Molecular Systems Biology (Apr 2016)
An inter‐species protein–protein interaction network across vast evolutionary distance
- Quan Zhong,
- Samuel J Pevzner,
- Tong Hao,
- Yang Wang,
- Roberto Mosca,
- Jörg Menche,
- Mikko Taipale,
- Murat Taşan,
- Changyu Fan,
- Xinping Yang,
- Patrick Haley,
- Ryan R Murray,
- Flora Mer,
- Fana Gebreab,
- Stanley Tam,
- Andrew MacWilliams,
- Amélie Dricot,
- Patrick Reichert,
- Balaji Santhanam,
- Lila Ghamsari,
- Michael A Calderwood,
- Thomas Rolland,
- Benoit Charloteaux,
- Susan Lindquist,
- Albert‐László Barabási,
- David E Hill,
- Patrick Aloy,
- Michael E Cusick,
- Yu Xia,
- Frederick P Roth,
- Marc Vidal
Affiliations
- Quan Zhong
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Samuel J Pevzner
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Yang Wang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Roberto Mosca
- 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
- Jörg Menche
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Mikko Taipale
- Whitehead Institute for Biomedical Research Cambridge MA USA
- Murat Taşan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Changyu Fan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Xinping Yang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Patrick Haley
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Ryan R Murray
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Flora Mer
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Fana Gebreab
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Stanley Tam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Andrew MacWilliams
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Amélie Dricot
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Patrick Reichert
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Balaji Santhanam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Michael A Calderwood
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Thomas Rolland
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Benoit Charloteaux
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Susan Lindquist
- Whitehead Institute for Biomedical Research Cambridge MA USA
- Albert‐László Barabási
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Patrick Aloy
- 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
- Michael E Cusick
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Yu Xia
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Frederick P Roth
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- DOI
- https://doi.org/10.15252/msb.20156484
- Journal volume & issue
-
Vol. 12,
no. 4
pp. n/a – n/a
Abstract
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