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Álvarez R, Garces F, Louis EJ, Dequin S, Camarasa C. Beyond S. cerevisiae for winemaking: Fermentation-related trait diversity in the genus Saccharomyces. Food Microbiol 2023; 113:104270. [PMID: 37098430 DOI: 10.1016/j.fm.2023.104270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
Saccharomyces cerevisiae is the yeast of choice for most inoculated wine fermentations worldwide. However, many other yeast species and genera display phenotypes of interest that may help address the environmental and commercial challenges the wine industry has been facing in recent years. This work aimed to provide, for the first time, a systematic phenotyping of all Saccharomyces species under winemaking conditions. For this purpose, we characterized the fermentative and metabolic properties of 92 Saccharomyces strains in synthetic grape must at two different temperatures. The fermentative potential of alternative yeasts was higher than expected, as nearly all strains were able to complete fermentation, in some cases more efficiently than commercial S. cerevisiae strains. Various species showed interesting metabolic traits, such as high glycerol, succinate and odour-active compound production, or low acetic acid production, compared to S. cerevisiae. Altogether, these results reveal that non-cerevisiae Saccharomyces yeasts are especially interesting for wine fermentation, as they may offer advantages over both S. cerevisiae and non-Saccharomyces strains. This study highlights the potential of alternative Saccharomyces species for winemaking, paving the way for further research and, potentially, for their industrial exploitation.
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Mozzachiodi S, Tattini L, Llored A, Irizar A, Škofljanc N, D'Angiolo M, De Chiara M, Barré BP, Yue JX, Lutazi A, Loeillet S, Laureau R, Marsit S, Stenberg S, Albaud B, Persson K, Legras JL, Dequin S, Warringer J, Nicolas A, Liti G. Aborting meiosis allows recombination in sterile diploid yeast hybrids. Nat Commun 2021; 12:6564. [PMID: 34772931 PMCID: PMC8589840 DOI: 10.1038/s41467-021-26883-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
Hybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation.
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Grants
- This work was supported by Agence Nationale de la Recherche (ANR-11-LABX-0028-01, ANR-13-BSV6-0006-01, ANR-15-IDEX-01, ANR-16-CE12-0019 and ANR-18-CE12-0004), Fondation pour la Recherche Médicale (FRM EQU202003010413), CEFIPRA, Cancéropôle PACA (AAP Equipment 2018), Meiogenix and the Swedish Research Council (2014-6547, 2014-4605 and 2018-03638). S.Mo. is funded by the convention CIFRE 2016/0582 between Meiogenix and ANRT. The Institut Curie NGS platform is supported by ANR-10-EQPX-03 (Equipex), ANR-10-INBS-09-08 (France Génomique Consortium), ITMO-CANCER and SiRIC INCA-DGOS (4654 program).
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Affiliation(s)
- Simone Mozzachiodi
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- Meiogenix, 38, rue Servan, Paris, 75011, France
| | | | - Agnes Llored
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Neža Škofljanc
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | | | | | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Angela Lutazi
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Sophie Loeillet
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
| | - Raphaelle Laureau
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Medical Center, New York, NY, USA
| | - Souhir Marsit
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
- Département de Biologie Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Benoit Albaud
- Institut Curie, ICGEX NGS Platform, Paris, 75005, France
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jean-Luc Legras
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Alain Nicolas
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- Meiogenix, 38, rue Servan, Paris, 75011, France
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
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Becerra-Rodríguez C, Taghouti G, Portier P, Dequin S, Casal M, Paiva S, Galeote V. Yeast Plasma Membrane Fungal Oligopeptide Transporters Display Distinct Substrate Preferences despite Their High Sequence Identity. J Fungi (Basel) 2021; 7:jof7110963. [PMID: 34829250 PMCID: PMC8625066 DOI: 10.3390/jof7110963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023] Open
Abstract
Fungal Oligopeptide Transporters (Fot) Fot1, Fot2 and Fot3 have been found in Saccharomyces cerevisiae wine strains, but not in strains from other environments. In the S. cerevisiae wine strain EC1118, Fot1 and Fot2 are responsible for a broader range of oligopeptide utilization in comparison with strains not containing any Fot. This leads to better fermentation efficiency and an increased production of desirable organoleptic compounds in wine. Despite the benefits associated with Fot activity in S. cerevisiae within the wine environment, little is known about this family of transporters in yeast. The presence of Fot1, Fot2 and Fot3 in S. cerevisiae wine strains is due to horizontal gene transfer from the yeast Torulaspora microellipsoides, which harbors Fot2Tm, FotX and FotY proteins. Sequence analyses revealed that Fot family members have a high sequence identity in these yeast species. In this work, we aimed to further characterize the different Fot family members in terms of subcellular localization, gene expression in enological fermentation and substrate specificity. Using CRISPR/Cas9, we constructed S. cerevisiae wine strains containing each different Fot as the sole oligopeptide transporter to analyze their oligopeptide preferences by phenotype microarrays. The results of oligopeptide consumption show that Fot counterparts have different di-/tripeptide specificities, suggesting that punctual sequence divergence between FOT genes can be crucial for substrate recognition, binding and transport activity. FOT gene expression levels in different S. cerevisiae wine strains during enological fermentation, together with predicted binding motifs for transcriptional regulators in nitrogen metabolism, indicate that these transporters may be under the control of the Nitrogen Catabolite Repression (NCR) system. Finally, we demonstrated that Fot1 is located in the yeast plasma membrane. This work contributes to a better understanding of this family of oligopeptide transporters, which have demonstrated a key role in the utilization of oligopeptides by S. cerevisiae in enological fermentation.
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Affiliation(s)
- Carmen Becerra-Rodríguez
- SPO, Univ. Montpellier, INRAE, Institut Agro, F-34060 Montpellier, France; (C.B.-R.); (S.D.)
- Centre of Environmental and Molecular Biology, Department of Biology, Campus of Gualtar, University of Minho, 4710-057 Braga, Portugal; (M.C.); (S.P.)
| | - Géraldine Taghouti
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France; (G.T.); (P.P.)
| | - Perrine Portier
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France; (G.T.); (P.P.)
| | - Sylvie Dequin
- SPO, Univ. Montpellier, INRAE, Institut Agro, F-34060 Montpellier, France; (C.B.-R.); (S.D.)
| | - Margarida Casal
- Centre of Environmental and Molecular Biology, Department of Biology, Campus of Gualtar, University of Minho, 4710-057 Braga, Portugal; (M.C.); (S.P.)
| | - Sandra Paiva
- Centre of Environmental and Molecular Biology, Department of Biology, Campus of Gualtar, University of Minho, 4710-057 Braga, Portugal; (M.C.); (S.P.)
| | - Virginie Galeote
- SPO, Univ. Montpellier, INRAE, Institut Agro, F-34060 Montpellier, France; (C.B.-R.); (S.D.)
- Correspondence:
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4
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Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family. eLife 2020; 9:55336. [PMID: 32338594 PMCID: PMC7282813 DOI: 10.7554/elife.55336] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023] Open
Abstract
The mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera close to Saccharomyces. Here we show that HO is structurally and phylogenetically related to a family of unorthodox homing genetic elements found in Torulaspora and Lachancea yeasts. These WHO elements home into the aldolase gene FBA1, replacing its 3' end each time they integrate. They resemble inteins but they operate by a different mechanism that does not require protein splicing. We show that a WHO protein cleaves Torulaspora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene conversion or NHEJ. The DNA rearrangement steps during WHO element homing are very similar to those during mating-type switching, and indicate that HO is a domesticated WHO-like element. In the same way as a sperm from a male and an egg from a female join together to form an embryo in most animals, yeast cells have two sexes that coordinate how they reproduce. These are called “mating types” and, rather than male or female, an individual yeast cell can either be mating type “a” or “alpha”. Every yeast cell contains the genes for both mating types, and each cell’s mating type is determined by which of those genes it has active. Only one mating type gene can be ‘on’ at a time, but some yeast species can swap mating type on demand by switching the corresponding genes ‘on’ or ‘off’. This switch is unusual. Rather than simply activate one of the genes it already has, the yeast cell keeps an inactive version of each mating type gene tucked away, makes a copy of the gene it wants to be active and pastes that copy into a different location in its genome. To do all of this yeast need another gene called HO. This gene codes for an enzyme that cuts the DNA at the location of the active mating type gene. This makes an opening that allows the cell to replace the ‘a’ gene with the ‘alpha’ gene, or vice versa. This system allows yeast cells to continue mating even if all the cells in a colony start off as the same mating type. But, cutting into the DNA is risky, and can damage the health of the cell. So, why did yeast cells evolve a system that could cause them harm? To find out where the HO gene came from, Coughlan et al. searched through all the available genomes from yeast species for other genes with similar sequences and identified a cluster which they nicknamed “weird HO” genes, or WHO genes for short. Testing these genes revealed that they also code for enzymes that make cuts in the yeast genome, but the way the cell repairs the cuts is different. The WHO genes are jumping genes. When the enzyme encoded by a WHO gene makes a cut in the genome, the yeast cell copies the gene into the gap, allowing the gene to ‘jump’ from one part of the genome to another. It is possible that this was the starting point for the evolution of the HO gene. Changes to a WHO gene could have allowed it to cut into the mating type region of the yeast genome, giving the yeast an opportunity to ‘domesticate’ it. Over time, the yeast cell stopped the WHO gene from jumping into the gap and started using the cut to change its mating type. Understanding how cells adapt genes for different purposes is a key question in evolutionary biology. There are many other examples of domesticated jumping genes in other organisms, including in the human immune system. Understanding the evolution of HO not only sheds light on how yeast mating type switching evolved, but on how other species might harness and adapt their genes.
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Affiliation(s)
- Aisling Y Coughlan
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | | | - Alexandre Ar Martos
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Virginie Galeote
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Kevin P Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
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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: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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Deroite A, Legras JL, Rigou P, Ortiz-Julien A, Dequin S. Lipids modulate acetic acid and thiol final concentrations in wine during fermentation by Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids. AMB Express 2018; 8:130. [PMID: 30097818 PMCID: PMC6086921 DOI: 10.1186/s13568-018-0657-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 12/23/2022] Open
Abstract
Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids are typically used for white wine fermentation because of their cryotolerance. One group of these hybrids presents a unique ability to release thiol varietal aroma products as well as excessive amounts of acetic acid under specific conditions, which is detrimental for wine organoleptic quality. The aim of this work is to better assess the effects of lipids, sugar concentrations and temperature on the production of acetic acid and thiols during wine fermentation. To this end, we used a Box–Behnken experimental design and response surface modeling on the production of acetic acid and thiols in S. cerevisiae × S. kudriavzevii hybrids from the Eg8 family during fermentation of a synthetic must. We showed that these hybrids produced lower levels of acetic acid when the initial lipid concentration was increased, whereas they produced greater levels when the initial sugar concentration was high. Moreover, we found that lipids had a positive impact on the final concentrations of 4-methyl-4-mercaptopentan-2-one and 3-mercaptohexan-1-ol (3MH), giving box tree and citrus flavors, respectively. The increase of 3MH was concomitant with a decrease of 3-mercaptohexyl acetate (3MHA) characterized by a passion fruit aroma, indicating that lipid addition reduces the rate of 3MH acetylation into 3MHA. These results highlight the key role of lipid management in acetic acid metabolism and thiol release by S. cerevisiae × S. kudriavzevii hybrids and underline its technological interest in alcoholic fermentation to avoid the overproduction of volatile acidity while favoring the release of volatile thiols.
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Eder M, Sanchez I, Brice C, Camarasa C, Legras JL, Dequin S. QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation. BMC Genomics 2018; 19:166. [PMID: 29490607 PMCID: PMC5831830 DOI: 10.1186/s12864-018-4562-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/20/2018] [Indexed: 01/07/2023] Open
Abstract
Background The volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermented beverages, such as wine. Although the metabolic pathways and genes behind yeast fermentative aroma formation are well described, little is known about the genetic mechanisms underlying variations between strains in the production of these aroma compounds. To increase our knowledge about the links between genetic variation and volatile production, we performed quantitative trait locus (QTL) mapping using 130 F2-meiotic segregants from two S. cerevisiae wine strains. The segregants were individually genotyped by next-generation sequencing and separately phenotyped during wine fermentation. Results Using different QTL mapping strategies, we were able to identify 65 QTLs in the genome, including 55 that influence the formation of 30 volatile secondary metabolites, 14 with an effect on sugar consumption and central carbon metabolite production, and 7 influencing fermentation parameters. For ethyl lactate, ethyl octanoate and propanol formation, we discovered 2 interacting QTLs each. Within 9 of the detected regions, we validated the contribution of 13 genes in the observed phenotypic variation by reciprocal hemizygosity analysis. These genes are involved in nitrogen uptake and metabolism (AGP1, ALP1, ILV6, LEU9), central carbon metabolism (HXT3, MAE1), fatty acid synthesis (FAS1) and regulation (AGP2, IXR1, NRG1, RGS2, RGT1, SIR2) and explain variations in the production of characteristic sensorial esters (e.g., 2-phenylethyl acetate, 2-metyhlpropyl acetate and ethyl hexanoate), higher alcohols and fatty acids. Conclusions The detection of QTLs and their interactions emphasizes the complexity of yeast fermentative aroma formation. The validation of underlying allelic variants increases knowledge about genetic variation impacting metabolic pathways that lead to the synthesis of sensorial important compounds. As a result, this work lays the foundation for tailoring S. cerevisiae strains with optimized volatile metabolite production for fermented beverages and other biotechnological applications. Electronic supplementary material The online version of this article (10.1186/s12864-018-4562-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Eder
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Isabelle Sanchez
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France.,MISTEA, INRA, SupAgro, F-34060, Montpellier, France
| | - Claire Brice
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Carole Camarasa
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Jean-Luc Legras
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Sylvie Dequin
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France.
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8
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Brice C, Cubillos FA, Dequin S, Camarasa C, Martínez C. Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen. PLoS One 2018; 13:e0192383. [PMID: 29432462 PMCID: PMC5809068 DOI: 10.1371/journal.pone.0192383] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/20/2018] [Indexed: 11/25/2022] Open
Abstract
Saccharomyces cerevisiae strains are genetically diverse, largely as a result of human efforts to develop strains specifically adapted to various fermentation processes. These adaptive pressures from various ecological niches have generated behavioral differences among these strains, particularly in terms of their nitrogen consumption capacities. In this work, we characterize this phenotype by the specific quantity of nitrogen consumed under oenological fermentation conditions using a new approach. Indeed, unlike previous studies, our experiments were conducted in an environment containing excess nitrogen, eliminating the nitrogen limitation/starvation factor that is generally observed in fermentation processes. Using these conditions, we evaluated differences in the nitrogen consumption capacities for a set of five strains from diverse origins. The strains presented extremely different phenotypes and variations in their capacities to take up nitrogen from a wine fermentation environment. These variations reflect the differences in the nitrogen uptake capacities between wine and non-wine strains. Finally, the strains differed in their ability to adapt to the nitrogen composition of the environment, leading to variations in the cellular stress states, fermentation performances and the activity of the nitrogen sensing signaling pathway.
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Affiliation(s)
- Claire Brice
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco A. Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Millennium Institute for Integrative Systems and Synthetic Biology (MII-SSB), Santiago, Chile
| | - Sylvie Dequin
- UMR SPO: INRA, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Carole Camarasa
- UMR SPO: INRA, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
- * E-mail:
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9
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Rollero S, Mouret JR, Bloem A, Sanchez I, Ortiz-Julien A, Sablayrolles JM, Dequin S, Camarasa C. Quantitative 13 C-isotope labelling-based analysis to elucidate the influence of environmental parameters on the production of fermentative aromas during wine fermentation. Microb Biotechnol 2017; 10:1649-1662. [PMID: 28695583 PMCID: PMC5658611 DOI: 10.1111/1751-7915.12749] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/28/2017] [Accepted: 05/24/2017] [Indexed: 02/02/2023] Open
Abstract
Nitrogen and lipids are key nutrients of grape must that influence the production of fermentative aromas by wine yeast, and we have previously shown that a strong interaction exists between these two nutrients. However, more than 90% of the acids and higher alcohols (and their acetate ester derivatives) were derived from intermediates produced by the carbon central metabolism (CCM). The objective of this study was to determine how variations in nitrogen and lipid resources can modulate the contribution of nitrogen and carbon metabolisms for the production of fermentative aromas. A quantitative analysis of metabolism using 13C‐labelled leucine and valine showed that nitrogen availability affected the part of the catabolism of N‐containing compounds, the formation of α‐ketoacids from CCM and the redistribution of fluxes around these precursors, explaining the optimum production of higher alcohols occurring at an intermediate nitrogen content. Moreover, nitrogen content modulated the total production of acids and higher alcohols differently, through variations in the redox state of cells. We also demonstrated that the phytosterol content, modifying the intracellular availability of acetyl‐CoA, can influence the flux distribution, especially the formation of higher alcohols and the conversion of α‐ketoisovalerate to α‐ketoisocaproate.
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Affiliation(s)
- Stéphanie Rollero
- UMR SPO: INRA, Universite Montpellier, Montpellier SupAgro, 34060, Montpellier, France.,Lallemand SAS, 31700, Blagnac, France
| | - Jean-Roch Mouret
- UMR SPO: INRA, Universite Montpellier, Montpellier SupAgro, 34060, Montpellier, France
| | - Audrey Bloem
- UMR SPO: INRA, Universite Montpellier, Montpellier SupAgro, 34060, Montpellier, France
| | - Isabelle Sanchez
- UMR SPO: INRA, Universite Montpellier, Montpellier SupAgro, 34060, Montpellier, France
| | | | | | - Sylvie Dequin
- UMR SPO: INRA, Universite Montpellier, Montpellier SupAgro, 34060, Montpellier, France
| | - Carole Camarasa
- UMR SPO: INRA, Universite Montpellier, Montpellier SupAgro, 34060, Montpellier, France
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10
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Magalhães F, Krogerus K, Castillo S, Ortiz-Julien A, Dequin S, Gibson B. Exploring the potential of Saccharomyces eubayanus as a parent for new interspecies hybrid strains in winemaking. FEMS Yeast Res 2017; 17:3950269. [DOI: 10.1093/femsyr/fox049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Affiliation(s)
- Frederico Magalhães
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, PO Box 16100, FI-00076 Espoo, Finland
| | - Kristoffer Krogerus
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, PO Box 16100, FI-00076 Espoo, Finland
| | - Sandra Castillo
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
| | | | - Sylvie Dequin
- SPO, INRA, SupAgro, Université de Montpellier, 34060 Montpellier, France
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
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11
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Ferreira D, Galeote V, Sanchez I, Legras JL, Ortiz-Julien A, Dequin S. Yeast multistress resistance and lag-phase characterisation during wine fermentation. FEMS Yeast Res 2017; 17:3950270. [DOI: 10.1093/femsyr/fox051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 07/06/2017] [Indexed: 01/08/2023] Open
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12
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Coi AL, Bigey F, Mallet S, Marsit S, Zara G, Gladieux P, Galeote V, Budroni M, Dequin S, Legras JL. Genomic signatures of adaptation to wine biological ageing conditions in biofilm-forming flor yeasts. Mol Ecol 2017; 26:2150-2166. [PMID: 28192619 DOI: 10.1111/mec.14053] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/31/2017] [Indexed: 12/16/2022]
Abstract
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological ageing are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and population structure analysis based on single nucleotide polymorphisms revealed a group of flor yeasts separated from wine yeasts. A combination of methods revealed several highly differentiated regions between wine and flor yeasts, and analyses using codon-substitution models for detecting molecular adaptation identified sites under positive selection in the high-affinity transporter gene ZRT1. The cross-population composite likelihood ratio revealed selective sweeps at three regions, including in the hexose transporter gene HXT7, the yapsin gene YPS6 and the membrane protein coding gene MTS27. Our analyses also revealed that the biological ageing environment has led to the accumulation of numerous mutations in proteins from several networks, including Flo11 regulation and divalent metal transport. Together, our findings suggest that the tuning of FLO11 expression and zinc transport networks are a distinctive feature of the genetic changes underlying the domestication of flor yeasts. Our study highlights the multiplicity of genomic changes underlying yeast adaptation to man-made habitats and reveals that flor/wine yeast lineage can serve as a useful model for studying the genomics of adaptive divergence.
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Affiliation(s)
- A L Coi
- Dipartimento di Agraria, Università di Sassari, 07100, Sassari, Italy
| | - F Bigey
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - S Mallet
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - S Marsit
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - G Zara
- Dipartimento di Agraria, Università di Sassari, 07100, Sassari, Italy
| | - P Gladieux
- INRA, UMR BGPI, 34398, Montpellier, France
| | - V Galeote
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - M Budroni
- Dipartimento di Agraria, Università di Sassari, 07100, Sassari, Italy
| | - S Dequin
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - J L Legras
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
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13
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Coi AL, Legras JL, Zara G, Dequin S, Budroni M. A set of haploid strains available for genetic studies ofSaccharomyces cerevisiaeflor yeasts. FEMS Yeast Res 2016; 16:fow066. [DOI: 10.1093/femsyr/fow066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 12/20/2022] Open
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14
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Legras JL, Moreno-Garcia J, Zara S, Zara G, Garcia-Martinez T, Mauricio JC, Mannazzu I, Coi AL, Bou Zeidan M, Dequin S, Moreno J, Budroni M. Flor Yeast: New Perspectives Beyond Wine Aging. Front Microbiol 2016; 7:503. [PMID: 27148192 PMCID: PMC4830823 DOI: 10.3389/fmicb.2016.00503] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/29/2016] [Indexed: 11/24/2022] Open
Abstract
The most important dogma in white-wine production is the preservation of the wine aroma and the limitation of the oxidative action of oxygen. In contrast, the aging of Sherry and Sherry-like wines is an aerobic process that depends on the oxidative activity of flor strains of Saccharomyces cerevisiae. Under depletion of nitrogen and fermentable carbon sources, these yeast produce aggregates of floating cells and form an air–liquid biofilm on the wine surface, which is also known as velum or flor. This behavior is due to genetic and metabolic peculiarities that differentiate flor yeast from other wine yeast. This review will focus first on the most updated data obtained through the analysis of flor yeast with -omic tools. Comparative genomics, proteomics, and metabolomics of flor and wine yeast strains are shedding new light on several features of these special yeast, and in particular, they have revealed the extent of proteome remodeling imposed by the biofilm life-style. Finally, new insights in terms of promotion and inhibition of biofilm formation through small molecules, amino acids, and di/tri-peptides, and novel possibilities for the exploitation of biofilm immobilization within a fungal hyphae framework, will be discussed.
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Affiliation(s)
- Jean-Luc Legras
- SPO, Institut National de la Recherche Agronomique - SupAgro, Université de Montpellier Montpellier, France
| | - Jaime Moreno-Garcia
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba Cordoba, Spain
| | - Severino Zara
- Department of Agricultural Sciences, University of Sassari Sassari, Italy
| | - Giacomo Zara
- Department of Agricultural Sciences, University of Sassari Sassari, Italy
| | - Teresa Garcia-Martinez
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba Cordoba, Spain
| | - Juan C Mauricio
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba Cordoba, Spain
| | - Ilaria Mannazzu
- Department of Agricultural Sciences, University of Sassari Sassari, Italy
| | - Anna L Coi
- Department of Agricultural Sciences, University of Sassari Sassari, Italy
| | - Marc Bou Zeidan
- Department of Agri-Food Sciences, Holy Spirit University of Kaslik Jounieh, Lebanon
| | - Sylvie Dequin
- SPO, Institut National de la Recherche Agronomique - SupAgro, Université de Montpellier Montpellier, France
| | - Juan Moreno
- Department of Agricultural Chemistry, Agrifood Campus of International Excellence ceiA3, University of Cordoba Cordoba, Spain
| | - Marilena Budroni
- Department of Agricultural Sciences, University of Sassari Sassari, Italy
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15
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Nidelet T, Brial P, Camarasa C, Dequin S. Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments. Microb Cell Fact 2016; 15:58. [PMID: 27044358 PMCID: PMC4820951 DOI: 10.1186/s12934-016-0456-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background S. cerevisiae has attracted considerable interest in recent years as a model for ecology and evolutionary biology, revealing a substantial genetic and phenotypic diversity. However, there is a lack of knowledge on the diversity of metabolic networks within this species. Results To identify the metabolic and evolutionary constraints that shape metabolic fluxes in S. cerevisiae, we used a dedicated constraint-based model to predict the central carbon metabolism flux distribution of 43 strains from different ecological origins, grown in wine fermentation conditions. In analyzing these distributions, we observed a highly contrasted situation in flux variability, with quasi-constancy of the glycolysis and ethanol synthesis yield yet high flexibility of other fluxes, such as the pentose phosphate pathway and acetaldehyde production. Furthermore, these fluxes with large variability showed multimodal distributions that could be linked to strain origin, indicating a convergence between genetic origin and flux phenotype. Conclusions Flux variability is pathway-dependent and, for some flux, a strain origin effect can be found. These data highlight the constraints shaping the yeast operative central carbon network and provide clues for the design of strategies for strain improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0456-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thibault Nidelet
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
| | - Pascale Brial
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - Carole Camarasa
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - Sylvie Dequin
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
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16
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Rollero S, Mouret JR, Sanchez I, Camarasa C, Ortiz-Julien A, Sablayrolles JM, Dequin S. Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain. Microb Cell Fact 2016; 15:32. [PMID: 26861624 PMCID: PMC4748530 DOI: 10.1186/s12934-016-0434-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/27/2016] [Indexed: 01/08/2023] Open
Abstract
Background Fermentative aromas play a key role in the organoleptic profile of young wines. Their production depends both on yeast strain and fermentation conditions. A present-day trend in the wine industry consists in developing new strains with aromatic properties using adaptive evolution approaches. An evolved strain, Affinity™ ECA5, overproducing esters, was recently obtained. In this study, dynamics of nitrogen consumption and of the fermentative aroma synthesis of the evolved and its ancestral strains were compared and coupled with a transcriptomic analysis approach to better understand the metabolic reshaping of Affinity™ ECA5. Results Nitrogen assimilation was different between the two strains, particularly amino acids transported by carriers regulated by nitrogen catabolite repression. We also observed differences in the kinetics of fermentative aroma production, especially in the bioconversion of higher alcohols into acetate esters. Finally, transcriptomic data showed that the enhanced bioconversion into acetate esters by the evolved strain was associated with the repression of genes involved in sterol biosynthesis rather than an enhanced expression of ATF1 and ATF2 (genes coding for the enzymes responsible for the synthesis of acetate esters from higher alcohols). Conclusions An integrated approach to yeast metabolism—combining transcriptomic analyses and online monitoring data—showed differences between the two strains at different levels. Differences in nitrogen source consumption were observed suggesting modifications of NCR in the evolved strain. Moreover, the evolved strain showed a different way of managing the lipid source, which notably affected the production of acetate esters, likely because of a greater availability of acetyl-CoA for the evolved strain. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0434-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphanie Rollero
- INRA, UMR1083, 34060, Montpellier, France. .,SupAgro, UMR1083, 34060, Montpellier, France. .,Universite Montpellier, UMR1083, 34060, Montpellier, France. .,Lallemand SAS, 31700, Blagnac, France.
| | - Jean-Roch Mouret
- INRA, UMR1083, 34060, Montpellier, France. .,SupAgro, UMR1083, 34060, Montpellier, France. .,Universite Montpellier, UMR1083, 34060, Montpellier, France.
| | - Isabelle Sanchez
- INRA, UMR1083, 34060, Montpellier, France. .,SupAgro, UMR1083, 34060, Montpellier, France. .,Universite Montpellier, UMR1083, 34060, Montpellier, France.
| | - Carole Camarasa
- INRA, UMR1083, 34060, Montpellier, France. .,SupAgro, UMR1083, 34060, Montpellier, France. .,Universite Montpellier, UMR1083, 34060, Montpellier, France.
| | | | - Jean-Marie Sablayrolles
- INRA, UMR1083, 34060, Montpellier, France. .,SupAgro, UMR1083, 34060, Montpellier, France. .,Universite Montpellier, UMR1083, 34060, Montpellier, France.
| | - Sylvie Dequin
- INRA, UMR1083, 34060, Montpellier, France. .,SupAgro, UMR1083, 34060, Montpellier, France. .,Universite Montpellier, UMR1083, 34060, Montpellier, France.
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17
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Marsit S, Sanchez I, Galeote V, Dequin S. Horizontally acquired oligopeptide transporters favour adaptation ofSaccharomyces cerevisiaewine yeast to oenological environment. Environ Microbiol 2016; 18:1148-61. [DOI: 10.1111/1462-2920.13117] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Souhir Marsit
- INRA; UMR1083 Sciences pour l'Oenology; Montpellier France
| | | | | | - Sylvie Dequin
- INRA; UMR1083 Sciences pour l'Oenology; Montpellier France
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18
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Tilloy V, Cadière A, Ehsani M, Dequin S. Reducing alcohol levels in wines through rational and evolutionary engineering of Saccharomyces cerevisiae. Int J Food Microbiol 2015. [DOI: 10.1016/j.ijfoodmicro.2015.06.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Tapsoba F, Legras JL, Savadogo A, Dequin S, Traore AS. Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages. Int J Food Microbiol 2015. [DOI: 10.1016/j.ijfoodmicro.2015.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras JL, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol Ecol 2015; 24:5412-27. [PMID: 26248006 DOI: 10.1111/mec.13341] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.
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Affiliation(s)
- Pedro Almeida
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Raquel Barbosa
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Yumi Imanishi
- Department of Applied Material and Life Science, College of Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama, 236-8501, Japan
| | - Kiminori Shimizu
- Medical Mycology Research Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8673, Japan
| | - Benedetta Turchetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali & Industrial Yeasts Collection DBVPG, Università degli Studi di Perugia, Borgo XX Giugno, 74 - 06121, Perugia, Italy
| | - Jean-Luc Legras
- Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France
| | - Marta Serra
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Sylvie Dequin
- Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France
| | - Arnaud Couloux
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France
| | - Julie Guy
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France
| | - Douda Bensasson
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Paula Gonçalves
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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Abstract
Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. This review summarizes current knowledge and recent advances on the diversity and evolutionary history of Saccharomyces cerevisiae wine yeasts, focusing on the domestication fingerprints identified in these strains.
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Affiliation(s)
- Souhir Marsit
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Sylvie Dequin
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
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22
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Franco-Duarte R, Bigey F, Carreto L, Mendes I, Dequin S, Santos MAS, Pais C, Schuller D. Intrastrain genomic and phenotypic variability of the commercialSaccharomyces cerevisiaestrain Zymaflore VL1 reveals microevolutionary adaptation to vineyard environments. FEMS Yeast Res 2015; 15:fov063. [DOI: 10.1093/femsyr/fov063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
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23
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Marsit S, Mena A, Bigey F, Sauvage FX, Couloux A, Guy J, Legras JL, Barrio E, Dequin S, Galeote V. Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts. Mol Biol Evol 2015; 32:1695-707. [PMID: 25750179 PMCID: PMC4476156 DOI: 10.1093/molbev/msv057] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although an increasing number of horizontal gene transfers have been reported in eukaryotes, experimental evidence for their adaptive value is lacking. Here, we report the recent transfer of a 158-kb genomic region between Torulaspora microellipsoides and Saccharomyces cerevisiae wine yeasts or closely related strains. This genomic region has undergone several rearrangements in S. cerevisiae strains, including gene loss and gene conversion between two tandemly duplicated FOT genes encoding oligopeptide transporters. We show that FOT genes confer a strong competitive advantage during grape must fermentation by increasing the number and diversity of oligopeptides that yeast can utilize as a source of nitrogen, thereby improving biomass formation, fermentation efficiency, and cell viability. Thus, the acquisition of FOT genes has favored yeast adaptation to the nitrogen-limited wine fermentation environment. This finding indicates that anthropic environments offer substantial ecological opportunity for evolutionary diversification through gene exchange between distant yeast species.
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Affiliation(s)
- Souhir Marsit
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Adriana Mena
- Department of Genetics, University of Valencia, and Department of Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - Frédéric Bigey
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - François-Xavier Sauvage
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Arnaud Couloux
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, Evry, France
| | - Julie Guy
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, Evry, France
| | - Jean-Luc Legras
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Eladio Barrio
- Department of Genetics, University of Valencia, and Department of Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - Sylvie Dequin
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Virginie Galeote
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
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Liu J, Martin-Yken H, Bigey F, Dequin S, François JM, Capp JP. Natural yeast promoter variants reveal epistasis in the generation of transcriptional-mediated noise and its potential benefit in stressful conditions. Genome Biol Evol 2015; 7:969-84. [PMID: 25762217 PMCID: PMC4419794 DOI: 10.1093/gbe/evv047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The increase in phenotypic variability through gene expression noise is proposed to be an evolutionary strategy in selective environments. Differences in promoter-mediated noise between Saccharomyces cerevisiae strains could have been selected for thanks to the benefit conferred by gene expression heterogeneity in the stressful conditions, for instance, those experienced by industrial strains. Here, we used a genome-wide approach to identify promoters conferring high noise levels in the industrial wine strain EC1118. Many promoters of genes related to environmental factors were identified, some of them containing genetic variations compared with their counterpart in the laboratory strain S288c. Each variant of eight promoters has been fused to yeast-Enhanced Green Fluorescent Protein and integrated in the genome of both strains. Some industrial variants conferred higher expression associated, as expected, with lower noise, but other variants either increased or decreased expression without modifying variability, so that they might exhibit different levels of transcriptional-mediated noise at equal mean. At different induction conditions giving similar expression for both variants of the CUP1 promoter, we indeed observed higher noise with the industrial variant. Nevertheless, this difference was only observed in the industrial strain, revealing epistasis in the generation of promoter-mediated noise. Moreover, the increased expression variability conferred by this natural yeast promoter variant provided a clear benefit in the face of an environmental stress. Thus, modulation of gene expression noise by a combination of promoter modifications and trans-influences might be a possible adaptation mechanism in yeast.
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Affiliation(s)
- Jian Liu
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Hélène Martin-Yken
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Frédéric Bigey
- INRA, UMR 1083 Sciences Pour l'Œnologie, Montpellier, France
| | - Sylvie Dequin
- INRA, UMR 1083 Sciences Pour l'Œnologie, Montpellier, France
| | - Jean-Marie François
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Jean-Pascal Capp
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
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Rollero S, Bloem A, Camarasa C, Sanchez I, Ortiz-Julien A, Sablayrolles JM, Dequin S, Mouret JR. Combined effects of nutrients and temperature on the production of fermentative aromas by Saccharomyces cerevisiae during wine fermentation. Appl Microbiol Biotechnol 2014; 99:2291-304. [PMID: 25412578 DOI: 10.1007/s00253-014-6210-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/27/2014] [Accepted: 11/01/2014] [Indexed: 11/30/2022]
Abstract
Volatile compounds produced by yeast during fermentation greatly influence the organoleptic qualities of wine. We developed a model to predict the combined effects of initial nitrogen and phytosterol content and fermentation temperature on the production of volatile compounds. We used a Box-Behnken design and response surface modeling to study the response of Lalvin EC1118® to these environmental conditions. Initial nitrogen content had the greatest influence on most compounds; however, there were differences in the value of fermentation parameters required for the maximal production of the various compounds. Fermentation parameters affected differently the production of isobutanol and isoamyl alcohol, although their synthesis involve the same enzymes and intermediate. We found differences in regulation of the synthesis of acetates of higher alcohols and ethyl esters, suggesting that fatty acid availability is the main factor influencing the synthesis of ethyl esters whereas the production of acetates depends on the activity of alcohol acetyltransferases. We also evaluated the effect of temperature on the total production of three esters by determining gas-liquid balances. Evaporation largely accounted for the effect of temperature on the accumulation of esters in liquid. Nonetheless, the metabolism of isoamyl acetate and ethyl octanoate was significantly affected by this parameter. We extended this study to other strains. Environmental parameters had a similar effect on aroma production in most strains. Nevertheless, the regulation of the synthesis of fermentative aromas was atypical in two strains: Lalvin K1M® and Affinity™ ECA5, which produces a high amount of aromatic compounds and was obtained by experimental evolution.
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Crépin L, Sanchez I, Nidelet T, Dequin S, Camarasa C. Efficient ammonium uptake and mobilization of vacuolar arginine by Saccharomyces cerevisiae wine strains during wine fermentation. Microb Cell Fact 2014; 13:109. [PMID: 25134990 PMCID: PMC4244049 DOI: 10.1186/s12934-014-0109-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Under N-limiting conditions, Saccharomyces cerevisiae strains display a substantial variability in their biomass yield from consumed nitrogen -in particular wine yeasts exhibit high growth abilities- that is correlated with their capacity to complete alcoholic fermentation, a trait of interest for fermented beverages industries. The aim of the present work was to assess the contribution of nitrogen availability to the strain-specific differences in the ability to efficiently use N-resource for growth and to identify the underlying mechanisms. We compared the profiles of assimilation of several nitrogen sources (mostly ammonium, glutamine, and arginine) for high and low biomass-producing strains in various conditions of nitrogen availability. We also analyzed the intracellular fate of nitrogen compounds. Results Strains clustered into two groups at initial nitrogen concentrations between 85 and 385 mg N.L−1: high biomass producers that included wine strains, were able to complete fermentation of 240 g.L−1 glucose and quickly consume nitrogen, in contrast to low biomass producers. The two classes of strains exhibited distinctive characteristics that contributed to their differential capacity to produce biomass. The contribution of each characteristic varied according to nitrogen availability. In high biomass producers, the high rate of ammonium uptake resulted in an important consumption of this preferred nitrogen source that promoted the growth of these yeasts when nitrogen was provided in excess. Both classes of yeast accumulated poor nitrogen sources, mostly arginine, in vacuoles during the first stages of growth. However, at end of the growth phase when nitrogen had become limiting, high biomass producers more efficiently used this vacuolar nitrogen fraction for protein synthesis and further biomass formation than low biomass producers. Conclusions Overall, we demonstrate that the efficient management of the nitrogen resource, including efficient ammonium uptake and efficient use of the amino acids stored in vacuoles during the late stages of growth, might lead to high biomass production by wine yeasts. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0109-0) contains supplementary material, which is available to authorized users.
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Mouret JR, Cadiere A, Aguera E, Rollero S, Ortiz-Julien A, Sablayrolles JM, Dequin S. Dynamics and quantitative analysis of the synthesis of fermentative aromas by an evolved wine strain of Saccharomyces cerevisiae. Yeast 2014; 32:257-69. [PMID: 24989462 DOI: 10.1002/yea.3028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/17/2014] [Accepted: 06/22/2014] [Indexed: 01/26/2023] Open
Abstract
We performed a dynamic and quantitative analysis of the synthesis of fermentative aromas by an aromatic wine yeast, ECA5, obtained by adaptive evolution. During fermentation at pilot scale on synthetic and natural musts, ECA5 produced volatile compounds (higher alcohols and their acetates, ethyl esters) at higher rates than the ancestral strain, with the exception of propanol. Marked differences in the chronology of synthesis of several compounds were observed between the two strains. Overproduction of phenyl ethanol occurred mainly during the growth phase for ECA5, consistent with its higher flux through the pentose phosphate pathway, which plays a key role in biosynthetic processes. The kinetics of production of isobutanol and isoamyl alcohol were differently affected by different media (synthetic or natural must) and, in particular, according to the nature of the sterols in the media (ergosterol or phytosterols). We also observed differences in the chronology of synthesis of ethyl acetate and isoamyl acetate or ethyl esters, suggesting that the regulation of the synthesis of these compounds in the evolved strain differs from that in the ancestral strain. This study shows that a dynamic analysis of volatile compounds, using high acquisition frequency online gas chromatography, can provide novel insights into the synthesis and regulation of aromas and is thus a potentially powerful tool for strain characterization.
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Mendes I, Franco-Duarte R, Umek L, Fonseca E, Drumonde-Neves J, Dequin S, Zupan B, Schuller D. Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLoS One 2013; 8:e66523. [PMID: 23874393 PMCID: PMC3713011 DOI: 10.1371/journal.pone.0066523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 05/06/2013] [Indexed: 11/29/2022] Open
Abstract
Saccharomyces cerevisiae strains from diverse natural habitats harbour a vast amount of phenotypic diversity, driven by interactions between yeast and the respective environment. In grape juice fermentations, strains are exposed to a wide array of biotic and abiotic stressors, which may lead to strain selection and generate naturally arising strain diversity. Certain phenotypes are of particular interest for the winemaking industry and could be identified by screening of large number of different strains. The objective of the present work was to use data mining approaches to identify those phenotypic tests that are most useful to predict a strain's potential for winemaking. We have constituted a S. cerevisiae collection comprising 172 strains of worldwide geographical origins or technological applications. Their phenotype was screened by considering 30 physiological traits that are important from an oenological point of view. Growth in the presence of potassium bisulphite, growth at 40°C, and resistance to ethanol were mostly contributing to strain variability, as shown by the principal component analysis. In the hierarchical clustering of phenotypic profiles the strains isolated from the same wines and vineyards were scattered throughout all clusters, whereas commercial winemaking strains tended to co-cluster. Mann-Whitney test revealed significant associations between phenotypic results and strain's technological application or origin. Naïve Bayesian classifier identified 3 of the 30 phenotypic tests of growth in iprodion (0.05 mg/mL), cycloheximide (0.1 µg/mL) and potassium bisulphite (150 mg/mL) that provided most information for the assignment of a strain to the group of commercial strains. The probability of a strain to be assigned to this group was 27% using the entire phenotypic profile and increased to 95%, when only results from the three tests were considered. Results show the usefulness of computational approaches to simplify strain selection procedures.
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Affiliation(s)
- Inês Mendes
- CBMA (Centre of Molecular and Environmental Biology)/Department of Biology/University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology)/Department of Biology/University of Minho, Braga, Portugal
| | - Lan Umek
- Faculty of Administration, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Elza Fonseca
- CBMA (Centre of Molecular and Environmental Biology)/Department of Biology/University of Minho, Braga, Portugal
| | - João Drumonde-Neves
- CBMA (Centre of Molecular and Environmental Biology)/Department of Biology/University of Minho, Braga, Portugal
- Research Center for Agricultural Technology – Department of Agricultural Sciences, University of Azores, Ponta Delgada, São Miguel, Azores, Portugal
| | - Sylvie Dequin
- INRA (Institut National de la Recherche), UMR1083, Sciences pour l'Enologie, Montpellier, France
| | - Blaz Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Dorit Schuller
- CBMA (Centre of Molecular and Environmental Biology)/Department of Biology/University of Minho, Braga, Portugal
- * E-mail:
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Maisonnave P, Sanchez I, Moine V, Dequin S, Galeote V. Stuck fermentation: Development of a synthetic stuck wine and study of a restart procedure. Int J Food Microbiol 2013; 163:239-47. [DOI: 10.1016/j.ijfoodmicro.2013.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/22/2013] [Accepted: 03/10/2013] [Indexed: 11/15/2022]
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Cadière A, Aguera E, Caillé S, Ortiz-Julien A, Dequin S. Pilot-scale evaluation the enological traits of a novel, aromatic wine yeast strain obtained by adaptive evolution. Food Microbiol 2012; 32:332-7. [PMID: 22986198 DOI: 10.1016/j.fm.2012.07.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 05/11/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
Abstract
In the competitive context of the wine market, there is a growing interest for novel wine yeast strains that have an overall good fermentation capacity and that contribute favorably to the organoleptic quality of wine. Using an adaptive evolution strategy based on growth on gluconate as sole carbon source, we recently obtained wine yeasts with improved characteristics in laboratory-scale fermentations. The characteristics included enhanced fermentation rate, decreased formation of acetate and greater production of fermentative aroma. We report an evaluation of the potential value of the evolved strain ECA5™ for winemaking, by comparing its fermentation performance and metabolite production to those of the parental strain in pilot-scale fermentation trials, with various grape cultivars and winemaking conditions. We show that the evolved strain has outstanding attributes relative to the parental wine yeast strain, and in particular the production of less volatile acidity and greater production of desirable volatile esters, important for the fruity/flowery character of wines. This study highlights the potential of evolutionary engineering for the generation of strains with a broad range of novel properties, appropriate for rapid application in the wine industry.
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Celton M, Sanchez I, Goelzer A, Fromion V, Camarasa C, Dequin S. A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. BMC Genomics 2012; 13:317. [PMID: 22805527 PMCID: PMC3431268 DOI: 10.1186/1471-2164-13-317] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 06/28/2012] [Indexed: 01/26/2023] Open
Abstract
Background Redox homeostasis is essential to sustain metabolism and growth. We recently reported that yeast cells meet a gradual increase in imposed NADPH demand by progressively increasing flux through the pentose phosphate (PP) and acetate pathways and by exchanging NADH for NADPH in the cytosol, via a transhydrogenase-like cycle. Here, we studied the mechanisms underlying this metabolic response, through a combination of gene expression profiling and analyses of extracellular and intracellular metabolites and 13 C-flux analysis. Results NADPH oxidation was increased by reducing acetoin to 2,3-butanediol in a strain overexpressing an engineered NADPH-dependent butanediol dehydrogenase cultured in the presence of acetoin. An increase in NADPH demand to 22 times the anabolic requirement for NADPH was accompanied by the intracellular accumulation of PP pathway metabolites consistent with an increase in flux through this pathway. Increases in NADPH demand were accompanied by the successive induction of several genes of the PP pathway. NADPH-consuming pathways, such as amino-acid biosynthesis, were upregulated as an indirect effect of the decrease in NADPH availability. Metabolomic analysis showed that the most extreme modification of NADPH demand resulted in an energetic problem. Our results also highlight the influence of redox status on aroma production. Conclusions Combined 13 C-flux, intracellular metabolite levels and microarrays analyses revealed that NADPH homeostasis, in response to a progressive increase in NADPH demand, was achieved by the regulation, at several levels, of the PP pathway. This pathway is principally under metabolic control, but regulation of the transcription of PP pathway genes can exert a stronger effect, by redirecting larger amounts of carbon to this pathway to satisfy the demand for NADPH. No coordinated response of genes involved in NADPH metabolism was observed, suggesting that yeast has no system for sensing NADPH/NADP+ ratio. Instead, the induction of NADPH-consuming amino-acid pathways in conditions of NADPH limitation may indirectly trigger the transcription of a set of PP pathway genes.
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Celton M, Goelzer A, Camarasa C, Fromion V, Dequin S. A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metab Eng 2012; 14:366-79. [PMID: 22709677 DOI: 10.1016/j.ymben.2012.03.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/22/2012] [Accepted: 03/16/2012] [Indexed: 11/28/2022]
Abstract
Controlling the amounts of redox cofactors to manipulate metabolic fluxes is emerging as a useful approach to optimizing byproduct yields in yeast biotechnological processes. Redox cofactors are extensively interconnected metabolites, so predicting metabolite patterns is challenging and requires in-depth knowledge of how the metabolic network responds to a redox perturbation. Our aim was to analyze comprehensively the metabolic consequences of increased cytosolic NADPH oxidation during yeast fermentation. Using a genetic device based on the overexpression of a modified 2,3-butanediol dehydrogenase catalyzing the NADPH-dependent reduction of acetoin into 2,3-butanediol, we increased the NADPH demand to between 8 and 40-fold the anabolic demand. We developed (i) a dedicated constraint-based model of yeast fermentation and (ii) a constraint-based modeling method based on the dynamical analysis of mass distribution to quantify the in vivo contribution of pathways producing NADPH to the maintenance of redox homeostasis. We report that yeast responds to NADPH oxidation through a gradual increase in the flux through the PP and acetate pathways, providing 80% and 20% of the NADPH demand, respectively. However, for the highest NADPH demand, the model reveals a saturation of the PP pathway and predicts an exchange between NADH and NADPH in the cytosol that may be mediated by the glycerol-DHA futile cycle. We also reveal the contribution of mitochondrial shuttles, resulting in a net production of NADH in the cytosol, to fine-tune the NADH/NAD(+) balance. This systems level study helps elucidate the physiological adaptation of yeast to NADPH perturbation. Our findings emphasize the robustness of yeast to alterations in NADPH metabolism and highlight the role of the glycerol-DHA cycle as a redox valve, providing additional NADPH from NADH under conditions of very high demand.
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Affiliation(s)
- Magalie Celton
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France.
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Damon C, Vallon L, Zimmermann S, Haider MZ, Galeote V, Dequin S, Luis P, Fraissinet-Tachet L, Marmeisse R. A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J 2011; 5:1871-80. [PMID: 21654847 PMCID: PMC3223307 DOI: 10.1038/ismej.2011.67] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 04/26/2011] [Accepted: 04/29/2011] [Indexed: 11/08/2022]
Abstract
Functional environmental genomics has the potential to identify novel biological functions that the systematic sequencing of microbial genomes or environmental DNA may fail to uncover. We targeted the functions expressed by soil eukaryotes using a metatranscriptomic approach based on the use of soil-extracted polyadenylated messenger RNA to construct environmental complementary DNA expression libraries. Functional complementation of a yeast mutant defective in di/tripeptide uptake identified a novel family of oligopeptide transporters expressed by fungi. This family has a patchy distribution in the Basidiomycota and Ascomycota and is present in the genome of a Saccharomyces cerevisiae wine strain. High throughput phenotyping of yeast mutants expressing two environmental transporters showed that they both displayed broad substrate specificity and could transport more than 60-80 dipeptides. When expressed in Xenopus oocytes one environmental transporter induced currents upon dipeptide addition, suggesting proton-coupled co-transport of dipeptides. This transporter was also able to transport specifically cysteine. Deletion of the two copies of the corresponding gene family members in the genome of the wine yeast strain severely reduced the number of dipeptides that it could assimilate. These results demonstrate that these genes are functional and can be used by fungi to efficiently scavenge the numerous, low concentration, oligopeptides continuously generated in soils by proteolysis.
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Affiliation(s)
- Coralie Damon
- Université de Lyon, Université Lyon 1, CNRS, UMR5557 d'Ecologie Microbienne, Villeurbanne, France
| | - Laurent Vallon
- Université de Lyon, Université Lyon 1, CNRS, UMR5557 d'Ecologie Microbienne, Villeurbanne, France
| | - Sabine Zimmermann
- CNRS, UMR5004 Biochimie et Physiologie Moléculaire des Plantes, Montpellier, France
| | - Muhammad Z Haider
- CNRS, UMR5004 Biochimie et Physiologie Moléculaire des Plantes, Montpellier, France
| | | | - Sylvie Dequin
- INRA, UMR1083 Sciences pour l'Oenologie, Montpellier, France
| | - Patricia Luis
- Université de Lyon, Université Lyon 1, CNRS, UMR5557 d'Ecologie Microbienne, Villeurbanne, France
| | | | - Roland Marmeisse
- Université de Lyon, Université Lyon 1, CNRS, UMR5557 d'Ecologie Microbienne, Villeurbanne, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ambroset C, Petit M, Brion C, Sanchez I, Delobel P, Guérin C, Chiapello H, Nicolas P, Bigey F, Dequin S, Blondin B. Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. G3 (Bethesda) 2011; 1:263-81. [PMID: 22384338 PMCID: PMC3276144 DOI: 10.1534/g3.111.000422] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/20/2011] [Indexed: 12/31/2022]
Abstract
The genetic basis of the phenotypic diversity of yeast is still poorly understood. Wine yeast strains have specific abilities to grow and ferment under stressful conditions compared with other strains, but the genetic basis underlying these traits is unknown. Understanding how sequence variation influences such phenotypes is a major challenge to address adaptation mechanisms of wine yeast. We aimed to identify the genetic basis of fermentation traits and gain insight into their relationships with variations in gene expression among yeast strains. We combined fermentation trait QTL mapping and expression profiling of fermenting cells in a segregating population from a cross between a wine yeast derivative and a laboratory strain. We report the identification of QTL for various fermentation traits (fermentation rates, nitrogen utilization, metabolites production) as well as expression QTL (eQTL). We found that many transcripts mapped to several eQTL hotspots and that two of them overlapped with QTL for fermentation traits. A QTL controlling the maximal fermentation rate and nitrogen utilization overlapping with an eQTL hotspot was dissected. We functionally demonstrated that an allele of the ABZ1 gene, localized in the hotspot and involved in p-aminobenzoate biosynthesis, controls the fermentation rate through modulation of nitrogen utilization. Our data suggest that the laboratory strain harbors a defective ABZ1 allele, which triggers strong metabolic and physiological alterations responsible for the generation of the eQTL hotspot. They also suggest that a number of gene expression differences result from some alleles that trigger major physiological disturbances.
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Affiliation(s)
- Chloé Ambroset
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Maud Petit
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Christian Brion
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Isabelle Sanchez
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Pierre Delobel
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Cyprien Guérin
- INRA, UR1077 Mathématique Informatique et Génome, F-78352 Jouy-en-Josas, France
| | - Hélène Chiapello
- INRA, UR1077 Mathématique Informatique et Génome, F-78352 Jouy-en-Josas, France
| | - Pierre Nicolas
- INRA, UR1077 Mathématique Informatique et Génome, F-78352 Jouy-en-Josas, France
| | - Frédéric Bigey
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Sylvie Dequin
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Bruno Blondin
- Montpellier SupAgro, UMR 1083 Sciences pour l'Oenologie, F-34060 Montpellier, and
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Galeote V, Bigey F, Beyne E, Novo M, Legras JL, Casaregola S, Dequin S. Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation. PLoS One 2011; 6:e17872. [PMID: 21423766 PMCID: PMC3053389 DOI: 10.1371/journal.pone.0017872] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/11/2011] [Indexed: 11/18/2022] Open
Abstract
We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.
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MESH Headings
- Base Sequence
- Blotting, Southern
- Chromosome Breakpoints
- Chromosomes, Fungal/genetics
- DNA, Circular/genetics
- DNA, Fungal/genetics
- Diploidy
- Electrophoresis, Gel, Pulsed-Field
- Evolution, Molecular
- Extrachromosomal Inheritance/genetics
- Gene Amplification/genetics
- Gene Dosage/genetics
- Genetic Variation
- Genome, Fungal/genetics
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis, Insertional/genetics
- Saccharomyces cerevisiae/genetics
- Wine/microbiology
- Zygosaccharomyces/genetics
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Affiliation(s)
| | - Frédéric Bigey
- INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France
| | | | - Maite Novo
- INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France
| | | | - Serge Casaregola
- CIRM-Levures, INRA, UMR1319 Micalis, AgroParisTech, Thiverval-Grignon, France
| | - Sylvie Dequin
- INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France
- * E-mail:
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38
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Galeote V, Novo M, Salema-Oom M, Brion C, Valério E, Gonçalves P, Dequin S. FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter. Microbiology (Reading) 2010; 156:3754-3761. [DOI: 10.1099/mic.0.041673-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transport of glucose and fructose in the yeast Saccharomyces cerevisiae plays a crucial role in controlling the rate of wine fermentation. In S. cerevisiae, hexoses are transported by facilitated diffusion via hexose carriers (Hxt), which prefer glucose to fructose. However, utilization of fructose by wine yeast is critically important at the end of fermentation. Here, we report the characterization of a fructose transporter recently identified by sequencing the genome of the commercial wine yeast strain EC1118 and found in many other wine yeasts. This transporter is designated Fsy1p because of its homology with the Saccharomyces pastorianus fructose/H+ symporter Fsy1p. A strain obtained by transformation of the V5 hxt1-7Δ mutant with FSY1 grew well on fructose, but to a much lesser extent on glucose as the sole carbon source. Sugar uptake and symport experiments showed that FSY1 encodes a proton-coupled symporter with high affinity for fructose (K
m 0.24±0.04 mM). Using real-time RT-PCR, we also investigated the expression pattern of FSY1 in EC1118 growing on various carbon sources. FSY1 was repressed by high concentrations of glucose or fructose and was highly expressed on ethanol as the sole carbon source. The characteristics of this transporter indicate that its acquisition could confer a significant advantage to S. cerevisiae during the wine fermentation process. This transporter is a good example of acquisition of a new function in yeast by horizontal gene transfer.
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Affiliation(s)
- Virginie Galeote
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France
| | - Maïté Novo
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France
| | - Madalena Salema-Oom
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Christian Brion
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France
| | - Elisabete Valério
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Paula Gonçalves
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Sylvie Dequin
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France
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Cadière A, Galeote V, Dequin S. The Saccharomyces cerevisiae zinc factor protein Stb5p is required as a basal regulator of the pentose phosphate pathway. FEMS Yeast Res 2010; 10:819-27. [PMID: 20738406 DOI: 10.1111/j.1567-1364.2010.00672.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In Saccharomyces cerevisiae, the oxidative stress-activated zinc cluster protein Stb5p activates genes involved in NADPH production and most genes of the pentose phosphate (PP) pathway. To gain insight into the role of Stb5p, we studied the behaviour of stb5 deletion mutants during aerobic and anaerobic growth on glucose. stb5 mutants were auxotrophic for methionine and pyrimidine nucleotides. The methionine auxotrophy phenotype was air dependent, suggesting an impaired aerobic NADPH status. Consistent with this, the acetate level was reduced and the α-ketoglutarate level was increased in the stb5 mutant. stb5 cells also required pyrimidine nucleotides for aerobic and anaerobic growth, consistent with a reduction in 5-phosphoribosyl-1-pyrophosphate production caused by a reduced flux through the PP pathway. Strains overexpressing STB5 could not grow on glucose. This growth defect was restored by overproduction of an NADPH-butanediol dehydrogenase, which reoxidizes the excess NADPH in the oxidative PP pathway. These findings suggest a major role for the transcription factor Stb5p in maintaining a basal flux through the PP pathway to meet the NADPH requirements for aerobic growth, and to provide the nucleotide precursors. Our data also demonstrate the potential use of a system based on overproduction of this transcription factor to increase flux through the PP pathway.
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Affiliation(s)
- Axelle Cadière
- INRA, UMR1083 Sciences pour l'nologie, Montpellier, France Lallemand SAS, Blagnac, France
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40
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Ehsani M, Fernández MR, Biosca JA, Dequin S. Reversal of coenzyme specificity of 2,3-butanediol dehydrogenase fromSaccharomyces cerevisaeand in vivo functional analysis. Biotechnol Bioeng 2009; 104:381-9. [DOI: 10.1002/bit.22391] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Heux S, Cadiere A, Dequin S. Glucose utilization of strains lacking PGI1 and expressing a transhydrogenase suggests differences in the pentose phosphate capacity among Saccharomyces cerevisiae strains. FEMS Yeast Res 2007; 8:217-24. [PMID: 18036177 DOI: 10.1111/j.1567-1364.2007.00330.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Saccharomyces cerevisiae strains lacking phosphoglucose isomerase (pgi1) cannot use the pentose phosphate (PP) pathway to oxidize glucose, which has been explained by the lack of mechanism for reoxidation of the NADPH surplus. Consistent with this, the defective growth on glucose of a ENYpgi1 strain can be partially restored by expressing the Escherichia coli transhydrogenase udhA. In this work it was found that growth of V5 (wine yeast-derived) and FY1679 (isogenic to S288C) pgi1 mutants is not rescued by expression of udhA. Moreover, the flux through the PP pathway of 11 S. cerevisiae strains from various origins was estimated, by calculating the ratio between the enzymatic activity of the G6PDH and HXK, placed at the glycolysis-PP pathway branch point. The results show that ENY.WA-1A exhibited the highest ratio (1.5-3-fold) and the highest G6PDH activity. Overexpression of ZWF1 encoding the G6PDH in V5pgi1udhA did not rescue growth on glucose, suggesting that steps downstream the G6PDH might limit the PP pathway in this strain. As a whole, these data highlight a great intraspecies diversity in the PP pathway capacity among S. cerevisiae strains and suggest that a low capacity may be the prime limiting factor in glucose oxidation through this pathway.
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Affiliation(s)
- Stéphanie Heux
- UMR1083 Sciences pour l'Oenologie, INRA, Montpellier, France
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42
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Schuller D, Pereira L, Alves H, Cambon B, Dequin S, Casal M. Genetic characterization of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments. Yeast 2007; 24:625-36. [PMID: 17534867 DOI: 10.1002/yea.1496] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One hundred isolates of the commercial Saccharomyces cerevisiae strain Zymaflore VL1 were recovered from spontaneous fermentations carried out with grapes collected from vineyards located close to wineries in the Vinho Verde wine region of Portugal. Isolates were differentiated based on their mitochondrial DNA restriction patterns and the evaluation of genetic polymorphisms was carried out by microsatellite analysis, interdelta sequence typing and pulsed-field gel electrophoresis (PFGE). Genetic patterns were compared to those obtained for 30 isolates of the original commercialized Zymaflore VL1 strain. Among the 100 recovered isolates we found a high percentage of chromosomal size variations, most evident for the smaller chromosomes III and VI. Complete loss of heterozygosity was observed for two isolates that had also lost chromosomal heteromorphism; their growth and fermentative capacity in a synthetic must medium was also affected. A considerably higher number of variant patterns for interdelta sequence amplifications was obtained for grape-derived strains compared to the original VL1 isolates. Our data show that the long-term presence of strain VL1 in natural grapevine environments induced genetic changes that can be detected using different fingerprinting methods. The observed genetic changes may reflect adaptive mechanisms to changed environmental conditions that yeast cells encounter during their existence in nature.
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Affiliation(s)
- Dorit Schuller
- Centro de Biologia (CB-UM), Departamento de Biologia, Universidade do Minho, Braga, Portugal.
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Camarasa C, Faucet V, Dequin S. Role in anaerobiosis of the isoenzymes for Saccharomyces cerevisiae fumarate reductase encoded by OSM1 and FRDS1. Yeast 2007; 24:391-401. [PMID: 17345583 DOI: 10.1002/yea.1467] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Saccharomyces cerevisiae possesses both a cytoplasmic and a mitochondrial fumarate reductase, encoded by FRDS1 and OSM1, respectively. While previous studies have shown that mutants lacking FRDS1 and OSM1 cannot grow under anaerobiosis (Arikawa et al., 1998), the physiological role of fumarate reductase (FR) remains poorly understood. Here, we report that an osm1 frds1 mutant is unable to grow anaerobically, even with glutamate as a sole nitrogen source, when succinate can be produced by the TCA oxidative branch. We also show that the growth of the mutant is not restored by adding acetoin, an alternative sink for NADH oxidation, but it is at least partly restored by the addition of oxygen or menadione, which can oxidize FADH(2) in addition to NADH. These data indicate that the growth inhibition of the mutant is due to an inability to reoxidize FAD, rather than an indirect effect on NADH or an inability to produce succinate per se. During anaerobic growth, FRDS1 expression was two to eight times higher than that of OSM1, and fumarate reductase activity was higher in the osm1 mutant than in the frds1 mutant. FRDS1 expression was induced by anaerobiosis, and this induction was abolished in a rox1 mutant. We conclude that the formation of succinate is strictly required for the reoxidation of FADH(2) during anaerobiosis, and that it is regulated through the control of FRDS1 expression when oxygen is limiting. Based on these data, we discuss the potential role of fumarate reductase in the regeneration of the FAD-prosthetic group of essential flavoproteins.
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Affiliation(s)
- Carole Camarasa
- UMR1083 Sciences pour l'Oenologie, INRA, 2 Place Viala, F-34060 Montpellier, France.
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44
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Galeote VA, Alexandre H, Bach B, Delobel P, Dequin S, Blondin B. Sfl1p acts as an activator of the HSP30 gene in Saccharomyces cerevisiae. Curr Genet 2007; 52:55-63. [PMID: 17594096 DOI: 10.1007/s00294-007-0136-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 05/22/2007] [Accepted: 05/23/2007] [Indexed: 10/23/2022]
Abstract
In the yeast, environmental challenges are known to induce both specific and general stress response. The HSP30 gene is strongly induced when cells are exposed to various stresses but this activation is largely independent of the major stress-related transcription factor Hsf1p and partly independent from Msn2p/Msn4p. In order to identify new potential regulators of HSP30 we isolated insertion mutants affected in HSP30 expression. We identified SFL1 gene encoding a protein previously shown to repress several genes. We show that Sfl1 is involved in the transcriptional activation of HSP30. Mutation of sfl1 reduces HSP30-lacZ expression under both basal and stress-induced conditions. We also show, using site-directed mutagenesis, that HSL motifs (Heat-Shock-Like putative DNA binding sequence) located in HSP30 promoter are required for HSP30 activation. Finally, a genome-wide analysis of the effects of SFL1 deletion on gene expression revealed that Sfl1p controls the expression of a small number of genes, with some being activated by the protein and others repressed. As a whole our data show that Sfl1p is a key component of the transcriptional control of the stress responsive gene HSP30. Moreover, we show that Sfl1, which was previously described as being a transcriptional repressor, can also act as an activator.
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45
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Valero E, Cambon B, Schuller D, Casal M, Dequin S. Biodiversity ofSaccharomycesyeast strains from grape berries of wine-producing areas using starter commercial yeasts. FEMS Yeast Res 2007; 7:317-29. [PMID: 17040482 DOI: 10.1111/j.1567-1364.2006.00161.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The use of commercial wine yeast strains as starters has grown extensively over the past two decades. In this study, a large-scale sampling plan was devised over a period of 3 years in three different vineyards in the south of France, to evaluate autochthonous wine yeast biodiversity in vineyards around wineries where active dry yeasts have been used as fermentation starters for more than 5 years. Seventy-two spontaneous fermentations were completed from a total of 106 grape samples, and 2160 colonies were isolated. Among these, 608 Saccharomyces strains were identified and 104 different chromosomal patterns found. The large majority of these (91) were found as unique patterns, indicating great biodiversity. There were differences in biodiversity according to the vineyard and year, showing that the biodiversity of Saccharomyces strains is influenced by climatic conditions and specific factors associated with the vineyards, such as age and size. Strains that were terroir yeast candidates were not found. The biodiversity of S. cerevisiae strains after harvest was similar to that in the early campaign; moreover, a temporal succession of S. cerevisiae strains is shown. This fact, together with the differences in biodiversity levels verifies that other factors were more important than commercial yeast utilization in the biodiversity of the vineyard.
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Affiliation(s)
- Eva Valero
- UMR Sciences pour l'Oenologie, Equipe Microbiologie, INRA, Montpellier, France
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46
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Heux S, Sablayrolles JM, Cachon R, Dequin S. Engineering a Saccharomyces cerevisiae wine yeast that exhibits reduced ethanol production during fermentation under controlled microoxygenation conditions. Appl Environ Microbiol 2006; 72:5822-8. [PMID: 16957200 PMCID: PMC1563617 DOI: 10.1128/aem.00750-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently showed that expressing an H(2)O-NADH oxidase in Saccharomyces cerevisiae drastically reduces the intracellular NADH concentration and substantially alters the distribution of metabolic fluxes in the cell. Although the engineered strain produces a reduced amount of ethanol, a high level of acetaldehyde accumulates early in the process (1 g/liter), impairing growth and fermentation performance. To overcome these undesirable effects, we carried out a comprehensive analysis of the impact of oxygen on the metabolic network of the same NADH oxidase-expressing strain. While reducing the oxygen transfer rate led to a gradual recovery of the growth and fermentation performance, its impact on the ethanol yield was negligible. In contrast, supplying oxygen only during the stationary phase resulted in a 7% reduction in the ethanol yield, but without affecting growth and fermentation. This approach thus represents an effective strategy for producing wine with reduced levels of alcohol. Importantly, our data also point to a significant role for NAD(+) reoxidation in controlling the glycolytic flux, indicating that engineered yeast strains expressing an NADH oxidase can be used as a powerful tool for gaining insight into redox metabolism in yeast.
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Affiliation(s)
- Stéphanie Heux
- UMR Sciences pour l'Oenologie, Microbiologie, INRA, 2 place Viala, F-34060 Montpellier Cedex 1, France
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Cambon B, Monteil V, Remize F, Camarasa C, Dequin S. Effects of GPD1 overexpression in Saccharomyces cerevisiae commercial wine yeast strains lacking ALD6 genes. Appl Environ Microbiol 2006; 72:4688-94. [PMID: 16820460 PMCID: PMC1489326 DOI: 10.1128/aem.02975-05] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The utilization of Saccharomyces cerevisiae strains overproducing glycerol and with a reduced ethanol yield is a potentially valuable strategy for producing wine with decreased ethanol content. However, glycerol overproduction is accompanied by acetate accumulation. In this study, we evaluated the effects of the overexpression of GPD1, coding for glycerol-3-phosphate dehydrogenase, in three commercial wine yeast strains in which the two copies of ALD6 encoding the NADP+-dependent Mg2+-activated cytosolic acetaldehyde dehydrogenase have been deleted. Under wine fermentation conditions, the engineered industrial strains exhibit fermentation performance and growth properties similar to those of the wild type. Acetate was produced at concentrations similar to that of the wild-type strains, whereas sugar was efficiently diverted to glycerol. The ethanol yield of the GPD1 ald6 industrial strains was 15 to 20% lower than that in the controls. However, these strains accumulated acetoin at considerable levels due to inefficient reduction to 2,3-butanediol. Due to the low taste and odor thresholds of acetoin and its negative sensorial impact on wine, novel engineering strategies will be required for a proper adjustment of the metabolites at the acetaldehyde branch point.
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Affiliation(s)
- Brigitte Cambon
- UMR Sciences pour l'Oenologie, Microbiologie, INRA, 2 Place Viala, F-34060 Montpellier Cedex 1, France
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Heux S, Cachon R, Dequin S. Cofactor engineering in Saccharomyces cerevisiae: Expression of a H2O-forming NADH oxidase and impact on redox metabolism. Metab Eng 2006; 8:303-14. [PMID: 16473032 DOI: 10.1016/j.ymben.2005.12.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 12/06/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
The pyridine nucleotides NAD(H) and NADP(H) play major roles in the formation of by-products. To analyse how Saccharomyces cerevisiae (S. cerevisiae) metabolism during growth on glucose might be altered when intracellular NADH pool is decreased, we expressed noxE encoding a water-forming NADH oxidase from Lactococcus lactis (L. lactis) in the S. cerevisiae strain V5. During batch fermentation under controlled microaeration conditions, expression of the NADH oxidase under the control of a yeast promoter lead to large decreases in the intracellular NADH concentration (five-fold) and NADH/NAD+ ratio (six-fold). This increased NADH consumption caused a large redistribution of metabolic fluxes. The ethanol, glycerol, succinate and hydroxyglutarate yields were significantly reduced as a result of the lower NADH availability, whereas the formation of more oxidized metabolites, acetaldehyde, acetate and acetoin was favoured. The biomass yield was low and consumption of glucose, at concentration above 10%, was impaired. The metabolic redistribution in cells expressing the NADH oxidase was a consequence of the maintenance of a redox balance and of the management of acetaldehyde formation, which accumulated at toxic levels early in the process.
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Affiliation(s)
- Stéphanie Heux
- UMR Sciences pour l'Oenologie, Microbiologie, INRA, 2 place Viala, F-34060 Montpellier Cedex 1, France
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Valero E, Schuller D, Cambon B, Casal M, Dequin S. Dissemination and survival of commercial wine yeast in the vineyard: A large-scale, three-years study. FEMS Yeast Res 2005; 5:959-69. [PMID: 15975857 DOI: 10.1016/j.femsyr.2005.04.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Revised: 04/05/2005] [Accepted: 04/19/2005] [Indexed: 11/20/2022] Open
Abstract
The use of commercial wine yeast strains as starters has been extensively generalised over the past two decades. In this study, a large-scale sampling plan was devised over a period of three years in six different vineyards to evaluate the dynamics and survival of industrial yeast strains in the vineyard. A total of 198 grape samples were collected at various distances from the wineries, before and after harvest, and yeast strains isolated after spontaneous fermentation were subsequently identified by molecular methods. Among 3780 yeast strains identified, 296 isolates had a genetic profile identical to that of commercial yeast strains. For a large majority (94%), these strains were recovered at very close proximity to the winery (10-200 m). Commercial strains were mostly found in the post-harvest samples, reflecting immediate dissemination. Analysis of population variations from year to year indicated that permanent implantation of commercial strains in the vineyard did not occur, but instead that these strains were subject to natural fluctuations of periodical appearance/disappearance like autochthonous strains. Our data show that dissemination of commercial yeast in the vineyard is restricted to short distances and limited periods of time and is largely favoured by the presence of water run-off.
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Affiliation(s)
- Eva Valero
- UMR Sciences pour l'Oenologie, Microbiologie, INRA, 34060 Montpellier Cedex 1, France
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50
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Schuller D, Alves H, Dequin S, Casal M. Ecological survey of Saccharomyces cerevisiae strains from vineyards in the Vinho Verde Region of Portugal. FEMS Microbiol Ecol 2005; 51:167-77. [PMID: 16329865 DOI: 10.1016/j.femsec.2004.08.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Revised: 08/06/2004] [Accepted: 08/11/2004] [Indexed: 10/26/2022] Open
Abstract
One thousand six hundred and twenty yeast isolates were obtained from 54 spontaneous fermentations performed from grapes collected in 18 sampling sites of three vineyards (Vinho Verde Wine Region in northwest Portugal) during the 2001-2003 harvest seasons. All isolates were analyzed by mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) and a pattern profile was verified for each isolate, resulting in a total of 297 different profiles, that all belonged to the species Saccharomyces cerevisiae. The strains corresponding to seventeen profiles showed a wider temporal and geographical distribution, being characterized by a generalized pattern of sporadic presence, absence and reappearance. One strain (ACP10) showed a more regional distribution with a perennial behavior. In different fermentations ACP10 was either dominant or not, showing that the final outcome of fermentation was dependent on the specific composition of the yeast community in the must. Few of the grape samples collected before harvest initiated a spontaneous fermentation, compared to the samples collected after harvest, in a time frame of about 2 weeks. The associated strains were also much more diversified: 267 patterns among 1260 isolates compared to 30 patterns among 360 isolates in the post- and pre-harvest samples, respectively. Fermenting yeast populations have never been characterized before in this region and the present work reports the presence of commercial yeast strains used by the wineries. The present study aims at the development of strategies for the preservation of biodiversity and genetic resources as a basis for further strain development.
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Affiliation(s)
- Dorit Schuller
- Departamento de Biologia, Centro de Biologia, Universidade do Minho, Braga, Portugal
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