Abstract
The theoretical investigation of the structure of metabolic systems has recently attracted increasing interest. In this chapter, the basic concepts of metabolic pathway analysis are described and various applications are outlined. In particular, the concepts of nullspace and elementary flux modes are explained. The presentation is illustrated by a simple example from tyrosine metabolism and a system describing lysine production in Corynebacterium glutamicum. The latter system gives rise to 37 elementary modes, 36 of which produce lysine with different molar yields. The examples illustrate that metabolic pathway analysis is a useful tool for better understanding the complex architecture of intracellular metabolism, for determining the pathways on which the molar conversion yield of a substrate-product pair under study is maximal, and for assigning functions to orphan genes (functional genomics). Moreover, problems emerging in the modeling of large networks are discussed. An outlook on current trends in the field concludes the chapter.
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References
Dandekar, T., Schuster, S., Snel, B., Huynen, M., and Bork, P. (1999) Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343, 115–124.
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., and Dandekar, T. (2002) Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18, 351–361.
Förster, J., Gombert, A. K., and Nielsen, J. (2002) A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol. Bioeng. 79, 703–712.
Van Dien, S. J. and Lidstrom, M. E. (2002) Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C3 and C4 metabolism. Biotechnol. Bioeng. 78, 296–312.
Romero, P., Wagg, J., Green, M. L., Kaiser, D., Krummenacker, M., and Karp, P. D. (2005) Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 6, R2.1–R2.17.
Mavrovouniotis, M. L., Stephanopoulos, G., and Stephanopoulos, G. (1990) Computer-aided synthesis of biochemical pathways. Biotechnol. Bioeng. 36, 1119–1132.
Schuster, S. and Hilgetag, C. (1994) On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 2, 165–182.
Alberty, R. A. (1996) Calculation of biochemical net reactions and pathways by using matrix operations. Biophys. J. 71, 507–515.
Stephanopoulos, G. and Simpson, T. W. (1997) Flux amplification in complex metabolic networks. Chem. Eng. Sci. 52, 2607–2627.
Seressiotis, A. and Bailey, J. E. (1988) MPS: an artificially intelligent software system for the analysis and synthesis of metabolic pathways. Biotechnol. Bioeng. 31, 587–602.
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.
Clarke, B. L. (1981) Complete set of steady states for the general stoichiometric dynamical system. J. Chem. Phys. 75, 4970–4979.
Heinrich, R. and Schuster, S. (1996) The Regulation of Cellular Systems, Chapman and Hall, New York, NY.
Schuster, S., Dandekar, T., and Fell, D. A. (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17, 53–60.
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., and Barabási, A. L. (2000) The large-scale organization of metabolic networks. Nature 407, 651–654.
Ma, H. and Zeng, A. P. (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19, 270–277.
Hofestädt, R. (1994) A petri net application to model metabolic processes. Syst. Anal. Mod. Simul. 16, 113–122.
Küffner, R., Zimmer, R., and Lengauer, T. (2000) Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16, 825–836.
Zevedei-Oancea, I. and Schuster, S. (2003) Topological analysis of metabolic networks based on Petri net theory. In Silico Biol. 3, 323–345.
Seo, H., Lee, D.-Y., Park, S., et al. (2001) Graph-theoretical identification of pathways for biochemical reactions. Biotechnol. Lett. 23, 1551–1557.
Fell, D. A. (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem. J. 286, 313–330.
Stephanopoulos, G. N., Aristidou, A. A., and Nielsen, J. (1998) Metabolic Engineering: Principles and Methodologies, Academic Press, San Diego, CA.
Wiechert, W. (2002) Modeling and simulation: tools for metabolic engineering. J. Biotechn. 94, 37–63.
Palsson, B. O. (2004) In silico biotechnology. Era of reconstruction and interrogation. Curr. Opin. Biotechnol. 15, 50–51.
Carlson, R. and Srienc, F. (2004) Fundamental Escherichia coli biochemical pathways for biomass and energy production: identification of reactions. Biotechnol. Bioeng. 85, 1–19.
Carlson, R., Fell, D., and Srienc, F. (2002) Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79, 121–134.
Cakir, T., Kirdar, B., and Ulgen, K. O. (2004) Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks. Biotechnol. Bioeng. 86, 251–260.
Poolman, M. G., Fell, D. A., and Raines, C. A. (2003) Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur. J. Biochem. 270, 430–439.
Cakir, T., Tacer, C. S., and Ulgen, K. O. (2004) Metabolic pathway analysis of enzyme-deficient human red blood cells. Biosystems 78, 49–67.
Liao, J. C., Hou, S. Y., and Chao, Y. P. (1996) Pathway analysis, engineering and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 52, 129–140.
Schuster, S., Dandekar, T., Mauch, K., Reuss, M., and Fell, D. (2000) Recent developments in metabolic pathway analysis and their potential implications for biotechnology and medicine. In: Technological and Medical Implications of Metabolic Control Analysis, (Cornish-Bowden, A. and Cárdenas, M. L., eds.), Kluwer, Dordrecht, The Netherlands, pp. 57–66.
Rohwer, J. M. and Botha, F. C. (2001) Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437–445.
Wilhelm, T., Behre, J., and Schuster, S. (2004) Analysis of structural robustness of metabolic networks. System Biology 1, 114–120.
Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., and Gilles, E. D. (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190–193.
Heinrich, R., Rapoport, S. M., and Rapoport, T. A. (1977) Metabolic regulation and mathematical models. Prog. Biophys. Mol. Biol. 32, 1–82.
Klamt, S., Schuster, S., and Gilles, E. D. (2002) Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol. Bioeng. 77, 734–751.
Fell, D. A. (1990) Substrate cycles: theoretical aspects of their role in metabolism. Comm. Theor. Biol. 6, 1–14.
Simpson, T. W., Follstad, B. D., and Stephanopoulos, G. (1999) Analysis of the pathway structure of metabolic networks. J. Biotechnol. 71, 207–223.
Lay, D. C. (2002) Linear Algebra and its Applications, Addison-Wesley, Boston, MA.
Pfeiffer, T., Sanchez-Valdenebro, I., Nuno, J. C., Montero, F., and Schuster, S. (1999) METATOOL: for studying metabolic networks. Bioinformatics 15, 251–257.
Schuster, S., Klamt, S., Weckwerth, W., Moldenhauer, F., and Pfeiffer, T. (2002) Use of network analysis of metabolic systems in bioengineering. Bioprocesses Biosyst. Eng. 24, 363–372.
Anderson, B. L. and Winawer, J. (2005) Image segmentation and lightness perception. Nature 434, 79–83.
Holter, N. S., Mitra, M., Maritan, A., Cieplak, M., Banavar, J. R., and Fedoroff, N. V. (2000) Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl. Acad. Sci. USA 97, 8409–8414.
Liebermeister, W. (2002) Linear modes of gene expression determined by independent component analysis. Bioinformatics 18, 51–60.
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.
Schuster, S., Hilgetag, C., Woods, J. H., and Fell, D. A. (2002) Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. J. Math. Biol. 45, 153–181.
Nussey, S. and Whitehead, S. (2001) Endocrinology. An Integrated Approach, BIOS Scientific Publishers Ltd, Oxford, UK.
Fischer, E. and Sauer, U. (2003) A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J. Biol. Chem. 278, 46,446–46,551.
Hers, H., G., and Hue, L. (1983) Gluconeogenesis and related aspects of glycolysis. Annu. Rev. Biochem. 52, 617–653.
Nozicka, F., Guddat, J., Hollatz, H., and Bank, B. (1974) Theorie der Linearen Parametrischen Optimierung, Akademie-Verlag, Berlin, Germany.
Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361–363.
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.
Wagner, C. (2004) Nullspace approach to determine the elementary modes of chemical reaction systems. J. Phys. Chem. B 108, 2425–2431.
Urbanczik, R. and Wagner, C. (2005) An improved algorithm for stoichiometric network analysis: theory and applications. Bioinformatics 21, 1203–1210.
Gagneur, J. and Klamt, S. (2004) Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5, 175.
Fell, D. A. and Small, J. R. (1986) Fat synthesis in adipose tissue. An examination of stoichiometric constraints. Biochem. J. 238, 781–786.
Watson, M. R. (1986) A discrete model of bacterial metabolism. Comput. Appl. Biosci. 2, 23–27.
Varma, A. and Palsson, B. O. (1993) Metabolic capabilities of Escherichia coli. I. Synthesis of biosynthetic precursors and cofactors. J. Theor. Biol. 165, 477–502.
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.
Mahadevan, R. and Schilling, C. H. (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5, 264–276.
Klamt, S. and Stelling, J. (2003) Two approaches for metabolic pathway analysis? Trends Biotechnol. 21, 64–69.
de Graaf, A. A. (2000) Metabolic flux analysis of Corynebacterium glutamicum. In: Bioreaction Engineering, Modelling and Control, (Schügerl, K. B. and Bellgardt, K. H., eds.), Springer, New York, NY, pp. 506–555.
Hermann, T. (2003) Industrial production of amino acids by coryneform bacteria. J. Biotechnol. 104, 155–172.
Schuster, S. (2004) Metabolic pathway analysis in biotechnology. In: Metabolic Engineering in the Post Genomic Era, (Kholodenko, B. N. and Westerhoff, H. V., eds.), Horizon Bioscience, Wymondham, UK, pp. 181–208.
von Mering, C., Jensen, L. J., Snel, B., et al. (2005) STRING: known and predicted protein protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433–D437.
Schilling, C. H. and Palsson, B. O. (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 203, 249–283.
Papin, J. A., Price, N. D., Edwards, J. S., and Palsson, B. O. (2002) The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215, 67–82.
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.
Vo, T. D., Greenberg, H. J., and Palsson, B. O. (2004) Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 279, 39,532–39,540.
Pachkov, M., Dandekar, T., Korbel, J., Bork, P., and Schuster, S. (2005) Pathway analysis of Mycoplasma pneumoniae nucleotide metabolism. Gene, in press.
Huynen, M. A., Snel, B., von Mering, C., and Bork, P. (2003) Functional prediction and protein networks. Curr. Opin. Cell Biol. 15, 191–198.
Osterman, A. and Overbeek, R. (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol. 7, 238–251.
Dandekar, T., Moldenhauer, F., Bulik, S., Bertram, H., and Schuster, S. (2003) A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. BioSystems 70, 255–270.
Klamt, S. and Gilles, E. D. (2004) Minimal cut sets in biochemical reaction networks. Bioinformatics 20, 226–234.
Fard, N. S. (1997) Determination of minimal cut sets of a complex fault tree. Comput. Ind. Eng. 33, 59–62.
Covert, M. and Palsson, B. (2003) Constraints-based models: regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221, 309–325.
Papin, J. A. and Palsson, B. O. (2004) Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J. Theor. Biol. 227, 283–297.
Campbell, K. S. (1999) Signal transduction from the B cell antigen-receptor. Curr. Opin. Immunol. 11, 256–264.
Papin, J. A. and Palsson, B. O. (2004) The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys. J. 87, 37–46.
Berg, J., Tymoczko, J., and Stryer, L. (2002) Biochemistry, Freeman, New York, NY.
Schuster, S., Kholodenko, B. N., and Westerhoff, H. V. (2000) Cellular information transfer regarded from stoichiometry and control analysis perspective. Biosystems 55, 73–81.
Carlson, R. and Srienc, F. (2004) Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol. Bioeng. 86, 149–162.
Pfeiffer, T., Schuster, S., and Bonhoeffer, T. (2001) Cooperation and competition in the evolution of ATP producing pathways. Science 292, 504–507.
Schuster, R. and Schuster, S. (1993) Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed. Comp. Appl. Biosci. 9, 79–85.
Poolman, M., Venkatesh, K., Pidcock, M., and Fell, D. (2004) A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus. Biotechnol. Bioeng. 88, 601–612.
Schilling, C. H., Edwards, J. S., Letscher, D., and Palsson, B. O. (2000) Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71, 286–306.
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Schuster, S., von Kamp, A., Pachkov, M. (2007). Understanding the Roadmap of Metabolism by Pathway Analysis. In: Weckwerth, W. (eds) Metabolomics. Methods in Molecular Biology™, vol 358. Humana Press. https://doi.org/10.1007/978-1-59745-244-1_12
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DOI: https://doi.org/10.1007/978-1-59745-244-1_12
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