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A Topological Characterization of Medium-Dependent Essential Metabolic Reactions
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
* Author to whom correspondence should be addressed.
Received: 1 August 2012; in revised form: 28 August 2012 / Accepted: 12 September 2012 / Published: 24 September 2012
Abstract: Metabolism has frequently been analyzed from a network perspective. A major question is how network properties correlate with biological features like growth rates, flux patterns and enzyme essentiality. Using methods from graph theory as well as established topological categories of metabolic systems, we analyze the essentiality of metabolic reactions depending on the growth medium and identify the topological footprint of these reactions. We find that the typical topological context of a medium-dependent essential reaction is systematically different from that of a globally essential reaction. In particular, we observe systematic differences in the distribution of medium-dependent essential reactions across three-node subgraphs (the network motif signature of medium-dependent essential reactions) compared to globally essential or globally redundant reactions. In this way, we provide evidence that the analysis of metabolic systems on the few-node subgraph scale is meaningful for explaining dynamic patterns. This topological characterization of medium-dependent essentiality provides a better understanding of the interplay between reaction deletions and environmental conditions.
Keywords: flux-balance analysis; metabolic networks; network motifs
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MDPI and ACS Style
Sonnenschein, N.; Marr, C.; Hütt, M.-T. A Topological Characterization of Medium-Dependent Essential Metabolic Reactions. Metabolites 2012, 2, 632-647.
Sonnenschein N, Marr C, Hütt M-T. A Topological Characterization of Medium-Dependent Essential Metabolic Reactions. Metabolites. 2012; 2(3):632-647.
Sonnenschein, Nikolaus; Marr, Carsten; Hütt, Marc-Thorsten. 2012. "A Topological Characterization of Medium-Dependent Essential Metabolic Reactions." Metabolites 2, no. 3: 632-647.