The evolution of modularity in bacterial metabolic networks

A. Kreimer, E. Borenstein, U. Gophna, E. Ruppin
2008 Proceedings of the National Academy of Sciences of the United States of America  
Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. Here, we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species. Three main determinants of metabolic network modularity are identified. First, network size is an important topological determinant of
more » ... modularity. Second, several environmental factors influence network modularity, with endosymbionts and mammal-specific pathogens having lower modularity scores than bacterial species that occupy a wider range of niches. Moreover, even among the pathogens, those that alternate between two distinct niches, such as insect and mammal, tend to have relatively high metabolic network modularity. Third, horizontal gene transfer is an important force that contributes significantly to metabolic modularity. We additionally reconstruct the metabolic network of ancestral bacterial species and examine the evolution of modularity across the tree of life. This reveals a trend of modularity decrease from ancestors to descendants that is likely the outcome of niche specialization and the incorporation of peripheral metabolic reactions. horizontal gene transfer ͉ lateral gene transfer ͉ systems biology ͉ bacterial evolution ͉ network modules Results We reconstructed the metabolic networks of 325 bacteria from their genome sequences [supporting information (SI) Dataset S1], of which 138 could be placed on a well established tree of life (21) (Fig. 1) . We then quantified the modularity of the network of each species by using Newman's algorithm (Methods). Subsequently, we used a phylogenetic reconstruction algorithm to infer the ancestral metabolic networks across the tree of life and quantify their modularity in a similar manner (Methods). The results of this analysis, assigning modularity scores to 138 contemporary metabolic networks and to 137 ancestral ones, are displayed in Fig.
doi:10.1073/pnas.0712149105 pmid:18460604 pmcid:PMC2383979 fatcat:awkppmfdyfb2jk2ubsj24gnkq4