Woojun Park

Korea University, Sŏul, Seoul, South Korea

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Publications (98)268.77 Total impact

  • Bora Shin · Woojun Park
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    ABSTRACT: Difficulties involved in treating drug-resistant pathogens have created a need for new therapies. In this study, we investigated the possibility of using oleanolic acid (OA), a natural pentacyclic triterpenoid, as a natural adjuvant for antibiotics against Acinetobacter baumannii. High concentrations of OA can kill cells, partly because it generates reactive oxygen species. Measurement of the fractional inhibitory concentration (FIC) for OA and time-kill experiments demonstrated that it only synergizes with aminoglycoside antibiotics (e.g., gentamicin, kanamycin). Other classes of antibiotics (e.g., ampicillin, rifampicin, norfloxacin, chloramphenicol, and tetracycline) have no interactions with OA. Microarray and quantitative reverse transcription-PCR analysis indicated that genes involved in ATP synthesis and cell membrane permeability, the gene encoding glycosyltransferase, peptidoglycan-related genes, phage-related genes, and DNA repair genes were upregulated under OA. OA highly induces the expression of adk, which encodes an adenylate kinase, and des6, which encodes a linoleoyl-CoA desaturase, and deletion of these genes increased FICs; these observations indicate that adk and des6 are involved in the synergism of OA with aminoglycosides. Data obtained using 8-anilino-1-naphthalenesulfonic acid, fluorescence-conjugated gentamicin, and membrane fatty acid analysis indicates that adk and des6 are involved in changes in membrane permeability. Proton-motive force and ATP synthesis tests show that those genes are also involved in energy metabolism. Taken together, our data show that OA boosts aminoglycoside uptake by changing membrane permeability and energy metabolism in A. baumannii.
    PLoS ONE 09/2015; 10(9):e0137751. DOI:10.1371/journal.pone.0137751 · 3.23 Impact Factor
  • Jisun Kim · Youjung Cho · In-Ae Jang · Woojun Park
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    ABSTRACT: Two-dimensional gel electrophoresis was conducted to investigate the effect of H2O2 on whole protein expression in Acinetobacter oleivorans DR1. Functional classification of 13 upregulated proteins using MALDI-TOF mass spectrometry showed relationships with oxidative stress, energy production and conversion, nucleotide and amino acid metabolism, membrane-related, ion transport, and chaperone-related functions. Alignment of OxyR-binding regions from Pseudomonas aeruginosa and Escherichia coli with promoters of identified proteins revealed that only ahpC, ahpF, and trxB (thioredoxin-disulfide reductase) genes, along with a newly found oprC (putative outer membrane receptor protein) gene, have OxyR-binding sites. The oxyR and ahpC mutants were more sensitive to H2O2 and showed growth defects in both nutritional and n-hexadecane-amended media. Four catalases present in the genome of A. oleivorans DR1 were not detected, which led us to confirm the expression and activity of those catalases in the presence of H2O2. The expression patterns of the four catalase genes differed at different concentrations of H2O2. Interestingly, the promoters of both known OxyR-controlled katG gene (AOLE_17390) and putative small catalase gene (AOLE_09800) have OxyR-binding sites. Gel-shift assay confirmed OxyR binding to the promoter regions of newly identified OxyR-controlled genes encoding OprC and a putative catalase. Hierarchical expression and OxyR-binding of several OxyR-controlled genes suggested that concentration is an important factor in inducing the set of genes under H2O2 stress.
    Applied Microbiology and Biotechnology 08/2015; DOI:10.1007/s00253-015-6914-5 · 3.34 Impact Factor
  • Jisun Kim · Woojun Park
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    ABSTRACT: Indole is an organic compound that is widespread in microbial communities inhabiting diverse habitats, like the soil environment and human intestines. Measurement of indole production is a traditional method for the identification of microbial species. Escherichia coli can produce millimolar concentrations of indole in the stationary growth phase under nutrient-rich conditions. Indole has received considerable attention because of its remarkable effects on various biological functions of the microbial communities, for example, biofilm formation, motility, virulence, plasmid stability, and antibiotic resistance. Indole may function as an intercellular signaling molecule, like a quorum-sensing signal. Nevertheless, a receptor system for indole and the function of this compound in coordinated behavior of a microbial population (which are requirements for a true signaling molecule) have not yet been confirmed. Recent findings suggest that a long-known quorum-sensing regulator, E. coli's SdiA, cannot recognize indole and that this compound may simply cause membrane disruption and energy reduction, which can lead to various changes in bacterial physiology including unstable folding of a quorum-sensing regulator. Indole appears to be responsible for acquisition of antibiotic resistance via the formation of persister cells and activation of an exporter. This review highlights and summarizes the current knowledge about indole as a multitrophic molecule among bacteria, together with recently identified new avenues of research.
    The Journal of Microbiology 07/2015; 53(7):421-8. DOI:10.1007/s12275-015-5273-3 · 1.44 Impact Factor
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    ABSTRACT: Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.
    Microbial Ecology 05/2015; DOI:10.1007/s00248-015-0624-5 · 3.12 Impact Factor
  • Jaejoon Jung · Woojun Park
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    ABSTRACT: Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.
    Applied Microbiology and Biotechnology 02/2015; 99(6). DOI:10.1007/s00253-015-6439-y · 3.34 Impact Factor
  • Aram Heo · Woojun Park
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    ABSTRACT: This study provides evidence that RecG regulates the expression of the OxyR-independent gene mexA in Pseudomonas aeruginosa PAO1. A reduction in mexA expression was observed in the absence of RecG but not OxyR by northern blot and quantitative real-time PCR analyses. The canonical palindromic RecG binding sequence was present upstream of the mexA promoter, and bound purified RecG and single strand-binding protein. These data reveal a novel mechanism of OxyR-independent gene transcription by RecG.
    Journal of Microbiology and Biotechnology 11/2014; 25(4). DOI:10.4014/jmb.1410.10011 · 1.53 Impact Factor
  • Source
    Aram Heo · Hyun-Jin Jang · Jung-Suk Sung · Woojun Park
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    ABSTRACT: The effects of antibiotics on environment-originated nonpathogenic Acinetobacter species have been poorly explored. To understand the antibiotic-resistance mechanisms that function in nonpathogenic Acinetobacter species, we used an RNA-sequencing (RNA-seq) technique to perform global gene-expression profiling of soil-borne Acinetobacter oleivorans DR1 after exposing the bacteria to 4 classes of antibiotics (ampicillin, Amp; kanamycin, Km; tetracycline, Tc; norfloxacin, Nor). Interestingly, the well-known two global regulators, the soxR and the rpoE genes are present among 41 commonly upregulated genes under all 4 antibiotic-treatment conditions. We speculate that these common genes are essential for antibiotic resistance in DR1. Treatment with the 4 antibiotics produced diverse physiological and phenotypic changes. Km treatment induced the most dramatic phenotypic changes. Examination of mutation frequency and DNA-repair capability demonstrated the induction of the SOS response in Acinetobacter especially under Nor treatment. Based on the RNA-seq analysis, the glyoxylate-bypass genes of the citrate cycle were specifically upregulated under Amp treatment. We also identified newly recognized non-coding small RNAs of the DR1 strain, which were also confirmed by Northern blot analysis. These results reveal that treatment with antibiotics of distinct classes differentially affected the gene expression and physiology of DR1 cells. This study expands our understanding of the molecular mechanisms of antibiotic-stress response of environment-originated bacteria and provides a basis for future investigations.
    PLoS ONE 10/2014; 9(10):e110215. DOI:10.1371/journal.pone.0110215 · 3.23 Impact Factor
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    ABSTRACT: Non-culture-based procedures were used to investigate plasmids showing ampicillin resistance properties in two different environments: remote mountain soil (Mt. Jeombong) and sludge (Tancheon wastewater treatment plant). Total DNA extracted from the environmental samples was directly transformed into Escherichia coli TOP10, and a single and three different plasmids were obtained from the mountain soil and sludge samples, respectively. Interestingly, the restriction fragment length polymorphism pattern of the plasmid from the mountain soil sample, designated pEMB1, was identical to the pattern of one of the three plasmids from the sludge sample. Complete DNA sequencing of plasmid pEMB1 (8,744 bp) showed the presence of six open reading frames, including a β-lactamase gene. Using BLASTX, the orf5 and orf6 genes were suggested to encode a CopG family transcriptional regulator and a plasmid stabilization system, respectively. Functional characterization of these genes using a knockout orf5 plasmid (pEMB1ΔparD) and the cloning and expression of orf6 (pET21bparE) indicated that these genes were antitoxin (parD) and toxin (parE) genes. Plasmid stability tests using pEMB1 and pEMB1ΔparDE in E. coli revealed that the orf5 and orf6 genes enhanced plasmid maintenance in the absence of ampicillin. Using a PCR-based survey, pEMB1-like plasmids were additionally detected in samples from other human-impacted sites (sludge samples) and two other remote mountain soil samples, suggesting that plasmids harboring a β-lactamase gene with a ParD-ParE toxin-antitoxin system occurs broadly in the environment. This study extends knowledge about the dissemination and persistence of antibiotic resistance genes in naturally occurring microbial populations.
    Applied and Environmental Microbiology 10/2014; 81(1). DOI:10.1128/AEM.02691-14 · 3.67 Impact Factor
  • Source
    Hyerim Hong · Jaejoon Jung · Woojun Park
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    ABSTRACT: Acquisition of the extracellular tetracycline (TC) resistance plasmid pAST2 affected host gene expression and phenotype in the oil-degrading soil bacterium, Acinetobacter oleivorans DR1. Whole-transcriptome profiling of DR1 cells harboring pAST2 revealed that all the plasmid genes were highly expressed under TC conditions, and the expression levels of many host chromosomal genes were modulated by the presence of pAST2. The host energy burden imposed by replication of pAST2 led to (i) lowered ATP concentrations, (ii) downregulated expression of many genes involved in cellular growth, and (iii) reduced growth rate. Interestingly, some phenotypes were restored by deleting the plasmid-encoded efflux pump gene tetH, suggesting that the membrane integrity changes resulting from the incorporation of efflux pump proteins also resulted in altered host response under the tested conditions. Alteration of membrane integrity by tetH deletion was shown by measuring permeability of fluorescent probe and membrane hydrophobicity. The presence of the plasmid conferred peroxide and superoxide resistance to cells, but only peroxide resistance was diminished by tetH gene deletion, suggesting that the plasmid-encoded membrane-bound efflux pump protein provided peroxide resistance. The downregulation of fimbriae-related genes presumably led to reduced swimming motility, but this phenotype was recovered by tetH gene deletion. Our data suggest that not only the plasmid replication burden, but also its encoded efflux pump protein altered host chromosomal gene expression and phenotype, which also alters the ecological fitness of the host in the environment.
    PLoS ONE 09/2014; 9(9):e107716. DOI:10.1371/journal.pone.0107716 · 3.23 Impact Factor
  • Jisun Kim · Woojun Park
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    ABSTRACT: Pseudomonas putida is widely distributed in nature and is capable of degrading various organic compounds due to its high metabolic versatility. The survival capacity of P. putida stems from its frequent exposure to various endogenous and exogenous oxidative stresses. Oxidative stress is an unavoidable consequence of interactions with various reactive oxygen species (ROS)-inducing agents existing in various niches. ROS could facilitate the evolution of bacteria by mutating genomes. Aerobic bacteria maintain defense mechanisms against oxidative stress throughout their evolution. To overcome the detrimental effects of oxidative stress, P. putida has developed defensive cellular systems involving induction of stress-sensing proteins and detoxification enzymes as well as regulation of oxidative stress response networks. Genetic responses to oxidative stress in P. putida differ markedly from those observed in Escherichia coli and Salmonella spp. Two major redox-sensing transcriptional regulators, SoxR and OxyR, are present and functional in the genome of P. putida. However, the novel regulators FinR and HexR control many genes belonging to the E. coli SoxR regulon. Oxidative stress can be generated by exposure to antibiotics, and iron homeostasis in P. putida is crucial for bacterial cell survival during treatment with antibiotics. This review highlights and summarizes current knowledge of oxidative stress in P. putida, as a model soil bacterium, together with recent studies from molecular genetics perspectives.
    Applied Microbiology and Biotechnology 06/2014; 98(16). DOI:10.1007/s00253-014-5883-4 · 3.34 Impact Factor
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    Sangwon Han · Jaejoon Jung · Woojun Park
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    ABSTRACT: L-asparaginase from gram-positive bacteria has been poorly explored. We conducted recombinant overexpression and purification of L-asparaginase from Staphylococcus sp. OJ82 (SoAsn) isolated from Korean fermented seafood to evaluate its biotechnological potential as an anti-leukemic agent. SoAsn was expressed in Escherichia coli BL21 (DE3) with an estimated molecular mass of 37.5 kDa determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Consistent with asparaginase in gram-negative bacteria, Size-exclusion chromatography determined SoAsn as a homodimer. Interestingly, optimal temperature of SoAsn was 37°C and over 90% of activity retained between 37°C and 50°C, and its thermal stability range was narrower than that of commercial E. coli L-asparaginase (EcAsn). Both SoAsn and EcAsn were active between pH 9 and pH 10, although their overall pH-dependent enzyme activities were slightly different. The Km value of SoAsn was 2.2 mM, which is higher than that of EcAsn. Among 8 metals tested for enzyme activity, cobalt and magnesium were greatly enhanced the SoAsn and EcAsn activity, respectively. Interestingly, SoAsn retained more than 60% of its activity under 2M NaCl conditions, but the activity of EcAsn was reduced to 48%. Overall, biochemical characteristics of SoAsn was similar to those of EcAsn, but its kinetics, cofactor requirements, and NaCl tolerance differed from those of EcAsn.
    Journal of Microbiology and Biotechnology 05/2014; 24(8). DOI:10.4014/jmb.1405.05021 · 1.53 Impact Factor
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    ABSTRACT: A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using pyrosequencing 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, while there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure was not significantly affected by the presence of antibiotics or by the exposure of T. molitor larvae to a highly diverse soil bacteria community. A negative relationship was identified between bacterial diversity and ampicillin concentration; however, no negative relationship was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in the bacterial community size estimated using the 16S rRNA gene copy number. A detailed phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species. Some Spiroplasma species are known to be insect pathogens; however, the T. molitor larvae did not experience any harmful effects arising from the presence of Spiroplasma species, indicating that Spiroplasma in the gut of T. molitor larvae do not act as a pathogen to the host. A comparison with the bacterial communities found in other insects (Apis and Solenopsis) showed that the Spiroplasma species found in this study were specific to T. molitor.
    Journal of Microbiology and Biotechnology 05/2014; 24(7). · 1.53 Impact Factor
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    ABSTRACT: Bacterial community and metabolites were analyzed in a flatfish jeotgal, a Korean fermented seafood. Inverse relationship of pH and 16S rRNA gene copy number was identified during fermentation. Lactobacillus was the predominant bacterial genus. Increase of Firmicutes was a common characteristic shared by other fermented seafood. Fructose, glucose, and maltose were the major metabolites.
    Bioscience Biotechnology and Biochemistry 05/2014; 78(5):908-10. DOI:10.1080/09168451.2014.895659 · 1.06 Impact Factor
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    ABSTRACT: Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.
    Microbial Ecology 04/2014; 68(2). DOI:10.1007/s00248-014-0420-7 · 3.12 Impact Factor
  • Hyerim Hong · Woojun Park
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    ABSTRACT: Tetracycline (TC)-sensing bioreporters using green fluorescent protein (GFP) were generated in Escherichia coli and solvent-tolerant Acinetobacter oleivorans. A TC-inducible promoter, tetH promoter, and a TetR repressor of the pAST2 plasmid recovered from sludge were used to construct plasmid-based and chromosome-based bioreporters. Two host plasmids with a broad range, pRK415 and pBBR1MCS2, and three randomly chosen chromosomal sites were used to create the reporter strains. Although the copy numbers of the two plasmids in A. oleivorans were greater than those in E. coli, GFP expression from the tetH promoter and growth under TC were significantly higher in E. coli. Thus, the E. coli bioreporter had higher GFP expression driven by TC, and the two plasmids differed in terms of their sensitivity. Our data reflected mosaic evolution of the constructed plasmids, suggesting that the plasmid replication efficiency and the tetH promoter strength differed in the two different hosts. Among the tested TC compounds, doxycycline (DC) was the most effective in promoting GFP expression. qRT-PCR data confirmed that the expression of the tetH promoter in the original pAST2 plasmid produced the most rapid response to DC. E. coli- and A. oleivorans-based plasmid reporters could detect 5 and 30 nM DC, respectively. Insertion of the GFP reporter into different positions of the A. oleivorans chromosome resulted in variations of GFP expression. Our stable A. oleivorans chromosomal bioreporter was functional in the presence of toxic organic solvents. Furthermore, the field test showed that strain A. oleivorans DR1-Tet1 could act as a sensitive bioreporter in activated sludge for DC detection.
    Applied Microbiology and Biotechnology 02/2014; 98(11). DOI:10.1007/s00253-014-5566-1 · 3.34 Impact Factor
  • Sungjong Choi · Jaejoon Jung · Che Ok Jeon · Woojun Park
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    ABSTRACT: Bacteria belonging to the Staphylococcus genus reside in various natural environments; however, only disease-associated Staphylococcus strains have received attention while ecological function and physiologies of non-pathogenic strains were often neglected. Because high level of tolerance against NaCl is a common trait of Staphylococcus, we investigated the characteristics of halotolerance in Staphylococcus sp. OJ82 isolated from fermented seafood containing a high concentration of NaCl. Among the 292 isolates screened, OJ82 showed the highest β-galactosidase and extracellular protease activities under high-salt conditions. Comparative genomic analysis with other Staphylococcus strains showed that (a) replication origins are highly conserved, (b) the OJ82 strain has a high number of amino acid transport- and metabolism-related genes, and (c) OJ82 has many unique proteins (15 %) and 12 prophage-related genomic islands. RNA-seq analysis under high-salt conditions showed that genes involved in cell membranes, transport, osmotic stress, ATP synthesis, and translation are highly expressed. OJ82 may use the ribulose monophosphate pathway to detoxify some toxic intermediates under high-salt conditions. Six new and three known non-coding small RNAs of the OJ82 strain were also found in the RNA-seq analysis. Genomic and transcriptomic analyses identified target β-galactosidase and extracellular protease. Interestingly, the OJ82 strain became resistant to bacteriocin produced by the Bacillus strain only under high-salt conditions. Our data showed that the OJ82 strain adapted to high-salt conditions by expressing core cellular processes (translation, ATP production) and defense genes (membrane synthesis, compatible solute transports, ribulose monophosphate pathway) could survive bacteriocin exposure under high-salt conditions.
    Applied Microbiology and Biotechnology 12/2013; 98(2). DOI:10.1007/s00253-013-5436-2 · 3.34 Impact Factor
  • Hyerim Hong · Hyeok-Jin Ko · In-Geol Choi · Woojun Park
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    ABSTRACT: We used culture-dependent and culture-independent methods to extract previously undescribed plasmids harboring tetracycline (TC) resistance genes from activated sludge. The extracted plasmids were transformed into naturally competent Acinetobacter oleivorans DR1 to recover a non-Escherichia coli-based plasmid. The transformed cells showed 80-100-fold higher TC resistance than the wild-type strain. Restriction length polymorphism performed using 30 transformed cells showed four different types of plasmids. Illumina-based whole sequencing of the four plasmids identified three previously unreported plasmids and one previously reported plasmid. All plasmids carried TC resistance-related genes (tetL, tetH), tetracycline transcriptional regulators (tetR), and mobilization-related genes. As per expression analysis, TC resistance genes were functional in the presence of TC. The recovered plasmids showed mosaic gene acquisition through horizontal gene transfer. Membrane fluidity, hydrophobicity, biofilm formation, motility, growth rate, sensitivity to stresses, and quorum sensing signals of the transformed cells were different from those of the wild-type cells. Plasmid-bearing cells seemed to have an energy burden for maintaining and expressing plasmid genes. Our data showed that acquisition of TC resistance through plasmid uptake is related to loss of biological fitness. Thus, cells acquiring antibiotic resistance plasmids can survive in the presence of antibiotics, but must pay ecological costs.
    Microbial Ecology 12/2013; 67(2). DOI:10.1007/s00248-013-0343-8 · 3.12 Impact Factor
  • Jisun Kim · Woojun Park
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    ABSTRACT: Quorum sensing (QS)-dependent biofilm formation and motility were controlled by AqsR in Acinetobacter oleivorans DR1. QS-controlled phenotypes appeared to be inhibited by indole, and the aqsR mutant had the same phenotypes. We demonstrated that the turnover rate of AqsR became more rapid without the AHL signal and that indole could increase the expression of many protease and chaperone proteins. The addition of exogenous indole decreased the expression of two AqsR-targeted genes, which were AOLE_03905 (putative surface adhesion protein) and AOLE_11355 (L-asparaginase). The overexpression of AqsR in Escherichia coli was impossible with the indole treatment. Surprisingly, our [35S]-methionine pulse labeling data demonstrated that the stability and folding of the AqsR protein decreased in the presence of indole without changing the aqsR mRNA expression in E. coli. Interestingly, indole resulted in a loss of TraR-dependent traG expression in an Agrobacterium tumefaciens indicator strain. However, when indole was added after incubation with exogenous AHL, indole could not inhibit the TraR-dependent expression of the traG promoter. This indicated that AHL-bound TraR could be protective against indole, but TraR without AHL could not be active in the presence of indole. Here, we provided evidence for the first time showing that the indole effect on QS-controlled bacterial phenotypes is due to inhibited QS regulator folding and not a reduced QS signal.
    Microbiology 09/2013; 159(Pt_12). DOI:10.1099/mic.0.070615-0 · 2.56 Impact Factor
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    Jaejoon Jung · Woojun Park
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    ABSTRACT: Alishewanella species are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history of Alishewanella species is reflected in their genomes, we performed comparative genomic and transcriptomic analyses of A. jeotgali, A. aestuarii, and A. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred in A. jeotgali and A. agri but not in A. aestuarii. Habitat differentiation of A. agri from a marine environment to a terrestrial environment was proposed because the species-specific genes of A. agri were similar to those of soil bacteria, whereas those of A. jeotgali and A. aestuarii were more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses in Alishewanella species, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated that A. agri had a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2 Alishewanella species. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3 Alishewanella species. Our comparative genomic and transcriptomic data revealed that Alishewanella species have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways in Alishewanella species are highly conserved, although stress responses of each Alishewanella species differed under pectin culture conditions.
    Applied and Environmental Microbiology 08/2013; 79(20). DOI:10.1128/AEM.02350-13 · 3.67 Impact Factor
  • Jisun Kim · Jaemin Noh · Woojun Park
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    ABSTRACT: Antibiotic resistance of soil-borne Acinetobacter species has been poorly explored. In this study, norfloxacin resistance of a soil bacterium, Acinetobacter oleivorans DR1 was investigated. Frequencies of mutant appearance of all tested non-pathogenic Acinetobacter strains were lower than those of pathogenic strains under minimum inhibitory concentration (MIC). When the quinolone-resistance-determining region (QRDR) of the gyrA gene were examined, only one mutant (His78Asn) out of 10 resistant variants had a mutation. Whole transcriptome analysis using a RNA-seq demonstrated that genes involved in SOS response and DNA repair were significantly up-regulated by norfloxacin. Determining the MICs of survival cells after norfloxacin treatment confirmed some of those cells were indeed persister cells. Ten colonies, randomly selected from amongst those that survived in the presence of norfloxacin, did not exhibit increased MIC. Thus, both low mutation frequency of the target gene and SOS reponse under norfloxacin suggested that persister formation might contribute to resistance of DR1 against norfloxacin. Persister frequency increased without a change in MIC when stationary phase cells, low growth rates conditions, and growth deficient dnaJ mutant were used. Taken together, our comprehensive approach, which included mutational analysis of target gene, persister formation assays, and RNA sequencing, indicated that DR1 survival when exposed to norfloxacin is related not only to target gene mutation but also to persister formation possibly through upregulation of SOS response and DNA repair genes.
    Journal of Microbiology and Biotechnology 08/2013; 23(9). · 1.53 Impact Factor

Publication Stats

1k Citations
268.77 Total Impact Points


  • 2006–2015
    • Korea University
      • Department of Environmental Science and Ecological Engineering
      Sŏul, Seoul, South Korea
  • 2012
    • Seoul National University
      • Department of Biological Sciences
      Sŏul, Seoul, South Korea
    • Dongguk University
      • Department of Life Science
      Sŏul, Seoul, South Korea
  • 2009–2011
    • Chung-Ang University
      • School of Biological Sciences
      Seoul, Seoul, South Korea
  • 2002–2011
    • Cornell University
      • Department of Microbiology
      Ithaca, New York, United States
  • 2006–2008
    • Gyeongsang National University
      Shinshū, South Gyeongsang, South Korea