Metabolic network modularity arising from simple growth processes

Abstract

Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous studies have suggested a theoretical model, which proposes that a change in the evolutionary goal (system-specific purpose) increases network modularity, and this hypothesis was supported by statistical data analysis. Nevertheless, further investigation has uncovered additional possibilities that might explain the origin of network modularity. In this work, we propose an evolving network model without tuning parameters to describe metabolic networks. We demonstrate, quantitatively, that metabolic network modularity can arise from simple growth processes, independent of the change in the evolutionary goal. Our model is applicable to a wide range of organisms, and appears to suggest that metabolic network modularity can be more simply determined than previously thought. Nonetheless, our proposition does not serve to contradict the previous model; it strives to provide an insight from a different angle in the ongoing efforts to understand metabolic evolution, with the hope of eventually achieving the synthetic engineering of metabolic networks.

11 pages, 7 figures

References in corpus (14)

• Modularity and community structure in networks
• Community detection in graphs
• Finding community structure in very large networks
• The large-scale organization of metabolic networks
• Specificity and stability in topology of protein networks
• Link Prediction in Complex Networks: A Survey
• Hierarchical Organization in Complex Networks
• Evolution of complex modular biological networks
• Toolbox model of evolution of prokaryotic metabolic networks and their regulation
• Metabolic robustness and network modularity: A model study
• The Blind Watchmaker Network: Scale-freeness and Evolution
• On Gene Duplication Models for Evolving Regulatory Networks
• Neutral theory of chemical reaction networks
• Selective pressure on metabolic network structures as measured from the random blind-watchmaker network

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