• Title/Summary/Keyword: metabolic flux analysis

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Modeling of in Silico Microbe System based on the Combination of a Hierarchical Regulatory Network with Metabolic Network (계층적 유전자 조절 네트워크와 대사 네트워크를 통합한 가상 미생물 시스템의 모델링)

  • Lee, Sung-Gun;Han, Sang-Il;Kim, Kyung-Hoon;Kim, Young-Han;Hwang, Kyu-Suk
    • Journal of Institute of Control, Robotics and Systems
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    • v.11 no.10
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    • pp.843-850
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    • 2005
  • FBA(flux balance analysis) with Boolean rules for representing regulatory events has correctly predicted cellular behaviors, such as optimal flux distribution, maximal growth rate, metabolic by-product, and substrate concentration changes, with various environmental conditions. However, until now, since FBA has not taken into account a hierarchical regulatory network, it has limited the representation of the whole transcriptional regulation mechanism and interactions between specific regulatory proteins and genes. In this paper, in order to solve these problems, we describe the construction of hierarchical regulatory network with defined symbols and the introduction of a weight for representing interactions between symbols. Finally, the whole cellular behaviors with time were simulated through the linkage of a hierarchical regulatory network module and dynamic simulation module including FBA. The central metabolic network of E. coli was chosen as the basic model to identify our suggested modeling method.

Development of L-Threonine Producing Recombinant Escherichia coli using Metabolic Control Analysis (대사 조절 분석 기법을 이용한 L-Threonine 생산 재조합 대장균 개발)

  • Choi, Jong-Il;Park, Young-Hoon;Yang, Young-Lyeol
    • KSBB Journal
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    • v.22 no.1
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    • pp.62-65
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    • 2007
  • New strain development strategy using kinetic models and metabolic control analysis was investigated. In this study, previously reported mathematical models describing the enzyme kinetics of intracellular threonine synthesis were modified for mutant threonine producer Escherichia coli TF5015. Using the modified models, metabolic control analysis was carried out to identify the rate limiting step by evaluating the flux control coefficient on the overall threonine synthesis flux exerted by individual enzymatic reactions. The result suggested the production of threonine could be enhanced most efficiently by increasing aspartate semialdehyde dehydrogenase (asd) activity of this strain. Amplification of asd gene in recombinant strain TF5015 (pCL-$P_{aroF}$-asd) increased the threonine production up to 23%, which is much higher than 14% obtained by amplifying aspartate kinse (thrA), other gene in threonine biosynthesis pathway.

Identification of Factors Regulating Escherichia coli 2,3-Butanediol Production by Continuous Culture and Metabolic Flux Analysis

  • Lu, Mingshou;Lee, Soo-Jin;Kim, Bo-Rim;Park, Chang-Hun;Oh, Min-Kyu;Park, Kyung-Moon;Lee, Sang-Yup;Lee, Jin-Won
    • Journal of Microbiology and Biotechnology
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    • v.22 no.5
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    • pp.659-667
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    • 2012
  • 2,3-Butanediol (2,3-BDO) is an organic compound with a wide range of industrial applications. Although Escherichia coli is often used for the production of organic compounds, the wild-type E. coli does not contain two essential genes in the 2,3-BDO biosynthesis pathway, and cannot ferment 2,3-BDO. Therefore, a 2,3-BDO biosynthesis mutant strain of Escherichia coli was constructed and cultured. To determine the optimum culture factors for 2,3-BDO production, experiments were conducted under different culture environments ranging from strongly acidic to neutral pH. The extracellular metabolite profiles were obtained using high-performance liquid chromatography (HPLC), and the intracellular metabolite profiles were analyzed by ultra-performance liquid chromatography and quadruple time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Metabolic flux analysis (MFA) was used to integrate these profiles. The metabolite profiles showed that 2,3-BDO production favors an acidic environment (pH 5), whereas cell mass favors a neutral environment. Furthermore, when the pH of the culture fell below 5, both the cell growth and 2,3-BDO production were inhibited.

A Novel Draft Genome-Scale Reconstruction Model of Isochrysis sp: Exploring Metabolic Pathways for Sustainable Aquaculture Innovations

  • Abhishek Sengupta;Tushar Gupta;Aman Chakraborty;Sudeepti Kulshrestha;Ritu Redhu;Raya Bhattacharjya;Archana Tiwari;Priyanka Narad
    • Microbiology and Biotechnology Letters
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    • v.52 no.2
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    • pp.141-151
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    • 2024
  • Isochrysis sp. is a sea microalga that has become a species of interest because of the extreme lipid content and rapid growth rate of this organism indicating its potential for efficient biofuel production. Using genome sequencing/genome-scale modeling for the prediction of Isochrysis sp. metabolic utilities there is high scope for the identification of essential pathways for the extraction of byproducts of interest at a higher rate. In our work, we design and present iIsochr964, a genome-scale metabolic model of Isochrysis sp. including 4315 reactions, 934 genes, and 1879 metabolites, which are distributed among fourteen compartments. For model validation, experimental culture, and isolation of Isochrysis sp. were performed and biomass values were used for validation of the genome-scale model. OptFlux was instrumental in uncovering several novel metabolites that influence the organism's metabolism by increasing the flux of interacting metabolites, such as Malonyl-CoA, EPA, Protein and others. iIsochr964 provides a compelling resource of metabolic understanding to revolutionize its industrial applications, thereby fostering sustainable development and allowing estimations and simulations of the organism metabolism under varying physiological, chemical, and genetic conditions. It is also useful in principle to provide a systemic view of Isochrysis sp. metabolism, efficiently guiding research and granting context to omics data.

Effect of carbon substrate on the intracellular fluxes in succinic acid producing Escherichia coli.

  • Hong, Soon-Ho;Lee, Dong-Yup;Kim, Tae-Yong;Lee, Sang-Yup;Park, Sun-Won
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2003.10a
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    • pp.251-257
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    • 2003
  • Metabolic engineering has become a new paradigm for the more efficient production of desired bioproducts. Metabolic engineering can be defined as directed modification of cellular metabolism and properties through the introduction, deletion, and modification of metabolic pathways by using recombinant DNA and other molecular biological tools. During the last decade, metabolic flux analysis(MFA) has become an essential tool fur metabolic engineering. By MFA, the intracellular metabolic fluxes can be quantified by the measurement of extracellular metabolite concentrations in combination with the stoichiometry of intracellular reactions and mass balances. The usefulness and functionality of MFA are demonstrated by applying to metabolic pathways in E. coli. First, a large-scale in silico E. coli model is constructed, and then the effects of carbon sources on intracellular flux distributions and succinic acid production were investigated on the basis of the uptake and secretion rates of the relevant metabolites. The results indicated that succinic acid yields increased in order of gluconate, glucose and sorbitol. Acetic acid and lactic acid were produced as major products rather than when gluconate and glucose were used carbon sources. The results indicated that among three carbon sources available, the most reduced substrate is sorbitol which yields efficient succinic acid production.

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