Biomedical subjects

Tae-Kwang Oh

Publications and source records attributed to Tae-Kwang Oh.

At least 19 recordsLinked to original sources

PubMed2006

MELDB: a database for microbial esterases and lipases.

MELDB is a comprehensive protein database of microbial esterases and lipases which are hydrolytic enzymes important in the modern industry. Proteins in MELDB are clustered into groups according to their sequence similarities based on a local pairwise alignment algorithm and a graph clustering algorithm (TribeMCL). This differs from traditional approaches that use global pairwise alignment and joining methods. Our procedure was able to reduce the noise caused by dubious alignment in the distantly related or unrelated regions in the sequences. In the database, 883 esterase and lipase sequences derived from microbial sources are deposited and conserved parts of each protein are identified. HMM profiles of each cluster were generated to classify unknown sequences. Contents of the database can be keyword-searched and query sequences can be aligned to sequence profiles and sequences themselves.

Amino Acid Sequence↗

PubMed2006

Brevundimonas kwangchunensis sp. nov., isolated from an alkaline soil in Korea.

Two Gram-negative, rod-shaped bacterial strains, KSL-102T and KSL-110, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by use of a polyphasic study. The two strains grew optimally at pH 7.0-8.0 and 30 degrees C without NaCl. They contained Q-10 as the predominant ubiquinone. The major fatty acids were C(18:1)omega7c and C(16:0) on trypticase soy agar, but 11-methyl C(18:1)omega7c was also a major component when the two strains were cultivated on LMG medium no. 221. Their DNA G + C contents were 68.4-68.7 mol%. Strains KSL-102T and KSL-110 exhibited three nucleotide differences in their 16S rRNA gene sequences and a mean DNA-DNA relatedness value of 85 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the two strains fell within the evolutionary radiation encompassed by the genus Brevundimonas. Levels of 16S rRNA gene sequence similarity between the two strains and the type strains of recognized Brevundimonas species ranged from 96.3 to 98.4%. DNA-DNA relatedness levels between the two strains and recognized Brevundimonas species were 8-21%. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-102T and KSL-110 were classified in the genus Brevundimonas as members of a novel species, for which the name Brevundimonas kwangchunensis sp. nov. is proposed. The type strain is KSL-102T (= KCTC 12380T = DSM 17033T).

Caulobacteraceae↗

PubMed2006

Gaetbulimicrobium brevivitae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat of the Yellow Sea in Korea.

A Gram-negative, non-spore-forming and rod-shaped gliding bacterium, designated strain SMK-19T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain SMK-19T grew optimally at 37 degrees C, in the presence of 2-3 % (w/v) NaCl and at pH 7.0-8.0. It contained MK-6 as the predominant menaquinone, and iso-C(17 : 0) 3-OH and iso-C(15 : 0) as the major fatty acids. Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and an amino-group-containing lipid that is ninhydrin-positive. The DNA G+C content was 36.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain SMK-19T formed a distinct evolutionary lineage within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain SMK-19T exhibited similarity values of <94.4 % to those of other members of the family Flavobacteriaceae. Strain SMK-19T was distinguished from phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic, phylogenetic and chemotaxonomic data, SMK-19T (= KCTC 12390T = DSM 17196T) was classified at the type strain of a novel genus and species, Gaetbulimicrobium brevivitae gen. nov., sp. nov.

Base Composition↗

PubMed2006

Dokdonella koreensis gen. nov., sp. nov., isolated from soil.

Two Gram-negative, motile, non-spore-forming and rod-shaped bacterial strains, DS-123T and DS-140, were isolated from soil and their taxonomic positions were investigated by a polyphasic study. Strains DS-123T and DS-140 grew optimally at 30 degrees C and pH 6.5 without NaCl. They contained Q-8 as the predominant ubiquione and iso-C(17 : 1)omega9c, iso-C(17 : 0) and iso-C(15 : 0) as the major fatty acids. Major polar lipids detected in the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an amino-group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 71.0 mol%. Strains DS-123T and DS-140 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA-DNA relatedness level of 92 %. Phylogenetic trees based on 16S rRNA gene sequences showed that strains DS-123T and DS-140 formed a distinct evolutionary lineage within the Gammaproteobacteria. The 16S rRNA gene sequences of strains DS-123T and DS-140 exhibited similarity values of less than 94.1 % to members of the Gammaproteobacteria. Strains DS-123T and DS-140 were distinguished from phylogenetically related genera by differences in some phenotypic properties. On the basis of phenotypic, phylogenetic and genetic data, it is proposed that strains DS-123T (= KCTC 12396T = DSM 17203T) and DS-140 be classified in a novel genus and species, Dokdonella koreensis gen. nov., sp. nov.

Base Composition↗

PubMed2006

Polaribacter dokdonensis sp. nov., isolated from seawater.

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5(T), was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25-28 degrees C and in the presence of 2 % (w/v) NaCl. Strain DSW-5(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0), iso-C(15 : 1) and iso-C(15 : 0) 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G + C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5(T) was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5(T) and the type strains of recognized Polaribacter species were in the range 96.2-96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5(T) (=KCTC 12392(T) = DSM 17204(T)) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

Flavobacteriaceae↗

PubMed2006

Porphyrobacter dokdonensis sp. nov., isolated from sea water.

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-74T, was isolated from sea water off the island of Dokdo, Korea, and its taxonomic position was investigated by a polyphasic study. Strain DSW-74T grew optimally at 37 degrees C and in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C17 : 1omega6c and C18 : 1omega7c as the major fatty acids. Its DNA G+C content was 65.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-74T was most closely related to Porphyrobacter species. Similarity values between the 16S rRNA gene sequence of strain DSW-74T and those of the type strains of recognized Porphyrobacter species and of Erythromicrobium ramosum were in the range 97.4-98.7 %. Strain DSW-74T exhibited 16S rRNA gene sequence similarity values of <97.5 % to recognized Erythrobacter species and the other species used in the phylogenetic analysis. DNA-DNA relatedness levels and differential phenotypic properties made it possible to categorize strain DSW-74T as representing a novel Porphyrobacter species. On the basis of the taxonomic data presented, it is proposed that DSW-74T (=KCTC 12395T=DSM 17193T) should be classified in the genus Porphyrobacter as the type strain of a novel species, Porphyrobacter dokdonensis sp. nov.

Alphaproteobacteria↗

PubMed2006

Donghaeana dokdonensis gen. nov., sp. nov., isolated from sea water.

A Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, DSW-6T, was isolated from sea water and subjected to a polyphasic study. Strain DSW-6T grew optimally at 25 degrees C, in the presence of 2 % (w/v) NaCl and at pH 7.0-8.0. It was characterized chemotaxonomically as having MK-6 as the predominant menaquinone and iso-C(15 : 0), anteiso-C(15 : 0), iso-C(17 : 0) 3-OH and C(15 : 0) as the major fatty acids (>10 % of total fatty acids). Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and amino-group-containing lipids that are ninhydrin-positive. The DNA G+C content was 36.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DSW-6(T) forms an independent line of descent within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain DSW-6T exhibited similarity values of less than 94.7 % to the sequences of other members of the family Flavobacteriaceae. Strain DSW-6T could be distinguished from other phylogenetically related genera by differences in several phenotypic properties. Therefore, in view of the combined phenotypic and phylogenetic data, it is proposed that strain DSW-6T (= KCTC 12402T = DSM 17205T) represents a novel genus and species, Donghaeana dokdonensis gen. nov., sp. nov.

Base Composition↗

PubMed2006

Colwellia aestuarii sp. nov., isolated from a tidal flat sediment in Korea.

A novel Colwellia-like bacterial strain, SMK-10T, was isolated from a tidal flat sediment in Korea and subjected to a polyphasic taxonomic analysis. Cells of strain SMK-10T were Gram-negative, motile, greyish yellow-pigmented, curved rods. Optimal growth occurred at 25-30 degrees C and in the presence of 2-3 % (w/v) NaCl. Strain SMK-10T contained Q-8 as the predominant ubiquinone and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, C(17 : 1), C(15 : 1) and iso-C(16 : 0) as major fatty acids. The DNA G+C content was 39.3 mol%. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain SMK-10T belonged to the genus Colwellia. 16S rRNA gene sequence similarity values (94.7-96.7 %) to the type strains of all other Colwellia species and various differential phenotypic properties were sufficient to distinguish strain SMK-10T from recognized Colwellia species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain SMK-10T (= KCTC 12480T = DSM 17314T) is classified as the type strain of a novel Colwellia species, for which the name Colwellia aestuarii sp. nov. is proposed.

Alteromonas↗

PubMed2006

Nocardioides lentus sp. nov., isolated from an alkaline soil.

Gram-positive, rod- or coccoid-shaped bacterial strains KSL-17T, KSL-18 and KSL-19 were isolated from an alkaline soil in Korea. They were subjected to analysis using polyphasic taxonomy. Strains KSL-17T, KSL-18 and KSL-19 grew optimally at pH 8.0 and 28 degrees C and in the presence of 0.5 % (w/v) NaCl. They were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C(16 : 0) as the major fatty acid. Their DNA G+C contents were in the range 74.6-74.8 mol%. Strains KSL-17T, KSL-18 and KSL-19 were identical in terms of their 16S rRNA gene sequences and exhibited a mean level of DNA-DNA relatedness of 85-90 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-17T, KSL-18 and KSL-19 formed a distinct phylogenetic lineage within the genus Nocardioides. The levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species were in the range 92.6-95.2 %. On the basis of phenotypic, genetic and phylogenetic data, strains KSL-17T (= KCTC 19039T = DSM 16315T), KSL-18 and KSL-19 should be classified as members of a novel species of the genus Nocardioides, for which the name Nocardioides lentus sp. nov. is proposed.

Actinobacteria↗

PubMed2006

Variovorax dokdonensis sp. nov., isolated from soil.

A Gram-negative, motile and oval- or rod-shaped bacterial strain, DS-43T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. The strain grew optimally at pH 7.0-8.0 and at 30 degrees C in the presence of 0.5 % (w/v) NaCl. Strain DS-43T had Q-8 as the predominant ubiquinone and C(16 : 0), C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)omega7c and C(17 : 0) cyclo as the major fatty acids, which are consistent with the corresponding data for the type strain (KCTC 12459T) of Variovorax paradoxus. The DNA G+C content was 66.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-43T was most closely related to Variovorax paradoxus, the only recognized species of the genus. The level of 16S rRNA gene sequence similarity between strain DS-43T and V. paradoxus IAM 12373T was 97.3 %. DNA-DNA relatedness data and differential phenotypic properties demonstrated that strain DS-43T is distinguishable from V. paradoxus. On the basis of phenotypic, phylogenetic and genetic data, it is proposed that strain DS-43T (=KCTC 12544T = CIP 108838T) be classified in the genus Variovorax as a member of a novel species, Variovorax dokdonensis sp. nov.

Comamonadaceae↗

PubMed2006

Stenotrophomonas dokdonensis sp. nov., isolated from soil.

A Gram-negative, rod-shaped, Stenotrophomonas-like bacterial strain, DS-16(T), was isolated from soil from Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-16(T) grew optimally at pH 6.0-7.0 and 30 degrees C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 1)omega9c as the major fatty acids. The DNA G + C content was 65.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-16(T) joined the cluster comprising Stenotrophomonas species. The levels of 16S rRNA gene sequence similarity between strain DS-16(T) and the type strains of Stenotrophomonas species ranged from 95.5 to 97.5 %. DNA-DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of strain DS-16(T), demonstrated that this novel strain differs from Stenotrophomonas species with validly published names. On the basis of phenotypic, phylogenetic and genetic data, strain DS-16(T) (=KCTC 12543(T) = CIP 108839(T)) should be classified in the genus Stenotrophomonas as a member of a novel species, for which the name Stenotrophomonas dokdonensis sp. nov. is proposed.

DNA, Bacterial↗

PubMed2006

Algoriphagus terrigena sp. nov., isolated from soil.

A Gram-negative, non-motile, non-spore-forming bacterial strain, DS-44T, was isolated from soil from Dokdo in Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 degrees C and in the presence of 2 % (w/v) NaCl. Strain DS-44T contained MK-7 as the predominant menaquinone and iso-C(15 : 0) and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH as the major fatty acids. The DNA G+C content was 49.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-44T belongs to the genus Algoriphagus of the phylum Bacteroidetes. Similarity values between the 16S rRNA gene sequences of strain DS-44T and those of the type strains of recognized Algoriphagus species were in the range 93.8-95.7 %, making it possible to categorize strain DS-44T as a species that is separate from previously described Algoriphagus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-44T (=KCTC 12545T = CIP 108837T) was classified in the genus Algoriphagus as the type strain of a novel species, for which the name Algoriphagus terrigena sp. nov. is proposed.

Cytophagaceae↗

PubMed2006

Flavobacterium soli sp. nov., isolated from soil.

A Gram-negative, rod-shaped Flavobacterium-like bacterial strain, DS-6T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-6T grew optimally at pH 7.0 and 25 degrees C in the presence of 0-0.5 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15:0 and iso-C17:0 3-OH as the major fatty acids. The DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DS-6T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-6T and the type strains of Flavobacterium species were below 95.4 %. Strain DS-6T differed from some phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, DS-6T (=KCTC 12542T=CIP 108840T) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium soli sp. nov. is proposed.

Bacterial Typing Techniques↗

PubMed2006

Pedobacter sandarakinus sp. nov., isolated from soil.

A Gram-negative, non-motile, rod-shaped bacterial strain, designated DS-27(T), was isolated from a soil sample, and its taxonomic position was investigated by using a polyphasic approach. The organism grew optimally at 30 degrees C and in the presence of 0-0.5 % (w/v) NaCl. Strain DS-27(T) contained MK-7 as the predominant menaquinone and iso-C(15 : 0), C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH and iso-C(17 : 0) 3-OH as the major fatty acids. The DNA G + C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-27(T) is most closely related to the genus Pedobacter of the family Sphingobacteriaceae. Similarity values between the 16S rRNA gene sequences of strain DS-27(T) and the type strains of recognized Pedobacter species ranged from 90.6 to 95.5 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to categorize strain DS-27(T) as representing a species that is separate from recognized Pedobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-27(T) (=KCTC 12559(T) = CIP 108922(T)) was classified in the genus Pedobacter as a member of a novel species, for which the name Pedobacter sandarakinus sp. nov. is proposed.

Culture Media↗

PubMed2005

The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase.

In many Gram-negative bacteria, including a number of pathogens such as Pseudomonas aeruginosa and Erwinia carotovora, virulence factor production and biofilm formation are linked to the quorum-sensing systems that use diffusible N-acyl-L-homoserine lactones (AHLs) as intercellular messenger molecules. A number of organisms also contain genes coding for lactonases that hydrolyze AHLs into inactive products, thereby blocking the quorum-sensing systems. Consequently, these enzymes attract intense interest for the development of antiinfection therapies. However, the catalytic mechanism of AHL-lactonase is poorly understood and subject to controversy. We here report a 2.0-angstroms resolution structure of the AHL-lactonase from Bacillus thuringiensis and a 1.7-angstroms crystal structure of its complex with L-homoserine lactone. Despite limited sequence similarity, the enzyme shows remarkable structural similarities to glyoxalase II and RNase Z proteins, members of the metallo-beta-lactamase superfamily. We present experimental evidence that AHL-lactonase is a metalloenzyme containing two zinc ions involved in catalysis, and we propose a catalytic mechanism for bacterial metallo-AHL-lactonases.

Bacillus thuringiensis↗

PubMed2005

Zinc in lipase L1 from Geobacillus stearothermophilus L1 and structural implications on thermal stability.

Lipase L1 from Geobacillus stearothermophilus L1 contains an unusual extra domain, making a tight intramolecular interaction with the main catalytic domain through a Zn2+-binding coordination. To elucidate the role of the Zn2+, we disrupted the Zn2+-binding site by mutating the zinc-ligand residues (H87A, D61A/H87A, and D61A/H81A/H87A/D238A). The activity vs. temperature profiles of the mutant enzymes showed that the disruption of the Zn2+-binding site resulted in a notable decrease in the optimal temperature for maximal activity from 60 to 45-50 degrees C. The mutations also abolished the Zn2+-induced thermal stabilization. The wild-type enzyme revealed a 34.6-fold increase in stabilization with the addition of Zn2+ at 60 degrees C, whereas the mutant enzymes exhibited no response to Zn2+. Additional circular dichroism spectroscopy studies also confirmed the structural stabilizing role of Zn2+ on lipase L1 at elevated temperatures.

Amino Acid Sequence↗

PubMed2005

Crystallization and preliminary crystallographic analysis of Bacillus thuringiensis AHL-lactonase.

The quorum sensing (QS) systems in Gram-negative bacteria are mostly associated with diffusible N-acyl-L-homoserine lactones (AHLs). AHL-degrading enzymes hydrolyze the AHLs into inactive molecules, thereby blocking the QS systems that are closely linked to virulence factor production and biofilm formation. Consequently, these enzymes have recently attracted intense interest for the development of anti-infection therapies for plants and animals. However, despite significant progress in the investigation of AHL-degrading enzymes, no structure is yet available. Accordingly, this study reports on the expression and purification of the AHL-lactonase from Bacillus thuringiensis subsp. kurstaki HD263, as well as the successful crystallization of the enzyme. High-quality native crystals were obtained and a complete data set collected at 2.0 A resolution. The native crystal was found to belong to the space group P2(1)2(1)2(1), with unit cell parameters a=52.7 A, b=55.9 A, and c=74.1 A and one molecule in the asymmetric unit. MAD data were also collected at 2.4 A resolution for a SeMet-substituted crystal.

Bacillus thuringiensis↗

PubMed2005

Analyses of enzyme II gene mutants for sugar transport and heterologous expression of fructokinase gene in Corynebacterium glutamicum ATCC 13032.

Corynebacterium glutamicum ATCC 13032 has four enzyme II (EII) genes of the phosphotransferase system in its genome encoding transporters for sucrose, glucose, fructose, and an unidentified EII. To analyze the function of these EII genes, they were inactivated via homologous recombination and the resulting mutants characterized for sugar utilization. Whereas the sucrose EII was the only transport system for sucrose in C. glutamicum, fructose and glucose were each transported by a second transporter in addition to their corresponding EII. In addition, the ptsF ptsG double mutant carrying deletions in the EII genes for fructose and glucose accumulated fructose in the culture broth when growing on sucrose. As no fructokinase gene exists in the C. glutamicum genome, the fructokinase gene from Clostridium acetobutylicum was expressed in C. glutamicum and resulted in the direct phosphorylation of fructose without any fructose efflux. Accordingly, since fructokinase could direct fructose flux to the pentose phosphate pathway for the supply of NADPH, fructokinase expression may be a potential strategy for enhancing amino acid production.

Corynebacterium glutamicum↗