Ju-Hoon Lee

Kyung Hee University, Sŏul, Seoul, South Korea

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Publications (32)104.79 Total impact

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    ABSTRACT: Amylosucrase (AS), a glucosyltransferase of the glycoside hydrolase 13 family, does not require a nucleotide-activated sugar as a glucosyl-donor. A gene (drpas) of Deinococcus radiopugnans encoding a putative AS was identified and cloned for characterization. The amino acid sequence revealed that drpas exhibited 76 and 74% identities with AS genes from D. geothermalis and D. radiodurans, respectively. Recombinant DRpAS exhibited AS activities. The ratios of hydrolysis, polymerization, and isomerization reactions were 5.8:82.7:11.5 at 40°C. The DRpAS was highly thermostable and produced more polymerization products than AS from D. radiodurans although the optimum growth temperature of both strains is 30°C.
    Food science and biotechnology 12/2014; 23(6). · 0.70 Impact Factor
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    ABSTRACT: Staphylococcus aureus is an important food-borne pathogen that causes a diverse diseases ranging from minor infections to life threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames (ORFs), 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that the strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252 according to a whole genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real food-borne outbreak in South Korea. This report would be helpful to extend our understanding about genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in food-borne outbreak.
    Journal of microbiology and biotechnology. 10/2014;
  • Hye-Jin Ku, Ju-Hoon Lee
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    ABSTRACT: Metagenomic analysis of human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting V6 to V9 regions with 580-bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.
    Journal of Microbiology and Biotechnology 04/2014; · 1.40 Impact Factor
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    ABSTRACT: PM1, a novel virulent bacteriophage that infects Pectobacterium carotovorum subsp. carotovorum, was isolated. Its morphological features were examined by electron microscopy, which indicated that this phage belongs to the family Myoviridae. It has a 55,098-bp genome, including a 2,665-bp terminal repeat. A total of 63 open reading frames (ORFs) were predicted, but only 20 ORFs possessed homology with functional proteins. There is one tRNA coding region, and the GC-content of the genome is 44.9 %. Most ORFs in bacteriophage PM1 showed high homology to enterobacteria phage ΦEcoM-GJ1 and Erwinia phage νB EamM-Y2. Like these bacteriophages, PM1 encodes an RNA polymerase, which is a hallmark of T7-like phages. There is no integrase or repressor, suggesting that PM1 is a virulent bacteriophage.
    Archives of Virology 03/2014; · 2.28 Impact Factor
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    ABSTRACT: Due to the emergence of antibiotic-resistant strains, bacteriophages are considered to be an alternative approach for the control of pathogens. In this study, the bacteriophages BPS10C and BPS13 were isolated and characterized to investigate their ability to control food-borne pathogenic Bacillus cereus. Phage BPS13 exhibited slightly higher host lysis activity compared with phage BPS10C. In addition, phage BPS13 exhibited greater stability under various pH and temperature conditions. To extend our knowledge of the lysis of B. cereus by these phages, their genomes were completely sequenced and analyzed, revealing that these phage genomes encode endolysin and two tail lysins, which are likely involved in host lysis and invasion mechanisms, respectively. These lysis-related proteins may increase the bactericidal activities of these phages, suggesting that they may be good candidates for the potential control of B. cereus.
    Archives of Virology 03/2014; · 2.28 Impact Factor
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    ABSTRACT: Thermococcus sp. strain ES1 is an anaerobic, hyperthermophilic archaeon from a hydrothermal vent that catabolizes sugars and peptides and produces H2S from S°, H2, acetate and CO2 as its primary metabolites. We present the complete genome sequence of this strain (1,957,742bp) with a focus on its substrate utilization and metabolite production capabilities. The sequence will contribute to the development of heterotrophic archaea for bioenergy production and biogeochemical modeling in hydrothermal environments.
    Journal of Biotechnology 01/2014; · 3.18 Impact Factor
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    ABSTRACT: Xanthomonas axonopodis pv. glycines 8ra is a causal agent of bacterial pustule disease in soybean. This bacterium possesses transcription activator-like (TAL) effectors which are useful for genetic/protein engineering applications in higher organisms including plants and humans. Here, we report that the draft genome sequence consists of 5,337,885-bp double-stranded DNA encoding 4,674 open reading frames (ORFs) in 13 different contigs. This genome sequence would be useful in applications of TAL effectors in genetic engineering and in elucidating virulence factors against plants.
    Journal of Biotechnology 01/2014; · 3.18 Impact Factor
  • Ju-Hoon Lee, Hakdong Shin, Sangryeol Ryu
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    ABSTRACT: The Bacillus cereus group phages infecting B. cereus, B. anthracis, and B. thuringiensis (Bt) have been studied at the molecular level and, recently, at the genomic level to control the pathogens B. cereus and B. anthracis and to prevent phage contamination of the natural insect pesticide Bt. A comparative phylogenetic analysis has revealed three different major phage groups with different morphologies (Myoviridae for group I, Siphoviridae for group II, and Tectiviridae for group III), genome size (group I > group II > group III), and lifestyle (virulent for group I and temperate for group II and III). A subsequent phage genome comparison using a dot plot analysis showed that phages in each group are highly homologous, substantiating the grouping of B. cereus phages. Endolysin is a host lysis protein that contains two conserved domains: a cell-wall-binding domain (CBD) and an enzymatic activity domain (EAD). In B. cereus sensu lato phage group I, four different endolysin groups have been detected, according to combinations of two types of CBD and four types of EAD. Group I phages have two copies of tail lysins and one copy of endolysin, but the functions of the tail lysins are still unknown. In the B. cereus sensu lato phage group II, the B. anthracis phages have been studied and applied for typing and rapid detection of pathogenic host strains. In the B. cereus sensu lato phage group III, the B. thuringiensis phages Bam35 and GIL01 have been studied to understand phage entry and lytic switch regulation mechanisms. In this review, we suggest that further study of the B. cereus group phages would be useful for various phage applications, such as biocontrol, typing, and rapid detection of the pathogens B. cereus and B. anthracis and for the prevention of phage contamination of the natural insect pesticide Bt.
    Archives of Virology 11/2013; · 2.28 Impact Factor
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    ABSTRACT: A novel Vibrio vulnificus-infecting bacteriophage SSP002 belonging to the Siphoviridae family was isolated from the coastal area of the Yellow Sea of South Korea. Host range analysis revealed that the growth inhibition of phage SSP002 is relatively specific to V. vulnificus strains from both clinical and environmental samples. In addition, a one-step growth curve analysis and bacteriophage stability test revealed a latent period of 65 min and a burst size of 23 ± 2 PFU as well as broad temperature range (20-60°C) and pH (pH 3-12) stabilities. The Tn5 transposon random mutation of the V. vulnificus and the partial DNA sequencing of the Tn5-inserted regions revealed that the flhA, flhB, fliF and fleQ mutants are resistant to SSP002 phage infection, suggesting that the flagellum may be the host receptor for infection. The subsequent construction of specific gene-inactivated mutants (flhA, flhB, fliF, and fleQ) and their complementation experiments substantiated this. Previously the genome of phage SSP002 was completely sequenced and analyzed. Comparative genomic analysis of phage SSP002 and V. parahaemolyticus vB_VpaS_MAR10 showed difference among their tail-related genes, supporting different host range in the species level, even though their genome sequences are highly similar. An additional mouse survival test showed that the administration of SSP002 phage at a multiplicity of infection of 1,000 significantly protects mice up to 2 months from the infection of V. vulnificus, suggesting that this phage may be a good candidate for the development of biocontrol agents against V. vulnificus infection.
    Applied and Environmental Microbiology 11/2013; · 3.95 Impact Factor
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    ABSTRACT: To understand phage infection and host lysis mechanisms with pathogenic Salmonella, a novel Salmonella Typhimurium-targeting bacteriophage SPN9CC, belonging to the Podoviridae family, was isolated and characterized. The phage infects S. Typhimurium via the O-antigen of lipopolysaccharide (LPS) and forms clear plaques with cloudy centers due to lysogen formation. Phylogenetic analysis of phage major capsid proteins (MCPs) revealed that this phage is a member of lysogen-forming P22-like phage group. However, comparative genomic analysis of SPN9CC with P22-like phages indicated that their lysogeny control regions and host lysis gene clusters share very low identities, suggesting that lysogen formation and host lysis mechanisms may be diverse among phages in this group. Analysis of the expression of SPN9CC host cell lysis genes encoding holin, endolysin, and Rz/Rz1-like proteins individually or in combinations in S. Typhimurium and E. coli hosts revealed that collaboration of these lysis proteins is important for lysis of both hosts, and holin is a key protein. To further investigate the role of the lysogeny control region in phage SPN9CC, a ΔcI mutant (SPN9CCM) of phage SPN9CC was constructed. The mutant does not produce a cloudy center in the plaques, suggesting that this mutant phage is virulent and no longer temperate. Subsequent comparative one-step growth analysis and challenge assays revealed that SPN9CCM has shorter eclipse/latent periods and a larger burst size as well as higher host lysis activity than SPN9CC. The present work indicates the possibility of engineering temperate phages as promising biocontrol agents similar to virulent phages.
    Applied and Environmental Microbiology 11/2013; · 3.95 Impact Factor
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    ABSTRACT: For molecular study of marine bacteria Pseudoalteromonas phenolica using bacteriophage, a novel bacteriophage, TW1, belonging to the family Siphoviridae, was isolated, and its genome was completely sequenced and analyzed. The phage TW1 genome consists of 39,940-bp-length double-stranded DNA with a GC content of 40.19 %, and it was predicted to have 62 open reading frames (ORFs), which were classified into functional groups, including phage structure, packaging, DNA metabolism, regulation, and additional function. The phage life style prediction using PHACTS showed that it may be a temperate phage. However, genes related to lysogeny and host lysis were not detected in the phage TW1 genome, indicating that annotation information about P. phenolica phages in the genome databases may not be sufficient for the functional prediction of their encoded proteins. This is the first report of a P. phenolica-infecting phage, and this phage genome study will provide useful information for further molecular research on P. phenolica and its phage, as well as their interactions.
    Archives of Virology 07/2013; · 2.28 Impact Factor
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    ABSTRACT: Staphylococcus aureus is a well-known pathogen that causes several serious diseases in humans and animals. As part of the efforts to control this pathogen, a newly isolated bacteriophage, SA12, which specifically targets S. aureus, was characterized, and its genome was completely sequenced. Host range and bacteriophage challenge tests demonstrated its specific and efficient host lysis of S. aureus. The genome of phage SA12 consists of 42,902 bp length double-stranded DNA with 58 predicted ORFs-encoding phage structure, DNA manipulation, packaging, host lysis, and regulation proteins. The characterization and genome study of phage SA12 in this report is useful for understanding S. aureus-targeting bacteriophages and provides basic information for the further development of phage-based biocontrol agents against S. aureus.
    Virus Genes 06/2013; · 1.84 Impact Factor
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    ABSTRACT: A novel flagellatropic phage of Salmonella enterica serovar Typhimurium called iEPS5 was isolated and characterized. iEPS5 has an icosahedral head and a long non-contractile tail with a tail fiber. Genome sequencing revealed a double-stranded DNA of 59,254 bp having 73 open reading frames (ORFs). To identify the receptor for iEPS5, Tn5 transposon insertion mutants of S. Typhimurium SL1344 that were resistant to the phage were isolated. All of the phage-resistant mutants were found to have mutations in genes involved in flagellar formation, suggesting that the flagellum is the adsorption target of this phage. Analysis of phage infection using the ΔmotA mutant, which is flagellated but non-motile, demonstrated the requirement of flagellar rotation for iEPS5 infection. Further analysis of phage infection using the ΔcheY mutant revealed that iEPS5 could infect host bacteria only when the flagellum is rotating counterclockwise (CCW). These results suggested that the CCW-rotating flagellar filament is essential for phage adsorption and required for successful infection by iEPS5. In contrast to the well-studied flagellatropic phage Chi, iEPS5 cannot infect the ΔfliK mutant that makes a polyhook without a flagellar filament, suggesting that these two flagellatropic phages utilize different infection mechanisms. Here, we present evidences that iEPS5 may inject its DNA into the flagellar filament for infection by assessing DNA transfer from SYBR-gold-labeled iEPS5 to the host bacteria.
    Applied and Environmental Microbiology 06/2013; · 3.95 Impact Factor
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    ABSTRACT: A cryptic plasmid, pMBLR00, from Leuconostoc mesenteroides subsp. mesenteroides KCTC 3733 was isolated, characterized, and used for the construction of a cloning vector to engineer Leuconostoc species. pMBLR00 is a rolling circle replication plasmid, containing 3,370 base pairs. Sequence analysis revealed that pMBLR00 has 3 open reading frames: Cop (copy number control protein), Rep (replication protein), and Mob (mobilization protein). pMBLR00 replicates by rolling circle replication, which was confirmed by the presence of a conserved double-stranded origin and single-stranded DNA intermediates. An Escherichia coli-Leuconostoc shuttle vector, pMBLR02, was constructed and was able to replicate in Leuconostoc citreum 95. pMBLR02 could be a useful genetic tool for metabolic engineering and the genetic study of Leuconostoc species.
    Journal of Microbiology and Biotechnology 05/2013; · 1.40 Impact Factor
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    ABSTRACT: Bacillus cereus causes food poisoning, resulting in vomiting and diarrhea, due to production of enterotoxins. As a means of controlling this food-borne pathogen, the virulent bacteriophage B4 was isolated and characterized. Bacterial challenge assays showed that phage B4 effectively inhibited growth of members of the B. cereus group as well as B. subtilis, and growth inhibition persisted for over 20 h. One-step growth analysis also revealed the host lysis activity of phage B4, with relatively short eclipse/latent times (10/15 min) and a large burst size (>200 PFU). The complete genome of phage B4, containing a 162-kb DNA with 277 ORFs, was analyzed. The endolysin encoded by the phage B4 genome accounts for the cell lysis activity of this phage. These results suggest that phage B4 has potential as a biological agent to control B. cereus propagation.
    Archives of Virology 05/2013; · 2.28 Impact Factor
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    ABSTRACT: Bacteriophage chi is a well-known phage that infects pathogens such as E. coli, Salmonella, and Serratia via bacterial flagella. To further understand its host-phage interaction and infection mechanism via host flagella, the genome was completely sequenced and analyzed. The phage genome contains 59,407-bp-length DNA with a GC content of 56.51 %, containing 75 open reading frames (ORFs) with no tRNA genes. Its annotation and functional analysis revealed that chi is evolutionarily very closely related to Enterobacter phage Enc34 and Providencia phage Redjac. However, most of the annotated genes encode hypothetical proteins, indicating that further genomic study of phage chi is required to elucidate the bacterial-flagellum-targeting infection mechanism of phage chi.
    Archives of Virology 04/2013; · 2.28 Impact Factor
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    ABSTRACT: Plasmid isolation of kimchi-derived Weissella cibaria KLC140 revealed six different plasmids. The smallest plasmid, pKW2124, was DNA sequenced and characterized, showing 2,124 bp with a GC content of 36.39% and five putative open reading frames (ORFs). In silico analysis of these ORFs showed ORF1 encodes a putative replication protein similar to rolling circular replication proteins from other lactic acid bacteria. However, a single-stranded intermediate was not detected when S1 nuclease was treated, suggesting it may follow theta replication. Interestingly, the replication initiation site of this plasmid is 100% identical to other plasmids from lactic acid bacteria, suggesting it may function for replication initiation. To construct a surface layer expression vector, pTSLGFP, slpA encoding the surface layer protein from Lactobacillus acidophilus was PCR amplified and fused with the gfp gene, forming a SLGFP fused gene. The plasmid pKW2124 was cloned into the XbaI site of pUC19, forming an Weissella-E. coli shuttle vector pKUW22. NheI-linearized pTSLGFP was ligated into pKUWCAT containing pKUW22 and the chloramphenicol acetyltransferase gene from pEK104, resulting in an 8.6 kb pKWCSLGFP surface layer expression vector. After transformation of this vector into W. cibaria KLC140, a GFP fluorescence signal was detected on the surface of the transformant, substantiating production of SLGFP fused protein and its secretion. This is the first report for construction of a Weissella surface layer expression vector, which may be useful for surface layer production of beneficial proteins in Weissella.
    Journal of Microbiology and Biotechnology 04/2013; 23(4):545-54. · 1.40 Impact Factor
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    ABSTRACT: Determination of the complete nucleotide sequence of a cryptic plasmid pMBLT00 from Leuconostoc mesenteriodes subsp. mesenteroides KCTC13302 revealed that it contains 20,721 base pairs (bp), a G + C content of 38.7%, and 18 open reading frames. Comparative sequence and mung been nuclease analyses of pMBLT00 showed that pMBLT00 replicates via the theta replication mechanism. A new, stable E. coli-Leuconostoc shuttle vector pMBLT02, which was constructed from a theta-replicating pMBLT00 replicon and an erythromycin resistance gene of pE194, was successfully introduced into Leuconostoc, Lactococcus lactis, and Pediococcus. This shuttle vector was used to engineer L. citreum 95 to overproduce d-lactate. The L. citreum 95 strain engineered using the plasmid pMBLT02 that overexpresses d-LDH exhibited enhanced production of optically pure d-lactate (61 g/L), 6-times more than that produced by the control strain, when cultured in a reactor supplemented with 140 g/L glucose. Therefore, the shuttle vector pMBLT02 can serve as a useful and stable plasmid vector for further development of a d-lactate overproduction system in other Leuconostoc strains and Lactococcus lactis.
    Applied and Environmental Microbiology 12/2012; · 3.95 Impact Factor
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    ABSTRACT: Pectobacterium carotovorum subsp. carotovorum, a member of the Enterobacteriaceae family, is an important plant-pathogenic bacterium causing significant economic losses worldwide. P. carotovorum subsp. carotovorum bacteriophage My1 was isolated from a soil sample. Its genome was completely sequenced and analyzed for the development of an effective biological control agent. Sequence and morphological analyses revealed that phage My1 is a T5-like bacteriophage and belongs to the family Siphoviridae. To date, there is no report of a Pectobacterium-targeting siphovirus genome sequence. Here, we announce the complete genome sequence of phage My1 and report the results of our analysis.
    Journal of Virology 10/2012; 86(20):11410-1. · 5.08 Impact Factor
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    ABSTRACT: Thermococcus sp. strain CL1 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a Paralvinella sp. polychaete worm living on an active deep-sea hydrothermal sulfide chimney on the Cleft Segment of the Juan de Fuca Ridge. To further understand the distinct characteristics of this archaeon at the genome level, its genome was completely sequenced and analyzed. Here, we announce the complete genome sequence (1,950,313 bp) of Thermococcus sp. strain CL1, with a focus on H(2)- and energy-producing capabilities and its amino acid biosynthesis and acquisition in an extreme habitat.
    Journal of bacteriology 09/2012; 194(17):4769-70. · 3.94 Impact Factor

Publication Stats

100 Citations
104.79 Total Impact Points

Institutions

  • 2012–2014
    • Kyung Hee University
      • Department of Food Science and Technology
      Sŏul, Seoul, South Korea
    • Institute for Mediterranean and Subtropical Horticulture "La Mayora"
      Málaga, Andalusia, Spain
    • National Academy of Agricultural Science (South Korea)
      Sŏul, Seoul, South Korea
    • University of Massachusetts Amherst
      • Department of Microbiology
      Amherst Center, Massachusetts, United States
  • 2013
    • Konkuk University
      • Division of Biological Sciences
      Sŏul, Seoul, South Korea
  • 2011–2013
    • Seoul National University
      • • Department of Agricultural Biotechnology
      • • Department of Food and Animal Biotechnology
      Seoul, Seoul, South Korea