TY - JOUR
T1 - An inter-species protein-protein interaction network across vast evolutionary distance
AU - Zhong, Quan
AU - Pevzner, Samuel J.
AU - Hao, Tong
AU - Wang, Yang
AU - Mosca, Roberto
AU - Menche, Jörg
AU - Taipale, Mikko
AU - Taşan, Murat
AU - Fan, Changyu
AU - Yang, Xinping
AU - Haley, Patrick
AU - Murray, Ryan R.
AU - Mer, Flora
AU - Gebreab, Fana
AU - Tam, Stanley
AU - MacWilliams, Andrew
AU - Dricot, Amélie
AU - Reichert, Patrick
AU - Santhanam, Balaji
AU - Ghamsari, Lila
AU - Calderwood, Michael A.
AU - Rolland, Thomas
AU - Charloteaux, Benoit
AU - Lindquist, Susan
AU - Barabási, Albert László
AU - Hill, David E.
AU - Aloy, Patrick
AU - Cusick, Michael E.
AU - Xia, Yu
AU - Roth, Frederick P.
AU - Vidal, Marc
N1 - Publisher Copyright:
© 2016 The Authors. Published under the terms of the CC BY 4.0 license.
PY - 2016/4/1
Y1 - 2016/4/1
N2 - 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. Synopsis An inter-species "inter-interactome" was generated by systematic mapping protein-protein interactions between human and yeast proteomes. Comparisons of the inter-species interactome with the two "parent" intra-species human and yeast networks reveal evolutionary constraints and plasticity of biological systems. The human and yeast proteomes widely retain the ability to form inter-species protein-protein interactions. Inter-species interactions significantly but not exclusively correspond to ancestral binding properties preserved in human and yeast proteins. Ancestral binding properties appear to underlie conserved and species-specific functions. An inter-species "inter-interactome" was generated by systematic mapping protein-protein interactions between human and yeast proteomes. Comparisons of the inter-species interactome with the two "parent" intra-species human and yeast networks reveal evolutionary constraints and plasticity of biological systems.
AB - 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. Synopsis An inter-species "inter-interactome" was generated by systematic mapping protein-protein interactions between human and yeast proteomes. Comparisons of the inter-species interactome with the two "parent" intra-species human and yeast networks reveal evolutionary constraints and plasticity of biological systems. The human and yeast proteomes widely retain the ability to form inter-species protein-protein interactions. Inter-species interactions significantly but not exclusively correspond to ancestral binding properties preserved in human and yeast proteins. Ancestral binding properties appear to underlie conserved and species-specific functions. An inter-species "inter-interactome" was generated by systematic mapping protein-protein interactions between human and yeast proteomes. Comparisons of the inter-species interactome with the two "parent" intra-species human and yeast networks reveal evolutionary constraints and plasticity of biological systems.
KW - Cross-species complementation
KW - Network evolution
KW - Selection
UR - http://www.scopus.com/inward/record.url?scp=84964490303&partnerID=8YFLogxK
U2 - 10.15252/msb.20156484
DO - 10.15252/msb.20156484
M3 - Article
C2 - 27107014
AN - SCOPUS:84964490303
SN - 1744-4292
VL - 12
JO - Molecular Systems Biology
JF - Molecular Systems Biology
IS - 4
M1 - 865
ER -