Hierarchical modularity of nested bow-ties in metabolic networks.

Jing Zhao,Yi-Xue Li,Hong Yu,Zhi-Wei Cao,Jian-Hua Luo

doi:10.1186/1471-2105-7-386

Abstract

BackgroundThe exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks.ResultsIn this work, metabolic networks of 75 organisms were investigated from a topological point of view. Network decomposition of three microbes (Escherichia coli, Aeropyrum pernix and Saccharomyces cerevisiae) shows that almost all of the sub-networks exhibit a highly modularized bow-tie topological pattern similar to that of the global metabolic networks. Moreover, these small bow-ties are hierarchically nested into larger ones and collectively integrated into a large metabolic network, and important features of this modularity are not observed in the random shuffled network. In addition, such a bow-tie pattern appears to be present in certain chemically isolated functional modules and spatially separated modules including carbohydrate metabolism, cytosol and mitochondrion respectively.ConclusionThe highly modularized bow-tie pattern is present at different levels and scales, and in different chemical and spatial modules of metabolic networks, which is likely the result of the evolutionary process rather than a random accident. Identification and analysis of such a pattern is helpful for understanding the design principles and facilitate the modelling of metabolic networks.

Highlights

The exploration of the structural topology and the organizing principles of genomebased large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks
An important finding is that metabolic networks, as well as other real-world complex networks, have topologies that differ markedly to those found in simple randomly connected networks [8], which suggests that their non-random structures could imply significant organizing principles of metabolic networks
The thick knot may reflect this flexibility, but further research will be needed to full explain these connections. In this survey we have attempted to reveal the topological features of graph models from the view of the design principle of metabolic networks

Summary

Introduction

The exploration of the structural topology and the organizing principles of genomebased large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. A large variety of metabolic reactions can be found in different organisms, metabolic networks are highly conserved across them. It remains a highly interesting and challenging problem to understand the architectural characteristics and "design" principles of the metabolic networks in relation to their function. An important finding is that metabolic networks, as well as other real-world complex networks, have topologies that differ markedly to those found in simple randomly connected networks [8], which suggests that their non-random structures could imply significant organizing principles of metabolic networks. Efforts have been directed towards the recognition of (page number not for citation purposes)

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Conclusion