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MBE Advance Access originally published online on October 20, 2004
Molecular Biology and Evolution 2005 22(3):421-425; doi:10.1093/molbev/msi024
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Molecular Biology and Evolution vol. 22 no. 3 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

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

José B. Pereira-Leal1, Benjamin Audit2, José M. Peregrin-Alvarez3 and Christos A. Ouzounis

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

E-mail: jleal{at}mrc-lmb.cam.ac.uk.

Protein interactions in the budding yeast have been shown to form a scale-free network, a feature of other organized networks such as 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-essential connections are long ranged and form a subnetwork where the giant component includes 97% of these proteins. Unexpectedly, this subnetwork displays an exponential connectivity distribution, in sharp contrast to 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-specific and taxon-specific proteins and interactions coalesce.

Key Words: protein interactions • essential proteins • network evolution • Saccharomyces cerevisiae


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