Understanding the roadmap of metabolism by pathway analysis.

Department of Bioinformatics, Friedrich-Schiller University of Jena, Germany.
Methods in Molecular Biology (Impact Factor: 1.29). 02/2007; 358:199-226. DOI: 10.1007/978-1-59745-244-1_12
Source: PubMed

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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    ABSTRACT: A homoserine auxotroph strain of Corynebacterium glutamicum accumulates storage compound trehalose with lysine when limited by growth. Industrially lysine is produced from C. glutamicum through aspartate biosynthetic pathway, where enzymatic activity of aspartate kinase is allosterically controlled by the concerted feedback inhibition of threonine plus lysine. Ample threonine in the medium supports growth and inhibits lysine production (phenotype-I) and its complete absence leads to inhibition of growth in addition to accumulating lysine and trehalose (phenotype-II). In this work, we demonstrate that as threonine concentration becomes limiting, metabolic state of the cell shifts from maximizing growth (phenotype-I) to maximizing trehalose phenotype (phenotype-II) in a highly sensitive manner (with a Hill coefficient of 4). Trehalose formation was linked to lysine production through stoichiometry of the network. The study demonstrated that the net flux of the population was a linear combination of the two optimal phenotypic states, requiring only two experimental measurements to evaluate the flux distribution. The property of linear combination of two extreme phenotypes was robust for various medium conditions including varying batch time, initial glucose concentrations and medium osmolality.
    Systems and Synthetic Biology 06/2013; 7(1-2). DOI:10.1007/s11693-013-9107-5
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    Friedrich-Schiller-University Jena, 02/2011, Degree: PhD