1
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Weng C, Faure AJ, Escobedo A, Lehner B. The energetic and allosteric landscape for KRAS inhibition. Nature 2024; 626:643-652. [PMID: 38109937 PMCID: PMC10866706 DOI: 10.1038/s41586-023-06954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Thousands of proteins have been validated genetically as therapeutic targets for human diseases1. However, very few have been successfully targeted, and many are considered 'undruggable'. This is particularly true for proteins that function via protein-protein interactions-direct inhibition of binding interfaces is difficult and requires the identification of allosteric sites. However, most proteins have no known allosteric sites, and a comprehensive allosteric map does not exist for any protein. Here we address this shortcoming by charting multiple global atlases of inhibitory allosteric communication in KRAS. We quantified the effects of more than 26,000 mutations on the folding of KRAS and its binding to six interaction partners. Genetic interactions in double mutants enabled us to perform biophysical measurements at scale, inferring more than 22,000 causal free energy changes. These energy landscapes quantify how mutations tune the binding specificity of a signalling protein and map the inhibitory allosteric sites for an important therapeutic target. Allosteric propagation is particularly effective across the central β-sheet of KRAS, and multiple surface pockets are genetically validated as allosterically active, including a distal pocket in the C-terminal lobe of the protein. Allosteric mutations typically inhibit binding to all tested effectors, but they can also change the binding specificity, revealing the regulatory, evolutionary and therapeutic potential to tune pathway activation. Using the approach described here, it should be possible to rapidly and comprehensively identify allosteric target sites in many proteins.
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Affiliation(s)
- Chenchun Weng
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andre J Faure
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Escobedo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- University Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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2
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Lemieux P, Bradley D, Dubé AK, Dionne U, Landry CR. Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins. Genetics 2024; 226:iyad175. [PMID: 37793087 PMCID: PMC10763533 DOI: 10.1093/genetics/iyad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 10/06/2023] Open
Abstract
Protein-protein interactions (PPIs) drive many cellular processes. Some interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of 2 paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the preduplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the most recent ancestor of the 2 domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that a SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity.
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Affiliation(s)
- Pascale Lemieux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec, Université Laval, Québec, QC, Canada G1R 2J6
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada M5G 1X5
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
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3
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Després PC, Cisneros AF, Alexander EMM, Sonigara R, Gagné-Thivierge C, Dubé AK, Landry CR. Asymmetrical dose responses shape the evolutionary trade-off between antifungal resistance and nutrient use. Nat Ecol Evol 2022; 6:1501-1515. [PMID: 36050399 DOI: 10.1038/s41559-022-01846-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/07/2022] [Indexed: 12/22/2022]
Abstract
Antimicrobial resistance is an emerging threat for public health. The success of resistance mutations depends on the trade-off between the benefits and costs they incur. This trade-off is largely unknown and uncharacterized for antifungals. Here, we systematically measure the effect of all amino acid substitutions in the yeast cytosine deaminase Fcy1, the target of the antifungal 5-fluorocytosine (5-FC, flucytosine). We identify over 900 missense mutations granting resistance to 5-FC, a large fraction of which appear to act through destabilization of the protein. The relationship between 5-FC resistance and growth sustained by cytosine deamination is characterized by a sharp trade-off, such that small gains in resistance universally lead to large losses in canonical enzyme function. We show that this steep relationship can be explained by differences in the dose-response functions of 5-FC and cytosine. Finally, we observe the same trade-off shape for the orthologue of FCY1 in Cryptoccocus neoformans, a human pathogen. Our results provide a powerful resource and platform for interpreting drug target variants in fungal pathogens as well as unprecedented insights into resistance-function trade-offs.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada.
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada.
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada.
| | - Angel F Cisneros
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada
| | - Emilie M M Alexander
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada
| | - Ria Sonigara
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
| | - Cynthia Gagné-Thivierge
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
| | - Alexandre K Dubé
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada.
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada.
- Centre de Recherche sur les Données Massives, Université Laval, Québec, Canada.
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada.
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4
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Dubé AK, Dandage R, Dibyachintan S, Dionne U, Després PC, Landry CR. Deep Mutational Scanning of Protein-Protein Interactions Between Partners Expressed from Their Endogenous Loci In Vivo. Methods Mol Biol 2022; 2477:237-259. [PMID: 35524121 DOI: 10.1007/978-1-0716-2257-5_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Deep mutational scanning (DMS) generates mutants of a protein of interest in a comprehensive manner. CRISPR-Cas9 technology enables large-scale genome editing with high efficiency. Using both DMS and CRISPR-Cas9 therefore allows us to investigate the effects of thousands of mutations inserted directly in the genome. Combined with protein-fragment complementation assay (PCA), which enables the quantitative measurement of protein-protein interactions (PPIs) in vivo, these methods allow for the systematic assessment of the effects of mutations on PPIs in living cells. Here, we describe a method leveraging DMS, CRISPR-Cas9, and PCA to study the effect of point mutations on PPIs mediated by protein domains in yeast.
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Affiliation(s)
- Alexandre K Dubé
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada.
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada.
| | - Rohan Dandage
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada
| | - Soham Dibyachintan
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada
- Department of Chemical Engineering, Indian Institute of Technology Bombay (IIT), Powai, Mumbai, Maharashtra, India
| | - Ugo Dionne
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec, Université Laval, Québec, QC, Canada
- Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Philippe C Després
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Christian R Landry
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada.
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, Canada.
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5
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Dandage R, Berger CM, Gagnon-Arsenault I, Moon KM, Stacey RG, Foster LJ, Landry CR. Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. Mol Biol Evol 2021; 38:1384-1401. [PMID: 33252673 PMCID: PMC8042767 DOI: 10.1093/molbev/msaa298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hybrids between species often show extreme phenotypes, including some that take place at the molecular level. In this study, we investigated the phenotypes of an interspecies diploid hybrid in terms of protein–protein interactions inferred from protein correlation profiling. We used two yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum, which are interfertile, but yet have proteins diverged enough to be differentiated using mass spectrometry. Most of the protein–protein interactions are similar between hybrid and parents, and are consistent with the assembly of chimeric complexes, which we validated using an orthogonal approach for the prefoldin complex. We also identified instances of altered protein–protein interactions in the hybrid, for instance, in complexes related to proteostasis and in mitochondrial protein complexes. Overall, this study uncovers the likely frequent occurrence of chimeric protein complexes with few exceptions, which may result from incompatibilities or imbalances between the parental proteomes.
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Affiliation(s)
- Rohan Dandage
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, la Structure et L'ingénierie des Protéines, Université Laval, Québec, QC, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada
| | - Caroline M Berger
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, la Structure et L'ingénierie des Protéines, Université Laval, Québec, QC, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada
| | - Isabelle Gagnon-Arsenault
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, la Structure et L'ingénierie des Protéines, Université Laval, Québec, QC, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Richard Greg Stacey
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Christian R Landry
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, la Structure et L'ingénierie des Protéines, Université Laval, Québec, QC, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, Canada
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6
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Liu Z, Miller D, Li F, Liu X, Levy SF. A large accessory protein interactome is rewired across environments. eLife 2020; 9:e62365. [PMID: 32924934 PMCID: PMC7577743 DOI: 10.7554/elife.62365] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022] Open
Abstract
To characterize how protein-protein interaction (PPI) networks change, we quantified the relative PPI abundance of 1.6 million protein pairs in the yeast Saccharomyces cerevisiae across nine growth conditions, with replication, for a total of 44 million measurements. Our multi-condition screen identified 13,764 pairwise PPIs, a threefold increase over PPIs identified in one condition. A few 'immutable' PPIs are present across all conditions, while most 'mutable' PPIs are rarely observed. Immutable PPIs aggregate into highly connected 'core' network modules, with most network remodeling occurring within a loosely connected 'accessory' module. Mutable PPIs are less likely to co-express, co-localize, and be explained by simple mass action kinetics, and more likely to contain proteins with intrinsically disordered regions, implying that environment-dependent association and binding is critical to cellular adaptation. Our results show that protein interactomes are larger than previously thought and contain highly dynamic regions that reorganize to drive or respond to cellular changes.
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Affiliation(s)
- Zhimin Liu
- Department of Biochemistry, Stony Brook UniversityStony BrookUnited States
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookUnited States
| | - Darach Miller
- Joint Initiative for Metrology in BiologyStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Fangfei Li
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookUnited States
- Department of Applied Mathematics and Statistics, Stony Brook UniversityStony BrookUnited States
| | - Xianan Liu
- Department of Biochemistry, Stony Brook UniversityStony BrookUnited States
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookUnited States
| | - Sasha F Levy
- Department of Biochemistry, Stony Brook UniversityStony BrookUnited States
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookUnited States
- Joint Initiative for Metrology in BiologyStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Applied Mathematics and Statistics, Stony Brook UniversityStony BrookUnited States
- SLAC National Accelerator LaboratoryMenlo ParkUnited States
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7
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Gauthier L, Stynen B, Serohijos AWR, Michnick SW. Genetics' Piece of the PI: Inferring the Origin of Complex Traits and Diseases from Proteome-Wide Protein-Protein Interaction Dynamics. Bioessays 2019; 42:e1900169. [PMID: 31854021 DOI: 10.1002/bies.201900169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/15/2019] [Indexed: 11/07/2022]
Abstract
How do common and rare genetic polymorphisms contribute to quantitative traits or disease risk and progression? Multiple human traits have been extensively characterized at the genomic level, revealing their complex genetic architecture. However, it is difficult to resolve the mechanisms by which specific variants contribute to a phenotype. Recently, analyses of variant effects on molecular traits have uncovered intermediate mechanisms that link sequence variation to phenotypic changes. Yet, these methods only capture a fraction of genetic contributions to phenotype. Here, in reviewing the field, it is proposed that complex traits can be understood by characterizing the dynamics of biochemical networks within living cells, and that the effects of genetic variation can be captured on these networks by using protein-protein interaction (PPI) methodologies. This synergy between PPI methodologies and the genetics of complex traits opens new avenues to investigate the molecular etiology of human diseases and to facilitate their prevention or treatment.
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Affiliation(s)
- Louis Gauthier
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Bram Stynen
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Adrian W R Serohijos
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Stephen W Michnick
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
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8
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Marchant A, Cisneros AF, Dubé AK, Gagnon-Arsenault I, Ascencio D, Jain H, Aubé S, Eberlein C, Evans-Yamamoto D, Yachie N, Landry CR. The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. eLife 2019; 8:46754. [PMID: 31454312 PMCID: PMC6711710 DOI: 10.7554/elife.46754] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/11/2019] [Indexed: 01/07/2023] Open
Abstract
Gene duplication is a driver of the evolution of new functions. The duplication of genes encoding homomeric proteins leads to the formation of homomers and heteromers of paralogs, creating new complexes after a single duplication event. The loss of these heteromers may be required for the two paralogs to evolve independent functions. Using yeast as a model, we find that heteromerization is frequent among duplicated homomers and correlates with functional similarity between paralogs. Using in silico evolution, we show that for homomers and heteromers sharing binding interfaces, mutations in one paralog can have structural pleiotropic effects on both interactions, resulting in highly correlated responses of the complexes to selection. Therefore, heteromerization could be preserved indirectly due to selection for the maintenance of homomers, thus slowing down functional divergence between paralogs. We suggest that paralogs can overcome the obstacle of structural pleiotropy by regulatory evolution at the transcriptional and post-translational levels.
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Affiliation(s)
- Axelle Marchant
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Angel F Cisneros
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | - Alexandre K Dubé
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Diana Ascencio
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Honey Jain
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Simon Aubé
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | - Chris Eberlein
- PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Daniel Evans-Yamamoto
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
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9
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Durand É, Gagnon-Arsenault I, Hallin J, Hatin I, Dubé AK, Nielly-Thibault L, Namy O, Landry CR. Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations. Genome Res 2019; 29:932-943. [PMID: 31152050 PMCID: PMC6581059 DOI: 10.1101/gr.239822.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 05/13/2019] [Indexed: 12/17/2022]
Abstract
Little is known about the rate of emergence of de novo genes, what their initial properties are, and how they spread in populations. We examined wild yeast populations (Saccharomyces paradoxus) to characterize the diversity and turnover of intergenic ORFs over short evolutionary timescales. We find that hundreds of intergenic ORFs show translation signatures similar to canonical genes, and we experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Compared with canonical genes, intergenic ORFs have lower translation efficiency, which could imply a lack of optimization for translation or a mechanism to reduce their production cost. Translated intergenic ORFs also tend to have sequence properties that are generally close to those of random intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared <110 kya, already show gene-like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary timescales.
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Affiliation(s)
- Éléonore Durand
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Johan Hallin
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Isabelle Hatin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Lou Nielly-Thibault
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Olivier Namy
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
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10
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Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomyces cerevisiae. Genetics 2018; 211:531-547. [PMID: 30546002 DOI: 10.1534/genetics.118.301727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
The Dam1 complex is an essential component of the outer kinetochore that mediates attachments between spindle microtubules and chromosomes. Dam1p, a subunit of the Dam1 complex, binds to microtubules and is regulated by Aurora B/Ipl1p phosphorylation. We find that overexpression of cAMP-dependent protein kinase (PKA) catalytic subunits (i.e., TPK1, TPK2, TPK3) is lethal in DAM1 mutants and increases the rate of chromosome loss in wild-type cells. Replacing an evolutionarily conserved PKA site (S31) in Dam1p with a nonphosphorylatable alanine suppressed the high-copy PKA dosage lethality in dam1-1 Consistent with Dam1p as a target of PKA, we find that in vitro PKA can directly phosphorylate S31 in Dam1p and we observed phosphorylation of S31 in Dam1p purified from asynchronously growing yeast cells. Cells carrying high-copy TPK2 or a Dam1p phospho-mimetic S31D mutant displayed a reduction in Dam1p localization at the kinetochore, suggesting that PKA phosphorylation plays a role in assembly and/or stability of the Dam1 complex. Furthermore, we observed spindle defects associated with S31 phosphorylation. Finally, we find that phosphorylation of Dam1p on S31 is reduced when glucose is limiting as well as during α-factor arrest, conditions that inhibit PKA activity. These observations suggest that the PKA site of Dam1p participates in regulating kinetochore activity. While PKA is a well-established effector of glucose signaling, our work shows for the first time that glucose-dependent PKA activity has an important function in chromosome segregation.
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11
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Stynen B, Abd-Rabbo D, Kowarzyk J, Miller-Fleming L, Aulakh SK, Garneau P, Ralser M, Michnick SW. Changes of Cell Biochemical States Are Revealed in Protein Homomeric Complex Dynamics. Cell 2018; 175:1418-1429.e9. [PMID: 30454649 PMCID: PMC6242466 DOI: 10.1016/j.cell.2018.09.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 01/22/2023]
Abstract
We report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins, or other small molecules based on "homomer dynamics" protein-fragment complementation assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating the confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health span-affecting drugs, the immunosuppressant rapamycin and the type 2 diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency and includes a change in protein-bound iron levels. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatment of diabetes, cancers, and other chronic diseases of aging.
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Affiliation(s)
- Bram Stynen
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Diala Abd-Rabbo
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC H3C 3J7, Canada
| | - Jacqueline Kowarzyk
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Leonor Miller-Fleming
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Garneau
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC H3C 3J7, Canada.
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12
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Diss G, Lehner B. The genetic landscape of a physical interaction. eLife 2018; 7:32472. [PMID: 29638215 PMCID: PMC5896888 DOI: 10.7554/elife.32472] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/02/2018] [Indexed: 12/26/2022] Open
Abstract
A key question in human genetics and evolutionary biology is how mutations in different genes combine to alter phenotypes. Efforts to systematically map genetic interactions have mostly made use of gene deletions. However, most genetic variation consists of point mutations of diverse and difficult to predict effects. Here, by developing a new sequencing-based protein interaction assay – deepPCA – we quantified the effects of >120,000 pairs of point mutations on the formation of the AP-1 transcription factor complex between the products of the FOS and JUN proto-oncogenes. Genetic interactions are abundant both in cis (within one protein) and trans (between the two molecules) and consist of two classes – interactions driven by thermodynamics that can be predicted using a three-parameter global model, and structural interactions between proximally located residues. These results reveal how physical interactions generate quantitatively predictable genetic interactions. Proteins, the molecular workhorses of the cell, are made of small units called amino acids attached together like the links of a chain. Each protein is composed of a unique combination of amino acids, which is determined by a specific sequence of DNA called a gene. A change in a gene – a mutation – can create a variation in the protein it codes for, for instance by swapping a type of amino acid for another. Different mutations in the same gene can alter a protein in different ways. Some of these changes are harmless, but other can hinder how the protein performs its role. For example, a small change in the structure of a protein could affect how it will bind to other molecules. It is possible for people to have identical mutations in the same genes, but experience different consequences. For instance, two persons could carry the same disease-inducing mutation, but one has a severe version of the condition and the other only mild symptoms. One reason is that changes in other genes cancel out or enhance the effect of a mutation. This phenomenon is known as a genetic interaction and it remains poorly understood, especially at the molecular level. Here, Diss and Lehner developed a method, called deepPCA, to study the consequences of mutations in proteins in the laboratory. The experiments focused on two human genes which code for two proteins that normally attach to each other. Two mutations were artificially created, either one in each gene, or two in one of them. Diss and Lehner then examined how strongly the two mutated proteins could still attach to each other. By repeating this process with over 120,000 different pairs of mutations, it became possible to study how one mutation can have different effects depending on the presence of other mutations in the same protein or in the binding partner. Overall, Diss and Lehner found that genetic interactions are the result of two mechanisms. In the first one, the two mutations together cause specific structural changes that modify how proteins bind to each other. In the second one, the changes solely depend on the magnitude of the initial, thermodynamic effects of individual mutations, but not on their specific physical and chemical properties. To predict the consequences of this second type of genetic interactions, knowing the identity or the exact effects of the two mutations is not necessary. Understanding and predicting genetic interactions is important to develop personalized medicine, where treatments are tailored based on the genetic make up of an individual. This knowledge will also help to study how genes have evolved together.
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Affiliation(s)
- Guillaume Diss
- Systems Biology Program, Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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13
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Diss G, Gagnon-Arsenault I, Dion-Coté AM, Vignaud H, Ascencio DI, Berger CM, Landry CR. Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science 2017; 355:630-634. [PMID: 28183979 DOI: 10.1126/science.aai7685] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/13/2017] [Indexed: 12/18/2022]
Abstract
The maintenance of duplicated genes is thought to protect cells from genetic perturbations, but the molecular basis of this robustness is largely unknown. By measuring the interaction of yeast proteins with their partners in wild-type cells and in cells lacking a paralog, we found that 22 out of 56 paralog pairs compensate for the lost interactions. An equivalent number of pairs exhibit the opposite behavior and require each other's presence for maintaining their interactions. These dependent paralogs generally interact physically, regulate each other's abundance, and derive from ancestral self-interacting proteins. This reveals that gene duplication may actually increase mutational fragility instead of robustness in a large number of cases.
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Affiliation(s)
- Guillaume Diss
- Département de Biologie, Université Laval, Québec, QC, Canada.,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.,EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Isabelle Gagnon-Arsenault
- Département de Biologie, Université Laval, Québec, QC, Canada.,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Anne-Marie Dion-Coté
- Département de Biologie, Université Laval, Québec, QC, Canada.,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Hélène Vignaud
- Département de Biologie, Université Laval, Québec, QC, Canada.,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Diana I Ascencio
- Département de Biologie, Université Laval, Québec, QC, Canada.,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.,Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Caroline M Berger
- Département de Biologie, Université Laval, Québec, QC, Canada.,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Christian R Landry
- Département de Biologie, Université Laval, Québec, QC, Canada. .,The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
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14
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Stynen B, Abd-rabbo D, Kowarzyk J, Miller-fleming L, Ralser M, Michnick S. A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State.. [DOI: 10.1101/190389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractWe report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins or other small molecules based on “homomer dynamics” Protein-fragment Complementation Assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health-span-affecting drugs, immunosuppressant rapamycin and type II diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatments of diabetes, cancers and other chronic diseases of aging.
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15
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Celaj A, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP, St Onge RP. Quantitative analysis of protein interaction network dynamics in yeast. Mol Syst Biol 2017; 13:934. [PMID: 28705884 PMCID: PMC5527849 DOI: 10.15252/msb.20177532] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many cellular functions are mediated by protein–protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment‐dependent protein complex dynamics, we used a DNA‐barcode‐based multiplexed protein interaction assay in Saccharomyces cerevisiae to measure in vivo abundance of 1,379 binary protein complexes under 14 environments. Many binary complexes (55%) were environment dependent, especially those involving transmembrane transporters. We observed many concerted changes around highly connected proteins, and overall network dynamics suggested that “concerted” protein‐centered changes are prevalent. Under a diauxic shift in carbon source from glucose to ethanol, a mass‐action‐based model using relative mRNA levels explained an estimated 47% of the observed variance in binary complex abundance and predicted the direction of concerted binary complex changes with 88% accuracy. Thus, we provide a resource of yeast protein interaction measurements across diverse environments and illustrate the value of this resource in revealing mechanisms of network dynamics.
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Affiliation(s)
- Albi Celaj
- 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, Sinai Health System, Toronto, ON, Canada
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Weihong Xu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Molly Miranda
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Ana Maria Aparicio
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Proctor
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Frederick P Roth
- 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, Sinai Health System, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
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16
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Schlecht U, Liu Z, Blundell JR, St Onge RP, Levy SF. A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions. Nat Commun 2017; 8:15586. [PMID: 28541284 PMCID: PMC5458509 DOI: 10.1038/ncomms15586] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.
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Affiliation(s)
- Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, Calfornia 94304, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Zhimin Liu
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - Jamie R Blundell
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.,Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, Calfornia 94304, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
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17
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Michnick SW, Levy ED, Landry CR, Kowarzyk J, Messier V. The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions. Cold Spring Harb Protoc 2016; 2016:2016/11/pdb.prot090027. [PMID: 27803252 DOI: 10.1101/pdb.prot090027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein-fragment complementation assays (PCAs) can be used to study protein-protein interactions (PPIs) in any living cell, in vivo or in vitro, in any subcellular compartment or membranes. Here, we present a detailed protocol for performing and analyzing a high-throughput PCA screening to study PPIs in yeast, using dihydrofolate reductase (DHFR) as the reporter protein. The DHFR PCA is a simple survival-selection assay in which Saccharomyces cerevisiae DHFR (scDHFR) is inhibited by methotrexate, thus preventing nucleotide synthesis and causing arrest of cell division. Complementation of cells with a methotrexate-insensitive murine DHFR restores nucleotide synthesis, allowing cell proliferation. The methotrexate-resistant DHFR has two mutations (L22F and F31S) and is 10,000 times less sensitive to methotrexate than wild-type scDHFR, but retains full catalytic activity. The DHFR PCA is sensitive enough for PPIs to be detected for open reading frame (ORF)-PCA fragments expressed off of their endogenous promoters.
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Affiliation(s)
- Stephen W Michnick
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100 Israel
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO-Québec Research Network on Protein Function, Structure and Engineering, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Jacqueline Kowarzyk
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Vincent Messier
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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18
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Filteau M, Vignaud H, Rochette S, Diss G, Chrétien AÈ, Berger CM, Landry CR. Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps. Brief Funct Genomics 2015; 15:130-7. [PMID: 26476431 DOI: 10.1093/bfgp/elv043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cellular architectures and signaling machineries are organized through protein-protein interactions (PPIs). High-throughput methods to study PPIs in yeast have opened a new perspective on the organization of the cell by allowing the study of whole protein interactomes. Recent investigations have moved from the description of this organization to the analysis of its dynamics by experimenting how protein interaction networks (PINs) are rewired in response to perturbations. Here we review studies that have used the budding yeast as an experimental system to explore these altered networks. Given the large space of possible PPIs and the diversity of potential genetic and environmental perturbations, high-throughput methods are an essential requirement to survey PIN perturbations on a large scale. Network perturbations are typically conceptualized as the removal of entire proteins (nodes), the modification of single PPIs (edges) or changes in growth conditions. These studies have revealed mechanisms of PPI regulation, PIN architectural organization, robustness and sensitivity to perturbations. Despite these major advances, there are still inherent limits to current technologies that lead to a trade-off between the number of perturbations and the number of PPIs that can be considered simultaneously. Nevertheless, as we exemplify here, targeted approaches combined with the existing resources remain extremely powerful to explore the inner organization of cells and their responses to perturbations.
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19
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Systematic identification of signal integration by protein kinase A. Proc Natl Acad Sci U S A 2015; 112:4501-6. [PMID: 25831502 DOI: 10.1073/pnas.1409938112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellular processes and homeostasis control in eukaryotic cells is achieved by the action of regulatory proteins such as protein kinase A (PKA). Although the outbound signals from PKA directed to processes such as metabolism, growth, and aging have been well charted, what regulates this conserved regulator remains to be systematically identified to understand how it coordinates biological processes. Using a yeast PKA reporter assay, we identified genes that influence PKA activity by measuring protein-protein interactions between the regulatory and the two catalytic subunits of the PKA complex in 3,726 yeast genetic-deletion backgrounds grown on two carbon sources. Overall, nearly 500 genes were found to be connected directly or indirectly to PKA regulation, including 80 core regulators, denoting a wide diversity of signals regulating PKA, within and beyond the described upstream linear pathways. PKA regulators span multiple processes, including the antagonistic autophagy and methionine biosynthesis pathways. Our results converge toward mechanisms of PKA posttranslational regulation by lysine acetylation, which is conserved between yeast and humans and that, we show, regulates protein complex formation in mammals and carbohydrate storage and aging in yeast. Taken together, these results show that the extent of PKA input matches with its output, because this kinase receives information from upstream and downstream processes, and highlight how biological processes are interconnected and coordinated by PKA.
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20
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Rochette S, Diss G, Filteau M, Leducq JB, Dubé AK, Landry CR. Genome-wide protein-protein interaction screening by protein-fragment complementation assay (PCA) in living cells. J Vis Exp 2015:52255. [PMID: 25867901 PMCID: PMC4401175 DOI: 10.3791/52255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Proteins are the building blocks, effectors and signal mediators of cellular processes. A protein's function, regulation and localization often depend on its interactions with other proteins. Here, we describe a protocol for the yeast protein-fragment complementation assay (PCA), a powerful method to detect direct and proximal associations between proteins in living cells. The interaction between two proteins, each fused to a dihydrofolate reductase (DHFR) protein fragment, translates into growth of yeast strains in presence of the drug methotrexate (MTX). Differential fitness, resulting from different amounts of reconstituted DHFR enzyme, can be quantified on high-density colony arrays, allowing to differentiate interacting from non-interacting bait-prey pairs. The high-throughput protocol presented here is performed using a robotic platform that parallelizes mating of bait and prey strains carrying complementary DHFR-fragment fusion proteins and the survival assay on MTX. This protocol allows to systematically test for thousands of protein-protein interactions (PPIs) involving bait proteins of interest and offers several advantages over other PPI detection assays, including the study of proteins expressed from their endogenous promoters without the need for modifying protein localization and for the assembly of complex reporter constructs.
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Affiliation(s)
- Samuel Rochette
- Département de Biologie, Institut de biologie intégrative et des systémes & PROTEO, Université Laval
| | - Guillaume Diss
- Département de Biologie, Institut de biologie intégrative et des systémes & PROTEO, Université Laval
| | - Marie Filteau
- Département de Biologie, Institut de biologie intégrative et des systémes & PROTEO, Université Laval
| | - Jean-Baptiste Leducq
- Département de Biologie, Institut de biologie intégrative et des systémes & PROTEO, Université Laval
| | - Alexandre K Dubé
- Département de Biologie, Institut de biologie intégrative et des systémes & PROTEO, Université Laval
| | - Christian R Landry
- Département de Biologie, Institut de biologie intégrative et des systémes & PROTEO, Université Laval;
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21
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Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties. Curr Opin Struct Biol 2014; 26:113-20. [DOI: 10.1016/j.sbi.2014.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/27/2014] [Accepted: 06/04/2014] [Indexed: 11/21/2022]
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22
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Rochette S, Gagnon-Arsenault I, Diss G, Landry CR. Modulation of the yeast protein interactome in response to DNA damage. J Proteomics 2013; 100:25-36. [PMID: 24262151 DOI: 10.1016/j.jprot.2013.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 10/10/2013] [Accepted: 11/05/2013] [Indexed: 01/24/2023]
Abstract
UNLABELLED Cells deploy diverse mechanisms to physiologically adapt to potentially detrimental perturbations. These mechanisms include changes in the organization of protein-protein interaction networks (PINs). Most PINs characterized to date are portrayed in a single environmental condition and are thus likely to miss important connections among biological processes. In this report, we show that the yeast DHFR-PCA on high-density arrays allows to detects modulations of protein-protein interactions (PPIs) in different conditions by testing more than 1000 PPIs in standard and in a drug-inducing DNA damage conditions. We identify 156 PPIs that show significant modulation in response to DNA damage. We provide evidence that modulated PPIs involve essential genes (NOP7, EXO84 and LAS17) playing critical roles in response to DNA damage. Additionally, we show that a significant proportion of PPI changes are likely explained by changes in protein localization and, to a lesser extent, protein abundance. The protein interaction modules affected by changing PPIs support the role of mRNA stability and translation, protein degradation and ubiquitylation and the regulation of the actin cytoskeleton in response to DNA damage. Overall, we provide a valuable tool and dataset for the study of the rewiring of PINs in response to environmental perturbations. BIOLOGICAL SIGNIFICANCE We show that the DHFR-PCA is a high-throughput method that allows the detection of changes in PPIs associated with different environmental conditions using DNA damage response as a testbed. We provide a valuable resource for the study of DNA damage in eukaryotic cells. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Samuel Rochette
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Guillaume Diss
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
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23
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Diss G, Dubé AK, Boutin J, Gagnon-Arsenault I, Landry CR. A systematic approach for the genetic dissection of protein complexes in living cells. Cell Rep 2013; 3:2155-67. [PMID: 23746448 DOI: 10.1016/j.celrep.2013.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/11/2013] [Accepted: 05/04/2013] [Indexed: 01/23/2023] Open
Abstract
Cells contain many important protein complexes involved in performing and regulating structural, metabolic, and signaling functions. One major challenge in cell biology is to elucidate the organization and mechanisms of robustness of these complexes in vivo. We developed a systematic approach to study structural dependencies within complexes in living cells by deleting subunits and measuring pairwise interactions among other components. We used our methodology to perturb two conserved eukaryotic complexes: the retromer and the nuclear pore complex. Our results identify subunits that are critical for the assembly of these complexes, reveal their structural architecture, and uncover mechanisms by which protein interactions are modulated. Our results also show that paralogous proteins play a key role in the robustness of protein complexes and shape their assembly landscape. Our approach paves the way for studying the response of protein interactomes to mutations and enhances our understanding of genotype-phenotype maps.
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Affiliation(s)
- Guillaume Diss
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
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24
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Diss G, Filteau M, Freschi L, Leducq JB, Rochette S, Torres-Quiroz F, Landry CR. Integrative avenues for exploring the dynamics and evolution of protein interaction networks. Curr Opin Biotechnol 2013; 24:775-83. [PMID: 23571097 DOI: 10.1016/j.copbio.2013.02.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/14/2013] [Accepted: 02/24/2013] [Indexed: 01/09/2023]
Abstract
Over the past decade, the study of protein interaction networks (PINs) has shed light on the organizing principles of living cells. However, PINs have been mostly mapped in one single condition. We outline three of the most promising avenues of investigation in this field, namely the study of first, how PINs are rewired by mutations and environmental perturbations; secondly, how inter-species interactions affect PIN achitectures; thirdly, what mechanisms and forces drive PIN evolution. These investigations will unravel the dynamics and condition dependence of PINs and will thus lead to a better functional annotation of network architecture. One major challenge to reach these goals is the integration of PINs with other cellular regulatory networks in the context of complex cellular phenotypes.
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Affiliation(s)
- Guillaume Diss
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), PROTEO, Université Laval, Québec, Canada G1V 0A6
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25
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Leducq JB, Charron G, Diss G, Gagnon-Arsenault I, Dubé AK, Landry CR. Evidence for the robustness of protein complexes to inter-species hybridization. PLoS Genet 2012; 8:e1003161. [PMID: 23300466 PMCID: PMC3531474 DOI: 10.1371/journal.pgen.1003161] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 10/26/2012] [Indexed: 01/11/2023] Open
Abstract
Despite the tremendous efforts devoted to the identification of genetic incompatibilities underlying hybrid sterility and inviability, little is known about the effect of inter-species hybridization at the protein interactome level. Here, we develop a screening platform for the comparison of protein-protein interactions (PPIs) among closely related species and their hybrids. We examine in vivo the architecture of protein complexes in two yeast species (Saccharomyces cerevisiae and Saccharomyces kudriavzevii) that diverged 5-20 million years ago and in their F1 hybrids. We focus on 24 proteins of two large complexes: the RNA polymerase II and the nuclear pore complex (NPC), which show contrasting patterns of molecular evolution. We found that, with the exception of one PPI in the NPC sub-complex, PPIs were highly conserved between species, regardless of protein divergence. Unexpectedly, we found that the architecture of the complexes in F1 hybrids could not be distinguished from that of the parental species. Our results suggest that the conservation of PPIs in hybrids likely results from the slow evolution taking place on the very few protein residues involved in the interaction or that protein complexes are inherently robust and may accommodate protein divergence up to the level that is observed among closely related species.
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Affiliation(s)
- Jean-Baptiste Leducq
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Canada
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26
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Gagnon-Arsenault I, Marois Blanchet FC, Rochette S, Diss G, Dubé AK, Landry CR. Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication. J Proteomics 2012; 81:112-25. [PMID: 23063722 DOI: 10.1016/j.jprot.2012.09.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/26/2012] [Accepted: 09/30/2012] [Indexed: 01/27/2023]
Abstract
Gene duplication plays a key role in the evolution of protein-protein interaction (PPI) networks. After a gene duplication event, paralogous proteins may diverge through the gain and loss of PPIs. This divergence can be explained by two non-exclusive mechanisms. First, mutations may accumulate in the coding sequences of the paralogs and affect their protein sequences, which can modify, for instance, their binding interfaces and thus their interaction specificity. Second, mutations may accumulate in the non-coding region of the genes and affect their regulatory sequences. The resulting changes in expression profiles can lead to paralogous proteins being differentially expressed and occurring in the cell with different sets of potential interaction partners. These changes could also alter splicing regulation and lead to the inclusion or exclusion of alternative exons. The evolutionary role of these regulatory mechanisms remains largely unexplored. We use bioinformatics analyses of existing PPI data and proteome-wide PPI screening to show that the divergence of transcriptional regulation between paralogs plays a significant role in determining their PPI specificity. Because many gene duplication events are followed by rapid changes in transcriptional regulation, our results suggest that PPI networks may be rewired by gene duplication, without the need for protein to diverge in their binding specificities. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Isabelle Gagnon-Arsenault
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, 1030 Avenue de la Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
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