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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 40, Issue 4 - Dec 2004
Volume 40, Issue 3 - Sep 2004
Volume 40, Issue 2 - Jun 2004
Volume 40, Issue 1 - Mar 2004
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Physiological and Molecular Characterization of NAD(P)H-Nitroreductase from Stenotrophomonas sp. OK-5
Ho Eun-Mi ; Kahng Hyung-Yeel ; Oh Kye-Heon ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 183~188
Stenotrophomonas sp. OK-5 capable of degrading TNT has been found to have three nitroreductase fractions designated as NTR fractions I, II, and III. NTR in a previous study. This study was attempted to reveal physiological and molecular characteristics of NTR fractions I, II, and III in strain OK-5. Several chemicals (e.g., EDTA, NaCl, dithiothreitol,
-mercaptoethanol) were tested for their effect on enzyme activity of NTRs, demonstrating that enzyme activities of NTR fractions I, II, and III from OK-5 were inhibited in the presence of
-mercaptoethanol. Substrate specificity test showed that NTR fractions I, II, and III all have over 70% enzyme activities for nitrobenzene or RDX as a substrate. N-terminal amino acid sequence of NTR fraction I from Stenotrophomonas sp. OK-5 was
and exhibited 70% sequence homology with that of NTR from Xanthomonas campestris. NTR I gene from Stenotrophomonas sp. OK-5 (SmOK5nrI) shared extensive sequence homology in deduced amino acid sequence of PCR product with NTRs from Xanthomonas campestris (81 %), X. axonopodis (75%), Streptomyces avermitilis(30%), whereas they had low homology with that from P. putida KT2440 (pnrB) (16%).
Bacterial Community Structure and Diversity Using 16S rDNA Analysis in the Intertidal Sediment of Ganghwa Island
Cho Hye Youn ; Lee Jung-Hyun ; Hyun Jung-Ho ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 189~198
T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in two layers (0-1cm, 6-7cm depth) of the sediment from Janghwari intertidal flat in Ganghwa Island. The results of T-RFLP (terminal-restriction fragment length polymorphism) analysis using restriction enzyme HhaI showed that the T-RFs of various size (
) bp) appeared evenly at the surface sediments but two T-RFs with 60(
)bp and 93 (
)bp predominated at 6-7cm depth. Analysis of partial sequences for 172 clones revealed that 98% of the clones were not matched with the sequences of cultured bacteria strains in the GenBank (
98%), and approximately 86% of them were classified as different phylotypes. Most clones belonged to
-Proteobacteria, Acidobacteria/Holophaga and green nonsulfur bacteria group. Proteobacteria group occupied the highest proportion in both layers (69% at 0-1cm depth and 46% at 6-7cm depth).
-Proteobacteria that are associated with oxidation and reduction of sulfur compounds were appeared to be dominant, and comprised 21.5% and 15.7% of total clones, respectively. Overall results indicated that extremely diverse bacterial groups were inhabiting in the sediment of Ganghwa intertidal flat, and bacterial communities associated with the behaviour of sulfur seemed to playa significant role in the biogeochemical environment in this anoxic sediment.
Characteristics of Parathion Hydrolase by Pseudomonas rhodesiae H5
Yun Nam Kyung ; Park Kyeong Ryang ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 199~204
The parathion hydrolase (OPH) produced by Pseudomonas rhodesiae H5 was purified by ammonium sulfate precipitation, DEAE-Toyopearl 650M ion exchange chromatography and Sephadex gel filtration chromatography. Parathion hydrolase from crude extracts of P. rhodesiae H5 has two components designated as OPH
, Optimum pH and temperature of OPH
were pH 7.2 and
, and pH 7.6 and
, respectively. The activation energy of OPH
for the hydrolysis of parathion was 3.01 ㎉/I, II, III in the temperature range of
, and Michaelis constant (
) for parathion was 69.2
. The activation energy of OPH
for the hydrolysis of parathion was 4.07㎉/㏖ in the temperature range of
, and Michaelis constant for parathion was 150.9
. Furthermore OPH
was completely inhibited by 1 mM
, but OPH
was less inhibited than OPH
by the metals used in this study.
Analysis of Microbial Communities During Cyanobacterial Bloom in Daechung Reservoir by DGGE
Ko So-Ra ; Park Seong-Joo ; Ahn Chi-Yong ; Choi Aeran ; Lee Jung-Sook ; Kim Hee-Sik ; Yoon Byung-Dae ; Oh Hee-Mock ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 205~210
The change of bacterial communities during cyanobacterial bloom was analyzed by DGGE in Daechung Reservoir from July to October in 2003. The traditional morphological analysis showed that the genera of Microcystis, Chroococcus, Oscillatoria, and Phormidium were dominated. The most frequent band in the DGGE profile by 16S rDNA sequence analysis was identified as Microcystis flos-aquae and the cyanobacterial bloom was peaked on September 2. Oscillatoria spp. were also identified and Aphanizomenon flos-aquae dominated in the middle of August. Judging from the analysis of the digitalized DGGE profiles using the cluster analysis technique, the microbial community on September 2 was considerably different from others. Consequently, it seems that the gene fingerprinting method can give not only the similar results to the traditional morphological method but also additional information on the bacterial species and similarity among the examined microbial communities.
Nucleotide Sequence of an Extracellular Phospholipase D Gene from Streptomyces somaliensis and Transphosphatidylation Activity of Its Enzyme
Jeong Sujin ; Lee Sun-Hee ; Uhm Tai-Boong ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 211~216
A bacterial strain JE-ll found to produce active extracellular phospholipase D (PLD) was selected from the soil isolates. It was identified as Streptomyces somaliensis on the basis of 16S rDNA sequence analysis, morphological and physiological characteristics. The gene (sspld) encoding S. somaliensis PLD was isolated and characterized. The open reading frame was suggested to encode 538 amino acids with a signal peptide of 33 amino acids. The deduced amino acid sequence of the sspld shared a sequence similarity of 70-88％ with PLDs of other Streptomyces sp. so far reported. The PLD converted phosphatidylcholine to phosphatidylglycerol or phosphatidylserine with the yield of 96 to 99％ (㏖/㏖), but did not act on inositol or ethanolamine as a transphosphatidylation donor.
Optimization of Culture Condition and Media Composition on the Production of Cordycepin by Cordyceps militaris.
Jo Sung-Jun ; Lee Tae-Hee ; Chae Dae-Hoon ; Han Yeong-Hwan ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 217~220
The effect of media composition and culture condition on mycelial growth and cordycepin (3'-deoxyadenosine) production was determined using Cordyceps spp. Among the strains of C. militaris and C. sinensis tested, C. militaris KCTC 6862, C. militaris DGUM 32003 and C. militaris KCTC 16932 were excellent for the production of cordycepin. The optimal temperature and pH for production of cordycepin were
and pH ranged from 6.0 to 10, respectively. Among various sources of carbon and nitrogen tested, glucose and tryptone were very excellent for the production of cordycepin, respectively. After 5days cultivation with 1% of tryptone with nitrogen source, 39mg/l of cordycepin was produced. However, addition of phosphorus sources reduced the production of cordycepin.
Cloning and Characterization of Novel Cytochrome P450 Hydroxylase Genes from Pseudonocardia autotrophica
Myeong Ji Seon ; Park Hyun-Joo ; Han Kyuboem ; Kim Sang-Nyun ; Kim Eung-Soo ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 221~225
Novel cytochrome P450 hydroxylase (CYP) genes were isolated and characterized from P. autotrophica cosmid DNA library using an actinomycete CYP-specific PCR product as a screening probe. The cosmids containing four unique CYP genes (pESK601, 602, 603, 604, 605) were identified, and the four CYP genes were completely sequenced to be homologous to other known Actinomycetes CYP genes involved in various secondary metabolic pathways. Among all novel actinomycete CYP genes found in P. autotrophica, the CYP genes present in pESK601 were revealed to be highly homologous to the CYP genes involved in polyene-type amphotericin and nystatin antibiotic biosynthesis. The nucleotide sequences of the CYP flanking region in pESK601 also revealed the polyene-type biosynthetic genes, implying the presence of a cryptic polyene-type antifungal biosynthetic gene cluster in P. autotrophica.
Partial Cloning of Histone Deacetylase Genes from Ganoderma lucidum.
Kim Sunkyung ; Kum Joohee ; Choi Hyoung T. ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 226~229
Histone deacetylase (HDAC) removes acetyl group in lysine residue of histone protein, which is transferred by histone acetylase. HDAC is important in the stabilization and regulation of gene expression in eukaryotic organisms. PCR has been carried out to clone HDAC genes using cDNA library and genomic DNA as the templates from Ganoderma lucidum isolated in Korea. One 470 bp cDNA gene fragment, and 3 genomic HDAC fragments (585 bp, 589 bp, 630 bp) were amplified. When their deduced amino acid sequences were compared with other fungal HDACs, they showed 59-72％ homology.
The Extracellular Enzyme Activities in Culture Broth of Sparassis crispa.
Kim Ji-Young ; Lim Chang-Soo ; Kim Jae-Yong ; Han Yeong-Hwan ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 230~231
The mycelia of Sparassis crispa DSMZ 5201 were cultivated at
for 15 days in yeast-malt extract-glucose broth (pH 4.0) and the filtrate was used as crude enzyme solution to determined the extracellular enzyme activity. The specific activity of
-amylase was 44.27 unit/protein. The specific activities of protease, CMCase,
-glucosidase, chitinase, exo-
-l,4-glucanase were relatively high. However, a very little activity of xylanase was found.
Resistance of Escherichia coli That Expresses Acetyl Xylan Esterase of Streptomyces coelicolor A3(2)
Kim Jae-heon ; Choi Won-ill ; Youn Seock-won ; Jung Sang Oun ; Oh Chung-Hun ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 232~236
We investigated hydrogen peroxide resistance of Escherichia coli possessing acetyl xylan esterase(AxeA) of Streptomyces coelicolor A3(2). The induction of AxeA production by isopropyl-
-thiogalactoside was confirmed by SDS-polyacrylamide gel electrophoresis. The differences in growth between induced and non-induced E. coli were determined by the changes in optical density of cultures after hydrogen peroxide treatment The lethal effect of hydrogen peroxide was observed for non-induced cultures at all concentrations tested in this study (lmM, 2.5mM and 5mM). However, cultures induced for AxeA production resisted the lethal effect, except at 5mM where cells were killed irrespective of the AxeA production. The axeA induction increased survival against 1.5mM hydrogen peroxide from 59% to 74%. In addition, AxeA producing E. coli showed increased survival at
, near maximum growth temperature. Therefore, it was concluded that AxeA conferred a cross-resistance upon the bacterium against both oxidative- and heat stress.
Detection Rate of Periodontopathogens Associated with Cardiovascular Diseases in Denture.
Lim Mi-Young ; Kim Hwa-Sook ; Jeong Jae-Heon ; Yang Ji-Youn ; Oh Sang-Ho ; Kook Joong-Ki ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 237~243
The aim of this study is to investigate the detection rate of putative periodontopathogens, Porphyromonas gingivalis, Tannerella forsythia, and Actiobacillus actinomycetemcomitans, related to cardiovascular diseases(CVD). Plaques were sampled from 15 subjects (4 sites of denture base and/or tooth) with sterilized explorers and were transported in IX PBS. The detection of periodontopathogens was performed by polymerase chain reaction with species-specific primers based on 16S rDNA. The PCR products were cloned into pGEM-T easy vector and its nucleotides were sequenced in order to confirm the specificity. Our data showed that the detection rate of P. gingivalis and T forsythia in denture base of edentulous patients was 25％ and 75％, respectively. And the detection rate of P. gingivalis and T.forsythia in denture base of patient having one more tooth was 91％. The results indicate that plaque of denture base may serve as reservoirs of oral bacteria related to CVD.
Influence of Elevated
on Denitrifying Bacterial Community in a Wetland Soil
Lee Seung-Hoon ; Kim Seonyoung ; Kang Hojeong ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 244~247
To investigate the effects of elevated
on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of
(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient
treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated
treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated
Sole-Carbon-Source Utilization Patterns of Oligotrophic and Psychrotrophic Bacteria Isolated from Lake Baikal.
Lee Geon-Hyoung ; Bae Myoung-Sook ; Park Suhk-Hwan ; Song Hong-Gyu ; Ahn Tae-Seok ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 248~253
To scrutinize the physiological diversity by BIOLOG microplate, the carbon source utilization patterns of 168 strains of oligotrophic bacteria and 132 strains of psychrotrophic bacteria isolated from Lake Baikal during 2000 and 2002 were investigated. Eighty-six percent (56 strains) of oxidase test positive group (GN-NENT group) and 89 % (92 strains) of oxidase test negative group (GN-ENT group) among oligotrophic bacteria, and 82% (85 strains) of oxidase test negative group among psychrotrophic bacteria were able to utilize
-D-glucose as a sole-carbon-source, and 93% (26 strains) of oxidase test positive group among psychrotrophic bacteria were able to utilize bromosuccinic acid as a sole-carbon-source. However, most strains except few oligotrophic bacteria with oxidase test negative group were not able to utilize
-D-lactose as a sole-carbon-source. Most dominant genus among 300 strains was Pseudomonas (49 strains). Other dominant genera belonged to Salmonella, Serratia, Buttiauxella, Pantoea, Yersinia, Brevundimonas, Hydrogenophaga, Photorhabdus, Sphingomonas, and Xenorhabdus. Our results by BIOLOG identification system were able to provide basic data to determine community-level carbon source utilization patterns and to accomplish the efficient and reliable identification for microbial community structure in Lake Baikal.
Treatment of Genomic DNA with Restriction Enzyme(s) Improves Amplification Efficiency by Polymerase Chain Reaction
Min Hae-Ki ; Chang Young-Hyo ;
The Korean Journal of Microbiology, volume 40, issue 3, 2004, Pages 254~256
Polymerase chain reaction (PCR) is a powerful tool for precisely amplifying selected DNA sequences that have had a broad impact on genomic studies. When examining human
- tryptase genes which have 95% DNA homology, inconsistent PCR amplification of genomic sequences hampered our progress. This study suggests that long PCR technique on the original DNA digested with restriction enzymes improves both efficiency and sensitivity of PCR. These improved results seem to derived from the effective denaturation of the original genomic DNA template or reduction of formation of secondary structures that block either primer annealing or extension in PCR. Elimination of homo- or hetero-duplex products derived from highly homologous genes provides an additional advantage in this study. This communication describes how the use of restriction enzymes improved these efficiencies, and also facilitated studies of highly homologous genes including tryptase genes.