1
|
Albillos‐Arenal S, Minebois R, Querol A, Barrio E. Understanding the role of GRE3 in the erythritol biosynthesis pathway in Saccharomyces uvarum and its implication in osmoregulation and redox homeostasis. Microb Biotechnol 2023; 16:1858-1871. [PMID: 37449952 PMCID: PMC10443344 DOI: 10.1111/1751-7915.14313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/10/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Erythritol is produced in yeasts via the reduction of erythrose into erythritol by erythrose reductases (ERs). However, the genes codifying for the ERs involved in this reaction have not been described in any Saccharomyces species yet. In our laboratory, we recently showed that, during alcoholic fermentation, erythritol is differentially produced by Saccharomyces cerevisiae and S. uvarum species, the latter being the largest producer. In this study, by using BLAST analysis and phylogenetic approaches the genes GRE3, GCY1, YPR1, ARA1 and YJR096W were identified as putative ERs in Saccharomyces cerevisiae Then, these genes were knocked out in our S. uvarum strain (BMV58) with higher erythritol biosynthesis compared to control S. cerevisiae wine strain, to evaluate their impact on erythritol synthesis and global metabolism. Among the mutants, the single deletion of GRE3 markedly impacts erythritol production, although ΔYPR1ΔGCY1ΔGRE3 was the combination that most decreased erythritol synthesis. Consistent with the increased production of fermentative by-products involved in redox balance in the Saccharomyces uvarum strain BMV58, erythritol synthesis increases at higher sugar concentrations, hinting it might be a response to osmotic stress. However, the expression of GRE3 in the S. uvarum strain was found to peak just before the start of the stationary phase, being consistent with the observation that erythritol increases at the start of the stationary phase, when there is low sugar in the medium and nitrogen sources are depleted. This suggests that GRE3 plays its primary function to help the yeast cells to maintain the redox balance during the last phases of fermentation.
Collapse
Affiliation(s)
| | - Romain Minebois
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA‐CSICPaternaSpain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA‐CSICPaternaSpain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA‐CSICPaternaSpain
- Departament de GenèticaUniversitat de ValènciaValènciaSpain
| |
Collapse
|
2
|
Barrio E, Hervás G, Gindri M, Friggens NC, Toral PG, Frutos P. Relationship between feed efficiency and resilience in dairy ewes subjected to acute underfeeding. J Dairy Sci 2023; 106:6028-6040. [PMID: 37474371 DOI: 10.3168/jds.2022-23174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/06/2023] [Indexed: 07/22/2023]
Abstract
Selection of dairy sheep based on production levels has caused a loss of rusticity, which might compromise their future resilience to nutritional challenges. Although refocusing breeding programs toward improved feed efficiency (FE) is expected, more-efficient ewes also seem to be more productive. As a first step to examine the relationship between FE and resilience in dairy sheep, in this study we explored the variation in the response to and the recovery from an acute nutritional challenge in high-yielding Assaf ewes phenotypically divergent for FE. First, feed intake, milk yield and composition, and body weight changes were recorded individually over a 3-wk period in a total of 40 sheep fed a total mixed ration (TMR) ad libitum. Data were used to calculate their FE index (FEI, defined as the difference between the actual and predicted intake estimated through net energy requirements for maintenance, production, and weight change). The highest and lowest FE ewes (H-FE and L-FE groups, respectively; 10 animals/group) were selected and then subjected to the nutritional challenge (i.e., withdrawing the TMR and limiting their diet only to the consumption of straw for 3 d). Afterward, sheep were fed again the TMR ad libitum. Temporal patterns of variation in performance traits, and ruminal fermentation and blood parameters were examined. A good consistency between FEI, residual feed intake, and feed conversion ratio was observed. Results supported that H-FE were more productive than L-FE sheep at similar intake level. Average time trends of milk yield generated by a piecewise model suggest that temporal patterns of variation in this trait would be related to prechallenge production level (i.e., H-FE presented quicker response and recovery than L-FE). Considering all studied traits, the overall response to and recovery from underfeeding was apparently similar or even better in H-FE than in L-FE. This would refute the initial hypothesis of a poorer resilience of more-efficient sheep to an acute underfeeding. However, the question remains whether a longer term feed restriction might impair the ability of H-FE ewes to maintain or revert to a high-production status, which would require further research.
Collapse
Affiliation(s)
- E Barrio
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - G Hervás
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain.
| | - M Gindri
- UMR 0791 Modélisation Systémique Appliquée aux Ruminants, INRAE, AgroParisTech, Université Paris-Saclay, 75005 Paris, France
| | - N C Friggens
- UMR 0791 Modélisation Systémique Appliquée aux Ruminants, INRAE, AgroParisTech, Université Paris-Saclay, 75005 Paris, France
| | - P G Toral
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - P Frutos
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| |
Collapse
|
3
|
Henriques D, Minebois R, dos Santos D, Barrio E, Querol A, Balsa-Canto E. A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii. Microbiol Spectr 2023; 11:e0351922. [PMID: 37227304 PMCID: PMC10269563 DOI: 10.1128/spectrum.03519-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
Saccharomyces kudriavzevii is a cold-tolerant species identified as a good alternative for industrial winemaking. Although S. kudriavzevii has never been found in winemaking, its co-occurrence with Saccharomyces cerevisiae in Mediterranean oaks is well documented. This sympatric association is believed to be possible due to the different growth temperatures of the two yeast species. However, the mechanisms behind the cold tolerance of S. kudriavzevii are not well understood. In this work, we propose the use of a dynamic genome-scale model to compare the metabolic routes used by S. kudriavzevii at two temperatures, 25°C and 12°C, to decipher pathways relevant to cold tolerance. The model successfully recovered the dynamics of biomass and external metabolites and allowed us to link the observed phenotype with exact intracellular pathways. The model predicted fluxes that are consistent with previous findings, but it also led to novel results which we further confirmed with intracellular metabolomics and transcriptomic data. The proposed model (along with the corresponding code) provides a comprehensive picture of the mechanisms of cold tolerance that occur within S. kudriavzevii. The proposed strategy offers a systematic approach to explore microbial diversity from extracellular fermentation data at low temperatures. IMPORTANCE Nonconventional yeasts promise to provide new metabolic pathways for producing industrially relevant compounds and tolerating specific stressors such as cold temperatures. The mechanisms behind the cold tolerance of S. kudriavzevii or its sympatric relationship with S. cerevisiae in Mediterranean oaks are not well understood. This study proposes a dynamic genome-scale model to investigate metabolic pathways relevant to cold tolerance. The predictions of the model would indicate the ability of S. kudriavzevii to produce assimilable nitrogen sources from extracellular proteins present in its natural niche. These predictions were further confirmed with metabolomics and transcriptomic data. This finding suggests that not only the different growth temperature preferences but also this proteolytic activity may contribute to the sympatric association with S. cerevisiae. Further exploration of these natural adaptations could lead to novel engineering targets for the biotechnological industry.
Collapse
Affiliation(s)
- David Henriques
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
| | - Romain Minebois
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | | | - Eladio Barrio
- Genomics Department, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | - Eva Balsa-Canto
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
| |
Collapse
|
4
|
Tapia SM, Macías LG, Pérez-Torrado R, Daroqui N, Manzanares P, Querol A, Barrio E. A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event. BMC Biol 2023; 21:102. [PMID: 37158891 PMCID: PMC10169451 DOI: 10.1186/s12915-023-01566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/16/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes. RESULTS Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces. CONCLUSIONS The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.
Collapse
Affiliation(s)
- Sebastián M Tapia
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Laura G Macías
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | | | - Noemi Daroqui
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Paloma Manzanares
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain.
- Departament de Genètica, Universitat de València, Valencia, Spain.
| |
Collapse
|
5
|
Contreras-Ruiz A, Alonso-del-Real J, Barrio E, Querol A. Saccharomyces cerevisiae wine strains show a wide range of competitive abilities and differential nutrient uptake behavior in co-culture with S. kudriavzevii. Food Microbiol 2023. [DOI: 10.1016/j.fm.2023.104276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
6
|
Tapia SM, Pérez‐Torrado R, Adam AC, Macías LG, Barrio E, Querol A. Adaptive evolution in the Saccharomyces kudriavzevii Aro4p promoted a reduced production of higher alcohols. Microb Biotechnol 2022; 15:2958-2969. [PMID: 36307988 PMCID: PMC9733642 DOI: 10.1111/1751-7915.14154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/30/2022] Open
Abstract
The use of unconventional yeast species in human-driven fermentations has attracted a lot of attention in the last few years. This tool allows the alcoholic beverage industries to solve problems related to climate change or the consumer demand for newer high-quality products. In this sense, one of the most attractive species is Saccharomyces kudriavzevii, which shows interesting fermentative traits such as the increased and diverse aroma compound production in wines. Specifically, it has been observed that different isolates of this species can produce higher amounts of higher alcohols such as phenylethanol compared with Saccharomyces cerevisiae. In this work, we have shed light on this feature relating it to the S. kudriavzevii aromatic amino acid anabolic pathway in which the enzyme Aro4p plays an essential role. Unexpectedly, we observed that the presence of the S. kudriavzevii ARO4 variant reduces phenylethanol production compared with the S. cerevisiae ARO4 allele. Our experiments suggest that this can be explained by increased feedback inhibition, which might be a consequence of the changes detected in the Aro4p amino end such as L26 Q24 that have been under positive selection in the S. kudriavzevii specie.
Collapse
Affiliation(s)
- Sebastián M. Tapia
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| | - Roberto Pérez‐Torrado
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| | - Ana Cristina Adam
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| | - Laura G. Macías
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain,Departament de GenèticaUniversitat de ValènciaValenciaSpain
| | - Eladio Barrio
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain,Departament de GenèticaUniversitat de ValènciaValenciaSpain
| | - Amparo Querol
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| |
Collapse
|
7
|
Tapia SM, Pérez-Torrado R, Adam AC, Macías LG, Barrio E, Querol A. Functional divergence in the proteins encoded by ARO80 from S. uvarum, S. kudriavzevii and S. cerevisiae explain differences in the aroma production during wine fermentation. Microb Biotechnol 2022; 15:2281-2291. [PMID: 35536034 PMCID: PMC9328738 DOI: 10.1111/1751-7915.14071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 11/27/2022] Open
Abstract
Phenylethanol (PE) and phenylethyl acetate (PEA) are commonly desired compounds in wine because of their rose‐like aroma. The yeast S. cerevisiae produces the PE either through de novo biosynthesis by shikimate pathway followed by the Ehrlich pathway or the direct phenylalanine catabolism via Ehrlich pathway, and then converted into PEA. Previous work demonstrated that, compared to S. cerevisiae, other Saccharomyces species, such as S. kudriavzevii and S. uvarum, produce higher concentrations of PE and PEA from the precursor phenylalanine, which indicates differential activities of the biosynthetic‐involved enzymes. A previous in‐silico analysis suggested that the transcriptional activator Aro80p is one of the best candidates to explain these differences. An improved functional analysis identified significant radical amino acid changes in the S. uvarum and S. kudriavzevii Aro80p that could impact the expression of the catabolic genes ARO9 and ARO10, and hence, the production of PE from phenylalanine. Indeed, wine S. cerevisiae strains carrying the S. uvarum and S. kudriavzevii ARO80 alleles increased the production of both compounds in the presence of phenylalanine by increasing the expression of ARO9 and ARO10. This study provides novel insights of the unidentified Aro80p regulatory region and the potential usage of alternatives ARO80 alleles to enhance the PE and PEA concentration in wine.
Collapse
Affiliation(s)
- Sebastián M Tapia
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Ana Cristina Adam
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Laura G Macías
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| |
Collapse
|
8
|
Macías LG, Flores MG, Adam AC, Rodríguez ME, Querol A, Barrio E, Lopes CA, Pérez-Torrado R. Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations. PLoS Genet 2021; 17:e1009872. [PMID: 34762651 PMCID: PMC8631656 DOI: 10.1371/journal.pgen.1009872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/05/2021] [Revised: 11/30/2021] [Accepted: 10/11/2021] [Indexed: 01/01/2023] Open
Abstract
Different species can find convergent solutions to adapt their genome to the same evolutionary constraints, although functional convergence promoted by chromosomal rearrangements in different species has not previously been found. In this work, we discovered that two domesticated yeast species, Saccharomyces cerevisiae, and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentation environments. We found two new heterologous chromosomal translocations in fermentative strains of S. uvarum at the SSU1 locus, involved in sulfite resistance, an antimicrobial additive widely used in food production. These are convergent events that share similarities with other SSU1 locus chromosomal translocations previously described in domesticated S. cerevisiae strains. In S. uvarum, the newly described VIIXVI and XIXVI chromosomal translocations generate an overexpression of the SSU1 gene and confer increased sulfite resistance. This study highlights the relevance of chromosomal rearrangements to promote the adaptation of yeast to anthropic environments. It is known that genetically distant species can arrive to similar evolutionary solutions during the adaptation to a specific environment, a phenomena known as convergent adaptation, and this frequently occurs after point mutations, gene duplications, or species hybridizations. In this work, we discovered a new example of convergent evolution in the adaptation of two wine fermentation yeast species to the presence of sulfite, an antimicrobial additive widely used in food production. We observed that two species, Saccharomyces cerevisiae and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentative environments. We describe new chromosomal translocations in S. uvarum strains that generate an overexpression of the SSU1 gene and confer increased sulfite resistance, a similar event that was already described in S. cerevisiae. Overall, this study describes a new case of convergent evolution in which the chromosomal rearrangements have a significant role in the adaptation of yeast to an environment created by humans to produce food.
Collapse
Affiliation(s)
- Laura G. Macías
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Melisa González Flores
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina–Universidad Nacional del Comahue), Neuquén, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Cinco Saltos, Río Negro, Argentina
| | - Ana Cristina Adam
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - María E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina–Universidad Nacional del Comahue), Neuquén, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Cipolletti, Río Negro, Argentina
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Christian Ariel Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina–Universidad Nacional del Comahue), Neuquén, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Cinco Saltos, Río Negro, Argentina
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- * E-mail:
| |
Collapse
|
9
|
Lairón-Peris M, Castiglioni GL, Routledge SJ, Alonso-Del-Real J, Linney JA, Pitt AR, Melcr J, Goddard AD, Barrio E, Querol A. Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid. Microb Genom 2021; 7. [PMID: 34448691 PMCID: PMC8549368 DOI: 10.1099/mgen.0.000628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
During industrial processes, yeasts are exposed to harsh conditions, which eventually lead to adaptation of the strains. In the laboratory, it is possible to use experimental evolution to link the evolutionary biology response to these adaptation pressures for the industrial improvement of a specific yeast strain. In this work, we aimed to study the adaptation of a wine industrial yeast in stress conditions of the high ethanol concentrations present in stopped fermentations and secondary fermentations in the processes of champagne production. We used a commercial Saccharomyces cerevisiae × S. uvarum hybrid and assessed its adaptation in a modified synthetic must (M-SM) containing high ethanol, which also contained metabisulfite, a preservative that is used during wine fermentation as it converts to sulfite. After the adaptation process under these selected stressful environmental conditions, the tolerance of the adapted strain (H14A7-etoh) to sulfite and ethanol was investigated, revealing that the adapted hybrid is more resistant to sulfite compared to the original H14A7 strain, whereas ethanol tolerance improvement was slight. However, a trade-off in the adapted hybrid was found, as it had a lower capacity to ferment glucose and fructose in comparison with H14A7. Hybrid genomes are almost always unstable, and different signals of adaptation on H14A7-etoh genome were detected. Each subgenome present in the adapted strain had adapted differently. Chromosome aneuploidies were present in S. cerevisiae chromosome III and in S. uvarum chromosome VII–XVI, which had been duplicated. Moreover, S. uvarum chromosome I was not present in H14A7-etoh and a loss of heterozygosity (LOH) event arose on S. cerevisiae chromosome I. RNA-sequencing analysis showed differential gene expression between H14A7-etoh and H14A7, which can be easily correlated with the signals of adaptation that were found on the H14A7-etoh genome. Finally, we report alterations in the lipid composition of the membrane, consistent with conserved tolerance mechanisms.
Collapse
Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Gabriel L Castiglioni
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Sarah J Routledge
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - John A Linney
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Andrew R Pitt
- College of Health and Life Sciences, Aston University, Birmingham, UK.,Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, UK
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands
| | - Alan D Goddard
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| |
Collapse
|
10
|
Lairón-Peris M, Routledge SJ, Linney JA, Alonso-del-Real J, Spickett CM, Pitt AR, Guillamón JM, Barrio E, Goddard AD, Querol A. Lipid Composition Analysis Reveals Mechanisms of Ethanol Tolerance in the Model Yeast Saccharomyces cerevisiae. Appl Environ Microbiol 2021; 87:e0044021. [PMID: 33771787 PMCID: PMC8174666 DOI: 10.1128/aem.00440-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 12/30/2022] Open
Abstract
Saccharomyces cerevisiae is an important unicellular yeast species within the biotechnological and the food and beverage industries. A significant application of this species is the production of ethanol, where concentrations are limited by cellular toxicity, often at the level of the cell membrane. Here, we characterize 61 S. cerevisiae strains for ethanol tolerance and further analyze five representatives with various ethanol tolerances. The most tolerant strain, AJ4, was dominant in coculture at 0 and 10% ethanol. Unexpectedly, although it does not have the highest noninhibitory concentration or MIC, MY29 was the dominant strain in coculture at 6% ethanol, which may be linked to differences in its basal lipidome. Although relatively few lipidomic differences were observed between strains, a significantly higher phosphatidylethanolamine concentration was observed in the least tolerant strain, MY26, at 0 and 6% ethanol compared to the other strains that became more similar at 10%, indicating potential involvement of this lipid with ethanol sensitivity. Our findings reveal that AJ4 is best able to adapt its membrane to become more fluid in the presence of ethanol and that lipid extracts from AJ4 also form the most permeable membranes. Furthermore, MY26 is least able to modulate fluidity in response to ethanol, and membranes formed from extracted lipids are least leaky at physiological ethanol concentrations. Overall, these results reveal a potential mechanism of ethanol tolerance and suggest a limited set of membrane compositions that diverse yeast species use to achieve this. IMPORTANCE Many microbial processes are not implemented at the industrial level because the product yield is poorer and more expensive than can be achieved by chemical synthesis. It is well established that microbes show stress responses during bioprocessing, and one reason for poor product output from cell factories is production conditions that are ultimately toxic to the cells. During fermentative processes, yeast cells encounter culture media with a high sugar content, which is later transformed into high ethanol concentrations. Thus, ethanol toxicity is one of the major stresses in traditional and more recent biotechnological processes. We have performed a multilayer phenotypic and lipidomic characterization of a large number of industrial and environmental strains of Saccharomyces to identify key resistant and nonresistant isolates for future applications.
Collapse
Affiliation(s)
- M. Lairón-Peris
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - S. J. Routledge
- College of Health and Life Sciences, Aston University, Birmingham, United Kingdom
| | - J. A. Linney
- College of Health and Life Sciences, Aston University, Birmingham, United Kingdom
| | - J. Alonso-del-Real
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - C. M. Spickett
- College of Health and Life Sciences, Aston University, Birmingham, United Kingdom
| | - A. R. Pitt
- College of Health and Life Sciences, Aston University, Birmingham, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - J. M. Guillamón
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - E. Barrio
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
- Genetics Department, University of Valencia, Valencia, Spain
| | - A. D. Goddard
- College of Health and Life Sciences, Aston University, Birmingham, United Kingdom
| | - A. Querol
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| |
Collapse
|
11
|
Minebois R, Lairón-Peris M, Barrio E, Pérez-Torrado R, Querol A. Metabolic differences between a wild and a wine strain of Saccharomyces cerevisiae during fermentation unveiled by multi-omic analysis. Environ Microbiol 2021; 23:3059-3076. [PMID: 33848053 DOI: 10.1111/1462-2920.15523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/30/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Saccharomyces cerevisiae, a widespread yeast present both in the wild and in fermentative processes, like winemaking. During the colonization of these human-associated fermentative environments, certain strains of S. cerevisiae acquired differential adaptive traits that enhanced their physiological properties to cope with the challenges imposed by these new ecological niches. The advent of omics technologies allowed unveiling some details of the molecular bases responsible for the peculiar traits of S. cerevisiae wine strains. However, the metabolic diversity within yeasts remained poorly explored, in particular that existing between wine and wild strains of S. cerevisiae. For this purpose, we performed a dual transcriptomic and metabolomic comparative analysis between a wild and a wine S. cerevisiae strains during wine fermentations performed at high and low temperatures. By using this approach, we could correlate the differential expression of genes involved in metabolic pathways, such as sulfur, arginine and thiamine metabolisms, with differences in the amounts of key metabolites that can explain some important differences in the fermentation performance between the wine and wild strains.
Collapse
Affiliation(s)
- Romain Minebois
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, E-46980, Spain
| | - María Lairón-Peris
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, E-46980, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, E-46980, Spain.,Departament de Genètica, Universitat de València, C/Doctor Moliner, 50, Burjassot, Valencia, E-46100, Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, E-46980, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, E-46980, Spain
| |
Collapse
|
12
|
Morard M, Ibáñez C, Adam AC, Querol A, Barrio E, Toft C. Genomic instability in an interspecific hybrid of the genus Saccharomyces: a matter of adaptability. Microb Genom 2020; 6:mgen000448. [PMID: 33021926 PMCID: PMC7660253 DOI: 10.1099/mgen.0.000448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022] Open
Abstract
Ancient events of polyploidy have been linked to huge evolutionary leaps in the tree of life, while increasing evidence shows that newly established polyploids have adaptive advantages in certain stress conditions compared to their relatives with a lower ploidy. The genus Saccharomyces is a good model for studying such events, as it contains an ancient whole-genome duplication event and many sequenced Saccharomyces cerevisiae are, evolutionary speaking, newly formed polyploids. Many polyploids have unstable genomes and go through large genome erosions; however, it is still unknown what mechanisms govern this reduction. Here, we sequenced and studied the natural S. cerevisiae × Saccharomyces kudriavzevii hybrid strain, VIN7, which was selected for its commercial use in the wine industry. The most singular observation is that its nuclear genome is highly unstable and drastic genomic alterations were observed in only a few generations, leading to a widening of its phenotypic landscape. To better understand what leads to the loss of certain chromosomes in the VIN7 cell population, we looked for genetic features of the genes, such as physical interactions, complex formation, epistatic interactions and stress responding genes, which could have beneficial or detrimental effects on the cell if their dosage is altered by a chromosomal copy number variation. The three chromosomes lost in our VIN7 population showed different patterns, indicating that multiple factors could explain the mechanisms behind the chromosomal loss. However, one common feature for two out of the three chromosomes is that they are among the smallest ones. We hypothesize that small chromosomes alter their copy numbers more frequently as a low number of genes is affected, meaning that it is a by-product of genome instability, which might be the chief driving force of the adaptability and genome architecture of this hybrid.
Collapse
Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Clara Ibáñez
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Ana C. Adam
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Program for Systems Biology of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), UV-CSIC, Valencia, Spain
| |
Collapse
|
13
|
Matos TTS, Teixeira JF, Macías LG, Santos ARO, Suh SO, Barrio E, Lachance MA, Rosa CA. Kluyveromyces osmophilus is not a synonym of Zygosaccharomyces mellis; reinstatement as Zygosaccharomyces osmophilus comb. nov. Int J Syst Evol Microbiol 2020; 70:3374-3378. [PMID: 32375978 DOI: 10.1099/ijsem.0.004182] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kluyveromyces osmophilus, a single-strain species isolated from Mozambique sugar, has been treated a synonym of Zygosaccharomyces mellis. Analyses of D1/D2 LSU rRNA gene sequences confirmed that the species belongs to the genus Zygosaccharomyces but showed it to be distinct from strains of Z. mellis. During studies of yeasts associated with stingless bees in Brazil, nine additional isolates of the species were obtained from unripe and ripe honey and pollen of Scaptotrigona cfr. bipunctata, as well as ripe honey of Tetragonisca angustula. The D1/D2 sequences of the Brazilian isolates were identical to those of the type strain of K. osmophilus CBS 5499 (=ATCC 22027), indicating that they represent the same species. Phylogenomic analyses using 4038 orthologous genes support the reinstatement of K. osmophilus as a member of the genus Zygosaccharomyces. We, therefore, propose the name Zygosaccharomyces osmophilus comb. nov. (lectotype ATCC 22027; MycoBank no. MB 833739).
Collapse
Affiliation(s)
- Thelma T S Matos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Juliana F Teixeira
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Laura G Macías
- Departament de Genètica, Universitat de València, València, Spain.,Departamento de Biotecnología de Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Alimentos (IATA)-CSIC, Valencia, Spain
| | - Ana Raquel O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Sung-Oui Suh
- Manufacturing Science and Technology Program, ATCC, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, València, Spain.,Departamento de Biotecnología de Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Alimentos (IATA)-CSIC, Valencia, Spain
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, N6A 5B7, London, Ontario, Canada
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| |
Collapse
|
14
|
Lairón-Peris M, Pérez-Través L, Muñiz-Calvo S, Guillamón JM, Heras JM, Barrio E, Querol A. Differential Contribution of the Parental Genomes to a S. cerevisiae × S. uvarum Hybrid, Inferred by Phenomic, Genomic, and Transcriptomic Analyses, at Different Industrial Stress Conditions. Front Bioeng Biotechnol 2020; 8:129. [PMID: 32195231 PMCID: PMC7062649 DOI: 10.3389/fbioe.2020.00129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/10/2020] [Indexed: 01/09/2023] Open
Abstract
In European regions of cold climate, S. uvarum can replace S. cerevisiae in wine fermentations performed at low temperatures. S. uvarum is a cryotolerant yeast that produces more glycerol, less acetic acid and exhibits a better aroma profile. However, this species exhibits a poor ethanol tolerance compared with S. cerevisiae. In the present study, we obtained by rare mating (non-GMO strategy), and a subsequent sporulation, an interspecific S. cerevisiae × S. uvarum spore-derivative hybrid that improves or maintains a combination of parental traits of interest for the wine industry, such as good fermentation performance, increased ethanol tolerance, and high glycerol and aroma productions. Genomic sequencing analysis showed that the artificial spore-derivative hybrid is an allotriploid, which is very common among natural hybrids. Its genome contains one genome copy from the S. uvarum parental genome and two heterozygous copies of the S. cerevisiae parental genome, with the exception of a monosomic S. cerevisiae chromosome III, where the sex-determining MAT locus is located. This genome constitution supports that the original hybrid from which the spore was obtained likely originated by a rare-mating event between a mating-competent S. cerevisiae diploid cell and either a diploid or a haploid S. uvarum cell of the opposite mating type. Moreover, a comparative transcriptomic analysis reveals that each spore-derivative hybrid subgenome is regulating different processes during the fermentation, in which each parental species has demonstrated to be more efficient. Therefore, interactions between the two subgenomes in the spore-derivative hybrid improve those differential species-specific adaptations to the wine fermentation environments, already present in the parental species.
Collapse
Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Laura Pérez-Través
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Sara Muñiz-Calvo
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | | | - Eladio Barrio
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| |
Collapse
|
15
|
Morard M, Benavent-Gil Y, Ortiz-Tovar G, Pérez-Través L, Querol A, Toft C, Barrio E. Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity. Microb Genom 2020; 6:e000333. [PMID: 32065577 PMCID: PMC7200066 DOI: 10.1099/mgen.0.000333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/15/2020] [Indexed: 01/03/2023] Open
Abstract
Interspecific hybridization has played an important role in the evolution of eukaryotic organisms by favouring genetic interchange between divergent lineages to generate new phenotypic diversity involved in the adaptation to new environments. This way, hybridization between Saccharomyces species, involving the fusion between their metabolic capabilities, is a recurrent adaptive strategy in industrial environments. In the present study, whole-genome sequences of natural hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii were obtained to unveil the mechanisms involved in the origin and evolution of hybrids, as well as the ecological and geographic contexts in which spontaneous hybridization and hybrid persistence take place. Although Saccharomyces species can mate using different mechanisms, we concluded that rare-mating is the most commonly used, but other mechanisms were also observed in specific hybrids. The preponderance of rare-mating was confirmed by performing artificial hybridization experiments. The mechanism used to mate determines the genomic structure of the hybrid and its final evolutionary outcome. The evolution and adaptability of the hybrids are triggered by genomic instability, resulting in a wide diversity of genomic rearrangements. Some of these rearrangements could be adaptive under the stressful conditions of the industrial environment.
Collapse
Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Yaiza Benavent-Gil
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Guadalupe Ortiz-Tovar
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Centro de Estudios Vitivinícolas de Baja California, México, CETYS Universidad, Ensenada, Baja California, Mexico
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Institute for Integrative and Systems Biology, Universitat de València and CSIC, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| |
Collapse
|
16
|
García-Ríos E, Nuévalos M, Barrio E, Puig S, Guillamón JM. A new chromosomal rearrangement improves the adaptation of wine yeasts to sulfite. Environ Microbiol 2019; 21:1771-1781. [PMID: 30859719 DOI: 10.1111/1462-2920.14586] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 11/27/2022]
Abstract
Sulfite-generating compounds are widely used during winemaking as preservatives because of its antimicrobial and antioxidant properties. Thus, wine yeast strains have developed different genetic strategies to increase its sulfite resistance. The most efficient sulfite detoxification mechanism in Saccharomyces cerevisiae uses a plasma membrane protein called Ssu1 to efflux sulfite. In wine yeast strains, two chromosomal translocations (VIIItXVI and XVtXVI) involving the SSU1 promoter region have been shown to upregulate SSU1 expression and, as a result, increase sulfite tolerance. In this study, we have identified a novel chromosomal rearrangement that triggers wine yeast sulfite adaptation. An inversion in chromosome XVI (inv-XVI) probably due to sequence microhomology, which involves SSU1 and GCR1 regulatory regions, increases the expression of SSU1 and the sulfite resistance of a commercial wine yeast strain. A detailed dissection of this chimeric SSU1 promoter indicates that both the removed SSU1 promoter sequence and the relocated GCR1 sequence contribute to SSU1 upregulation and sulfite tolerance. However, no relevant function has been attributed to the SSU1-promoter-binding transcription factor Fzf1. These results unveil a new genomic event that confers an evolutive advantage to wine yeast strains.
Collapse
Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Marcos Nuévalos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain.,Departament de Genètica, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| |
Collapse
|
17
|
Macías LG, Morard M, Toft C, Barrio E. Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation. Front Genet 2019; 10:187. [PMID: 30930934 PMCID: PMC6425871 DOI: 10.3389/fgene.2019.00187] [Citation(s) in RCA: 13] [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: 09/21/2018] [Accepted: 02/21/2019] [Indexed: 12/02/2022] Open
Abstract
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis behind these phenotypic differences of biotechnological interest by using a species-based comparative genomics approach. In this work, we sequenced, assembled and annotated two new genomes of S. kudriavzevii. We used a combination of different statistical methods to identify functional divergence, signatures of positive selection and acceleration of substitution rates at specific amino acid sites of proteins in S. kudriavzevii when compared to S. cerevisiae, and vice versa. We provide a list of candidate genes in which positive selection could be acting during the evolution of both S. cerevisiae and S. kudriavzevii clades. Some of them could be related to certain important differences in metabolism previously reported by other authors such us DAL3 and ARO4, involved in nitrogen assimilation and amino acid biosynthesis. In addition, three of those genes (FBA1, ZIP1, and RQC2) showed accelerated evolutionary rates in Sk branch. Finally, genes of the riboflavin biosynthesis were also among those genes with a significant higher rate of nucleotide substitution and those proteins have amino acid positions contributing to functional divergence.
Collapse
Affiliation(s)
- Laura G Macías
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Miguel Morard
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| |
Collapse
|
18
|
Alonso-Del-Real J, Pérez-Torrado R, Querol A, Barrio E. Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization. Environ Microbiol 2019; 21:1627-1644. [PMID: 30672093 DOI: 10.1111/1462-2920.14536] [Citation(s) in RCA: 29] [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] [Received: 09/05/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 01/01/2023]
Abstract
Grape must is a sugar-rich habitat for a complex microbiota which is replaced by Saccharomyces cerevisiae strains during the first fermentation stages. Interest on yeast competitive interactions has recently been propelled due to the use of alternative yeasts in the wine industry to respond to new market demands. The main issue resides in the persistence of these yeasts due to the specific competitive activity of S. cerevisiae. To gather deeper knowledge of the molecular mechanisms involved, we performed a comparative transcriptomic analysis during fermentation carried out by a wine S. cerevisiae strain and a strain representative of the cryophilic S. kudriavzevii, which exhibits high genetic and physiological similarities to S. cerevisiae, but also differences of biotechnological interest. In this study, we report that transcriptomic response to the presence of a competitor is stronger in S. cerevisiae than in S. kudriavzevii. Our results demonstrate that a wine S. cerevisiae industrial strain accelerates nutrient uptake and utilization to outcompete the co-inoculated yeast, and that this process requires cell-to-cell contact to occur. Finally, we propose that this competitive phenotype evolved recently, during the adaptation of S. cerevisiae to man-manipulated fermentative environments, since a non-wine S. cerevisiae strain, isolated from a North American oak, showed a remarkable low response to competition.
Collapse
Affiliation(s)
- Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, València, Spain
| |
Collapse
|
19
|
Morard M, Macías LG, Adam AC, Lairón-Peris M, Pérez-Torrado R, Toft C, Barrio E. Aneuploidy and Ethanol Tolerance in Saccharomyces cerevisiae. Front Genet 2019; 10:82. [PMID: 30809248 PMCID: PMC6379819 DOI: 10.3389/fgene.2019.00082] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 10/01/2018] [Accepted: 01/28/2019] [Indexed: 12/31/2022] Open
Abstract
Response to environmental stresses is a key factor for microbial organism growth. One of the major stresses for yeasts in fermentative environments is ethanol. Saccharomyces cerevisiae is the most tolerant species in its genus, but intraspecific ethanol-tolerance variation exists. Although, much effort has been done in the last years to discover evolutionary paths to improve ethanol tolerance, this phenotype is still hardly understood. Here, we selected five strains with different ethanol tolerances, and used comparative genomics to determine the main factors that can explain these phenotypic differences. Surprisingly, the main genomic feature, shared only by the highest ethanol-tolerant strains, was a polysomic chromosome III. Transcriptomic data point out that chromosome III is important for the ethanol stress response, and this aneuploidy can be an advantage to respond rapidly to ethanol stress. We found that chromosome III copy numbers also explain differences in other strains. We show that removing the extra chromosome III copy in an ethanol-tolerant strain, returning to euploidy, strongly compromises its tolerance. Chromosome III aneuploidy appears frequently in ethanol-tolerance evolution experiments, and here, we show that aneuploidy is also used by natural strains to enhance their ethanol tolerance.
Collapse
Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Laura G Macías
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Ana C Adam
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - María Lairón-Peris
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain
| |
Collapse
|
20
|
Querol A, Pérez-Torrado R, Alonso-Del-Real J, Minebois R, Stribny J, Oliveira BM, Barrio E. New Trends in the Uses of Yeasts in Oenology. Adv Food Nutr Res 2018; 85:177-210. [PMID: 29860974 DOI: 10.1016/bs.afnr.2018.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The most important factor in winemaking is the quality of the final product and the new trends in oenology are dictated by wine consumers and producers. Traditionally the red wine is the most consumed and more popular; however, in the last times, the wine companies try to attract other groups of populations, especially young people and women that prefer sweet, whites or rosé wines, very fruity and with low alcohol content. Besides the new trends in consumer preferences, there are also increased concerns on the effects of alcohol consumption on health and the effects of global climate change on grape ripening and wine composition producing wines with high alcohol content. Although S. cerevisiae is the most frequent species in wines, and the subject of most studies, S. uvarum and hybrids between Saccharomyces species such as S. cerevisiae×S. kudriavzevii and S. cerevisiae×S. uvarum are also involved in wine fermentations and can be preponderant in certain wine regions. New yeast starters of non-cerevisiae strains (S. uvarum) or hybrids (S. cerevisiae×S. uvarum and S. cerevisiae×S. kudriavzevii) can contribute to solve some problems of the wineries. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts, while fulfilling the requirements of the commercial yeasts, such as a good fermentative performance and aromatic profiles that are of great interest for the wine industry. In this review, we will analyze different applications of nonconventional yeasts to solve the current winemaking demands.
Collapse
Affiliation(s)
- Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain.
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Romain Minebois
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Jiri Stribny
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Bruno M Oliveira
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| |
Collapse
|
21
|
Ortiz-Tovar G, Pérez-Torrado R, Adam AC, Barrio E, Querol A. A comparison of the performance of natural hybrids Saccharomyces cerevisiae × Saccharomyces kudriavzevii at low temperatures reveals the crucial role of their S. kudriavzevii genomic contribution. Int J Food Microbiol 2018; 274:12-19. [PMID: 29574243 DOI: 10.1016/j.ijfoodmicro.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 10/29/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/17/2022]
Abstract
Fermentation performance at low temperature is a common approach to obtain wines with better aroma, and is critical in industrial applications. Natural hybrids S. cerevisiae × S. kudriavzevii, isolated from fermentations in cold-climate European countries, have provided an understanding of the mechanisms of adaptation to grow at low temperature. In this work, we studied the performance of 23 S. cerevisiae × S. kudriavzevii hybrids at low temperature (8, 12 and 24 °C) to characterize their phenotypes. Kinetic parameters and spot tests revealed a different ability to grow at low temperature. Interestingly, the genome content of the S. kudriavzevii in hybrids was moderately correlated with a shorter lag phase, and the genetic origin of hybrids influenced their performance at low temperature (8 °C). The parental expression of cold marker genes (NSR1, GUT2 and GPD1) showed that the relative expression of the S. kudriavzevii alleles was higher than the expression of the S. cerevisiae alleles in hybrids with a better growth at low-temperatures. These results suggest that the genomic contribution of S. kudriavzevii to hybrids is important for improving the fitness of these strains at low temperature.
Collapse
Affiliation(s)
- Guadalupe Ortiz-Tovar
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Ana Cris Adam
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain.
| |
Collapse
|
22
|
Peris D, Pérez-Torrado R, Hittinger CT, Barrio E, Querol A. On the origins and industrial applications ofSaccharomyces cerevisiae×Saccharomyces kudriavzeviihybrids. Yeast 2017; 35:51-69. [DOI: 10.1002/yea.3283] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/15/2017] [Accepted: 09/27/2017] [Indexed: 12/22/2022] Open
Affiliation(s)
- David Peris
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center; University of Wisconsin-Madison; Madison WI USA
- Department of Food Biotechnology; Institute of Agrochemistry and Food Technology (IATA), CSIC; Valencia Spain
| | - Roberto Pérez-Torrado
- Department of Food Biotechnology; Institute of Agrochemistry and Food Technology (IATA), CSIC; Valencia Spain
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center; University of Wisconsin-Madison; Madison WI USA
| | - Eladio Barrio
- Department of Food Biotechnology; Institute of Agrochemistry and Food Technology (IATA), CSIC; Valencia Spain
- Department of Genetics; University of Valencia; Valencia Spain
| | - Amparo Querol
- Department of Food Biotechnology; Institute of Agrochemistry and Food Technology (IATA), CSIC; Valencia Spain
| |
Collapse
|
23
|
Alonso-Del-Real J, Contreras-Ruiz A, Castiglioni GL, Barrio E, Querol A. The Use of Mixed Populations of Saccharomyces cerevisiae and S. kudriavzevii to Reduce Ethanol Content in Wine: Limited Aeration, Inoculum Proportions, and Sequential Inoculation. Front Microbiol 2017; 8:2087. [PMID: 29118746 PMCID: PMC5661026 DOI: 10.3389/fmicb.2017.02087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 09/08/2017] [Accepted: 10/11/2017] [Indexed: 01/03/2023] Open
Abstract
Saccharomyces cerevisiae is the most widespread microorganism responsible for wine alcoholic fermentation. Nevertheless, the wine industry is currently facing new challenges, some of them associate with climate change, which have a negative effect on ethanol content and wine quality. Numerous and varied strategies have been carried out to overcome these concerns. From a biotechnological point of view, the use of alternative non-Saccharomyces yeasts, yielding lower ethanol concentrations and sometimes giving rise to new and interesting aroma, is one of the trendiest approaches. However, S. cerevisiae usually outcompetes other Saccharomyces species due to its better adaptation to the fermentative environment. For this reason, we studied for the first time the use of a Saccharomyces kudriavzevii strain, CR85, for co-inoculations at increasing proportions and sequential inoculations, as well as the effect of aeration, to improve its fermentation performance in order to obtain wines with an ethanol yield reduction. An enhanced competitive performance of S. kudriavzevii CR85 was observed when it represented 90% of the cells present in the inoculum. Furthermore, airflow supply of 20 VVH to the fermentation synergistically improved CR85 endurance and, interestingly, a significant ethanol concentration reduction was achieved.
Collapse
Affiliation(s)
- Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Valencia, Spain
| | - Alba Contreras-Ruiz
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Gabriel L Castiglioni
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Valencia, Spain
| |
Collapse
|
24
|
Ibáñez C, Pérez-Torrado R, Morard M, Toft C, Barrio E, Querol A. RNAseq-based transcriptome comparison of Saccharomyces cerevisiae strains isolated from diverse fermentative environments. Int J Food Microbiol 2017; 257:262-270. [PMID: 28711856 DOI: 10.1016/j.ijfoodmicro.2017.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 05/30/2017] [Accepted: 07/02/2017] [Indexed: 11/18/2022]
Abstract
Transcriptome analyses play a central role in unraveling the complexity of gene expression regulation in Saccharomyces cerevisiae. This species, one of the most important microorganisms for humans given its industrial applications, shows an astonishing degree of genetic and phenotypic variability among different strains adapted to specific environments. In order to gain novel insights into the Saccharomyces cerevisiae biology of strains adapted to different fermentative environments, we analyzed the whole transcriptome of three strains isolated from wine, flor wine or mezcal fermentations. An RNA-seq transcriptome comparison of the different yeasts in the samples obtained during synthetic must fermentation highlighted the differences observed in the genes that encode mannoproteins, and in those involved in aroma, sugar transport, glycerol and alcohol metabolism, which are important under alcoholic fermentation conditions. These differences were also observed in the physiology of the strains after mannoprotein and aroma determinations. This study offers an essential foundation for understanding how gene expression variations contribute to the fermentation differences of the strains adapted to unequal fermentative environments. Such knowledge is crucial to make improvements in fermentation processes and to define targets for the genetic improvement or selection of wine yeasts.
Collapse
Affiliation(s)
- Clara Ibáñez
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Miguel Morard
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Christina Toft
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain.
| |
Collapse
|
25
|
Affiliation(s)
- Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| |
Collapse
|
26
|
Abstract
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.
Collapse
Affiliation(s)
- José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain.,Departamento de Genética, Universidad de ValenciaValencia, Spain
| |
Collapse
|
27
|
Alonso-Del-Real J, Lairón-Peris M, Barrio E, Querol A. Effect of Temperature on the Prevalence of Saccharomyces Non cerevisiae Species against a S. cerevisiae Wine Strain in Wine Fermentation: Competition, Physiological Fitness, and Influence in Final Wine Composition. Front Microbiol 2017; 8:150. [PMID: 28223968 PMCID: PMC5293751 DOI: 10.3389/fmicb.2017.00150] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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: 12/05/2016] [Accepted: 01/20/2017] [Indexed: 12/20/2022] Open
Abstract
Saccharomyces cerevisiae is the main microorganism responsible for the fermentation of wine. Nevertheless, in the last years wineries are facing new challenges due to current market demands and climate change effects on the wine quality. New yeast starters formed by non-conventional Saccharomyces species (such as S. uvarum or S. kudriavzevii) or their hybrids (S. cerevisiae x S. uvarum and S. cerevisiae x S. kudriavzevii) can contribute to solve some of these challenges. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts. However, S. cerevisiae can competitively displace other yeast species from wine fermentations, therefore the use of these new starters requires an analysis of their behavior during competition with S. cerevisiae during wine fermentation. In the present study we analyzed the survival capacity of non-cerevisiae strains in competition with S. cerevisiae during fermentation of synthetic wine must at different temperatures. First, we developed a new method, based on QPCR, to quantify the proportion of different Saccharomyces yeasts in mixed cultures. This method was used to assess the effect of competition on the growth fitness. In addition, fermentation kinetics parameters and final wine compositions were also analyzed. We observed that some cryotolerant Saccharomyces yeasts, particularly S. uvarum, seriously compromised S. cerevisiae fitness during competences at lower temperatures, which explains why S. uvarum can replace S. cerevisiae during wine fermentations in European regions with oceanic and continental climates. From an enological point of view, mixed co-cultures between S. cerevisiae and S. paradoxus or S. eubayanus, deteriorated fermentation parameters and the final product composition compared to single S. cerevisiae inoculation. However, in co-inoculated synthetic must in which S. kudriavzevii or S. uvarum coexisted with S. cerevisiae, there were fermentation performance improvements and the final wines contained less ethanol and higher amounts of glycerol. Finally, it is interesting to note that in co-inoculated fermentations, wine strains of S. cerevisiae and S. uvarum performed better than non-wine strains of the same species.
Collapse
Affiliation(s)
- Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC Valencia, Spain
| | - María Lairón-Peris
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSICValencia, Spain; Departament de Genètica, Universitat de ValènciaValència, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSICValencia, Spain; Departament de Genètica, Universitat de ValènciaValència, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC Valencia, Spain
| |
Collapse
|
28
|
Rodríguez ME, Pérez-Través L, Sangorrín MP, Barrio E, Querol A, Lopes CA. Saccharomyces uvarum
is Responsible for the Traditional Fermentation of Apple
CHICHA
in Patagonia. FEMS Yeast Res 2016; 17:fow109. [DOI: 10.1093/femsyr/fow109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2016] [Indexed: 11/12/2022] Open
|
29
|
Pérez-Través L, Lopes CA, Barrio E, Querol A. Stabilization process in Saccharomyces intra and interspecific hybrids in fermentative conditions. Int Microbiol 2016; 17:213-24. [PMID: 26421737 DOI: 10.2436/20.1501.01.224] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/18/2014] [Indexed: 11/15/2022]
Abstract
We evaluated the genetic stabilization of artificial intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae × S. kudriavzevii) hybrids under wine fermentative conditions. Large-scale transitions in genome size and genome reorganizations were observed during this process. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns recovered among the derived clones was observed for intraspecific hybrids, particularly for those obtained by rare-mating. Molecular marker analyses revealed that unstable clones could change during the industrial process to obtain active dry yeast. When no changes in molecular markers and ploidy were observed after this process, no changes in genetic composition were confirmed by comparative genome hybridization, considering the clone as a stable hybrid. According to our results, under these conditions, fermentation steps 3 and 5 (30-50 generations) would suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively.
Collapse
Affiliation(s)
- Laura Pérez-Través
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Food Biotechnology Department, Paterna, Valencia, Spain.,Genetics, University of Valencia, Valencia, Spain
| | - Christian A Lopes
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Food Biotechnology Department, Paterna, Valencia, Spain.,Institute for Research and Development in Process Engineering, Biotechnology and Alternative Energy, CONICET-UNCo, Faculty of Agricultural Sciences and Faculty of Engineering, National University of Comahue, Neuquen, Argentina
| | - Eladio Barrio
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Food Biotechnology Department, Paterna, Valencia, Spain.,Genetics, University of Valencia, Valencia, Spain
| | - Amparo Querol
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Food Biotechnology Department, Paterna, Valencia, Spain
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Pérez-Través L, Lopes CA, González R, Barrio E, Querol A. Physiological and genomic characterisation of Saccharomyces cerevisiae hybrids with improved fermentation performance and mannoprotein release capacity. Int J Food Microbiol 2015; 205:30-40. [DOI: 10.1016/j.ijfoodmicro.2015.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 03/14/2015] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
|
32
|
Beleña JM, Anta D, Barrio E, Nuñez M. Real-time ultrasound detection of correct intravenous placement of central venous catheters after ultrasound cannulation. ACTA ACUST UNITED AC 2014; 63:63-4. [PMID: 25530434 DOI: 10.1016/j.redar.2014.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/04/2014] [Accepted: 11/11/2014] [Indexed: 11/28/2022]
Affiliation(s)
- J M Beleña
- Servicio de Anestesiología y Reanimación, Hospital Universitario del Sureste, Arganda del Rey, Madrid, Spain.
| | - D Anta
- Servicio de Anestesiología y Reanimación, Hospital Universitario del Sureste, Arganda del Rey, Madrid, Spain
| | - E Barrio
- Servicio de Anestesiología y Reanimación, Hospital Universitario del Sureste, Arganda del Rey, Madrid, Spain
| | - M Nuñez
- Servicio de Anestesiología y Reanimación, Hospital Universitario Ramón y Cajal, Madrid, Spain
| |
Collapse
|
33
|
Rodríguez ME, Pérez-Través L, Sangorrín MP, Barrio E, Lopes CA. Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia. FEMS Yeast Res 2014; 14:948-65. [PMID: 25041507 DOI: 10.1111/1567-1364.12183] [Citation(s) in RCA: 51] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/29/2014] [Accepted: 07/07/2014] [Indexed: 12/27/2022] Open
Abstract
Mudai is a traditional fermented beverage, made from the seeds of the Araucaria araucana tree by Mapuche communities. The main goal of the present study was to identify and characterize the yeast microbiota responsible of Mudai fermentation as well as from A. araucana seeds and bark from different locations in Northern Patagonia. Only Hanseniaspora uvarum and a commercial bakery strain of Saccharomyces cerevisiae were isolated from Mudai and all Saccharomyces isolates recovered from A. araucana seed and bark samples belonged to the cryotolerant species Saccharomyces eubayanus and Saccharomyces uvarum. These two species were already reported in Nothofagus trees from Patagonia; however, this is the first time that they were isolated from A. araucana, which extends their ecological distribution. The presence of these species in A. araucana seeds and bark samples, led us to postulate a potential role for them as the original yeasts responsible for the elaboration of Mudai before the introduction of commercial S. cerevisiae cultures. The molecular and genetic characterization of the S. uvarum and S. eubayanus isolates and their comparison with European S. uvarum strains and S. eubayanus hybrids (S. bayanus and S. pastorianus), allowed their ecology and evolution us to be examined.
Collapse
Affiliation(s)
- M Eugenia Rodríguez
- Grupo de Biodiversidad y Biotecnología de Levaduras, Fac. Ingeniería, Instituto Multidisciplinario de Investigación y Desarrollo en Ingeniería de procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue), Facultad de Ingeniería, UNCo, Buenos Aires, Neuquén, Argentina; Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Comahue, Neuquén, Argentina
| | | | | | | | | |
Collapse
|
34
|
Pérez-Través L, Lopes CA, Querol A, Barrio E. On the complexity of the Saccharomyces bayanus taxon: hybridization and potential hybrid speciation. PLoS One 2014; 9:e93729. [PMID: 24705561 PMCID: PMC3976317 DOI: 10.1371/journal.pone.0093729] [Citation(s) in RCA: 47] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/10/2014] [Indexed: 11/18/2022] Open
Abstract
Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99–100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.
Collapse
Affiliation(s)
- Laura Pérez-Través
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (CSIC), València, Spain
| | - Christian A. Lopes
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (CSIC), València, Spain
- Grupo de Biodiversidad y Biotecnología de Levaduras, Instituto Multidisciplinario de Investigación y Desarrollo de la Patagonia Norte (IDEPA), CONICET-UNCo, Departmento Química, Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires, Neuquén, Argentina
| | - Amparo Querol
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (CSIC), València, Spain
| | - Eladio Barrio
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (CSIC), València, Spain
- Departament de Genètica, Universitat de València, València, Spain
- * E-mail:
| |
Collapse
|
35
|
Oliveira BM, Barrio E, Querol A, Pérez-Torrado R. Enhanced enzymatic activity of glycerol-3-phosphate dehydrogenase from the cryophilic Saccharomyces kudriavzevii. PLoS One 2014; 9:e87290. [PMID: 24498063 PMCID: PMC3907487 DOI: 10.1371/journal.pone.0087290] [Citation(s) in RCA: 47] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 12/26/2013] [Indexed: 11/18/2022] Open
Abstract
During the evolution of the different species classified within the Saccharomyces genus, each one has adapted to live in different environments. One of the most important parameters that have influenced the evolution of Saccharomyces species is the temperature. Here we have focused on the study of the ability of certain species as Saccharomyces kudriavzevii to grow at low temperatures, in contrast to Saccharomyces cerevisiae. We observed that S. kudriavzevii strains isolated from several regions are able to synthesize higher amounts of glycerol, a molecule that has been shown to accumulate in response to freeze and cold stress. To explain this observation at the molecular level we studied the expression of glycerol biosynthetic pathway genes and we observed a higher expression of GPD1 gene in S. kudriavzevii compared to S. cerevisiae in micro-vinification conditions. We observed higher enzymatic activity of Gpd1p in S. kudriavzevii in response to osmotic and cold stress. Also, we determined that S. kudriavzevii Gpd1p enzyme presents increased catalytic properties that will contribute to increase glycerol production. Finally, we evaluated the glycerol production with S. cerevisiae, S. kudriavzevii or a recombinant Gpd1p variant in the same background and observed that the S. kudriavzevii enzyme produced increased glycerol levels at 12 or 28°C. This suggests that glycerol is increased in S. kudriavzevii mainly due to increased Vmax of the Gpd1p enzyme. All these differences indicate that S. kudriavzevii has changed the metabolism to promote the branch of the glycolytic pathway involved in glycerol production to adapt to low temperature environments and maintain the NAD+/NADH ratio in alcoholic fermentations. This knowledge is industrially relevant due to the potential use, for example, of S. cerevisiae-S. kudriavzevii hybrids in the wine industry where glycerol content is an important quality parameter.
Collapse
Affiliation(s)
- Bruno M. Oliveira
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna (Valencia), Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna (Valencia), Spain
- Institut “Cavanilles” de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna (Valencia), Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980, Paterna (Valencia), Spain
- * E-mail:
| |
Collapse
|
36
|
Badotti F, Vilaça ST, Arias A, Rosa CA, Barrio E. Two interbreeding populations of Saccharomyces cerevisiae strains coexist in cachaça fermentations from Brazil. FEMS Yeast Res 2013; 14:289-301. [PMID: 24119212 DOI: 10.1111/1567-1364.12108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 07/12/2013] [Revised: 09/18/2013] [Accepted: 10/02/2013] [Indexed: 12/22/2022] Open
Abstract
In this study, the phylogenetic relationships between cachaça strains of Saccharomyces cerevisiae isolated from different geographical areas in Brazil were obtained on the basis of sequences of one mitochondrial (COX2) and three nuclear (EGT2, CAT8, and BRE5) genes. This analysis allowed us to demonstrate that different types of strains coexist in cachaça fermentations: wine strains, exhibiting alleles related or identical to those present in European wine strains; native strains, containing alleles similar to those found in strains isolated from traditional fermentations from Latin America, North America, Malaysian, Japan, or West Africa; and their intraspecific hybrids or 'mestizo' strains, heterozygous for both types of alleles. Wine strains and hybrids with high proportions of wine-type alleles predominate in southern and southeastern Brazil, where cachaça production coexists with winemaking. The high frequency of 'wine-type' alleles in these regions is probably due to the arrival of wine immigrant strains introduced from Europe in the nearby wineries due to the winemaking practices. However, in north and northeastern states, regions less suited or not suited for vine growing and winemaking, wine-type alleles are much less frequent because 'mestizo' strains with intermediate or higher proportions of 'native-type' alleles are predominant.
Collapse
Affiliation(s)
- Fernanda Badotti
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Department of Biotechnology, Institute of Agrochemistry and Food Technology, Paterna, València, Spain
| | | | | | | | | |
Collapse
|
37
|
Páez-Lerma JB, Arias-García A, Rutiaga-Quiñones OM, Barrio E, Soto-Cruz NO. Yeasts Isolated from the Alcoholic Fermentation ofAgave duranguensisDuring Mezcal Production. FOOD BIOTECHNOL 2013. [DOI: 10.1080/08905436.2013.840788] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
38
|
Rodríguez-Sifuentes L, Páez-Lerma J, Rutiaga-Quiñones O, Rojas-Contreras J, Ruiz-Baca E, Gutiérrez-Sánchez G, Barrio E, Soto-Cruz N. Identification of a yeast strain as a potential stuck wine fermentation restarter: a kinetic characterization. CyTA - Journal of Food 2013. [DOI: 10.1080/19476337.2013.776637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
39
|
Peris D, Lopes CA, Belloch C, Querol A, Barrio E. Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins. BMC Genomics 2012; 13:407. [PMID: 22906207 PMCID: PMC3468397 DOI: 10.1186/1471-2164-13-407] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [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: 09/22/2011] [Accepted: 04/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Interspecific hybrids between S. cerevisiae × S. kudriavzevii have frequently been detected in wine and beer fermentations. Significant physiological differences among parental and hybrid strains under different stress conditions have been evidenced. In this study, we used comparative genome hybridization analysis to evaluate the genome composition of different S. cerevisiae × S. kudriavzevii natural hybrids isolated from wine and beer fermentations to infer their evolutionary origins and to figure out the potential role of common S. kudriavzevii gene fraction present in these hybrids. RESULTS Comparative genomic hybridization (CGH) and ploidy analyses carried out in this study confirmed the presence of individual and differential chromosomal composition patterns for most S. cerevisiae × S. kudriavzevii hybrids from beer and wine. All hybrids share a common set of depleted S. cerevisiae genes, which also are depleted or absent in the wine strains studied so far, and the presence a common set of S. kudriavzevii genes, which may be associated with their capability to grow at low temperatures. Finally, a maximum parsimony analysis of chromosomal rearrangement events, occurred in the hybrid genomes, indicated the presence of two main groups of wine hybrids and different divergent lineages of brewing strains. CONCLUSION Our data suggest that wine and beer S. cerevisiae × S. kudriavzevii hybrids have been originated by different rare-mating events involving a diploid wine S. cerevisiae and a haploid or diploid European S. kudriavzevii strains. Hybrids maintain several S. kudriavzevii genes involved in cold adaptation as well as those related to S. kudriavzevii mitochondrial functions.
Collapse
Affiliation(s)
- David Peris
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Parc Científic, P,O, Box 22085, E-46071, Valencia, Spain
| | | | | | | | | |
Collapse
|
40
|
Fernández E, Barrio E, Luque M, De Miguel A, Fernández C, Cruz P. [Anaesthesia in a patient with Lesch-Nyhan syndrome]. ACTA ACUST UNITED AC 2012; 59:167-8. [PMID: 22985762 DOI: 10.1016/j.redar.2012.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 02/06/2012] [Indexed: 10/28/2022]
Affiliation(s)
- E Fernández
- Servicio de Anestesiología, Hospital General Universitario Gregorio Marañón, Madrid, España.
| | | | | | | | | | | |
Collapse
|
41
|
Peris D, Belloch C, Lopandić K, Álvarez-Pérez JM, Querol A, Barrio E. The molecular characterization of new types of Saccharomyces cerevisiae × S. kudriavzevii hybrid yeasts unveils a high genetic diversity. Yeast 2012; 29:81-91. [DOI: 10.1002/yea.2891] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 11/24/2011] [Indexed: 11/09/2022] Open
Affiliation(s)
- David Peris
- Institute Cavanilles of Biodiversity and Evolutionary Biology; University of Valencia; Spain
| | - Carmela Belloch
- Department of Biotecnology; Institute of Agrochemistry and Food Technology (CSIC); Valencia; Spain
| | - Ksenija Lopandić
- Austrian Centre of Biological Resources and Applied Mycology, Institute of Applied Microbiology; University of Natural Resources and Applied Life Sciences; Vienna; Austria
| | | | - Amparo Querol
- Department of Biotecnology; Institute of Agrochemistry and Food Technology (CSIC); Valencia; Spain
| | - Eladio Barrio
- Institute Cavanilles of Biodiversity and Evolutionary Biology; University of Valencia; Spain
| |
Collapse
|
42
|
Abstract
BACKGROUND AND AIMS Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. METHODS The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. KEY RESULTS Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. CONCLUSIONS This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.
Collapse
Affiliation(s)
- Concepción M Díez
- Departamento de Agronomía, Campus Universitario de Rabanales, Ctra. Madrid-Cádiz Km. 396, Córdoba, Spain.
| | | | | | | | | | | |
Collapse
|
43
|
Salvadó Z, Arroyo-López FN, Barrio E, Querol A, Guillamón JM. Quantifying the individual effects of ethanol and temperature on the fitness advantage of Saccharomyces cerevisiae. Food Microbiol 2011; 28:1155-61. [PMID: 21645814 DOI: 10.1016/j.fm.2011.03.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/08/2011] [Accepted: 03/21/2011] [Indexed: 10/18/2022]
Abstract
The presence of Saccharomyces cerevisiae in grape berries and fresh musts is usually very low. However, as fermentation progresses, the population levels of this species considerably increase. In this study, we use the concept of fitness advantage to measure how increasing ethanol concentrations (0-25%) and temperature values (4-46 °C) in wine fermentations affects competition between S. cerevisiae and several non-Saccharomyces yeasts (Hanseniaspora uvarum, Torulaspora delbrueckii, Candida zemplinina, Pichia fermentans and Kluyveromyces marxianus). We used a mathematical approach to model the hypothetical time needed for S. cerevisiae to impose itself on a mixed population of the non-Saccharomyces species described above. This approach also took into consideration the influence of environmental factors and the initial population levels of S. cerevisiae (0.1, 1.0 and 10.0%). Our results suggest that Saccharomyces niche construction via ethanol production does not provide a clear ecological advantage (at least not until the ethanol concentration exceeds 9%), whereas a temperature rise (above 15 °C) does give S. cerevisiae a considerable advantage. The initial frequency of S. cerevisiae considerably influences the time it needs to impose itself (until it reaches a final frequency of 99% in the mixed culture), the lowest time values being found at the highest initial frequency. In light of these results, the application of low temperatures in the wine industry could favor the growth and survival of non-Saccharomyces species for a longer period of time.
Collapse
Affiliation(s)
- Z Salvadó
- Departament de Bioquímica i Biotecnologia, Facultat de Enologia, Universitat Rovira i Virgili, C/Marcel·lí Domingo, s/n, 43007 Tarragona, Spain
| | | | | | | | | |
Collapse
|
44
|
Bautista-Gallego J, Rodríguez-Gómez F, Barrio E, Querol A, Garrido-Fernández A, Arroyo-López FN. Exploring the yeast biodiversity of green table olive industrial fermentations for technological applications. Int J Food Microbiol 2011; 147:89-96. [PMID: 21497408 DOI: 10.1016/j.ijfoodmicro.2011.03.013] [Citation(s) in RCA: 68] [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] [Received: 08/03/2010] [Revised: 02/21/2011] [Accepted: 03/22/2011] [Indexed: 11/18/2022]
Abstract
In recent years, there has been an increasing interest in identifying and characterizing the yeast populations associated with diverse types of table olive elaborations because of the many desirable technological properties of these microorganisms. In this work, a total of 199 yeast isolates were directly obtained from industrial green table olive fermentations and genetically identified by means of a RFLP analysis of the 5.8S-ITS region and sequencing of the D1/D2 domains of the 26S rDNA gene. Candida diddensiae, Saccharomyces cerevisiae and Pichia membranifaciens were the most abundant yeast species isolated from directly brined Aloreña olives, while for Gordal and Manzanilla cultivars they were Candida tropicalis, Pichia galeiformis and Wickerhamomyces anomalus. In the case of Gordal and Manzanilla green olives processed according to the Spanish style, the predominant yeasts were Debaryomyces etchellsii, C. tropicalis, P. galeiformis and Kluyveromyces lactis. Biochemical activities of technological interest were then qualitatively determined for isolates belonging to all yeast species. This preliminary screening identified two isolates of W. anomalus with interesting properties, such as a strong β-glucosidase and esterase activity, and a moderate catalase and lipolytic activity, which were also confirmed by quantitative assays. The results obtained in this survey show the potential use that some yeast species could have as starters, alone or in combination with lactic acid bacteria, during olive processing.
Collapse
Affiliation(s)
- J Bautista-Gallego
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa (CSIC), Avda, Padre García Tejero, Sevilla, Spain
| | | | | | | | | | | |
Collapse
|
45
|
Arroyo-López FN, Pérez-Través L, Querol A, Barrio E. Exclusion of Saccharomyces kudriavzevii from a wine model system mediated by Saccharomyces cerevisiae. Yeast 2011; 28:423-35. [DOI: 10.1002/yea.1848] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 02/02/2011] [Indexed: 11/06/2022] Open
|
46
|
de Llanos R, Hernández-Haro C, Barrio E, Querol A, Fernández-Espinar MT, Molina M. Differences in activation of MAP kinases and variability in the polyglutamine tract of Slt2 in clinical and non-clinical isolates of Saccharomyces cerevisiae. Yeast 2010; 27:549-61. [PMID: 20586115 DOI: 10.1002/yea.1799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The concept of Saccharomyces cerevisiae as an emerging opportunistic pathogen is relatively new and it is due to an increasing number of human infections during the past 20 years. There are still few studies addressing the mechanisms of infection of this yeast species. Moreover, little is known about how S. cerevisiae cells sense and respond to the harsh conditions imposed by the host, and whether this response is different between clinical isolates and non-pathogenic strains. In this regard, mitogen-activated protein kinase (MAPK) pathways constitute one of the major mechanisms for controlling transcriptional responses and, in some cases, virulence in fungi. Here we show differences among clinical and non-clinical isolates of S. cerevisiae in the level of activation of the MAPKs Kss1, which controls pseudohyphal and invasive growth, and Slt2, which is required for maintaining the integrity of the cell wall under stress conditions and in the absence of stimulating conditions. Moreover, we report for the first time the existence of length variability in SLT2 alleles of strains with a clinical origin. This is due to the expansion in the number of glutamine-encoding triplets in the microsatellite region coding for the polyglutamine (poly-Q) tract of this gene, which range from 12 to more than 38 repetitions. We suggest that this variability may influence biological features of the Slt2 protein, allowing it to adapt swiftly in order to survive in unusual environments.
Collapse
Affiliation(s)
- Rosa de Llanos
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, PO Box 73, 46100 Burjassot, Valencia, Spain
| | | | | | | | | | | |
Collapse
|
47
|
Arroyo-López FN, Salvadó Z, Tronchoni J, Guillamón JM, Barrio E, Querol A. Susceptibility and resistance to ethanol in Saccharomyces strains isolated from wild and fermentative environments. Yeast 2010; 27:1005-15. [PMID: 20824889 DOI: 10.1002/yea.1809] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 06/21/2010] [Indexed: 11/09/2022] Open
Abstract
In this work, we apply statistical modelling techniques to study the influence of increasing concentrations of ethanol on the overall growth of 29 yeast strains belonging to different Saccharomyces and non-Saccharomyces species. A modified Gompertz equation for decay was used to objectively estimate the noninhibitory concentration (NIC) and minimum inhibitory concentration (MIC) for the assayed strains to ethanol, which are related to the susceptibility and resistance of yeasts to this compound, respectively. A first ANOVA analysis, grouping strains as a function of their respective Saccharomyces species, revealed that S. cerevisiae was the yeast with the highest, and statistically significant, ethanol resistance value. Then, a second factorial ANOVA analysis, using the origin of strains (wild or fermentative) and their taxonomic classification (S. cerevisiae, S. paradoxus or S. bayanus var. uvarum) as categorical predictor variables, showed that no significant differences for the NIC and MIC parameters were found between both ecological niches within the same species, indicative that these physiological characteristics were presumably not modified throughout the adaptation to human-manipulated fermentative environments. Finally, differences among selected strains with respect to ethanol tolerance were correlated to the initial contents of unsaturated fatty acids, mainly oleic acid.
Collapse
Affiliation(s)
- F N Arroyo-López
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva. Universitat de València. Edifici d'Instituts, Parc Científic de Paterna. P.O. Box 22085, E-46071 València, Spain
| | | | | | | | | | | |
Collapse
|
48
|
Naumova ES, Naumov GI, Barrio E, Querol A. Mitochondrial DNA polymorphism of the yeast Saccharomyces bayanus var. uvarum. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710040144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
49
|
Castro JA, Barrio E, González A, Picornell A, Ramon MM, Moya A. Nucleotide diversity of a ND5 fragment confirms that population expansion is the most suitable explanation for the mtDNA haplotype polymorphism of Drosophila subobscura. Genetica 2010; 138:819-29. [PMID: 20559686 DOI: 10.1007/s10709-010-9464-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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: 06/24/2009] [Accepted: 05/17/2010] [Indexed: 02/07/2023]
Abstract
Results from mitochondria (mt) DNA restriction site analyses (RSAs) have revealed that wild populations of Drosophila subobscura are formed by two common (I and II) and some rare, often endemic, low-frequency haplotypes. In the study reported here, we analysed nucleotide diversity in a 942-bp fragment of the mtDNA ND5 gene in 48 D. subobscura individuals captured from three populations that showed haplotypes I, II or the less common ones, as well as in one additional individual belonging to D. guanche that was taken as an outgroup. RSAs and sequencing results were compared. The two approaches yielded similar nucleotide variability parameters, suggesting a consistency in the results obtained from mtDNA dynamics in natural populations of D. subobscura. Patterns of polymorphism at ND5 are most consistent with the hypothesis of population expansion after a bottleneck that may have occurred since the last glaciation or which may occur seasonally after the summer and winter. However, we cannot rule out that selection has a role in maintaining the two major haplotypes at intermediate frequencies in worldwide populations of D. subobscura.
Collapse
Affiliation(s)
- José A Castro
- Laboratori de Genètica, Departament de Biologia, Edifici Guillem Colom, Facultat de Ciències, Universitat de les Illes Balears, Campus de la UIB, Palma de Mallorca 07122, Balearic Islands, Spain.
| | | | | | | | | | | |
Collapse
|
50
|
Abstract
A simple and rapid method of yeast strain characterization based on mitochondrial DNA restriction analysis was applied to the control of wine fermentations conducted by active dry yeast strains. This molecular approach allows us to understand several important aspects of this process, such as the role of the active dry yeast strain and that of the natural Saccharomyces cerevisiae flora during vinification. In this paper, we demonstrate that the inoculated strain is really responsible for the fermentation but does not suppress significant development of natural strains during the first stages. During this early period, natural strains could have important effects on wine flavor.
Collapse
Affiliation(s)
- A Querol
- Departamento de Microbiología and Departamento de Genética, Facultad de Ciencias Biológicas, Universidad de Valencia, 46100 Burjasot, and Unidad de Bioingeniería, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
| | | | | | | |
Collapse
|