Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 116, Issue 10, Pages 4426-4433Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1818013116
Keywords
protein-protein interaction networks; molecular evolution; ecology; network resilience; network rewiring
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Funding
- NSF
- NIH
- Defense Advanced Research Projects Agency
- Boeing
- Stanford Data Science Initiative
- Chan Zuckerberg Biohub
- Stanford Center for Computational, Evolutionary, and Human Genomics
- John Templeton Foundation
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Phenotype robustness to environmental fluctuations is a common biological phenomenon. Although most phenotypes involve multiple proteins that interact with each other, the basic principles of how such interactome networks respond to environmental unpredictability and change during evolution are largely unknown. Here we study interactomes of 1,840 species across the tree of life involving a total of 8,762,166 protein-protein interactions. Our study focuses on the resilience of interactomes to network failures and finds that interactomes become more resilient during evolution, meaning that interactomes become more robust to network failures over time. In bacteria, we find that a more resilient interactome is in turn associated with the greater ability of the organism to survive in a more complex, variable, and competitive environment. We find that at the protein family level proteins exhibit a coordinated rewiring of interactions over time and that a resilient interactome arises through gradual change of the network topology. Our findings have implications for understanding molecular network structure in the context of both evolution and environment.
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