Showing papers by "Byung-Gee Kim published in 2006"

Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples.

Abstract: An important prerequisite for successful construction of a metagenome library is an efficient procedure for extracting DNA from environmental samples. We compared three indirect and four direct extraction methods, including a commercial kit, in terms of DNA yield, purity, and time requirement. A special focus was on methods that are appropriate for the extraction of environmental DNA (eDNA) from very limited sample sizes (0.1 g) to enable a highly parallel approach. Direct extraction procedures yielded on average 100-fold higher DNA amounts than indirect ones. A drawback of direct extraction was the small fragment sizeof approx 12 kb. The quality of the extracted DNA was evaluated by the ability of different restriction enzymes to digest the eDNA. Only the commercial kit and a direct extraction method using freeze-thaw cell lysis in combination with an in-gel patch electrophoresis with hydroxyapatite to remove humic acid substances yielded DNA, which was completely digested by all restriction enzymes. Moreover, only DNA extracted by these two procedures could be used as template for the amplification of fragments of several 16S rDNA, 18SrDNA groups under standard polymerase chain reaction conditions.

Heterologous expression of tylosin polyketide synthase and production of a hybrid bioactive macrolide in Streptomyces venezuelae

Abstract: Tylosin polyketide synthase (Tyl PKS) was heterologously expressed in an engineered strain of Streptomyces venezuelae bearing a deletion of pikromycin PKS gene cluster using two compatible low-copy plasmids, each under the control of a pikAI promoter. The mutant strain produced 0.5 mg/l of the 16-membered ring macrolactone, tylactone, after a 4-day culture, which is a considerably reduced culture period to reach the maximum production level compared to other Streptomyces hosts. To improve the production level of tylactone, several precursors for ethylmalonyl-CoA were fed to the growing medium, leading to a 2.8-fold improvement (1.4 mg/ml); however, switching the pikAI promoter to an actI promoter had no observable effect. In addition, a small amount of desosamine-glycosylated tylactone was detected from the extract of the mutant strain, revealing that the native glycosyltransferase DesVII displayed relaxed substrate specificity in accepting the 16-membered ring macrolactone to produce the glycosylated tylactone. These results demonstrate a successful attempt for a heterologous expression of Tyl PKS in S. venezuelae and introduce S. venezuelae as a rapid heterologous expression system for the production of secondary metabolites.

Synthesis of enantiomerically pure trans-(1R,2R)- and cis-(1S,2R)-1-amino-2-indanol by lipase and omega-transaminase.

Abstract: Syntheses of trans-(1R,2R) and cis-(1S,2R)-1-amino-2-indanol (AI) were accomplished by a series of enantioselective enzymatic reactions using lipase and transaminase (TA). Lipase catalysed enantioselective hydrolysis of 2-acetoxyindanone was employed to prepare (R)-2-hydroxy indanone (HI). trans-AI (5 mM) (de > 98%) was produced from 20 mM (R)-2- HI using omega-TA and 50 mM (S)-1-aminoindan as an amino donor in water-saturated ethyl acetate. For the production of cis-AI, the diastereomeric (2R)-AI was synthesized from (R)-2-HI using reductive amination, and the kinetic resolution was performed with omega-TA. The enantioselectivity of omega-TA for (2R)-AI was increased to 22.1 in the presence of 5% gamma-cyclodextrin. cis-AI (15.4 mM) (96% de) was obtained from 40 mM (2R)-AI using 30 mM pyruvate and omega-TA (25 mg) in 10 mL of 100 mM phosphate buffer (pH 7.0).

The identification and characterization of xenoantigenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney.

Abstract: The immunogenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney were identified and characterized using MALDI-TOF MS and ESI-QTOF-MS. The MALDI profile, investigated by incubation with exoglycosidases, showed a series of about 40 carbohydrates that were identified as high mannose glycans (Man3–9GlcNAc2) and complex bi-, tri-, and tetra-antennary glycans with and without core fucose. The antennae of many of the complex glycans were terminated with α-galactose residues, with the numbers of these residues ranging from one up to the number of antennae. Negative ion ESI-MS/MS spectra confirmed the location of the α-galactose residues on the ends of the antennae. This total glycan profile of the membrane proteins from porcine kidney will thus provide important information for the study of molecular interactions between antigenic carbohydrates and proteins in xenotransplantation.

Protective effect of Rosa laevigata against amyloid beta peptide-induced oxidative stress

Abstract: The amyloid beta (Abeta) peptide is known to increase free radical production in nerve cells, leading to cell death. To investigate the effect of Rosa laevigata against Abeta-induced oxidative damage, in vitro assays and in vivo behavioral tests were performed. R. laevigata showed cell protective effects against oxidative stress-induced cytotoxicity. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) reduction assay exhibited significant increase in cell viability when rat pheochromocytoma (PC 12) cells were treated with R. laevigata extracts. Administration of R. laevigata extracts to mice significantly reversed the Abeta-induced learning and memory impairment in in vivo behavioral tests. These results suggest that R. laevigata extracts can reduce the cytotoxicity of Abeta in PC 12 cells, possibly by the reduction of oxidative stress, and these extracts may be useful in the prevention of Alzheimer's disease.

Engineering aromatic L-amino acid transaminase for the asymmetric synthesis of constrained analogs of L-phenylalanine.

Abstract: An enzymatic asymmetric synthesis was carried out for the preparation of enantiomerically pure L-diphenylalanine using the rationally engineered aromatic L-amino acid transaminase (eAroATEs) obtained from Enterobacter sp. BK2K-1. To rationally redesign the enzyme, structural model was constructed by the homology modeling. The structural model was experimentally validated by the site-directed mutagenesis of the predicted pyridoxal-5′-phosphate (PLP) binding site and the substrate-recognition region, and the cell-free protein synthesis of mutated enzymes. It was suggested that Arg281 and Arg375 were the key residues to recognize the distal carboxylate and α-carboxylate group of the substrates, respectively. The model also predicted that Tyr66 forms hydrogen bond with the phosphate moiety of PLP and interacts with the side chain attached to β-carbon of the amino acid substrate. Among the various site-directed mutants, Y66L variant was able to synthesize L-diphenylalanine with 23% conversion yield for 10 h, whereas the wild-type AroATEs was inactive for the transamination between diphenylpyruvate and L-phenylalanine as amino acceptor and amino donor, respectively. © 2006 Wiley Periodicals, Inc.

Preparative synthesis of dTDP‐L‐rhamnose through combined enzymatic pathways

Abstract: dTDP-L-rhamnose, an important precursor of O-antigen, was prepared on a large scale from dTMP by executing an one-pot reaction in which six enzymes are involved. Two enzymes, dTDP-4-keto-6-deoxy-D-glucose 3,5-epimerase and dTDP-4-keto-rhamnose reductase, responsible for the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-L-rhamnose, were isolated from their putative sequences in the genome of Mesorhizobium loti, functionally expressed in Escherichia coli, and their enzymatic activities were identified. The two enzymes were combined with an enzymatic process for dTDP-4-keto-6-deoxy-D-glucose involving TMP kinase, acetate kinase, dTDP-glucose synthase, and dTDP-glucose 4,6-dehydratase, which allowed us to achieve a preparative scale synthesis of dTDP-L-rhamnose using dTMP and glucose-1-phosphate as starting materials. About 82% yield of dTDP-L-rhamnose was obtained based on initial dTMP concentration at 20 mM dTMP, 1 mM ATP, 10 mM NADH, 60 mM acetyl phosphate, and 80 mM glucose-1-phosphate. From the reaction with 20 ml volume, approximately 180 mg of dTDP-L-rhamnose was obtained in an overall yield of 60% after two-step purification, that is, anion exchange chromatography and gel filtration for desalting. The purified product was identified by HPLC, ESI-MS, and NMR, showing about 95% purity. © 2005 Wiley Periodicals, Inc.

Application of a temperature-controllable microreactor to simple and rapid protein identification using MALDI-TOF MS.

Abstract: We have carried out a simultaneous thermal denaturation and trypsin digestion of proteins using a temperature-controllable microreactor. This is a simple and rapid sample preparation technique for use before matrix-assisted laser desorption ionization time-of-flight mass spectrometry. In contrast to a conventional sample preparation method, which involves several chemical treatments, our sample preparation was performed using only trypsin digestion with the thermal denaturation of the target protein. Optimization of the reactor operational parameters for trypsin digestion using a temperature-controllable microreactor was carried out. The entire trypsin digestion procedure took about 11 min, and consisted of 1 min for the thermal denaturation of the sample protein (3 µl, 0.2 µM) at 85 °C, and 10 min for digestion of the protein at 37 °C. The resulting sequence coverage ranged from 24% to 57%, which was sufficient for practical protein identification.

Improved immobilized enzyme systems using spherical micro silica sol-gel enzyme beads

Abstract: Spherical micro silica sol-gel immobilized enzyme beads were prepared in an emulsion system using cyclohexanone and Triton-X 114. The beads were used for thein situ immobilization of transaminase, trypsin, and lipase. Immobilization during the sol to gel phase transition was investigated to determine the effect of the emulsifying solvents, surfactants, and mixing process on the formation of spherical micro sol-gel enzyme beads and their catalytic activity. The different combinations of sol-gel precursors affected both activity and the stability of the enzymes, which suggests that each enzyme has a unique preference for the silica gel matrix dependent upon the characteristics of the precursors. The resulting enzyme-entrapped micronsized beads were characterized and utilized for several enzyme reaction cycles. These results indicated improved stability compared to the conventional crushed form silica sol-gel immobilized enzyme systems.

Selection of peptides for lipopolysaccharide binding on to epoxy beads and selective detection of Gram-negative bacteria.

Abstract: Lipopolysaccharide (LPS)-binding peptides were enriched by using epoxy beads as a novel support to immobilize LPS for a phage displayed peptide library screening. The sequence of Phe-Ala-Pro-Trp (FAPW) was the most significant consensus motif of 10 selected clones, and Pro-Phe (PF) was the key dipeptide for binding at the apex of the loop to form a characteristic structure of CXXPFXXXC. Moreover, AWLPWAK, one of the highly conserved heptamer peptides, could detect specifically Gram-negative bacteria via a whole cell binding test at 106 cells ml−1.

Biochemical reactions on a microfluidic chip based on a precise fluidic handling method at the nanoliter scale

Abstract: A passive microfluidic delivery system using hydrophobic valving and pneumatic control was devised for microfluidic handling on a chip. The microfluidic metering, cutting, transport, and merging of two liquids on the chip were correctly performed. The error range of the accuracy of microfluid metering was below 4% on a 20 nL scale, which showed that microfluid was easily manipulated with the desired volume on a chip. For a study of the feasibility of biochemical reactions on the chip, a single enzymatic reaction, such as a β-galactosidase reaction was performed. The detection limit of the substrate,i.e. fluorescein di-β-galactopyranoside (FDG) of the β-galactosidase (6.7 fM), was about 76 pM. Additionally, multiple biochemical reactions such asin vitro protein synthesis of enhanced green fluorescence protein (EGFP) were successfully demonstrated at the nanoliter scale, which suggests that our microfluidic chip can be applied not only to miniaturization of various biochemical reactions, but also to development of the microfluidic biochemical reaction system requiring a precise nano-scale control.

Screening and Purification of a Novel Transaminase Catalyzing the Transamination of Aryl β-Amino Acid from Mesorhizobium sp. LUK

Abstract: Mesorhizobium sp. LUK, which utilizes 3-amino-3-phenylpropionic acid as the sole source of nitrogen with high enantioselectivity (E(S)>100), was isolated using enrichment culture. The enzyme involved in the utilization of (S)-3-amino-3-phenylpropionic acid was confirmed to be a transaminase and was purified by 235-folds with a specific activity of 0.72 U/mg. The molecular weight of the purified protein was ca. 47 kDa and the active enzyme was determined as a dimer on gel filtration chromatography. The N-terminal sequence was obtained from the purified protein. Spontaneous decarboxylation of produced β-keto acids was observed during the chiral resolution of 3-amino-3-phenylpropionic acid.

Asymmetric synthesis of unnaturall-amino acids using thermophilic aromaticl-amino acid transaminase

Abstract: Aromaticl-amino acid transaminase is an enzyme that is able to transfer the amino group froml-glutamate to unnatural aromatic α-keto acids to generate α-ketoglutarate and unnatural aromaticl-amino acids, respectively. Enrichment culture was used to isolate thermophilicBacillus sp. T30 expressing this enzyme for use in the synthesis of unnaturall-amino acids. The asymmetric syntheses ofl-homophenylalanine andl-phenylglycine resulted in conversion yields of >95% and >93% from 150 mM 2-oxo-4-phenylbutyrate and phenylglyoxylate, respectively, usingl-glutamate as an amino donor at 60°C. Synthesizedl-homophenylalanine andl-phenylglycine were optically pure (>99% enantiomeric excess) and continuously pre-cipitated in the reaction solution due to their low solubility at the given reaction pH. While the solubility of the α-keto acid substrates is dependent on temperature, the solubility of the unnaturall-amino acid products is dependent on the reaction pH. As the solubility difference between substrate and product at the given reaction pH is therefore larger at higher temperature, the thermophilic transaminase was successfully used to shift the reaction equilibrium toward rapid product formation.

Pro-antibiotic substrates for the identification of enantioselective hydrolases.

Abstract: A new growth-based screening method for the identification of enantioselective hydrolases, such as lipases and esterases, using pro-antibiotic substrates was devised. An enantioselective hydrolase could be identified by measuring growth rates of cells in liquid media containing (R)- or (S)-2-phenylbutyric chloramphenicol esters. This method can be applied to the screening of novel enantioselective microbes and to the high-throughput screening for the directed evolution of enantioselective hydrolytic enzymes.

Asymmetric synthesis of nonproteinogenic amino acids with l-amino acid transaminase: synthesis of (2S)-2-amino-4-oxo-4-phenylbutyric and (3E,2S)-2-amino-4-phenylbutenoic acids

Abstract: 2,4-Dioxo-4-phenylbutyric acid and 2-oxo-4-phenylbut-3-enoic acid are converted to the corresponding ( S )-2-amino acids by recombinant Escherichia coli whole cells over-expressing aromatic transaminase from Enterobacter sp. BK2K-1 (AroAT Es ) in high yields (68–78%) and high enantiomeric purity (>99%) using l -aspartic acid as an amino donor.

Lipase-catalyzed kinetic resolutions of racemic β- and γ-thiolactones

Abstract: Several racemic β- and γ-thiolactones were synthesized and kinetic resolutions of them were executed using lipases While a lipase from Pseudomonas cepacia (PCL) showed the highest enantioselectivity for ( S )-form (>99% ee S at 53% conversion, E > 100) in the kinetic resolution of racemic α-methyl-β-propiothiolactone ( rac -MPTL), it showed no hydrolysis activity in the kinetic resolution of α-benzyl-α-methyl-β-propiothiolactone ( rac -BMPTL), suggesting that the changes in the size of alkyl group from rac -MPTL to rac -BMPTL leads to lower hydrolysis activity and enantioselectivity In contrast, racemic γ-butyrothiolactones were hydrolyzed by several lipases with low enantioselectivity, whereas a lipase from Candida antarctica (CAL) showed moderate enantioselectivity for ( S )-form (>99% ee S at 76% conversion, E = 11) in the kinetic resolution of racemic α-methyl-γ-butyrothiolactone ( rac -MBTL) Computer-aided molecular modeling was also performed to investigate the enantioselectivites and activities of PCL toward β-propiothiolactones The computer modeling results suggest that the alkyl side chains of β-propiothiolactones and γ-butyrothiolactones interact with amino acid residues around hydrophobic crevice , which affects the activity of PCL

Fabrication of disposable protein chip for simultaneous sample detection

Abstract: In this study, we have described a method for the fabrication of a protein chip on silicon substrate using hydrophobic thin film and microfluidic channels, for the simultaneous detection of multiple targets in samples. The use of hydrophobic thin film provides for a physical, chemical, and biological barrier for protein patterning. The microfluidic channels create four protein patterned strips on the silicon surfaces with a high signal-to-noise ratio. The feasibility of the protein chips was determined in order to discriminate between each protein interaction in a mixture sample that included biotin, ovalbumin, hepatitis B antigen. In the fabrication of the multiplexed assay system, the utilization of the hydrophobic thin film and the microfluidic networks constitutes a more convenient method for the development of biosensors or biochips. This technique may be applicable to the simultaneous evaluation of multiple protein-protein interactions.