• Applied Biological Chemistry
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• v.27 no.2
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• pp.64-72
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• 1984

Alachlor, 2-chloro-2, '6'-diethyl-N-(methoxymethyl) acetanilide, which had been incubated in the flooded paddy soils yielded 1-formyl-2,3-dihydro-7-ethylindole, 2,6-diethylaniline, 2,6-diethylacetanilide, 2,6-diethyl-N-(methoxymethyl) acetanilide, 2-hydroxy-2, '6'-diethyl-N-(methoxymethyl) acetanilide, and three unidentifiable compounds as its degradation products. The water-soluble products of Alachlor in soil suspensions increased with incubation periods and similar results were obtained from the incubation of Rhizoctonia solani, as verified by use of the ring $-^{14}C-$labeled Alachlor. Streptomyces lavendulae Ru 3340-8 produced 2-hydroxy-2, '6'-diethyl-N-(methoxymethyl) acetanilide as the major degradation product as much as 25%, whereas Bacillus brevis IFO 3331, Bacillus cruciviae, and Pseudomonas putida did not produce it.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.91-95
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• 2005

In the multidimensional protein identification technology of high-throughput proteomics, we use one-dimensional gel electrophoresis and after the separation by two-dimensional liquid chromatography, the sample is analyzed by tandem mass spectrometry. In this study, we have analyzed the Pseudomonas Putida KT2440 protein. From the protein identification, the protein database was combined with its reversed sequence database. From the peptide selection whose error rate is less than 1%, the SEQUEST database search for the tandem mass spectral data identified 2,045 proteins. For each protein, we compared the molecular weight calibrated from 1D-gel band position with the theoretical molecular weight computed from the amino acid sequence, by defining a variable MW$_{corr}$ Since the bacterial proteome is simpler than human proteome considering the complexity and modifications, the proteome analysis result for the Pseudomonas Putida KT2440 could suggest a guideline to build the protocol to analyze human proteome data.

• Korean Journal Plant Pathology
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• v.11 no.4
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• pp.292-297
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• 1995

We developed an in vitro assay method for evaluating plant growth promotion and providing an evidence that the growth promotion is rendered by growth enhancing factors. The amendment of culture filtrates of Trichoderma harzianum T95 and Gliocladium virens G872 and G872B in Murashige and Skoog (MS) agar medium enhanced the cotyledon growth of cucumber in terms of fresh weight and primary leaf area of cucumber cotyledon cuttings, of which the treatment of G. virens G872B was the most effective. The mycelial culture filtrate of G872B was more effective in the growth promotion than its conidial germling filtrate. The addition of 1% sucrose in MS mineral medium with 0.1% culture filtrates of the antagonists (T95 and G872B) was optimum for enhancing the effect of the filtrates on the growth of cotyledon cuttings in vitro. When cucumber seeds treated with G872B, Pseudomonas putida Pf3 or the G872B-Pf3 mixture were planted in a greenhouse, the rate of seed germination, biomass of shoot and root, and yield of cucumber fruits were increased, especially by G872B or the G872B-Pf3 mixture. Correspondingly, cucumber fruit yields in early to middle-cycles of harvest were significantly greater in the plots of G872B than the control and Pf3-treated plots, and the final yield was highest in the plots of the G872B-Pf3 mixture applications.

• Journal of Microbiology
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• v.37 no.3
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• pp.141-147
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• 1999

Thirteen transcriptionally-fused carbon starvation mutants, derived from Pseudomonas putida ATCC 12633, were analyzed for their survivability and transcriptional induction profiles upon carbon starvation. One of these mutants, MK114, which exhibited the lowest survivability and the highest induction rate, was selected and further examined under different starvation (nitrogen and phosphate) and stress (osmolarity, H2O2, salts, alcohol, and heat) conditions. Under all tested conditions MK114 induced ${\beta}$-galactosidase activity, implying that the interrupted gene (cst114) is a general starvation and stress response gene. The rate of induction ranged from 2.6-fold for phosphate starvation to 3.7-fold for osmotic shock. The mini-Tn5 flanking DNA was cloned from the chromosome of MK114. The cloned DNA fragment exhibited carbon starvation activity, indicating that this fragment contains a carbon starvation-related promoter region. This region was partially sequenced. Possible physiological roles of Cst114 in a carbon sensing mechanism and in other stress responses are also discussed.

• Journal of Microbiology and Biotechnology
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• v.17 no.10
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• pp.1727-1732
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• 2007

Phenylacetic acid (PAA) is produced by many bacteria as an antifungal agent and also appears to be an environmentally toxic chemical. The object of this study was to detect PAA using Pseudomonas putida harboring a reporter plasmid that has a PAA-inducible promoter fused to a green fluorescent protein (GFP) gene. Pseudomonas putida KT2440 was used to construct a green fluorescent protein-based reporter fusion using the paaA promoter region to detect the presence of PAA. The reporter strain exhibited a high level of gfp expression in minimal medium containing PAA; however, the level of GFP expression diminished when glucose was added to the medium, whereas other carbon sources, such as succinate and pyruvate, showed no catabolic repression. Interestingly, overexpression of a paaF gene encoding PAA-CoA ligase minimized catabolic repression. The reporter strain could also successfully detect PAA produced by other PAA-producing bacteria. This GFP-based bioreporter provides a useful tool for detecting bacteria producing PAA.

• Journal of Microbiology and Biotechnology
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• v.25 no.11
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• pp.1928-1935
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• 2015

Microbial growth kinetics is often used to optimize environmental processes owing to its relation to the breakdown of substrate (contaminants). However, the quantification of bacterial populations in the environment is difficult owing to the challenges of monitoring a specific bacterial population within a diverse microbial community. Conventional methods are unable to detect and quantify the growth of individual strains separately in the mixed culture reactor. This work describes a novel quantitative PCR (qPCR)-based genomic approach to quantify each species in mixed culture and interpret its growth kinetics in the mixed system. Batch experiments were performed for both single and dual cultures of Pseudomonas putida and Escherichia coli K12 to obtain Monod kinetic parameters (μ_max and K_s). The growth curves and kinetics obtained by conventional methods (i.e., dry weight measurement and absorbance reading) were compared with that obtained by qPCR assay. We anticipate that the adoption of this qPCR-based genomic assay can contribute significantly to traditional microbial kinetics, modeling practice, and the operation of bioreactors, where handling of complex mixed cultures is required.

• Journal of Microbiology and Biotechnology
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• v.10 no.1
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• pp.35-42
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• 2000

Reaction characteristics of 4-methylcatechol 2,3-dioxygenase (4MC230) purified from Pseudomonas putida SU10 with a higher activity toward 4-methylcatechol than catechol or 3-cethylcatechol were studied by altering their physical and chemical properties. The enzyme exhibited a maximum activity at pH 7.5 and approximately 40% at pH 6.0 for 4-methylcatechol hydrolysis. The optimum temperature for the enzyme was around $35^{\circ}C$, since the enzyme was unstable at higher temperature. Acetone(10%) stabilized the 4MC230. The effects of solvent and other chemicals (inactivator or reactivator) for the reactivation of the 4MC230 were also investigated. Silver nitrate and hydrogen peroxid severely deactivated the enzyme and the deactivation by hydrogen peroxide severely deactivated the enzyme and the deactivation by hydrogen peroxide was mainly due to the oxidation of ferrous ion to ferric ion. Some solvents acted as an activator and protector for the enzyme from deactivation by hydrogen peroxide. Ascorbate, cysteine, or ferrous ion reactivated the deactivated enzyme by hydrogen peroxide. The addition of ferrous ion together with a reducing agent fully recovered the enzyme activity and increased its activity abut 2 times.

• Journal of environmental and Sanitary engineering
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• v.19 no.4 s.54
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• pp.19-24
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• 2004

The objective of this study was to develop a mechanistically based mathematical model that would consider the interdependence of VOCs transport, microbial activity, and sorptive interactions in a moist, unsaturated soil. Because the focus of the model was on description of natural attenuation, the advective VOCs transport that is induced in engineered remediation processes such as vapor extraction was not considered. The utility of the model was assessed through its ability to describe experimental observations from diffusion experiments using toluene as a representative VOCs in well-defined soil columns that contained a toluene degrading bacterium, Pseudomonas putida G7 md Fl, as the sole active microbial species. The gas-liquid mass-transfer was found to be a key parameter controlling the ability of bacteria to degrade VOCs. This finding indicates that soil size and geometry are likely to be important parameters in assessing the possible success of natural attenuation of VOCs in contaminated unsaturated soils. Therefore we found that Pseudomonas putida G7 and Fl were very effective to remove of refractory pollutants such as toluene in soil by Bio-filter

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.249-254
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• 1999

A catechol 2,3-dioxygenase (C23O) was purified to apparent homogeneity from Pseudomonas putida SU10 through several purification steps consisting of ammonium sulfate precipitation and chromatographies on DEAE 5PW, Superdex S-200, and Resource-Q. Gel filtration indicated a molecular mass under nondenaturing conditions of about 130 kDa. The enzyme has a subunit of 34 kDa as was determined by SDS-PAGE. These results suggest that the native enzyme is composed of four identical subunits. The N-terminal amino acid sequence (30 residues) of the enzyme has been determined and exhibits high identity with other extradiol dioxygenases. The reactivity of this enzyme towards catechol and methyl-substituted catechols is somewhat different from that seen for other catechol 2,3-dioxygenases, with 4-methylcatechol cleaved at a higher rate than catechol or 3-methylcatechol. $K_m$ values of the enzyme for these substrates are between 3.5 and 5.7 M.

• Journal of Microbiology
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• v.45 no.1
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• pp.15-20
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• 2007

The majority of soil microorganisms can derive ethylene from L-methionine (L-MET), while some rhizobacteria can hydrolyze 1-aminocyclopropane-1-carboxylate (ACC) due to their ACC-deaminase activity. In this study, three strains having either ACC-deaminase activity (Pseudomonas putida biotype A, $A_7$), or the ability to produce ethylene from L-MET (Acinetobacter calcoaceticus, $M_9$) or both (Pseudomonas fluorescens, $AM_3$) were used for inoculation. The highly ethylene specific bioassay of a classical 'triple' response in pea seedlings was used to investigate the effect of the inoculation with the rhizobacteria in the presence of 10 mM ACC or L-MET. The exogenous application of ACC had a concentration-dependent effect on the etiolated pea seedlings in creating the classical 'triple' response. The inoculation with P. putida diluted the effect of ACC, which was most likely due to its ACC-deaminase activity. Similarly, the application of $Co^{2+}$ reduced the ACC-imposed effect on etiolated pea seedlings. In contrast, the inoculation of A. calcoaceticus or P. fluorescens in the presence of L-MET caused a stronger classical 'triple' response in etiolated pea seedlings; most likely by producing ethylene from L-MET. This is the first study, to our knowledge, reporting on the comparative effect of rhizobacteria capable of utilizing ACC vs L-MET on etiolated pea seedlings.