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Nath SS, Villadsen J. Modeling dynamics of chemical reaction networks using electrical analogs: Application to autocatalytic reactions. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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2
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Nath SS, Nielsen LK, Villadsen J. Elucidating dynamics and mechanism of cyclic bioreaction networks using topologically-equivalent electrical circuits. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Narad P, Naresh G, Sengupta A. Metabolomics and flux balance analysis. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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4
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Jensen PR, Matos MRA, Sonnenschein N, Meier S. Combined In-Cell NMR and Simulation Approach to Probe Redox-Dependent Pathway Control. Anal Chem 2019; 91:5395-5402. [PMID: 30896922 DOI: 10.1021/acs.analchem.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic response of intracellular reaction cascades to changing environments is a hallmark of living systems. As metabolism is complex, mechanistic models have gained popularity for describing the dynamic response of cellular metabolism and for identifying target genes for engineering. At the same time, the detailed tracking of transient metabolism in living cells on the subminute time scale has become amenable using dynamic nuclear polarization-enhanced 13C NMR. Here, we suggest an approach combining in-cell NMR spectroscopy with perturbation experiments and modeling to obtain evidence that the bottlenecks of yeast glycolysis depend on intracellular redox state. In pre-steady-state glycolysis, pathway bottlenecks shift from downstream to upstream reactions within a few seconds, consistent with a rapid decline in the NAD+/NADH ratio. Simulations using mechanistic models reproduce the experimentally observed response and help identify unforeseen biochemical events. Remaining inaccuracies in the computational models can be identified experimentally. The combined use of rapid injection NMR spectroscopy and in silico simulations provides a promising method for characterizing cellular reactions with increasing mechanistic detail.
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Affiliation(s)
- Pernille R Jensen
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Marta R A Matos
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Nikolaus Sonnenschein
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Sebastian Meier
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
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5
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Souza SSD, Castro JDV, Porto LM. MODELING THE CORE METABOLISM OF Komagataeibacter hansenii ATCC 23769 TO EVALUATE NANOCELLULOSE BIOSYNTHESIS. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2018. [DOI: 10.1590/0104-6632.20180353s20170327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Matsuura T, Hosoda K, Shimizu Y. Robustness of a Reconstituted Escherichia coli Protein Translation System Analyzed by Computational Modeling. ACS Synth Biol 2018; 7:1964-1972. [PMID: 30004679 DOI: 10.1021/acssynbio.8b00228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Robustness against environmental changes is one of the major features of biological systems, but its origin is not well understood. We recently constructed a large-scale computational model of an Escherichia coli-based reconstituted in vitro translation system that enumerates all protein synthesis processes in detail. Our model synthesizes a formyl-Met-Gly-Gly tripeptide (MGG peptide) from 27 initial molecular components through 968 biochemical reactions. Among the 968 kinetic parameters, 483 are nonzero parameters, and the simulator was used to determine how perturbations of 483 individual reactions affect the complex reaction network. We found that even when the kinetic parameter was changed from 100- to 0.01-fold, 94% of the changes hardly affected the two indicators of reaction dynamics in MGG peptide synthesis, which represent the yield of the MGG peptide and the initial lag-time of the peptide synthesis. Moreover, none of the indicators increased proportionally to these changes: e.g., a 100-fold increase in the kinetic parameter increased the yield by only 2.2-fold at most, indicating the insensitivity of the reaction network to perturbation. Robustness and insensitivity are likely to be a common feature of large-scale biological reaction networks.
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Affiliation(s)
- Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazufumi Hosoda
- Institute for Academic Initiatives, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
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7
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Young EM, Zhao Z, Gielesen BE, Wu L, Benjamin Gordon D, Roubos JA, Voigt CA. Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast. Metab Eng 2018; 48:33-43. [DOI: 10.1016/j.ymben.2018.05.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 11/25/2022]
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8
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Vignolini T, Mengoni A, Fondi M. Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models. Methods Mol Biol 2018; 1716:177-196. [PMID: 29222754 DOI: 10.1007/978-1-4939-7528-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Intraspecific genomic exchanges happen frequently between bacteria living in the same natural environment and can also be performed artificially in the laboratory for basic research or genetic/metabolic engineering purposes. In silico metabolic reconstruction and simulation of the metabolism of the hybrid strains that result from these processes can be used to predict the phenotypic outcome of such genomic rearrangements; this can be especially helpful as a designing tool in the purview of synthetic biology. However, reconstructing the metabolism of a bacterium with a hybrid genome through in silico approaches is not a trivial task, as it requires taking into account the complex relationships existing between metabolic genes and how they change (or remain unchanged) when new genes are placed in a different genomic context. Furthermore, in order to "mix" the metabolic models of different bacterial strains one needs at least two different metabolic models to begin with, and reconstructing a genome-scale model from the ground up is a challenging task itself, requiring an intensive manual effort and a great deal of information. In this chapter, we propose two general protocols to address the aforementioned issues of: (1) quickly generating strain-specific metabolic models, given the relevant genomic sequence and an already existing, high-quality metabolic model of a different strain belonging to the same species, and (2) reconstructing the metabolic model of a hybrid strain containing genomic elements from two different parental strains.
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Affiliation(s)
- Tiziano Vignolini
- LENS, European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Florence, Italy.
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9
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Herold S, Krämer D, Violet N, King R. Rapid process synthesis supported by a unified modular software framework. Eng Life Sci 2017; 17:1202-1214. [PMID: 32624748 DOI: 10.1002/elsc.201600020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 10/12/2016] [Accepted: 01/05/2017] [Indexed: 11/11/2022] Open
Abstract
Although known to be very powerful, the widespread application of model-based techniques is still significantly hampered in the area of bio-processes. Reasons for this situation can be found along the whole chain to set up and implement such approaches. In a time-consuming step, models are typically hand-crafted. Whether alternatives of better models exist to actually fulfill the final goals is undocumented, most often even unknown. In a next step, model-based process control methods are hand-coded in an error-prone procedure. For many of these methods given in the literature, only simulation studies are shown, leaving the interested reader with the unanswered question whether the implementation of a specific method in a real process is viable. As the potentially time-consuming implementation of such a method presents a risk for a rapid process development, promising candidates may be overlooked. To remediate this unsatisfactory situation, a combination of theoretical methods and information technology is proposed here. By an exemplarily realized software tool, it is shown how such an environment helps to promote model-based optimization, supervision, and control of bio-processes and allows for an inexpensive test of new ideas as well in real-life experiments. The contribution concentrates on an overview of a possible software architecture with respect to necessary methods and a meaningful information strategy, highlighting some of the more crucial building blocks. Experimental results exploiting parts of the proposed methods are given for a yeast strain synthesizing a product of industrial interest.
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Affiliation(s)
- Sebastian Herold
- Chair of Measurement and Control Technische Universität Berlin Berlin Germany
| | - Dominik Krämer
- Chair of Measurement and Control Technische Universität Berlin Berlin Germany
| | - Norman Violet
- Department Experimental Toxicology and ZEBET Federal Institute for Risk Assessment Berlin Germany
| | - Rudibert King
- Chair of Measurement and Control Technische Universität Berlin Berlin Germany
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10
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Williams TC, Xu X, Ostrowski M, Pretorius IS, Paulsen IT. Positive-feedback, ratiometric biosensor expression improves high-throughput metabolite-producer screening efficiency in yeast. Synth Biol (Oxf) 2017; 2:ysw002. [PMID: 32995501 PMCID: PMC7513737 DOI: 10.1093/synbio/ysw002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/14/2016] [Accepted: 11/29/2016] [Indexed: 11/23/2022] Open
Abstract
Biosensors are valuable and versatile tools in synthetic biology that are used to modulate gene expression in response to a wide range of stimuli. Ligand responsive transcription factors are a class of biosensor that can be used to couple intracellular metabolite concentration with gene expression to enable dynamic regulation and high-throughput metabolite producer screening. We have established the Saccharomyces cerevisiae WAR1 transcriptional regulator and PDR12 promoter as an organic acid biosensor that can be used to detect varying levels of para-hydroxybenzoic acid (PHBA) production from the shikimate pathway and output green fluorescent protein (GFP) expression in response. The dynamic range of GFP expression in response to PHBA was dramatically increased by engineering positive-feedback expression of the WAR1 transcriptional regulator from its target PDR12 promoter. In addition, the noise in GFP expression at the population-level was controlled by normalising GFP fluorescence to constitutively expressed mCherry fluorescence within each cell. These biosensor modifications increased the high-throughput screening efficiency of yeast cells engineered to produce PHBA by 5,000-fold, enabling accurate fluorescence activated cell sorting isolation of producer cells that were mixed at a ratio of 1 in 10,000 with non-producers. Positive-feedback, ratiometric transcriptional regulator expression is likely applicable to many other transcription-factor/promoter pairs used in synthetic biology and metabolic engineering for both dynamic regulation and high-throughput screening applications.
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Affiliation(s)
- Thomas C Williams
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Xin Xu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Isak S Pretorius
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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11
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Yang Y, Guan Y, Villadsen J. System wide cofactor turnovers can propagate metabolic stability between pathways. Metab Eng Commun 2016; 3:196-204. [PMID: 29142824 PMCID: PMC5678836 DOI: 10.1016/j.meteno.2016.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/03/2016] [Indexed: 11/17/2022] Open
Abstract
Metabolic homeostasis, or low-level metabolic steady state, has long been taken for granted in metabolic engineering, and research priority has always been given to understand metabolic flux control and regulation of the reaction network. In the past, this has not caused concerns because the metabolic networks studied were invariably associated with living cells. Nowadays, there are needs to reconstruct metabolic networks, and so metabolic homeostasis cannot be taken for granted. For metabolic steady state, enzyme feedback control has been known to explain why metabolites in metabolic pathways can avoid accumulation. However, we reasoned that there are further contributing mechanisms. As a new methodology developed, we separated cofactor intermediates (CIs) from non-cofactor intermediates, and identified an appropriate type of open systems for operating putative reaction topologies. Furthermore, we elaborated the criteria to tell if a multi-enzyme over-all reaction path is of in vivo nature or not at the metabolic level. As new findings, we discovered that there are interactions between the enzyme feedback inhibition and the CI turnover, and such interactions may well lead to metabolic homeostasis, an emergent property of the system. To conclude, this work offers a new perspective for understanding the role of CIs and the presence of metabolic homeostasis in the living cell. In perspective, this work might provide clues for constructing non-natural metabolic networks using multi-enzyme reactions or by degenerating metabolic reaction networks from the living cell.
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Affiliation(s)
- Y. Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing & College of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Y.H. Guan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing & College of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - J. Villadsen
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2800, Denmark
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12
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Lomnitz JG, Savageau MA. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems. Sci Rep 2016; 6:32375. [PMID: 27578053 PMCID: PMC5006174 DOI: 10.1038/srep32375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/03/2016] [Indexed: 11/20/2022] Open
Abstract
An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values.
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Affiliation(s)
- Jason G Lomnitz
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Michael A Savageau
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA.,Department of Microbiology &Molecular Genetics, University of California, Davis, CA 95616 USA
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13
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Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Oyelade J, Isewon I, Rotimi S, Okunoren I. Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets. Bioinform Biol Insights 2016; 10:49-57. [PMID: 27199550 PMCID: PMC4869600 DOI: 10.4137/bbi.s37296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 01/15/2023] Open
Abstract
Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways. In this work, we built a qualitative PN model for the glycolysis pathway in P. falciparum and analyzed the model for its structural and quantitative properties using PN theory. From PlasmoCyc files, a total of 11 reactions were extracted; 6 of these were reversible and 5 were irreversible. These reactions were catalyzed by a total number of 13 enzymes. We extracted some of the essential reactions in the pathway using PN model, which are the possible drug targets without which the pathway cannot function. This model also helps to improve the understanding of the biological processes within this pathway.
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Affiliation(s)
- Jelili Oyelade
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Solomon Rotimi
- Department of Biological Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Ifeoluwa Okunoren
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
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15
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Coudreuse D. Insights from synthetic yeasts. Yeast 2016; 33:483-92. [PMID: 27145443 DOI: 10.1002/yea.3169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 12/17/2022] Open
Abstract
Synthetic biology is one of the most exciting strategies for the investigation of living organisms and lies at the intersection of biology and engineering. Originally developed in prokaryotes, the idea of deciphering biological phenomena through building artificial genetic circuits and studying their behaviours has rapidly demonstrated its potential in a broad range of fields in the life sciences. From the assembly of synthetic genomes to the generation of novel biological functions, yeast cells have imposed themselves as the most powerful eukaryotic model for this approach. However, we are only beginning to explore the possibilities of synthetic biology, and the perspectives it offers in a genetically amenable system such as yeasts are endless. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Damien Coudreuse
- SyntheCell Team, Institute of Genetics and Development of Rennes, CNRS UMR, 6290, Rennes, France
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16
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Ostermann S, Richhardt J, Bringer S, Bott M, Wiechert W, Oldiges M. (13)C Tracers for Glucose Degrading Pathway Discrimination in Gluconobacter oxydans 621H. Metabolites 2015; 5:455-74. [PMID: 26404385 PMCID: PMC4588806 DOI: 10.3390/metabo5030455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
Gluconobacter oxydans 621H is used as an industrial production organism due to its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. With glucose as the carbon source, up to 90% of the initial concentration is oxidized periplasmatically to gluconate and ketogluconates. Growth on glucose is biphasic and intracellular sugar catabolism proceeds via the Entner-Doudoroff pathway (EDP) and the pentose phosphate pathway (PPP). Here we studied the in vivo contributions of the two pathways to glucose catabolism on a microtiter scale. In our approach we applied specifically (13)C labeled glucose, whereby a labeling pattern in alanine was generated intracellularly. This method revealed a dynamic growth phase-dependent pathway activity with increased activity of EDP in the first and PPP in the second growth phase, respectively. Evidence for a growth phase-independent decarboxylation-carboxylation cycle around the pyruvate node was obtained from (13)C fragmentation patterns of alanine. For the first time, down-scaled microtiter plate cultivation together with (13)C-labeled substrate was applied for G. oxydans to elucidate pathway operation, exhibiting reasonable labeling costs and allowing for sufficient replicate experiments.
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Affiliation(s)
- Steffen Ostermann
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Leo-Brandt-Straße, 52428 Jülich, Germany.
| | - Janine Richhardt
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Leo-Brandt-Straße, 52428 Jülich, Germany.
| | - Stephanie Bringer
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Leo-Brandt-Straße, 52428 Jülich, Germany.
| | - Michael Bott
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Leo-Brandt-Straße, 52428 Jülich, Germany.
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Leo-Brandt-Straße, 52428 Jülich, Germany.
| | - Marco Oldiges
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Leo-Brandt-Straße, 52428 Jülich, Germany.
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17
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Ben Yahia B, Malphettes L, Heinzle E. Macroscopic modeling of mammalian cell growth and metabolism. Appl Microbiol Biotechnol 2015; 99:7009-24. [PMID: 26198881 PMCID: PMC4536272 DOI: 10.1007/s00253-015-6743-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/28/2015] [Accepted: 05/30/2015] [Indexed: 12/24/2022]
Abstract
We review major modeling strategies and methods to understand and simulate the macroscopic behavior of mammalian cells. These strategies comprise two important steps: the first step is to identify stoichiometric relationships for the cultured cells connecting the extracellular inputs and outputs. In a second step, macroscopic kinetic models are introduced. These relationships together with bioreactor and metabolite balances provide a complete description of a system in the form of a set of differential equations. These can be used for the simulation of cell culture performance and further for optimization of production.
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Affiliation(s)
- Bassem Ben Yahia
- />Biochemical Engineering Institute, Saarland University, Campus A1.5, D-66123 Saarbruecken, Germany
- />Upstream Process Sciences Biotech Sciences, UCB Pharma S.A., Avenue de l’Industrie, B-1420, Braine l’Alleud, Belgium
| | - Laetitia Malphettes
- />Upstream Process Sciences Biotech Sciences, UCB Pharma S.A., Avenue de l’Industrie, B-1420, Braine l’Alleud, Belgium
| | - Elmar Heinzle
- />Biochemical Engineering Institute, Saarland University, Campus A1.5, D-66123 Saarbruecken, Germany
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18
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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19
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Birkenmeier M, Mack M, Röder T. Thermodynamic and Probabilistic Metabolic Control Analysis of Riboflavin (Vitamin B2) Biosynthesis in Bacteria. Appl Biochem Biotechnol 2015; 177:732-52. [DOI: 10.1007/s12010-015-1776-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/28/2022]
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20
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Hartmann A, Schreiber F. Integrative analysis of metabolic models - from structure to dynamics. Front Bioeng Biotechnol 2015; 2:91. [PMID: 25674560 PMCID: PMC4306315 DOI: 10.3389/fbioe.2014.00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/30/2014] [Indexed: 01/09/2023] Open
Abstract
The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the context of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM (2) - Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.
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Affiliation(s)
- Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Falk Schreiber
- Monash University, Melbourne, VIC, Australia
- Martin-Luther-University Halle-Wittenberg, Halle, Germany
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21
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Are Dynamic Mechanistic Explanations Still Mechanistic? HISTORY, PHILOSOPHY AND THEORY OF THE LIFE SCIENCES 2015. [DOI: 10.1007/978-94-017-9822-8_12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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García Sánchez CE, Torres Sáez RG. Comparison and analysis of objective functions in flux balance analysis. Biotechnol Prog 2014; 30:985-91. [PMID: 25044958 DOI: 10.1002/btpr.1949] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/16/2014] [Indexed: 11/10/2022]
Abstract
Flux balance analysis (FBA) is currently one of the most important and used techniques for estimation of metabolic reaction rates (fluxes). This mathematical approach utilizes an optimization criterion in order to select a distribution of fluxes from the feasible space delimited by the metabolic reactions and some restrictions imposed over them, assuming that cellular metabolism is in steady state. Therefore, the obtained flux distribution depends on the specific objective function used. Multiple studies have been aimed to compare distinct objective functions at given conditions, in order to determine which of those functions produces values of fluxes closer to real data when used as objective in the FBA; in other words, what is the best objective function for modeling cell metabolism at a determined environmental condition. However, these comparative studies have been designed in very dissimilar ways, and in general, several factors that can change the ideal objective function in a cellular condition have not been adequately considered. Additionally, most of them have used only one dataset for representing one condition of cell growth, and different measuring techniques have been used. For these reasons, a rigorous study on the effect of factors such as the quantity of used data, the number and type of fluxes utilized as input data, and the selected classification of growth conditions, are required in order to obtain useful conclusions for these comparative studies, allowing limiting clearly the application range on any of those results.
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Affiliation(s)
- Carlos Eduardo García Sánchez
- Grupo de Investigación en Fluidos y Energía, Corporación Centro de Desarrollo Tecnológico del Gas, Parque Tecnológico UIS Guatiguará Km 2 vía Refugio, Piedecuesta, Santander, Colombia
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Sarrafzadeh MH, Schorr-Galindo S, La HJ, Oh HM. Aeration effects on metabolic events during sporulation of Bacillus thuringiensis. J Microbiol 2014; 52:597-603. [PMID: 24972809 DOI: 10.1007/s12275-014-3547-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 04/15/2014] [Accepted: 04/19/2014] [Indexed: 11/28/2022]
Abstract
The metabolism of Bacillus thuringiensis during its sporulation process was investigated under different concentrations of oxygen. At the beginning of sporulation, the aeration conditions were regulated to obtain different oxygen transfer rates (OTR) in four separate fermentations, representing interrupted, limited, non-limited, and saturated oxygenation, respectively. A higher OTR resulted in a higher pH, up to about 9 in the case of saturated oxygenation, while the interrupted oxygenation resulted in a significantly acidic culture. In contrast, the absence of oxygen resulted in rapid sporangia lysis and caused acidification of the medium, indicating a distinctly different sporangia composition and different metabolism. The bacterium also showed different CO2 production rates during sporulation, although a maximum point was observed in every case.With a higher OTR, the maximal value was observed after a longer time and at a lower value (40, 26, and 13 mmol/L/h for limited, non-limited, and saturated cases, respectively). Despite the exhaustion of glucose prior to the sporulation phase, the interrupted oxygenation resulted in acetate, lactate, and citrate in the medium with a maximum concentration of 4.8, 1.3, and 5.0 g/L, respectively. Notwithstanding, while the metabolic events differed visibly in the absence of oxygen, once sporulation was triggered, it was completed, even in the case of an interrupted oxygen supply.
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Affiliation(s)
- Mohammad H Sarrafzadeh
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, P.O. Box 11155-4563, Iran
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Villafaña-Rojas J, González-Reynoso O, Alcaraz-González V, González-García Y, González-Álvarez V, Solís-Pacheco JR, Aguilar-Uscanga B, Gómez-Hermosillo C. Asymptotic Observers a tool to estimate metabolite concentrations under transient state conditions in biological systems: Determination of intermediate metabolites in the pentose phosphate pathway of Saccharomyces cerevisiae. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Garcia-Albornoz MA, Nielsen J. Application of Genome-Scale Metabolic Models in Metabolic Engineering. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
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Cintolesi A, Rodríguez-Moyá M, Gonzalez R. Fatty acid oxidation: systems analysis and applications. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:575-85. [DOI: 10.1002/wsbm.1226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/26/2013] [Accepted: 03/29/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Angela Cintolesi
- Department of Chemical and Biomolecular Engineering; Rice University; Houston TX USA
| | - María Rodríguez-Moyá
- Department of Chemical and Biomolecular Engineering; Rice University; Houston TX USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering; Rice University; Houston TX USA
- Department of Bioengineering; Rice University; Houston TX USA
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Klanchui A, Vorapreeda T, Vongsangnak W, Khannapho C, Cheevadhanarak S, Meechai A. Systems biology and metabolic engineering of Arthrospira cell factories. Comput Struct Biotechnol J 2012; 3:e201210015. [PMID: 24688675 PMCID: PMC3962090 DOI: 10.5936/csbj.201210015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/19/2012] [Accepted: 11/22/2012] [Indexed: 12/24/2022] Open
Abstract
Arthrospira are attractive candidates to serve as cell factories for production of many valuable compounds useful for food, feed, fuel and pharmaceutical industries. In connection with the development of sustainable bioprocessing, it is a challenge to design and develop efficient Arthrospira cell factories which can certify effective conversion from the raw materials (i.e. CO2 and sun light) into desired products. With the current availability of the genome sequences and metabolic models of Arthrospira, the development of Arthrospira factories can now be accelerated by means of systems biology and the metabolic engineering approach. Here, we review recent research involving the use of Arthrospira cell factories for industrial applications, as well as the exploitation of systems biology and the metabolic engineering approach for studying Arthrospira. The current status of genomics and proteomics through the development of the genome-scale metabolic model of Arthrospira, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies are discussed. At the end, the perspective and future direction on Arthrospira cell factories for industrial biotechnology are presented.
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Affiliation(s)
- Amornpan Klanchui
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), KlongLuang, Pathumthani, Thailand
| | - Tayvich Vorapreeda
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu 215006, China
| | - Chiraphan Khannapho
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand ; Devision of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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Xu C, Liu L, Zhang Z, Jin D, Qiu J, Chen M. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl Microbiol Biotechnol 2012. [DOI: 10.1007/s00253-012-4543-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Veloz T, Razeto-Barry P, Dittrich P, Fajardo A. Reaction networks and evolutionary game theory. J Math Biol 2012. [DOI: 10.1007/s00285-012-0626-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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García Sánchez CE, Vargas García CA, Torres Sáez RG. Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives. PLoS One 2012; 7:e43006. [PMID: 22912775 PMCID: PMC3415429 DOI: 10.1371/journal.pone.0043006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/16/2012] [Indexed: 11/21/2022] Open
Abstract
Background The main objective of flux balance analysis (FBA) is to obtain quantitative predictions of metabolic fluxes of an organism, and it is necessary to use an appropriate objective function to guarantee a good estimation of those fluxes. Methodology In this study, the predictive performance of FBA was evaluated, using objective functions arising from the linear combination of different cellular objectives. This approach is most suitable for eukaryotic cells, owing to their multiplicity of cellular compartments. For this reason, Saccharomyces cerevisiae was used as model organism, and its metabolic network was represented using the genome-scale metabolic model iMM904. As the objective was to evaluate the predictive performance from the FBA using the kind of objective function previously described, substrate uptake and oxygen consumption were the only input data used for the FBA. Experimental information about microbial growth and exchange of metabolites with the environment was used to assess the quality of the predictions. Conclusions The quality of the predictions obtained with the FBA depends greatly on the knowledge of the oxygen uptake rate. For the most of studied classifications, the best predictions were obtained with “maximization of growth”, and with some combinations that include this objective. However, in the case of exponential growth with unknown oxygen exchange flux, the objective function “maximization of growth, plus minimization of NADH production in cytosol, plus minimization of NAD(P)H consumption in mitochondrion” gave much more accurate estimations of fluxes than the obtained with any other objective function explored in this study.
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Affiliation(s)
- Carlos Eduardo García Sánchez
- Escuela de Ingeniería Química, Grupo de Investigación en Bioquímica y Microbiología, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia.
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Moisset P, Vaisman D, Cintolesi A, Urrutia J, Rapaport I, Andrews B, Asenjo J. Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters. Biotechnol Bioeng 2012; 109:2325-39. [DOI: 10.1002/bit.24503] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 11/12/2022]
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Rohwer JM. Kinetic modelling of plant metabolic pathways. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2275-92. [PMID: 22419742 DOI: 10.1093/jxb/ers080] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
This paper provides a review of kinetic modelling of plant metabolic pathways as a tool for analysing their control and regulation. An overview of different modelling strategies is presented, starting with those approaches that only require a knowledge of the network stoichiometry; these are referred to as structural. Flux-balance analysis, metabolic flux analysis using isotope labelling, and elementary mode analysis are briefly mentioned as three representative examples. The main focus of this paper, however, is a discussion of kinetic modelling, which requires, in addition to the stoichiometry, a knowledge of the kinetic properties of the constituent pathway enzymes. The different types of kinetic modelling analysis, namely time-course simulation, steady-state analysis, and metabolic control analysis, are explained in some detail. An overview is presented of strategies for obtaining model parameters, as well as software tools available for simulation of such models. The kinetic modelling approach is exemplified with discussion of three models from the general plant physiology literature. With the aid of kinetic modelling it is possible to perform a control analysis of a plant metabolic system, to identify potential targets for biotechnological manipulation, as well as to ascertain the regulatory importance of different enzymes (including isoforms of the same enzyme) in a pathway. Finally, a framework is presented for extending metabolic models to the whole-plant scale by linking biochemical reactions with diffusion and advective flow through the phloem. Future challenges include explicit modelling of subcellular compartments, as well as the integration of kinetic models on the different levels of the cellular and organizational hierarchy.
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Affiliation(s)
- Johann M Rohwer
- Triple-J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa.
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Chao TC, Hansmeier N. The current state of microbial proteomics: Where we are and where we want to go. Proteomics 2012; 12:638-50. [DOI: 10.1002/pmic.201100381] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 08/15/2011] [Accepted: 08/22/2011] [Indexed: 11/11/2022]
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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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Dimitrov S, Pavlov T, Veith G, Mekenyan O. Simulation of chemical metabolism for fate and hazard assessment. I: approach for simulating metabolism. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:699-718. [PMID: 21999104 DOI: 10.1080/1062936x.2011.623323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Information regarding the metabolism of xenobiotic chemicals plays a central role in regulatory risk assessments. In regulatory programmes where metabolism studies are required, the studies of metabolic pathways are often incomplete and the identification of activated metabolites and important degradation products are limited by analytical methods. Because so many more new chemicals are being produced than can be assessed for potential hazards, setting assessment priorities among the thousands of untested chemicals requires methods for predictive hazard identification which can be derived directly from chemical structure and their likely metabolites. In a series of papers we are sharing our experience in the computerized management of metabolic data and the development of simulators of metabolism for predicting the environmental fate and (eco)toxicity of chemicals. The first paper of the series presents a knowledge-based formalism for the computer simulation of non-intermediary metabolism for untested chemicals, with an emphasis on qualitative and quantitative aspects of modelling metabolism.
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Affiliation(s)
- S Dimitrov
- Laboratory of Mathematical Chemistry, University, Bourgas, Bulgaria
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Petri Net Based Metabolic Network Parameters Fitting with GPU Acceleration. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abo-Hashesh M, Wang R, Hallenbeck PC. Metabolic engineering in dark fermentative hydrogen production; theory and practice. BIORESOURCE TECHNOLOGY 2011; 102:8414-8422. [PMID: 21470849 DOI: 10.1016/j.biortech.2011.03.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/03/2011] [Accepted: 03/07/2011] [Indexed: 05/26/2023]
Abstract
Dark fermentation is an attractive option for hydrogen production since it could use already existing reactor technology and readily available substrates without requiring a direct input of solar energy. However, a number of improvements are required before the rates and yields of such a process approach those required for a practical process. Among the options for achieving the required advances, metabolic engineering offers some powerful tools for remodeling microbes to increase product production rates and molar yields. Here we review the current metabolic engineering tool box that is available, discuss the current status of engineering efforts as applied to dark hydrogen production, and suggest areas for future improvements.
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Affiliation(s)
- Mona Abo-Hashesh
- Département de Microbiologie et Immunologie, Université de Montréal, CP 6128 Succursale Centre-ville, Montréal, Québec, Canada H3C 3J7
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McMullen JP, Jensen KF. Rapid Determination of Reaction Kinetics with an Automated Microfluidic System. Org Process Res Dev 2011. [DOI: 10.1021/op100300p] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan P. McMullen
- Department of Chemical Engineering, Novartis-MIT Center for Continuous Manufacturing, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Klavs F. Jensen
- Department of Chemical Engineering, Novartis-MIT Center for Continuous Manufacturing, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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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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van Berlo RJP, de Ridder D, Daran JM, Daran-Lapujade PAS, Teusink B, Reinders MJT. Predicting metabolic fluxes using gene expression differences as constraints. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:206-216. [PMID: 21071808 DOI: 10.1109/tcbb.2009.55] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A standard approach to estimate intracellular fluxes on a genome-wide scale is flux-balance analysis (FBA), which optimizes an objective function subject to constraints on (relations between) fluxes. The performance of FBA models heavily depends on the relevance of the formulated objective function and the completeness of the defined constraints. Previous studies indicated that FBA predictions can be improved by adding regulatory on/off constraints. These constraints were imposed based on either absolute or relative gene expression values. We provide a new algorithm that directly uses regulatory up/down constraints based on gene expression data in FBA optimization (tFBA). Our assumption is that if the activity of a gene drastically changes from one condition to the other, the flux through the reaction controlled by that gene will change accordingly. We allow these constraints to be violated, to account for posttranscriptional control and noise in the data. These up/down constraints are less stringent than the on/off constraints as previously proposed. Nevertheless, we obtain promising predictions, since many up/down constraints can be enforced. The potential of the proposed method, tFBA, is demonstrated through the analysis of fluxes in yeast under nine different cultivation conditions, between which approximately 5,000 regulatory up/down constraints can be defined. We show that changes in gene expression are predictive for changes in fluxes. Additionally, we illustrate that flux distributions obtained with tFBA better fit transcriptomics data than previous methods. Finally, we compare tFBA and FBA predictions to show that our approach yields more biologically relevant results.
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Affiliation(s)
- Rogier J P van Berlo
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.
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Chen X, Alonso AP, Allen DK, Reed JL, Shachar-Hill Y. Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. Metab Eng 2010; 13:38-48. [PMID: 21129495 DOI: 10.1016/j.ymben.2010.11.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 10/20/2010] [Accepted: 11/16/2010] [Indexed: 01/28/2023]
Abstract
Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and ¹³C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes.
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Affiliation(s)
- Xuewen Chen
- Department of Plant Biology, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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Likhoshvai VA, Khlebodarova TM, Ree MT, Kolchanov NA. Metabolic engineering in silico. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810070021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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De Mey M, Taymaz-Nikerel H, Baart G, Waegeman H, Maertens J, Heijnen JJ, van Gulik WM. Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions. Metab Eng 2010; 12:477-87. [PMID: 20447466 DOI: 10.1016/j.ymben.2010.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/12/2010] [Accepted: 04/26/2010] [Indexed: 11/28/2022]
Abstract
The design and application of a BioScope, a mini plug-flow reactor for carrying out pulse response experiments, specifically designed for Escherichia coli is presented. Main differences with the previous design are an increased volume-specific membrane surface for oxygen transfer and significantly decreased sampling intervals. The characteristics of the new device (pressure drop, residence time distribution, plug-flow behavior and O2 mass transfer) were determined and evaluated. Subsequently, 2.8 mM glucose perturbation experiments on glucose-limited aerobic E. coli chemostat cultures were carried out directly in the chemostat as well as in the BioScope (for two time frames: 8 and 40 s). It was ensured that fully aerobic conditions were maintained during the perturbation experiments. To avoid metabolite leakage during quenching, metabolite quantification (glycolytic and TCA-cycle intermediates and nucleotides) was carried out with a differential method, whereby the amounts measured in the filtrate were subtracted from the amounts measured in total broth. The dynamic metabolite profiles obtained from the BioScope perturbations were very comparable with the profiles obtained from the chemostat perturbation. This agreement demonstrates that the BioScope is a promising device for studying in vivo kinetics in E. coli that shows much faster response (< 10 s) in comparison with eukaryotes.
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Affiliation(s)
- Marjan De Mey
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Amicarelli A, di Sciascio F, Toibero JM, Alvarez H. Including dissolved oxygen dynamics into the Bt δ-endotoxins production process model and its application to process control. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2010. [DOI: 10.1590/s0104-66322010000100004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wittmann C. Analysis and engineering of metabolic pathway fluxes in Corynebacterium glutamicum. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 120:21-49. [PMID: 20140657 DOI: 10.1007/10_2009_58] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Gram-positive soil bacterium Corynebacterium glutamicum was discovered as a natural overproducer of glutamate about 50 years ago. Linked to the steadily increasing economical importance of this microorganism for production of glutamate and other amino acids, the quest for efficient production strains has been an intense area of research during the past few decades. Efficient production strains were created by applying classical mutagenesis and selection and especially metabolic engineering strategies with the advent of recombinant DNA technology. Hereby experimental and computational approaches have provided fascinating insights into the metabolism of this microorganism and directed strain engineering. Today, C. glutamicum is applied to the industrial production of more than 2 million tons of amino acids per year. The huge achievements in recent years, including the sequencing of the complete genome and efficient post genomic approaches, now provide the basis for a new, fascinating era of research - analysis of metabolic and regulatory properties of C. glutamicum on a global scale towards novel and superior bioprocesses.
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Affiliation(s)
- Christoph Wittmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Gaussstrasse 17, 38106, Braunschweig, Germany,
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Heijnen JJ. Impact of thermodynamic principles in systems biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 121:139-62. [PMID: 20490971 DOI: 10.1007/10_2009_63] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects will be demonstrated both theoretically and experimentally.
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Affiliation(s)
- J J Heijnen
- Department Biotechnology, Bioprocess technology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands,
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