An inter‐species protein–protein interaction network across vast evolutionary distance
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‐functi...
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| Format: | Article |
| Language: | English |
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Springer Nature
2016-04-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.20156484 |
| _version_ | 1827014782526423040 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Quan Zhong |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-07T16:37:34Z |
| format | Article |
| id | doaj.art-8947e4a722804e5f9ef09601ac31c1ba |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2025-02-18T14:13:19Z |
| publishDate | 2016-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-8947e4a722804e5f9ef09601ac31c1ba2024-10-28T09:23:27ZengSpringer NatureMolecular Systems Biology1744-42922016-04-0112411910.15252/msb.20156484An inter‐species protein–protein interaction network across vast evolutionary distanceQuan Zhong0Samuel J Pevzner1Tong Hao2Yang Wang3Roberto Mosca4Jörg Menche5Mikko Taipale6Murat Taşan7Changyu Fan8Xinping Yang9Patrick Haley10Ryan R Murray11Flora Mer12Fana Gebreab13Stanley Tam14Andrew MacWilliams15Amélie Dricot16Patrick Reichert17Balaji Santhanam18Lila Ghamsari19Michael A Calderwood20Thomas Rolland21Benoit Charloteaux22Susan Lindquist23Albert‐László Barabási24David E Hill25Patrick Aloy26Michael E Cusick27Yu Xia28Frederick P Roth29Marc Vidal30Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteJoint IRB‐BSC‐CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and TechnologyCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteWhitehead Institute for Biomedical ResearchCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteWhitehead Institute for Biomedical ResearchCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteJoint IRB‐BSC‐CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and TechnologyCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteAbstract 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.https://doi.org/10.15252/msb.20156484Cross‐species complementationNetwork evolutionSelection |
| spellingShingle | 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 An inter‐species protein–protein interaction network across vast evolutionary distance Molecular Systems Biology Cross‐species complementation Network evolution Selection |
| title | An inter‐species protein–protein interaction network across vast evolutionary distance |
| title_full | An inter‐species protein–protein interaction network across vast evolutionary distance |
| title_fullStr | An inter‐species protein–protein interaction network across vast evolutionary distance |
| title_full_unstemmed | An inter‐species protein–protein interaction network across vast evolutionary distance |
| title_short | An inter‐species protein–protein interaction network across vast evolutionary distance |
| title_sort | inter species protein protein interaction network across vast evolutionary distance |
| topic | Cross‐species complementation Network evolution Selection |
| url | https://doi.org/10.15252/msb.20156484 |
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