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MBE Advance Access originally published online on August 24, 2005
Molecular Biology and Evolution 2006 23(1):30-39; doi:10.1093/molbev/msi249
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org

Research Article

Protein Function, Connectivity, and Duplicability in Yeast

Anuphap Prachumwat* and Wen-Hsiung Li{dagger}

* Committee on Genetics, University of Chicago; and {dagger} Department of Ecology and Evolution, University of Chicago

E-mail: whli{at}uchicago.edu.

Protein-protein interaction networks have evolved mainly through connectivity rewiring and gene duplication. However, how protein function influences these processes and how a network grows in time have not been well studied. Using protein-protein interaction data and genomic data from the budding yeast, we first examined whether there is a correlation between the age and connectivity of yeast proteins. A steady increase in connectivity with protein age is observed for yeast proteins except for those that can be traced back to Eubacteria. Second, we investigated whether protein connectivity and duplicability vary with gene function. We found a higher average duplicability for proteins interacting with external environments than for proteins localized within intracellular compartments. For example, proteins that function in the cell periphery (mainly transporters) show a high duplicability but are lowly connected. Conversely, proteins that function within the nucleus (e.g., transcription, RNA and DNA metabolisms, and ribosome biogenesis and assembly) are highly connected but have a low duplicability. Finally, we found a negative correlation between protein connectivity and duplicability.

Key Words: protein interaction network • protein connectivity • gene duplicability • network evolution • protein localization


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