Preferential attachment in the evolution of metabolic networks.
BACKGROUND
Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. Here we have investigated preferential attachment in the context of metabolic networks.


RESULTS
The connectivities of the enzymes in the metabolic network of Escherichia coli were determined and representatives for these enzymes were located in 11 eukaryotes, 17 archaea and 46 bacteria. E. coli enzymes which have representatives in eukaryotes have a higher average connectivity while enzymes which are represented only in the prokaryotes, and especially the enzymes only present in betagamma-proteobacteria, have lower connectivities than expected by chance. Interestingly, the enzymes which have been proposed as candidates for horizontal gene transfer have a higher average connectivity than the other enzymes. Furthermore, It was found that new edges are added to the highly connected enzymes at a faster rate than to enzymes with low connectivities which is consistent with preferential attachment.


CONCLUSIONS
Here, we have found indications of preferential attachment in the metabolic network of E. coli. A possible biological explanation for preferential attachment growth of metabolic networks is that novel enzymes created through gene duplication maintain some of the compounds involved in the original reaction, throughout its future evolution. In addition, we found that enzymes which are candidates for horizontal gene transfer have a higher average connectivity than other enzymes. This indicates that while new enzymes are attached preferentially to highly connected enzymes, these highly connected enzymes have sometimes been introduced into the E. coli genome by horizontal gene transfer. We speculate that E. coli has adjusted its metabolic network to a changing environment by replacing the relatively central enzymes for better adapted orthologs from other prokaryotic species.
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Sara
S
Stockholm Bioinformatics Center, Department of Biochemistry and Biophyhsics, Albanova University Center, Stockholm University, Stockholm SE-10691, Sweden. sara@sbc.su.se
Kraulis
Per
P
Elofsson
Arne
A
D001419:Bacteria / Q000378:metabolism; D018407:Bacterial Physiological Phenomena; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000502:physiology; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D015966:Gene Expression Regulation, Fungal; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D005821:Genetic Techniques; D016680:Genome, Bacterial; D008660:Metabolism; D008954:Models, Biological; D015233:Models, Statistical; D010802:Phylogeny; D025941:Protein Interaction Mapping; D020033:Protein Isoforms; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D012641:Selection, Genetic
D029968:Escherichia coli Proteins; D020033:Protein Isoforms