N305D) only enabled N-Rne to support survival of E. roli cells when the mutant N-Rne was over-expressed. Analysis of copy number of ColEl-type plasmid revealed that effects of amino acid substitution on the ability of N-Rne to support cellular growth stemmed from their differential effects on the ribonucleolytic activity of N-Rne in the cell. These results imply that the genetic system developed in this study can be used to isolate mutant RNase E with various phenotypes, which would help to unveil a functional role of each subdomain of the protein in the regulation of RNA stability in E. coli.
Isolation and Characterization of an Alkaline Protease Produced by Bacillus subtilis JK-1
Kim, Ji-Yeon ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 331~336
A bacterium producing the alkaline pretense was isolated from Chungkookjoug, and was identified as Bacillus subtilis JK-1 based on morphological, physiological and biochemical characteristics, as well as phylogenetic analysis using 16S rRNA gene sequence. The optimum pH and temperature of the pretense activity were pH 9.0 and
, respectively. This enzyme was stable at the temperatures
. The maximum alkaline pretense production was obtained when 1.0% (w/v) xylose, 1.0% (w/v) yeast extract and 0.3% (w/v)
were used as carbon source, nitrogen source and mineral source. Under the optimal condition, growth of the isolate was reached at stationary phase after 12 hr followed by incubation, the alkaline pretense production reached a maximum level with
Plasmid Profiles of Pseudomonas syringae pv. syringae Isolated from Kiwifruit Plants in Korea and the Copper Resistance Determinant
Park, So-Yeon ; Han, Hyo-Shim ; Lee, Young-Sun ; Koh, Young-Jin ; Shin, Jong-Sup ; Jung, Jae-Sung ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 337~340
Pseudomonas syringae Pv. syringae is a causal agent of bacterial blossom blight of kiwifruit in Korea. Eleven strains of the pathogen were isolated from different kiwifruit orchards in Korea and the plasmid profiles were obtained by pulsed-field gel electrophoresis. They could be clustered into six groups according to the number and size of plasmids. The number of plasmids per strain and size of these plasmids ranged from 0 to 4 and from 22 to 160 kb, respectively. Among them, four strains belonging to Group III which harbored two plasmids were resistant to copper sulfate. Southern blot hybridization of the plasmid DNA indicated that the copper resistance determinant was carried on a 48 kb plasmid.
Isolation and Characterization of High Viscosity Polysaccharide Producing Endophytic Bacteria from Pueraria Root
Whang, Kyung-Sook ; Choi, Seung-Hyun ; Han, Song-Ih ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 341~345
Fifty endophytic bacteria, which produced slime around the colonies, were isolated from Pueraria roots. In particular, HDN-14, TDG-3, and TNB-3 strains, which appeared to be high viscosity producers, were selected. These strains produced high levels of polysaccharides in Puerara root medium extract. The purified polysaccharide was digested with 1N HCI and analyzed by HPLC, with glucose (
), maltose (
), and fructose (
) detected as constitutive sugars. When determined by the homology relationship of the 16S rDNA sequence with the relative taxa, the HDN-14 and TNB-3 strains were closely (
) related to the Pseudomonas
, while TDG-3 were closely (
) related to Pseudomonas
, and Pseudomonas
. The major cellular Pseudomonas acids are
, with these strains being further differentiated in species belonging to the genus Pseudomonas.
Changes in Coagulase Serotype of Staphylococcus aureus Isolates in Busan, 1994-2005
Hwang, Soo-Myung ; Kim, Tae-Un ;
The Korean Journal of Microbiology, volume 43, issue 4, 2007, Pages 346~350
We analyzed the phenotypic changes in coagulase serotype of S. aureus isolated from clinical sources and nasal cavities of healthy persons,
. A total of 715 isolates, 408 methicillin resistant S. aureus (MRSA) from clinical sources and 307 methicillin-susceptible S. aureus (MSSA), were classified into eight coagulase sero-types, I to VIII. The most prevalent serotype in MRSA was type II (54.3%, 222/408) and followed IV (24.7%), III (10.9%), and V (5.2%), whereas the majorities in MSSA were type VII (30.9%, 95/307), IV (22.2%), V (22.2%) and II (7.1%). Among the isolates collected periods, significant changes of coagulase serotypes in both strains were observed. In MRSA strains, the serotype V was not detected until 1997, but rapidly increased to 18.5% (20/108) in 2005, and the serotypes III decreased from 27% (31/115) in 1994 to 0.9% (1/108) in 2005. A similar trend in MSSA strains was observed but serotype II strain was not detected in 2005. The antigenic shift and changes in the coagulase of S. aureus were confirmed.