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Zimmermann J, Kaleta C, Waschina S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol 2021; 22:81. [PMID: 33691770 PMCID: PMC7949252 DOI: 10.1186/s13059-021-02295-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.
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Affiliation(s)
- Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
| | - Christoph Kaleta
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
| | - Silvio Waschina
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
- Christian-Albrechts-University Kiel, Institute of Human Nutrition and Food Science, Nutriinformatics, Heinrich-Hecht-Platz 10, Kiel, 24118 Germany
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2
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Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep 2018; 8:11678. [PMID: 30076366 PMCID: PMC6076258 DOI: 10.1038/s41598-018-30149-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
In order to provide timely treatment for organ damage initiated by therapeutic drugs or exposure to environmental toxicants, we first need to identify markers that provide an early diagnosis of potential adverse effects before permanent damage occurs. Specifically, the liver, as a primary organ prone to toxicants-induced injuries, lacks diagnostic markers that are specific and sensitive to the early onset of injury. Here, to identify plasma metabolites as markers of early toxicant-induced injury, we used a constraint-based modeling approach with a genome-scale network reconstruction of rat liver metabolism to incorporate perturbations of gene expression induced by acetaminophen, a known hepatotoxicant. A comparison of the model results against the global metabolic profiling data revealed that our approach satisfactorily predicted altered plasma metabolite levels as early as 5 h after exposure to 2 g/kg of acetaminophen, and that 10 h after treatment the predictions significantly improved when we integrated measured central carbon fluxes. Our approach is solely driven by gene expression and physiological boundary conditions, and does not rely on any toxicant-specific model component. As such, it provides a mechanistic model that serves as a first step in identifying a list of putative plasma metabolites that could change due to toxicant-induced perturbations.
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Affiliation(s)
- Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA.
| | - Martha L Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA.
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA.
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3
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Machado D, Herrgård MJ, Rocha I. Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Comput Biol 2016; 12:e1005140. [PMID: 27711110 PMCID: PMC5053500 DOI: 10.1371/journal.pcbi.1005140] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/13/2016] [Indexed: 12/05/2022] Open
Abstract
Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene level by explicitly accounting for the individual fluxes of enzymes (and subunits) encoded by each gene. We show how this can be applied to different kinds of constraint-based analysis: flux distribution prediction, gene essentiality analysis, random flux sampling, elementary mode analysis, transcriptomics data integration, and rational strain design. In each case we demonstrate how this approach can lead to improved phenotype predictions and a deeper understanding of the genotype-to-phenotype link. In particular, we show that a large fraction of reaction-based designs obtained by current strain design methods are not actually feasible, and show how our approach allows using the same methods to obtain feasible gene-based designs. We also show, by extensive comparison with experimental 13C-flux data, how simple reformulations of different simulation methods with gene-wise objective functions result in improved prediction accuracy. The model transformation proposed in this work enables existing constraint-based methods to be used at the gene level without modification. This automatically leverages phenotype analysis from reaction to gene level, improving the biological insight that can be obtained from genome-scale models.
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Affiliation(s)
- Daniel Machado
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Markus J. Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsølm, Denmark
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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4
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Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7863706. [PMID: 27595107 PMCID: PMC4993939 DOI: 10.1155/2016/7863706] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 06/16/2016] [Indexed: 11/23/2022]
Abstract
Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments.
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Hyötyläinen T, Jerby L, Petäjä EM, Mattila I, Jäntti S, Auvinen P, Gastaldelli A, Yki-Järvinen H, Ruppin E, Orešič M. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nat Commun 2016; 7:8994. [PMID: 26839171 DOI: 10.1038/ncomms9994] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/22/2015] [Indexed: 12/14/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD.
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Affiliation(s)
- Tuulia Hyötyläinen
- Department of Systems Medicine, Steno Diabetes Center, Niels Steensens Vej 6, Gentofte, DK-2820, Denmark.,VTT Technical Research Centre of Finland, Espoo, FI-02044 VTT, Finland
| | - Livnat Jerby
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Elina M Petäjä
- Department of Medicine, Division of Diabetes, University of Helsinki, Helsinki, FI-00014, Finland.,Minerva Foundation Institute for Medical Research, Helsinki FI-00290, Finland
| | - Ismo Mattila
- Department of Systems Medicine, Steno Diabetes Center, Niels Steensens Vej 6, Gentofte, DK-2820, Denmark.,VTT Technical Research Centre of Finland, Espoo, FI-02044 VTT, Finland
| | - Sirkku Jäntti
- VTT Technical Research Centre of Finland, Espoo, FI-02044 VTT, Finland.,Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki FI-00014, Finland
| | - Amalia Gastaldelli
- Institute of Clinical Physiology, National Research Council, Pisa 56124, Italy
| | - Hannele Yki-Järvinen
- Department of Medicine, Division of Diabetes, University of Helsinki, Helsinki, FI-00014, Finland.,Minerva Foundation Institute for Medical Research, Helsinki FI-00290, Finland
| | - Eytan Ruppin
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.,Center for BioInformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland 20742, USA
| | - Matej Orešič
- Department of Systems Medicine, Steno Diabetes Center, Niels Steensens Vej 6, Gentofte, DK-2820, Denmark.,VTT Technical Research Centre of Finland, Espoo, FI-02044 VTT, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku FI-20520, Finland
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6
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Jamshidi N, Raghunathan A. Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Front Microbiol 2015; 6:1032. [PMID: 26500611 PMCID: PMC4594423 DOI: 10.3389/fmicb.2015.01032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/11/2015] [Indexed: 12/12/2022] Open
Abstract
Constraint-based models have become popular methods for systems biology as they enable the integration of complex, disparate datasets in a biologically cohesive framework that also supports the description of biological processes in terms of basic physicochemical constraints and relationships. The scope, scale, and application of genome scale models have grown from single cell bacteria to multi-cellular interaction modeling; host-pathogen modeling represents one of these examples at the current horizon of constraint-based methods. There are now a small number of examples of host-pathogen constraint-based models in the literature, however there has not yet been a definitive description of the methodology required for the functional integration of genome scale models in order to generate simulation capable host-pathogen models. Herein we outline a systematic procedure to produce functional host-pathogen models, highlighting steps which require debugging and iterative revisions in order to successfully build a functional model. The construction of such models will enable the exploration of host-pathogen interactions by leveraging the growing wealth of omic data in order to better understand mechanism of infection and identify novel therapeutic strategies.
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Affiliation(s)
- Neema Jamshidi
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA ; Department of Radiological Sciences, University of California, Los Angeles Los Angeles, CA, USA
| | - Anu Raghunathan
- Chemical Engineering Division, National Chemical Laboratory Pune, India
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7
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Ish-Am O, Kristensen DM, Ruppin E. Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media. PLoS One 2015; 10:e0123785. [PMID: 25894004 PMCID: PMC4403854 DOI: 10.1371/journal.pone.0123785] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 03/08/2015] [Indexed: 11/22/2022] Open
Abstract
One of the basic postulates of molecular evolution is that functionally important genes should evolve slower than genes of lesser significance. Essential genes, whose knockout leads to a lethal phenotype are considered of high functional importance, yet whether they are truly more conserved than nonessential genes has been the topic of much debate, fuelled by a host of contradictory findings. Here we conduct the first large-scale study utilizing genome-scale metabolic modeling and spanning many bacterial species, which aims to answer this question. Using the novel Media Variation Analysis, we examine the range of conservation of essential vs. nonessential metabolic genes in a given species across all possible media. We are thus able to obtain for the first time, exact upper and lower bounds on the levels of differential conservation of essential genes for each of the species studied. The results show that bacteria do exhibit an overall tendency for differential conservation of their essential genes vs. their non-essential ones, yet this tendency is highly variable across species. We show that the model bacterium E. coli K12 may or may not exhibit differential conservation of essential genes depending on its growth medium, shedding light on previous experimental studies showing opposite trends.
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Affiliation(s)
- Oren Ish-Am
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - David M. Kristensen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eytan Ruppin
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Dept. of Computer Science and the Center for Bioinformatics & Computational Biology, the University of Maryland, Maryland, United States of America
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8
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Carbonell P, Trosset JY. Overcoming drug resistance through in silico prediction. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 11:101-7. [PMID: 24847659 DOI: 10.1016/j.ddtec.2014.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Prediction tools are commonly used in pre-clinical research to assist target selection, to optimize drug potency or to predict the pharmacological profile of drug candidates. In silico prediction and overcoming drug resistance is a new opportunity that creates a high interest in pharmaceutical research. This review presents two main in silico strategies to meet this challenge: a structure-based approach to study the influence of mutations on the drug-target interaction and a system-biology approach to identify resistance pathways for a given drug. In silico screening of synergies between therapeutic and resistant pathways through biological network analysis is an example of technique to escape drug resistance. Structure-based drug design and in silico system biology are complementary approaches to reach few objectives at once: increase efficiency, reduce toxicity and overcoming drug resistance.
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9
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Yizhak K, Le Dévédec SE, Rogkoti VM, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration. Mol Syst Biol 2014; 10:744. [PMID: 25086087 PMCID: PMC4299514 DOI: 10.15252/msb.20134993] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over the last decade, the field of cancer metabolism has mainly focused on studying the role of
tumorigenic metabolic rewiring in supporting cancer proliferation. Here, we perform the first
genome-scale computational study of the metabolic underpinnings of cancer migration. We build
genome-scale metabolic models of the NCI-60 cell lines that capture the Warburg effect (aerobic
glycolysis) typically occurring in cancer cells. The extent of the Warburg effect in each of these
cell line models is quantified by the ratio of glycolytic to oxidative ATP flux (AFR), which is
found to be highly positively associated with cancer cell migration. We hence predicted that
targeting genes that mitigate the Warburg effect by reducing the AFR may specifically inhibit cancer
migration. By testing the anti-migratory effects of silencing such 17 top predicted genes in four
breast and lung cancer cell lines, we find that up to 13 of these novel predictions significantly
attenuate cell migration either in all or one cell line only, while having almost no effect on cell
proliferation. Furthermore, in accordance with the predictions, a significant reduction is observed
in the ratio between experimentally measured ECAR and OCR levels following these perturbations.
Inhibiting anti-migratory targets is a promising future avenue in treating cancer since it may
decrease cytotoxic-related side effects that plague current anti-proliferative treatments.
Furthermore, it may reduce cytotoxic-related clonal selection of more aggressive cancer cells and
the likelihood of emerging resistance.
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Affiliation(s)
- Keren Yizhak
- The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Sylvia E Le Dévédec
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Vasiliki Maria Rogkoti
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Franziska Baenke
- Gene Expression Analysis Laboratory, Cancer Research UK, London Research Institute, London, UK
| | - Vincent C de Boer
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - Christian Frezza
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Almut Schulze
- Gene Expression Analysis Laboratory, Cancer Research UK, London Research Institute, London, UK
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Eytan Ruppin
- The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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10
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Jerby L, Ruppin E. Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling. Clin Cancer Res 2013; 18:5572-84. [PMID: 23071359 DOI: 10.1158/1078-0432.ccr-12-1856] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The metabolism of cancer cells is reprogrammed in various ways to support their growth and survival. Studying these phenomena to develop noninvasive diagnostic tools and selective treatments is a promising avenue. Metabolic modeling has recently emerged as a new way to study human metabolism in a systematic, genome-scale manner by using pertinent high-throughput omics data. This method has been shown in various studies to provide fairly accurate estimates of the metabolic phenotype and its modifications following genetic and environmental perturbations. Here, we provide an overview of genome-scale metabolic modeling and its current use to model human metabolism in health and disease. We then describe the initial steps made using it to study cancer metabolism and how it may be harnessed to enhance ongoing experimental efforts to identify drug targets and biomarkers for cancer in a rationale-based manner.
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Affiliation(s)
- Livnat Jerby
- The Blavatnik School of Computer Science, Tel Aviv University, Israel.
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11
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Hyötyläinen T. Novel methodologies in metabolic profiling with a focus on molecular diagnostic applications. Expert Rev Mol Diagn 2012; 12:527-38. [PMID: 22702368 DOI: 10.1586/erm.12.33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The metabolome contains all the biological end points of genomic, transcriptomic and proteomic perturbations, also including the influence of gut microbiota and the environment, giving a direct picture of an organism's ongoing metabolic state. Metabolomics thus has the potential to be an effective tool for early diagnosis of disease, and also to be a predictor of treatment response and survival. In recent years, the development of instrumental systems has enabled more comprehensive coverage of the metabolome. Advances in mass spectrometry and chromatography have particularly improved both the efficiency of nontargeted metabolic profiling as well as the sensitivity and reliability of targeted analyses. Mass spectrometric techniques are also increasingly becoming accepted as a routine diagnostic tool in clinical laboratories. This review summarizes the most recent advances and current challenges in metabolomics, with a focus on mass spectrometric methods utilized in biomarker research, highlighted with selected examples.
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12
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Abstract
Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism's physiological response to different metabolites and environments. Biolog phenotype assays achieve this by coupling tetrazolium dyes with minimally defined nutrients to measure the impact of hundreds of carbon, nitrogen, phosphorous, and sulfur sources on redox reactions that result from compound-induced effects on the electron transport chain. Over the years, we have used Biolog's reproducible and highly sensitive assays to distinguish closely related bacterial isolates, to understand their metabolic differences, and to model their metabolic behavior using flux balance analysis. This chapter describes Biolog phenotype microarray system components, reagents, and methods, particularly as they apply to bacterial identification, characterization, and metabolic analysis.
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Affiliation(s)
- April Shea
- Bacteriology Division, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, USA
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Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z. MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC SYSTEMS BIOLOGY 2011; 5:20. [PMID: 21276275 PMCID: PMC3045322 DOI: 10.1186/1752-0509-5-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 01/31/2011] [Indexed: 01/20/2023]
Abstract
Background Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. Results MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. Conclusions We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys.
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Affiliation(s)
- Stephan Pabinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
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14
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Kavun Ozbayraktar FB, Ulgen KO. Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation. Biosystems 2011; 104:63-75. [PMID: 21215790 DOI: 10.1016/j.biosystems.2011.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 11/09/2010] [Accepted: 01/03/2011] [Indexed: 12/20/2022]
Abstract
The first elaborate metabolic model of Saccharomyces cerevisiae sphingolipid metabolism was reconstructed in silico. The model considers five different states of sphingolipid hydroxylation, rendering it unique among other models. It is aimed to clarify the significance of hydroxylation on sphingolipids and hence to interpret the preferences of the cell between different metabolic pathway branches under different stress conditions. The newly constructed model was validated by single, double and triple gene deletions with experimentally verified phenotypes. Calcium sensitivity and deletion mutations that may suppress calcium sensitivity were examined by CSG1 and CSG2 related deletions. The model enabled the analysis of complex sphingolipid content of the plasma membrane coupled with diacylglycerol and phosphatidic acid biosynthesis and ATP consumption in in silico cell. The flux data belonging to these critically important key metabolites are integrated with the fact of phytoceramide induced cell death to propose novel potential drug targets for cancer therapeutics. In conclusion, we propose that IPT1, GDA1, CSG and AUR1 gene deletions may be novel candidates of drug targets for cancer therapy according to the results of flux balance and variability analyses coupled with robustness analysis.
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15
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Staphylococcus aureus TargetArray: comprehensive differential essential gene expression as a mechanistic tool to profile antibacterials. Antimicrob Agents Chemother 2010; 54:3659-70. [PMID: 20547796 DOI: 10.1128/aac.00308-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread emergence of antibiotic-resistant bacteria and a lack of new pharmaceutical development have catalyzed a need for new and innovative approaches for antibiotic drug discovery. One bottleneck in antibiotic discovery is the lack of a rapid and comprehensive method to identify compound mode of action (MOA). Since a hallmark of antibiotic action is as an inhibitor of essential cellular targets and processes, we identify a set of 308 essential genes in the clinically important pathogen Staphylococcus aureus. A total of 446 strains differentially expressing these genes were constructed in a comprehensive platform of sensitized and resistant strains. A subset of strains allows either target underexpression or target overexpression by heterologous promoter replacements with a suite of tetracycline-regulatable promoters. A further subset of 236 antisense RNA-expressing clones allows knockdown expression of cognate targets. Knockdown expression confers selective antibiotic hypersensitivity, while target overexpression confers resistance. The antisense strains were configured into a TargetArray in which pools of sensitized strains were challenged in fitness tests. A rapid detection method measures strain responses toward antibiotics. The TargetArray antibiotic fitness test results show mechanistically informative biological fingerprints that allow MOA elucidation.
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Milne CB, Kim PJ, Eddy JA, Price ND. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol J 2010; 4:1653-70. [PMID: 19946878 DOI: 10.1002/biot.200900234] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. While the use of in silico models is still in its early stages for delivering to industry, significant initial successes have been achieved. For the cases presented here, genome-scale models predict engineering strategies to enhance properties of interest in an organism or to inhibit harmful mechanisms of pathogens. Going forward, genome-scale in silico models promise to extend their application and analysis scope to become a trans-formative tool in biotechnology.
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Affiliation(s)
- Caroline B Milne
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
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Kim HU, Kim TY, Lee SY. Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. ACTA ACUST UNITED AC 2010; 6:339-48. [DOI: 10.1039/b916446d] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Abstract
A metabolic model can be represented as a bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualization of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for other organisms.
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Affiliation(s)
- P B Warren
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK.
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Fang X, Wallqvist A, Reifman J. A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. BMC SYSTEMS BIOLOGY 2009; 3:92. [PMID: 19754970 PMCID: PMC2759933 DOI: 10.1186/1752-0509-3-92] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 09/15/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND Because metabolism is fundamental in sustaining microbial life, drugs that target pathogen-specific metabolic enzymes and pathways can be very effective. In particular, the metabolic challenges faced by intracellular pathogens, such as Mycobacterium tuberculosis, residing in the infected host provide novel opportunities for therapeutic intervention. RESULTS We developed a mathematical framework to simulate the effects on the growth of a pathogen when enzymes in its metabolic pathways are inhibited. Combining detailed models of enzyme kinetics, a complete metabolic network description as modeled by flux balance analysis, and a dynamic cell population growth model, we quantitatively modeled and predicted the dose-response of the 3-nitropropionate inhibitor on the growth of M. tuberculosis in a medium whose carbon source was restricted to fatty acids, and that of the 5'-O-(N-salicylsulfamoyl) adenosine inhibitor in a medium with low-iron concentration. CONCLUSION The predicted results quantitatively reproduced the experimentally measured dose-response curves, ranging over three orders of magnitude in inhibitor concentration. Thus, by allowing for detailed specifications of the underlying enzymatic kinetics, metabolic reactions/constraints, and growth media, our model captured the essential chemical and biological factors that determine the effects of drug inhibition on in vitro growth of M. tuberculosis cells.
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Affiliation(s)
- Xin Fang
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U,S, Army Medical Research and Materiel Command, Ft, Detrick, MD 21702, USA.
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Selvarasu S, Karimi IA, Ghim GH, Lee DY. Genome-scale modeling and in silico analysis of mouse cell metabolic network. MOLECULAR BIOSYSTEMS 2009; 6:152-61. [PMID: 20024077 DOI: 10.1039/b912865d] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genome-scale metabolic modeling has been successfully applied to a multitude of microbial systems, thus improving our understanding of their cellular metabolisms. Nevertheless, only a handful of works have been done for describing mammalian cells, particularly mouse, which is one of the important model organisms, providing various opportunities for both biomedical research and biotechnological applications. Presented herein is a genome-scale mouse metabolic model that was systematically reconstructed by improving and expanding the previous generic model based on integrated biochemical and genomic data of Mus musculus. The key features of the updated model include additional information on gene-protein-reaction association, and improved network connectivity through lipid, amino acid, carbohydrate and nucleotide biosynthetic pathways. After examining the model predictability both quantitatively and qualitatively using constraints-based flux analysis, the structural and functional characteristics of the mouse metabolism were investigated by evaluating network statistics/centrality, gene/metabolite essentiality and their correlation. The results revealed that overall mouse metabolic network is topologically dominated by highly connected and bridging metabolites, and functionally by lipid metabolism that most of essential genes and metabolites are from. The current in silico mouse model can be exploited for understanding and characterizing the cellular physiology, identifying potential cell engineering targets for the enhanced production of recombinant proteins and developing diseased state models for drug targeting.
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Affiliation(s)
- Suresh Selvarasu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Engineering Drive 4, Singapore.
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Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC SYSTEMS BIOLOGY 2009; 3:38. [PMID: 19356237 PMCID: PMC2678070 DOI: 10.1186/1752-0509-3-38] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 04/08/2009] [Indexed: 01/10/2023]
Abstract
BACKGROUND Infections with Salmonella cause significant morbidity and mortality worldwide. Replication of Salmonella typhimurium inside its host cell is a model system for studying the pathogenesis of intracellular bacterial infections. Genome-scale modeling of bacterial metabolic networks provides a powerful tool to identify and analyze pathways required for successful intracellular replication during host-pathogen interaction. RESULTS We have developed and validated a genome-scale metabolic network of Salmonella typhimurium LT2 (iRR1083). This model accounts for 1,083 genes that encode proteins catalyzing 1,087 unique metabolic and transport reactions in the bacterium. We employed flux balance analysis and in silico gene essentiality analysis to investigate growth under a wide range of conditions that mimic in vitro and host cell environments. Gene expression profiling of S. typhimurium isolated from macrophage cell lines was used to constrain the model to predict metabolic pathways that are likely to be operational during infection. CONCLUSION Our analysis suggests that there is a robust minimal set of metabolic pathways that is required for successful replication of Salmonella inside the host cell. This model also serves as platform for the integration of high-throughput data. Its computational power allows identification of networked metabolic pathways and generation of hypotheses about metabolism during infection, which might be used for the rational design of novel antibiotics or vaccine strains.
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Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA. Predicting biological system objectives de novo from internal state measurements. BMC Bioinformatics 2008; 9:43. [PMID: 18218092 PMCID: PMC2258290 DOI: 10.1186/1471-2105-9-43] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 01/24/2008] [Indexed: 01/15/2023] Open
Abstract
Background Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells to optimally produce byproducts of commercial value, such as bioethanol, as well as molecular compounds for disease therapy. Flux balance analysis (FBA) is an optimization framework that aids in this interrogation by generating predictions of optimal flux distributions in cellular networks. Critical features of FBA are the definition of a biologically relevant objective function (e.g., maximizing the rate of synthesis of biomass, a unit of measurement of cellular growth) and the subsequent application of linear programming (LP) to identify fluxes through a reaction network. Despite the success of FBA, a central remaining challenge is the definition of a network objective with biological meaning. Results We present a novel method called Biological Objective Solution Search (BOSS) for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables. Specifically, BOSS identifies a system objective by defining a putative stoichiometric "objective reaction," adding this reaction to the existing set of stoichiometric constraints arising from known interactions within a network, and maximizing the putative objective reaction via LP, all the while minimizing the difference between the resultant in silico flux distribution and available experimental (e.g., isotopomer) flux data. This new approach allows for discovery of objectives with previously unknown stoichiometry, thus extending the biological relevance from earlier methods. We verify our approach on the well-characterized central metabolic network of Saccharomyces cerevisiae. Conclusion We illustrate how BOSS offers insight into the functional organization of biochemical networks, facilitating the interrogation of cellular design principles and development of cellular engineering applications. Furthermore, we describe how growth is the best-fit objective function for the yeast metabolic network given experimentally-measured fluxes.
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Affiliation(s)
- Erwin P Gianchandani
- Department of Biomedical Engineering University of Virginia Box 800759, Health System Charlottesville, VA 22908 USA.
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Pinney JW, Papp B, Hyland C, Wambua L, Westhead DR, McConkey GA. Metabolic reconstruction and analysis for parasite genomes. Trends Parasitol 2007; 23:548-54. [PMID: 17950669 DOI: 10.1016/j.pt.2007.08.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 08/20/2007] [Accepted: 08/20/2007] [Indexed: 01/29/2023]
Abstract
With the completion of sequencing projects for several parasite genomes, efforts are ongoing to make sense of this mass of information in terms of the gene products encoded and their interactions in the growth, development and survival of parasites. The emerging science of systems biology aims to explain the complex relationship between genotype and phenotype by using network models. One area in which this approach has been particularly successful is in the modeling of metabolism. With an accurate picture of the set of metabolic reactions encoded in a genome, it is now possible to identify enzymes or transporters that might be viable targets for new drugs. Because these predictions greatly depend on the quality and completeness of the genome annotation, there are substantial efforts in the scientific community to increase the numbers of metabolic enzymes identified. In this review, we discuss the opportunities for using metabolic reconstruction and analysis tools in parasitology research, and their applications to protozoan parasites.
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Affiliation(s)
- John W Pinney
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK
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Warren PB, Jones JL. Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism. PHYSICAL REVIEW LETTERS 2007; 99:108101. [PMID: 17930409 DOI: 10.1103/physrevlett.99.108101] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Indexed: 05/25/2023]
Abstract
It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is to minimize free energy consumption given a free energy drain corresponding to growth. The interpretation is distinct from conventional nonequilibrium thermodynamics, although it does satisfy a minimum entropy production principle. It can be used to motivate extensions of constraint-based modeling, for example, to microbial ecosystems.
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Affiliation(s)
- Patrick B Warren
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, United Kingdom
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Schwarz R, Liang C, Kaleta C, Kühnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S, Dandekar T. Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 2007; 8:313. [PMID: 17725829 PMCID: PMC2020486 DOI: 10.1186/1471-2105-8-313] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 08/28/2007] [Indexed: 01/29/2023] Open
Abstract
Background Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network. Results YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network performance analysis (calculation of flux modes as well as target and robustness tests). YANAsquare comes as an easy-to-setup program package in Java. It is fully compatible and integrates the programs YANA (translation of gene expression values into flux distributions, metabolite network dissection) and Metatool (elementary mode calculation). As application examples we set-up and model the phospholipid network in the phagosome and genome-scale metabolic maps of S.aureus, S.epidermidis and S.saprophyticus as well as test their robustness against enzyme impairment. Conclusion YANAsquare is an application software for rapid setup, visualization and analysis of small, larger and genome-scale metabolic networks.
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Affiliation(s)
- Roland Schwarz
- Department of Bioinformatics, Biocenter Am Hubland, D-97074 University of Würzburg, Germany
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter Am Hubland, D-97074 University of Würzburg, Germany
| | - Christoph Kaleta
- Bio Systems Analysis Group, Department of Mathematics and Computer Science, Friedrich Schiller University Jena, Germany
| | - Mark Kühnel
- Cell Biology Program, EMBL Heidelberg, Germany
| | - Eik Hoffmann
- Department of Cell Biology and Biosystems Technology, Albert-Einstein-Str. 3, D-18059 University of Rostock, Germany
| | - Sergei Kuznetsov
- Department of Cell Biology and Biosystems Technology, Albert-Einstein-Str. 3, D-18059 University of Rostock, Germany
| | - Michael Hecker
- Institute for Microbiology, Friedrich-Ludwig-Jahn-Str. 15, D-17487 University of Greifswald, Germany
| | | | - Stefan Schuster
- Department of Bioinformatics, Ernst-Abbe-Platz 2, D-07743 University of Jena, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter Am Hubland, D-97074 University of Würzburg, Germany
- Structural and Computational Biology, EMBL Heidelberg, Germany
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Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 2007; 104:1777-82. [PMID: 17267599 PMCID: PMC1794290 DOI: 10.1073/pnas.0610772104] [Citation(s) in RCA: 936] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Indexed: 01/19/2023] Open
Abstract
Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype-phenotype relationships. We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resulting genome-scale (or global) network can be used (i) for the discovery of missing information, (ii) for the formulation of an in silico model, and (iii) as a structured context for analyzing high-throughput biological data sets. Our comprehensive evaluation of the literature revealed many gaps in the current understanding of human metabolism that require future experimental investigation. Mathematical analysis of network structure elucidated the implications of intracellular compartmentalization and the potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets within the context of the reconstruction enabled a global assessment of functional metabolic states. These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.
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Affiliation(s)
- Natalie C. Duarte
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Scott A. Becker
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Neema Jamshidi
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Ines Thiele
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Monica L. Mo
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Thuy D. Vo
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Rohith Srivas
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
| | - Bernhard Ø. Palsson
- Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412
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