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Open Access Highly Accessed Research article

Comparative genomics of metabolic networks of free-living and parasitic eukaryotes

Barbara Nerima12, Daniel Nilsson1 and Pascal Mäser134*

Author Affiliations

1 Institute of Cell Biology, University of Bern, Switzerland

2 National Livestock Resources Research Institute, Tororo, Uganda

3 Swiss Tropical and Public Health Institute, Basel, Switzerland

4 University of Basel, Basel, Switzerland

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BMC Genomics 2010, 11:217  doi:10.1186/1471-2164-11-217

Published: 31 March 2010

Abstract

Background

Obligate endoparasites often lack particular metabolic pathways as compared to free-living organisms. This phenomenon comprises anabolic as well as catabolic reactions. Presumably, the corresponding enzymes were lost in adaptation to parasitism. Here we compare the predicted core metabolic graphs of obligate endoparasites and non-parasites (free living organisms and facultative parasites) in order to analyze how the parasites' metabolic networks shrunk in the course of evolution.

Results

Core metabolic graphs comprising biochemical reactions present in the presumed ancestor of parasites and non-parasites were reconstructed from the Kyoto Encyclopedia of Genes and Genomes. While the parasites' networks had fewer nodes (metabolites) and edges (reactions), other parameters such as average connectivity, network diameter and number of isolated edges were similar in parasites and non-parasites. The parasites' networks contained a higher percentage of ATP-consuming reactions and a lower percentage of NAD-requiring reactions. Control networks, shrunk to the size of the parasites' by random deletion of edges, were scale-free but exhibited smaller diameters and more isolated edges.

Conclusions

The parasites' networks were smaller than those of the non-parasites regarding number of nodes or edges, but not regarding network diameters. Network integrity but not scale-freeness has acted as a selective principle during the evolutionary reduction of parasite metabolism. ATP-requiring reactions in particular have been retained in the parasites' core metabolism while NADH- or NADPH-requiring reactions were lost preferentially.