title: Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.
abstract: BACKGROUND
  As 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  We 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.
authors: Bioinformatics Laboratory and National Laboratory of Bromacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. zhangyong@moon.ibp.ac.cn
authors: Yong
authors: Y
authors: Zhang
authors: Shaojuan
authors: S
authors: Li
authors: Geir
authors: G
authors: Skogerbø
authors: Zhihua
authors: Z
authors: Zhang
authors: Xiaopeng
authors: X
authors: Zhu
authors: Zefeng
authors: Z
authors: Zhang
authors: Shiwei
authors: S
authors: Sun
authors: Hongchao
authors: H
authors: Lu
authors: Baochen
authors: B
authors: Shi
authors: Runsheng
authors: R
authors: Chen