• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.812-821
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• 2007

The ecosystems of certain abandoned mines contain arsenic-resistant bacteria capable of performing detoxification when an ars gene is present in the bacterial genome. The ars gene has already been isolated from Pseudomonas putida and identified as a member of the membrane transport regulatory deoxyribonucleic acid family. The arsenite-oxidizing bacterial strains isolated in the present study were found to grow in the presence of 66.7 mM sodium arsenate($V;\;Na_2HAsO_4{\cdot}7H_2O$), yet experienced inhibited growth when the sodium arsenite($III;\;NaAsO_2$) concentration was higher than 26 mM. Batch experiment results showed that Pseudomonas putida strain OS-5 completely oxidized 1 mM of As(III) to As(V) within 35 h. An arsB gene encoding a membrane transport regulatory protein was observed in arsenite-oxidizing Pseudomonas putida strain OS-5, whereas arsB, arsH, and arrA were detected in strain OS-19, arsD and arsB were isolated from strain RW-18, and arsR, arsD, and arsB were found in E. coli strain OS-80. The leader gene of arsR, -arsD, was observed in a weak acid position. Thus, for bacteria exposed to weak acidity, the ars system may cause changes to the ecosystems of As-contaminated mines. Accordingly, the present results suggest that arsR, arsD, arsAB, arsA, arsB, arsC, arsH, arrA, arrB, aoxA, aoxB, aoxC, aoxD, aroA, and aroB may be useful for arsenite-oxidizing bacteria in abandoned arsenic-contaminated mines.

• Journal of Microbiology and Biotechnology
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• v.17 no.9
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• pp.1504-1512
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• 2007

The fpr gene, which encodes a ferredoxin-$NADP^+$ reductase, is known to participate in the reversible redox reactions between $NADP^+$/NADPH and electron carriers, such as ferredoxin or flavodoxin. The role of Fpr and its regulatory protein, FinR, in Pseudomonas putida KT2440 on the oxidative and osmotic stress responses has already been characterized [Lee at al. (2006). Biochem. Biophys. Res. Commun. 339, 1246-1254]. In the genome of P. putida KT2440, another Fpr homolog (FprB) has a 35.3% amino acid identity with Fpr. The fprB gene was cloned and expressed in Escherichia coli. The diaphorase activity assay was conducted using purified FprB to identify the function of FprB. In contrast to the fpr gene, the induction of fprB was not affected by oxidative stress agents, such as paraquat, menadione, $H_2O_2$, and t-butyl hydroperoxide. However, a higher level of fprB induction was observed under osmotic stress. Targeted disruption of fprB by homologous recombination resulted in a growth defect under high osmotic conditions. Recovery of oxidatively damaged aconitase activity was faster for the fprB mutant than for the fpr mutant, yet still slower than that for the wild type. Therefore, these data suggest that the catalytic function of FprB may have evolved to augment the function of Fpr in P. putida KT2440.

• Korean journal of applied entomology
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• v.22 no.3 s.56
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• pp.186-192
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• 1983

The growth of germ tube of Fusarium oxysporum f. sp. cucumerinum was remarkably inhibited on the water agar treated with 100ppm of Fe-EDDHA, a synthetic iron chelating agent, whereas germination rate of microconidia did not show much differences compare with that of non treated water agar. Both of the germination and the germ tube elongation of microconidia were suppressed significantly in King's B agar by the bacterial siderophores produced by Pseudomonas putida. The highest germination of the chlamydospores was obtained in the soil added with $0.25\%$ of glucose plus $0.05\%$ of asparagine. The chlamydospores of cucumber wil fungus germinated about $14\%$ in rhizosphere soil of 2 day-old cucumber seedlings within 48 hours, and the germination was enhanced notably in rhizosphere soil of 10 day-old seedling. But the rates of germination was not increased according to cucumber growth age after 10 day-old seedling. The effect of P. putida and Fe-EDDHA on the germination on chlamydospores in conducive soil was not pronounced in the non-rhizosphere soil added with nutrient. However, the germination was suppressed significantly both in rhizosphere soil and in rhizosphere soil added with nutrient. The suppression of chlamydospore germination was greater in the bacteria inoculated soil than that in Fe-EDDHA treated soil.

• Journal of Food Hygiene and Safety
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• v.16 no.3
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• pp.232-240
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• 2001

One hundred twenty five bacterial isolates were obtained from the brown blotch-diseased oyster mushrooms collected from markets. Among them, 45 were determined as pathogenic bacteria and white line forming organisms(WLFO) were 6 strains and white line reaction organisms (WLRO) were 6 strains. All of the white line forming isolates were identified as Pseudomonas tolaasii which is a known pathogen of brown blotch disease of oyster mushroom by GC-MIS(Gas chromatography-microbial identification system). Six of the white line reacting organisms were identified as P. chlomraphis, P. fluorescens biotype A and type C. The rest of them were P gingeri, P. agarici, P. fluorescens biotype B, P. chloroyaphis, non-pathogenic P. tolaasii, P. putida biotype A and B etc. For spectrum of activity of tolaasin, culture filtrates from pathogenic isolates were examined by browning of mushroom tissue and pitting of mushroom caps. The weak pathogenic bacteria didn't induce browning or pitting of mushroom tissue. On the other hand, strong pathogenic isolates showed browning and pitting reaction on mushroom. An extracellular toxin produced by P. tolaasii, was investigated. The hemolysis activity test of 6 strains identified as P. tolaasii were 0.8∼0.9 at 600 nm and 3 strains of WLRO were 0.9∼1.0 and Pseudomonas app. were 1.0∼1.2. Observation of fresh mushroom tissue using confocal laser scanning microscopy was carried out for images of optical sectioning and vertical sectioning. Also images of brown blotch diseased oyster mushroom tissue after contamination P. tolaasii was obtained by CLSM.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.835-842
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• 2014

Haloperoxidase (HPO, E.C.1.11.1.7) is a metal-containing enzyme oxidizing halonium species, which can be used in the synthesis of halogenated organic compounds, for instance in the production of antimicrobial agents, cosmetics, etc., in the presence of halides and $H_2O_2$. To isolate and evaluate a novel non-metal HPO using a culture-independent method, a cassette PCR library was constructed from marine seawater in Japan. We first isolated a novel HPO gene from Pseudomonas putida ATCC11172 by PCR for constructing the chimeric HPO library (HPO11172). HPO11172 showed each single open-reading frame of 828 base pairs coding for 276 amino acids, respectively, and showed 87% similarity with P. putida IF-3 sequences. Approximately 600 transformants screened for chimeric genes between P. putida ATCC11173 and HPO central fragments were able to identify 113 active clones. Among them, we finally isolated 20 novel HPO genes. Sequence analyses of the obtained 20 clones showed higher homology genes with P. putida or Sinorhizobium or Streptomyces strains. Although the HPO A9 clone showed the lowest homology with HPO11172, clones in group B, including CS19, showed a relatively higher homology of 80%, with 70% identy. E. coli cells expressing these HPO chimeric genes were able to successfully bioconvert chlorodimedone with KBr or KCl as substrate.

• Journal of Microbiology and Biotechnology
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• v.19 no.4
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• pp.362-367
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• 2009

In recombinant strains, many proteins and enzymes are expressed as inactive and insoluble inclusion bodies. For soluble expression of an active form of StyB, an NADH-flavin oxidoreductase, several recombinant Escherichia coli strains were developed and tested. Among them, strain BL21(DE3)pLysS effectively produced an active and soluble form of StyB as about 9% of the total protein content, when cultivated at $20^{\circ}C$ with 0.5 mM IPTG. The solubly expressed StyB has the highest oxidoreductase activity at pH 6.5-7.5 and $37^{\circ}C$. Substrate dependence profiles of the StyB-catalyzed reaction showed that the maximum specific activity($V_m$) and half saturation constant($K_m$) were $1,867{\pm}148\;U/mg$ protein and $51.6{\pm}11{\mu}M$ for NADH, and $1,274{\pm}34\;U/mg$ protein and $8.2{\pm}1.2{\mu}M$ for FAD, respectively. This indicates that solubly produced StyB has 6- to 9-fold higher oxidoreductase activities than the in vitro refolded StyB from inclusion bodies.

• KSBB Journal
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• v.29 no.4
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• pp.244-249
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• 2014

Biosynthesis pathway of medium-chain-length (MCL) polyhydroxyalkanoates (PHA) from fatty acid ${\beta}$-oxidation pathway was constructed in recombinant Escherichia coli by introducing the Pseudomonas sp. 61-3 PHA synthase gene (phaC2) and the maoC genes from Pseudomonas putida, Sinorhizobium meliloti, and Ralstonia eutropha. The metabolic link between fatty acid ${\beta}$-oxidation pathway and PHA biosynthesis pathway was constructed by MaoC, which is homologous to P. aeruginosa (R)-specific enoyl-CoA hydratase (PhaJ1). When the E. coli W3110 strains expressing the phaC2 gene and one of the maoC genes from P. putida, Sinorhizobium meliloti, and Ralstonia eutropha were cultured in LB medium containing 2 g/L of sodium decanoate as a carbon source, MCL-PHA that mainly consists of 3-hydroxyhexanoate (3HHx), 3-hydroxyoctanoate (3HO) and 3-hydroxydecanoate (3HD), was produced. The monomer composition of PHA and PHA contents varied depending on MaoC employed for the production of PHA. The highest PHA content of 18.7 wt% was achieved in recombinant E. coli W3110 expressing the phaC2 gene and the P. putida maoC gene. These results suggest that MCL-PHA biosynthesis pathway can be constructed in recombinant E. coli strains from the b-oxidation pathway by employing MaoC able to supply (R)-3-hydroxyacyl-CoA, the substrate of PHA synthase.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.48-55
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• 2004

Six strains of an obligate predatory bdellovibrio isolate that preys on Burkholderia glumae in rice paddy field water and rhizosphere soil, were identified and characterized. The numbers of Bdellovibrio cells varied from $3.2{\times}10^3$ to $9.2{\times}10^3$ plaque-forming unit/g after enrichment in cells of B. glumae. Prey range tests with six Bdellovibrio strains and 17 prey strains of rice-pathogenic, antibiosis-related, or nitrogen-fixing bacteria resulted in unique predation patterns in related prey cells. Strain BG282 had the widest prey range on 7 plant pathogenic bacteria among the 17 prey strains tested. However, no predation occurred with strains of Azospirillum brasilense, Paenibacillus polymyxa, Pseudomonas fluorescens, P. putida, and Serratia marcescens that are associated with antibiosis or nitrogen fixation in the rice ecosystem. Identification was confirmed by the presence of typical bdelloplast in the prey cells of B. glumae and by a PCR assay using B. bacteriovorus-specific primers. Furthermore, 16S rDNA sequencing of the six bdellovibrio strains showed a homology range of 97.2% to 99.2% to the type strain of B. bacteriovorus.

• Korean Journal of Environmental Biology
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• v.29 no.1
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• pp.52-60
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• 2011

Today, the weather is changing continually, due to the progress of global warming. As the weather changes, the habitats of different organisms will change as well. It cannot be predicted whether or not the weather will change with each passing day. In particular, the biological distribution of the areas climate change affects constitutes a major factor in determining the natural state of indigenous plants; additionally, plants are constantly exposed to rhizospheric microorganisms, which are bound to be sensitive to these changes. Interest has grown in the relationship between plants and rhizopheric microorganisms. As a result of this interest we elected to research and experiment further. We researched the dominant changes that occur between plants and rhizospheric organisms due to global warming. First, we used temperature as a variable. We employed four different temperatures and four different sites: room temperature ($27^{\circ}C$), $+2^{\circ}C$, $+4^{\circ}C$, and $+6^{\circ}C$. The four different sites we used were populated by the following species: Pinus deniflora, Pinus koraiensis, Quercus acutissima, and Alnus japonica. We counted colonies of these plants and divided them. Then, using 16S rRNA analysis we identified the microorganisms. In conclusion, we identified the following genera, which were as follows: 10 species of Bacillus, 2 Enterobacter species, 4 Pseudomonas species, 1 Arthrobacter species, 1 Chryseobacterium species, and 1 Rhodococcus species. Among these genera, the dominant species in Pinus deniflora was discovered in the same genus, but a different species dominated at $33^{\circ}C$. Additionally, that of Pinus koraiensis changed in both genus and species which changed into the Chryseobacrterium genus from the Bacilus genus at $33^{\circ}C$.

• Journal of Microbiology and Biotechnology
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• v.31 no.2
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• pp.259-271
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• 2021

Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catBICIAI and catBIICIIAII) on the chromosome play an important role. The catI and catII operons are co-transcribed, whereas catAI and catAII are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatRI and CatRII occupy an additional downstream site, designated as the activation binding site. Notably, CatRI binds to both the catI and catII promoters with high affinity, while CatRII binds weakly. This is likely caused by a T to G mutation in the G/T-N11-A motif. Specifically, we found that CatRI and CatRII regulate catBICIAI and catBIICIIAII in a cooperative manner, which provides new insights into naphthalene degradation.