Lee SW

References (21)

Title : Eucalyptus globulus leaf-isolated isorhapontin serves as a natural insecticide via acetylcholinesterase inhibition - Park_2024_Pestic.Biochem.Physiol_200_105834
Author(s) : Park JY , Kang SD , Son YG , Kim JY , Lee G , Kim KD , Lee SW
Ref : Pestic Biochem Physiol , 200 :105834 , 2024
Abstract : Acetylcholinesterase (AChE) inhibitors cause insect death by preventing the hydrolysis of the neurotransmitter acetylcholine, which overstimulates the nervous system. In this study, isorhapontin, isolated from E. globulus leaves, was evaluated as a natural insecticide with AChE inhibition at 12.5 microM. Using kinetic analyses, we found that isorhapontin acted as a competitive inhibitor that binds to the active site of AChE. The inhibition constant (K(i)) was 6.1 microM. Furthermore, isorhapontin and resveratrol, which have basic skeletons, were predicted to bind to the active site of AChE via molecular docking. A comparison of the hydrogen bonding between the two stilbenes revealed characteristic differences in their interactions with amino acids. In isorhapontin, Trp83, Gly149, Tyr162, Tyr324, and Tyr370 interacted with the sugar moiety. These results suggest that with further development, isorhapontin can be used as an insecticide alternative.
ESTHER : Park_2024_Pestic.Biochem.Physiol_200_105834
PubMedSearch : Park_2024_Pestic.Biochem.Physiol_200_105834
PubMedID: 38582576

Title : Identification of a Second Type of AHL-lactonase from Rhodococcus sp. BH4, belonging to the alpha\/beta Hydrolase Superfamily - Ryu_2020_J.Microbiol.Biotechnol__
Author(s) : Ryu DH , Lee SW , Mikolaityte V , Kim YW , Jeong HY , Lee SJ , Lee CH , Lee JK
Ref : J Microbiol Biotechnol , : , 2020
Abstract : N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the alpha/beta hydrolase family. Purified recombinant JydB demonstrated a high hydrolytic activity against various AHLs. Kinetic analysis of JydB revealed a high catalytic efficiency (kcat/KM) against C4-HSL and 3-oxo-C6 HSL, ranging from 1.88 x 10(6) to 1.45 x 10(6) M(-1) s(-1), with distinctly low KM values (0.16 - 0.24 mM). This study affirms that the AHL degrading activity and biofilm inhibition ability of Rhodococcus sp. BH4 may be due to the presence of multiple quorum quenching enzymes, including two types of AHL-lactonases, in addition to AHL-acylase and oxidoreductase, for which the genes have yet to be described.
ESTHER : Ryu_2020_J.Microbiol.Biotechnol__
PubMedSearch : Ryu_2020_J.Microbiol.Biotechnol__
PubMedID: 32160697

Title : Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome - Kim_2019_PLoS.One_14_e0210298
Author(s) : Kim SH , Kang PA , Han K , Lee SW , Rhee S
Ref : PLoS ONE , 14 :e0210298 , 2019
Abstract : Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity. In this study, we determined the crystal structures of EstDL136 and in a complex with Cm. Consistent with the high sequence similarity, the structure of EstDL136 is homologous to that of the HSL family. The active site of EstDL136 is a relatively shallow pocket that could accommodate Cm as a substrate as opposed to the long acyl chain substrates typical of the HSL family. Mutational analyses further suggested that several residues in the vicinity of the active site play roles in the Cm-binding of EstDL136. These results provide structural and functional insights into a metagenome-derived EstDL136.
ESTHER : Kim_2019_PLoS.One_14_e0210298
PubMedSearch : Kim_2019_PLoS.One_14_e0210298
PubMedID: 30645605
Gene_locus related to this paper: 9bact-g3cr02

Title : Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum - Lee_2018_J.Biotechnol_270_30
Author(s) : Lee MH , Khan R , Tao W , Choi K , Lee SY , Lee JW , Hwang EC , Lee SW
Ref : J Biotechnol , 270 :30 , 2018
Abstract : Autoinducers are indispensable for bacterial cell-cell communication. However, due to the reliance on culture-based techniques, few autoinducer-hydrolyzing enzymes are known. In this study, we characterized soil metagenome-derived unique enzymes capable of hydrolyzing 3-hydroxypalmitic acid methyl ester (3-OH PAME), an autoinducer of the plant pathogenic bacterium Ralstonia solanacearum. Among 146 candidate lipolytic clones from a soil metagenome library, 4 unique enzymes capable of hydrolyzing the autoinducer 3-OH PAME, termed ELP86, ELP96, ELP104, and EstDL33, were selected and characterized. Phylogenetic analysis revealed that metagenomic enzymes were novel esterase/lipase candidates as they clustered as novel subfamilies of family I, V, X, and family XI. The purified enzymes displayed various levels of hydrolytic activities towards 3-OH PAME with optimum activity at 40-50 degrees C and pH 7-10. Interestingly, ELP104 also displayed N-(3-oxohexanoyl)-L-homoserine lactone hydrolysis activity. Heterologous expression of the gene encoding 3-OH PAME hydrolase in R. solanacearum significantly decreased exopolysaccharide production without affecting bacterial growth. mRNA transcription analysis revealed that genes regulated by quorum-sensing, such as phcA and xpsR, were significantly down-regulated in the stationary growth phase of R. solanacearum. Therefore, metagenomic enzymes are capable of quorum-quenching by hydrolyzing the autoinducer 3-OH PAME, which could be used as a biocontrol strategy against bacterial wilt.
ESTHER : Lee_2018_J.Biotechnol_270_30
PubMedSearch : Lee_2018_J.Biotechnol_270_30
PubMedID: 29407418
Gene_locus related to this paper: 9zzzz-a0a223he11 , 9zzzz-a0a223heg6 , 9zzzz-a0a223he13

Title : Inactivation of chloramphenicol and florfenicol by a novel chloramphenicol hydrolase - Tao_2012_Appl.Environ.Microbiol_78_6295
Author(s) : Tao W , Lee MH , Wu J , Kim NH , Kim JC , Chung E , Hwang EC , Lee SW
Ref : Applied Environmental Microbiology , 78 :6295 , 2012
Abstract : Chloramphenicol and florfenicol are broad-spectrum antibiotics. Although the bacterial resistance mechanisms to these antibiotics have been well documented, hydrolysis of these antibiotics has not been reported in detail. This study reports the hydrolysis of these two antibiotics by a specific hydrolase that is encoded by a gene identified from a soil metagenome. Hydrolysis of chloramphenicol has been recognized in cell extracts of Escherichia coli expressing a chloramphenicol acetate esterase gene, estDL136. A hydrolysate of chloramphenicol was identified as p-nitrophenylserinol by liquid chromatography-mass spectroscopy and proton nuclear magnetic resonance spectroscopy. The hydrolysis of these antibiotics suggested a promiscuous amidase activity of EstDL136. When estDL136 was expressed in E. coli, EstDL136 conferred resistance to both chloramphenicol and florfenicol on E. coli, due to their inactivation. In addition, E. coli carrying estDL136 deactivated florfenicol faster than it deactivated chloramphenicol, suggesting that EstDL136 hydrolyzes florfenicol more efficiently than it hydrolyzes chloramphenicol. The nucleotide sequences flanking estDL136 encode proteins such as amidohydrolase, dehydrogenase/reductase, major facilitator transporter, esterase, and oxidase. The most closely related genes are found in the bacterial family Sphingomonadaceae, which contains many bioremediation-related strains. Whether the gene cluster with estDL136 in E. coli is involved in further chloramphenicol degradation was not clear in this study. While acetyltransferases for chloramphenicol resistance and drug exporters for chloramphenicol or florfenicol resistance are often detected in numerous microbes, this is the first report of enzymatic hydrolysis of florfenicol resulting in inactivation of the antibiotic.
ESTHER : Tao_2012_Appl.Environ.Microbiol_78_6295
PubMedSearch : Tao_2012_Appl.Environ.Microbiol_78_6295
PubMedID: 22752166
Gene_locus related to this paper: 9bact-g3cr00 , 9bact-g3cr02

Title : Monitoring of carbamate and organophosphate resistance levels in Nilaparvata lugens based on bioassay and quantitative sequencing - Kwon_2012_J.Asia.Pac.Entomol_15_635
Author(s) : Kwon DH , Min S , Lee SW , Park JH , Lee SH
Ref : Journal of Asia-Pacific Entomology , 15 :635 , 2012
Abstract : The resistance levels to carbamate (CB) and organophosphate (OP) insecticides were determined by topical application in 14 field strains of Nilaparvata lugens. The resistance levels of N. lugens to CB and OP were 1.3 ~ 47.5-fold and 1.4 ~ 14.4-fold higher than a susceptible strain, respectively. A quantitative sequencing (QS) protocol was established to determine the allele frequencies of four acetylcholinesterase point mutations putatively associated with CB and OP resistance. The allele frequencies of the four mutations (G119A, F/Y330S, F331H and I332L) in field strains ranged from ca. 0.0 ~ 51.7%, 0.0 ~ 88.9%, 5.1 ~ 56.0% and 6.7 ~ 57.3%, respectively. The F331H and I332L were tightly linked to each other, suggesting that these mutations may occur simultaneously. In correlation analysis, G119A was not well correlated with actual resistance levels (r2 = < 0.232), whereas F331H and I332L showed a better correlation with the resistance levels of benzofuranyl methylcarbamates (r2 = 0.595). This finding indicates that F331H and I332L mutation frequencies may be used as molecular markers for detecting carbamate resistance in N. lugens. A QS protocol detecting the F331H and I332L mutation frequencies could therefore be employed as a supportive tool for the rapid monitoring of CB insecticide resistance levels in N. lugens.
ESTHER : Kwon_2012_J.Asia.Pac.Entomol_15_635
PubMedSearch : Kwon_2012_J.Asia.Pac.Entomol_15_635
PubMedID:

Title : Cloning of the acetylcholinesterase 1 gene and identification of point mutations putatively associated with carbofuran resistance in Nilaparvata lugens - Kwon_2012_Pestic.Biochem.Physiol_103_94
Author(s) : Kwon DH , Cha DJ , Kim YH , Lee SW , Lee SH
Ref : Pesticide Biochemistry and Physiology , 103 :94 , 2012
Abstract : Molecular mechanisms of carbofuran resistance in the brown planthopper, Nilaparvata lugens Stl, were investigated. A carbofuran-resistant strain (CAS) showed approximately 45.5- and 15.1-fold resistance compared with a susceptible strain (SUS) and a non-selected field strain (FM), respectively. Activities of the esterase and mixed-function oxidase were approximately 2.8- and 1.6-fold higher, respectively, in the CAS strain than in the SUS strain, suggesting that these enzymes play a minor role in carbofuran resistance. Interestingly, the insensitivity of acetylcholinesterase (AChE) to carbofuran was approximately 5.5- and 3.7-fold higher in the CAS strain compared to the SUS and FM strains, respectively, indicating that AChE insensitivity is associated with carbofuran resistance. Western blot analysis identified two kinds of AChEs, of which the type-1 AChE (encoded from Nlace1, which is paralogous to the Drosophila AChE gene) was determined to be the major catalytic AChE in N. lugens. The open reading frame of Nlace1 is composed of 1989 bp (approximately 74 kD) and revealed 52.5% and 24.3% amino acid sequence identities to those of Nephotettix cincticeps and Drosophila melanogaster, respectively. Screening of point mutations identified four amino acid substitutions (G119A, F/Y330S, F331H and H332L) in the CAS strain that likely contribute to AChE insensitivity. The frequencies of these mutations were well correlated with resistance levels, confirming that they are associated with reduced sensitivity to carbofuran in N. lugens. These point mutations can be useful as genetic markers for monitoring resistance levels in field populations of N. lugens.
ESTHER : Kwon_2012_Pestic.Biochem.Physiol_103_94
PubMedSearch : Kwon_2012_Pestic.Biochem.Physiol_103_94
PubMedID:
Gene_locus related to this paper: nillu-ACHE1

Title : Characterization of two metagenome-derived esterases that reactivate chloramphenicol by counteracting chloramphenicol acetyltransferase - Tao_2011_J.Microbiol.Biotechnol_21_1203
Author(s) : Tao W , Lee MH , Yoon MY , Kim JC , Malhotra S , Wu J , Hwang EC , Lee SW
Ref : J Microbiol Biotechnol , 21 :1203 , 2011
Abstract : Function-driven metagenomic analysis is a powerful approach to screening for novel biocatalysts. In this study, we investigated lipolytic enzymes selected from an alluvial soil metagenomic library, and identified two novel esterases, EstDL26 and EstDL136. EstDL26 and EstDL136 reactivated chloramphenicol from its acetyl derivates by counteracting the chloramphenicol acetyltransferase (CAT) activity in Escherichia coli. These two enzymes showed only 27% identity in amino acid sequence to each other; however both preferentially hydrolyzed short-chain p-nitrophenyl esters (< or =C5) and showed mesophilic properties. In vitro, EstDL136 catalyzed the deacetylation of 1- and 3- acetyl and 1,3-diacetyl derivates; in contrast, EstDL26 was not capable of the deacetylation at C1, indicating a potential regioselectivity. EstDL26 and EstDL136 were similar to microbial hormone-sensitive lipase (HSL), and since chloramphenicol acetate esterase (CAE) activity was detected from two other soil esterases in the HSL family, this suggests a distribution of CAE among the soil microorganisms. The isolation and characterization of EstDL26 and EstDL136 in this study may be helpful in understanding the diversity of CAE enzymes and their potential role in releasing active chloramphenicol in the producing bacteria.
ESTHER : Tao_2011_J.Microbiol.Biotechnol_21_1203
PubMedSearch : Tao_2011_J.Microbiol.Biotechnol_21_1203
PubMedID: 22210605
Gene_locus related to this paper: 9bact-g3cr00 , 9bact-g3cr02

Title : Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110 - Han_2011_J.Bacteriol_193_1183
Author(s) : Han JI , Choi HK , Lee SW , Orwin PM , Kim J , Laroe SL , Kim TG , O'Neil J , Leadbetter JR , Lee SY , Hur CG , Spain JC , Ovchinnikova G , Goodwin L , Han C
Ref : Journal of Bacteriology , 193 :1183 , 2011
Abstract : Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions.
ESTHER : Han_2011_J.Bacteriol_193_1183
PubMedSearch : Han_2011_J.Bacteriol_193_1183
PubMedID: 21183664
Gene_locus related to this paper: varps-c5cla8 , varps-c5cld3 , varps-c5cle8 , varps-c5cmg7 , varps-c5cmn3 , varps-c5cmq5 , varps-c5cn77 , varps-c5cpt8 , varps-c5cqf4 , varps-c5crj1 , varps-c5crm2 , varps-c5csa3 , varps-c5csp0 , varps-c5ct29 , varps-c5ct59 , varps-c5ctz6 , varps-c5cu01 , varps-c5cu02 , varps-c5cuk9 , varps-c5cw29 , varps-c5czm3 , varps-c5czm7 , varps-c5czs2 , varps-c5czw9 , varps-c5czx0 , varps-c5czz1 , varps-c5d0w2 , varps-c5d1f5 , varps-c5d1m4 , varps-c5d1p7 , varps-c5d1r3 , varps-c5d033 , varpd-t1x730 , varps-c5cyt5 , varps-rutd

Title : Isolation and characterization of a family VII esterase derived from alluvial soil metagenomic library - Tao_2011_J.Microbiol_49_178
Author(s) : Tao W , Lee MH , Wu J , Kim NH , Lee SW
Ref : J Microbiol , 49 :178 , 2011
Abstract : A novel esterase gene, estDL30, was isolated from an alluvial metagenomic library using function-driven screening. estDL30 consisted of 1,524 nucleotides and encoded a 507-amino acid protein. Sequence analysis revealed that EstDL30 is similar to many type B carboxylesterases, containing a G-E-S-A-G pentapeptide with a catalytic Ser residue. Phylogenetic analysis suggested that EstDL30 belongs to the family VII lipases, together with esterases from Bacillus subtilis (P37967), Streptomyces coelicolor A3(2) (CAA22794), and Arthrobacter oxydans (Q01470). Purified EstDL30 showed its highest catalytic efficiency toward p-nitrophenyl butyrate, with a k (cat) of 2293 s(-1) and k (cat)/K (m) of 176.4 s(-1)mM(-1); however, little activity was detected when the acyl chain length exceeded C(8). Biochemical characterization of EstDL30 revealed that it is an alkaline esterase that possesses maximal activity at pH 8 and 40 degrees C. The effects of denaturants and divalent cations were also investigated. EstDL30 tolerated well the presence of methanol and Tween 20. Its activity was strongly inhibited by 1 mM Cu(2+) and Zn(2+), but stimulated by Fe(2+). The unique properties of EstDL30, its high activity under alkaline conditions and stability in the presence of organic solvents, may render it applicable to organic synthesis.
ESTHER : Tao_2011_J.Microbiol_49_178
PubMedSearch : Tao_2011_J.Microbiol_49_178
PubMedID: 21538236
Gene_locus related to this paper: 9bact-g1ard1

Title : Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp - Bogdanove_2011_J.Bacteriol_193_5450
Author(s) : Bogdanove AJ , Koebnik R , Lu H , Furutani A , Angiuoli SV , Patil PB , Van Sluys MA , Ryan RP , Meyer DF , Han SW , Aparna G , Rajaram M , Delcher AL , Phillippy AM , Puiu D , Schatz MC , Shumway M , Sommer DD , Trapnell C , Benahmed F , Dimitrov G , Madupu R , Radune D , Sullivan S , Jha G , Ishihara H , Lee SW , Pandey A , Sharma V , Sriariyanun M , Szurek B , Vera-Cruz CM , Dorman KS , Ronald PC , Verdier V , Dow JM , Sonti RV , Tsuge S , Brendel VP , Rabinowicz PD , Leach JE , White FF , Salzberg SL
Ref : Journal of Bacteriology , 193 :5450 , 2011
Abstract : Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
ESTHER : Bogdanove_2011_J.Bacteriol_193_5450
PubMedSearch : Bogdanove_2011_J.Bacteriol_193_5450
PubMedID: 21784931
Gene_locus related to this paper: xanax-XAC4055 , xanca-CATD , xanca-estA1 , xanca-XCC0080 , xanca-XCC3164 , xanor-q5h5n1

Title : A new esterase EstD2 isolated from plant rhizosphere soil metagenome - Lee_2010_Appl.Microbiol.Biotechnol_88_1125
Author(s) : Lee MH , Hong KS , Malhotra S , Park JH , Hwang EC , Choi HK , Kim YS , Tao W , Lee SW
Ref : Applied Microbiology & Biotechnology , 88 :1125 , 2010
Abstract : Soil metagenome constitutes a reservoir for discovering novel enzymes from the unculturable microbial diversity. From three plant rhizosphere metagenomic libraries comprising a total of 142,900 members of recombinant plasmids, we obtained 14 recombinant fosmids that exhibited lipolytic activity. A selected recombinant plasmid, pFLP-2, which showed maximum lipolytic activity, was further analyzed. DNA sequence analysis of the subclone in pUC119, pELP-2, revealed an open reading frame of 1,191 bp encoding a 397-amino-acid protein. Purified EstD2 exhibited maximum enzymatic activity towards p-nitrophenyl butyrate, indicating that it is an esterase. Purified EstD2 showed optimal activity at 35 degC and at pH 8.0. The K(m) and K(cat) values were determined to be 79.4 uM and 120.5/s, respectively. The esterase exhibited an increase in enzymatic activity in the presence of 15% butanol and 15% methanol. Phylogenetic analysis revealed that the lipolytic protein EstD2 may be a member of a novel family of lipolytic enzymes. Several hypothetical protein homologs of EstD2 were found in the database. A hypothetical protein from Phenylobacterium zucineum HLK1, a close homolog of EstD2, displayed lipolytic activity when the corresponding gene was expressed in Escherichia coli. Our results suggest that the other hypothetical protein homologs of EstD2 might also be members of this novel family.
ESTHER : Lee_2010_Appl.Microbiol.Biotechnol_88_1125
PubMedSearch : Lee_2010_Appl.Microbiol.Biotechnol_88_1125
PubMedID: 20683720
Gene_locus related to this paper: 9bact-e2d695

Title : Genome sequences of Escherichia coli B strains REL606 and BL21(DE3) - Jeong_2009_J.Mol.Biol_394_644
Author(s) : Jeong H , Barbe V , Lee CH , Vallenet D , Yu DS , Choi SH , Couloux A , Lee SW , Yoon SH , Cattolico L , Hur CG , Park HS , Segurens B , Kim SC , Oh TK , Lenski RE , Studier FW , Daegelen P , Kim JF
Ref : Journal of Molecular Biology , 394 :644 , 2009
Abstract : Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
ESTHER : Jeong_2009_J.Mol.Biol_394_644
PubMedSearch : Jeong_2009_J.Mol.Biol_394_644
PubMedID: 19786035
Gene_locus related to this paper: eco57-b3a913 , ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-YfhR

Title : Characterization of carboxylesterase-mediated pirimicarb resistance in Myzus persicae - Kwon_2009_Pestic.Biochem.Physiol_93_120
Author(s) : Kwon DH , Choi BR , Lee SW , Clark JM , Lee SH
Ref : Pesticide Biochemistry and Physiology , 93 :120 , 2009
Abstract : The biochemical and molecular mechanisms of pirimicarb resistance were investigated in a pirimicarb-resistant (Pc-R) strain of Myzus persicae. The Pc-R strain showed a 131-fold resistance to pirimicarb but no or slight cross-resistance to other organophosphate and carbamate insecticides. Interestingly, the strain showed a moderate level of cross-resistance to neonicotinoids. Sequence analysis of the acetylcholinesterase (AChE) gene revealed that the Ser431Phe mutation, previously known to be associated with AChE insensitivity, was saturated in the Pc-R strain, and the AChE insensitivity caused by the mutation is likely a major pirimicarb resistance mechanism. In addition, detoxifying enzyme assays suggested that enhanced carboxylesterase (CbE) activity is associated with pirimicarb resistance as a supporting mechanism. The higher CbE activity in the Pc-R strain was determined to be mainly due to a pI 4.9 esterase by native isoelectricfocusing. The resistance-associated CbE was further identified as the E4 type by native two-dimensional gel electrophoresis in conjunction with matrix-assisted laser desorption ionization-time of flight mass spectrometry. The gene copy number and transcription level of the E4 CbE were increased 4.0- and 10.5-fold in the Pc-R strain, respectively, suggesting that both gene duplication and transcriptional regulation of E4 CbE are associated with pirimicarb resistance.
ESTHER : Kwon_2009_Pestic.Biochem.Physiol_93_120
PubMedSearch : Kwon_2009_Pestic.Biochem.Physiol_93_120
PubMedID:

Title : Molecular characterization of two acetylcholinesterase cDNAs in Pediculus human lice - Lee_2007_J.Med.Entomol_44_72
Author(s) : Lee SW , Kasai S , Komagata O , Kobayashi M , Agui N , Kono Y , Tomita T
Ref : Journal of Medical Entomology , 44 :72 , 2007
Abstract : Two cDNA sequences encoding Drosophila Ace-orthologous and -paralogous acetylcholinesterase precursors (AO- and AP-AChE precursors, respectively), were identified from the body louse, Pediculus humanus humanus L. In vitro inhibition studies with an insecticide-susceptible body louse strain exhibited a simplex inhibitory response of AChE. The I50 values of fenitroxon and carbaryl were estimated to be 2.2 and 1.9 microM for the susceptible lice, respectively. The mRNA level of AP-AChE gene was 3.1- and 9.3-fold higher than that of AO-AChE gene in the abdomen and the combined parts of the head and thorax, respectively, suggesting, due to its abundance, the potential significance of the AP-AChE isoform in Pediculus human lice in association with the efficacy of AChE-targeting pediculicides.
ESTHER : Lee_2007_J.Med.Entomol_44_72
PubMedSearch : Lee_2007_J.Med.Entomol_44_72
PubMedID: 17294923
Gene_locus related to this paper: pedhb-ACHE1 , pedhb-ACHE2 , pedhc-ACHE1 , pedhc-ACHE2

Title : A 12-week, double-blind, placebo-controlled trial of galantamine adjunctive treatment to conventional antipsychotics for the cognitive impairments in chronic schizophrenia - Lee_2007_Int.Clin.Psychopharmacol_22_63
Author(s) : Lee SW , Lee JG , Lee BJ , Kim YH
Ref : Int Clin Psychopharmacol , 22 :63 , 2007
Abstract : The objective of the study was to study the effects of acetylcholinesterase inhibitors on cognition in patients with schizophrenia. We conducted a 12-week, double-blind, placebo-controlled trial of galantamine as adjunctive treatment to conventional antipsychotic drugs on 24 patients with schizophrenia. The 24 patients had been stabilized on conventional antipsychotic drugs (chlorpromazine equivalent dose of 1390 mg/day) for a minimum of 3 months before their enrollment into the study. The patients were evaluated at baseline, and after 6 and 12 weeks using the Korean version of Mini Mental State Examination, Brief Psychiatric Rating Scale, and a standard neuropsychological battery. Compared with placebo, galantamine produced a small and nonsignificant change in the cognitive measures, but the score for recognition on the Rey Complex Figure Test improved significantly in patients given galantamine (P<0.05). Of the several domains of cognitive functions assessed, galantamine tended to improve the score for recognition on the Hopkins Verbal Learning Test and for color on the Stroop Test (P<0.1), but these results were not statistically significant. The scores on the Korean version of Mini Mental State Examination did not change significantly in patients with galantamine, and the psychiatric symptoms did not change. The addition of galantamine to the conventional antipsychotic medication of patients with schizophrenia does not produce a change in the cognitive function or state of psychopathology.
ESTHER : Lee_2007_Int.Clin.Psychopharmacol_22_63
PubMedSearch : Lee_2007_Int.Clin.Psychopharmacol_22_63
PubMedID: 17293705

Title : Selection and characterization of forest soil metagenome genes encoding lipolytic enzymes - Hong_2007_J.Microbiol.Biotechnol_17_1655
Author(s) : Hong KS , Lim HK , Chung EJ , Park EJ , Lee MH , Kim JC , Choi GJ , Cho KY , Lee SW
Ref : J Microbiol Biotechnol , 17 :1655 , 2007
Abstract : A metagenome is a unique resource to search for novel microbial enzymes from the unculturable microorganisms in soil. A forest soil metagenomic library using a fosmid and soil microbial DNA from Gwangneung forest, Korea, was constructed in Escherichia coli and screened to select lipolytic genes. A total of seven unique lipolytic clones were selected by screening of the 31,000-member forest soil metagenome library based on tributyrin hydrolysis. The ORFs for lipolytic activity were subcloned in a high copy number plasmid by screening the secondary shortgun libraries from the seven clones. Since the lipolytic enzymes were well secreted in E. coli into the culture broth, the lipolytic activity of the subclones was confirmed by the hydrolysis of p-nitrophenyl butyrate using culture broth. Deduced amino acid sequence analysis of the identified ORFs for lipolytic activity revealed that 4 genes encode hormone-sensitive lipase (HSL) in lipase family IV. Phylogenetic analysis indicated that 4 proteins were clustered with HSL in the database and other metagenomic HSLs. The other 2 genes and 1 gene encode non-heme peroxidase-like enzymes of lipase family V and a GDSL family esterase/lipase in family II, respectively. The gene for the GDSL enzyme is the first description of the enzyme from metagenomic screening.
ESTHER : Hong_2007_J.Microbiol.Biotechnol_17_1655
PubMedSearch : Hong_2007_J.Microbiol.Biotechnol_17_1655
PubMedID: 18156781
Gene_locus related to this paper: 9bact-bol3I1 , 9bact-b0l3i3

Title : Metabolism of PyracDofos in Housefly, Musca domestica - Lee_2005_J.Asia.Pac.Entomol_8_387
Author(s) : Lee SW , Shono T , Tashiro S , Ohta K
Ref : Journal of Asia-Pacific Entomology , 8 :387 , 2005
Abstract : In vivo metabolism of pyraclofos, (R, S)-[0-1-(4-chlorophenyl) pyrazol-4-yl O-ethyl S-n-propyl phosphorothioate], labeled with 14C on the benzene ring was studied in the housefly, Musca domestica. The metabolism of pyraclofos produced five main metabolites: EHP-CHP {1-(4-chlorophenyl) pyrazol-4-yl O-ethyl hydrogen phosphate}, formed by the cleavage of the n-propyl-S-P bond after oxidation of the S atom, CHP {1-(4-chlorophenyl)-4-hydroxy-pyrazole}, formed from cleavage of the P-O-aryl bond, CHP-sulfate, formed from the sulfate conjugate of CHP, CHP-glucose, formed from the glucose conjugate of CHP, and SHP-CHP {1-(4-chlorophenyl) pyrazol-4-yl S-n propyl hydrogen phosphorothioate}, formed from the cleavage of the P-O-ethyl bond. The proposed metabolic pathways of pyraclofos in the housefly are: cleavage of the P-O-aryl bond resulting in CHP and its conjugates, and cleavage of the P-S-n-propyl bond after oxidation of the sulfur atom resulting in EHP-CHP.
ESTHER : Lee_2005_J.Asia.Pac.Entomol_8_387
PubMedSearch : Lee_2005_J.Asia.Pac.Entomol_8_387
PubMedID:

Title : Screening for novel lipolytic enzymes from uncultured soil microorganisms - Lee_2004_Appl.Microbiol.Biotechnol_65_720
Author(s) : Lee SW , Won K , Lim HK , Kim JC , Choi GJ , Cho KY
Ref : Applied Microbiology & Biotechnology , 65 :720 , 2004
Abstract : The construction and screening of metagenomic libraries constitute a valuable resource for obtaining novel biocatalysts. In this work, we present the construction of a metagenomic library in Escherichia coli using fosmid and microbial DNA directly isolated from forest topsoil and screened for lipolytic enzymes. The library consisted of 33,700 clones with an average DNA insert size of 35 kb. Eight unique lipolytic active clones were obtained from the metagenomic library on the basis of tributyrin hydrolysis. Subsequently, secondary libraries in a high-copy-number plasmid were generated to select lipolytic subclones and to characterize the individual genes responsible for the lipolytic activity. DNA sequence analysis of six genes revealed that the enzymes encoded by the metagenomic genes for lipolytic activity were novel with 34-48% similarity to known enzymes. They had conserved sequences similar to those in the hormone-sensitive lipase family. Based on their deduced amino acid similarity, the six genes encoding lipolytic enzymes were further divided into three subgroups, the identities among which ranged from 33% to 45%. The six predicted gene products were successfully expressed in E. coli and secreted into the culture broth. Most of the secreted enzymes showed a catalytic activity for hydrolysis of p-nitrophenyl butyrate (C(4)) but not p-nitrophenyl palmitate (C(16)).
ESTHER : Lee_2004_Appl.Microbiol.Biotechnol_65_720
PubMedSearch : Lee_2004_Appl.Microbiol.Biotechnol_65_720
PubMedID: 15365646
Gene_locus related to this paper: 9bact-q6rjl0 , 9bact-q6rjl2 , 9bact-q6rjm3

Title : Inhibition of tumor cell growth by RTP\/rit42 and its responsiveness to p53 and DNA damage - Kurdistani_1998_Cancer.Res_58_4439
Author(s) : Kurdistani SK , Arizti P , Reimer CL , Sugrue MM , Aaronson SA , Lee SW
Ref : Cancer Research , 58 :4439 , 1998
Abstract : Through a differential screening technique, we have identified a cDNA clone with differential expression in normal versus tumor cells. This clone, designated rit42 (reduced in tumor, 42 kDa), was previously isolated as a homocysteine-inducible gene in human endothelial cells (RTP), and the same or a highly related androgen-responsive gene in mouse has also been identified. Both Northern blot analysis and in situ hybridization demonstrated a significantly diminished expression in tumor cells, including those derived from breast and prostate when compared with normal cells. It was shown that RTP/rit42 mRNA cycles with cell division, peaking at G1 and G2-M, with lower expression in S phase. The biphasic expression of RTP/rit42 mRNA was absent in tumor cells. Introduction of rit42 cDNA into human cancer cells reduced cell growth both in vitro and in nude mice. Moreover, analysis of a tetracycline-regulated p53-inducible system in null-p53 cell lines showed that RTP/rit42 mRNA expression increased concomitantly with p53 expression and followed a similar time course. In addition, DNA-damaging agents induced RTP/rit42 expression in a p53-dependent manner but independent of a p53-mediated G1 arrest. Immunofluorescence analysis of a FLAG epitope-tagged RTP/rit42 protein revealed a cytoplasmic localization pattern with redistribution to the nucleus upon DNA damage. We have localized RTP/rit42 to human chromosome 8q24.3. Taken together, these results are consistent with a growth inhibitory role for RTP/rit42, and its down-regulation may contribute to the tumor malignant phenotype.
ESTHER : Kurdistani_1998_Cancer.Res_58_4439
PubMedSearch : Kurdistani_1998_Cancer.Res_58_4439
PubMedID: 9766676
Gene_locus related to this paper: human-NDRG1

Title : [3H]nimodipine specific binding to cardiac myocytes and subcellular fractions - DePover_1983_Biochem.Biophys.Res.Commun_113_185
Author(s) : DePover A , Lee SW , Matlib MA , Whitmer K , Davis BA , Powell T , Schwartz A
Ref : Biochemical & Biophysical Research Communications , 113 :185 , 1983
Abstract : [3H]Nimodipine binding was studied in isolated myocytes from rat heart and in partially purified sarcolemma, sarcoplasmic reticulum and mitochondrial fractions from dog heart. In isolated myocytes, the density of [3H]nimodipine specific sites (10(6) per cell) was close to density of [3H]QNB sites (0.8 x 10(6) per cell) and higher than that of [3H]DHA sites (0.2 x 10(6) per cell). During subcellular fractionation, [3H]nimodipine binding did not copurify with plasma membrane markers. The highest densities were found in fractions enriched in sarcolemma or in sarcoplasmic reticulum. No specific binding was found in mitochondria. These results indicate that the localization of [3H]nimodipine sites is not restricted to areas of the plasma membrane rich in beta-adrenoceptors, muscarinic receptors and sodium pump sites.
ESTHER : DePover_1983_Biochem.Biophys.Res.Commun_113_185
PubMedSearch : DePover_1983_Biochem.Biophys.Res.Commun_113_185
PubMedID: 6860335