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Komiya Y, Sakazaki Y, Goto T, Kawabata F, Suzuki T, Sato Y, Sawano S, Nakamura M, Tatsumi R, Ikeuchi Y, Arihara K, Mizunoya W. Eicosapentaenoic acid increases proportion of type 1 muscle fibers through PPARδ and AMPK pathways in rats. iScience 2024; 27:109816. [PMID: 38779480 PMCID: PMC11108975 DOI: 10.1016/j.isci.2024.109816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/07/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Muscle fiber type composition (% slow-twitch and % fast-twitch fibers) is associated with metabolism, with increased slow-twitch fibers alleviating metabolic disorders. Previously, we reported that dietary fish oil intake induced a muscle fiber-type transition in a slower direction in rats. The aim of this study was to determine the functionality of eicosapentaenoic acid (EPA), a unique fatty acid in fish oil, to skeletal muscle fiber type and metabolism in rats. Here, we showed that dietary EPA promotes whole-body oxidative metabolism and improves muscle function by increasing proportion of slow-twitch type 1 fibers in rats. Transcriptomic and metabolomic analyses revealed that EPA supplementation activated the peroxisome proliferator-activated receptor δ (PPARδ) and AMP-activated protein kinase (AMPK) pathways in L6 myotube cultures, which potentially increasing slow-twitch fiber share. This highlights the role of EPA as an exercise-mimetic dietary component that improves metabolism and muscle function, with potential benefits for health and athletic performance.
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Affiliation(s)
- Yusuke Komiya
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Yuka Sakazaki
- Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Tsuyoshi Goto
- Division of Food Science & Biotechnology, Kyoto University, Kyoto, Japan
| | - Fuminori Kawabata
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Takahiro Suzuki
- Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yusuke Sato
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Shoko Sawano
- Department of Food and Life Science, School of Life and Environmental Science, Azabu University, Sagamihara, Japan
| | - Mako Nakamura
- Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Ryuichi Tatsumi
- Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoshihide Ikeuchi
- Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Keizo Arihara
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Wataru Mizunoya
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Japan
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Wang X, Wei Z, Gu M, Zhu L, Hai C, Di A, Wu D, Bai C, Su G, Liu X, Yang L, Li G. Loss of Myostatin Alters Mitochondrial Oxidative Phosphorylation, TCA Cycle Activity, and ATP Production in Skeletal Muscle. Int J Mol Sci 2022; 23:ijms232415707. [PMID: 36555347 PMCID: PMC9779574 DOI: 10.3390/ijms232415707] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Myostatin (MSTN) is an important negative regulator of skeletal muscle growth in animals. A lack of MSTN promotes lipolysis and glucose metabolism but inhibits oxidative phosphorylation (OXPHOS). Here, we aimed to investigate the possible mechanism of MSTN regulating the mitochondrial energy homeostasis of skeletal muscle. To this end, MSTN knockout mice were generated by the CRISPR/Cas9 technique. Expectedly, the MSTN null (Mstn-/-) mouse has a hypermuscular phenotype. The muscle metabolism of the Mstn-/- mice was detected by an enzyme-linked immunosorbent assay, indirect calorimetry, ChIP-qPCR, and RT-qPCR. The resting metabolic rate and body temperature of the Mstn-/- mice were significantly reduced. The loss of MSTN not only significantly inhibited the production of ATP by OXPHOS and decreased the activity of respiratory chain complexes, but also inhibited key rate-limiting enzymes related to the TCA cycle and significantly reduced the ratio of NADH/NAD+ in the Mstn-/- mice, which then greatly reduced the total amount of ATP. Further ChIP-qPCR results confirmed that the lack of MSTN inhibited both the TCA cycle and OXPHOS, resulting in decreased ATP production. The reason may be that Smad2/3 is not sufficiently bound to the promoter region of the rate-limiting enzymes Idh2 and Idh3a of the TCA cycle, thus affecting their transcription.
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Affiliation(s)
- Xueqiao Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Zhuying Wei
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Mingjuan Gu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lin Zhu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Chao Hai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Anqi Di
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Di Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Xuefei Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
- Correspondence: (L.Y.); (G.L.)
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010070, China
- Correspondence: (L.Y.); (G.L.)
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Bian J, Liao Y, Liu R, An X, Hu C, Liu H, Qu J. Synergy of cyano groups and cobalt single atoms in graphitic carbon nitride for enhanced bio-denitrification. WATER RESEARCH 2022; 218:118465. [PMID: 35461103 DOI: 10.1016/j.watres.2022.118465] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Bio-denitrification plays a crucial role in the purification of nitrogen contaminated water, yet the low efficiency of the pure biological system often leads to the accumulation of harmful intermediates. Semi-biological catalysis provides an effective approach to improving the reaction efficiency through hybridizing artificial nanomaterials with natural organisms, yet the application of this strategy in bio-denitrification is limited. In this study, the effect of surface engineered carbon nitride on the denitrification capability of denitrifying bacteria was investigated. We found that cyano groups availed the biotic-abiotic interactions, while immobilized cobalt single atoms attenuated the local electrostatic repulsion. This synergistic effect endowed carbon nitride modified with cobalt atoms and cyano groups (Co/C3N4-C) with the unexpected acceleration of bio-denitrification reaction, without the accumulation of harmful intermediates. According to the metabolomics analysis, this improvement was attributed to the moderate metabolic adaptation caused by nanoelicitor, which induced dramatically boosted electron transfer and energy supply for extracellular polymeric substance (EPS) secretion. The elevation of intracellular iron level increased the activities of denitrification reductase, which was evidenced by metatranscriptomic analysis. Our results not only demonstrate the great potential of carbon nitride as an artificial elicitor for biological regulation, but also shed light on comprehending the complicated biotic-abiotic interactions for versatile application.
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Affiliation(s)
- Jiyong Bian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xiaoqiang An
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Chengzhi Hu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Afeyan NB, Cooney CL. Professor Daniel I.C. Wang: A Legacy of Education, Innovation, Publication, and Leadership. Biotechnol Bioeng 2020; 117:3615-3627. [PMID: 33616929 PMCID: PMC7839494 DOI: 10.1002/bit.27644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Noubar B. Afeyan
- Flagship Ventures, One Memorial Drive7th FloorCambridgeMassachusetts
- Sloan School of Management, Massachusetts Institute of Technology50 Memorial DriveCambridgeMassachusetts
| | - Charles L. Cooney
- Department of Chemical EngineeringMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMassachusetts
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Sugrue E, Coombes D, Wood D, Zhu T, Donovan KA, Dobson RCJ. The lid domain is important, but not essential, for catalysis of Escherichia coli pyruvate kinase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:761-772. [PMID: 32978636 DOI: 10.1007/s00249-020-01466-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/24/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022]
Abstract
Pyruvate kinase catalyses the final step of the glycolytic pathway in central energy metabolism. The monomeric structure comprises three domains: a catalytic TIM-barrel, a regulatory domain involved in allosteric activation, and a lid domain that encloses the substrates. The lid domain is thought to close over the TIM-barrel domain forming contacts with the substrates to promote catalysis and may be involved in stabilising the activated state when the allosteric activator is bound. However, it remains unknown whether the lid domain is essential for pyruvate kinase catalytic or regulatory function. To address this, we removed the lid domain of Escherichia coli pyruvate kinase type 1 (PKTIM+Reg) using protein engineering. Biochemical analyses demonstrate that, despite the absence of key catalytic residues in the lid domain, PKTIM+Reg retains a low level of catalytic activity and has a reduced binding affinity for the substrate phosphoenolpyruvate. The enzyme retains allosteric activation, but the regulatory profile of the enzyme is changed relative to the wild-type enzyme. Analytical ultracentrifugation and small-angle X-ray scattering data show that, beyond the loss of the lid domain, the PKTIM+Reg structure is not significantly altered and is consistent with the wild-type tetramer that is assembled through interactions at the TIM and regulatory domains. Our results highlight the contribution of the lid domain for facilitating pyruvate kinase catalysis and regulation, which could aid in the development of small molecule inhibitors for pyruvate kinase and related lid-regulated enzymes.
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Affiliation(s)
- Elena Sugrue
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - David Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Tong Zhu
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Katherine A Donovan
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
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Ramos JRC, Rath AG, Genzel Y, Sandig V, Reichl U. A dynamic model linking cell growth to intracellular metabolism and extracellular by-product accumulation. Biotechnol Bioeng 2020; 117:1533-1553. [PMID: 32022250 DOI: 10.1002/bit.27288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 12/12/2019] [Accepted: 01/26/2020] [Indexed: 12/16/2022]
Abstract
Mathematical modeling of animal cell growth and metabolism is essential for the understanding and improvement of the production of biopharmaceuticals. Models can explain the dynamic behavior of cell growth and product formation, support the identification of the most relevant parameters for process design, and significantly reduce the number of experiments to be performed for process optimization. Few dynamic models have been established that describe both extracellular and intracellular dynamics of growth and metabolism of animal cells. In this study, a model was developed, which comprises a set of 33 ordinary differential equations to describe batch cultivations of suspension AGE1.HN.AAT cells considered for the production of α1-antitrypsin. This model combines a segregated cell growth model with a structured model of intracellular metabolism. Overall, it considers the viable cell concentration, mean cell diameter, viable cell volume, concentration of extracellular substrates, and intracellular concentrations of key metabolites from the central carbon metabolism. Furthermore, the release of metabolic by-products such as lactate and ammonium was estimated directly from the intracellular reactions. Based on the same set of parameters, this model simulates well the dynamics of four independent batch cultivations. Analysis of the simulated intracellular rates revealed at least two distinct cellular physiological states. The first physiological state was characterized by a high glycolytic rate and high lactate production. Whereas the second state was characterized by efficient adenosine triphosphate production, a low glycolytic rate, and reactions of the TCA cycle running in the reverse direction from α-ketoglutarate to citrate. Finally, we show possible applications of the model for cell line engineering and media optimization with two case studies.
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Affiliation(s)
- João R C Ramos
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Alexander G Rath
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, AMINO GmbH, Frellstedt, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Volker Sandig
- Bioprocess Engineering, ProBioGen AG, Berlin, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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7
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Application of a genome-scale model in tandem with enzyme assays for identification of metabolic signatures of high and low CHO cell producers. Metab Eng Commun 2019; 9:e00097. [PMID: 31720213 PMCID: PMC6838488 DOI: 10.1016/j.mec.2019.e00097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
Biopharmaceutical industrial processes are based on high yielding stable recombinant Chinese Hamster Ovary (CHO) cells that express monoclonal antibodies. However, the process and feeding regimes need to be adapted for each new cell line, as they all have a slightly different metabolism and product performance. A main limitation for accelerating process development is that the metabolic pathways underlying this physiological variability are not yet fully understood. This study describes the evolution of intracellular fluxes during the process for 4 industrial cell lines, 2 high producers and 2 low producers (n = 3), all of them producing a different antibody. In order to understand from a metabolic point of view the phenotypic differences observed, and to find potential targets for improving specific productivity of low producers, the analysis was supported by a tailored genome-scale model and was validated with enzymatic assays performed at different days of the process. A total of 59 reactions were examined from different key pathways, namely glycolysis, pentose phosphate pathway, TCA cycle, lipid metabolism, and oxidative phosphorylation. The intracellular fluxes did not show a metabolic correlation between high producers, but the degree of similitude observed between cell lines could be confirmed with additional experimental observations. The whole analysis led to a better understanding of the metabolic requirements for all the cell lines, allowed to the identification of metabolic bottlenecks and suggested targets for further cell line engineering. This study is a successful application of a curated genome-scale model to multiple industrial cell lines, which makes the metabolic model suitable for process platform.
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Li MY, Ebel B, Blanchard F, Paris C, Guedon E, Marc A. Control of IgG glycosylation by in situ and real-time estimation of specific growth rate of CHO cells cultured in bioreactor. Biotechnol Bioeng 2019; 116:985-993. [PMID: 30636319 DOI: 10.1002/bit.26914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 12/04/2018] [Accepted: 01/09/2019] [Indexed: 12/19/2022]
Abstract
The cell-specific growth rate (µ) is a critical process parameter for antibody production processes performed by animal cell cultures, as it describes the cell growth and reflects the cell physiological state. When there are changes in these parameters, which are indicated by variations of µ, the synthesis and the quality of antibodies are often affected. Therefore, it is essential to monitor and control the variations of µto assure the antibody production and achieve high product quality. In this study, a novel approach for on-line estimation of µ was developed based on the process analytical technology initiative by using an in situ dielectric spectroscopy. Critical moments, such as significant µ decreases, were successfully detected by this method, in association with changes in cell physiology as well as with an accumulation of nonglycosylated antibodies. Thus, this method was used to perform medium renewals at the appropriate time points, maintaining the values of µ close to its maximum. Using this method, we demonstrated that the physiological state of cells remained stable, the quantity and the glycosylation quality of antibodies were assured at the same time, leading to better process performances compared with the reference feed-harvest cell cultures carried out by using off-line nutrient measurements.
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Affiliation(s)
- Meng-Yao Li
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, Vandœuvre-lès-Nancy, France
| | - Bruno Ebel
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, Vandœuvre-lès-Nancy, France
| | - Fabrice Blanchard
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, Vandœuvre-lès-Nancy, France
| | - Cédric Paris
- Structural and Metabolomics Analyses Platform, SF4242, Université de Lorraine, EFABA, Vandœuvre-lès-Nancy, France
| | - Emmanuel Guedon
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, Vandœuvre-lès-Nancy, France
| | - Annie Marc
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, Vandœuvre-lès-Nancy, France
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Linezolid Inhibited Synthesis of ATP in Mitochondria: Based on GC-MS Metabolomics and HPLC Method. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3128270. [PMID: 30410924 PMCID: PMC6206563 DOI: 10.1155/2018/3128270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/28/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
Linezolid has been widely used in serious infections for its effective inhibiting effect against multidrug-resistant gram-positive pathogens. However, linezolid caused severe adverse reactions, such as thrombocytopenia, anaemia, optic neuropathy, and near-fatal serotonin syndrome. In order to investigate the toxicity of linezolid, twenty-four Sprague-Dawley rats were randomly divided into: control group (n=7), low-group (n=8), and high-group (n=9). The rats of low-group and high-group were given by gavage with linezolid 60 and 120 mg/kg/day for 7 days, respectively. The serum concentration of linezolid was determined by high performance liquid chromatography (HPLC); blood metabolic change was analyzed by gas chromatography-mass spectrometer (GC-MS). Adenosine triphosphate (ATP) concentration in HepG2-C3A after being cultured with linezolid was determined by HPLC. The results showed that there were six metabolites and nine metabolites had statistical differences in low-group and high-group (P<0.05). The trimethyl phosphate was the most significant indicator in those changed metabolites. Except for d-glucose which was slightly increased in low-group, octadecanoic acid, cholest-5-ene, hexadecanoic acid, α-linolenic acid, eicosapentaenoic acid, 9,12-Octadecadienoic acid, and docosahexaenoic acid were all decreased in low-group and high-group. ATP concentration was decreased in HepG2-C3A after cultured with linezolid. In conclusion, the toxicity of linezolid is related to its serum concentration. Linezolid may inhibit the synthesis of ATP and fatty acid.
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Quiroga-Campano AL, Panoskaltsis N, Mantalaris A. Energy-based culture medium design for biomanufacturing optimization: A case study in monoclonal antibody production by GS-NS0 cells. Metab Eng 2018; 47:21-30. [PMID: 29501926 DOI: 10.1016/j.ymben.2018.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/25/2018] [Indexed: 01/30/2023]
Abstract
Demand for high-value biologics, a rapidly growing pipeline, and pressure from competition, time-to-market and regulators, necessitate novel biomanufacturing approaches, including Quality by Design (QbD) principles and Process Analytical Technologies (PAT), to facilitate accelerated, efficient and effective process development platforms that ensure consistent product quality and reduced lot-to-lot variability. Herein, QbD and PAT principles were incorporated within an innovative in vitro-in silico integrated framework for upstream process development (UPD). The central component of the UPD framework is a mathematical model that predicts dynamic nutrient uptake and average intracellular ATP content, based on biochemical reaction networks, to quantify and characterize energy metabolism and its adaptive response, metabolic shifts, to maintain ATP homeostasis. The accuracy and flexibility of the model depends on critical cell type/product/clone-specific parameters, which are experimentally estimated. The integrated in vitro-in silico platform and the model's predictive capacity reduced burden, time and expense of experimentation resulting in optimal medium design compared to commercially available culture media (80% amino acid reduction) and a fed-batch feeding strategy that increased productivity by 129%. The framework represents a flexible and efficient tool that transforms, improves and accelerates conventional process development in biomanufacturing with wide applications, including stem cell-based therapies.
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Affiliation(s)
- Ana L Quiroga-Campano
- CPSE, BSEL, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, United Kingdom.
| | - Nicki Panoskaltsis
- CPSE, BSEL, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, United Kingdom; Department of Haematology, Imperial College London, Northwick Park & St. Mark's Campus, Harrow, United Kingdom.
| | - Athanasios Mantalaris
- CPSE, BSEL, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, United Kingdom.
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A Predictive Model for Energy Metabolism and ATP Balance in Mammalian Cells: Towards the Energy-Based Optimization of mAb Production. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/b978-0-444-63428-3.50268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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12
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Kiparissides A, Pistikopoulos EN, Mantalaris A. On the model-based optimization of secreting mammalian cell (GS-NS0) cultures. Biotechnol Bioeng 2014; 112:536-48. [DOI: 10.1002/bit.25457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/01/2014] [Accepted: 09/05/2014] [Indexed: 12/16/2022]
Affiliation(s)
- A. Kiparissides
- Centre for Process Systems Engineering; Department of Chemical Engineering; Imperial College London; London SW7 2AZ UK
| | - E. N. Pistikopoulos
- Centre for Process Systems Engineering; Department of Chemical Engineering; Imperial College London; London SW7 2AZ UK
| | - A. Mantalaris
- Centre for Process Systems Engineering; Department of Chemical Engineering; Imperial College London; London SW7 2AZ UK
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13
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Lohr V, Hädicke O, Genzel Y, Jordan I, Büntemeyer H, Klamt S, Reichl U. The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis. BMC Biotechnol 2014; 14:72. [PMID: 25077436 PMCID: PMC4124504 DOI: 10.1186/1472-6750-14-72] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 07/16/2014] [Indexed: 01/10/2023] Open
Abstract
Background In human vaccine manufacturing some pathogens such as Modified Vaccinia Virus Ankara, measles, mumps virus as well as influenza viruses are still produced on primary material derived from embryonated chicken eggs. Processes depending on primary cell culture, however, are difficult to adapt to modern vaccine production. Therefore, we derived previously a continuous suspension cell line, AGE1.CR.pIX, from muscovy duck and established chemically-defined media for virus propagation. Results To better understand vaccine production processes, we developed a stoichiometric model of the central metabolism of AGE1.CR.pIX cells and applied flux variability and metabolic flux analysis. Results were compared to literature dealing with mammalian and insect cell culture metabolism focusing on the question whether cultured avian cells differ in metabolism. Qualitatively, the observed flux distribution of this avian cell line was similar to distributions found for mammalian cell lines (e.g. CHO, MDCK cells). In particular, glucose was catabolized inefficiently and glycolysis and TCA cycle seem to be only weakly connected. Conclusions A distinguishing feature of the avian cell line is that glutaminolysis plays only a minor role in energy generation and production of precursors, resulting in low extracellular ammonia concentrations. This metabolic flux study is the first for a continuous avian cell line. It provides a basis for further metabolic analyses to exploit the biotechnological potential of avian and vertebrate cell lines and to develop specific optimized cell culture processes, e.g. vaccine production processes.
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Affiliation(s)
- Verena Lohr
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr, 1, 39106 Magdeburg, Germany.
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Young JD. Metabolic flux rewiring in mammalian cell cultures. Curr Opin Biotechnol 2013; 24:1108-15. [PMID: 23726154 DOI: 10.1016/j.copbio.2013.04.016] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 03/28/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022]
Abstract
Continuous cell lines (CCLs) engage in 'wasteful' glucose and glutamine metabolism that leads to accumulation of inhibitory byproducts, primarily lactate and ammonium. Advances in techniques for mapping intracellular carbon fluxes and profiling global changes in enzyme expression have led to a deeper understanding of the molecular drivers underlying these metabolic alterations. However, recent studies have revealed that CCLs are not necessarily entrenched in a glycolytic or glutaminolytic phenotype, but instead can shift their metabolism toward increased oxidative metabolism as nutrients become depleted and/or growth rate slows. Progress to understand dynamic flux regulation in CCLs has enabled the development of novel strategies to force cultures into desirable metabolic phenotypes, by combining fed-batch feeding strategies with direct metabolic engineering of host cells.
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Affiliation(s)
- Jamey D Young
- Department of Chemical and Biomolecular Engineering, PMB 351604, Vanderbilt University, Nashville, TN 37235-1604, USA; Department of Molecular Physiology and Biophysics, PMB 351604, Vanderbilt University, Nashville, TN 37235-1604, USA.
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15
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Templeton N, Dean J, Reddy P, Young JD. Peak antibody production is associated with increased oxidative metabolism in an industrially relevant fed-batch CHO cell culture. Biotechnol Bioeng 2013; 110:2013-24. [PMID: 23381838 DOI: 10.1002/bit.24858] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 01/11/2013] [Accepted: 01/22/2013] [Indexed: 12/18/2022]
Abstract
Cell metabolism can vary considerably over the course of a typical fed-batch antibody production process. However, the intracellular pathway alterations associated with various phases of growth and antibody production have yet to be fully elucidated using industrially relevant production hosts. Therefore, we performed (13)C labeling experiments and metabolic flux analysis (MFA) to characterize CHO cell metabolism during four separate phases of a fed-batch culture designed to closely represent industrial process conditions. First, we found that peak specific growth rate was associated with high lactate production and minimal TCA cycling. Conversely, we found that lactate metabolism switched from net production to net consumption as the culture transitioned from peak growth to peak antibody production. During the peak antibody production phase, energy was primarily generated through oxidative phosphorylation, which was also associated with elevated oxidative pentose phosphate pathway (oxPPP) activity. Interestingly, as TCA cycling and antibody production reached their peaks, specific growth rate continued to diminish as the culture entered stationary phase. However, TCA cycling and oxPPP activity remained high even as viable cell density began to decline. Overall, we found that a highly oxidative state of metabolism corresponded with peak antibody production, whereas peak cell growth was characterized by a highly glycolytic metabolic state.
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Affiliation(s)
- Neil Templeton
- Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, Nashville, TN 37235, USA
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16
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Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG. Advanced stoichiometric analysis of metabolic networks of mammalian systems. Crit Rev Biomed Eng 2012; 39:511-34. [PMID: 22196224 DOI: 10.1615/critrevbiomedeng.v39.i6.30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties. Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis. Although application of these tools into well-known microbial systems is extensive in the literature, various barriers prevent them from being utilized in mammalian cells. Limited experimental data, complex regulatory mechanisms, and the requirement of more complex nutrient media are some major obstacles in mammalian cell systems. However, mammalian cells have been used to produce therapeutic proteins, to characterize disease states or related abnormal metabolic conditions, and to analyze the toxicological effects of some medicinally important drugs. Therefore, there is a growing need for extending metabolic engineering principles to mammalian cells in order to understand their underlying metabolic functions. In this review article, advanced metabolic engineering tools developed for stoichiometric analysis including MFA, FBA, and MPA are described. Applications of these tools in mammalian cells are discussed in detail, and the challenges and opportunities are highlighted.
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Affiliation(s)
- Mehmet A Orman
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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17
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Selvarasu S, Ho YS, Chong WPK, Wong NSC, Yusufi FNK, Lee YY, Yap MGS, Lee DY. Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture. Biotechnol Bioeng 2012; 109:1415-29. [DOI: 10.1002/bit.24445] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 11/08/2022]
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18
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Gerdtzen ZP. Modeling metabolic networks for mammalian cell systems: general considerations, modeling strategies, and available tools. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:71-108. [PMID: 21984615 DOI: 10.1007/10_2011_120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Over the past decades, the availability of large amounts of information regarding cellular processes and reaction rates, along with increasing knowledge about the complex mechanisms involved in these processes, has changed the way we approach the understanding of cellular processes. We can no longer rely only on our intuition for interpreting experimental data and evaluating new hypotheses, as the information to analyze is becoming increasingly complex. The paradigm for the analysis of cellular systems has shifted from a focus on individual processes to comprehensive global mathematical descriptions that consider the interactions of metabolic, genomic, and signaling networks. Analysis and simulations are used to test our knowledge by refuting or validating new hypotheses regarding a complex system, which can result in predictive capabilities that lead to better experimental design. Different types of models can be used for this purpose, depending on the type and amount of information available for the specific system. Stoichiometric models are based on the metabolic structure of the system and allow explorations of steady state distributions in the network. Detailed kinetic models provide a description of the dynamics of the system, they involve a large number of reactions with varied kinetic characteristics and require a large number of parameters. Models based on statistical information provide a description of the system without information regarding structure and interactions of the networks involved. The development of detailed models for mammalian cell metabolism has only recently started to grow more strongly, due to the intrinsic complexities of mammalian systems, and the limited availability of experimental information and adequate modeling tools. In this work we review the strategies, tools, current advances, and recent models of mammalian cells, focusing mainly on metabolism, but discussing the methodology applied to other types of networks as well.
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Affiliation(s)
- Ziomara P Gerdtzen
- Department of Chemical Engineering and Biotechnology, Millennium Institute for Cell Dynamics and Biotechnology: a Centre for Systems Biology, University of Chile, Beauchef 850, Santiago, Chile,
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19
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Kishikawa JI, Fujikawa M, Imamura H, Yasuda K, Noji H, Ishii N, Mitani S, Yokoyama K. MRT letter: Expression of ATP sensor protein in Caenorhabditis elegans. Microsc Res Tech 2011; 75:15-9. [PMID: 22038755 DOI: 10.1002/jemt.21103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/08/2011] [Indexed: 11/08/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is the major energy currency and is involved in many biological processes. The ATP-monitoring system for cells in animals can be helpful to study the relationship between energy metabolism and biological processes. The fluorescent ATP biosensor ATeam (ATP indicator based on Epsilon subunit for Analytical Measurements), which has been reported to monitor ATP levels in cultured cells on the basis of fluorescence resonance energy transfer (FRET), was introduced into nematodes by microinjection and UV-irradiation method. To confirm whether ATeam functions as an ATP sensor in nematode cells, the authors measured FRET of ATeam in cells of transgenic nematode. The ATeam was expressed in target cells in nematode. In vulva cells, ATP levels in the cytosol were higher than those in mitochondria. ATeam also sensed ATP level change in cultured cells from the transgenic nematode. These experiments indicated that ATeam is available for detection of changes in ATP levels in nematode cells.
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Affiliation(s)
- Jun-ichi Kishikawa
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, Japan
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20
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Guan YH, Kemp RB. On-line heat flux measurements improve the culture medium for the growth and productivity of genetically engineered CHO cells. Cytotechnology 2011; 30:107-20. [PMID: 19003360 DOI: 10.1023/a:1008038515285] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With the increasingly competitive commercial production of target proteins by hybridoma and genetically engineered cells, there is an urgent requirement for biosensors to monitor and control on-line and in real time the growth of cultured cells. Since growth is accompanied by an enthalpy change, heat dissipation measured by calorimetry could act as an index for metabolic flow rate. Recombinant CHO cell suspensions producing interferon-gamma were pumped to an on-line flow calorimeter. The results showed that an early reflection of metabolic change is size-specific heat flux obtained from dividing heat flow rate by the capacitance change of the cell suspension, using the on-line probe of a dielectric spectroscope. Comparison of heat flux with glucose and glutamine fluxes indicated that the former most accurately reflected decreased metabolic activity. Possibly this was due to accumulation of lactate and ammonia resulting from catabolic substrates being used as biosynthetic precursors. Thus, the heat flux probe is an ideal on-line biosensor for fed-batch culture. A stoichiometric growth reaction was formulated and data for material and heat fluxes incorporated into it. This showed that cell demand for glucose and glutamine was in the stoichiometric ratio of approximately 3:1 rather than the approximately 5:1 in the medium. It was demonstrated that the set of stoichiometric coefficients in the reaction were related through the extent of reaction (advancement) to overall metabolic activity (flux). The fact that this approach can be used for medium optimisation is the basis for an amino-acid-enriched medium which improved cell growth while decreasing catabolic fluxes.
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Affiliation(s)
- Y H Guan
- Institute of Biological Sciences, University of Wales, Edward Llwyd Building, Aberystwyth, SY23 3DA, UK
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21
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Goudar CT, Piret JM, Konstantinov KB. Estimating cell specific oxygen uptake and carbon dioxide production rates for mammalian cells in perfusion culture. Biotechnol Prog 2011; 27:1347-57. [DOI: 10.1002/btpr.646] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 04/01/2011] [Indexed: 11/08/2022]
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22
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Advancing biopharmaceutical process development by system-level data analysis and integration of omics data. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2011; 127:133-63. [PMID: 21290218 DOI: 10.1007/10_2010_98] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of efficient bioprocesses is essential for cost-effective manufacturing of recombinant therapeutic proteins. To achieve further process improvement and process rationalization comprehensive data analysis of both process data and phenotypic cell-level data is essential. Here, we present a framework for advanced bioprocess data analysis consisting of multivariate data analysis (MVDA), metabolic flux analysis (MFA), and pathway analysis for mapping of large-scale gene expression data sets. This data analysis platform was applied in a process development project with an IgG-producing Chinese hamster ovary (CHO) cell line in which the maximal product titer could be increased from about 5 to 8 g/L.Principal component analysis (PCA), k-means clustering, and partial least-squares (PLS) models were applied to analyze the macroscopic bioprocess data. MFA and gene expression analysis revealed intracellular information on the characteristics of high-performance cell cultivations. By MVDA, for example, correlations between several essential amino acids and the product concentration were observed. Also, a grouping into rather cell specific productivity-driven and process control-driven processes could be unraveled. By MFA, phenotypic characteristics in glycolysis, glutaminolysis, pentose phosphate pathway, citrate cycle, coupling of amino acid metabolism to citrate cycle, and in the energy yield could be identified. By gene expression analysis 247 deregulated metabolic genes were identified which are involved, inter alia, in amino acid metabolism, transport, and protein synthesis.
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23
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Niklas J, Heinzle E. Metabolic flux analysis in systems biology of mammalian cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2011; 127:109-32. [PMID: 21432052 DOI: 10.1007/10_2011_99] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reaction rates or metabolic fluxes reflect the integrated phenotype of genome, transcriptome and proteome interactions, including regulation at all levels of the cellular hierarchy. Different methods have been developed in the past to analyse intracellular fluxes. However, compartmentation of mammalian cells, varying utilisation of multiple substrates, reversibility of metabolite uptake and production, unbalanced growth behaviour and adaptation of cells to changing environment during cultivation are just some reasons that make metabolic flux analysis (MFA) in mammalian cell culture more challenging compared to microorganisms. In this article MFA using the metabolite balancing methodology and the advantages and disadvantages of (13)C MFA in mammalian cell systems are reviewed. Application examples of MFA in the optimisation of cell culture processes for the production of biopharmaceuticals are presented with a focus on the metabolism of the main industrial workhorse. Another area in which mammalian cell culture plays a key role is in medical and toxicological research. It is shown that MFA can be used to understand pathophysiological mechanisms and can assist in understanding effects of drugs or other compounds on cellular metabolism.
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Affiliation(s)
- Jens Niklas
- Biochemical Engineering Institute, Saarland University, Campus A 1.5, 66123, Saarbrücken, Germany
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24
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Zamorano F, Wouwer AV, Bastin G. A detailed metabolic flux analysis of an underdetermined network of CHO cells. J Biotechnol 2010; 150:497-508. [PMID: 20869402 DOI: 10.1016/j.jbiotec.2010.09.944] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 09/14/2010] [Accepted: 09/15/2010] [Indexed: 10/19/2022]
Abstract
In this article the metabolic flux analysis of growing CHO-320 cells is performed for a detailed metabolic network which involves 100 reactions and embraces all the significant pathways describing the metabolism of CHO cells. The purpose is to investigate the efficiency of the flux analysis when it is based on a relatively small set of extracellular measurements that can be easily achieved in most laboratories. In this case the flux analysis problem leads to a generally underdetermined mass balance system, as data are not sufficient to uniquely define the metabolic fluxes. Our main contribution is to show that, provided the system of mass balance equations is well-posed, although it is underdetermined, very narrow intervals may be found for most fluxes. The importance of checking the well-posedness of the problem is emphasized and the influence of the number of available measurements on the accuracy of the metabolic flux intervals is systematically investigated. In all cases the computed flux intervals are bounded and a single well defined value is obtained for the formation rates of the cellular macromolecules (proteins, DNA, RNA, lipids) that are not measured. The potential gain of a simple theoretical assumption regarding the metabolism of Threonine is also discussed and compared with an optimal solution calculated by maximizing the biomass formation rate. Alternative network structures obtained by inverting the direction of reversible reactions are also considered. Finally, the results of the metabolic flux analysis are exploited to estimate the total energy production resulting from the metabolism of growing CHO-320 cells.
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Affiliation(s)
- F Zamorano
- Department of Automatic Control, University of Mons, Boulevard Dolez 31, 7000 Mons, Belgium.
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25
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Bioreactors and bioseparation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 122:105-50. [PMID: 20396995 DOI: 10.1007/10_2010_70] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Along with the rapid development of life science, great attention has been increasingly given to the biotechnological products of cell cultivation technology. In the course of industrialization, bioreactor and bioproduct separation techniques are the two essential technical platforms. In this chapter, the current situation and development prospects of bioreactor techniques in China are systematically discussed, starting with the elucidation of bioreactor processes and the principle of process optimization. Separation technology for biological products is also briefly introduced.At present, a series of bioreactors made by Chinese enterprises have been widely used for laboratory microbial cultivation, process optimization studies, and large-scale production. In the course of bioprocess optimization studies, the complicated bioprocesses in a bioreactor could be resolved into different reaction processes on three scales, namely genetic, cellular, and bioreactor scales. The structural varieties and nonlinear features of various scales of bioprocess systems was discussed through considering the mutual effects of different scale events, namely material flux, energy flux, and information flux, and the optimization approach for bioprocesses was proposed by taking the analysis of metabolic flux and multiscale consideration as a core strategy.In order to realize such an optimization approach, a bioreactor system based on association analysis of multiscale parameters was elaborated, and process optimization of many biological products were materialized, which resulted in great improvement in production efficiency. In designing and manufacturing large-scale bioreactors, the principle of scaling up a process incorporated with flow field study and physiological features in a bioreactor was suggested according to the criterion for the scale-up of cellular physiological and metabolic traits. The flow field features of a bioreactor were investigated through computational fluid dynamics (CFD), and the design of a bioreactor configuration was carried out depending on multiscale studies of parameters correlation in a bioprocess. With respect to the development trend of bioreactor studies in China, the significance of the development of microbioreactors for high throughput strain screening and large-scale bioreactors for animal cell cultivation were put forward. Finally, the importance of studies of systems biology for bioprocesses based on bioinformation processing was raised, and the necessity of establishing a bioprocess information database and local area network (LAN) were emphasized as well.Bioseparation engineering plays a key role in biotechnology production. At present, many difficulties need to be resolved in the area. Scientists of China have made considerable progress in bioseparation engineering. This progress includes chromatography media, recycling aqueous two-phase systems (ATPS), affinity precipitation, molecular imprinting, renaturation and modification of proteins, protein fractionation using ultrafiltration (UF), ion liquid separation of bioproducts, reverse micellar extraction, etc. The preparation of bioseparation materials, as well as part of bioseparation process research development in the past 5 years, are introduced here.
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26
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Selvarasu S, Wong VV, Karimi IA, Lee DY. Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling. Biotechnol Bioeng 2009; 102:1494-504. [DOI: 10.1002/bit.22186] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Mukwena NT, Al-Rubeai M. Apoptosis and its suppression in hepatocytes culture. Cytotechnology 2008; 46:79-95. [PMID: 19003264 DOI: 10.1007/s10616-005-8306-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Accepted: 05/18/2005] [Indexed: 11/25/2022] Open
Abstract
In order to achieve the goal of developing extracorporeal liver support devices, it is necessary to optimise bioprocess environment such that viability and function are maximised. Optimising culture medium composition and controlling the constitution of the cellular microenvironment within the bioreactor have for many years been considered vital to achieving these aims. Coupled to this is the need to understand apoptosis, the prime suspect in the demise of animal cultures, including those of hepatocytes. Results presented here show that absent nutrients including glucose and amino acids play a substantial part in the induction of apoptosis. The use of chemical apoptosis inhibitors was utilised to investigate key components of hepatic apoptosis where caspases, predominantly caspase 8, were implicated in staurosporine (STS)-induced HepZ apoptosis. Caspase 9 and 3 activation although recorded was of less significance. Interestingly, these results were not consistent with those of mitochondrial membrane depolarisation where inhibition of caspase activation appeared to drive depolarisation. Inhibition of mitochondrial permeability transition and use of anti-oxidants was unsuccessful in reducing apoptosis, caspase activation and mitochondrial membrane depolarisation. In further studies, the anti-apoptotic gene bcl-2 was over-expressed in HepZ, resulting in a cell line that was more robust and resistant to death induced by glucose and cystine deprivation and treatment with STS. Bcl-2 did not however show significant cytoprotectivity where apoptosis was stimulated by deprivation of glutamine and serum. Overall, results indicated that although apoptosis can be curbed by use of chemical inhibitors and genetic manipulation, their success is dependent on apoptotic stimuli.
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Affiliation(s)
- Nyaradzo T Mukwena
- Department of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK
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28
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Zhou F, Bi JX, Zeng AP, Yuan JQ. A macrokinetic and regulator model for myeloma cell culture based on metabolic balance of pathways. Process Biochem 2006. [DOI: 10.1016/j.procbio.2006.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Afeyan NB, Cooney CL. Professor Daniel I.C. Wang: A legacy of education, innovation, publication, and leadership. Biotechnol Bioeng 2006; 95:206-217. [PMID: 16933287 DOI: 10.1002/bit.21078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Noubar B Afeyan
- Flagship Ventures, One Memorial Drive, 7th Floor, Cambridge, Massachusetts
- Sloan School of Management, Massachusetts Institute of Technology, 50 Memorial Drive, Cambridge, Massachusetts
| | - Charles L Cooney
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307
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Gambhir A, Korke R, Lee J, Fu PC, Europa A, Hu WS. Analysis of cellular metabolism of hybridoma cells at distinct physiological states. J Biosci Bioeng 2005; 95:317-27. [PMID: 16233414 DOI: 10.1016/s1389-1723(03)80062-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2002] [Accepted: 08/26/2002] [Indexed: 10/27/2022]
Abstract
Hybridoma cells were cultivated in a chemically defined medium in continuous cultures. These cultures reached different steady states marked by distinctive cell metabolism depending on the culture conditions leading to the steady state. Those steady states with different metabolism are characterized by different stoichiometric ratios of lactate production to glucose consumption (deltaL/deltaG). The specific consumption rates of glucose, glutamine and other amino acids are reduced when DeltaL DeltaG reduces. Those steady states do not have a few discrete values of deltaL/deltaGs , rather they span from a high deltaL/deltaG state (> 1.0) to an intermediate state (0.1 < or = deltaL/deltaG < or = 1.0), and reduces even further at a low deltaL/deltaG state (< 0.1). Metabolic flux analysis was performed to compare energy metabolism of cells in cultures representing these three distinct metabolic states. The material balance on carbon and nitrogen was facilitated by the use of chemically defined medium. The formation of biomass was systematically estimated. It was revealed that all glycolysis and TCA cycle fluxes are reduced as deltaL/deltaG decreases. At the low deltaL/deltaG state, a reduction in amino acid specific consumption rate is accompanied by a reduction in all the fluxes around pyruvate. The analysis also shows that the outflux from the TCA cycle to form pyruvate, which contributes to lactate formation, is possibly linked to the higher consumption rate of amino acids at the high deltaL/deltaG state. Taken together the results suggest the amino acid metabolism plays an important role in reducing lactate production in mammalian cell culture.
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Affiliation(s)
- Anshu Gambhir
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455-0132, USA
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31
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Henry O, Perrier M, Kamen A. Metabolic flux analysis of HEK-293 cells in perfusion cultures for the production of adenoviral vectors. Metab Eng 2005; 7:467-76. [PMID: 16198135 DOI: 10.1016/j.ymben.2005.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 08/05/2005] [Accepted: 08/09/2005] [Indexed: 11/29/2022]
Abstract
To meet increasing needs of adenovirus vectors for gene therapy programs, development of efficient and reproducible production processes is required. Perfusion cultures were employed to allow infection at greater cell concentrations. In an effort to define culture conditions resulting in enhanced productivities, experiments performed at different feed rates and infected at various cell densities were compared using metabolic flux analysis. The highest specific product yields were achieved in experiments performed at high perfusion rates and/or low cell concentrations. The intracellular flux analysis revealed that these experiments exhibited greater glycolytic fluxes, slightly higher TCA fluxes, and greater ATP production rates at the time of infection. In contrast, cultures infected at high cell density and/or low medium renewal rates were characterized by a more efficient utilization of glucose at the time of infection, but the specific product yields achieved were lower. The intracellular flux analysis provided a rational basis for the implementation of a feeding strategy that allowed successful infection at a density of 5x10(6)cells/ml.
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Affiliation(s)
- O Henry
- Institut de Recherche en Biotechnologie, CNRC, 6100 avenue Royalmount, and Ecole Polytechnique de Montréal, Campus de l'Université de Montréal, Montréal, Qué., Canada
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32
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Bcl-2 over-expression reduced the serum dependency and improved the nutrient metabolism in a NS0 cells culture. BIOTECHNOL BIOPROC E 2005. [DOI: 10.1007/bf02932022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Keane JT, Ryan D, Gray PP. Effect of shear stress on expression of a recombinant protein by Chinese hamster ovary cells. Biotechnol Bioeng 2003; 81:211-20. [PMID: 12451557 DOI: 10.1002/bit.10472] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A flow chamber was used to impart a steady laminar shear stress on a recombinant Chinese hamster ovary (CHO) cell line expressing human growth hormone (hGH). The cells were subjected to shear stress ranging from 0.005 to 0.80 N m(-2). The effect of shear stress on the cell specific glucose uptake, cell specific hGH, and lactate productivity rates were calculated. No morphological changes to the cells were observed over the range of shear stresses examined. When the cells were subjected to 0.10 N m(-2) shear in protein-free media without Pluronic F-68, recombinant protein production ceased with no change in cell morphology, whereas control cultures were expressing hGH at 0.35 microg/10(6 )cells/h. Upon addition of the shear protectants, Pluronic F-68 (0.2% [w/v]) or fetal bovine serum (1.0% [v/v] FBS), the productivity of the cells was restored. The effect of increasing shear stress on the cells in protein-free medium containing Pluronic F-68 was also investigated. Cell specific metabolic rates were calculated for cells under shear stress and for no-shear control cultures performed in parallel, with shear stress rates expressed as a percentage of those obtained for control cultures. Upon increasing shear from 0.005 to 0.80 N m(-2), the cell specific hGH productivity decreased from 100% at 0.005 N m(-2) to 49% at 0.80 N m(-2) relative to the no-shear control. A concurrent increase in the glucose uptake rate from 115% at 0.01 N m(-2) to 142% at 0.80 N m(-2), and decreased lactate productivity from 92% to 50%, revealed a change in the yield of products from glucose compared with the static control. It was shown that shear stress, at sublytic levels in medium containing Pluronic F-68, could decrease hGH specific productivity.
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Affiliation(s)
- Julian T Keane
- Department of Biotechnology, University of New South Wales, Sydney 2052, Australia.
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34
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Protein production by large-scale mammalian cell culture. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0167-7306(03)38035-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Xie L, Pilbrough W, Metallo C, Zhong T, Pikus L, Leung J, Auniņs JG, Zhou W. Serum-free suspension cultivation of PER.C6(R) cells and recombinant adenovirus production under different pH conditions. Biotechnol Bioeng 2002; 80:569-79. [PMID: 12355468 DOI: 10.1002/bit.10443] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
PER.C6(R) cell growth, metabolism, and adenovirus production were studied in head-to-head comparisons in stirred bioreactors under different pH conditions. Cell growth rate was found to be similar in the pH range of 7.1-7.6, while a long lag phase and a slower growth rate were observed at pH 6.8. The specific consumption rates of glucose and glutamine decreased rapidly over time during batch cell growth, as did the specific lactate and ammonium production rates. Cell metabolism in both infected and uninfected cultures was very sensitive to culture pH, resulting in dramatic differences in glucose/glutamine consumption and lactate/ammonium production under different pH conditions. It appeared that glucose metabolism was suppressed at low pH but the efficiency of energy production from glucose was enhanced. Adenovirus infection resulted in profound changes in cell growth and metabolism. Cell growth was largely arrested under all pH conditions, while glucose consumption and lactate production were elevated post virus infection. Virus infection induced a reduction in glutamine consumption at low pH but an increase at high pH. The optimal pH for adenovirus production was found to be 7.3 under the experimental conditions used in the study. Deviations from this optimum resulted in significant reductions of virus productivity. The results indicate that culture pH is a very critical process parameter in PER.C6(R) cell culture and adenovirus production.
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Affiliation(s)
- Liangzhi Xie
- Fermentation and Cell Culture, BioProcess R&D, Merck Research Laboratories, Sumneytown Pike, West Point, Pennsylvania 19486, USA.
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Zhao Y, Lin YH. Distribution of ATP and reducing equivalents in Corynebacterium glutamicum during amino acid resolution. Process Biochem 2002. [DOI: 10.1016/s0032-9592(02)00033-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Nadeau I, Gilbert PA, Jacob D, Perrier M, Kamen A. Low-protein medium affects the 293SF central metabolism during growth and infection with adenovirus. Biotechnol Bioeng 2002; 77:91-104. [PMID: 11745177 DOI: 10.1002/bit.10128] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this study the metabolism of 293SF cells grown in serum-free and low-protein medium was analyzed. This cell line is known for its ability to replicate recombinant adenovirus, mainly used in gene therapy applications. A complete model composed of the main glycolytic, glutaminolytic, and amino acids pathways, as well as the internalization fluxes of certain compounds into the mitochondria, is used for metabolic flux calculations. The pentose-phosphate cycle is also added to the biochemical reactions set and was independently measured with labeled 14C-glucose. Different feeding strategies in two different media were analyzed with the model, and the theoretical ATP production was also calculated. The two media were similar in their glucose and amino acid composition, but one contained BSA at 1g/L whereas the other had a very low protein content. Use of low-protein medium resulted in up to fourfold higher adenoviral vector production. In this medium, glucose utilization was more efficient, as it entered the TCA cycle more efficiently. Also, lower glutamine and amino acids consumption were observed as well as lower lactate and ammonia production. This increased TCA activity led to a twofold higher ATP production in the low-protein medium.
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Affiliation(s)
- I Nadeau
- Institut de recherche en biotechnologie, CNRC, 6100 avenue Royalmount, Montréal, Québec H4P 2R2, Canada
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Burgard AP, Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng 2001; 74:364-75. [PMID: 11427938 DOI: 10.1002/bit.1127] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An optimization-based procedure for studying the response of metabolic networks after gene knockouts or additions is introduced and applied to a linear flux balance analysis (FBA) Escherichia coli model. Both the gene addition problem of optimally selecting which foreign genes to recombine into E. coli, as well as the gene deletion problem of removing a given number of existing ones, are formulated as mixed-integer optimization problems using binary 0-1 variables. The developed modeling and optimization framework is tested by investigating the effect of gene deletions on biomass production and addressing the maximum theoretical production of the 20 amino acids for aerobic growth on glucose and acetate substrates. In the gene deletion study, the smallest gene set necessary to achieve maximum biomass production in E. coli is determined for aerobic growth on glucose. The subsequent gene knockout analysis indicates that biomass production decreases monotonically, rendering the metabolic network incapable of growth after only 18 gene deletions. In the gene addition study, the E. coli flux balance model is augmented with 3,400 non-E. coli reactions from the KEGG database to form a multispecies model. This model is referred to as the Universal model. This study reveals that the maximum theoretical production of six amino acids could be improved by the addition of only one or two genes to the native amino acid production pathway of E. coli, even though the model could choose from 3,400 foreign reaction candidates. Specifically, manipulation of the arginine production pathway showed the most promise with 8.75% and 9.05% predicted increases with the addition of genes for growth on glucose and acetate, respectively. The mechanism of all suggested enhancements is either by: 1) improving the energy efficiency and/or 2) increasing the carbon conversion efficiency of the production route.
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Affiliation(s)
- A P Burgard
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Energetics and carbon metabolism during growth of microalgal cells under photoautotrophic, mixotrophic and cyclic light-autotrophic/dark-heterotrophic conditions. Biochem Eng J 2000; 6:87-102. [PMID: 10959082 DOI: 10.1016/s1369-703x(00)00080-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chlorella pyrenoidosa was cultivated under photoautotrophic, mixotrophic and cyclic light-autotrophic/dark-heterotrophic conditions. The influence of light on the carbon and energy metabolism of microalgae was investigated by the use of metabolic flux analysis. The respiratory activity of microalgae in the light was assessed from the autotrophic flux distribution. Results showed that the glycolytic pathway, tricarboxylic acid cycle and mitochondrial oxidative phosphorylation maintained high activities during illumination, indicating little effect of light on these pathways, while the flux through the pentose phosphate pathway during illumination was very small due to the light-mediated regulation. The theoretical yields of biomass on ATP decreased in the following order: heterotrophic culture>mixotrophic culture>autotrophic culture, and a significant amount of the available ATP was required for maintenance processes in microalgal cells. The energy conversion efficiency between the supplied energy to culture, the absorbed energy by cells and the free energy conserved in ATP were analyzed for the different cultures. Analysis showed that the heterotrophic culture generated more ATP from the supplied energy than the autotrophic and mixotrophic cultures. The maximum thermodynamic efficiency of ATP production from the absorbed energy, which was calculated from the metabolic fluxes at zero growth rate, was the highest in the heterotrophic culture and as low as 16% in the autotrophic culture. By evaluating the energy economy through the energy utilization efficiency, it was found that the biomass yield on the supplied energy was the lowest in the autotrophic cultivation, and the cyclic culture gave the most efficient utilization of energy for biomass production.
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Xie L, Wang DIC. Material balance studies on animal cell metabolism using a stoichiometrically based reaction network. Biotechnol Bioeng 2000; 52:579-90. [DOI: 10.1002/(sici)1097-0290(19961205)52:5<579::aid-bit5>3.0.co;2-g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Simpson NH, Singh RP, Perani A, Goldenzon C, Al-Rubeai M. In hybridoma cultures, deprivation of any single amino acid leads to apoptotic death, which is suppressed by the expression of the bcl-2 gene. Biotechnol Bioeng 1998; 59:90-8. [PMID: 10099318 DOI: 10.1002/(sici)1097-0290(19980705)59:1<90::aid-bit12>3.0.co;2-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The transfection of murine hybridomas with the apoptosis suppressor gene bcl-2 has been reported to result in the extension of batch culture duration, leading to significant improvements in culture productivity. In the present study, the effect of deprivation, individually, of each amino acid found in culture medium was examined to characterize the chemical environment of the culture in terms of its propensity to induce apoptosis. When cells were deprived of each amino acid, individually for 48 h, the majority of cell deaths in each case occurred by apoptosis, with essential amino acids being clearly most effective. For nearly all the amino acids, the viability of the bcl-2 cell line cultures was greater than 70% after 48 h, representing a substantial improvement in viability over control cell line cultures. Time course studies revealed that the induction of death could be divided into two phases. Initially, following the deprivation of a single essential amino acid, there was a period of time during which all the control cell line cultures retained high viability. The duration of this phase varied from 15 h in the case of lysine deprivation, through to 40 h in the case methionine deprivation. In the second phase of deprivation, the cultures exhibited an abrupt and rapid collapse in viability. The time taken for the viability to fall to 50% was similar for each amino acid. In every case, the duration of both phases of the bcl-2 cultures was considerably extended. Specific utilization rates were increased during the control cultures relative to the bcl-2 cultures for both the growth phase (ranging between 2% and 57% higher than the bcl-2 cultures) and the death phase (ranging between 172% to 1900% higher than the bcl-2 culture).
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Affiliation(s)
- N H Simpson
- Centre for Bioprocess Engineering, School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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