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Origin of structural difference in metabolic networks with respect to temperature.

ABSTRACT: BACKGROUND: Metabolism is believed to adaptively shape-shift with changing environment. In recent years, a structural difference with respect to temperature, which is an environmental factor, has been revealed in metabolic networks, implying that metabolic networks transit with temperature. Subsequently, elucidatation of the origin of these structural differences due to temperature is important for understanding the evolution of life. However, the origin has yet to be clarified due to the complexity of metabolic networks. RESULTS: Consequently, we propose a simple model with a few parameters to explain the transitions. We first present mathematical solutions of this model using mean-field approximation, and demonstrate that this model can reproduce structural properties, such as heterogeneous connectivity and hierarchical modularity, in real metabolic networks both qualitatively and quantitatively. We next show that the model parameters correlate with optimal growth temperature. In addition, we present a relationship between multiple cyclic properties and optimal growth temperature in metabolic networks. CONCLUSION: From the proposed model, we find that such structural properties are determined by the emergence of a short-cut path, which reduces the minimum distance between two nodes on a graph. Furthermore, we investigate correlations between model parameters and growth temperature; as a result, we find that the emergence of the short-cut path tends to be inhibited with increasing temperature. In addition, we also find that the short-cut path bypasses a relatively long path at high temperature when the emergence of the new path is not inhibited. Even further, additional network analysis provides convincing evidence of the reliability of the proposed model and its conclusions on the possible origins of differences in metabolic network structure.

SUBMITTER: Takemoto K

PROVIDER: S-EPMC2564917 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND: Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. RESULTS: We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. CONCLUSIONS: The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and biochemical correlations can act both to diversify and to narrow down metabolic evolution.

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Origin of structural difference in metabolic networks with respect to temperature.

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