Genome-Scale Metabolic Models: Reconstruction and Analysis
Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme–reaction r
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duction The vast amount of available genome sequence databases for organisms and the development of high throughput bioinformatics and experimental techniques have led to intense efforts to functionally characterize these genomes and build genome-scale datasets for a variety of organisms like Neisseria meningitidis (1). Genomescale metabolic network models are an example of this. Whereas enzyme kinetics are often unknown, the stoichiometry of the reaction the enzyme catalyzes is in most cases well established. The reaction stoichiometry of the biochemical reactions that are present forms
Myron Christodoulides (ed.), Neisseria meningitidis: Advanced Methods and Protocols, Methods in Molecular Biology, vol. 799, DOI 10.1007/978-1-61779-346-2_7, © Springer Science+Business Media, LLC 2012
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G.J.E. Baart and D.E. Martens
the basis of a genome-scale network in which the different metabolic reactions are connected through their common substrates and products. Whether a metabolic reaction can take place inside an organism can primarily be reconstructed using the information provided in the annotated genome combined with information from curated databases and literature. Such a genome-scale network thus represents the metabolic potential of the organism and hence is valuable in understanding its metabolic capabilities. Genomescale metabolic models have been built for several organisms (2, 3) and have been used to analyze cultivation data, get a better understanding of cellular metabolism (1, 4), develop metabolic engineering strategies (5–8), design media and processes (1, 7, 9, 10), assess theoretical capabilities (2), and even for online control of the process (11), which illustrates its usefulness for process development and optimization. In this chapter, an introduction to genome-scale metabolic network reconstruction and the constraint-based modeling approach is presented.
2. Materials For the genome-scale metabolic network reconstruction and constraint-based modeling methods described below, the following software materials can be used. 1. Major online bioinformatics databases (see Table 1). 2. Software for metabolic network analysis (see Table 2). 3. Tools for assigning putative gene function, e.g., BLAST or InParanoid. 4. Automated tools for metabolic network reconstruction, e.g., Pathologic (Pathway Tools) and AUTOGRAPH.
3. Methods 3.1. Metabolic Network Reconstruction
Before a metabolic model for a given microorganism (or specific phenotype) can be used to gain new insights into its metabolic capabilities or evolutionary history, it must first be built from the available (scattered) genomic, biochemical, and physiological information. This process is known as model reconstruction and has been extensively reviewed before (12, 13). The process of model reconstruction is schematically shown in Fig. 1. It starts with the functional annotation of a sequenced genome, meaning that for each open reading frame (ORF) a function is sought using literature and pathway databases. Part of the functionally annotated
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