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Banderas A, Hofmann M, Cordier C, Le Bec M, Elizondo-Cantú MC, Chiron L, Pouzet S, Lifschytz Y, Ji W, Amir A, Scolari V, Hersen P. Optogenetic control of pheromone gradients and mating behavior in budding yeast. Life Sci Alliance 2025; 8:e202403078. [PMID: 40216553 PMCID: PMC11992364 DOI: 10.26508/lsa.202403078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 03/25/2025] [Accepted: 03/25/2025] [Indexed: 04/14/2025] Open
Abstract
During mating in budding yeast, cells use pheromones to locate each other and fuse. This model system has shaped our current understanding of signal transduction and cell polarization in response to extracellular signals. The cell populations producing extracellular signal landscapes themselves are, however, less well understood, yet crucial for functionally testing quantitative models of cell polarization and for controlling cell behavior through bioengineering approaches. Here we engineered optogenetic control of pheromone landscapes in mating populations of budding yeast, hijacking the mating-pheromone pathway to achieve spatial control of growth, cell morphology, cell-cell fusion, and distance-dependent gene expression in response to light. Using our tool, we were able to spatially control and shape pheromone gradients, allowing the use of a biophysical model to infer the properties of large-scale gradients generated by mating populations in a single, quantitative experimental setup, predicting that the shape of such gradients depends quantitatively on population parameters. Spatial optogenetic control of diffusible signals and their degradation provides a controllable signaling environment for engineering artificial communication and cell-fate systems in gel-embedded cell populations without the need for physical manipulation.
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Affiliation(s)
- Alvaro Banderas
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
- INM - Leibniz Institute for New Materials, Campus D2 2, Saarbrücken, Germany
| | - Maud Hofmann
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - Céline Cordier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - Matthias Le Bec
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - M Carolina Elizondo-Cantú
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - Lionel Chiron
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - Sylvain Pouzet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - Yotam Lifschytz
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Wencheng Ji
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Ariel Amir
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Vittore Scolari
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Paris, France
| | - Pascal Hersen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
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Marr RA, Moore J, Formby S, Martiniuk JT, Hamilton J, Ralli S, Konwar K, Rajasundaram N, Hahn A, Measday V. Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade. G3 (BETHESDA, MD.) 2023; 13:jkad130. [PMID: 37307358 PMCID: PMC10411583 DOI: 10.1093/g3journal/jkad130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023]
Abstract
Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The "wine circle/Region B", a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.
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Affiliation(s)
- R Alexander Marr
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Jackson Moore
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Sean Formby
- Koonkie Canada Inc., 321 Water Street Suite 501, Vancouver, BC V6B 1B8, Canada
| | - Jonathan T Martiniuk
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
- Food Science Graduate Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jonah Hamilton
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Sneha Ralli
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, 8888 University Drive East K9625, Burnaby, BC V5A 1S6, Canada
| | - Kishori Konwar
- Koonkie Canada Inc., 321 Water Street Suite 501, Vancouver, BC V6B 1B8, Canada
| | - Nisha Rajasundaram
- Koonkie Canada Inc., 321 Water Street Suite 501, Vancouver, BC V6B 1B8, Canada
| | - Aria Hahn
- Koonkie Canada Inc., 321 Water Street Suite 501, Vancouver, BC V6B 1B8, Canada
| | - Vivien Measday
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
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3
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Galeota-Sprung B, Fernandez A, Sniegowski P. Changes to the mtDNA copy number during yeast culture growth. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211842. [PMID: 35814911 PMCID: PMC9257595 DOI: 10.1098/rsos.211842] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
We show that the mitochondrial DNA (mtDNA) copy number in growing cultures of the yeast Saccharomyces cerevisiae increases by a factor of up to 4, being lowest (approx. 10 per haploid genome) and stable during rapid fermentative growth, and highest at the end of the respiratory phase. When yeast are grown on glucose, the onset of the mtDNA copy number increase coincides with the early stages of the diauxic shift, and the increase continues through respiration. A lesser yet still substantial copy number increase occurs when yeast are grown on a nonfermentable carbon source, i.e. when there is no diauxic shift. The mtDNA copy number increase during and for some time after the diauxic shift is not driven by an increase in cell size. The copy number increase occurs in both haploid and diploid strains but is markedly attenuated in a diploid wild isolate that is a ready sporulator. Strain-to-strain differences in mtDNA copy number are least apparent in fermentation and most apparent in late respiration or stationary phase. While changes in mitochondrial morphology and function were previously known to accompany changes in physiological state, it had not been previously shown that the mtDNA copy number changes substantially over time in a clonal growing culture. The mtDNA copy number in yeast is therefore a highly dynamic phenotype.
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Affiliation(s)
- Ben Galeota-Sprung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy Fernandez
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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Thomasson KM, Franks A, Teotónio H, Proulx SR. Testing the adaptive value of sporulation in budding yeast using experimental evolution. Evolution 2021; 75:1889-1897. [PMID: 34029382 DOI: 10.1111/evo.14265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/16/2021] [Indexed: 11/28/2022]
Abstract
Saccharomyces yeast grow through mitotic cell division, converting resources into biomass. When cells experience starvation, sporulation is initiated and meiosis produces haploid cells inside a protective ascus. The protected spore state does not acquire resources and is partially protected from desiccation, heat, and caustic chemicals. Because cells cannot both be protected and acquire resources simultaneously, committing to sporulation represents a trade-off between current and future reproduction. Recent work has suggested that passaging through insect guts selects for spore formation, as surviving insect ingestion represents a major way that yeasts are vectored to new food sources. We subjected replicate populations from five yeast strains to passaging through insects, and evolved control populations by pipette passaging. We assayed populations for their propensity to sporulate after resource depletion. We found that ancestral domesticated strains produced fewer spores, and all strains evolved increased spore production in response to passaging through flies, but domesticated strains responded less. Exposure to flies led to a more rapid shift to sporulation that was more extreme in wild-derived strains. Our results indicate that insect passaging selects for spore production and suggest that domestication led to genetic canalization of the response to cues in the environment and initiation of sporulation.
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Affiliation(s)
- Kelly M Thomasson
- Department of Ecology, Evolution, and Marine Biology, UC Santa Barbara, Santa Barbara, California 93106
| | - Alexander Franks
- Department of Probability and Statistics, UC Santa Barbara, Santa Barbara, California 93106
| | - Henrique Teotónio
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Superieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Stephen R Proulx
- Department of Ecology, Evolution, and Marine Biology, UC Santa Barbara, Santa Barbara, California 93106
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5
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Anders A, Colin R, Banderas A, Sourjik V. Asymmetric mating behavior of isogamous budding yeast. SCIENCE ADVANCES 2021; 7:7/24/eabf8404. [PMID: 34117059 PMCID: PMC8195471 DOI: 10.1126/sciadv.abf8404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/28/2021] [Indexed: 05/12/2023]
Abstract
Anisogamy, the size difference between small male and large female gametes, is known to enable selection for sexual dimorphism and behavioral differences between sexes. Nevertheless, even isogamous species exhibit molecular asymmetries between mating types, which are known to ensure their self-incompatibility. Here, we show that different properties of the pheromones secreted by the MATa and MATα mating types of budding yeast lead to asymmetry in their behavioral responses during mating in mixed haploid populations, which resemble behavioral asymmetries between gametes in anisogamous organisms. MATa behaves as a random searcher that is stimulated in proportion to the fraction of MATα partner cells within the population, whereas MATα behaves as a short-range directional distance sensor. Mathematical modeling suggests that the observed asymmetric responses can enhance efficiency of mating and might thus provide a selective advantage. Our results demonstrate that the emergence of asymmetric mating behavior did not require anisogamy-based sexual selection.
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Affiliation(s)
- Alexander Anders
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Alvaro Banderas
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Laboratoire Physico Chimie Curie, CNRS UMR168, Institut Curie, Paris, France
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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6
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Fischer G, Liti G, Llorente B. The budding yeast life cycle: More complex than anticipated? Yeast 2020; 38:5-11. [PMID: 33197073 DOI: 10.1002/yea.3533] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 11/07/2022] Open
Abstract
The budding yeast, Saccharomyces cerevisiae, has served as a model for nearly a century to understand the principles of the eukaryotic life cycle. The canonical life cycle of S. cerevisiae comprises a regular alternation between haploid and diploid phases. Haploid gametes generated by sporulation are expected to quickly restore the diploid phase mainly through inbreeding via intratetrad mating or haploselfing, thereby promoting genome homozygotization. However, recent large population genomics data unveiled that heterozygosity and polyploidy are unexpectedly common. This raises the interesting paradox of a haplo-diplobiontic species being well-adapted to inbreeding and able to maintain high levels of heterozygosity and polyploidy, thereby suggesting an unanticipated complexity of the yeast life cycle. Here, we propose that unprogrammed mating type switching, heterothallism, reduced spore formation and viability, cell-cell fusion and dioecy could play key and uncharted contributions to generate and maintain heterozygosity through polyploidization.
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Affiliation(s)
- Gilles Fischer
- CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Sorbonne Université, Paris, France
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
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7
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Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, Marcet-Houben M, Gabaldon T, Schuller D, Sampaio JP, Dequin S. Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Mol Biol Evol 2019; 35:1712-1727. [PMID: 29746697 PMCID: PMC5995190 DOI: 10.1093/molbev/msy066] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g., amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations.
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Affiliation(s)
- Jean-Luc Legras
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Virginie Galeote
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Carole Camarasa
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Souhir Marsit
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Thibault Nidelet
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Arnaud Couloux
- Centre National de Séquençage, Institut de Genomique, Genoscope, Evry Cedex, France
| | - Julie Guy
- Centre National de Séquençage, Institut de Genomique, Genoscope, Evry Cedex, France
| | - Ricardo Franco-Duarte
- CBMA, Department of Biology, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Dorit Schuller
- CBMA, Department of Biology, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Sylvie Dequin
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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8
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Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E. Mismatch Repair Incompatibilities in Diverse Yeast Populations. Genetics 2017; 205:1459-1471. [PMID: 28193730 PMCID: PMC5378106 DOI: 10.1534/genetics.116.199513] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/10/2017] [Indexed: 11/18/2022] Open
Abstract
An elevated mutation rate can provide cells with a source of mutations to adapt to changing environments. We identified a negative epistatic interaction involving naturally occurring variants in the MLH1 and PMS1 mismatch repair (MMR) genes of Saccharomyces cerevisiae We hypothesized that this MMR incompatibility, created through mating between divergent S. cerevisiae, yields mutator progeny that can rapidly but transiently adapt to an environmental stress. Here we analyzed the MLH1 and PMS1 genes across 1010 S. cerevisiae natural isolates spanning a wide range of ecological sources (tree exudates, Drosophila, fruits, and various fermentation and clinical isolates) and geographical sources (Europe, America, Africa, and Asia). We identified one homozygous clinical isolate and 18 heterozygous isolates containing the incompatible MMR genotype. The MLH1-PMS1 gene combination isolated from the homozygous clinical isolate conferred a mutator phenotype when expressed in the S288c laboratory background. Using a novel reporter to measure mutation rates, we showed that the overall mutation rate in the homozygous incompatible background was similar to that seen in compatible strains, indicating the presence of suppressor mutations in the clinical isolate that lowered its mutation rate. This observation and the identification of 18 heterozygous isolates, which can lead to MMR incompatible genotypes in the offspring, are consistent with an elevated mutation rate rapidly but transiently facilitating adaptation. To avoid long-term fitness costs, the incompatibility is apparently buffered by mating or by acquiring suppressors. These observations highlight effective strategies in eukaryotes to avoid long-term fitness costs associated with elevated mutation rates.
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Affiliation(s)
- Duyen T Bui
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Anne Friedrich
- Université de Strasbourg, Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie, Unité Mixte de Recherche, 7156, F-67000 Strasbourg, France
| | - Najla Al-Sweel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice, 06107 Nice, France
| | - Joseph Schacherer
- Université de Strasbourg, Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie, Unité Mixte de Recherche, 7156, F-67000 Strasbourg, France
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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9
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Banderas A, Koltai M, Anders A, Sourjik V. Sensory input attenuation allows predictive sexual response in yeast. Nat Commun 2016; 7:12590. [PMID: 27557894 PMCID: PMC5007329 DOI: 10.1038/ncomms12590] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 07/14/2016] [Indexed: 12/22/2022] Open
Abstract
Animals are known to adjust their sexual behaviour depending on mate competition. Here we report similar regulation for mating behaviour in a sexual unicellular eukaryote, the budding yeast Saccharomyces cerevisiae. We demonstrate that pheromone-based communication between the two mating types, coupled to input attenuation by recipient cells, enables yeast to robustly monitor relative mate abundance (sex ratio) within a mixed population and to adjust their commitment to sexual reproduction in proportion to their estimated chances of successful mating. The mechanism of sex-ratio sensing relies on the diffusible peptidase Bar1, which is known to degrade the pheromone signal produced by mating partners. We further show that such a response to sexual competition within a population can optimize the fitness trade-off between the costs and benefits of mating response induction. Our study thus provides an adaptive explanation for the known molecular mechanism of pheromone degradation in yeast. Cells of the yeast Saccharomyces cerevisiae can mate with other cells of opposite mating type. Here, the authors show that the combination of a pheromone and a pheromone-degrading enzyme allows yeast cells to monitor relative mate abundance within a population and adjust their commitment to sexual reproduction.
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Affiliation(s)
- Alvaro Banderas
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Mihaly Koltai
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany
| | - Alexander Anders
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany
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10
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Abstract
The reproductive ecology of Saccharomyces cerevisiae is still largely unknown. Recent evidence of interspecific hybridization, high levels of strain heterozygosity, and prion transmission suggest that outbreeding occurs frequently in yeasts. Nevertheless, the place where yeasts mate and recombine in the wild has not been identified. We found that the intestine of social wasps hosts highly outbred S. cerevisiae strains as well as a rare S. cerevisiae×S. paradoxus hybrid. We show that the intestine of Polistes dominula social wasps favors the mating of S. cerevisiae strains among themselves and with S. paradoxus cells by providing a succession of environmental conditions prompting cell sporulation and spores germination. In addition, we prove that heterospecific mating is the only option for European S. paradoxus strains to survive in the gut. Taken together, these findings unveil the best hidden secret of yeast ecology, introducing the insect gut as an environmental alcove in which crosses occur, maintaining and generating the diversity of the ascomycetes.
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11
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Masneuf-Pomarede I, Bely M, Marullo P, Albertin W. The Genetics of Non-conventional Wine Yeasts: Current Knowledge and Future Challenges. Front Microbiol 2016; 6:1563. [PMID: 26793188 PMCID: PMC4707289 DOI: 10.3389/fmicb.2015.01563] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/23/2015] [Indexed: 11/13/2022] Open
Abstract
Saccharomyces cerevisiae is by far the most widely used yeast in oenology. However, during the last decade, several other yeasts species has been purposed for winemaking as they could positively impact wine quality. Some of these non-conventional yeasts (Torulaspora delbrueckii, Metschnikowia pulcherrima, Pichia kluyveri, Lachancea thermotolerans, etc.) are now proposed as starters culture for winemakers in mixed fermentation with S. cerevisiae, and several others are the subject of various studies (Hanseniaspora uvarum, Starmerella bacillaris, etc.). Along with their biotechnological use, the knowledge of these non-conventional yeasts greatly increased these last 10 years. The aim of this review is to describe the last updates and the current state-of-art of the genetics of non-conventional yeasts (including S. uvarum, T. delbrueckii, S. bacillaris, etc.). We describe how genomics and genetics tools provide new data into the population structure and biodiversity of non-conventional yeasts in winemaking environments. Future challenges will lie on the development of selection programs and/or genetic improvement of these non-conventional species. We discuss how genetics, genomics and the advances in next-generation sequencing will help the wine industry to develop the biotechnological use of non-conventional yeasts to improve the quality and differentiation of wines.
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Affiliation(s)
- Isabelle Masneuf-Pomarede
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
- Bordeaux Sciences AgroGradignan, France
| | - Marina Bely
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
| | - Philippe Marullo
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
- BiolaffortBordeaux, France
| | - Warren Albertin
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
- ENSCBP, Bordeaux INPPessac, France
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12
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Boisnard S, Zhou Li Y, Arnaise S, Sequeira G, Raffoux X, Enache-Angoulvant A, Bolotin-Fukuhara M, Fairhead C. Efficient Mating-Type Switching in Candida glabrata Induces Cell Death. PLoS One 2015; 10:e0140990. [PMID: 26491872 PMCID: PMC4619647 DOI: 10.1371/journal.pone.0140990] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/02/2015] [Indexed: 01/05/2023] Open
Abstract
Candida glabrata is an apparently asexual haploid yeast that is phylogenetically closer to Saccharomyces cerevisiae than to Candida albicans. Its genome contains three MAT-like cassettes, MAT, which encodes either MATa or MATalpha information in different strains, and the additional loci, HML and HMR. The genome also contains an HO gene homolog, but this yeast has never been shown to switch mating-types spontaneously, as S. cerevisiae does. We have recently sequenced the genomes of the five species that, together with C. glabrata, make up the Nakaseomyces clade. All contain MAT-like cassettes and an HO gene homolog. In this work, we express the HO gene of all Nakaseomyces and of S. cerevisiae in C. glabrata. All can induce mating-type switching, but, despite the larger phylogenetic distance, the most efficient endonuclease is the one from S. cerevisiae. Efficient mating-type switching in C. glabrata is accompanied by a high cell mortality, and sometimes results in conversion of the additional cassette HML. Mortality probably results from the cutting of the HO recognition sites that are present, in HML and possibly HMR, contrary to what happens naturally in S. cerevisiae. This has implications in the life-cycle of C. glabrata, as we show that efficient MAT switching is lethal for most cells, induces chromosomal rearrangements in survivors, and that the endogenous HO is probably rarely active indeed.
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Affiliation(s)
- Stéphanie Boisnard
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
- Génétique Quantitative et Évolution–Le Moulon, INRA–Université Paris-Sud–CNRS–AgroParisTech, Batiment 400, UFR des Sciences, F 91405, Orsay, CEDEX, France
- * E-mail:
| | - Youfang Zhou Li
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
- Génétique Quantitative et Évolution–Le Moulon, INRA–Université Paris-Sud–CNRS–AgroParisTech, Batiment 400, UFR des Sciences, F 91405, Orsay, CEDEX, France
| | - Sylvie Arnaise
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
| | - Gregory Sequeira
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
| | - Xavier Raffoux
- Génétique Quantitative et Évolution–Le Moulon, INRA–Université Paris-Sud–CNRS–AgroParisTech, Batiment 400, UFR des Sciences, F 91405, Orsay, CEDEX, France
| | - Adela Enache-Angoulvant
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
- Hôpital de Bicêtre, Le Kremlin Bicêtre, APHP, France
| | - Monique Bolotin-Fukuhara
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
- Génétique Quantitative et Évolution–Le Moulon, INRA–Université Paris-Sud–CNRS–AgroParisTech, Batiment 400, UFR des Sciences, F 91405, Orsay, CEDEX, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621 CNRS, F-91405, Orsay, CEDEX, France
- Génétique Quantitative et Évolution–Le Moulon, INRA–Université Paris-Sud–CNRS–AgroParisTech, Batiment 400, UFR des Sciences, F 91405, Orsay, CEDEX, France
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13
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Bui DT, Dine E, Anderson JB, Aquadro CF, Alani EE. A Genetic Incompatibility Accelerates Adaptation in Yeast. PLoS Genet 2015; 11:e1005407. [PMID: 26230253 PMCID: PMC4521705 DOI: 10.1371/journal.pgen.1005407] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/01/2015] [Indexed: 12/21/2022] Open
Abstract
During mismatch repair (MMR) MSH proteins bind to mismatches that form as the result of DNA replication errors and recruit MLH factors such as Mlh1-Pms1 to initiate excision and repair steps. Previously, we identified a negative epistatic interaction involving naturally occurring polymorphisms in the MLH1 and PMS1 genes of baker’s yeast. Here we hypothesize that a mutagenic state resulting from this negative epistatic interaction increases the likelihood of obtaining beneficial mutations that can promote adaptation to stress conditions. We tested this by stressing yeast strains bearing mutagenic (incompatible) and non-mutagenic (compatible) mismatch repair genotypes. Our data show that incompatible populations adapted more rapidly and without an apparent fitness cost to high salt stress. The fitness advantage of incompatible populations was rapid but disappeared over time. The fitness gains in both compatible and incompatible strains were due primarily to mutations in PMR1 that appeared earlier in incompatible evolving populations. These data demonstrate a rapid and reversible role (by mating) for genetic incompatibilities in accelerating adaptation in eukaryotes. They also provide an approach to link experimental studies to observational population genomics. In nature, bacterial populations with high mutation rates can adapt faster to new environments by acquiring beneficial mutations. However, such populations also accumulate harmful mutations that reduce their fitness. We show that the model eukaryote baker’s yeast can use a similar mutator strategy to adapt to new environments. The mutator state that we observed resulted from an incompatibility involving two genes, MLH1 and PMS1, that work together to remove DNA replication errors through a spellchecking mismatch repair mechanism. This incompatibility can occur through mating between baker’s yeast from different genetic backgrounds, yielding mutator offspring containing an MLH1-PMS1 combination not present in either parent. Interestingly, these offspring adapted more rapidly to stress, compared to the parental strains, and did so without an overall loss in fitness. DNA sequencing analyses of baker’s yeast strains from across the globe support the presence of incompatible hybrid yeast strains in nature. These observations provide a powerful model to understand how the segregation of defects in DNA mismatch repair can serve as an effective strategy to enable eukaryotes to adapt to changing environments.
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Affiliation(s)
- Duyen T. Bui
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Elliot Dine
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - James B. Anderson
- Department of Biology, University of Toronto, Mississauga, Ontario, Canada
| | - Charles F. Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Eric E. Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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14
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Miller EL, Greig D. Spore germination determines yeast inbreeding according to fitness in the local environment. Am Nat 2014; 185:291-301. [PMID: 25616146 DOI: 10.1086/679347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Gene combinations conferring local fitness may be destroyed by mating with individuals that are adapted to a different environment. This form of outbreeding depression provides an evolutionary incentive for self-fertilization. We show that the yeast Saccharomyces paradoxus tends to self-fertilize when it is well adapted to its local environment but tends to outcross when it is poorly adapted. This behavior could preserve combinations of genes when they are beneficial and break them up when they are not, thereby helping adaptation. Haploid spores must germinate before mating, and we found that fitter spores had higher rates of germination across a 24-hour period, increasing the probability that they mate with germinated spores from the same meiotic tetrad. The ability of yeast spores to detect local conditions before germinating and mating suggests the novel possibility that these gametes directly sense their own adaptation and plastically adjust their breeding strategy accordingly.
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Affiliation(s)
- Eric L Miller
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
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15
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Boynton PJ, Greig D. The ecology and evolution of non-domesticated Saccharomyces species. Yeast 2014; 31:449-62. [PMID: 25242436 PMCID: PMC4282469 DOI: 10.1002/yea.3040] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 12/13/2022] Open
Abstract
Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by domestication. Instead, ecologists and evolutionary biologists are focusing on close relatives of S. cerevisiae, the seven species in the genus Saccharomyces. The best-studied Saccharomyces yeast, after S. cerevisiae, is S. paradoxus, an oak tree resident throughout the northern hemisphere. In addition, several more members of the genus Saccharomyces have recently been discovered. Some Saccharomyces species are only found in nature, while others include both wild and domesticated strains. Comparisons between domesticated and wild yeasts have pinpointed hybridization, introgression and high phenotypic diversity as signatures of domestication. But studies of wild Saccharomyces natural history, biogeography and ecology are only beginning. Much remains to be understood about wild yeasts' ecological interactions and life cycles in nature. We encourage researchers to continue to investigate Saccharomyces yeasts in nature, both to place S. cerevisiae biology into its ecological context and to develop the genus Saccharomyces as a model clade for ecology and evolution.
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Affiliation(s)
| | - Duncan Greig
- Max Planck Institute for Evolutionary BiologyPlön, Germany
- Galton Laboratory, Department of Genetics, Evolution and Environment, University College LondonUK
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16
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Abstract
Sexual reproduction is ubiquitous throughout the eukaryotic kingdom, but the capacity of pathogenic fungi to undergo sexual reproduction has been a matter of intense debate. Pathogenic fungi maintained a complement of conserved meiotic genes but the populations appeared to be clonally derived. This debate was resolved first with the discovery of an extant sexual cycle and then unisexual reproduction. Unisexual reproduction is a distinct form of homothallism that dispenses with the requirement for an opposite mating type. Pathogenic and nonpathogenic fungi previously thought to be asexual are able to undergo robust unisexual reproduction. We review here recent advances in our understanding of the genetic and molecular basis of unisexual reproduction throughout fungi and the impact of unisex on the ecology and genomic evolution of fungal species.
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Affiliation(s)
- Kevin C Roach
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Marianna Feretzaki
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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17
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Diener C, Schreiber G, Giese W, del Rio G, Schröder A, Klipp E. Yeast mating and image-based quantification of spatial pattern formation. PLoS Comput Biol 2014; 10:e1003690. [PMID: 24967739 PMCID: PMC4072512 DOI: 10.1371/journal.pcbi.1003690] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 05/14/2014] [Indexed: 12/25/2022] Open
Abstract
Communication between cells is a ubiquitous feature of cell populations and is frequently realized by secretion and detection of signaling molecules. Direct visualization of the resulting complex gradients between secreting and receiving cells is often impossible due to the small size of diffusing molecules and because such visualization requires experimental perturbations such as attachment of fluorescent markers, which can change diffusion properties. We designed a method to estimate such extracellular concentration profiles in vivo by using spatiotemporal mathematical models derived from microscopic analysis. This method is applied to populations of thousands of haploid yeast cells during mating in order to quantify the extracellular distributions of the pheromone α-factor and the activity of the aspartyl protease Bar1. We demonstrate that Bar1 limits the range of the extracellular pheromone signal and is critical in establishing α-factor concentration gradients, which is crucial for effective mating. Moreover, haploid populations of wild type yeast cells, but not BAR1 deletion strains, create a pheromone pattern in which cells differentially grow and mate, with low pheromone regions where cells continue to bud and regions with higher pheromone levels and gradients where cells conjugate to form diploids. However, this effect seems to be exclusive to high-density cultures. Our results show a new role of Bar1 protease regulating the pheromone distribution within larger populations and not only locally inside an ascus or among few cells. As a consequence, wild type populations have not only higher mating efficiency, but also higher growth rates than mixed MATabar1Δ/MATα cultures. We provide an explanation of how a rapidly diffusing molecule can be exploited by cells to provide spatial information that divides the population into different transcriptional programs and phenotypes. Haploid budding yeast cells cannot actively move to find a mating partner, like some flagellated bacteria do. Instead they must grow a so-called shmoo – a mating projection – precisely into the direction of a potential partner. They communicate with each other by releasing pheromones into their environment, which are sensed by cells of the opposite mating type. This serves the localization of nearby cells and initiates growth arrest and mating. Paradoxically, yeast cells also secrete the protease Bar1 that destroys pheromones. To visualize the resulting pheromone distribution and understand the effect on mating efficiency, we combined fluorescence imaging and mathematical modeling. We observed that the controlled destruction of pheromones by the yeast cells is beneficial to communication since it causes relatively higher pheromone concentrations in areas where cells are dense and vanishing pheromone concentrations elsewhere. This allows the population to maintain two different cellular behaviors at the same time, i.e. mating and continued growth, a behavior which disappears when we genetically delete the gene for the pheromone-destroying protein.
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Affiliation(s)
- Christian Diener
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, México D.F, México
| | | | - Wolfgang Giese
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gabriel del Rio
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, México D.F, México
| | - Andreas Schröder
- Institut für Mathematik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
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18
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Smith C, Pomiankowski A, Greig D. Size and competitive mating success in the yeast Saccharomyces cerevisiae.. Behav Ecol 2014; 25:320-327. [PMID: 24616602 PMCID: PMC3945744 DOI: 10.1093/beheco/art117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/19/2013] [Accepted: 11/19/2013] [Indexed: 01/28/2023] Open
Abstract
In unicellular organisms like yeast, mating with the right partner is critical to future fitness because each individual can only mate once. Because cell size is important for viability, mating with a partner of the right size could be a significant advantage. To investigate this idea, we manipulated the size of unmated yeast cells and showed that their viability depended on environmental conditions; large cells do better on rich medium and small cells do better on poor medium. We also found that the fitness of offspring is determined by the size of their parents. Finally, we demonstrated that when a focal cell of one mating type was placed with a large and a small cell of the opposite mating type, it was more likely to mate with the cell that was closer to the optimum size for growth in a given environment. This pattern was not generated by differences in passive mating efficiency of large and small cells across environments but by competitive mating behavior, mate preference, or both. We conclude that the most likely mechanism underlying this interesting behavior is that yeast cells compete for mates by producing pheromone signals advertising their viability, and cells with the opportunity to choose prefer to mate with stronger signalers because such matings produce more viable offspring.
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Affiliation(s)
- Carl Smith
- The Galton Laboratory, Department of Genetics, Evolution, and Environment, University College London , Gower Street , London WC1E 6BT , UK
| | - Andrew Pomiankowski
- The Galton Laboratory, Department of Genetics, Evolution, and Environment, University College London , Gower Street , London WC1E 6BT , UK , ; CoMPLEX, University College London , Gower Street , London WC1E 6BT , UK , and
| | - Duncan Greig
- The Galton Laboratory, Department of Genetics, Evolution, and Environment, University College London , Gower Street , London WC1E 6BT , UK , ; Max Planck Institute for Evolutionary Biology , August Thienemann Strasse 2 , Plön 24306 , Germany
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19
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Abstract
Yeast prions are infectious proteins that spread exclusively by mating. The frequency of prions in the wild therefore largely reflects the rate of spread by mating counterbalanced by prion growth slowing effects in the host. We recently showed that the frequency of outcross mating is about 1% of mitotic doublings with 23–46% of total matings being outcrosses. These findings imply that even the mildest forms of the [PSI+], [URE3] and [PIN+] prions impart > 1% growth/survival detriment on their hosts. Our estimate of outcrossing suggests that Saccharomyces cerevisiae is far more sexual than previously thought and would therefore be more responsive to the adaptive effects of natural selection compared with a strictly asexual yeast. Further, given its large effective population size, a growth/survival detriment of > 1% for yeast prions should strongly select against prion-infected strains in wild populations of Saccharomyces cerevisiae.
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Affiliation(s)
- Amy C Kelly
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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20
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López-Villavicencio M, Debets AJM, Slakhorst M, Giraud T, Schoustra SE. Deleterious effects of recombination and possible nonrecombinatorial advantages of sex in a fungal model. J Evol Biol 2013; 26:1968-78. [PMID: 23848947 DOI: 10.1111/jeb.12196] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/03/2013] [Accepted: 05/08/2013] [Indexed: 01/19/2023]
Abstract
Why sexual reproduction is so prevalent in nature remains a major question in evolutionary biology. Most of the proposed advantages of sex rely on the benefits obtained from recombination. However, it is still unclear whether the conditions under which these recombinatorial benefits would be sufficient to maintain sex in the short term are met in nature. Our study addresses a largely overlooked hypothesis, proposing that sex could be maintained in the short term by advantages due to functions linked with sex, but not related to recombination. These advantages would be so essential that sex could not be lost in the short term. Here, we used the fungus Aspergillus nidulans to experimentally test predictions of this hypothesis. Specifically, we were interested in (i) the short-term deleterious effects of recombination, (ii) possible nonrecombinatorial advantages of sex particularly through the elimination of mutations and (iii) the outcrossing rate under choice conditions in a haploid fungus able to reproduce by both outcrossing and haploid selfing. Our results were consistent with our hypotheses: we found that (i) recombination can be strongly deleterious in the short term, (ii) sexual reproduction between individuals derived from the same clonal lineage provided nonrecombinatorial advantages, likely through a selection arena mechanism, and (iii) under choice conditions, outcrossing occurs in a homothallic species, although at low rates.
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Affiliation(s)
- M López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, Paris, France.
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21
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Poole AM, Kobayashi T, Ganley ARD. A positive role for yeast extrachromosomal rDNA circles? Extrachromosomal ribosomal DNA circle accumulation during the retrograde response may suppress mitochondrial cheats in yeast through the action of TAR1. Bioessays 2012; 34:725-9. [PMID: 22706794 PMCID: PMC3563013 DOI: 10.1002/bies.201200037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anthony M Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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22
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Tazzyman SJ, Seymour RM, Pomiankowski A, Greig D. Mate choice among yeast gametes can purge deleterious mutations. J Evol Biol 2012; 25:1463-71. [PMID: 22594920 DOI: 10.1111/j.1420-9101.2012.02539.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Meiosis in Saccharomyces yeast produces four haploid gametes that usually fuse with each other, an extreme form of self-fertilization among the products of a single meiosis known as automixis. The gametes signal to each other with sex pheromone. Better-quality gametes produce stronger signals and are preferred as mates. We suggest that the function of this signalling system is to enable mate choice among the four gametes from a single meiosis and so to promote the clearance of deleterious mutations. To support this claim, we construct a mathematical model that shows that signalling during automixis (i) improves the long-term fitness of a yeast colony and (ii) lowers its mutational load. We also show that the benefit to signalling is greater with larger numbers of segregating mutations.
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Affiliation(s)
- S J Tazzyman
- CoMPLEX, University College London, Gower St., London, UK.
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23
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Billiard S, López-Villavicencio M, Hood ME, Giraud T. Sex, outcrossing and mating types: unsolved questions in fungi and beyond. J Evol Biol 2012; 25:1020-38. [PMID: 22515640 DOI: 10.1111/j.1420-9101.2012.02495.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Variability in the way organisms reproduce raises numerous, and still unsolved, questions in evolutionary biology. In this study, we emphasize that fungi deserve a much greater emphasis in efforts to address these questions because of their multiple advantages as model eukaryotes. A tremendous diversity of reproductive modes and mating systems can be found in fungi, with many evolutionary transitions among closely related species. In addition, fungi show some peculiarities in their mating systems that have received little attention so far, despite the potential for providing insights into important evolutionary questions. In particular, selfing can occur at the haploid stage in addition to the diploid stage in many fungi, which is generally not possible in animals and plants but has a dramatic influence upon the structure of genetic systems. Fungi also present several advantages that make them tractable models for studies in experimental evolution. Here, we briefly review the unsolved questions and extant hypotheses about the evolution and maintenance of asexual vs. sexual reproduction and of selfing vs. outcrossing, focusing on fungal life cycles. We then propose how fungi can be used to address these long-standing questions and advance our understanding of sexual reproduction and mating systems across all eukaryotes.
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Affiliation(s)
- S Billiard
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, Villeneuve d'Ascq Cedex, France.
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24
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Abstract
In response to nitrogen starvation in the presence of a poor carbon source, diploid cells of the yeast Saccharomyces cerevisiae undergo meiosis and package the haploid nuclei produced in meiosis into spores. The formation of spores requires an unusual cell division event in which daughter cells are formed within the cytoplasm of the mother cell. This process involves the de novo generation of two different cellular structures: novel membrane compartments within the cell cytoplasm that give rise to the spore plasma membrane and an extensive spore wall that protects the spore from environmental insults. This article summarizes what is known about the molecular mechanisms controlling spore assembly with particular attention to how constitutive cellular functions are modified to create novel behaviors during this developmental process. Key regulatory points on the sporulation pathway are also discussed as well as the possible role of sporulation in the natural ecology of S. cerevisiae.
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25
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HERRERA CM, POZO MI, BAZAGA P. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast. Mol Ecol 2011; 20:4395-407. [DOI: 10.1111/j.1365-294x.2011.05217.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2011; 108:1987-92. [PMID: 21245305 DOI: 10.1073/pnas.1012544108] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We carried out a population genomic survey of Saccharomyces cerevisiae diploid isolates and find that many budding yeast strains have high levels of genomic heterozygosity, much of which is likely due to outcrossing. We demonstrate that variation in heterozygosity among strains is correlated with a life-history trade-off that involves how readily yeast switch from asexual to sexual reproduction under nutrient stress. This trade-off is reflected in a negative relationship between sporulation efficiency and pseudohyphal development and correlates with variation in the expression of RME1, a transcription factor with pleiotropic effects on meiosis and filamentous growth. Selection for alternate life-history strategies in natural versus human-associated environments likely contributes to differential maintenance of genomic heterozygosity through its effect on the frequency that yeast lineages experience sexual cycles and hence the opportunity for inbreeding. In addition to elevated levels of heterozygosity, many strains exhibit large genomic regions of loss-of-heterozygosity (LOH), suggesting that mitotic recombination has a significant impact on genetic variation in this species. This study provides new insights into the roles that both outcrossing and mitotic recombination play in shaping the genome architecture of Saccharomyces cerevisiae. This study also provides a unique case where stark differences in the genomic distribution of genetic variation among individuals of the same species can be largely explained by a life-history trade-off.
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