Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BACKGROUND
Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems.


RESULTS
Metabolic networks are naturally represented as directed hypergraphs in such a way that metabolites are nodes and enzyme-catalyzed reactions form (hyper)edges. The familiar operations from set algebra (union, intersection, and difference) form a natural basis for both the pairwise comparison of networks and identification of distinct metabolic features of a set of algorithms. We report here on an implementation of this approach and its application to the procaryotes.


CONCLUSIONS
We demonstrate that metabolic networks contain valuable phylogenetic information by comparing phylogenies obtained from network comparisons with 16S RNA phylogenies. The algebraic approach to metabolic networks is suitable to study metabolic innovations in two sets of organisms, free living microbes and Pyrococci, as well as obligate intracellular pathogens.
Forst
Christian V
CV
Bioscience Division, Los Alamos National Laboratory, Mailstop M888, PO Box 1663, Los Alamos, NM 87545, USA. chris@lanl.gov
Flamm
Christoph
C
Hofacker
Ivo L
IL
Stadler
Peter F
PF
D000465:Algorithms; D003198:Computer Simulation; D019143:Evolution, Molecular; D008954:Models, Biological; D009716:Numerical Analysis, Computer-Assisted; D010802:Phylogeny; D015398:Signal Transduction / Q000502:physiology*