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Lo Y, Bruxaux J, Rodríguez de la Vega RC, O'Donnell S, Snirc A, Coton M, Le Piver M, Le Prieur S, Roueyre D, Dupont J, Houbraken J, Debuchy R, Ropars J, Giraud T, Branca A. Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evol Appl 2023; 16:1637-1660. [PMID: 37752962 PMCID: PMC10519415 DOI: 10.1111/eva.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.
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Affiliation(s)
- Ying‐Chu Lo
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Jade Bruxaux
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | | | - Samuel O'Donnell
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Alodie Snirc
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Stéphanie Le Prieur
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS‐MNHN, Muséum National d'Histoire NaturelleParis Cedex 05France
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity InstituteUtrechtThe Netherlands
| | - Robert Debuchy
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Tatiana Giraud
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Antoine Branca
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- IDEEV – Laboratoire Evolution, Génomes Comportement, EcologieCNRS Université Paris Saclay UMR 9191, IRD UMR 247Gif‐sur‐YvetteFrance
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2
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Kessi-Pérez EI, Acuña E, Bastías C, Fundora L, Villalobos-Cid M, Romero A, Khaiwal S, De Chiara M, Liti G, Salinas F, Martínez C. Single nucleotide polymorphisms associated with wine fermentation and adaptation to nitrogen limitation in wild and domesticated yeast strains. Biol Res 2023; 56:43. [PMID: 37507753 PMCID: PMC10385942 DOI: 10.1186/s40659-023-00453-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
For more than 20 years, Saccharomyces cerevisiae has served as a model organism for genetic studies and molecular biology, as well as a platform for biotechnology (e.g., wine production). One of the important ecological niches of this yeast that has been extensively studied is wine fermentation, a complex microbiological process in which S. cerevisiae faces various stresses such as limited availability of nitrogen. Nitrogen deficiencies in grape juice impair fermentation rate and yeast biomass production, leading to sluggish or stuck fermentations, resulting in considerable economic losses for the wine industry. In the present work, we took advantage of the "1002 Yeast Genomes Project" population, the most complete catalogue of the genetic variation in the species and a powerful resource for genotype-phenotype correlations, to study the adaptation to nitrogen limitation in wild and domesticated yeast strains in the context of wine fermentation. We found that wild and domesticated yeast strains have different adaptations to nitrogen limitation, corroborating their different evolutionary trajectories. Using a combination of state-of-the-art bioinformatic (GWAS) and molecular biology (CRISPR-Cas9) methodologies, we validated that PNP1, RRT5 and PDR12 are implicated in wine fermentation, where RRT5 and PDR12 are also involved in yeast adaptation to nitrogen limitation. In addition, we validated SNPs in these genes leading to differences in fermentative capacities and adaptation to nitrogen limitation. Altogether, the mapped genetic variants have potential applications for the genetic improvement of industrial yeast strains.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- 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
| | - Eric Acuña
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Camila Bastías
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Leyanis Fundora
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Manuel Villalobos-Cid
- Departamento de Ingeniería Informática, Program for the Development of Sustainable Production Systems (PDSPS), Facultad de Ingeniería, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Andrés Romero
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sakshi Khaiwal
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Francisco Salinas
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - 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.
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3
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The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges. Comput Struct Biotechnol J 2022; 20:5698-5712. [PMID: 36320937 PMCID: PMC9596735 DOI: 10.1016/j.csbj.2022.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022] Open
Abstract
Protein phosphorylation is the most common and versatile post-translational modification occurring in eukaryotes. In yeast, protein phosphorylation is fundamental for maintaining cell growth and adapting to sudden changes in environmental conditions by regulating cellular processes and activating signal transduction pathways. Protein kinases catalyze the reversible addition of phosphate groups to target proteins, thereby regulating their activity. In Saccharomyces cerevisiae, kinases are classified into six major groups based on structural and functional similarities. The NPR/Hal family of kinases comprises nine fungal-specific kinases that, due to lack of similarity with the remaining kinases, were classified to the “Other” group. These kinases are primarily implicated in regulating fundamental cellular processes such as maintaining ion homeostasis and controlling nutrient transporters’ concentration at the plasma membrane. Despite their biological relevance, these kinases remain poorly characterized and explored. This review provides an overview of the information available regarding each of the kinases from the NPR/Hal family, including their known biological functions, mechanisms of regulation, and integration in signaling pathways in S. cerevisiae. Information gathered for non-Saccharomyces species of biotechnological or clinical relevance is also included.
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Schrevens S, Sanglard D. Hijacking Transposable Elements for Saturation Mutagenesis in Fungi. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:633876. [PMID: 37744130 PMCID: PMC10512250 DOI: 10.3389/ffunb.2021.633876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 09/26/2023]
Abstract
Transposable elements are present in almost all known genomes, these endogenous transposons have recently been referred to as the mobilome. They are now increasingly used in research in order to make extensive mutant libraries in different organisms. Fungi are an essential part of our lives on earth, they influence the availability of our food and they live inside our own bodies both as commensals and pathogenic organisms. Only few fungal species have been studied extensively, mainly due to the lack of appropriate molecular genetic tools. The use of transposon insertion libraries can however help to rapidly advance our knowledge of (conditional) essential genes, compensatory mutations and drug target identification in fungi. Here we give an overview of some recent developments in the use of different transposons for saturation mutagenesis in different fungi.
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Affiliation(s)
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
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Rogers CM, Lee CY, Parkins S, Buehler NJ, Wenzel S, Martínez-Márquez F, Takagi Y, Myong S, Bochman ML. The yeast Hrq1 helicase stimulates Pso2 translesion nuclease activity and thereby promotes DNA interstrand crosslink repair. J Biol Chem 2020; 295:8945-8957. [PMID: 32371399 PMCID: PMC7335788 DOI: 10.1074/jbc.ra120.013626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
DNA interstrand crosslink (ICL) repair requires a complex network of DNA damage response pathways. Removal of the ICL lesions is vital, as they are physical barriers to essential DNA processes that require the separation of duplex DNA, such as replication and transcription. The Fanconi anemia (FA) pathway is the principal mechanism for ICL repair in metazoans and is coupled to DNA replication. In Saccharomyces cerevisiae, a vestigial FA pathway is present, but ICLs are predominantly repaired by a pathway involving the Pso2 nuclease, which is hypothesized to use its exonuclease activity to digest through the lesion to provide access for translesion polymerases. However, Pso2 lacks translesion nuclease activity in vitro, and mechanistic details of this pathway are lacking, especially relative to FA. We recently identified the Hrq1 helicase, a homolog of the disease-linked enzyme RecQ-like helicase 4 (RECQL4), as a component of Pso2-mediated ICL repair. Here, using genetic, biochemical, and biophysical approaches, including single-molecule FRET (smFRET)- and gel-based nuclease assays, we show that Hrq1 stimulates the Pso2 nuclease through a mechanism that requires Hrq1 catalytic activity. Importantly, Hrq1 also stimulated Pso2 translesion nuclease activity through a site-specific ICL in vitro We noted that stimulation of Pso2 nuclease activity is specific to eukaryotic RecQ4 subfamily helicases, and genetic and biochemical data suggest that Hrq1 likely interacts with Pso2 through their N-terminal domains. These results advance our understanding of FA-independent ICL repair and establish a role for the RecQ4 helicases in the repair of these detrimental DNA lesions.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Samuel Parkins
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicholas J Buehler
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francisco Martínez-Márquez
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA.
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Valero E, Tronchoni J, Morales P, Gonzalez R. Autophagy is required for sulfur dioxide tolerance in Saccharomyces cerevisiae. Microb Biotechnol 2019; 13:599-604. [PMID: 31638329 PMCID: PMC7017813 DOI: 10.1111/1751-7915.13495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/18/2019] [Accepted: 10/01/2019] [Indexed: 01/17/2023] Open
Abstract
Sulfiting agents are among the most widely used preservatives in the food and beverages industries, including winemaking, and one of their main functions is inhibition of spoilage microorganisms. We have used a whole genome quantitative fitness analysis in order to improve our knowledge on yeast tolerance to sulfites. Apart from the contribution of sulfite efflux to tolerance, results point to vesicle‐mediated transport, autophagy and vacuolar activity as the main cellular functions required to survive sulfite challenges. The involvement of autophagic and vacuolar functions in sulfite tolerance was further confirmed by pairwise competition using a newly constructed atg2‐defective strain, as well as by showing induction of ATG8 expression by sulfite. Autophagy is required for the turnover of proteins and subcellular structures damaged by sulfite. In addition, the requirement for vacuolar functions might be related to its role in intracellular pH homeostasis. Finally, the involvement of the sulfite pump Ssu1 and the transcription factor Fzf1 in sulfite tolerance by Saccharomyces cerevisiae was confirmed; a result that validates the experimental approach used in this work. These findings have relevance for understanding sulfite toxicity and tolerance, as well as for the eventual design of strategies aiming to control yeast spoilage.
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Affiliation(s)
- Eva Valero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
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James TY, Michelotti LA, Glasco AD, Clemons RA, Powers RA, James ES, Simmons DR, Bai F, Ge S. Adaptation by Loss of Heterozygosity in Saccharomyces cerevisiae Clones Under Divergent Selection. Genetics 2019; 213:665-683. [PMID: 31371407 PMCID: PMC6781901 DOI: 10.1534/genetics.119.302411] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/29/2019] [Indexed: 01/14/2023] Open
Abstract
Loss of heterozygosity (LOH) is observed during vegetative growth and reproduction of diploid genotypes through mitotic crossovers, aneuploidy caused by nondisjunction, and gene conversion. We aimed to test the role that LOH plays during adaptation of two highly heterozygous Saccharomyces cerevisiae genotypes to multiple environments over a short time span in the laboratory. We hypothesized that adaptation would be observed through parallel LOH events across replicate populations. Using genome resequencing of 70 clones, we found that LOH was widespread with 5.2 LOH events per clone after ∼500 generations. The most common mode of LOH was gene conversion (51%) followed by crossing over consistent with either break-induced replication or double Holliday junction resolution. There was no evidence that LOH involved nondisjunction of whole chromosomes. We observed parallel LOH in both an environment-specific and environment-independent manner. LOH largely involved recombining existing variation between the parental genotypes, but also was observed after de novo, presumably beneficial, mutations occurred in the presence of canavanine, a toxic analog of arginine. One highly parallel LOH event involved the ENA salt efflux pump locus on chromosome IV, which showed repeated LOH to the allele from the European parent, an allele originally derived by introgression from S. paradoxus Using CRISPR-engineered LOH we showed that the fitness advantage provided by this single LOH event was 27%. Overall, we found extensive evidence that LOH could be adaptive and is likely to be a greater source of initial variation than de novo mutation for rapid evolution of diploid genotypes.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Alexander D Glasco
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Robert A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ellen S James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Fengyan Bai
- Institute of Microbiology, Chinese Academy of Sciences, State Key Laboratory of Mycology, Chaoyang District, Beijing 100101, China
| | - Shuhua Ge
- Technology Development and Transfer Center, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100029, China
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8
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Marullo P, Durrens P, Peltier E, Bernard M, Mansour C, Dubourdieu D. Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study. BMC Genomics 2019; 20:680. [PMID: 31462217 PMCID: PMC6714461 DOI: 10.1186/s12864-019-5959-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. Among them, high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes. RESULTS In this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genes VHS1 and OYE2 characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (> 240 g/L of sugar) carried out at high temperatures (> 28 °C). Phenotypes impacted were mostly related to the late stage of alcoholic fermentation during the stationary growth phase of yeast. CONCLUSIONS Our findings illustrate the complex genetic determinism of stuck fermentation and open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.
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Affiliation(s)
- Philippe Marullo
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
- Biolaffort, 33100 Bordeaux, France
| | - Pascal Durrens
- CNRS UMR 5800, University of Bordeaux, 33405 Talence, France
- Inria Bordeaux Sud-Ouest, Joint team Pleiade Inria/INRA/CNRS, 33405 Talence, France
| | - Emilien Peltier
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
- Biolaffort, 33100 Bordeaux, France
| | - Margaux Bernard
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
- Biolaffort, 33100 Bordeaux, France
| | | | - Denis Dubourdieu
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
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9
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Lang GI, Rice AM. Evolution unscathed: Darwin Devolvesargues on weak reasoning that unguided evolution is a destructive force, incapable of innovation. Evolution 2019. [DOI: 10.1111/evo.13710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gregory I. Lang
- Department of Biological SciencesLehigh University, Bethlehem Pennsylvania 18015
| | - Amber M. Rice
- Department of Biological SciencesLehigh University, Bethlehem Pennsylvania 18015
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10
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Seixas I, Barbosa C, Mendes-Faia A, Güldener U, Tenreiro R, Mendes-Ferreira A, Mira NP. Genome sequence of the non-conventional wine yeast Hanseniaspora guilliermondii UTAD222 unveils relevant traits of this species and of the Hanseniaspora genus in the context of wine fermentation. DNA Res 2019; 26:67-83. [PMID: 30462193 PMCID: PMC6379042 DOI: 10.1093/dnares/dsy039] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/16/2018] [Indexed: 12/21/2022] Open
Abstract
Hanseanispora species, including H. guilliermondii, are long known to be abundant in wine grape-musts and to play a critical role in vinification by modulating, among other aspects, the wine sensory profile. Despite this, the genetics and physiology of Hanseniaspora species remains poorly understood. The first genomic sequence of a H. guilliermondii strain (UTAD222) and the discussion of its potential significance are presented in this work. Metabolic reconstruction revealed that H. guilliermondii is not equipped with a functional gluconeogenesis or glyoxylate cycle, nor does it harbours key enzymes for glycerol or galactose catabolism or for biosynthesis of biotin and thiamine. Also, no fructose-specific transporter could also be predicted from the analysis of H. guilliermondii genome leaving open the mechanisms underlying the fructophilic character of this yeast. Comparative analysis involving H. guilliermondii, H. uvarum, H. opuntiae and S. cerevisiae revealed 14 H. guilliermondii-specific genes (including five viral proteins and one β-glucosidase). Furthermore, 870 proteins were only found within the Hanseniaspora proteomes including several β-glucosidases and decarboxylases required for catabolism of biogenic amines. The release of H. guilliermondii genomic sequence and the comparative genomics/proteomics analyses performed, is expected to accelerate research focused on Hanseniaspora species and to broaden their application in the wine industry and in other bio-industries in which they could be explored as cell factories.
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Affiliation(s)
- Isabel Seixas
- WM&B—Laboratory of Wine Microbiology & Biotechnology, Department of Biology and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisbon, Portugal
| | - Catarina Barbosa
- WM&B—Laboratory of Wine Microbiology & Biotechnology, Department of Biology and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisbon, Portugal
| | - Arlete Mendes-Faia
- WM&B—Laboratory of Wine Microbiology & Biotechnology, Department of Biology and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisbon, Portugal
| | - Ulrich Güldener
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus von-Imhof-Forum 3, Freising, Germany
| | - Rogério Tenreiro
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisbon, Portugal
| | - Ana Mendes-Ferreira
- WM&B—Laboratory of Wine Microbiology & Biotechnology, Department of Biology and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisbon, Portugal
- To whom correspondence should be addressed. Tel. +351218419181. (N.P.M.); Tel. +351 259 350 550. (A.M.-F.)
| | - Nuno P Mira
- Department of Bioengineering, iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon, Portugal
- To whom correspondence should be addressed. Tel. +351218419181. (N.P.M.); Tel. +351 259 350 550. (A.M.-F.)
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11
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Bleuven C, Dubé AK, Nguyen GQ, Gagnon‐Arsenault I, Martin H, Landry CR. A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology. Microbiologyopen 2018; 8:e00773. [PMID: 30569485 PMCID: PMC6612553 DOI: 10.1002/mbo3.773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 01/24/2023] Open
Abstract
While the use of barcoded collections of laboratory microorganisms and the development of barcode-based cell tracking are rapidly developing in genetics and genomics research, tools to track natural populations are still lacking. The yeast Saccharomyces paradoxus is an emergent microbial model in ecology and evolution. More than five allopatric and sympatric lineages have been identified and hundreds of strains have been isolated for this species, allowing to assess the impact of natural diversity on complex traits. We constructed a collection of 550 barcoded and traceable strains of S. paradoxus, including all three North American lineages SpB, SpC, and SpC*. These strains are diploid, many have their genome fully sequenced and are barcoded with a unique 20 bp sequence that allows their identification and quantification. This yeast collection is functional for competitive experiments in pools as the barcodes allow to measure each lineage's and individual strains' fitness in common conditions. We used this tool to demonstrate that in the tested conditions, there are extensive genotype-by-environment interactions for fitness among S. paradoxus strains, which reveals complex evolutionary potential in variable environments. This barcoded collection provides a valuable resource for ecological genomics studies that will allow gaining a better understanding of S. paradoxus evolution and fitness-related traits.
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Affiliation(s)
- Clara Bleuven
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada
| | - Alexandre K. Dubé
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Guillaume Q. Nguyen
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQuébecCanada
| | - Isabelle Gagnon‐Arsenault
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Hélène Martin
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Christian R. Landry
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
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12
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Hypoxia and iron requirements are the main drivers in transcriptional adaptation of Kluyveromyces lactis during wine aerobic fermentation. Int J Food Microbiol 2017; 246:40-49. [DOI: 10.1016/j.ijfoodmicro.2017.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 01/06/2023]
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13
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Eldarov MA, Kishkovskaia SA, Tanaschuk TN, Mardanov AV. Genomics and biochemistry of Saccharomyces cerevisiae wine yeast strains. BIOCHEMISTRY (MOSCOW) 2017; 81:1650-1668. [DOI: 10.1134/s0006297916130046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Salvadó Z, Ramos-Alonso L, Tronchoni J, Penacho V, García-Ríos E, Morales P, Gonzalez R, Guillamón JM. Genome-wide identification of genes involved in growth and fermentation activity at low temperature in Saccharomyces cerevisiae. Int J Food Microbiol 2016; 236:38-46. [PMID: 27442849 DOI: 10.1016/j.ijfoodmicro.2016.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/23/2016] [Accepted: 07/09/2016] [Indexed: 01/17/2023]
Abstract
Fermentation at low temperatures is one of the most popular current winemaking practices because of its reported positive impact on the aromatic profile of wines. However, low temperature is an additional hurdle to develop Saccharomyces cerevisiae wine yeasts, which are already stressed by high osmotic pressure, low pH and poor availability of nitrogen sources in grape must. Understanding the mechanisms of adaptation of S. cerevisiae to fermentation at low temperature would help to design strategies for process management, and to select and improve wine yeast strains specifically adapted to this winemaking practice. The problem has been addressed by several approaches in recent years, including transcriptomic and other high-throughput strategies. In this work we used a genome-wide screening of S. cerevisiae diploid mutant strain collections to identify genes that potentially contribute to adaptation to low temperature fermentation conditions. Candidate genes, impaired for growth at low temperatures (12°C and 18°C), but not at a permissive temperature (28°C), were deleted in an industrial homozygous genetic background, wine yeast strain FX10, in both heterozygosis and homozygosis. Some candidate genes were required for growth at low temperatures only in the laboratory yeast genetic background, but not in FX10 (namely the genes involved in aromatic amino acid biosynthesis). Other genes related to ribosome biosynthesis (SNU66 and PAP2) were required for low-temperature fermentation of synthetic must (SM) in the industrial genetic background. This result coincides with our previous findings about translation efficiency with the fitness of different wine yeast strains at low temperature.
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Affiliation(s)
- Zoel Salvadó
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain; Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Lucía Ramos-Alonso
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Vanessa Penacho
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Estéfani García-Ríos
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain.
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15
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Gonzalez R, Morales P, Tronchoni J, Cordero-Bueso G, Vaudano E, Quirós M, Novo M, Torres-Pérez R, Valero E. New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae. Front Microbiol 2016; 7:1545. [PMID: 27733850 PMCID: PMC5039201 DOI: 10.3389/fmicb.2016.01545] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/15/2016] [Indexed: 01/17/2023] Open
Abstract
Adaptation to changes in osmolarity is fundamental for the survival of living cells, and has implications in food and industrial biotechnology. It has been extensively studied in the yeast Saccharomyces cerevisiae, where the Hog1 stress activated protein kinase was discovered about 20 years ago. Hog1 is the core of the intracellular signaling pathway that governs the adaptive response to osmotic stress in this species. The main endpoint of this program is synthesis and intracellular retention of glycerol, as a compatible osmolyte. Despite many details of the signaling pathways and yeast responses to osmotic challenges have already been described, genome-wide approaches are contributing to refine our knowledge of yeast adaptation to hypertonic media. In this work, we used a quantitative fitness analysis approach in order to deepen our understanding of the interplay between yeast cells and the osmotic environment. Genetic requirements for proper growth under osmotic stress showed both common and specific features when hypertonic conditions were induced by either glucose or sorbitol. Tolerance to high-glucose content requires mitochondrial function, while defective protein targeting to peroxisome, GID-complex function (involved in negative regulation of gluconeogenesis), or chromatin dynamics, result in poor survival to sorbitol-induced osmotic stress. On the other side, the competitive disadvantage of yeast strains defective in the endomembrane system is relieved by hypertonic conditions. This finding points to the Golgi-endosome system as one of the main cell components negatively affected by hyperosmolarity. Most of the biological processes highlighted in this analysis had not been previously related to osmotic stress but are probably relevant in an ecological and evolutionary context.
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Affiliation(s)
- Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Gustavo Cordero-Bueso
- Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz Cádiz, Spain
| | - Enrico Vaudano
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-Centro di Ricerca per l'Enologia Asti, Italy
| | | | - Maite Novo
- Departamento de Bioquímica y Biotecnología, Universitat Rovira i Virgili Tarragona, Spain
| | - Rafael Torres-Pérez
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Eva Valero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide Sevilla, Spain
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16
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Curiel JA, Salvadó Z, Tronchoni J, Morales P, Rodrigues AJ, Quirós M, Gonzalez R. Identification of target genes to control acetate yield during aerobic fermentation with Saccharomyces cerevisiae. Microb Cell Fact 2016; 15:156. [PMID: 27627879 PMCID: PMC5024518 DOI: 10.1186/s12934-016-0555-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 01/01/2023] Open
Abstract
Background Aerobic fermentation of grape must, leading to respiro-fermentative metabolism of sugars, has been proposed as way of reducing alcohol content in wines. Two factors limit the usefulness of Saccharomyces cerevisiae for this application, the Crabtree effect, and excess volatile acidity under aerobic conditions. This work aimed to explore the impact on ethanol acetate production of different S. cerevisiae strains deleted for genes previously related with the Crabtree phenotype. Results Recombinant strains were constructed on a wine industrial genetic background, FX10. All yeast strains, including FX10, showed respiro-fermentative metabolism in natural grape must under aerobic conditions, as well as a concomitant reduction in ethanol yield. This indicates that the Crabtree effect is not a major constrain for reaching relevant respiration levels in grape must. Indeed, only minor differences in ethanol yield were observed between the original and some of the recombinant strains. In contrast, some yeast strains showed a relevant reduction of acetic acid production. This was identified as a positive feature for the feasibility of alcohol level reduction by respiration. Reduced acetic acid production was confirmed by a thorough analysis of these and some additional deletion strains (involving genes HXK2, PYK1, REG1, PDE2 and PDC1). Some recombinant yeasts showed altered production of glycerol and pyruvate derived metabolites. Conclusions REG1 and PDC1 deletion strains showed a strong reduction of acetic acid yield in aerobic fermentations. Since REG1 defective strains may be obtained by non-GMO approaches, these gene modifications show good promise to help reducing ethanol content in wines. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0555-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Antonio Curiel
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain
| | - Zoel Salvadó
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain
| | - Jordi Tronchoni
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain
| | - Pilar Morales
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain
| | - Alda Joao Rodrigues
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain
| | - Manuel Quirós
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain.,Evolva Biotech A/S, Copenhagen Ø, Denmark
| | - Ramón Gonzalez
- Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, Departamento de Enología, Instituto de Ciencias de la Vid y del Vino, Finca La Grajera, Ctra. De Burgos Km. 6, 26007, Logroño, La Rioja, Spain.
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17
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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] [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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18
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Chen Z, Zheng Z, Yi C, Wang F, Niu Y, Li H. Intracellular metabolic changes in Saccharomyces cerevisiae and promotion of ethanol tolerance during the bioethanol fermentation process. RSC Adv 2016. [DOI: 10.1039/c6ra19254h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
During the batch bioethanol fermentation process, although Saccharomyces cerevisiae cells are challenged by accumulated ethanol, our previous work showed that the ethanol tolerance of S. cerevisiae increased as fermentation time increased.
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Affiliation(s)
- Ze Chen
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Zhou Zheng
- Key Laboratory of Marine Bioactive Substance
- The First Institute of Oceanography
- State Oceanic Administration (SOA)
- Qingdao 266061
- China
| | - Chenfeng Yi
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Fenglian Wang
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Yuanpu Niu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Hao Li
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
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19
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Barbosa C, Mendes-Faia A, Lage P, Mira NP, Mendes-Ferreira A. Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii. Microb Cell Fact 2015; 14:124. [PMID: 26314747 PMCID: PMC4552253 DOI: 10.1186/s12934-015-0318-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/14/2015] [Indexed: 02/01/2023] Open
Abstract
Background The introduction of yeast starter cultures consisting in a blend of Saccharomyces cerevisiae and non-Saccharomyces yeast strains is emerging for production of wines with improved complexity of flavor. The rational use of this approach is, however, dependent on knowing the impact that co-inoculation has in the physiology of S. cerevisiae. In this work the transcriptome of S.cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniasporaguilliermondii, this being the first time that this relevant yeast–yeast interaction is examined at a genomic scale. Results Co-inoculation with H. guilliermondii reduced the overall genome-wide transcriptional response of S. cerevisiae throughout the fermentation, which was attributable to a lower fermentative activity of S. cerevisiae while in the mixed-fermentation. Approximately 350 genes S. cerevisiae genes were found to be differently expressed (FDR < 0.05) in response to the presence of H. guilliermondii in the fermentation medium. Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. The differences in the aromatic profiles of wines obtained in the single and in the mixed-fermentations correlated with the differential expression of S. cerevisiae genes encoding enzymes required for formation of aroma compounds. Conclusions By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. The availability of nutrients, in particular, of nitrogen and vitamins, stands out as a factor that may determine population dynamics, fermentative activity and by-product formation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0318-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catarina Barbosa
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal.
| | - Arlete Mendes-Faia
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI-Biosystems and Integrative Sciences Institute, Campo Grande, Lisbon, Portugal.
| | - Patrícia Lage
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal.
| | - Nuno P Mira
- iBB-Institute for Bioengineering and Biosciences, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal. .,Department of Bioengineering, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Ana Mendes-Ferreira
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI-Biosystems and Integrative Sciences Institute, Campo Grande, Lisbon, Portugal.
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20
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Yeast toxicogenomics: lessons from a eukaryotic cell model and cell factory. Curr Opin Biotechnol 2015; 33:183-91. [DOI: 10.1016/j.copbio.2015.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/16/2015] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
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21
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Mangado A, Tronchoni J, Morales P, Novo M, Quirós M, Gonzalez R. An impaired ubiquitin ligase complex favors initial growth of auxotrophic yeast strains in synthetic grape must. Appl Microbiol Biotechnol 2014; 99:1273-86. [PMID: 25620600 DOI: 10.1007/s00253-014-6126-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/28/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
Abstract
We used experimental evolution in order to identify genes involved in the adaptation of Saccharomyces cerevisiae to the early stages of alcoholic fermentation. Evolution experiments were run for about 200 generations, in continuous culture conditions emulating the initial stages of wine fermentation. We performed whole-genome sequencing of four adapted strains from three independent evolution experiments. Mutations identified in these strains pointed to the Rsp5p-Bul1/2p ubiquitin ligase complex as the preferred evolutionary target under these experimental conditions. Rsp5p is a multifunctional enzyme able to ubiquitinate target proteins participating in different cellular processes, while Bul1p is an Rsp5p substrate adaptor specifically involved in the ubiquitin-dependent internalization of Gap1p and other plasma membrane permeases. While a loss-of-function mutation in BUL1 seems to be enough to confer a selective advantage under these assay conditions, this did not seem to be the case for RSP5 mutated strains, which required additional mutations, probably compensating for the detrimental effect of altered Rsp5p activity on essential cellular functions. The power of this experimental approach is illustrated by the identification of four independent mutants, each with a limited number of SNPs, affected within the same pathway. However, in order to obtain information relevant for a specific biotechnological process, caution must be taken in the choice of the background yeast genotype (as shown in this case for auxotrophies). In addition, the use of very stable continuous fermentation conditions might lead to the selection of a rather limited number of adaptive responses that would mask other possible targets for genetic improvement.
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Affiliation(s)
- Ana Mangado
- Instituto de Ciencias de la Vid y del Vino, ICVV, (CSIC-Universidad de La Rioja-Gobierno de La Rioja), Madre de Dios 51, 26006, Logroño, La Rioja, Spain
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22
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Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome. PLoS One 2014; 9:e108089. [PMID: 25272156 PMCID: PMC4182726 DOI: 10.1371/journal.pone.0108089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/11/2014] [Indexed: 02/03/2023] Open
Abstract
Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.
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