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Cisneros AF, Nielly-Thibault L, Mallik S, Levy ED, Landry CR. Mutational biases favor complexity increases in protein interaction networks after gene duplication. Mol Syst Biol 2024; 20:549-572. [PMID: 38499674 DOI: 10.1038/s44320-024-00030-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Biological systems can gain complexity over time. While some of these transitions are likely driven by natural selection, the extent to which they occur without providing an adaptive benefit is unknown. At the molecular level, one example is heteromeric complexes replacing homomeric ones following gene duplication. Here, we build a biophysical model and simulate the evolution of homodimers and heterodimers following gene duplication using distributions of mutational effects inferred from available protein structures. We keep the specific activity of each dimer identical, so their concentrations drift neutrally without new functions. We show that for more than 60% of tested dimer structures, the relative concentration of the heteromer increases over time due to mutational biases that favor the heterodimer. However, allowing mutational effects on synthesis rates and differences in the specific activity of homo- and heterodimers can limit or reverse the observed bias toward heterodimers. Our results show that the accumulation of more complex protein quaternary structures is likely under neutral evolution, and that natural selection would be needed to reverse this tendency.
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Affiliation(s)
- Angel F Cisneros
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Lou Nielly-Thibault
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
| | - Saurav Mallik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada.
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada.
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada.
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada.
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada.
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Rouleau FD, Dubé AK, Gagnon-Arsenault I, Dibyachintan S, Pageau A, Després PC, Lagüe P, Landry CR. Deep mutational scanning of Pneumocystis jirovecii dihydrofolate reductase reveals allosteric mechanism of resistance to an antifolate. PLoS Genet 2024; 20:e1011252. [PMID: 38683847 DOI: 10.1371/journal.pgen.1011252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
Pneumocystis jirovecii is a fungal pathogen that causes pneumocystis pneumonia, a disease that mainly affects immunocompromised individuals. This fungus has historically been hard to study because of our inability to grow it in vitro. One of the main drug targets in P. jirovecii is its dihydrofolate reductase (PjDHFR). Here, by using functional complementation of the baker's yeast ortholog, we show that PjDHFR can be inhibited by the antifolate methotrexate in a dose-dependent manner. Using deep mutational scanning of PjDHFR, we identify mutations conferring resistance to methotrexate. Thirty-one sites spanning the protein have at least one mutation that leads to resistance, for a total of 355 high-confidence resistance mutations. Most resistance-inducing mutations are found inside the active site, and many are structurally equivalent to mutations known to lead to resistance to different antifolates in other organisms. Some sites show specific resistance mutations, where only a single substitution confers resistance, whereas others are more permissive, as several substitutions at these sites confer resistance. Surprisingly, one of the permissive sites (F199) is without direct contact to either ligand or cofactor, suggesting that it acts through an allosteric mechanism. Modeling changes in binding energy between F199 mutants and drug shows that most mutations destabilize interactions between the protein and the drug. This evidence points towards a more important role of this position in resistance than previously estimated and highlights potential unknown allosteric mechanisms of resistance to antifolate in DHFRs. Our results offer unprecedented resources for the interpretation of mutation effects in the main drug target of an uncultivable fungal pathogen.
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Affiliation(s)
- Francois D Rouleau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Department of Biology, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Department of Biology, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
| | - Soham Dibyachintan
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, Canada
| | - Alicia Pageau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, Canada
| | - Philippe C Després
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, Canada
| | - Patrick Lagüe
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, Canada
- Department of Biology, Science and Engineering Faculty, Université Laval, Québec, Québec, Canada
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Dibyachintan S, Dube AK, Bradley D, Lemieux P, Dionne U, Landry CR. Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network. bioRxiv 2024:2024.02.23.581840. [PMID: 38464075 PMCID: PMC10925128 DOI: 10.1101/2024.02.23.581840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Paralogous genes are often redundant for long periods of time before they diverge in function. While their functions are preserved, paralogous proteins can accumulate mutations that, through epistasis, could impact their fate in the future. By quantifying the impact of all single-amino acid substitutions on the binding of two myosin proteins to their interaction partners, we find that the future evolution of these proteins is highly contingent on their regulatory divergence and the mutations that have silently accumulated in their protein binding domains. Differences in the promoter strength of the two paralogs amplify the impact of mutations on binding in the lowly expressed one. While some mutations would be sufficient to non-functionalize one paralog, they would have minimal impact on the other. Our results reveal how functionally equivalent protein domains could be destined to specific fates by regulatory and cryptic coding sequence changes that currently have little to no functional impact.
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Affiliation(s)
- Soham Dibyachintan
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Alexandre K Dube
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - David Bradley
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Pascale Lemieux
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Ugo Dionne
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Current affiliation: Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Christian R Landry
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
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Hénault M, Marsit S, Charron G, Landry CR. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate. eLife 2024; 12:RP89277. [PMID: 38411604 PMCID: PMC10911583 DOI: 10.7554/elife.89277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis (Hénault et al., 2020) by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy, and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants, and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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Després PC, Dubé AK, Grenier J, Picard MÈ, Shi R, Landry CR. Compensatory mutations potentiate constructive neutral evolution by gene duplication. bioRxiv 2024:2024.02.12.579783. [PMID: 38405844 PMCID: PMC10888846 DOI: 10.1101/2024.02.12.579783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Protein functions generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicate and evolve an homodimeric enzyme to examine if and how this could happen. We identify hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.
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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, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
| | - Jordan Grenier
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event. Mol Biol Evol 2023; 40:msad246. [PMID: 37979156 PMCID: PMC10699747 DOI: 10.1093/molbev/msad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Whole-genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in Saccharomyces cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post-WGD. In S. cerevisiae, HRR25 encodes the casein kinase 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post-WGD and non-WGD species, and have nonconserved cellular localization, consistent with their ongoing loss of function. The analysis in Naumovozyma castellii shows that the noncomplementing ohnolog is expressed at a lower level and has become nonessential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa Campus, South Goa, India
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
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8
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. bioRxiv 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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9
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event. bioRxiv 2023:2023.10.02.560513. [PMID: 37873368 PMCID: PMC10592909 DOI: 10.1101/2023.10.02.560513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in S. cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post WGD. In S. cerevisiae, HRR25 encodes the casein kinase (CK) 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis in N. castelli shows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa campus, Zuarinagar, South Goa, Goa, India
- Current address: Department of Bioengineering, University of California, CA 90095, United States
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Current address: Département de Biochimie, Université de Sherbrooke, Québec, J1K 0A5, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
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Durand R, Jalbert-Ross J, Fijarczyk A, Dubé AK, Landry CR. Cross-feeding affects the target of resistance evolution to an antifungal drug. PLoS Genet 2023; 19:e1011002. [PMID: 37856537 PMCID: PMC10617708 DOI: 10.1371/journal.pgen.1011002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Pathogenic fungi are a cause of growing concern. Developing an efficient and safe antifungal is challenging because of the similar biological properties of fungal and host cells. Consequently, there is an urgent need to better understand the mechanisms underlying antifungal resistance to prolong the efficacy of current molecules. A major step in this direction would be to be able to predict or even prevent the acquisition of resistance. We leverage the power of experimental evolution to quantify the diversity of paths to resistance to the antifungal 5-fluorocytosine (5-FC), commercially known as flucytosine. We generated hundreds of independent 5-FC resistant mutants derived from two genetic backgrounds from wild isolates of Saccharomyces cerevisiae. Through automated pin-spotting, whole-genome and amplicon sequencing, we identified the most likely causes of resistance for most strains. Approximately a third of all resistant mutants evolved resistance through a pleiotropic drug response, a potentially novel mechanism in response to 5-FC, marked by cross-resistance to fluconazole. These cross-resistant mutants are characterized by a loss of respiration and a strong tradeoff in drug-free media. For the majority of the remaining two thirds, resistance was acquired through loss-of-function mutations in FUR1, which encodes an important enzyme in the metabolism of 5-FC. We describe conditions in which mutations affecting this particular step of the metabolic pathway are favored over known resistance mutations affecting a step upstream, such as the well-known target cytosine deaminase encoded by FCY1. This observation suggests that ecological interactions may dictate the identity of resistance hotspots.
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Affiliation(s)
- Romain Durand
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 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 (CRDM), Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
| | - Jordan Jalbert-Ross
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 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 (CRDM), Université Laval, Québec, Canada
| | - Anna Fijarczyk
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 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 (CRDM), 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, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 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 (CRDM), 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, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 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 (CRDM), Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
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11
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Aubé S, Nielly-Thibault L, Landry CR. Evolutionary trade-off and mutational bias could favor transcriptional over translational divergence within paralog pairs. PLoS Genet 2023; 19:e1010756. [PMID: 37235586 DOI: 10.1371/journal.pgen.1010756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
How changes in the different steps of protein synthesis-transcription, translation and degradation-contribute to differences of protein abundance among genes is not fully understood. There is however accumulating evidence that transcriptional divergence might have a prominent role. Here, we show that yeast paralogous genes are more divergent in transcription than in translation. We explore two causal mechanisms for this predominance of transcriptional divergence: an evolutionary trade-off between the precision and economy of gene expression and a larger mutational target size for transcription. Performing simulations within a minimal model of post-duplication evolution, we find that both mechanisms are consistent with the observed divergence patterns. We also investigate how additional properties of the effects of mutations on gene expression, such as their asymmetry and correlation across levels of regulation, can shape the evolution of paralogs. Our results highlight the importance of fully characterizing the distributions of mutational effects on transcription and translation. They also show how general trade-offs in cellular processes and mutation bias can have far-reaching evolutionary impacts.
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Affiliation(s)
- Simon Aubé
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives, Université Laval, Québec, Québec, Canada
| | - Lou Nielly-Thibault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives, Université Laval, Québec, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives, Université Laval, Québec, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
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12
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Kienzle L, Bettinazzi S, Choquette T, Brunet M, Khorami HH, Jacques JF, Moreau M, Roucou X, Landry CR, Angers A, Breton S. A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics. BMC Biol 2023; 21:111. [PMID: 37198654 DOI: 10.1186/s12915-023-01609-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. RESULTS We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. CONCLUSIONS Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.
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Affiliation(s)
- Laura Kienzle
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Stefano Bettinazzi
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Thierry Choquette
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Marie Brunet
- Service de génétique médicale, Département de pédiatrie, Université de Sherbrooke, Sherbrooke, Canada
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
| | | | - Jean-François Jacques
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Mathilde Moreau
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, 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
| | - Annie Angers
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal, Canada.
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13
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Plante S, Moon KM, Lemieux P, Foster LJ, Landry CR. Breaking spore dormancy in budding yeast transforms the cytoplasm and the solubility of the proteome. PLoS Biol 2023; 21:e3002042. [PMID: 37079504 PMCID: PMC10118125 DOI: 10.1371/journal.pbio.3002042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/21/2023] [Indexed: 04/21/2023] Open
Abstract
The biophysical properties of the cytoplasm are major determinants of key cellular processes and adaptation. Many yeasts produce dormant spores that can withstand extreme conditions. We show that spores of Saccharomyces cerevisiae exhibit extraordinary biophysical properties, including a highly viscous and acidic cytosol. These conditions alter the solubility of more than 100 proteins such as metabolic enzymes that become more soluble as spores transit to active cell proliferation upon nutrient repletion. A key regulator of this transition is the heat shock protein, Hsp42, which shows transient solubilization and phosphorylation, and is essential for the transformation of the cytoplasm during germination. Germinating spores therefore return to growth through the dissolution of protein assemblies, orchestrated in part by Hsp42 activity. The modulation of spores' molecular properties are likely key adaptive features of their exceptional survival capacities.
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Affiliation(s)
- Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec), Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Université Laval, Québec (Québec), Canada
- Département de biologie, Université Laval, Québec (Québec), Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec (Québec), Canada
- Centre de recherche en données massives (CRDM), Université Laval, Québec (Québec), Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver (British Columbia), Canada
| | - Pascale Lemieux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec), Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Université Laval, Québec (Québec), Canada
- Département de biologie, Université Laval, Québec (Québec), Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec (Québec), Canada
- Centre de recherche en données massives (CRDM), Université Laval, Québec (Québec), Canada
| | - Leonard J Foster
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver (British Columbia), Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec), Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Université Laval, Québec (Québec), Canada
- Département de biologie, Université Laval, Québec (Québec), Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec (Québec), Canada
- Centre de recherche en données massives (CRDM), Université Laval, Québec (Québec), Canada
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14
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Biot-Pelletier D, Bettinazzi S, Gagnon-Arsenault I, Dubé AK, Bédard C, Nguyen THM, Fiumera HL, Breton S, Landry CR. Evolutionary trajectories are contingent on mitonuclear interactions. Mol Biol Evol 2023; 40:7079771. [PMID: 36929911 PMCID: PMC10072823 DOI: 10.1093/molbev/msad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/02/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths towards higher fitness. To test this prediction, we submitted 1344 populations derived from seven mitonuclear genotypes of Saccharomyces cerevisiae to more than 300 generations of experimental evolution in conditions that either select for a mitochondrial function, or that do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.
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Affiliation(s)
- Damien Biot-Pelletier
- Institut de biologie intégrative et des systèmes, Université Laval, Québec QC Canada.,Département de biologie, Université Laval, Québec QC Canada.,Centre de recherche en données massives (CRDM), 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
| | - Stefano Bettinazzi
- Département de sciences biologiques, Université de Montréal, Montréal QC Canada
| | - Isabelle Gagnon-Arsenault
- Institut de biologie intégrative et des systèmes, Université Laval, Québec QC Canada.,Département de biologie, Université Laval, Québec QC Canada.,Centre de recherche en données massives (CRDM), 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.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec QC Canada
| | - Alexandre K Dubé
- Institut de biologie intégrative et des systèmes, Université Laval, Québec QC Canada.,Département de biologie, Université Laval, Québec QC Canada.,Centre de recherche en données massives (CRDM), 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.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec QC Canada
| | - Camille Bédard
- Institut de biologie intégrative et des systèmes, Université Laval, Québec QC Canada.,Département de biologie, Université Laval, Québec QC Canada.,Centre de recherche en données massives (CRDM), 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
| | - Tuc H M Nguyen
- Department of Biological Sciences, Binghamton University, Binghamton NY USA
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton NY USA
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal QC Canada
| | - Christian R Landry
- Institut de biologie intégrative et des systèmes, Université Laval, Québec QC Canada.,Département de biologie, Université Laval, Québec QC Canada.,Centre de recherche en données massives (CRDM), 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.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec QC Canada
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15
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Peris D, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 2023; 14:690. [PMID: 36755033 PMCID: PMC9908912 DOI: 10.1038/s41467-023-36139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
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Grants
- R01 GM080669 NIGMS NIH HHS
- T32 GM007133 NIGMS NIH HHS
- We thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing Illumina and Sanger sequencing facilities and services; Maria Sardi, Audrey Gasch, and Ursula Bond for providing strains; Sean McIlwain for providing guidance for genome ultra-scaffolding; Yury V. Bukhman for discussing applications of the Growth Curve Analysis Tool (GCAT); Mick McGee for HPLC analysis; Raúl Ortíz-Merino for assistance during YGAP annotations; Jessica Leigh for assistance with PopART; Cecile Ané for suggestions about BUCKy utilization and phylogenetic network analyses; Samina Naseeb and Daniela Delneri for sharing preliminary multi-locus Saccharomyces jurei data; and Branden Timm, Brian Kyle, and Dan Metzger for computational assistance. Some computations were performed on Tirant III of the Spanish Supercomputing Network (‘‘Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin-Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. DP is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. QKL was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB-1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. CRL holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by a NSERC Discovery Grant.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain.
| | - Emily J Ubbelohde
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Meihua Christina Kuang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Kominek
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin A Koshalek
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Katie Hyma
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Guillaume Charron
- Canada Natural Resources, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Carla Gonçalves
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Qi-Ming Wang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Russel L Wrobel
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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16
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Cisneros AF, Gagnon-Arsenault I, Dubé AK, Després PC, Kumar P, Lafontaine K, Pelletier JN, Landry CR. Epistasis between promoter activity and coding mutations shapes gene evolvability. Sci Adv 2023; 9:eadd9109. [PMID: 36735790 PMCID: PMC9897669 DOI: 10.1126/sciadv.add9109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
The evolution of protein-coding genes proceeds as mutations act on two main dimensions: regulation of transcription level and the coding sequence. The extent and impact of the connection between these two dimensions are largely unknown because they have generally been studied independently. By measuring the fitness effects of all possible mutations on a protein complex at various levels of promoter activity, we show that promoter activity at the optimal level for the wild-type protein masks the effects of both deleterious and beneficial coding mutations. Mutations that are deleterious at low activity but masked at optimal activity are slightly destabilizing for individual subunits and binding interfaces. Coding mutations that increase protein abundance are beneficial at low expression but could potentially incur a cost at high promoter activity. We thereby demonstrate that promoter activity in interaction with protein properties can dictate which coding mutations are beneficial, neutral, or deleterious.
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Affiliation(s)
- Angel F. Cisneros
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
| | - Alexandre K. Dubé
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
| | - Philippe C. Després
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
| | - Pradum Kumar
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Kiana Lafontaine
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, H3C 3J7, Montréal, Canada
| | - Joelle N. Pelletier
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, H3C 3J7, Montréal, Canada
- Département de chimie, Faculté des arts et des sciences, Université de Montréal, H3C 3J7, Montréal, Canada
| | - Christian R. Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
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17
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Landry CR, Liti G. Editorial overview: evolutionary genetics: how a tiny model system enables big discoveries. Curr Opin Genet Dev 2022; 77:102000. [PMID: 36270218 DOI: 10.1016/j.gde.2022.102000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Christian R Landry
- Département de biologie, Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec City, Québec, Canada.
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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18
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Bédard C, Cisneros AF, Jordan D, Landry CR. Correlation between protein abundance and sequence conservation: what do recent experiments say? Curr Opin Genet Dev 2022; 77:101984. [PMID: 36162152 DOI: 10.1016/j.gde.2022.101984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 01/27/2023]
Abstract
Cells evolve in a space of parameter values set by physical and chemical forces. These constraints create associations among cellular properties. A particularly strong association is the negative correlation between the rate of evolution of proteins and their abundance in the cell. Highly expressed proteins evolve slower than lowly expressed ones. Multiple hypotheses have been put forward to explain this relationship, including, for instance, the requirement for higher mRNA stability, misfolding avoidance, and misinteraction avoidance for highly expressed proteins. Here, we review some of these hypotheses, their predictions, and how they are supported to finally discuss recent experiments that have been performed to test these predictions.
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Affiliation(s)
- Camille Bédard
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada. https://twitter.com/@CamilleBed17
| | - Angel F Cisneros
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada. https://twitter.com/@AngelFCC119
| | - David Jordan
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada. https://twitter.com/@DavidJordan1997
| | - Christian R Landry
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada.
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19
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Dionne U, Percival LJ, Chartier FJM, Landry CR, Bisson N. SRC homology 3 domains: multifaceted binding modules. Trends Biochem Sci 2022; 47:772-784. [PMID: 35562294 DOI: 10.1016/j.tibs.2022.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.
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Affiliation(s)
- Ugo Dionne
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Lily J Percival
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Manchester, UK
| | - François J M Chartier
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Christian R Landry
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Institute of Integrative and Systems Biology, Université Laval, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC, Canada; Department of Biology, Université Laval, Quebec, QC, Canada.
| | - Nicolas Bisson
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada.
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21
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Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Riffo FC, Dashko S, Dimitrov R, Fisher KJ, Gibson BR, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast 2022; 39:4-24. [PMID: 35146791 DOI: 10.1002/yea.3699] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.
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Affiliation(s)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Graham Bell
- Biology Department and Redpath Museum, McGill University, Québec, Canada
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Neža Čadež
- Biotechnical Faculty, Food Science and Technology Department, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco Cubillos Riffo
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sofia Dashko
- DSM Food Specialties, Center for Food Innovation, AX, Delft, The Netherlands
| | - Roumen Dimitrov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kaitlin J Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian R Gibson
- Technische Universität Berlin, Institute of Food Technology and Food Chemistry, Chair of Brewing and Beverage Technology, Berlin, Germany
| | - Dilnora Gouliamova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Duncan Greig
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Lina Heistinger
- ETH Zurich, Department of Biology, Institute of Biochemistry, Switzerland
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Canada.,PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Canada.,Centre de Recherche sur les Données Massives, Université Laval, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Canada
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dana Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, USA
| | | | - Uroš Petrovič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.,Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia
| | | | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Pablo Villarreal
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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22
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Diss G, Landry CR. Corrigendum: Combining the Dihydrofolate Reductase Protein-Fragment Complementation Assay with Gene Deletions to Establish Genotype-to-Phenotype Maps of Protein Complexes and Interaction Networks. Cold Spring Harb Protoc 2022; 2022:pdb.corr107813. [PMID: 34983864 DOI: 10.1101/pdb.corr107813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Michnick SW, Levy ED, Landry CR, Kowarzyk J, Messier V. Corrigendum: The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions. Cold Spring Harb Protoc 2022; 2022:pdb.corr107812. [PMID: 34983863 DOI: 10.1101/pdb.corr107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Hénault M, Marsit S, Charron G, Landry CR. Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance. Genome Res 2022; 32:2043-2056. [PMID: 36351770 PMCID: PMC9808621 DOI: 10.1101/gr.276885.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. Although uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but the recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which led to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism, and the emergence of reproductive isolation.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
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25
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Després PC, Dubé AK, Yachie N, Landry CR. High-Throughput Gene Mutagenesis Screening Using Base Editing. Methods Mol Biol 2022; 2477:331-348. [PMID: 35524126 DOI: 10.1007/978-1-0716-2257-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Base editing is a CRISPR-Cas9 genome engineering tool that allows programmable mutagenesis without the creation of double-stranded breaks. Here, we describe the design and execution of large-scale base editing screens using the Target-AID base editor in yeast. Using this approach, thousands of sites can be mutated simultaneously. The effects of these mutations on fitness can be measured using a pooled growth competition assay followed by DNA sequencing of gRNAs as barcodes.
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Affiliation(s)
- 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.
| | - 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
| | - Nozomu Yachie
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - 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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27
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Dandage R, Landry CR. Identifying features of genome evolution to exploit cancer vulnerabilities. Cell Syst 2021; 12:1127-1130. [PMID: 34914903 DOI: 10.1016/j.cels.2021.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cancer treatment strategies include exploiting genetic vulnerabilities offered by synthetic lethal (SL) interactions between paralogs. In this issue of Cell Systems, De Kegel et al. (2021) apply a machine learning approach to predict robust SL paralogs in the human genome, highlighting genome evolutionary features as key predictors.
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Affiliation(s)
- Rohan Dandage
- Département de biologie, Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; Département de biochimie, microbiologie et bio-informatique, Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; The Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; Centre de recherche en données massive (CRDM), Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada
| | - Christian R Landry
- Département de biologie, Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; Département de biochimie, microbiologie et bio-informatique, Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; The Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada; Centre de recherche en données massive (CRDM), Université Laval, 1030 Avenue de la médecine, Québec, QC G1V 0A6, Canada.
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28
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Abstract
Mutation rates and spectra vary between species and among populations. Hybridization can contribute to this variation, but its role remains poorly understood. Estimating mutation rates requires controlled conditions where the effect of natural selection can be minimized. One way to achieve this is through mutation accumulation experiments coupled with genome sequencing. Here, we investigate 400 mutation accumulation lines initiated from 11 genotypes spanning intralineage, interlineage, and interspecific crosses of the yeasts Saccharomyces paradoxus and S. cerevisiae and propagated for 770 generations. We find significant differences in mutation rates and spectra among crosses, which are not related to the level of divergence of parental strains but are specific to some genotype combinations. Differences in number of generations and departures from neutrality play a minor role, whereas polyploidy and loss of heterozygosity impact mutation rates in some of the hybrid crosses in an opposite way.
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Affiliation(s)
- Anna Fijarczyk
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Mathieu Hénault
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Souhir Marsit
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Guillaume Charron
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
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29
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Berger CS, Laroche J, Maaroufi H, Martin H, Moon KM, Landry CR, Foster LJ, Aubin-Horth N. The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions. Parasit Vectors 2021; 14:436. [PMID: 34454597 PMCID: PMC8400842 DOI: 10.1186/s13071-021-04933-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Manipulative parasites are thought to liberate molecules in their external environment, acting as manipulation factors with biological functions implicated in their host's physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative parasite. It is necessary to study the molecular interaction between a manipulative parasite and its host to better understand how such alterations evolve. METHODS Here, we used proteomics to characterize the secretome of a model cestode with a complex life cycle based on trophic transmission. We studied Schistocephalus solidus during the life stage in which behavioural changes take place in its obligatory intermediate fish host, the threespine stickleback (Gasterosteus aculeatus). We produced a novel genome sequence and assembly of S. solidus to improve protein coding gene prediction and annotation for this parasite. We then described the whole worm's proteome and its secretome during fish host infection using LC-MS/MS. RESULTS A total of 2290 proteins were detected in the proteome of S. solidus, and 30 additional proteins were detected specifically in the secretome. We found that the secretome contains proteases, proteins with neural and immune functions, as well as proteins involved in cell communication. We detected receptor-type tyrosine-protein phosphatases, which were reported in other parasitic systems to be manipulation factors. We also detected 12 S. solidus-specific proteins in the secretome that may play important roles in host-parasite interactions. CONCLUSIONS Our results suggest that S. solidus liberates molecules with putative host manipulation functions in the host and that many of them are species-specific.
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Affiliation(s)
- Chloé Suzanne Berger
- Département de Biologie, Université Laval, Quebec, QC Canada
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Quebec, QC Canada
- Ressources Aquatiques Québec (RAQ), Institut Des Sciences de La Mer de Rimouski, Quebec, Canada
| | - Jérôme Laroche
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Quebec, QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Quebec, QC Canada
| | - Hélène Martin
- Département de Biologie, Université Laval, Quebec, QC Canada
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Quebec, QC Canada
- Département de Biochimie, Microbiologie Et Bioinformatique, Université Laval, Quebec, QC Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Christian R. Landry
- Département de Biologie, Université Laval, Quebec, QC Canada
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Quebec, QC Canada
- Département de Biochimie, Microbiologie Et Bioinformatique, Université Laval, Quebec, QC Canada
- PROTEO, Le Réseau Québécois de Recherche Sur La Fonction, la structure et l’ingénierie des protéines, Université Laval, Quebec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Quebec, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Nadia Aubin-Horth
- Département de Biologie, Université Laval, Quebec, QC Canada
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Quebec, QC Canada
- Ressources Aquatiques Québec (RAQ), Institut Des Sciences de La Mer de Rimouski, Quebec, Canada
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30
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Drouin M, Hénault M, Hallin J, Landry CR. Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids. Front Fungal Biol 2021; 2:729264. [PMID: 37744137 PMCID: PMC10512236 DOI: 10.3389/ffunb.2021.729264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 09/26/2023]
Abstract
Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading to TE propagation. Recent studies in yeast did not find any increase in transposition rate in hybrids. However, this does not rule out the possibility that the transcriptional or translational activity of TEs increases following hybridization because of a disruption of the host TE control mechanisms. Thus, whether total expression of a TE family is higher in hybrids than in their parental species remains to be examined. We leveraged publically available RNA-seq and ribosomal profiling data on yeast artificial hybrids of the Saccharomyces genus and performed differential expression analysis of their LTR retrotransposons (Ty elements). Our analyses of total mRNA levels show that Ty elements are generally not differentially expressed in hybrids, even when the hybrids are exposed to a low temperature stress condition. Overall, only 2/26 Ty families show significantly higher expression in the S. cerevisiae × S. uvarum hybrids while there are 3/26 showing significantly lower expression in the S. cerevisiae x S. paradoxus hybrids. Our analysis of ribosome profiling data of S. cerevisiae × S. paradoxus hybrids shows similar translation efficiency of Ty in both parents and hybrids, except for Ty1_cer showing higher translation efficiency. Overall, our results do not support the hypothesis that hybridization could act as a systematic trigger of TE expression in yeast and suggest that the impact of hybridization on TE activity is strain and TE specific.
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Affiliation(s)
- Marika Drouin
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
| | - Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
| | - Johan Hallin
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
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31
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Suzuki G, Saito Y, Seki M, Evans-Yamamoto D, Negishi M, Kakoi K, Kawai H, Landry CR, Yachie N, Mitsuyama T. Machine learning approach for discrimination of genotypes based on bright-field cellular images. NPJ Syst Biol Appl 2021; 7:31. [PMID: 34290253 PMCID: PMC8295336 DOI: 10.1038/s41540-021-00190-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Morphological profiling is a combination of established optical microscopes and cutting-edge machine vision technologies, which stacks up successful applications in high-throughput phenotyping. One major question is how much information can be extracted from an image to identify genetic differences between cells. While fluorescent microscopy images of specific organelles have been broadly used for single-cell profiling, the potential ability of bright-field (BF) microscopy images of label-free cells remains to be tested. Here, we examine whether single-gene perturbation can be discriminated based on BF images of label-free cells using a machine learning approach. We acquired hundreds of BF images of single-gene mutant cells, quantified single-cell profiles consisting of texture features of cellular regions, and constructed a machine learning model to discriminate mutant cells from wild-type cells. Interestingly, the mutants were successfully discriminated from the wild type (area under the receiver operating characteristic curve = 0.773). The features that contributed to the discrimination were identified, and they included those related to the morphology of structures that appeared within cellular regions. Furthermore, functionally close gene pairs showed similar feature profiles of the mutant cells. Our study reveals that single-gene mutant cells can be discriminated from wild-type cells based on BF images, suggesting the potential as a useful tool for mutant cell profiling.
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Affiliation(s)
- Godai Suzuki
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, 169-8555, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Motoaki Seki
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Daniel Evans-Yamamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0035, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Mikiko Negishi
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Kentaro Kakoi
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Hiroki Kawai
- Research and Development Department, LPIXEL Inc., Tokyo, 100-0004, Japan
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systémes, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de sciences et génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0035, Japan.
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan.
- School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T1Z3, Canada.
| | - Toutai Mitsuyama
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan.
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Marsit S, Hénault M, Charron G, Fijarczyk A, Landry CR. The neutral rate of whole-genome duplication varies among yeast species and their hybrids. Nat Commun 2021; 12:3126. [PMID: 34035259 PMCID: PMC8149824 DOI: 10.1038/s41467-021-23231-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/19/2021] [Indexed: 11/09/2022] Open
Abstract
Hybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD may allow hybrids to thrive by increasing fitness, restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. Here we show, by measuring the spontaneous rate of WGD of more than 1300 yeast crosses evolved under relaxed selection, that some genotypes or combinations of genotypes are more prone to WGD, including some hybrids between closely related species. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.
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Affiliation(s)
- S Marsit
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada.
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada.
| | - M Hénault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada
| | - G Charron
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - A Fijarczyk
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada
| | - C R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada.
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada.
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Berger CM, Landry CR. Yeast proteins do not practice social distancing as species hybridize. Curr Genet 2021; 67:755-759. [PMID: 33948708 PMCID: PMC8096128 DOI: 10.1007/s00294-021-01188-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/12/2021] [Indexed: 11/26/2022]
Abstract
With the current COVID-19 pandemic, we all realized how important interactions are. Interactions are everywhere. At the cellular level, protein interactions play a key role and their ensemble, also called interactome, is often referred as the basic building blocks of life. Given its importance, the maintenance of the integrity of the interactome is a real challenge in the cell. Many events during evolution can disrupt interactomes and potentially result in different characteristics for the organisms. However, the molecular underpinnings of changes in interactions at the cellular level are still largely unexplored. Among the perturbations, hybridization puts in contact two different interactomes, which may lead to many changes in the protein interaction network of the hybrid, including gains and losses of interactions. We recently investigated the fate of the interactomes after hybridization between yeast species using a comparative proteomics approach. A large-scale conservation of the interactions was observed in hybrids, but we also noticed the presence of proteostasis-related changes. This suggests that, despite a general robustness, small differences may accumulate in hybrids and perturb their protein physiology. Here, we summarize our work with a broader perspective on the importance of interactions.
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Affiliation(s)
- Caroline M Berger
- Département de Biologie, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada.
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada.
- Le réseau québécois de recherche sur la fonction, la structure et l'ingénierie de protéines, PROTEO, Université Laval, Quebec, QC, G1V0A6, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Quebec, QC, G1V0A6, Canada.
| | - Christian R Landry
- Département de Biologie, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada
- Le réseau québécois de recherche sur la fonction, la structure et l'ingénierie de protéines, PROTEO, Université Laval, Quebec, QC, G1V0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Quebec, QC, G1V0A6, Canada
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35
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Bautista C, Marsit S, Landry CR. Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions. Evol Appl 2021; 14:758-769. [PMID: 33767750 PMCID: PMC7980265 DOI: 10.1111/eva.13155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022] Open
Abstract
Hybridization may increase the probability of adaptation to extreme stresses. This advantage could be caused by an increased genome plasticity in hybrids, which could accelerate the search for adaptive mutations. High ultraviolet (UV) radiation is a particular challenge in terms of adaptation because it affects the viability of organisms by directly damaging DNA, while also challenging future generations by increasing mutation rate. Here we test whether hybridization accelerates adaptive evolution in response to DNA damage, using yeast as a model. We exposed 180 populations of hybrids between species (Saccharomyces cerevisiae and Saccharomyces paradoxus) and their parental strains to UV mimetic and control conditions for approximately 100 generations. Although we found that adaptation occurs in both hybrids and parents, hybrids achieved a lower rate of adaptation, contrary to our expectations. Adaptation to DNA damage conditions comes with a large and similar cost for parents and hybrids, suggesting that this cost is not responsible for the lower adaptability of hybrids. We suggest that the lower adaptive potential of hybrids in this condition may result from the interaction between DNA damage and the inherent genetic instability of hybrids.
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Affiliation(s)
- Carla Bautista
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
- Département de Biochimie, de Microbiologie et de Bio‐informatiqueFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
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36
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Plante S, Landry CR. Closely related budding yeast species respond to different ecological signals for spore activation. Yeast 2020; 38:81-89. [PMID: 33202071 DOI: 10.1002/yea.3538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/27/2020] [Accepted: 11/10/2020] [Indexed: 01/20/2023] Open
Abstract
Spore activation is one of the most important developmental decisions in fungi as it initiates the transition from dormant and stress-resistant cells to vegetative cells. Because in many species mating follows spore activation and germination, signals that trigger this developmental transition can also contribute to species reproductive barriers. Here, we examine the biochemical signals triggering spore activation in a natural species complex of budding yeast, Saccharomyces paradoxus (lineages SpA, SpB, SpC and SpC*). We first demonstrate that we can quantitatively monitor spore activation in these closely related lineages. Second, we dissect the composition of culture media to identify components necessary and/or sufficient to activate spores in the four lineages. We show that, contrary to expectation, glucose is necessary but not sufficient to trigger spore activation. We also show that two of the North American lineages (SpC and SpC*) diverge from the other North American (SpB) and European (SpA) lineages in terms of germination signal as their spore activation requires inorganic phosphate. Our results show that the way budding yeast interpret environmental conditions during spore activation diverged among closely related and incipient species, which means that it may play a role in their ecological differentiation and reproductive isolation. TAKE AWAY: Sensing of multiple compounds allows spore activation in non-domesticated budding yeast. Spore activation cues differ among Saccharomyces paradoxus lineages. Dextrose and phosphate signal activation in SpC and SpC* spores.
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Affiliation(s)
- Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, Québec, Canada.,Département de biologie, Université Laval, Québec, Québec, Canada.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, Québec, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, Québec, Canada.,Département de biologie, Université Laval, Québec, Québec, Canada.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, Québec, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, Québec, Canada
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37
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Abstract
Germination is an important developmental process that supports resumption of growth in dormant spores. The study of the mechanisms underlying germination requires a pure spore population devoid of other cell types. This article describes the sporulation of wild Saccharomyces cerevisiae and Saccharomyces paradoxus strains, and the isolation and purification of ascospores. We also describe a method to synchronously induce germination in a spore population as well as to measure spore activation. This procedure can be applied, for example, to the study of environmental conditions that trigger germination. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Sporulation Basic Protocol 2: Spore purification Basic Protocol 3: Germination induction Support Protocol 1: Flow cytometry analysis Support Protocol 2: Heat-shock resistance measurement.
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Affiliation(s)
- Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (Québec), Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, (Québec), Canada.,Département de Biologie, Université Laval, Québec, (Québec), Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, (Québec), Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, (Québec), Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (Québec), Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, (Québec), Canada.,Département de Biologie, Université Laval, Québec, (Québec), Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, (Québec), Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, (Québec), Canada
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38
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Hénault M, Marsit S, Charron G, Landry CR. The effect of hybridization on transposable element accumulation in an undomesticated fungal species. eLife 2020; 9:e60474. [PMID: 32955438 PMCID: PMC7584455 DOI: 10.7554/elife.60474] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can profoundly impact the evolution of genomes and species. A long-standing hypothesis suggests that hybridization could deregulate TEs and trigger their accumulation, although it received mixed support from studies mostly in plants and animals. Here, we tested this hypothesis in fungi using incipient species of the undomesticated yeast Saccharomyces paradoxus. Population genomic data revealed no signature of higher transposition in natural hybrids. As we could not rule out the elimination of past transposition increase signatures by natural selection, we performed a laboratory evolution experiment on a panel of artificial hybrids to measure TE accumulation in the near absence of selection. Changes in TE copy numbers were not predicted by the level of evolutionary divergence between the parents of a hybrid genotype. Rather, they were highly dependent on the individual hybrid genotypes, showing that strong genotype-specific deterministic factors govern TE accumulation in yeast hybrids.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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39
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Horianopoulos LC, Gluck-Thaler E, Benoit Gelber I, Cowen LE, Geddes-McAlister J, Landry CR, Schwartz IS, Scott JA, Sellam A, Sheppard DC, Spribille T, Subramaniam R, Walker AK, Harris SD, Shapiro RS, Gerstein AC. The Canadian Fungal Research Network: current challenges and future opportunities. Can J Microbiol 2020; 67:13-22. [PMID: 32717148 DOI: 10.1139/cjm-2020-0263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fungi critically impact the health and function of global ecosystems and economies. In Canada, fungal researchers often work within silos defined by subdiscipline and institutional type, complicating the collaborations necessary to understand the impacts fungi have on the environment, economy, and plant and animal health. Here, we announce the establishment of the Canadian Fungal Research Network (CanFunNet, https://fungalresearch.ca), whose mission is to strengthen and promote fungal research in Canada by facilitating dialogue among scientists. We summarize the challenges and opportunities for Canadian fungal research that were discussed at CanFunNet's inaugural meeting in 2019, and identify 4 priorities for our community: (i) increasing collaboration among scientists, (ii) studying diversity in the context of ecological disturbance, (iii) preserving culture collections in the absence of sustained funding, and (iv) leveraging diverse expertise to attract trainees. We have gathered additional information to support our recommendations, including a survey identifying underrepresentation of fungal-related courses at Canadian universities, a list of Canadian fungaria and culture collections, and a case study of a human fungal pathogen outbreak. We anticipate that these discussions will help prioritize fungal research in Canada, and we welcome all researchers to join this nationwide effort to enhance knowledge dissemination and funding advocacy.
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Affiliation(s)
- Linda C Horianopoulos
- Department of Microbiology and Immunology, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Emile Gluck-Thaler
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Isabelle Benoit Gelber
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, QC H4B 1R6, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jennifer Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, 474-570 Gordon Street, Guelph, ON N1G 1Y2, Canada
| | - Christian R Landry
- Département de biologie and Département de biochimie, microbiologie et bio-informatique, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, 8440 112 Street NW, Edmonton, AB T6G 2R7, Canada
| | - James A Scott
- Dalla Lana School of Public Health, University of Toronto, 223 College Street, Toronto, ON, M5T 1R4, Canada
| | - Adnane Sellam
- Department of Microbiology, Infectious Disease and Immunology, Montreal Heart Institute, Université de Montréal, 5000, rue Bélanger, Montréal, QC H1T 1C8, Canada
| | - Donald C Sheppard
- Department of Microbiology and Immunology, McGill University, 3775, rue University, Room 511, Montréal, QC H3A 2B4.,McGill Interdisciplinary Initiative in Infection and Immunity, 3666 McTavish Street, 2nd Floor, Montréal, QC H3Y 1Y2, Canada
| | - Toby Spribille
- Department of Biological Sciences, University of Alberta, 11335 Saskatchewan Drive NW, Edmonton, AB T6G 2H5, Canada
| | - Rajagopal Subramaniam
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Allison K Walker
- Department of Biology, Acadia University, 33 Westwood Avenue, Room 302, Wolfville, NS B4P 2R6, Canada
| | - Steven D Harris
- Department of Biological Sciences, University of Manitoba, Biological Sciences Building, Winnipeg, MB R3T 2N2, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, 474-570 Gordon Street, Guelph, ON N1G 1Y2, Canada
| | - Aleeza C Gerstein
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB R3T 2N2, Canada.,Department of Statistics, University of Manitoba, 318 Machray Hall, Winnipeg, MB R3T 2N2, Canada
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40
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Abstract
Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Motoaki Seki
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Christian R Landry
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada.
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
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41
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Hallin J, Cisneros AF, Hénault M, Fijarczyk A, Dandage R, Bautista C, Landry CR. Similarities in biological processes can be used to bridge ecology and molecular biology. Evol Appl 2020; 13:1335-1350. [PMID: 32684962 PMCID: PMC7359829 DOI: 10.1111/eva.12961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/17/2020] [Accepted: 03/16/2020] [Indexed: 01/10/2023] Open
Abstract
Much of the research in biology aims to understand the origin of diversity. Naturally, ecological diversity was the first object of study, but we now have the necessary tools to probe diversity at molecular scales. The inherent differences in how we study diversity at different scales caused the disciplines of biology to be organized around these levels, from molecular biology to ecology. Here, we illustrate that there are key properties of each scale that emerge from the interactions of simpler components and that these properties are often shared across different levels of organization. This means that ideas from one level of organization can be an inspiration for novel hypotheses to study phenomena at another level. We illustrate this concept with examples of events at the molecular level that have analogs at the organismal or ecological level and vice versa. Through these examples, we illustrate that biological processes at different organization levels are governed by general rules. The study of the same phenomena at different scales could enrich our work through a multidisciplinary approach, which should be a staple in the training of future scientists.
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Affiliation(s)
- Johan Hallin
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
| | - Angel F Cisneros
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
| | - Mathieu Hénault
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
| | - Anna Fijarczyk
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
| | - Rohan Dandage
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
| | - Carla Bautista
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
| | - Christian R Landry
- Département de biochimie de microbiologie et de bio-informatique Faculté des sciences et de génie Université Laval Québec Canada.,Département de biologie Faculté des sciences et de génie Université Laval Québec Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS) 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
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Cooke SJ, Nguyen VM, Anastakis D, Scott SD, Turetsky MR, Amirfazli A, Hearn A, Milton CE, Loewen L, Smith EE, Norris DR, Lavoie KL, Aiken A, Ansari D, Antle AN, Babel M, Bailey J, Bernstein DM, Birnbaum R, Bourassa C, Calcagno A, Campana A, Chen B, Collins K, Connelly CE, Denov M, Dupont B, George E, Gregory-Eaves I, High S, Hill JM, Jackson PL, Jette N, Jurdjevic M, Kothari A, Khairy P, Lamoureux SA, Ladner K, Landry CR, Légaré F, Lehoux N, Leuprecht C, Lieverse AR, Luczak A, Mallory ML, Manning E, Mazalek A, Murray SJ, Newman LL, Oosterveld V, Potvin P, Reimer-Kirkham S, Rowsell J, Stacey D, Tighe SL, Vocadlo DJ, Wilson AE, Woolford A. Diverse perspectives on interdisciplinarity from Members of the College of the Royal Society of Canada. Facets (Ott) 2020. [DOI: 10.1139/facets-2019-0044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Various multiple-disciplinary terms and concepts (although most commonly “interdisciplinarity,” which is used herein) are used to frame education, scholarship, research, and interactions within and outside academia. In principle, the premise of interdisciplinarity may appear to have many strengths; yet, the extent to which interdisciplinarity is embraced by the current generation of academics, the benefits and risks for doing so, and the barriers and facilitators to achieving interdisciplinarity, represent inherent challenges. Much has been written on the topic of interdisciplinarity, but to our knowledge there have been few attempts to consider and present diverse perspectives from scholars, artists, and scientists in a cohesive manner. As a team of 57 members from the Canadian College of New Scholars, Artists, and Scientists of the Royal Society of Canada (the College) who self-identify as being engaged or interested in interdisciplinarity, we provide diverse intellectual, cultural, and social perspectives. The goal of this paper is to share our collective wisdom on this topic with the broader community and to stimulate discourse and debate on the merits and challenges associated with interdisciplinarity. Perhaps the clearest message emerging from this exercise is that working across established boundaries of scholarly communities is rewarding, necessary, and is more likely to result in impact. However, there are barriers that limit the ease with which this can occur (e.g., lack of institutional structures and funding to facilitate cross-disciplinary exploration). Occasionally, there can be significant risk associated with doing interdisciplinary work (e.g., lack of adequate measurement or recognition of work by disciplinary peers). Solving many of the world’s complex and pressing problems (e.g., climate change, sustainable agriculture, the burden of chronic disease, and aging populations) demands thinking and working across long-standing, but in some ways restrictive, academic boundaries. Academic institutions and key support structures, especially funding bodies, will play an important role in helping to realize what is readily apparent to all who contributed to this paper—that interdisciplinarity is essential for solving complex problems; it is the new norm. Failure to empower and encourage those doing this research will serve as a great impediment to training, knowledge, and addressing societal issues.
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Affiliation(s)
- Steven J. Cooke
- Institute of Environmental and Interdisciplinary Sciences, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Vivian M. Nguyen
- Institute of Environmental and Interdisciplinary Sciences, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Dimitry Anastakis
- History Department, Trent University, 1600 West Bank Dr., Peterborough, ON K9L 0G2, Canada
| | - Shannon D. Scott
- Faculty of Nursing, Edmonton Clinic Health Academy, University of Alberta, 11405-87 Ave., Edmonton, AB T6G 1C9, Canada
| | - Merritt R. Turetsky
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Alidad Amirfazli
- Department of Mechanical Engineering, York University, 4700 Keele St., Toronto, ON M3J 1P3, Canada
| | - Alison Hearn
- Faculty of Information and Media Studies, Western University, London, ON N6A 5B7, Canada
| | - Cynthia E. Milton
- Département d’histoire, Université de Montréal, 2900 Edouard Montpetit Blvd, Montréal, QC H3T 1J4, Canada
| | - Laura Loewen
- Desautels Faculty of Music, University of Manitoba, 150 Dafoe Rd. W, Winnipeg, MB R3T 2N2, Canada
| | - Eric E. Smith
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB T4N 2N1, Canada
| | - D. Ryan Norris
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada
- Nature Conservancy of Canada, 245 Eglington Avenue East, Toronto, ON M4P 3J1, Canada
| | - Kim L. Lavoie
- Department of Psychology, University of Quebec at Montreal and CIUSSS-NIM Hopital du Sacre-Coeur de Montreal, CP 8888, succursale Centre-ville, Montreal, QC H3C 3P8, Canada
| | - Alice Aiken
- Faculty of Health and Office of the Vice-President, Research and Innovation, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Daniel Ansari
- Department of Psychology & Faculty of Education, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Alissa N. Antle
- School of Interactive Arts and Technology, Simon Fraser University, 250—13450 102 Avenue, Surrey, BC V3T 0A3, Canada
| | - Molly Babel
- Department of Linguistics, University of British Columbia, 2613 West Mall, Vancouver, BC V6T 1Z4, Canada
| | - Jane Bailey
- Faculty of Law (Common Law), University of Ottawa, 57 Louis Pasteur St, Ottawa, ON K1N 6N5, Canada
| | - Daniel M. Bernstein
- Department of Psychology, Kwantlen Polytechnic University, 12666-72nd Ave., Surrey, BC V3W 2M8, Canada
| | - Rachel Birnbaum
- School of Social Work and Childhood Studies and Interdisciplinary Programs, King’s University College at Western, 266 Epworth Avenue, London, ON N6A 2M3, Canada
| | - Carrie Bourassa
- Indigenous Health, Department of Community Health & Epidemiology, College of Medicine, University of Saskatchewan, 104 Clinic Place, Saskatoon, SK S7N 2Z4, Canada
| | - Antonio Calcagno
- Department of Philosophy, King’s University College at Western University, 266 Epworth Avenue, London, ON N6A 2M3, Canada
| | - Aurélie Campana
- Département de science politique, Faculté des sciences sociales, Université Laval, 1030 avenue des Sciences humaines, Québec, QC G1V 0A6, Canada
| | - Bing Chen
- Department of Civil Engineering, Memorial University, 240 Prince Philip Drive, St. John’s, NL A1A 3X5, Canada
| | - Karen Collins
- Department of Communication Arts, University of Waterloo, 200 University Ave W., Waterloo, ON N2L 3G1, Canada
| | - Catherine E. Connelly
- DeGroote School of Business, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4M4, Canada
| | - Myriam Denov
- School of Social Work, McGill University, 3506 University Street, Montreal, QC H3A 2A7, Canada
| | - Benoît Dupont
- Centre international de criminologie comparée, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Eric George
- École des medias, The Université du Québec à Montréal, 405 Rue Sainte-Catherine Est, Montréal, QC H2L 2C4, Canada
| | - Irene Gregory-Eaves
- Department of Biology, McGill University, 1205 Dr. Penfield Ave, Montreal, QC H3A 1B1, Canada
| | - Steven High
- Department of History, Concordia University, 1455 de Maisonneuve Blvd Ouest, Montreal, QC H3G 1M8, Canada
| | - Josephine M. Hill
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Philip L. Jackson
- École de psychologie, Université Laval, 2325 Allée des Bibliothèques, Québec, QC G1V 0A6, Canada
| | - Nathalie Jette
- Departments of Neurology and Population Health Sciences & Policy, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Mark Jurdjevic
- Department of History, York University-Glendon Campus, 2275 Bayview Ave, Toronto, ON M4N 3M6, Canada
| | - Anita Kothari
- Faculty of Health Studies, Western University, 1151 Richmond St, London, ON N6A 3K7, Canada
| | - Paul Khairy
- Department of Medicine, Montreal Heart Institute, University of Montreal, 5000 Bélanger, Montreal, QC H1T 1C8, Canada
| | - Sylvie A. Lamoureux
- Faculty of Arts, Official Languages and Bilingualism Institute, Université d’Ottawa, 70 Laurier Est, Ottawa, ON K1N 6N5, Canada
| | - Kiera Ladner
- Political Studies, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Christian R. Landry
- Département de biologie & Département de biochimie, microbiologie et bioinformatique, Université Laval, 1030 Avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - François Légaré
- INRS, Centre Énergie Matériaux Télécommunications, 1650, boulevard Lionel-Boulet, Québec, QC J3X 1S2, Canada
| | - Nadia Lehoux
- Department of Mechanical Engineering, Pavillon Pouliot, Université Laval, 1065 avenue de la Médecine, Québec, QC G1V OA6, Canada
| | - Christian Leuprecht
- Department of Political Science and Economics, Royal Military College of Canada, P.O. Box 17000, Station Forces, Kingston, ON K7K 7B4, Canada
| | - Angela R. Lieverse
- Department of Archaeology and Anthropology, University of Saskatchewan, 55 Campus Dr., Saskatoon, SK S7N 5B1, Canada
| | - Artur Luczak
- Canadian Center for Behavioural Neuroscience, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
| | - Mark L. Mallory
- Department of Biology, Acadia University, 15 University Dr., Wolfville, NS B4P 2R6, Canada
| | - Erin Manning
- Film Studies and Studio Art, Concordia University, 1455 de Maisonneuve W, Montreal, QC H3G 1M8, Canada
| | - Ali Mazalek
- Synaesthetic Media Lab, Ryerson University, Bell Trinity Square N103, 483 Bay St., Toronto, ON M5G 2E1, Canada
| | - Stuart J. Murray
- Department of English Language and Literature and Department of Health Sciences, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Lenore L. Newman
- Department of Geography, University of the Fraser Valley, 33844 King Rd., Abbotsford, BC V2S 7M8, Canada
| | - Valerie Oosterveld
- Faculty of Law, Western University, 1151 Richmond St., London, ON N6A 3K7, Canada
| | - Patrice Potvin
- Département de didactique, Faculté des sciences de l’éducation, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Sheryl Reimer-Kirkham
- School of Nursing, Trinity Western University, 7600 Glover Rd., Langley, BC V2Y 1Y1, Canada
| | - Jennifer Rowsell
- Department of Educational Studies, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Dawn Stacey
- School of Nursing, Faculty of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Susan L. Tighe
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - David J. Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC V5A 1S6, Canada
| | - Anne E. Wilson
- Psychology Department, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON N2L 3C5, Canada
| | - Andrew Woolford
- Department of Sociology and Criminology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Abstract
A gene duplication can lead to all sorts of problems in a cell. However, it can also lead to all sorts of benefits. Beneficial or not, the gene duplicates might be kept in the genome because of several different reasons. For instance, if natural selection works towards optimizing one function of a gene at the expense of another, then gene duplication could resolve this conflict by separating the functions in two genes. Here, we outline evolutionary incentives to keep a duplicated gene in the genome, focusing on divergence in expression and trade-off resolution as featured in a new and exciting paper published in this edition of PLOS Biology.
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Affiliation(s)
- Johan Hallin
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), 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
| | - Christian R. Landry
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), 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
- * E-mail:
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Charron G, Marsit S, Hénault M, Martin H, Landry CR. Spontaneous whole-genome duplication restores fertility in interspecific hybrids. Nat Commun 2019; 10:4126. [PMID: 31511504 PMCID: PMC6739354 DOI: 10.1038/s41467-019-12041-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/19/2019] [Indexed: 11/21/2022] Open
Abstract
Interspecies hybrids often show some advantages over parents but also frequently suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out genetic incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in species such as fungi that can also propagate asexually. Here, to test this, we evolve in parallel and under relaxed selection more than 600 diploid yeast inter-specific hybrids that span from 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occur in both hybrids between young and well-established species. Our results show that the instability of ploidy in hybrid is an accessible path to spontaneous fertility recovery. Hybridization across species can lead to offspring with reduced fertility. Here, the authors experimentally evolve yeast and show that whole-genome duplication during asexual reproduction can restore fertility in hybrids over a relatively short evolutionary timespan.
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Affiliation(s)
- Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Hélène Martin
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada. .,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada. .,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada. .,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.
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45
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Abstract
The protective redundancy of paralogous genes partly relies on the fact that they carry their functions independently. However, a significant fraction of paralogous proteins may form functionally dependent pairs, for instance, through heteromerization. As a consequence, one could expect these heteromeric paralogs to be less protective against deleterious mutations. To test this hypothesis, we examined the robustness landscape of gene loss-of-function by CRISPR-Cas9 in more than 450 human cell lines. This landscape shows regions of greater deleteriousness to gene inactivation as a function of key paralog properties. Heteromeric paralogs are more likely to occupy such regions owing to their high expression and large number of protein-protein interaction partners. Further investigation revealed that heteromers may also be under stricter dosage balance, which may also contribute to the higher deleteriousness upon gene inactivation. Finally, we suggest that physical dependency may contribute to the deleteriousness upon loss-of-function as revealed by the correlation between the strength of interactions between paralogs and their higher deleteriousness upon loss of function.
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Affiliation(s)
- Rohan Dandage
- Département de BiologieUniversité LavalQuébecQCCanada
- Département de Biochimie, Microbiologie et Bio‐InformatiqueUniversité LavalQuébecQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- The Québec Network for Research on Protein Function, Engineering, and Applications (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Christian R Landry
- Département de BiologieUniversité LavalQuébecQCCanada
- Département de Biochimie, Microbiologie et Bio‐InformatiqueUniversité LavalQuébecQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- The Québec Network for Research on Protein Function, Engineering, and Applications (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
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46
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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47
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Nielly-Thibault L, Landry CR. Differences Between the Raw Material and the Products of de Novo Gene Birth Can Result from Mutational Biases. Genetics 2019; 212:1353-1366. [PMID: 31227545 PMCID: PMC6707459 DOI: 10.1534/genetics.119.302187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/14/2019] [Indexed: 12/03/2022] Open
Abstract
Proteins are among the most important constituents of biological systems. Because all protein-coding genes have a noncoding ancestral form, the properties of noncoding sequences and how they shape the birth of novel proteins may influence the structure and function of all proteins. Differences between the properties of young proteins and random expectations from noncoding sequences have previously been interpreted as the result of natural selection. However, interpreting such deviations requires a yet-unattained understanding of the raw material of de novo gene birth and its relation to novel functional proteins. We mathematically show that the average properties and selective filtering of the "junk" polypeptides of which this raw material is composed are not the only factors influencing the properties of novel functional proteins. We find that in some biological scenarios, they also depend on the variance of the properties of junk polypeptides and their correlation with the rate of allelic turnover, which may itself depend on mutational biases. This suggests for instance that any property of polypeptides that accelerates their exploration of the sequence space could be overrepresented in novel functional proteins, even if it has a limited effect on adaptive value. To exemplify the use of our general theoretical results, we build a simple model that predicts the mean length and mean intrinsic disorder of novel functional proteins from the genomic GC content and a single evolutionary parameter. This work provides a theoretical framework that can guide the prediction and interpretation of results when studying the de novo emergence of protein-coding genes.
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Affiliation(s)
- Lou Nielly-Thibault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biologie, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec, Quebec G1V 0A6, Canada
- PROTEO, Quebec, Quebec G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biologie, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec, Quebec G1V 0A6, Canada
- PROTEO, Quebec, Quebec G1V 0A6, Canada
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48
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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49
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Eberlein C, Hénault M, Fijarczyk A, Charron G, Bouvier M, Kohn LM, Anderson JB, Landry CR. Author Correction: Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nat Commun 2019; 10:2199. [PMID: 31086180 PMCID: PMC6513852 DOI: 10.1038/s41467-019-09702-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Chris Eberlein
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
| | - Mathieu Hénault
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Anna Fijarczyk
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Matteo Bouvier
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Christian R Landry
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada. .,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada.
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50
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Eberlein C, Hénault M, Fijarczyk A, Charron G, Bouvier M, Kohn LM, Anderson JB, Landry CR. Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nat Commun 2019; 10:923. [PMID: 30804385 PMCID: PMC6389940 DOI: 10.1038/s41467-019-08809-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/31/2019] [Indexed: 01/30/2023] Open
Abstract
Hybridization can result in reproductively isolated and phenotypically distinct lineages that evolve as independent hybrid species. How frequently hybridization leads to speciation remains largely unknown. Here we examine the potential recurrence of hybrid speciation in the wild yeast Saccharomyces paradoxus in North America, which comprises two endemic lineages SpB and SpC, and an incipient hybrid species, SpC*. Using whole-genome sequences from more than 300 strains, we uncover the hybrid origin of another group, SpD, that emerged from hybridization between SpC* and one of its parental species, the widespread SpB. We show that SpD has the potential to evolve as a novel hybrid species, because it displays phenotypic novelties that include an intermediate transcriptome profile, and partial reproductive isolation with its most abundant sympatric parental species, SpB. Our findings show that repetitive cycles of divergence and hybridization quickly generate diversity and reproductive isolation, providing the raw material for speciation by hybridization. Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.
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Affiliation(s)
- Chris Eberlein
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
| | - Mathieu Hénault
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Anna Fijarczyk
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Matteo Bouvier
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Christian R Landry
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada. .,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada.
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