1
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Maslanka R, Bednarska S, Zadrag-Tecza R. Virtually identical does not mean exactly identical: Discrepancy in energy metabolism between glucose and fructose fermentation influences the reproductive potential of yeast cells. Arch Biochem Biophys 2024; 756:110021. [PMID: 38697344 DOI: 10.1016/j.abb.2024.110021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The physiological efficiency of cells largely depends on the possibility of metabolic adaptations to changing conditions, especially on the availability of nutrients. Central carbon metabolism has an essential role in cellular function. In most cells is based on glucose, which is the primary energy source, provides the carbon skeleton for the biosynthesis of important cell macromolecules, and acts as a signaling molecule. The metabolic flux between pathways of carbon metabolism such as glycolysis, pentose phosphate pathway, and mitochondrial oxidative phosphorylation is dynamically adjusted by specific cellular economics responding to extracellular conditions and intracellular demands. Using Saccharomyces cerevisiae yeast cells and potentially similar fermentable carbon sources i.e. glucose and fructose we analyzed the parameters concerning the metabolic status of the cells and connected with them alteration in cell reproductive potential. Those parameters were related to the specific metabolic network: the hexose uptake - glycolysis and activity of the cAMP/PKA pathway - pentose phosphate pathway and biosynthetic capacities - the oxidative respiration and energy generation. The results showed that yeast cells growing in a fructose medium slightly increased metabolism redirection toward respiratory activity, which decreased pentose phosphate pathway activity and cellular biosynthetic capabilities. These differences between the fermentative metabolism of glucose and fructose, lead to long-term effects, manifested by changes in the maximum reproductive potential of cells.
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Affiliation(s)
- Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland.
| | - Sabina Bednarska
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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2
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Contreras‐Ruiz A, Minebois R, Alonso‐del‐Real J, Barrio E, Querol A. Differences in metabolism among Saccharomyces species and their hybrids during wine fermentation. Microb Biotechnol 2024; 17:e14476. [PMID: 38801338 PMCID: PMC11129674 DOI: 10.1111/1751-7915.14476] [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: 02/12/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
This study aimed to investigate how parental genomes contribute to yeast hybrid metabolism using a metabolomic approach. Previous studies have explored central carbon and nitrogen metabolism in Saccharomyces species during wine fermentation, but this study analyses the metabolomes of Saccharomyces hybrids for the first time. We evaluated the oenological performance and intra- and extracellular metabolomes, and we compared the strains according to nutrient consumption and production of the main fermentative by-products. Surprisingly, no common pattern was observed for hybrid genome influence; each strain behaved differently during wine fermentation. However, this study suggests that the genome of the S. cerevisiae species may play a more relevant role in fermentative metabolism. Variations in biomass/nitrogen ratios were also noted, potentially linked to S. kudriavzevii and S. uvarum genome contributions. These results open up possibilities for further research using different "omics" approaches to comprehend better metabolic regulation in hybrid strains with genomes from different species.
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Affiliation(s)
- Alba Contreras‐Ruiz
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Romain Minebois
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Javier Alonso‐del‐Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
- Departament de GenèticaUniversitat de ValènciaValènciaSpain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
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3
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Vion C, Brambati M, Da Costa G, Richard T, Marullo P. Endo metabolomic profiling of flor and wine yeasts reveals a positive correlation between intracellular metabolite load and the specific glycolytic flux during wine fermentation. Front Microbiol 2023; 14:1227520. [PMID: 37928666 PMCID: PMC10620685 DOI: 10.3389/fmicb.2023.1227520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
This study explored the intracellular metabolic variations between 17 strains of Saccharomyces cerevisiae belonging to two different genetic populations: flor and wine yeasts, in the context of alcoholic fermentation. These two populations are closely related as they share the same ecological niche but display distinct genetic characteristics. A protocol was developed for intracellular metabolites extraction and 1H-NMR analysis. This methodology allowed us to identify and quantify 21 intracellular metabolites at two different fermentation steps: the exponential and stationary phases. This work provided evidence of significant differences in the abundance of intracellular metabolites, which are strain- and time-dependent, thus revealing complex interactions. Moreover, the differences in abundance appeared to be correlated with life-history traits such as average cell size and specific glycolytic flux, which revealed unsuspected phenotypic correlations between metabolite load and fermentation activity.
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Affiliation(s)
- Charlotte Vion
- Biolaffort, Bordeaux, France
- UMR Oenologie 1366, Université de Bordeaux, INRAE, Bordeaux INP, BSA, ISVV, Paris, France
| | - Mathilde Brambati
- Biolaffort, Bordeaux, France
- UMR Oenologie 1366, Université de Bordeaux, INRAE, Bordeaux INP, BSA, ISVV, Paris, France
| | - Grégory Da Costa
- UMR Oenologie 1366, Université de Bordeaux, INRAE, Bordeaux INP, BSA, ISVV, Paris, France
| | - Tristan Richard
- UMR Oenologie 1366, Université de Bordeaux, INRAE, Bordeaux INP, BSA, ISVV, Paris, France
| | - Philippe Marullo
- Biolaffort, Bordeaux, France
- UMR Oenologie 1366, Université de Bordeaux, INRAE, Bordeaux INP, BSA, ISVV, Paris, France
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4
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Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast. Nat Ecol Evol 2022; 6:763-773. [PMID: 35484218 DOI: 10.1038/s41559-022-01730-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/10/2022] [Indexed: 01/05/2023]
Abstract
Deleterious mutations are generally considered to be irrelevant for morphological evolution. However, they could be compensated by conditionally beneficial mutations, thereby providing access to new adaptive paths. Here we use high-dimensional phenotyping of laboratory-evolved budding yeast lineages to demonstrate that new cellular morphologies emerge exceptionally rapidly as a by-product of gene loss and subsequent compensatory evolution. Unexpectedly, the capacities for invasive growth, multicellular aggregation and biofilm formation also spontaneously evolve in response to gene loss. These multicellular phenotypes can be achieved by diverse mutational routes and without reactivating the canonical regulatory pathways. These ecologically and clinically relevant traits originate as pleiotropic side effects of compensatory evolution and have no obvious utility in the laboratory environment. The extent of morphological diversity in the evolved lineages is comparable to that of natural yeast isolates with diverse genetic backgrounds and lifestyles. Finally, we show that both the initial gene loss and subsequent compensatory mutations contribute to new morphologies, with their synergistic effects underlying specific morphological changes. We conclude that compensatory evolution is a previously unrecognized source of morphological diversity and phenotypic novelties.
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5
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Different life strategies in genetic backgrounds of the Saccharomyces cerevisiae yeast cells. Fungal Biol 2022; 126:498-510. [DOI: 10.1016/j.funbio.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
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6
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Growth response of Saccharomyces cerevisiae strains to stressors associated to the vine cycle. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Petrizzelli MS, de Vienne D, Nidelet T, Noûs C, Dillmann C. Data integration uncovers the metabolic bases of phenotypic variation in yeast. PLoS Comput Biol 2021; 17:e1009157. [PMID: 34264947 PMCID: PMC8315545 DOI: 10.1371/journal.pcbi.1009157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/27/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
The relationship between different levels of integration is a key feature for understanding the genotype-phenotype map. Here, we describe a novel method of integrated data analysis that incorporates protein abundance data into constraint-based modeling to elucidate the biological mechanisms underlying phenotypic variation. Specifically, we studied yeast genetic diversity at three levels of phenotypic complexity in a population of yeast obtained by pairwise crosses of eleven strains belonging to two species, Saccharomyces cerevisiae and S. uvarum. The data included protein abundances, integrated traits (life-history/fermentation) and computational estimates of metabolic fluxes. Results highlighted that the negative correlation between production traits such as population carrying capacity (K) and traits associated with growth and fermentation rates (Jmax) is explained by a differential usage of energy production pathways: a high K was associated with high TCA fluxes, while a high Jmax was associated with high glycolytic fluxes. Enrichment analysis of protein sets confirmed our results. This powerful approach allowed us to identify the molecular and metabolic bases of integrated trait variation, and therefore has a broad applicability domain. The integration of data at different levels of cellular organization is an important goal in computational biology for understanding the way the genotypic variation translates into phenotypic variation. Novel profiling technologies and accurate high-throughput phenotyping now allows genomic, transcriptomic, metabolic and proteomic characterization of a large number of individuals under various environmental conditions. However, the metabolic fluxes remain difficult to measure. In this work, we take advantage of recent advances in genome-scale functional annotation and constraint-based metabolic modeling to provide a mathematical framework that allows to estimate internal cellular fluxes from protein abundances and elucidate the biological mechanisms underlying phenotypic variation. Applied to yeast as a model system, this approach highlights that the negative correlation between production traits such as maximum population size and growth and fermentation traits is explained by a differential usage of energy production pathways. The ability to identify molecular and metabolic bases of the variation of integrated traits through population studies has a broad applicability domain.
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Affiliation(s)
- Marianyela Sabina Petrizzelli
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE–Le Moulon, Gif-sur-Yvette, France
- Institut Curie, PSL Research University, Paris, France
- INSERM, U900, Paris, France
- CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
- * E-mail:
| | - Dominique de Vienne
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE–Le Moulon, Gif-sur-Yvette, France
| | - Thibault Nidelet
- SPO, INRAE, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE–Le Moulon, Gif-sur-Yvette, France
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8
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Oenological Potential of Autochthonous Saccharomyces cerevisiae Yeast Strains from the Greek Varieties of Agiorgitiko and Moschofilero. BEVERAGES 2021. [DOI: 10.3390/beverages7020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nemea and Mantinia are famous wine regions in Greece known for two indigenous grape varieties, Agiorgitiko and Moschofilero, which produce high quality PDO wines. In the present study, indigenous Saccharomyces cerevisiae yeast strains were isolated and identified from spontaneous alcoholic fermentation of Agiorgitiko and Moschofilero musts in order to evaluate their oenological potential. Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) recovered the presence of five distinct profiles from a total of 430 yeast isolates. The five obtained strains were evaluated at microvinifications trials and tested for basic oenological and biochemical parameters including sulphur dioxide and ethanol tolerance as well as H2S production in sterile grape must. The selected autochthonous yeast strains named, Soi2 (Agiorgitiko wine) and L2M (Moschofilero wine), were evaluated also in industrial (4000L) fermentations to assess their sensorial and oenological characteristics. The volatile compounds of the produced wines were determined by GC-FID. Our results demonstrated the feasibility of using Soi2 and L2M strains in industrial fermentations for Agiorgitiko and Moschofilero grape musts, respectively.
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9
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Lifestyle, Lineage, and Geographical Origin Influence Temperature-Dependent Phenotypic Variation across Yeast Strains during Wine Fermentation. Microorganisms 2020; 8:microorganisms8091367. [PMID: 32906626 PMCID: PMC7565122 DOI: 10.3390/microorganisms8091367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/17/2022] Open
Abstract
Saccharomyces cerevisiae yeasts are a diverse group of single-celled eukaryotes with tremendous phenotypic variation in fermentation efficiency, particularly at different temperatures. Yeast can be categorized into subsets based on lifestyle (Clinical, Fermentation, Laboratory, and Wild), genetic lineage (Malaysian, Mosaic, North American, Sake, West African, and Wine), and geographical origin (Africa, Americas, Asia, Europe, and Oceania) to start to understand their ecology; however, little is known regarding the extent to which these groupings drive S. cerevisiae fermentative ability in grape juice at different fermentation temperatures. To investigate the response of yeast within the different subsets, we quantified fermentation performance in grape juice by measuring the lag time, maximal fermentation rate (Vmax), and fermentation finishing efficiency of 34 genetically diverse S. cerevisiae strains in grape juice at five environmentally and industrially relevant temperatures (10, 15, 20, 25, and 30 °C). Extensive multivariate analysis was applied to determine the effects of lifestyle, lineage, geographical origin, strain, and temperature on yeast fermentation phenotypes. We show that fermentation capability is inherent to S. cerevisiae and that all factors are important in shaping strain fermentative ability, with temperature having the greatest impact, and geographical origin playing a lesser role than lifestyle or genetic lineage.
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10
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Vandermeulen MD, Cullen PJ. New Aspects of Invasive Growth Regulation Identified by Functional Profiling of MAPK Pathway Targets in Saccharomyces cerevisiae. Genetics 2020; 216:95-116. [PMID: 32665277 PMCID: PMC7463291 DOI: 10.1534/genetics.120.303369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022] Open
Abstract
MAPK pathways are drivers of morphogenesis and stress responses in eukaryotes. A major function of MAPK pathways is the transcriptional induction of target genes, which produce proteins that collectively generate a cellular response. One approach to comprehensively understand how MAPK pathways regulate cellular responses is to characterize the individual functions of their transcriptional targets. Here, by examining uncharacterized targets of the MAPK pathway that positively regulates filamentous growth in Saccharomyces cerevisiae (fMAPK pathway), we identified a new role for the pathway in negatively regulating invasive growth. Specifically, four targets were identified that had an inhibitory role in invasive growth: RPI1, RGD2, TIP1, and NFG1/YLR042cNFG1 was a highly induced unknown open reading frame that negatively regulated the filamentous growth MAPK pathway. We also identified SFG1, which encodes a transcription factor, as a target of the fMAPK pathway. Sfg1p promoted cell adhesion independently from the fMAPK pathway target and major cell adhesion flocculin Flo11p, by repressing genes encoding presumptive cell-wall-degrading enzymes. Sfg1p also contributed to FLO11 expression. Sfg1p and Flo11p regulated different aspects of cell adhesion, and their roles varied based on the environment. Sfg1p also induced an elongated cell morphology, presumably through a cell-cycle delay. Thus, the fMAPK pathway coordinates positive and negative regulatory proteins to fine-tune filamentous growth resulting in a nuanced response. Functional analysis of other pathways' targets may lead to a more comprehensive understanding of how signaling cascades generate biological responses.
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Affiliation(s)
| | - Paul J Cullen
- Department of Biological Sciences, University at Buffalo, New York 14260-1300
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11
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Tondini F, Onetto CA, Jiranek V. Early adaptation strategies of Saccharomyces cerevisiae and Torulaspora delbrueckii to co-inoculation in high sugar grape must-like media. Food Microbiol 2020; 90:103463. [DOI: 10.1016/j.fm.2020.103463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/18/2019] [Accepted: 02/18/2020] [Indexed: 12/28/2022]
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12
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Ginovart M, Carbó R, Blanco M, Portell X. Digital Image Analysis of Yeast Single Cells Growing in Two Different Oxygen Concentrations to Analyze the Population Growth and to Assist Individual-Based Modeling. Front Microbiol 2018; 8:2628. [PMID: 29354112 PMCID: PMC5758558 DOI: 10.3389/fmicb.2017.02628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/15/2017] [Indexed: 11/22/2022] Open
Abstract
Nowadays control of the growth of Saccharomyces to obtain biomass or cellular wall components is crucial for specific industrial applications. The general aim of this contribution is to deal with experimental data obtained from yeast cells and from yeast cultures to attempt the integration of the two levels of information, individual and population, to progress in the control of yeast biotechnological processes by means of the overall analysis of this set of experimental data, and to assist in the improvement of an individual-based model, namely, INDISIM-Saccha. Populations of S. cerevisiae growing in liquid batch culture, in aerobic and microaerophilic conditions, were studied. A set of digital images was taken during the population growth, and a protocol for the treatment and analyses of the images obtained was established. The piecewise linear model of Buchanan was adjusted to the temporal evolutions of the yeast populations to determine the kinetic parameters and changes of growth phases. In parallel, for all the yeast cells analyzed, values of direct morphological parameters, such as area, perimeter, major diameter, minor diameter, and derived ones, such as circularity and elongation, were obtained. Graphical and numerical methods from descriptive statistics were applied to these data to characterize the growth phases and the budding state of the yeast cells in both experimental conditions, and inferential statistical methods were used to compare the diverse groups of data achieved. Oxidative metabolism of yeast in a medium with oxygen available and low initial sugar concentration can be taken into account in order to obtain a greater number of cells or larger cells. Morphological parameters were analyzed statistically to identify which were the most useful for the discrimination of the different states, according to budding and/or growth phase, in aerobic and microaerophilic conditions. The use of the experimental data for subsequent modeling work was then discussed and compared to simulation results generated with INDISIM-Saccha, which allowed us to advance in the development of this yeast model, and illustrated the utility of data at different levels of observation and the needs and logic behind the development of a microbial individual-based model.
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Affiliation(s)
- Marta Ginovart
- Department of Mathematics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Rosa Carbó
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Mónica Blanco
- Department of Mathematics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Xavier Portell
- Cranfield Soil and Agrifood Institute, Cranfield University, Bedfordshire, United Kingdom
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13
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Stelkens RB, Miller EL, Greig D. Asynchronous spore germination in isogenic natural isolates ofSaccharomyces paradoxus. FEMS Yeast Res 2016; 16:fow012. [DOI: 10.1093/femsyr/fow012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/18/2022] Open
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14
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Legrand J, Bolotin-Fukuhara M, Bourgais A, Fairhead C, Sicard D. Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Res 2015; 16:fov112. [PMID: 26684721 DOI: 10.1093/femsyr/fov112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 12/14/2022] Open
Abstract
The Nakaseomyces clade consists of a group of six hemiascomyceteous yeasts (Candida glabrata, Nakaseomyces delphensis, C. nivarensis, C. bracarensis, C. castelli, N. bacillisporus), phylogenetically close to the yeast Saccharomyces cerevisiae, their representative being the well-known pathogenic yeast C. glabrata. Four species had been previously examined for their carbon assimilation properties and found to have similar properties to S. cerevisiae (repression of respiration in high glucose-i.e. Crabtree positivity-and being a facultative anaerobe). We examined here the complete set of the six species for their carbon metabolic gene content. We also measured different metabolic and life-history traits (glucose consumption rate, population growth rate, carrying capacity, cell size, cell and biomass yield). We observed deviations from the glycolytic gene redundancy observed in S. cerevisiae presumed to be an important property for the Crabtree positivity, especially for the two species C. castelli and N. bacillisporus which frequently have only one gene copy, but different life strategies. Therefore, we show that the decrease in carbon metabolic gene copy cannot be simply associated with a reduction of glucose consumption rate and can be counterbalanced by other beneficial genetic variations.
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Affiliation(s)
- Judith Legrand
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Monique Bolotin-Fukuhara
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Aurélie Bourgais
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Cécile Fairhead
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France INRA, UMR 1083 Sciences pour l'oenologie, 34060 Montpellier Cedex 2, France
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15
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Accelerating Mutational Load Is Not Due to Synergistic Epistasis or Mutator Alleles in Mutation Accumulation Lines of Yeast. Genetics 2015; 202:751-63. [PMID: 26596348 DOI: 10.1534/genetics.115.182774] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022] Open
Abstract
Much of our knowledge about the fitness effects of new mutations has been gained from mutation accumulation (MA) experiments. Yet the fitness effect of single mutations is rarely measured in MA experiments. This raises several issues, notably for inferring epistasis for fitness. The acceleration of fitness decline in MA lines has been taken as evidence for synergistic epistasis, but establishing the role of epistasis requires measuring the fitness of genotypes carrying known numbers of mutations. Otherwise, accelerating fitness loss could be explained by increased genetic mutation rates. Here we segregated mutations accumulated over 4800 generations in haploid and diploid MA lines of the yeast Saccharomyces cerevisiae. We found no correspondence between an accelerated fitness decline and synergistic epistasis among deleterious mutations in haploid lines. Pairs of mutations showed no overall epistasis. Furthermore, several lines of evidence indicate that genetic mutation rates did not increase in the MA lines. Crucially, segregant fitness analyses revealed that MA accelerated in both haploid and diploid lines, even though the fitness of diploid lines was nearly constant during the MA experiment. This suggests that the accelerated fitness decline in haploids was caused by cryptic environmental factors that increased mutation rates in all lines during the last third of the lines' transfers. In addition, we provide new estimates of deleterious mutation rates, including lethal mutations, and highlight that nearly all the mutational load we observed was due to one or two mutations having a large effect on fitness.
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16
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da Silva T, Albertin W, Dillmann C, Bely M, la Guerche S, Giraud C, Huet S, Sicard D, Masneuf-Pomarede I, de Vienne D, Marullo P. Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions. PLoS One 2015; 10:e0123834. [PMID: 25946464 PMCID: PMC4422614 DOI: 10.1371/journal.pone.0123834] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/21/2015] [Indexed: 11/18/2022] Open
Abstract
Despite its biotechnological interest, hybridization, which can result in hybrid vigor, has not commonly been studied or exploited in the yeast genus. From a diallel design including 55 intra- and interspecific hybrids between Saccharomyces cerevisiae and S. uvarum grown at two temperatures in enological conditions, we analyzed as many as 35 fermentation traits with original statistical and modeling tools. We first showed that, depending on the types of trait--kinetics parameters, life-history traits, enological parameters and aromas -, the sources of variation (strain, temperature and strain * temperature effects) differed in a large extent. Then we compared globally three groups of hybrids and their parents at two growth temperatures: intraspecific hybrids S. cerevisiae * S. cerevisiae, intraspecific hybrids S. uvarum * S. uvarum and interspecific hybrids S. cerevisiae * S. uvarum. We found that hybridization could generate multi-trait phenotypes with improved oenological performances and better homeostasis with respect to temperature. These results could explain why interspecific hybridization is so common in natural and domesticated yeast, and open the way to applications for wine-making.
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Affiliation(s)
- Telma da Silva
- INRA, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Warren Albertin
- ENSCBP—Bordeaux INP, Pessac, France
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | - Christine Dillmann
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Marina Bely
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | | | | | | | - Delphine Sicard
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Isabelle Masneuf-Pomarede
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Bordeaux Sciences Agro, Gradignan, France
| | - Dominique de Vienne
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Philippe Marullo
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
- * E-mail:
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17
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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: 0.7] [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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18
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Ibstedt S, Stenberg S, Bagés S, Gjuvsland AB, Salinas F, Kourtchenko O, Samy JKA, Blomberg A, Omholt SW, Liti G, Beltran G, Warringer J. Concerted evolution of life stage performances signals recent selection on yeast nitrogen use. Mol Biol Evol 2014; 32:153-61. [PMID: 25349282 DOI: 10.1093/molbev/msu285] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection.
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Affiliation(s)
- Sebastian Ibstedt
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Simon Stenberg
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
| | - Sara Bagés
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Arne B Gjuvsland
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
| | | | - Olga Kourtchenko
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jeevan K A Samy
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stig W Omholt
- Department of Biotechnology, Faculty of Natural Sciences and Technology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, Nice, France
| | - Gemma Beltran
- Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, Tarragona, Spain
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
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19
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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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20
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Spor A, Kvitek DJ, Nidelet T, Martin J, Legrand J, Dillmann C, Bourgais A, de Vienne D, Sherlock G, Sicard D. Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast. Evolution 2013; 68:772-790. [PMID: 24164389 DOI: 10.1111/evo.12302] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 10/14/2013] [Indexed: 12/26/2022]
Abstract
Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the population converged toward a different multivariate phenotype. However, the evolution of most traits, including fitness components, was constrained by history. Phenotypic convergence was partly associated with the selection of mutations in genes involved in the same pathway. By further investigating the convergence in one gene, BMH1, mutated in 20% of the evolved populations, we show that both the history and the environment influenced the types of mutations (missense/nonsense), their location within the gene itself, as well as their effects on multiple traits. However, these effects could not be easily predicted from ancestors' phylogeny or past selection. Combined, our data highlight the role of pleiotropy and epistasis in shaping a rugged fitness landscape.
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Affiliation(s)
- Aymé Spor
- Univ Paris-Sud, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France
| | - Daniel J Kvitek
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | - Juliette Martin
- Université Lyon 1; CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, 7 passage du, Vercors F-69367, France
| | - Judith Legrand
- Univ Paris-Sud, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France
| | - Christine Dillmann
- Univ Paris-Sud, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France
| | - Aurélie Bourgais
- CNRS, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France
| | - Dominique de Vienne
- Univ Paris-Sud, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Delphine Sicard
- Univ Paris-Sud, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France
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21
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Albertin W, Marullo P, Bely M, Aigle M, Bourgais A, Langella O, Balliau T, Chevret D, Valot B, da Silva T, Dillmann C, de Vienne D, Sicard D. Linking post-translational modifications and variation of phenotypic traits. Mol Cell Proteomics 2012; 12:720-35. [PMID: 23271801 DOI: 10.1074/mcp.m112.024349] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymes can be post-translationally modified, leading to isoforms with different properties. The phenotypic consequences of the quantitative variability of isoforms have never been studied. We used quantitative proteomics to dissect the relationships between the abundances of the enzymes and isoforms of alcoholic fermentation, metabolic traits, and growth-related traits in Saccharomyces cerevisiae. Although the enzymatic pool allocated to the fermentation proteome was constant over the culture media and the strains considered, there was variation in abundance of individual enzymes and sometimes much more of their isoforms, which suggests the existence of selective constraints on total protein abundance and trade-offs between isoforms. Variations in abundance of some isoforms were significantly associated to metabolic traits and growth-related traits. In particular, cell size and maximum population size were highly correlated to the degree of N-terminal acetylation of the alcohol dehydrogenase. The fermentation proteome was found to be shaped by human selection, through the differential targeting of a few isoforms for each food-processing origin of strains. These results highlight the importance of post-translational modifications in the diversity of metabolic and life-history traits.
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Affiliation(s)
- Warren Albertin
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
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22
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Jasmin JN, Zeyl C. Life-history evolution and density-dependent growth in experimental populations of yeast. Evolution 2012. [PMID: 23206137 DOI: 10.1111/j.1558-5646.2012.01711.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We studied the evolution of the correlation between growth rate r and yield K in experimental lineages of the yeast Saccharomyces cerevisiae. First, we isolated a single clone every approximately 250 generations from each of eight populations selected in a glucose-limited medium for 5000 generations at approximately 6.6 population doublings per day (20 clones per line × 8 lines) and measured its growth rate and yield in a new, galactose-limited medium (with ∼1.3 doubling per day). For most lines, r on galactose increased throughout the 5000 generations of selection on glucose whereas K on galactose declined. Next, we selected these 160 glucose-adapted clones in the galactose environment for approximately 120 generations and measured changes in r and K in galactose. In general, growth rate increased and yield declined, and clones that initially grew slowly on galactose improved more than did faster clones. We found a negative correlation between r and K among clones both within each line and across all clones. We provide evidence that this relationship is not heritable and is a negative environmental correlation rather than a genetic trade-off.
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Affiliation(s)
- Jean-Nicolas Jasmin
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina 27106, USA.
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23
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Zakrzewska A, van Eikenhorst G, Burggraaff JEC, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ. Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol Biol Cell 2011; 22:4435-46. [PMID: 21965291 PMCID: PMC3216668 DOI: 10.1091/mbc.e10-08-0721] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A genome-wide analysis of the acquisition of stress cross-tolerance shows that reduction of growth rate is an important determinant of severe stress survival. Cellular functions important for the coupling of growth rate to stress resistance are identified, as are those required for cross-tolerance acquisition independent of growth rate reduction. All organisms have evolved to cope with changes in environmental conditions, ensuring the optimal combination of proliferation and survival. In yeast, exposure to a mild stress leads to an increased tolerance for other stresses. This suggests that yeast uses information from the environment to prepare for future threats. We used the yeast knockout collection to systematically investigate the genes and functions involved in severe stress survival and in the acquisition of stress (cross-) tolerance. Besides genes and functions relevant for survival of heat, acid, and oxidative stress, we found an inverse correlation between mutant growth rate and stress survival. Using chemostat cultures, we confirmed that growth rate governs stress tolerance, with higher growth efficiency at low growth rates liberating the energy for these investments. Cellular functions required for stress tolerance acquisition, independent of the reduction in growth rate, were involved in vesicular transport, the Rpd3 histone deacetylase complex, and the mitotic cell cycle. Stress resistance and acquired stress tolerance in Saccharomyces cerevisiae are governed by a combination of stress-specific and general processes. The reduction of growth rate, irrespective of the cause of this reduction, leads to redistribution of resources toward stress tolerance functions, thus preparing the cells for impending change.
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Affiliation(s)
- Anna Zakrzewska
- Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, Netherlands
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24
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Granek JA, Kayıkçı Ö, Magwene PM. Pleiotropic signaling pathways orchestrate yeast development. Curr Opin Microbiol 2011; 14:676-81. [PMID: 21962291 DOI: 10.1016/j.mib.2011.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 08/31/2011] [Accepted: 09/07/2011] [Indexed: 12/15/2022]
Abstract
Developmental phenotypes in Saccharomyces cerevisiae and related yeasts include responses such as filamentous growth, sporulation, and the formation of biofilms and complex colonies. These developmental phenotypes are regulated by evolutionarily conserved, nutrient-responsive signaling networks. The signaling mechanisms that control development in yeast are highly pleiotropic--all the known pathways contribute to the regulation of multiple developmental outcomes. This degree of pleiotropy implies that perturbations of these signaling pathways, whether genetic, biochemical, or environmentally induced, can manifest in multiple (and sometimes unexpected) ways. We summarize the current state of knowledge of developmental pleiotropy in yeast and discuss its implications for understanding functional relationships.
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Affiliation(s)
- Joshua A Granek
- Department of Biology and IGSP Center for Systems Biology, Duke University, Box 90338, Durham, NC 27708, USA
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25
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Camarasa C, Sanchez I, Brial P, Bigey F, Dequin S. Phenotypic landscape of Saccharomyces cerevisiae during wine fermentation: evidence for origin-dependent metabolic traits. PLoS One 2011; 6:e25147. [PMID: 21949874 PMCID: PMC3174997 DOI: 10.1371/journal.pone.0025147] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 08/29/2011] [Indexed: 01/01/2023] Open
Abstract
The species Saccharomyces cerevisiae includes natural strains, clinical isolates, and a large number of strains used in human activities. The aim of this work was to investigate how the adaptation to a broad range of ecological niches may have selectively shaped the yeast metabolic network to generate specific phenotypes. Using 72 S. cerevisiae strains collected from various sources, we provide, for the first time, a population-scale picture of the fermentative metabolic traits found in the S. cerevisiae species under wine making conditions. Considerable phenotypic variation was found suggesting that this yeast employs diverse metabolic strategies to face environmental constraints. Several groups of strains can be distinguished from the entire population on the basis of specific traits. Strains accustomed to growing in the presence of high sugar concentrations, such as wine yeasts and strains obtained from fruits, were able to achieve fermentation, whereas natural yeasts isolated from “poor-sugar” environments, such as oak trees or plants, were not. Commercial wine yeasts clearly appeared as a subset of vineyard isolates, and were mainly differentiated by their fermentative performances as well as their low acetate production. Overall, the emergence of the origin-dependent properties of the strains provides evidence for a phenotypic evolution driven by environmental constraints and/or human selection within S. cerevisiae.
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26
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Population size drives industrial Saccharomyces cerevisiae alcoholic fermentation and is under genetic control. Appl Environ Microbiol 2011; 77:2772-84. [PMID: 21357433 DOI: 10.1128/aem.02547-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Alcoholic fermentation (AF) conducted by Saccharomyces cerevisiae has been exploited for millennia in three important human food processes: beer and wine production and bread leavening. Most of the efforts to understand and improve AF have been made separately for each process, with strains that are supposedly well adapted. In this work, we propose a first comparison of yeast AFs in three synthetic media mimicking the dough/wort/grape must found in baking, brewing, and wine making. The fermentative behaviors of nine food-processing strains were evaluated in these media, at the cellular, populational, and biotechnological levels. A large variation in the measured traits was observed, with medium effects usually being greater than the strain effects. The results suggest that human selection targeted the ability to complete fermentation for wine strains and trehalose content for beer strains. Apart from these features, the food origin of the strains did not significantly affect AF, suggesting that an improvement program for a specific food processing industry could exploit the variability of strains used in other industries. Glucose utilization was analyzed, revealing plastic but also genetic variation in fermentation products and indicating that artificial selection could be used to modify the production of glycerol, acetate, etc. The major result was that the overall maximum CO(2) production rate (V(max)) was not related to the maximum CO(2) production rate per cell. Instead, a highly significant correlation between V(max) and the maximum population size was observed in all three media, indicating that human selection targeted the efficiency of cellular reproduction rather than metabolic efficiency. This result opens the way to new strategies for yeast improvement.
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27
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Sicard D, Legras JL. Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol 2011; 334:229-36. [PMID: 21377618 DOI: 10.1016/j.crvi.2010.12.016] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Yeasts of the Saccharomyces sensu stricto species complex are able to convert sugar into ethanol and CO(2) via fermentation. They have been used for thousands years by mankind for fermenting food and beverages. In the Neolithic times, fermentations were probably initiated by naturally occurring yeasts, and it is unknown when humans started to consciously add selected yeast to make beer, wine or bread. Interestingly, such human activities gave rise to the creation of new species in the Saccharomyces sensu stricto complex by interspecies hybridization or polyploidization. Within the S. cerevisiae species, they have led to the differentiation of genetically distinct groups according to the food process origin. Although the evolutionary history of wine yeast populations has been well described, the histories of other domesticated yeasts need further investigation.
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Affiliation(s)
- Delphine Sicard
- Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France.
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28
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Wang S, Spor A, Nidelet T, Montalent P, Dillmann C, de Vienne D, Sicard D. Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae. Appl Environ Microbiol 2011; 77:452-9. [PMID: 21075872 PMCID: PMC3020566 DOI: 10.1128/aem.00808-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 10/26/2010] [Indexed: 12/24/2022] Open
Abstract
Adaptation is the process whereby a population or species becomes better fitted to its habitat through modifications of various life history traits which can be positively or negatively correlated. The molecular factors underlying these covariations remain to be elucidated. Using Saccharomyces cerevisiae as a model system, we have investigated the effects on life history traits of varying the dosage of genes involved in the transformation of resources into energy. Changing gene dosage for each of three glycolytic enzyme genes (hexokinase 2, phosphoglucose isomerase, and fructose-1,6-bisphosphate aldolase) resulted in variation in enzyme activities, glucose consumption rate, and life history traits (growth rate, carrying capacity, and cell size). However, the range of effects depended on which enzyme was expressed differently. Most interestingly, these changes revealed a genetic trade-off between carrying capacity and cell size, supporting the discovery of two extreme life history strategies already described in yeast populations: the "ants," which have lower glycolytic gene dosage, take up glucose slowly, and have a small cell size but reach a high carrying capacity, and the "grasshoppers," which have higher glycolytic gene dosage, consume glucose more rapidly, and allocate it to a larger cell size but reach a lower carrying capacity. These results demonstrate antagonist pleiotropy for glycolytic genes and show that altered dosage of a single gene drives a switch between two life history strategies in yeast.
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Affiliation(s)
- Shaoxiao Wang
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Aymé Spor
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Thibault Nidelet
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Pierre Montalent
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Christine Dillmann
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Dominique de Vienne
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
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29
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Spor A, Nidelet T, Simon J, Bourgais A, de Vienne D, Sicard D. Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae. BMC Evol Biol 2009; 9:296. [PMID: 20028531 PMCID: PMC2804673 DOI: 10.1186/1471-2148-9-296] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/22/2009] [Indexed: 01/14/2023] Open
Abstract
Background Variation of resource supply is one of the key factors that drive the evolution of life-history strategies, and hence the interactions between individuals. In the yeast Saccharomyces cerevisiae, two life-history strategies related to different resource utilization have been previously described in strains from different industrial origins. In this work, we analyzed metabolic traits and life-history strategies in a broader collection of yeast strains sampled in various ecological niches (forest, human body, fruits, laboratory and industrial environments). Results By analysing the genetic and plastic variation of six life-history and three metabolic traits, we showed that S. cerevisiae populations harbour different strategies depending on their ecological niches. On one hand, the forest and laboratory strains, referred to as extreme "ants", reproduce quickly, reach a large carrying capacity and a small cell size in fermentation, but have a low reproduction rate in respiration. On the other hand, the industrial strains, referred to as extreme "grasshoppers", reproduce slowly, reach a small carrying capacity but have a big cell size in fermentation and a high reproduction rate in respiration. "Grasshoppers" have usually higher glucose consumption rate than "ants", while they produce lower quantities of ethanol, suggesting that they store cell resources rather than secreting secondary products to cross-feed or poison competitors. The clinical and fruit strains are intermediate between these two groups. Conclusions Altogether, these results are consistent with a niche-driven evolution of S. cerevisiae, with phenotypic convergence of populations living in similar habitat. They also revealed that competition between strains having contrasted life-history strategies ("ants" and "grasshoppers") seems to occur at low frequency or be unstable since opposite life-history strategies appeared to be maintained in distinct ecological niches.
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Affiliation(s)
- Aymé Spor
- Univ Paris-Sud, UMR de Génétique Végétale, INRA/Univ Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, F-91190, France.
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Albertin W, Marullo P, Aigle M, Bourgais A, Bely M, Dillmann C, DE Vienne D, Sicard D. Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J Evol Biol 2009; 22:2157-70. [PMID: 19765175 DOI: 10.1111/j.1420-9101.2009.01828.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Partial or whole-genome duplications have played a major role in the evolution of new species. We have investigated the variation of ploidy level in a panel of domesticated strains of Saccharomyces cerevisiae coming from different geographical origins. Segregation studies and crosses with tester strains of different ploidy levels showed that part of the strains were well-balanced autotetraploids displaying tetrasomic inheritance. The presence of up to four different alleles for various loci is consistent with a polyploidization mechanism relying on the fusion of two nonreduced meiospores coming from two S. cerevisiae strains. Autotetraploidy was also in accordance with karyotype and flow cytometry analyses. Interestingly, most bakery strains were tetraploids, suggesting a link between ploidy level and human use. The null or drastically reduced fertility of the hybrids between tetraploid and diploid strains indicated that domesticated S. cerevisiae strains are composed of two groups isolated by post-zygotic reproductive barriers.
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Affiliation(s)
- W Albertin
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
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