The evolution of modularity in bacterial metabolic networks

@article{kbg-embmn-2008, abstract = {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 network 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. 10.1073/pnas.0712149105}, author = {Kreimer, Anat and Borenstein, Elhanan and Gophna, Uri and Ruppin, Eytan }, citeulike-article-id = {2763285}, doi = {10.1073/pnas.0712149105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {dataset\_interactions, network\_modules}, month = {May}, pages = {0712149105+}, posted-at = {2008-05-14 15:48:53}, priority = {2}, title = {The evolution of modularity in bacterial metabolic networks}, url = {http://dx.doi.org/10.1073/pnas.0712149105}, year = {2008} }

TY - JOUR ID - kbg-embmn-2008 L3 - citeulike-article-id:2763285 TI - The evolution of modularity in bacterial metabolic networks JF - Proceedings of the National Academy of Sciences SP - 0712149105 N2 - 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 network 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. 10.1073/pnas.0712149105 KW - dataset_interactions KW - network_modules AU - Kreimer, Anat AU - Borenstein, Elhanan AU - Gophna, Uri AU - Ruppin, Eytan PY - 2008/05/06/ UR - http://dx.doi.org/10.1073/pnas.0712149105 ER -