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Design and Application of Genome-Scale Reconstructed Metabolic Models

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Microbial Gene Essentiality: Protocols and Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 416))

Abstract

In this chapter, the process for the reconstruction of genome-scale metabolic networks is described, and some of the main applications of such models are illustrated. The reconstruction process can be viewed as an iterative process where information obtained from several sources is combined to construct a preliminary set of reactions and constraints. This involves steps such as genome annotation; identification of the reactions from the annotated genome sequence and available literature; determination of the reaction stoichiometry; definition of compartmentation and assignment of localization; determination of the biomass composition; measurement, calculation, or fitting of energy requirements; and definition of additional constraints. The reaction and constraint sets, after debugging, may be integrated into a stoichiometric model that can be used for simulation using tools such as Flux Balance Analysis (Section 3.8). From the flux distributions obtained, physiologic parameters such as growth yields or minimal medium components can be calculated, and their distance from similar experimental data provides a basis from where the model may need to be improved.

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References

  1. Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., and Palsson, B. O. (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429, 92–96.

    Article  CAS  PubMed  Google Scholar 

  2. Tomita, M. (2001) Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19, 205–210.

    Article  CAS  PubMed  Google Scholar 

  3. Edwards, J. S., and Palsson, B. O. (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274, 17410–17416.

    Article  CAS  PubMed  Google Scholar 

  4. Covert, M. W., Schilling, C. H., Famili, I., Edwards, J. S., Goryanin, I. I., Selkov, E., and Palsson, B. O. (2001) Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26, 179–186.

    Article  CAS  PubMed  Google Scholar 

  5. Patil, K. R., Akesson, M., and Nielsen, J. (2004) Use of genome-scale microbial models for metabolic engineering. Curr. Opin. Biotechnol. 15, 1–6.

    Article  Google Scholar 

  6. Price, N. D., Papin, J. A., Schilling, C. H., and Palsson, B. O. (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 21, 162–169.

    Article  CAS  PubMed  Google Scholar 

  7. Notebaart, R. A., van Enckevort, F. H. J., Francke, C., Siezen, R. J., and Teusink, B. (2006) Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 7, 296.

    Article  PubMed  Google Scholar 

  8. Kitano, H., Funahashi, A., Matsuoka, Y., and Oda, K. (2005) Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23, 961–966.

    Article  CAS  PubMed  Google Scholar 

  9. Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361–363.

    Article  CAS  PubMed  Google Scholar 

  10. Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531.

    Article  CAS  PubMed  Google Scholar 

  11. Segre, D., Zucker, J., Katz, J., Lin, X., D’Haeseleer, P., Rindone, W. P., et al. (2003) From annotated genomes to metabolic flux models and kinetic parameter fitting. OMICS 7, 301–316.

    Article  CAS  PubMed  Google Scholar 

  12. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504.

    Article  CAS  PubMed  Google Scholar 

  13. Duarte, N. C., Herrgard, M. J., and Palsson, B. O. (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14, 1298–1309.

    Article  CAS  PubMed  Google Scholar 

  14. Reed, J. L., and Palsson, B. O. (2003) Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185, 2692–2699.

    Article  CAS  PubMed  Google Scholar 

  15. Karp, P. D., Riley, M., Saier, M., Paulsen, I. T., Collado-Vides, J., Paley, S. et al. (2002) The MetaCyc Database. Nucleic Acids Res. 30, 56–58.

    Article  CAS  PubMed  Google Scholar 

  16. Covert, M. W., Schilling, C. H., and Palsson, B. (2001) Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213, 73–88.

    Article  CAS  PubMed  Google Scholar 

  17. Cox, S. J., Levanon, S. S., Bennett, G. N., and San, K. Y. (2005) Genetically constrained metabolic flux analysis. Metab. Eng. 7, 445–456.

    Article  CAS  PubMed  Google Scholar 

  18. Reed, J. L., Vo, T. D., Schilling, C. H., and Palsson, B. O (2003). An expanded genomescale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4, R54.

    Article  PubMed  Google Scholar 

  19. Forster, J., Famili, I., Fu, P., Palsson, B. O., and Nielsen, J. (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13, 244–253.

    Article  CAS  PubMed  Google Scholar 

  20. David, H., Akesson, M., and Nielsen, J. (2003) Reconstruction of the central carbon metabolism of Aspergillus niger. Eur. J. Biochem. 270, 4243–4253.

    Article  CAS  PubMed  Google Scholar 

  21. Varma, A., and Palsson, B. O. (1993) Metabolic capabilities of Escherichia coli: II. optimal growth patterns. J. Theor. Biol. 165, 503–522.

    Article  CAS  Google Scholar 

  22. Varma, A., and Palsson, B. O. (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60, 3724–3731.

    CAS  PubMed  Google Scholar 

  23. Famili, I., Forster, J., Nielsen, J., and Palsson, B. O. (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. U.S.A. 100, 13134–13139.

    Article  CAS  PubMed  Google Scholar 

  24. Stephanopoulos, G., Aristidou, A., and Nielsen, J. (1998) Metabolic Engineering. San Diego: Academic Press.

    Google Scholar 

  25. Christensen, B., and Nielsen, J. (2000) Metabolic network analysis. A powerful tool in metabolic engineering. Adv. Biochem. Eng. Biotechnol. 66, 209–231.

    CAS  PubMed  Google Scholar 

  26. Edwards, J. S., Ibarra, R. U., and Palsson, B. O. (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125–130.

    Article  CAS  PubMed  Google Scholar 

  27. Edwards, J. S., and Palsson, B. O. (2000) Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16, 927–939.

    Article  CAS  PubMed  Google Scholar 

  28. Edwards, J. S., and Palsson, B. O. (2000) Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1, 1.

    Article  CAS  PubMed  Google Scholar 

  29. Papp, B., Pal, C., and Hurst, L. D. (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429, 661–664.

    Article  CAS  PubMed  Google Scholar 

  30. Segre, D., Vitkup, D., and Church, G. M. (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 99, 15112–15117.

    Article  CAS  PubMed  Google Scholar 

  31. Shlomi, T., Berkman, O., and Ruppin, E. (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. U.S.A. 102, 7695–7700.

    Article  CAS  PubMed  Google Scholar 

  32. Burgard, A. P., Pharkya, P., and Maranas, C. D. (2003) OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84, 647–657.

    Article  CAS  PubMed  Google Scholar 

  33. Burgard, A. P., and Maranas, C. D. (2001) Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74, 364–375.

    Article  CAS  PubMed  Google Scholar 

  34. Pharkya, P., Burgard, A. P., and Maranas, C. D. (2003) Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol. Bioeng. 84, 887–899.

    Article  CAS  PubMed  Google Scholar 

  35. Patil, K. R., Rocha, I., Forster, J., and Nielsen, J. (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6, 308.

    Article  PubMed  Google Scholar 

  36. Covert, M. W., and Palsson, B. O. (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28058–28064.

    Article  CAS  PubMed  Google Scholar 

  37. Akesson, M., Forster, J., and Nielsen, J. (2004) Integration of gene expression data into genome-scale metabolic models. Metab. Eng. 6, 285–293.

    Article  CAS  PubMed  Google Scholar 

  38. Ibarra, R. U., Edwards, J. S., and Palsson, B. O. (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186–189.

    Article  CAS  PubMed  Google Scholar 

  39. Price, N. D., Papin, J. A., and Palsson, B. O. (2002) Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 12, 760–769.

    CAS  PubMed  Google Scholar 

  40. Schuster, S., Fell, D. A., and Dandekar, T. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18, 326–332.

    Article  CAS  PubMed  Google Scholar 

  41. Lee, S., Phalakornkule, C., Domach, M. M., and Grossmann, I. E. (2000) Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput. Chem. Eng. 24, 711–716.

    Article  CAS  Google Scholar 

  42. Schilling, C. H., Letscher, D., and Palsson, B. O. (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203, 229–248.

    Article  CAS  PubMed  Google Scholar 

  43. Edwards, J. S., and Palsson, B. O. (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. U.S.A. 97, 5528–5533.

    Article  CAS  PubMed  Google Scholar 

  44. Schilling, C. H., Covert, M. W., Famili, I., Church, G. M., Edwards, J. S., and Palsson, B. O. (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184, 4582–4593.

    Article  CAS  PubMed  Google Scholar 

  45. Thiele, I., Vo, T. D., Price, N. D., and Palsson, B. O. (2005) Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single-and double-deletion mutants. J. Bacteriol. 187, 5818–5830.

    Article  CAS  PubMed  Google Scholar 

  46. Kuepfer, L., Sauer, U., and Blank, L. M. (2005) Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 15, 1421–1430.

    Article  CAS  PubMed  Google Scholar 

  47. Yeh, W., Hanekamp, T., Tsoka, S., Karp, P. D., and Altman, R. B. (2004) Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res. 14, 917–924.

    Article  CAS  PubMed  Google Scholar 

  48. Tsoka, S., Simon, D., and Ouzounis, C. A. (2004) Automated metabolic reconstruction for Methanococcus jannaschii. Archaea 1, 223–229.

    Article  CAS  PubMed  Google Scholar 

  49. Sheikh, K., Forster, J., and Nielsen, L. K. (2005) Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol. Prog. 21, 112–121.

    Article  CAS  PubMed  Google Scholar 

  50. Oliveira, A. P., Nielsen, J., and Forster, J. (2005) Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5, 39.

    Article  PubMed  Google Scholar 

  51. Teusink, B., van Enckevort, F. H. J., Francke, C., Wiersma, A., Wegkamp, A., Smid, E. J., and Siezen, R. J. (2005) In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: Comparing predictions of nutrient requirements with those from growth experiments. Appl. Environ. Microbiol. 71, 7253–7262.

    Article  CAS  PubMed  Google Scholar 

  52. Becker, S. A., and Palsson, B. O. (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol. 5, 8.

    Article  PubMed  Google Scholar 

  53. Heinemann, M., Kummel, A., Ruinatscha, R., and Panke, S. (2005) In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol. Bioeng. 92, 850–864.

    Article  CAS  PubMed  Google Scholar 

  54. Feist, A. M., Scholten, J. C. M., Palsson, B. O., Brockman, F., and Ideker, T. (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol. Syst. Biol. 2, 4.

    Article  Google Scholar 

  55. Borodina, I., Krabben, P., and Nielsen, J. (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 15, 820–829.

    Article  CAS  PubMed  Google Scholar 

  56. Karp, P. D., Paley, S., and Romero, P. (2002) The Pathway Tools software. Bioinformatics 18(Suppl 1), S225–S232.

    PubMed  Google Scholar 

  57. Klamt, S., Stelling, J., Ginkel, M., and Gilles, E. D. (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19, 261–269.

    Article  CAS  PubMed  Google Scholar 

  58. Lee, S. Y., Lee, D.-Y., and Hong, S. H. (2003) MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform. 14, 23–33.

    CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, Braga, Portugal

    Isabel Rocha

  2. Fluxome Sciences A/S, Lyngby, Denmark

    Jochen Förster

  3. Center for Microbial Biotechnology Biocentrum, Technical University of Denmark, Lyngby, Denmark

    Jens Nielsen

Authors
  1. Isabel Rocha
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  2. Jochen Förster
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  3. Jens Nielsen
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Editor information

Editors and Affiliations

  1. Burnham Institute for Medical Research, La Jolla, California

    Andrei L. Osterman

  2. Fellowship for Interpretation of Genomes (FIG), Burr Ridge, Illinois

    Svetlana Y. Gerdes

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© 2008 Humana Press Inc., a part of Springer Science+Business Media, LLC

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Rocha, I., Förster, J., Nielsen, J. (2008). Design and Application of Genome-Scale Reconstructed Metabolic Models. In: Osterman, A.L., Gerdes, S.Y. (eds) Microbial Gene Essentiality: Protocols and Bioinformatics. Methods in Molecular Biology™, vol 416. Humana Press. https://doi.org/10.1007/978-1-59745-321-9_29

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  • DOI: https://doi.org/10.1007/978-1-59745-321-9_29

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-378-7

  • Online ISBN: 978-1-59745-321-9

  • eBook Packages: Springer Protocols

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