• BMB Reports
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• 제41권8호
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• pp.609-614
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• 2008

The concentrations and catalytic activities of enzymes control metabolic rates. Previous studies have focused on enzyme concentrations because there are no genome-wide techniques used for the measurement of enzyme activity. We propose a method for evaluating the significance of enzyme activity by integrating metabolic network topologies and genome-wide microarray gene expression profiles. We quantified the enzymatic activity of reactions and report the 388 significant reactions in five perturbation datasets. For the 388 enzymatic reactions, we identified 70 that were significantly regulated (P-value < 0.001). Thirty-one of these reactions were part of anaerobic metabolism, 23 were part of low-pH aerobic metabolism, 8 were part of high-pH anaerobic metabolism, 3 were part of low-pH aerobic reactions, and 5 were part of high-pH anaerobic metabolism.

• Journal of Microbiology and Biotechnology
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• 제16권7호
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• pp.1139-1143
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• 2006

Various techniques and strategies have been developed for the identification of intracellular metabolic conditions, and among them, isotope balance-based flux analysis with gas chromatography/mass spectrometry (GC/ MS) has recently become popular. Even though isotope balance-based flux analysis allows a more accurate estimation of intracellular fluxes, its application has been restricted to relatively small metabolic systems because of the limited number of measurable metabolites. In this paper, a strategy for incorporating isotope balance-based flux data obtained for a small network into metabolic flux analysis was examined as a feasible alternative allowing more accurate quantification of intracellular flux distribution in a large metabolic system. To impose GC/MS based data into a large metabolic network and obtain optimum flux distribution profile, data reconciliation procedure was applied. As a result, metabolic flux values of 308 intracellular reactions could be estimated from 29 GC/ MS based fluxes with higher accuracy.

• Biotechnology and Bioprocess Engineering:BBE
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• 제7권5호
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• pp.237-251
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• 2002

The recent progress on metabolic systems engineering was reviewed based on our recent research results in terms of (1) metabolic signal flow diagram approach, (2) metabolic flux analysis (MFA) in particular with intracellular isotopomer distribution using NMR and/or GC-MS, (3) synthesis and optimization of metabolic flux distribution (MFD), (4) modification of MFD by gene manipulation and by controlling culture environment, (5) metabolic control analysis (MCA), (6) design of metabolic regulation structure, and (7) identification of unknown pathways with isotope tracing by NMR. The main characteristics of metabolic engineering is to treat metabolism as a network or entirety instead of individual reactions. The applications were made for poly-3-hydroxybutyrate (PHB) production using Ralstonia eutropha and recombinant Escherichia coli, lactate production by recombinant Saccharomyces cerevisiae, pyruvate production by vitamin auxotrophic yeast Toluropsis glabrata, lysine production using Corynebacterium glutamicum, and energetic analysis of photosynthesic microorganisms such as Cyanobateria. The characteristics of each approach were reviewed with their applications. The approach based on isotope labeling experiments gives reliable and quantitative results for metabolic flux analysis. It should be recognized that the next stage should be toward the investigation of metabolic flux analysis with gene and protein expressions to uncover the metabolic regulation in relation to genetic modification and/ or the change in the culture condition.

• Korean Chemical Engineering Research
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• 제51권2호
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• pp.226-232
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• 2013

부탄올을 생산하는 발효반응기에서는 아세톤, 부탄올 그리고 에탄올을 주로 생산하는 Clostridium acetobutylicum이 사용된다. 본 연구에서는 이 미생물을 이용한 발효공정의 개발을 위하여, Clostridium acetobutylicum ATCC824의 대사망의 동적 모델이 제안되었다. 많은 효소기반의 대사반응들로 구성된 대사망의 복잡성과 대사반응속도식의 비선형적 특성 때문에, 유전 알고리듬과 Levenberg-Marquardt 알고리듬이 결합된 효율적인 최적화 기법을 이용하여 회분식 발효반응기의 실험 결과값으로 58개의 반응속도상수들을 결정하였다. 그리고 이 반응속도상수 결정의 정확도를 제고하기 위하여, 유전자 조작을 통해 특정 대사경로를 차단한 미생물을 이용했을 때의 실험과 초기 글루코스의 농도를 다르게 한 실험들을 수행하여 개발된 대사망의 동적모델을 분석하였다. 결과적으로, 본 연구를 통해서 개발된 대사망 모델의 정확도를 확인하였고, 이를 활용하여 발효반응공정의 생산성 향상을 위한 적절한 클로스트리듐의 개발과 발효반응기의 최적화를 위한 연구에 기여할 수 있을 것으로 기대된다.

• Journal of Microbiology and Biotechnology
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• 제33권10호
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• pp.1351-1360
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• 2023

Endocrine-disrupting chemicals (EDCs) are compounds that disturb hormonal homeostasis by binding to receptors. EDCs are metabolized through hepatic enzymes, causing altered transcriptional activities of hormone receptors, and thus necessitating the exploration of the potential endocrine-disrupting activities of EDC-derived metabolites. Accordingly, we have developed an integrative workflow for evaluating the post-metabolic activity of potential hazardous compounds. The system facilitates the identification of metabolites that exert hormonal disruption through the integrative application of an MS/MS similarity network and predictive biotransformation based on known hepatic enzymatic reactions. As proof-of-concept, the transcriptional activities of 13 chemicals were evaluated by applying the in vitro metabolic module (S9 fraction). Identified among the tested chemicals were three thyroid hormone receptor (THR) agonistic compounds that showed increased transcriptional activities after phase I+II reactions (T3, 309.1 ± 17.3%; DITPA, 30.7 ± 1.8%; GC-1, 160.6 ± 8.6% to the corresponding parents). The metabolic profiles of these three compounds showed common biotransformation patterns, particularly in the phase II reactions (glucuronide conjugation, sulfation, GSH conjugation, and amino acid conjugation). Data-dependent exploration based on molecular network analysis of T3 profiles revealed that lipids and lipid-like molecules were the most enriched biotransformants. The subsequent subnetwork analysis proposed 14 additional features, including T4 in addition to 9 metabolized compounds that were annotated by prediction system based on possible hepatic enzymatic reaction. The other 10 THR agonistic negative compounds showed unique biotransformation patterns according to structural commonality, which corresponded to previous in vivo studies. Our evaluation system demonstrated highly predictive and accurate performance in determining the potential thyroid-disrupting activity of EDC-derived metabolites and for proposing novel biotransformants.

• Toxicological Research
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• 제23권3호
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• pp.189-196
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• 2007

Cytochrome P450 (P450) enzymes are the major catalysts involved in the biotransformation of various drugs, pollutants, carcinogens, and many endogenous compounds. Most of chemical carcinogens are not active by themselves but they require metabolic activation. P450 isozymes playa pivotal role in the metabolic activation. The activation of arylamines and heterocyclic arylamines (HAAs) involves critical N-hydroxylation, usually by P450. CYP1A2 plays an important role in these reactions. Broad exposure to many of these compounds might cause carcinogenicity in animals and humans. On the other hand, P450s can be also involved in the bioactivation of other chemicals including alcohols, aflatoxin B1, acetaminophen, and trichloroethylene, both in humans and in experimental animals. Understanding the P450 metabolic activation of many chemicals is necessary to develop rational strategies for prevention of their toxicities in human health. An important part is the issues of extrapolation between species in predicting risks and variation of P450 enzyme activities in humans.

• 한국환경농학회지
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• 제15권2호
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• pp.246-261
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• 1996

현재 사용되고 있는 유기합성 농약의 중요한 부분을 차지하고 있는 유기인계 농약의 대부분은 분자에 황 원자를 포함하고 있으며 환경이나 생체 내에서 대사되어 활성화 되거나 무독화 된다. 이에 관련된 다양한 반응 중 산화반응이 주요 대사반응으로 여겨지는데 이산화대사에 의해 생성된 대사물의 특성도 중요하거니와 반응 중 생성되는 반응성 중간체에 대한 연구는 대사반응의 경로 및 기작 구명에 필수적이고 농약의 독성학적 특성을 이해하는 데에 중요한 위치를 차지하고 있다. 본 총설은 유기인계 농약을 중심으로 관련 유기인 화합물을 대상으로 산화대사 반응 중 생성되는 반응성 중간체에 대한 연구들을 그 구조구명과 반응 기작면에서 다루었다.

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1994년도 제2회 추계심포지움
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• pp.135-140
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• 1994

Over past decades, numerous in vitro model has been developed to investigate drug metabolism. In the order of complexity we found the isolated perfused liver, hepatocytes in co-culture with epithelial cells, hepatocytes in suspension and in primary culture and subcellular hepatic microsomal fractions. Because they can be easily prepared from both animals (pharmacological and toxicological species) and humans (whole livers as well as biopsies obtained during surgery) hepatocytes in primary culture provide the most powerful model to better elucidate drug behavior at an early stage of preclinical development such as : 1. the characterization of main biotransformation reactions. 2. the identification of phase I and phase II isozymes involved in such reactions 3. the evaluation of interspecies differences allowing the selection of a second toxicological animal species more closely related to man on the basis of metabolic profiles 4. the detection of the inducing and/or inhibitory effects of a drug on metabolic enzymes, the prediction of drug interactions 5. the estimation of inter-individual variability in biotransformation reactions. The use of hepatocytes, and in particular those obstained from humans, at an early stage of drug development allows the obtention of more predictive preclinical data and a better knowledge of drug behavior in humans before the first administration of the drug in healthy volunteers.

• KSBB Journal
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• 제24권3호
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• pp.287-290
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• 2009

최근 미생물을 이용하여 기존에 화학산업을 통하여 생산되어지던 여러 화학물질 혹은 대사산물을 생산하려는 연구가 활발히 이루어지고 있다. 이러한 연구를 통하여 미생물의 대사특성을 개량하기 위하여는, 미생물의 대사 특성을 분석하는 연구가 일차적으로 수행되어져야 한다. 본 연구에서는 대사network간의 기능적 연관성을 분석하기 위하여 transcriptome 연구에 주로 활용되던 ARACNE 기법이 활용되었다. 특정 대사 subpathway들이 미생물 균주들 사이에 존재하는 패턴이 유사하다면 그 대사 subpathway들이 서로 기능적 상관관계를 가지고 있을 가능성이 높다는 가정 하에, ARACNE를 활용하여 미생물들의 subrathway들의 존재 패턴을 분석함으로서 각 subpathway 사이의 기능적 상관관계를 분석하여 보았다. 본 연구에 활용된 새로운 대사network 분석기법을 활용한다면 더욱 효율적인 대사network 분석연구가 수행될 수 있을 것이라 기대된다.

• Journal of Microbiology and Biotechnology
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• 제13권4호
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• pp.571-577
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• 2003

The intracellular metabolic fluxes can be calculated by metabolic flux analysis, which uses a stoichiometric model for the intracellulal reactions along with mass balances around the intracellular metabolites. In this study, metabolic flux analyses were carried out to estimate flux distributions for the maximum in silico yields of various metabolites in Escherichia coli. The maximum in silico yields of acetic acid and lactic acid were identical to their theoretical yields. On the other hand, the in silico yields of succinic acid and ethanol were only 83% and 6.5% of their theoretical yields, respectively. The lower in silico yield of succinic acid was found to be due to the insufficient reducing power. but this lower yield could be increased to its theoretical yield by supplying more reducing power. The maximum theoretical yield of ethanol could be achieved, when a reaction catalyzed by pyruvate decarboxylase was added in the metabolic network. Futhermore, optimal metabolic pathways for the production of various metabolites could be proposed, based on the results of metabolic flux analyses. In the case of succinic acid production, it was found that the pyruvate carboxylation pathway should be used for its optimal production in E. coli rather than the phosphoenolpyruvate carboxylation pathway.