Abstract
BackgroundAs phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective.ResultsWe reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees. Similarity values for each pair of trees ranged from 0.044 to 0.297. Using the quartet method, single pathways trees were merged into a comprehensive tree containing information from a large part of the entire metabolic networks. This tree showed considerably higher similarity (0.386) to the corresponding 16S rRNA-based tree than any tree based on a single pathway, but was, on the other hand, sufficiently distinct to preserve unique phylogenetic information not reflected by the 16S rRNA tree.ConclusionWe observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms. The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.
Highlights
As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components
Taxonomiac distributions of pathways In order to obtain an overview of the distribution of pathways relative to the phylogenetic classification of the 184 organisms studied, we produced a grid showing the fraction of organisms in each Kyoto encyclopedia of genes and genomes (KEGG) [2] category containing a given pathway, based on the definition given in Methods (Figure 1)
Pathway topologies can be regarded as the results of a compromise between phylogenetic information inherited from the last common ancestor and evolutionary pressure causing more rapid shifts in metabolic structure, and varying similarity values may reflect the strength of the two factors
Summary
As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. Other groups have reconstructed the phylogenies based on the enzyme content of entire metabolic networks [8,9] One of these groups used a method based on the combination of sequence information and graph topology [3,4]. The combination of these two sources of information was used for analyzing protein-protein interaction networks, known as PathBLAST [10,11]. These studies have provided valuable insight into the evolution of metabolism; as phylogenetic trees they have generally diverged substantially from trees based on 16S rRNA, the most used molecule for phylogeny reconstruction. One group showed that trees based on different subsets of metabolic networks were different [9], and another result indicated a similar situation when several different pathways were used to construct trees separately [5], just like when different molecules are used for reconstructing phylogenies [12]
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