title: A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.
abstract: 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.
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Tommy V
authors.initials: TV
authors.lastname: Vo
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Jishnu
authors.initials: J
authors.lastname: Das
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Meyer
authors.affiliation: Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Nicolas A
authors.initials: NA
authors.lastname: Cordero
authors.affiliation: Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Nurten
authors.initials: N
authors.lastname: Akturk
authors.affiliation: Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Medicine, Weill Cornell College of Medicine, New York, NY 10021, USA.
authors.forename: Xiaomu
authors.initials: X
authors.lastname: Wei
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Fair
authors.affiliation: Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Degatano
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Fragoza
authors.affiliation: Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Lisa G
authors.initials: LG
authors.lastname: Liu
authors.affiliation: Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Center, Wako, Saitama 351-0198, Japan.
authors.forename: Akihisa
authors.initials: A
authors.lastname: Matsuyama
authors.affiliation: University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
authors.forename: Michelle
authors.initials: M
authors.lastname: Trickey
authors.affiliation: Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Sachi
authors.initials: S
authors.lastname: Horibata
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Grimson
authors.affiliation: University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Yamano
authors.affiliation: Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Center, Wako, Saitama 351-0198, Japan.
authors.forename: Minoru
authors.initials: M
authors.lastname: Yoshida
authors.affiliation: Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada.
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Pleiss
authors.affiliation: Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0C3, Canada.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA. Electronic address: haiyuan.yu@cornell.edu.
authors.forename: Haiyuan
authors.initials: H
authors.lastname: Yu
mesh_terms: D030562:Databases, Protein; D004194:Disease / Q000235:genetics; D019143:Evolution, Molecular; D006801:Humans; D025341:Principal Component Analysis; D060066:Protein Interaction Maps; D020543:Proteome / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D012568:Schizosaccharomyces / Q000378:metabolism*; D029702:Schizosaccharomyces pombe Proteins / Q000378:metabolism*
chemical_list: D020543:Proteome; D029702:Schizosaccharomyces pombe Proteins