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Schuster S, Ewald J, Kaleta C. Modeling the energy metabolism in immune cells. Curr Opin Biotechnol 2021; 68:282-291. [PMID: 33770632 DOI: 10.1016/j.copbio.2021.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/16/2021] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
In this review, we summarize and briefly discuss various approaches to modeling the metabolism in human immune cells, with a focus on energy metabolism. These approaches include metabolic reconstruction, elementary modes, and flux balance analysis, which are often subsumed under constraint-based modeling. Further approaches are evolutionary game theory and kinetic modeling. Many immune cells such as macrophages show the Warburg effect, meaning that glycolysis is upregulated upon activation. We outline a minimal model for explaining that effect using optimization. The effect of a confrontation with pathogen cells on immunometabolism is highlighted. Models describing the differences between M1 and M2 macrophages, ROS production in neutrophils, and tryptophan metabolism are discussed. Obstacles and future prospects are outlined.
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Affiliation(s)
- Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany.
| | - Jan Ewald
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany
| | - Christoph Kaleta
- Medical Systems Biology Group, Institute of Experimental Medicine, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
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Pyruvate cycle increases aminoglycoside efficacy and provides respiratory energy in bacteria. Proc Natl Acad Sci U S A 2018; 115:E1578-E1587. [PMID: 29382755 DOI: 10.1073/pnas.1714645115] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The emergence and ongoing spread of multidrug-resistant bacteria puts humans and other species at risk for potentially lethal infections. Thus, novel antibiotics or alternative approaches are needed to target drug-resistant bacteria, and metabolic modulation has been documented to improve antibiotic efficacy, but the relevant metabolic mechanisms require more studies. Here, we show that glutamate potentiates aminoglycoside antibiotics, resulting in improved elimination of antibiotic-resistant pathogens. When exploring the metabolic flux of glutamate, it was found that the enzymes that link the phosphoenolpyruvate (PEP)-pyruvate-AcCoA pathway to the TCA cycle were key players in this increased efficacy. Together, the PEP-pyruvate-AcCoA pathway and TCA cycle can be considered the pyruvate cycle (P cycle). Our results show that inhibition or gene depletion of the enzymes in the P cycle shut down the TCA cycle even in the presence of excess carbon sources, and that the P cycle operates routinely as a general mechanism for energy production and regulation in Escherichia coli and Edwardsiella tarda These findings address metabolic mechanisms of metabolite-induced potentiation and fundamental questions about bacterial biochemistry and energy metabolism.
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Hunt KA, Folsom JP, Taffs RL, Carlson RP. Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. ACTA ACUST UNITED AC 2014; 30:1569-78. [PMID: 24497502 DOI: 10.1093/bioinformatics/btu021] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
MOTIVATION Elementary flux mode analysis (EFMA) decomposes complex metabolic network models into tractable biochemical pathways, which have been used for rational design and analysis of metabolic and regulatory networks. However, application of EFMA has often been limited to targeted or simplified metabolic network representations due to computational demands of the method. RESULTS Division of biological networks into subnetworks enables the complete enumeration of elementary flux modes (EFMs) for metabolic models of a broad range of complexities, including genome-scale. Here, subnetworks are defined using serial dichotomous suppression and enforcement of flux through model reactions. Rules for selecting appropriate reactions to generate subnetworks are proposed and tested; three test cases, including both prokaryotic and eukaryotic network models, verify the efficacy of these rules and demonstrate completeness and reproducibility of EFM enumeration. Division of models into subnetworks is demand-based and automated; computationally intractable subnetworks are further divided until the entire solution space is enumerated. To demonstrate the strategy's scalability, the splitting algorithm was implemented using an EFMA software package (EFMTool) and Windows PowerShell on a 50 node Microsoft high performance computing cluster. Enumeration of the EFMs in a genome-scale metabolic model of a diatom, Phaeodactylum tricornutum, identified ∼2 billion EFMs. The output represents an order of magnitude increase in EFMs computed compared with other published algorithms and demonstrates a scalable framework for EFMA of most systems.
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Affiliation(s)
- Kristopher A Hunt
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USACenter for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USA
| | - James P Folsom
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USACenter for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USA
| | - Reed L Taffs
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USACenter for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USA
| | - Ross P Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USACenter for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980 and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3920, USA
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Dandekar T, Astrid F, Jasmin P, Hensel M. Salmonella enterica: a surprisingly well-adapted intracellular lifestyle. Front Microbiol 2012; 3:164. [PMID: 22563326 PMCID: PMC3342586 DOI: 10.3389/fmicb.2012.00164] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/12/2012] [Indexed: 11/15/2022] Open
Abstract
The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole (SCV) in host cells. We summarize latest results on metabolic requirements for Salmonella during infection. This includes intracellular phenotypes of mutant strains based on metabolic modeling and experimental tests, isotopolog profiling using 13C-compounds in intracellular Salmonella, and complementation of metabolic defects for attenuated mutant strains towards a comprehensive understanding of the metabolic requirements of the intracellular lifestyle of Salmonella. Helpful for this are also genomic comparisons. We outline further recent studies and which analyses of intracellular phenotypes and improved metabolic simulations were done and comment on technical required steps as well as progress involved in the iterative refinement of metabolic flux models, analyses of mutant phenotypes, and isotopolog analyses. Salmonella lifestyle is well-adapted to the SCV and its specific metabolic requirements. Salmonella metabolism adapts rapidly to SCV conditions, the metabolic generalist Salmonella is quite successful in host infection.
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Affiliation(s)
- Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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Fuchs TM, Eisenreich W, Kern T, Dandekar T. Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Front Microbiol 2012; 3:23. [PMID: 22347216 PMCID: PMC3271275 DOI: 10.3389/fmicb.2012.00023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 01/13/2012] [Indexed: 02/03/2023] Open
Abstract
Listeria monocytogenes is a foodborne human pathogen that can cause invasive infection in susceptible animals and humans. For proliferation within hosts, this facultative intracellular pathogen uses a reservoir of specific metabolic pathways, transporter, and enzymatic functions whose expression requires the coordinated activity of a complex regulatory network. The highly adapted metabolism of L. monocytogenes strongly depends on the nutrient composition of various milieus encountered during infection. Transcriptomic and proteomic studies revealed the spatial-temporal dynamic of gene expression of this pathogen during replication within cultured cells or in vivo. Metabolic clues are the utilization of unusual C(2)- and C(3)-bodies, the metabolism of pyruvate, thiamine availability, the uptake of peptides, the acquisition or biosynthesis of certain amino acids, and the degradation of glucose-phosphate via the pentose phosphate pathway. These examples illustrate the interference of in vivo conditions with energy, carbon, and nitrogen metabolism, thus affecting listerial growth. The exploitation, analysis, and modeling of the available data sets served as a first attempt to a systemic understanding of listerial metabolism during infection. L. monocytogenes might serve as a model organism for systems biology of a Gram-positive, facultative intracellular bacterium.
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Affiliation(s)
- Thilo M. Fuchs
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Technische Universität MünchenFreising, Germany
- Lehrstuhl für Mikrobielle Ökologie, Department Biowissenschaften, Wissenschaftszentrum Weihenstephan, Technische Universität MünchenFreising, Germany
| | | | - Tanja Kern
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Technische Universität MünchenFreising, Germany
| | - Thomas Dandekar
- Abteilung Bioinformatik, Theodor-Boveri-Institut (Biozentrum), Universität WürzburgWürzburg, Germany
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Faust K, Croes D, van Helden J. Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems 2011; 105:109-21. [PMID: 21645586 DOI: 10.1016/j.biosystems.2011.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/23/2011] [Accepted: 05/05/2011] [Indexed: 01/06/2023]
Abstract
The analysis of a variety of data sets (transcriptome arrays, phylogenetic profiles, etc.) yields groups of functionally related genes. In order to determine their biological function, associated gene groups are often projected onto known pathways or tested for enrichment of known functions. However, these approaches are not flexible enough to deal with variations or novel pathways. During the last decade, we developed and refined an approach that predicts metabolic pathways from a global metabolic network encompassing all known reactions and their substrates/products, by extracting a subgraph connecting at best a set of seed nodes (compounds, reactions, enzymes or enzyme-coding genes). In this review, we summarize this work, while discussing the problems and pitfalls but also the advantages and applications of network-based metabolic pathway prediction.
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Affiliation(s)
- Karoline Faust
- Research Group of Bioinformatics and (Eco-)Systems Biology (BSB), VIB - Vrije Universiteit Brussel, Pleinlaan, Belgium
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