Metabolic innovations towards the human lineage.
BACKGROUND
We describe a function-driven approach to the analysis of metabolism which takes into account the phylogenetic origin of biochemical reactions to reveal subtle lineage-specific metabolic innovations, undetectable by more traditional methods based on sequence comparison. The origins of reactions and thus entire pathways are inferred using a simple taxonomic classification scheme that describes the evolutionary course of events towards the lineage of interest. We investigate the evolutionary history of the human metabolic network extracted from a metabolic database, construct a network of interconnected pathways and classify this network according to the taxonomic categories representing eukaryotes, metazoa and vertebrates.


RESULTS
It is demonstrated that lineage-specific innovations correspond to reactions and pathways associated with key phenotypic changes during evolution, such as the emergence of cellular organelles in eukaryotes, cell adhesion cascades in metazoa and the biosynthesis of complex cell-specific biomolecules in vertebrates.


CONCLUSIONS
This phylogenetic view of metabolic networks puts gene innovations within an evolutionary context, demonstrating how the emergence of a phenotype in a lineage provides a platform for the development of specialized traits.
Freilich
Shiri
S
The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK. shirifre@post.tau.ac.il
Goldovsky
Leon
L
Ouzounis
Christos A
CA
Thornton
Janet M
JM
D002784:Cholesterol / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006028:Glycosphingolipids / Q000378:metabolism; D006031:Glycosylation; D006801:Humans; D053858:Metabolic Networks and Pathways; D008957:Models, Genetic; D010802:Phylogeny
D006028:Glycosphingolipids; D002784:Cholesterol
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