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

doi:10.15252/msb.20156484

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

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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, …

Molecular systems biology, Vol.12(4), pp.865-n/a

04/2016

DOI: https://doi.org/10.15252/msb.20156484

PMID: 27107014

Résumé

Computational Biology - methods

Databases, Protein

Evolution, Molecular

Fungal Proteins - metabolism

Humans

Protein Interaction Mapping - methods

Proteome - metabolism

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.

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Titre: An inter-species protein-protein interaction network across vast evolutionary distance
Créateurs - sans rôle: Quan Zhong - 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
Samuel J Pevzner - 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
Tong Hao - 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
Yang Wang - 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
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 Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, 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 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
Changyu Fan - 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
Xinping Yang - 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
Patrick Haley - 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
Ryan R Murray - 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
Flora Mer - 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
Fana Gebreab - 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
Stanley Tam - 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
Andrew MacWilliams - 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
Amélie Dricot - 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
Patrick Reichert - 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
Balaji Santhanam - 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
Lila Ghamsari - 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
Michael A Calderwood - Dana-Farber Cancer Institute
Thomas Rolland - 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
Benoit Charloteaux - 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
Susan Lindquist - 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
Albert-László Barabási - 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
David E Hill - Dana-Farber Cancer Institute
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 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
Michael E Cusick - 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
Yu Xia - 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
Frederick P Roth
Marc Vidal - 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
Détails de publication: Molecular systems biology, Vol.12(4), pp.865-n/a
Note de subvention: Intramural NIH HHS R01 HG006061 / NHGRI NIH HHS U41 HG001715 / NHGRI NIH HHS R01 HG001715 / NHGRI NIH HHS U01 HG001715 / NHGRI NIH HHS R01-HG006061 / NHGRI NIH HHS R01-HG001715 / NHGRI NIH HHS
Identifiants: 99149620109311
Unité académique: Centre de Recherche en Biologie Cellulaire de Montpellier - CRBM
Langue: English
Type de ressource: Journal article