Modular co-evolution of metabolic networks

In this work, the functional and evolutionary modularity of Homo sapiens (H. sapiens) metabolic network were investigated from a topological point of view. Network decomposition shows that the metabolic network is organized in a highly modular core-periphery way, in which the core modules are tightly linked together and perform basic metabolism functions, whereas the periphery modules only interact with few modules and accomplish relatively independent and specialized functions. Moreover, over half of the modules exhibit co-evolutionary feature and belong to specific evolutionary ages. Peripheral modules tend to evolve more cohesively and faster than core modules do.The correlation between functional, evolutionary and topological modularity suggests that the evolutionary history and functional requirements of metabolic systems have been imprinted in the architecture of metabolic networks. Such systems level analysis could demonstrate how the evolution of genes may be placed in a genome-scale network context, giving a novel perspective on molecular evolution.Cellular functions are carried out in a modular way, and functional modules are basic building blocks of cellular organization [1]. From the perspective of molecular biology, a functional module is regarded as a group of spatially isolated or chemically specific biological components that work together for a discrete biological function. Various functional modules such as protein complexes [2-4], signalling/metabolic pathways [5-8] and transcriptional clusters [9,10] have been detected from functional genomic techniques or bioinformatics analyses of genomic data. Recent studies suggest, to varying degrees, functional modules correlate with evolutionary modules [11], the latter being defined as cohesive evolutionary blocks in cellular systems [12,13]. It was found that genes within functional modules tend to evolve in a coordinated way [12-15], while some fraction of evolutionary modules (or phylogenetic modules)