Abstract
BackgroundCellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life. Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics.DescriptionThe Molecular Ancestry Network (MANET) project traces evolution of protein architecture in biomolecular networks. We describe metabolic MANET, a database that links information in the Structural Classification of Proteins (SCOP), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and phylogenetic reconstructions depicting the evolution of protein fold architecture. Metabolic MANET literally 'paints' the ancestries of enzymes derived from rooted phylogenomic trees directly onto over one hundred metabolic subnetworks, enabling the study of evolutionary patterns at global and local levels. An initial analysis of painted subnetworks reveals widespread enzymatic recruitment and an early origin of amino acid metabolism.ConclusionMANET maps evolutionary relationships directly and globally onto biological networks, and can generate and test hypotheses related to evolution of metabolism. We anticipate its use in the study of other networks, such as signaling and other protein-protein interaction networks.
Highlights
Cellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life
Molecular Ancestry Network (MANET) maps evolutionary relationships directly and globally onto biological networks, and can generate and test hypotheses related to evolution of metabolism
The MANET database project traces the evolution of protein structure in biomolecular networks with bioinformatic, phylogenetic, and statistical methods
Summary
Cellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life. Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics. Metabolic MANET literally 'paints' the ancestries of enzymes derived from rooted phylogenomic trees directly onto over one hundred metabolic subnetworks, enabling the study of evolutionary patterns at global and local levels. Cellular metabolism represents a collection of enzymatic reactions and transport processes that convert metabolites into molecules capable of supporting cellular life. It is the best-studied biological network, with highly branched pathways describing the enzymatic processing of metabolites. How metabolic networks function and change as organisms increased in complexity remains an important question, making metabolism an (page number not for citation purposes)
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