title: Evolution of protein-protein interaction networks in yeast.
abstract: Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE), which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide null expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.
authors.affiliation: School of Computer Science, Carleton University, Ottawa, Canada.
authors.forename: Andrew
authors.initials: A
authors.lastname: Schoenrock
authors.affiliation: Department of Biology, Carleton University, Ottawa, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Burnside
authors.affiliation: Department of Biology, Carleton University, Ottawa, Canada.
authors.forename: Houman
authors.initials: H
authors.lastname: Moteshareie
authors.affiliation: School of Computer Science, Carleton University, Ottawa, Canada.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Pitre
authors.affiliation: Department of Biology, Carleton University, Ottawa, Canada.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Hooshyar
authors.affiliation: Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada.
authors.forename: James R
authors.initials: JR
authors.lastname: Green
authors.affiliation: Department of Biology, Carleton University, Ottawa, Canada.
authors.forename: Ashkan
authors.initials: A
authors.lastname: Golshani
authors.affiliation: School of Computer Science, Carleton University, Ottawa, Canada.
authors.forename: Frank
authors.initials: F
authors.lastname: Dehne
authors.affiliation: Department of Biology, Carleton University, Ottawa, Canada.
authors.forename: Alex
authors.initials: A
authors.lastname: Wong
mesh_terms: D019143:Evolution, Molecular; D053263:Gene Regulatory Networks / Q000502:physiology*; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins