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Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

An inter-species protein-protein interaction network across vast evolutionary distance.

Author information

1
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Biological Sciences, Wright State University, Dayton, OH, USA marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.
2
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Biomedical Engineering, Boston University, Boston, MA, USA Boston University School of Medicine, Boston, MA, USA.
3
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
4
Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona Catalonia, Spain.
5
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA, USA.
6
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
7
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.
8
Whitehead Institute for Biomedical Research, Cambridge, MA, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
9
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA, USA Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
10
Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona Catalonia, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
11
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Bioengineering, McGill University, Montreal, QC, Canada marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.
12
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada Canadian Institute for Advanced Research, Toronto, ON, Canada marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.
13
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.

Abstract

In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an "inter-interactome" approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter-interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra-species networks. Although substantially reduced relative to intra-species networks, the levels of functional overlap in the yeast-human inter-interactome network uncover significant remnants of co-functionality widely preserved in the two proteomes beyond human-yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co-functionality. Such non-functional interactions, however, represent a reservoir from which nascent functional interactions may arise.

KEYWORDS:

Cross‐species complementation; Network evolution; Selection

PMID:
27107014
PMCID:
PMC4848758
DOI:
10.15252/msb.20156484
[Indexed for MEDLINE]
Free PMC Article

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