Kye-Heon Oh

Adaptive and cross-protective responses of Pseudomonas sp. DJ-12 to several aromatics and other stress shocks.

Pseudomonas sp. DJ-12 cells were subjected to mild treatments of stress such as exposure to biphenyl, 4-chlorobiphenyl (4CB), 4-hydroxybenzoate (4HBA), ethanol, and heat, and then were examined for production of stress-shock proteins and morphological changes. The adapted cells were then subjected to lethal stress conditions such as 200 mm 4CB, 100 mm biphenyl, 10 mm 4HBA, 20% ethanol, and 46°C to examine crossly protective responses to the stresses. Several stress-shock proteins including DnaK and GroEL were newly synthesized in the adapted cells. Some of them were commonly produced by those stresses separately treated. The cells treated with these aromatic hydrocarbons showed destructive openings on the cell envelopes. On the other hand, those cells treated with ethanol or heat displayed irregular rod shapes with wrinkled surfaces. The adapted cells to each stress under sublethal conditions exhibited increased resistance to the same stress of lethal conditions. The cells adapted with 5 mm 4HBA showed greater protection for survival than those adapted by other stresses. In addition, those adapted cells showed increased resistance to other stresses as a cross-protection phenomenon. The cells adapted to 42°C exhibited markedly increased resistance to the lethal stresses of 46°C as well as to 20% ethanol.

Analysis of TNT (2,4,6-trinitrotoluene)-inducible cellular responses and stress shock proteome in Stenotrophomonas sp. OK-5.

In this study, the cellular responses of Stenotrophomonas sp. OK-5 to explosive 2,4,6-trinitrotoluene (TNT) have been extensively analyzed. The stress shock proteins, which might contribute to enhancing cellular resistance to TNT-mediated toxicity, were induced at different concentrations of TNT used as a substrate for cell culture of Stenotrophomonas sp. OK-5 capable of utilizing TNT. Proteomic analysis for 2-DE of soluble protein fractions from the culture of OK-5 exposed to TNT demonstrated approximately 300 spots on the silver-stained gel ranging from pH 3 to pH 10. Among them, 10 spots significantly induced and expressed in response to TNT were selected and analyzed. As the result of internal amino acid sequencing with ESI-Q TOF mass spectrometry, TNT-mediated stress shock proteins such as DnaK, OmpW, and OsmC were identified and characterized. Survival of strain OK-5 was periodically monitored in the presence of different concentrations of TNT along with the production of the stress shock proteins. Cells of strain OK-5 pre-exposed to TNT had in improved survival tolerance. Analysis of total cellular fatty acids in strain OK-5 suggested that several saturated or unsaturated fatty acids might increase or decrease under TNT-mediated stress condition. Scanning electron microscopy of cells treated with 0.8 mM TNT for 12 h revealed irregular rod shapes with wrinkled surfaces.

Induction of Stress Shock Proteins DnaK and GroEL by Phenoxyherbicide 2,4-D in Burkholderia sp. YK-2 Isolated from Rice Field

The purpose of this work was to investigate the induction of stress shock proteins in Burkholderia sp. YK-2 in response to the phenoxyherbicide 2,4-dichlorophenoxyacetic acid (2,4-D). The stress shock proteins, which contribute to the resistance of the cytotoxic effect of 2,4-D, were induced at different 2,4-D concentrations in exponentially growing cultures of Burkholderia sp. YK-2. This response involved the induction of a 43-kDa DnaK and 41-kDa GroEL proteins, characterized by SDS-PAGE and Western blot by use of the anti-DnaK and anti-GroEL monoclonal antibodies. The total stress shock proteins were analyzed by 2-D PAGE. Survival of Burkholderia sp. YK-2 with time in the presence of different concentrations of 2,4-D was monitored, and viable counts paralleled the induction of the stress shock proteins in this strain.

Proteome analysis of aniline-induced proteins in Acinetobacter lwoffii K24.

Acinetobacter lwoffii K24 is a soil bacterium that can use aniline as a sole carbon and nitrogen source (by β-ketoadipate pathway genes (cat genes)) and has two copies of catABC gene separately located on the chromosome. In order to identify aniline-induced proteins, two-dimensional electrophoresis (2-DE) was applied to soluble protein fractions of A. lwoffii K24 cultured in aniline and succinate media. In the range of pH3–10, more than 370 spots were detected on the silver stained gels. Interestingly, more than 20 spots were selectively induced on aniline-cultured bacteria. Twenty-three protein spots of A. lwoffii K24 were analyzed by N-terminal microsequencing and internal microsequencing with in-gel digestion. Of 20 aniline induced protein spots, we identified six β-ketoadipate pathway genes, one subunit of amino group transfer (putative subunit of aniline oxygenase), malate dehydrogenase, putative ABC transporter, putative hydrolase, HHDD isomerase, and five unknown proteins. Especially in case of two catechol 1,2-dioxygenases (CDI1 and CDI2), more than three isotypes were detected on the 2D gel. This study showed that the proteome analysis of A. lwoffii K24 may be helpful for identification of genes induced by aniline and understanding of their function in the cell.

Synergistic anti-bacterial and proteomic effects of epigallocatechin gallate on clinical isolates of imipenem-resistant Klebsiella pneumoniae.

Imipenem-resistant Klebsiella pneumoniae (IRKP) were used to explore the synergistic anti-bacterial and proteomic effects of imipenem alone or in combination with epigallocatechin gallate (EGCg). The minimal inhibitory concentrations (MICs) of EGCG for 12 clinically isolated IRKP strains ranged from 300 to 650 μg/ml. Each of the 12 IRKP strains experienced a 4- to 64-fold reduction in the MIC of imipenem upon co-incubation with 0.25 × MIC level of EGCg. The time-kill method was used on the 12 IRKP clinical isolates to evaluate the bactericidal activities of imipenem alone or with EGCg. Compared to imipenem alone, EGCg with imipenem demonstrated enhanced bactericidal activity. Two-dimensional polyacrylamide gel electrophoresis identified eight down-regulated and four up-regulated proteins in the IRKP strain upon exposure to 1 × MIC of EGCg. Analysis of the outer membrane protein profiles of IRKP cultures treated with EGCg revealed unique changes in outer membrane proteins. In addition, scanning electron microscopic analysis demonstrated the presence of cells with wrinkled surfaces containing perforations and irregular rod-shaped forms after treatment with EGCg or imipenem. These studies demonstrate that EGCg can synergize the bacterial activity of imipenem and differentially stimulate the expression of various proteins in IRKP.

Evaluation of carbazole degradation by Pseudomonas rhodesiae strain KK1 isolated from soil contaminated with coal tar.

In this study, strain KK1 isolated from coal tar‐contaminated soil was found to be able to mineralize carbazole as a sole source of carbon by radiorespirometric analysis. KK1 cells pregrown on phenanthrene were able to mineralize carbazole much more rapidly than cells pregrown on naphthalene, suggesting a possible close linkage between the pathways for carbazole and phenanthrene catabolism. Also, Rieske‐type iron sulfur center sequence of dioxygenase from KK1 was analyzed to evaluate carbazole catabolism by KK1. A gene cloned out from KK1 using a universal dioxygenase primer set was found a dioxygenase for initial catabolism of carbazole based on deduced amino acid sequences. Northern hybridization using the putative carbazole dixoygenase gene fragment as a probe provided the information that catabolism of carbazole might be greatly activated in phenanthrene‐grown cells. Analysis of PLFAs extracted from KK1 cells exposed to carbazole revealed that lipids 10:0 3OH, 17:0 cyclo, and 18:0 were representatives produced or significantly increased in response to carbazole. Strain KK1 was identified as Pseudomonas species with 94% confidence when BIOLOG system was applied, as Pseudomonas sp. with over 90% confidence by total cellular compositions of fatty acid, and as Pseudomonas rhodesiae with 99% confidence by 16S rRNA sequence. Accordingly, strain KK1 was identified as Pseudomonas rhodesiae based on combination of the data, and designated Pseudomonas rhodesiae KK1. The phylogenetic tree based on 16S rRNA suggested that strain KK1 was far away in the phylogenetic distance from the strains that can degrade carbazole.

Physiological and cellular responses of the 2,4-D degrading bacterium, Burkholderia cepacia YK-2, to the phenoxyherbicides 2,4-D and 2,4,5-T.

Our previous research has demonstrated that novel 43-kDa DnaK and 41-kDa GroEL proteins are synthesized in Burkholderia sp. YK-2 in response to sublethal concentrations of 2,4-D stress [Cho et al. (2000) Curr Microbiol 41:33–38]. In this study, we have extended this work to examine the cellular responses of strain YK-2 to stresses induced in response to the phenoxyherbicides 2,4-D or 2,4,5-T. Strain YK-2 exhibited a more sensitive response to 2,4,5-T stress than to 2,4-D stress, as shown in physiological and morphological changes, suggesting a greater cytotoxic effect of 2,4,5-T. SEM analyses revealed the presence of perforations and irregular rod forms with wrinkled surfaces for cells treated with either herbicide. These irregularities were found more frequently for 2,4,5-T-treated cells than for 2,4-D-treated cells. Analysis of cellular fatty acids showed similar effects in the shifts of total cellular fatty acid composition in response to 2,4-D and 2,4,5-T. Strain YK-2 could degrade 2.25 mM 2,4-D completely during 28 h of incubation with transient production of 2,4-dichlorophenol as a metabolite; however, 2,4,5-T was not catabolized at any of the concentrations tested. BIOLOG and 16S rDNA analyses revealed that strain YK-2 was 98% similar to the Burkholderia cepacia species cluster; therefore, we have designated this strain as B. cepacia YK-2.

Biological removal of explosive 2,4,6-trinitrotoluene byStenotrophomonas sp. OK-5 in bench-scale bioreactors

The biological removal of 2,4,6-trinitrotoluene (TNT) was studied in a bench-scale bioreactor using a bacterial culture of strain OK-5 originally isolated from soil samples contaminated with TNT. The TNT was completely removed within 4 days of incubation in a 2.5 L benchscale bioreactor containing a newly developed medium. The TNT was catabolized in the presence of different supplemented carbons. Only minimal growth was observed in the killed controls and cultures that only received TNT during the incubation period. This catabolism was affected by the concentration ratio of the substrate to the biomass. The addition of various nitrogen sources produced a delayed effect for the TNT degradation. Tween 80 enhanced the degradation of TNT under these conditions. Two metabolic intermediates were detected and identified as 2-amino-4,6-dinitrotoluene and 4-amino-2,6-dinitrotoluene based on HPLC and GC-MS analyses, respectively. Strain OK-5 was characterized using the BIOLOG system and fatty acid profile produced by a microbial identification system equipped with a Hewlett packard HP 5890 II gas chromatograph. As such, the bacterium was identified as aStenotrophomonas species and designated asStenotrophomonas sp. OK-5.

Biodegradation of the Phenoxy Herbicide MCPA by Microbial Consortia Isolated from a Rice Field

The phenoxy herbicide 4-methyl-2-chlorophenoxyacetic acid (MCPA) is widely used as a broad leaf weed controller (Loos 1975; Que Hee and Sutherland 1981). MCPA is readily susceptible to biodegradation and MCPA-degrading bacteria are relatively ubiquitous in soils with histories of previous applications. The pathway of MCPA biodegradation has been elucidated in several bacteria, including Pseudomonas spp. (Gaunt and Evans 1971 ; Kilpi et al. 1980). Some species of Alcaligenes (Pieper et al. 1988) and Flavobacterium (Horvath et al. 1990) can also degrade MCPA as the sole source of carbon and energy. Enzymes involved in the degradative pathway of MCPA are commonly plasmid borne in Pseudomonas spp. (Fisher et al. 1978). MCPA degradation in soils has also been elucidated in previous studies (Soderquist and Crosby 1975; Smith and Hayden 1981; Smith and LaFond 1990).

Comparative analysis of 2,4,6-trinitrotoluene (TNT)-induced cellular responses and proteomes in Pseudomonas sp. HK-6 in two types of media

TNT-induced cellular responses and proteomes in Pseudomonas sp. HK-6 were comparatively analyzed in two different media: basal salts (BS) and Luria broth (LB). HK-6 cells could not degrade more than 0.5 mM TNT with BS medium, while in LB medium, they exhibited the enhanced capability to degrade as much as 3.0 mM TNT. Analysis of total cellular fatty acids in HK-6 cells suggested that the relative abundance of several saturated or unsaturated fatty acids is altered under TNT-mediated stress conditions. Scanning electron microscopy showed the presence of perforations, irregular rod formations, and wrinkled extracellular surfaces in cells under TNT stress. Proteomic analysis of soluble protein fractions from HK-6 cultures grown with TNT as a substrate revealed 11 protein spots induced by TNT. Among these, seven proteins (including Alg8, AlgB, NirB, and the AhpC/Tsa family) were detected only in LB medium containing TNT. The proteins AspS, Tsf, and assimilatory nitrate reductase were increasingly expressed only in BS medium containing TNT. The protein dGTPase was found to be induced and expressed when cells were grown in either type of TNT-containing media. These results provide a better understanding of the cytotoxicity and survival mechanism used by Pseudomonas sp. HK-6 when placed under TNT stress conditions.