A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human

• Published in: Cell 2016-01, Vol.164 (1-2), p.310-323
• Main Authors: Vo, Tommy V., Das, Jishnu, Meyer, Michael J., Cordero, Nicolas A., Akturk, Nurten, Wei, Xiaomu, Fair, Benjamin J., Degatano, Andrew G., Fragoza, Robert, Liu, Lisa G., Matsuyama, Akihisa, Trickey, Michelle, Horibata, Sachi, Grimson, Andrew, Yamano, Hiroyuki, Yoshida, Minoru, Roth, Frederick P., Pleiss, Jeffrey A., Xia, Yu, Yu, Haiyuan
• Format: Article
• Language: English
• Subjects: Databases, Protein; Disease - genetics; Evolution, Molecular; Humans; Principal Component Analysis; Protein Interaction Maps; Proteome - metabolism; Saccharomyces cerevisiae - metabolism; Schizosaccharomyces - metabolism; Schizosaccharomyces pombe Proteins - metabolism
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2015.11.037

Here, we present FissionNet, a proteome-wide binary protein interactome for S. pombe, comprising 2,278 high-quality interactions, of which ∼50% were previously not reported in any species. FissionNet unravels previously unreported interactions implicated in processes such as gene silencing and pre-mRNA splicing. We developed a rigorous network comparison framework that accounts for assay sensitivity and specificity, revealing extensive species-specific network rewiring between fission yeast, budding yeast, and human. Surprisingly, although genes are better conserved between the yeasts, S. pombe interactions are significantly better conserved in human than in S. cerevisiae. Our framework also reveals that different modes of gene duplication influence the extent to which paralogous proteins are functionally repurposed. Finally, cross-species interactome mapping demonstrates that coevolution of interacting proteins is remarkably prevalent, a result with important implications for studying human disease in model organisms. Overall, FissionNet is a valuable resource for understanding protein functions and their evolution. [Display omitted] •A proteome-wide network of 2,278 high-quality binary S. pombe protein interactions•Species-specific interaction rewiring among yeasts and human•Gene duplication modes shape the functional fate of paralogous proteins•Cross-species interactome mapping uncovers extensive coevolution FissionNet is a proteome-wide binary interactome network for S. pombe. Comparative analyses of FissionNet with protein networks in budding yeast and human reveal how protein networks evolve, principles of gene repurposing following duplication, and insights into species-specific alterations of function.