Evolution of resilience in protein interactomes across the tree of life

Author:

Zitnik Marinka,Sosič Rok,Feldman Marcus W.,Leskovec Jure

Abstract

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.

Funder

National Science Foundation

HHS | National Institutes of Health

DOD | Defense Advanced Research Projects Agency

Boeing

Stanford Data Science Inititative

Chan Zuckerberg BioHub

SU | Center for Computational, Evolutionary and Human Genomics, Stanford University

John Templeton Foundation

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

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