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MBE Advance Access published online on October 20, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi024
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 13, 2004

Research Article

An Exponential Core in the Heart of the Yeast Protein Interaction Network

José B. Pereira-Leal 1* *, Benjamin Audit 1 *, José M. Peregrin-Alvarez 1, and Christos A. Ouzounis 1

1 Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD - UK

* To whom correspondence should be addressed.
José B. Pereira-Leal, E-mail: jleal{at}mrc-lmb.cam.ac.uk


  Abstract

Protein interactions in the budding yeast have been shown to form a scale-free network, a feature of other organized networks like bacterial and archaeal metabolism and the world wide web. Here, we study the connections established by yeast proteins and discover a preferential attachment between essential proteins. The essential connections are long-ranged and form a sub-network where the giant component includes 97% of these proteins. Unexpectedly, this sub-network displays an exponential connectivity distribution, in sharp contrast with the scale-free topology of the complete network. Furthermore, the wide phylogenetic extent of these core proteins and interactions provides evidence that they represent the ancestral state of the yeast protein interaction network. Finally, we propose that this core exponential network may represent a generic scaffold around which organism- and taxon-specific proteins and interactions coalesce.

Keywords: protein interactions; essential proteins; network evolution; Saccharomyces cerevisiae.

*These authors contributed equally to this work


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