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Volatile Aroma Compound Production Is Affected by Growth Rate in S. cerevisiae. Appl Environ Microbiol 2022; 88:e0150922. [PMID: 36377958 PMCID: PMC9746289 DOI: 10.1128/aem.01509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The initial growth rate of a yeast strain is a key parameter in the production of fermented beverages. Fast growth is linked with higher fermentative capacity and results in less slow and stuck fermentations unable to reach the expected final gravity. As concentrations of metabolites are in a constant state of flux, quantitative data on how growth rate affects the production of aromatic compounds becomes an important factor for brewers. Chemostats allow to set and keep a specific dilution rate throughout the fermentation and are ideal system to study the effect of growth on aroma production. In this study, we ran chemostats alongside batch and fed-batch cultures, compared volatile profiles detected at different growth rates, and identified those affected by the different feeding profiles. Specifically, we quantified six abundant aroma compounds produced in anaerobic glucose-limited continuous cultivations of S. cerevisiae at different dilution rates. We found that volatile production was affected by the growth rate in four out of six compounds assayed, with higher alcohols and esters following opposite trends. Batch and fed-batch fermentations were devised to study the extent by which the final concentration of volatile compounds is influenced by glucose availability. Compared with the batch system, fed-batch fermentations, where the yeast growth was artificially limited by a slow constant release of nutrients in the media, resulted in a significant increase in concentration of higher alcohols, mirroring the results obtained in continuous fermentations. This study paves the way to further process development optimization for the production of fermented beverages. IMPORTANCE The production of fermentation beverages will need to quickly adapt to changes in both the climate and customer demands, requiring the development of new strains and processes. Breakthroughs in the field are hindered by the limited knowledge on the interplay between physiology and aroma compound production in yeast. No quantitative data on how growth rate affects aroma profile is available in the literature to guide optimization of the complex flavors in fermented beverages. In this study, we exploited the chemostat system, alongside with batch and fed-batch cultures, to compare volatile profiles at different growth rates. We identified the aromatic compounds affected by the different feeding profiles and nutrient limitations. Moreover, we uncovered the correlation between yeast growth, esters, and higher alcohols production. This study showcases the potential of the application of feeding profiles for the manipulation of aroma in the craft beverage industry.
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2
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Effect of low temperature on the shaping of yeast-derived metabolite compositions during wine fermentation. Food Res Int 2022; 162:112016. [DOI: 10.1016/j.foodres.2022.112016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
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3
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Mendoza SN, Saa PA, Teusink B, Agosin E. Metabolic Modeling of Wine Fermentation at Genome Scale. Methods Mol Biol 2022; 2399:395-454. [PMID: 35604565 DOI: 10.1007/978-1-0716-1831-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wine fermentation is an ancient biotechnological process mediated by different microorganisms such as yeast and bacteria. Understanding of the metabolic and physiological phenomena taking place during this process can be now attained at a genome scale with the help of metabolic models. In this chapter, we present a detailed protocol for modeling wine fermentation using genome-scale metabolic models. In particular, we illustrate how metabolic fluxes can be computed, optimized and interpreted, for both yeast and bacteria under winemaking conditions. We also show how nutritional requirements can be determined and simulated using these models in relevant test cases. This chapter introduces fundamental concepts and practical steps for applying flux balance analysis in wine fermentation, and as such, it is intended for a broad microbiology audience as well as for practitioners in the metabolic modeling field.
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Affiliation(s)
| | - Pedro A Saa
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bas Teusink
- Systems Biology Lab, AIMMS, Vrije Universiteit, Amsterdam, The Netherlands
| | - Eduardo Agosin
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
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4
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Zhang L, Huang C, Johansen PG, Petersen MA, Poojary MM, Lund MN, Jespersen L, Arneborg N. The utilisation of amino acids by Debaryomyces hansenii and Yamadazyma triangularis associated with cheese. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Heavey MK, Anselmo AC. Modulating Oral Delivery and Gastrointestinal Kinetics of Recombinant Proteins via Engineered Fungi. AAPS J 2021; 23:76. [PMID: 34009532 PMCID: PMC8195623 DOI: 10.1208/s12248-021-00606-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022] Open
Abstract
A new modality in microbe-mediated drug delivery has recently emerged wherein genetically engineered microbes are used to locally deliver recombinant therapeutic proteins to the gastrointestinal tract. These engineered microbes are often referred to as live biotherapeutic products (LBPs). Despite advanced genetic engineering and recombinant protein expression approaches, little is known on how to control the spatiotemporal dynamics of LBPs and their secreted therapeutics within the gastrointestinal tract. To date, the fundamental pharmacokinetic analyses for microbe-mediated drug delivery systems have not been described. Here, we explore the pharmacokinetics of an engineered, model protein-secreting Saccharomyces cerevisiae, which serves as an ideal organism for the oral delivery of complex, post-translationally modified proteins. We establish three methods to modulate the pharmacokinetics of an engineered, recombinant protein-secreting fungi system: (i) altering oral dose of engineered fungi, (ii) co-administering antibiotics, and (iii) altering recombinant protein secretion titer. Our findings establish the fundamental pharmacokinetics which will be essential in controlling downstream therapeutic response for this new delivery modality.
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Affiliation(s)
- Mairead K Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, North Carolina, 27599, Chapel Hill, USA
| | - Aaron C Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, North Carolina, 27599, Chapel Hill, USA.
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6
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Influence of Temperature during Pre-Fermentative Maceration and Alcoholic Fermentation on the Phenolic Composition of 'Cabernet Sauvignon' Wines. Foods 2021; 10:foods10051053. [PMID: 34064824 PMCID: PMC8150270 DOI: 10.3390/foods10051053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/17/2022] Open
Abstract
This study presents the effects of different working temperatures on the transfer of compounds during the pre-fermentative and fermentative stages of the wine making process with ‘Cabernet Sauvignon’ grapes. Two different procedures have been evaluated. Firstly, the pre-fermentative maceration of the crushed grapes at two different temperatures (20 °C and 10 °C). Then, the alcoholic fermentation under two different sets of conditions, the fermentation at a constant temperature of 20 °C and the fermentation under a positive temperature gradient from 10 to 20 °C. According to the experimental results, the phenolic contents (total phenolics, total anthocyanins, and total tannins) were mainly conditioned by the fermentation temperature, however the pre-fermentative conditions also affected the content levels of these compounds. Furthermore, the use of a fermentation temperature gradient improved the organoleptic characteristics of the wines. However, the color was not as stable as that of wines produced through fermentation at a higher constant temperature. Consequently, the implementation of a temperature gradient during the alcoholic fermentation process is recommended and a longer period at high temperature over the last phase of the process would be desirable to obtain aromatic wines with the desirable color stability.
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7
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Lifestyle, Lineage, and Geographical Origin Influence Temperature-Dependent Phenotypic Variation across Yeast Strains during Wine Fermentation. Microorganisms 2020; 8:microorganisms8091367. [PMID: 32906626 PMCID: PMC7565122 DOI: 10.3390/microorganisms8091367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/17/2022] Open
Abstract
Saccharomyces cerevisiae yeasts are a diverse group of single-celled eukaryotes with tremendous phenotypic variation in fermentation efficiency, particularly at different temperatures. Yeast can be categorized into subsets based on lifestyle (Clinical, Fermentation, Laboratory, and Wild), genetic lineage (Malaysian, Mosaic, North American, Sake, West African, and Wine), and geographical origin (Africa, Americas, Asia, Europe, and Oceania) to start to understand their ecology; however, little is known regarding the extent to which these groupings drive S. cerevisiae fermentative ability in grape juice at different fermentation temperatures. To investigate the response of yeast within the different subsets, we quantified fermentation performance in grape juice by measuring the lag time, maximal fermentation rate (Vmax), and fermentation finishing efficiency of 34 genetically diverse S. cerevisiae strains in grape juice at five environmentally and industrially relevant temperatures (10, 15, 20, 25, and 30 °C). Extensive multivariate analysis was applied to determine the effects of lifestyle, lineage, geographical origin, strain, and temperature on yeast fermentation phenotypes. We show that fermentation capability is inherent to S. cerevisiae and that all factors are important in shaping strain fermentative ability, with temperature having the greatest impact, and geographical origin playing a lesser role than lifestyle or genetic lineage.
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Vieira D, Esteves S, Santiago C, Conde-Sousa E, Fernandes T, Pais C, Soares P, Franco-Duarte R. Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes. Microorganisms 2020; 8:E1001. [PMID: 32635509 PMCID: PMC7409325 DOI: 10.3390/microorganisms8071001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 01/30/2023] Open
Abstract
The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains' technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine-associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains' technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species.
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Affiliation(s)
- Daniel Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Soraia Esteves
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Carolina Santiago
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Eduardo Conde-Sousa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- CMUP—Centro de Matemática da Universidade do Porto, 4169-007 Porto, Portugal
| | - Ticiana Fernandes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Ricardo Franco-Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (D.V.); (S.E.); (C.S.); (E.C.-S.); (T.F.); (C.P.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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9
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Kulkarni SD, Zhou F, Sen ND, Zhang H, Hinnebusch AG, Lorsch JR. Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae. BMC Biol 2019; 17:101. [PMID: 31810458 PMCID: PMC6898956 DOI: 10.1186/s12915-019-0718-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Translation of an mRNA in eukaryotes starts at an AUG codon in most cases, but near-cognate codons (NCCs) such as UUG, ACG, and AUU can also be used as start sites at low levels in Saccharomyces cerevisiae. Initiation from NCCs or AUGs in the 5'-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. RESULTS Using reporter assays, we found that changes in growth temperature can affect translation from NCC start sites in yeast cells, suggesting the possibility that gene expression could be regulated by temperature by altering use of different uORF start codons. Using ribosome profiling, we provide evidence that growth temperature regulates the efficiency of translation of nearly 200 uORFs in S. cerevisiae. Of these uORFs, most that start with an AUG codon have increased translational efficiency at 37 °C relative to 30 °C and decreased efficiency at 20 °C. For translationally regulated uORFs starting with NCCs, we did not observe a general trend for the direction of regulation as a function of temperature, suggesting mRNA-specific features can determine the mode of temperature-dependent regulation. Consistent with this conclusion, the position of the uORFs in the 5'-leader relative to the 5'-cap and the start codon of the main ORF correlates with the direction of temperature-dependent regulation of uORF translation. We have identified several novel cases in which changes in uORF translation are inversely correlated with changes in the translational efficiency of the downstream main ORF. Our data suggest that translation of these mRNAs is subject to temperature-dependent, uORF-mediated regulation. CONCLUSIONS Our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae.
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Affiliation(s)
- Shardul D Kulkarni
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Neelam Dabas Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Present Address: School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Hongen Zhang
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Su Y, Gamero A, Rodríguez ME, Lopes CA, Querol A, Guillamón JM. Interspecific hybridisation among diverse Saccharomyces species: A combined biotechnological solution for low-temperature and nitrogen-limited wine fermentations. Int J Food Microbiol 2019; 310:108331. [DOI: 10.1016/j.ijfoodmicro.2019.108331] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/30/2019] [Accepted: 08/25/2019] [Indexed: 12/24/2022]
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11
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Sun ZG, Wang MQ, Wang YP, Xing S, Hong KQ, Chen YF, Guo XW, Xiao DG. Identification by comparative transcriptomics of core regulatory genes for higher alcohol production in a top-fermenting yeast at different temperatures in beer fermentation. Appl Microbiol Biotechnol 2019; 103:4917-4929. [DOI: 10.1007/s00253-019-09807-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/29/2022]
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12
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Talukder AA, Adnan N, Siddiqa A, Miah R, Tuli JF, Khan ST, Dey SK, Lertwattanasakul N, Yamada M. Fuel ethanol production using xylose assimilating and high ethanol producing thermosensitive Saccharomyces cerevisiae isolated from date palm juice in Bangladesh. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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García-Ríos E, Guillén A, de la Cerda R, Pérez-Través L, Querol A, Guillamón JM. Improving the Cryotolerance of Wine Yeast by Interspecific Hybridization in the Genus Saccharomyces. Front Microbiol 2019; 9:3232. [PMID: 30671041 PMCID: PMC6331415 DOI: 10.3389/fmicb.2018.03232] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/12/2018] [Indexed: 12/02/2022] Open
Abstract
Fermentations carried out at low temperatures (10–15°C) enhance the production and retention of flavor volatiles, but also increase the chances of slowing or arresting the process. Notwithstanding, as Saccharomyces cerevisiae is the main species responsible for alcoholic fermentation, other species of the genus Saccharomyces, such as cryophilic species Saccharomyces eubayanus, Saccharomyces kudriavzevii and Saccharomyces uvarum, are better adapted to low-temperature fermentations during winemaking. In this work, a Saccharomyces cerevisiae × S. uvarum hybrid was constructed to improve the enological features of a wine S. cerevisiae strain at low temperature. Fermentations of white grape musts were performed, and the phenotypic differences between parental and hybrid strains under different temperature conditions were examined. This work demonstrates that hybridization constitutes an effective approach to obtain yeast strains with desirable physiological features, like low-temperature fermentation capacity, which genetically depend on the expression of numerous genes (polygenic character). As this interspecific hybridization approach is not considered a GMO, the genetically improved strains can be quickly transferred to the wine industry.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Alba Guillén
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Roberto de la Cerda
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
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Mechanisms of Yeast Adaptation to Wine Fermentations. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:37-59. [PMID: 30911888 DOI: 10.1007/978-3-030-13035-0_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cells face genetic and/or environmental changes in order to outlast and proliferate. Characterization of changes after stress at different "omics" levels is crucial to understand the adaptation of yeast to changing conditions. Wine fermentation is a stressful situation which yeast cells have to cope with. Genome-wide analyses extend our cellular physiology knowledge by pointing out the mechanisms that contribute to sense the stress caused by these perturbations (temperature, ethanol, sulfites, nitrogen, etc.) and related signaling pathways. The model organism, Saccharomyces cerevisiae, was studied in response to industrial stresses and changes at different cellular levels (transcriptomic, proteomic, and metabolomics), which were followed statically and/or dynamically in the short and long terms. This chapter focuses on the response of yeast cells to the diverse stress situations that occur during wine fermentations, which induce perturbations, including nutritional changes, ethanol stress, temperature stress, oxidative stress, etc.
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Su Y, Origone AC, Rodríguez ME, Querol A, Guillamón JM, Lopes CA. Fermentative behaviour and competition capacity of cryotolerant Saccharomyces species in different nitrogen conditions. Int J Food Microbiol 2018; 291:111-120. [PMID: 30496940 DOI: 10.1016/j.ijfoodmicro.2018.11.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/12/2018] [Accepted: 11/18/2018] [Indexed: 01/03/2023]
Abstract
The selection of yeasts with low nitrogen requirement is a current need in winemaking. In this work, we analysed nitrogen requirements of strains belonging to the cryotolerant species S. uvarum, S. eubayanus and S. kudriavzevii, in order to evaluate their potential for conducting the fermentation of low nitrogen content grape musts. Our result demonstrated that S. eubayanus is the species less influenced by the increasing nitrogen concentrations in both growth and fermentation conditions. Strains showing the best behaviours, S. eubayanus NPCC 1285 and S. uvarum NPCC 1317, were selected to be tested in mixed cultures with S. cerevisiae T73 at different temperatures (12 °C, 20 °C and 28 °C) in synthetic grape must with different nitrogen concentrations (60, 140 and 300 mg/L YAN). The cryotolerant strains dominated the fermentations carried out at 12 °C while S. cerevisiae prevailed at 28 °C independently from the nitrogen concentration. At intermediate temperature, 20 °C, S. eubayanus mono and mixed cultures showed the best fermentative behaviour especially with low and intermediate nitrogen concentration. In summary, cryotolerant Saccharomyces species, particularly S. eubayanus, could be interesting tools to avoid fermentations stucks caused by low nitrogen content in grape musts.
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Affiliation(s)
- Ying Su
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Carrer del Catedràtic Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Andrea Cecilia Origone
- 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, Buenos Aires 1400, 8300, Neuquén, Argentina
| | - María Eugenia 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, Buenos Aires 1400, 8300, Neuquén, Argentina; Facultad de Ciencias Médicas, Universidad Nacional del Comahue, 8324 Cipolletti, Río Negro, Argentina
| | - Amparo Querol
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Carrer del Catedràtic Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Carrer del Catedràtic Agustín Escardino Benlloch, 7, 46980 Paterna, 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, Buenos Aires 1400, 8300, Neuquén, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, 8303 Cinco Saltos, Río Negro, Argentina.
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16
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Grape and Wine Metabolomics to Develop New Insights Using Untargeted and Targeted Approaches. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4040092] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chemical analysis of grape juice and wine has been performed for over 50 years in a targeted manner to determine a limited number of compounds using Gas Chromatography, Mass-Spectrometry (GC-MS) and High Pressure Liquid Chromatography (HPLC). Therefore, it only allowed the determination of metabolites that are present in high concentration, including major sugars, amino acids and some important carboxylic acids. Thus, the roles of many significant but less concentrated metabolites during wine making process are still not known. This is where metabolomics shows its enormous potential, mainly because of its capability in analyzing over 1000 metabolites in a single run due to the recent advancements of high resolution and sensitive analytical instruments. Metabolomics has predominantly been adopted by many wine scientists as a hypothesis-generating tool in an unbiased and non-targeted way to address various issues, including characterization of geographical origin (terroir) and wine yeast metabolic traits, determination of biomarkers for aroma compounds, and the monitoring of growth developments of grape vines and grapes. The aim of this review is to explore the published literature that made use of both targeted and untargeted metabolomics to study grapes and wines and also the fermentation process. In addition, insights are also provided into many other possible avenues where metabolomics shows tremendous potential as a question-driven approach in grape and wine research.
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17
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Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains. Metab Eng 2018; 49:178-191. [PMID: 30138679 DOI: 10.1016/j.ymben.2018.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/13/2018] [Accepted: 08/17/2018] [Indexed: 01/22/2023]
Abstract
Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of 'omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the 'low-alcohol' phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.
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18
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Kunthiphun S, Chokreansukchai P, Hondee P, Tanasupawat S, Savarajara A. Diversity and characterization of cultivable oleaginous yeasts isolated from mangrove forests. World J Microbiol Biotechnol 2018; 34:125. [PMID: 30083778 DOI: 10.1007/s11274-018-2507-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/20/2018] [Indexed: 12/20/2022]
Abstract
A total of 198 yeasts were isolated from 140 samples collected from 7 mangrove forests in 4 provinces of Thailand, and were found to belong to 30 genera, 45 described species and at least 12 undescribed species based on their 26S rRNA (D1/D2 domain) gene sequence. The most prevalent species was Candida tropicalis, followed by Candida pseudolambica and Rhodosporidium paludigena. Lipid accumulation, as determined by Nile red staining, of the isolated yeasts revealed that 69 and 18 strains were positive and strongly positive, respectively, while quantitative analysis of the intracellular lipid accumulated in the latter indicated that 10 of these strains, Pseudozyma tsukubaensis (YWT7-2 and YWT7-3), Rhodotorula sphaerocarpa (YWW6-1 and SFL14-1SF), Saitozyma podzolica (YWT1-1, NS3-3 and NS10-2), Prototheca zopfii var. hydrocarbonea OMS6-1 and Prototheca sp. (YMTW3-1 and YMTS5-2), were oleaginous. In this study we found that under nitrogen depletion condition (155 C/N ratio) Pseudozyma tsukubaensis YWT7-2 accumulated the highest level of intracellular lipid at 32.4% (w/w, dry cell weight), with a broadly similar fatty acid composition to that in palm oil.
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Affiliation(s)
- Sineenath Kunthiphun
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Puthita Chokreansukchai
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Patcharaporn Hondee
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Ancharida Savarajara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
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19
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Di Gianvito P, Perpetuini G, Tittarelli F, Schirone M, Arfelli G, Piva A, Patrignani F, Lanciotti R, Olivastri L, Suzzi G, Tofalo R. Impact of Saccharomyces cerevisiae strains on traditional sparkling wines production. Food Res Int 2018; 109:552-560. [DOI: 10.1016/j.foodres.2018.04.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/16/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
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20
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Enhanced arginine biosynthesis and lower proteolytic profile as indicators of Saccharomyces cerevisiae stress in stationary phase during fermentation of high sugar grape must: A proteomic evidence. Food Res Int 2018; 105:1011-1018. [DOI: 10.1016/j.foodres.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 11/19/2022]
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21
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Huseyin CE, Rubio RC, O'Sullivan O, Cotter PD, Scanlan PD. The Fungal Frontier: A Comparative Analysis of Methods Used in the Study of the Human Gut Mycobiome. Front Microbiol 2017; 8:1432. [PMID: 28824566 PMCID: PMC5534473 DOI: 10.3389/fmicb.2017.01432] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/14/2017] [Indexed: 01/20/2023] Open
Abstract
The human gut is host to a diverse range of fungal species, collectively referred to as the gut "mycobiome". The gut mycobiome is emerging as an area of considerable research interest due to the potential roles of these fungi in human health and disease. However, there is no consensus as to what the best or most suitable methodologies available are with respect to characterizing the human gut mycobiome. The aim of this study is to provide a comparative analysis of several previously published mycobiome-specific culture-dependent and -independent methodologies, including choice of culture media, incubation conditions (aerobic versus anaerobic), DNA extraction method, primer set and freezing of fecal samples to assess their relative merits and suitability for gut mycobiome analysis. There was no significant effect of media type or aeration on culture-dependent results. However, freezing was found to have a significant effect on fungal viability, with significantly lower fungal numbers recovered from frozen samples. DNA extraction method had a significant effect on DNA yield and quality. However, freezing and extraction method did not have any impact on either α or β diversity. There was also considerable variation in the ability of different fungal-specific primer sets to generate PCR products for subsequent sequence analysis. Through this investigation two DNA extraction methods and one primer set was identified which facilitated the analysis of the mycobiome for all samples in this study. Ultimately, a diverse range of fungal species were recovered using both approaches, with Candida and Saccharomyces identified as the most common fungal species recovered using culture-dependent and culture-independent methods, respectively. As has been apparent from ecological surveys of the bacterial fraction of the gut microbiota, the use of different methodologies can also impact on our understanding of gut mycobiome composition and therefore requires careful consideration. Future research into the gut mycobiome needs to adopt a common strategy to minimize potentially confounding effects of methodological choice and to facilitate comparative analysis of datasets.
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Affiliation(s)
- Chloe E Huseyin
- Teagasc Food Research Centre, TeagascFermoy, Ireland.,APC Microbiome Institute, Biosciences Institute, University College CorkCork, Ireland.,School of Microbiology, University College CorkCork, Ireland
| | - Raul Cabrera Rubio
- Teagasc Food Research Centre, TeagascFermoy, Ireland.,APC Microbiome Institute, Biosciences Institute, University College CorkCork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, TeagascFermoy, Ireland.,APC Microbiome Institute, Biosciences Institute, University College CorkCork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, TeagascFermoy, Ireland.,APC Microbiome Institute, Biosciences Institute, University College CorkCork, Ireland
| | - Pauline D Scanlan
- APC Microbiome Institute, Biosciences Institute, University College CorkCork, Ireland
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22
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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] [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.
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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.
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23
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Integrating transcriptomics and metabolomics for the analysis of the aroma profiles of Saccharomyces cerevisiae strains from diverse origins. BMC Genomics 2017; 18:455. [PMID: 28595605 PMCID: PMC5465573 DOI: 10.1186/s12864-017-3816-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/24/2017] [Indexed: 01/22/2023] Open
Abstract
Background During must fermentation thousands of volatile aroma compounds are formed, with higher alcohols, acetate esters and ethyl esters being the main aromatic compounds contributing to floral and fruity aromas. The action of yeast, in particular Saccharomyces cerevisiae, on the must components will build the architecture of the wine flavour and its fermentation bouquet. The objective of the present work was to better understand the molecular and metabolic bases of aroma production during a fermentation process. For such, comparative transcriptomic and metabolic analysis was performed at two time points (5 and 50 g/L of CO2 released) in fermentations conducted by four yeast strains from different origins and/or technological applications (cachaça, sake, wine, and laboratory), and multivariate factorial analyses were used to rationally identify new targets for improving aroma production. Results Results showed that strains from cachaça, sake and wine produced higher amounts of acetate esters, ethyl esters, acids and higher alcohols, in comparison with the laboratory strain. At fermentation time T1 (5 g/L CO2 released), comparative transcriptomics of the three S. cerevisiae strains from different fermentative environments in comparison with the laboratory yeast S288c, showed an increased expression of genes related with tetracyclic and pentacyclic triterpenes metabolism, involved in sterol synthesis. Sake strain also showed upregulation of genes ADH7 and AAD6, involved in the formation of higher alcohols in the Ehrlich pathway. For fermentation time point T2 (50 g/L CO2 released), again sake strain, but also VL1 strain, showed an increased expression of genes involved in formation of higher alcohols in the Ehrlich pathway, namely ADH7, ADH6 and AAD6, which is in accordance with the higher levels of methionol, isobutanol, isoamyl alcohol and phenylethanol observed. Conclusions Our approach revealed successful to integrate data from several technologies (HPLC, GC-MS, microarrays) and using different data analysis methods (PCA, MFA). The results obtained increased our knowledge on the production of wine aroma and flavour, identifying new gene in association to the formation of flavour active compounds, mainly in the production of fatty acids, and ethyl and acetate esters. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3816-1) contains supplementary material, which is available to authorized users.
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24
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Tronchoni J, García-Ríos E, Guillamón JM, Querol A, Pérez-Torrado R. Transcriptomic analysis of Saccharomyces cerevisiae x Saccharomyceskudriavzevii hybrids during low temperature winemaking. F1000Res 2017; 6:679. [PMID: 29067162 PMCID: PMC5635440 DOI: 10.12688/f1000research.11550.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Although Saccharomyces cerevisiae is the most frequently isolated species in wine fermentation, and the most studied species, other species and interspecific hybrids have greatly attracted the interest of researchers in this field in the last few years, given their potential to solve new winemaking industry challenges. S. cerevisiae x S. kudriavzevii hybrids exhibit good fermentative capabilities at low temperatures, and produce wines with smaller alcohol quantities and larger glycerol quantities, which can be very useful to solve challenges in the winemaking industry such as the necessity to enhance the aroma profile. METHODS In this study, we performed a transcriptomic study of S. cerevisiae x S. kudriavzevii hybrids in low temperature winemaking conditions. RESULTS The results revealed that the hybrids have acquired both fermentative abilities and cold adaptation abilities, attributed to S. cerevisiae and S. kudriavzevii parental species, respectively, showcasing their industrially relevant characteristics. For several key genes, we also studied the contribution to gene expression of each of the alleles of S. cerevisiae and S. kudriavzevii in the S. cerevisiae x S. kudriavzevii hybrids. From the results, it is not clear how important the differential expression of the specific parental alleles is to the phenotype of the hybrids. CONCLUSIONS This study shows that the fermentative abilities of S. cerevisiae x S. kudriavzevii hybrids at low temperatures do not seem to result from differential expression of specific parental alleles of the key genes involved in this phenotype.
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Affiliation(s)
- Jordi Tronchoni
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain.,Instituto de Ciencias de la Vid y del Vino (ICVV), Gobierno de La Rioja-CSIC-Universidad de La Rioja, Logroño, La Rioja, Spain
| | - Estéfani García-Ríos
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
| | - Jose Manuel Guillamón
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
| | - Roberto Pérez-Torrado
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
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25
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Benet M, Miguel A, Carrasco F, Li T, Planells J, Alepuz P, Tordera V, Pérez-Ortín JE. Modulation of protein synthesis and degradation maintains proteostasis during yeast growth at different temperatures. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:794-802. [PMID: 28461260 DOI: 10.1016/j.bbagrm.2017.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 02/03/2023]
Abstract
To understand how cells regulate each step in the flow of gene expression is one of the most fundamental goals in molecular biology. In this work, we have investigated several protein turnover-related steps in the context of gene expression regulation in response to changes in external temperature in model yeast Saccharomyces cerevisiae. We have found that the regulation of protein homeostasis is stricter than mRNA homeostasis. Although global translation and protein degradation rates are found to increase with temperature, the increase of the catalytic activity of ribosomes is higher than the global translation rate suggesting that yeast cells adapt the amount of translational machinery to the constraints imposed by kinetics in order to minimize energy costs. Even though the transcriptional machinery is subjected to the same constraints, we observed interesting differences between transcription and translation, which may be related to the different energy costs of the two processes as well as the differential functions of mRNAs and proteins.
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Affiliation(s)
- Marta Benet
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Ana Miguel
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Fany Carrasco
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Tianlu Li
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Jordi Planells
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Vicente Tordera
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
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26
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Deed RC, Fedrizzi B, Gardner RC. Saccharomyces cerevisiae FLO1 Gene Demonstrates Genetic Linkage to Increased Fermentation Rate at Low Temperatures. G3 (BETHESDA, MD.) 2017; 7:1039-1048. [PMID: 28143947 PMCID: PMC5345705 DOI: 10.1534/g3.116.037630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/25/2017] [Indexed: 01/14/2023]
Abstract
Low fermentation temperatures are of importance to food and beverage industries working with Saccharomyces cerevisiae Therefore, the identification of genes demonstrating a positive impact on fermentation kinetics is of significant interest. A set of 121 mapped F1 progeny, derived from a cross between haploid strains BY4716 (a derivative of the laboratory yeast S288C) and wine yeast RM11-1a, were fermented in New Zealand Sauvignon Blanc grape juice at 12.5°. Analyses of five key fermentation kinetic parameters among the F1 progeny identified a quantitative trait locus (QTL) on chromosome I with a significant degree of linkage to maximal fermentation rate (Vmax) at low temperature. Independent deletions of two candidate genes within the region, FLO1 and SWH1, were constructed in the parental strains (with S288C representing BY4716). Fermentation of wild-type and deletion strains at 12.5 and 25° confirmed that the genetic linkage to Vmax corresponds to the S288C version of the FLO1 allele, as the absence of this allele reduced Vmax by ∼50% at 12.5°, but not at 25°. Reciprocal hemizygosity analysis (RHA) between S288C and RM11-1a FLO1 alleles did not confirm the prediction that the S288C version of FLO1 was promoting more rapid fermentation in the opposing strain background, suggesting that the positive effect on Vmax derived from S288C FLO1 may only provide an advantage in haploids, or is dependent on strain-specific cis or trans effects. This research adds to the growing body of evidence demonstrating the role of FLO1 in providing stress tolerance to S. cerevisiae during fermentation.
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Affiliation(s)
- Rebecca C Deed
- School of Chemical Sciences, University of Auckland, 1010, New Zealand
- School of Biological Sciences, University of Auckland, 1010, New Zealand
| | - Bruno Fedrizzi
- School of Chemical Sciences, University of Auckland, 1010, New Zealand
| | - Richard C Gardner
- School of Biological Sciences, University of Auckland, 1010, New Zealand
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27
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Ballester-Tomás L, Prieto JA, Gil JV, Baeza M, Randez-Gil F. The Antarctic yeast Candida sake: Understanding cold metabolism impact on wine. Int J Food Microbiol 2017; 245:59-65. [PMID: 28131961 DOI: 10.1016/j.ijfoodmicro.2017.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/15/2017] [Accepted: 01/19/2017] [Indexed: 12/26/2022]
Abstract
Current winemaking trends include low-temperature fermentations and using non-Saccharomyces yeasts as the most promising tools to produce lower alcohol and increased aromatic complexity wines. Here we explored the oenological attributes of a C. sake strain, H14Cs, isolated in the sub-Antarctic region. As expected, the cold sea water yeast strain showed greater cold growth, Na+-toxicity resistance and freeze tolerance than the S. cerevisiae QA23 strain, which we used as a commercial wine yeast control. C. sake H14Cs was found to be more sensitive to ethanol. The fermentation trials of low-sugar content must demonstrated that C. sake H14Cs allowed the cold-induced lag phase of growth to be eliminated and also notably reduced the ethanol (-30%) and glycerol (-50%) content in wine. Instead C. sake produced sorbitol as a compatible osmolyte. Finally, the inspection of the main wine volatile compounds revealed that C. sake produced more higher alcohols than S. cerevisiae. In conclusion, our work evidences that using the Antarctic C. sake H14Cs yeast improves low-temperature must fermentations and has the potential to provide a wine with less ethanol and also particular attributes.
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Affiliation(s)
- Lidia Ballester-Tomás
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Av. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain
| | - Jose A Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Av. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain
| | - Jose V Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Av. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain; Food Technology Area, Faculty of Pharmacy, University of Valencia, Av. Vicente Andrés Estellés s/n, 46100 Burjassot, Valencia, Spain
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Av. Agustín Escardino, 7, 46980 Paterna, Valencia, Spain.
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28
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García-Ríos E, Querol A, Guillamón JM. iTRAQ-based proteome profiling of Saccharomyces cerevisiae and cryotolerant species Saccharomyces uvarum and Saccharomyces kudriavzevii during low-temperature wine fermentation. J Proteomics 2016; 146:70-9. [PMID: 27343759 DOI: 10.1016/j.jprot.2016.06.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED Temperature is one of the most important parameters to affect the duration and rate of alcoholic fermentation and final wine quality. Some species of the Saccharomyces genus have shown better adaptation at low temperature than Saccharomyces cerevisiae, which was the case of cryotolerant yeasts Saccharomyces uvarum and Saccharomyces kudriavzevii. In an attempt to detect inter-specific metabolic differences, we characterized the proteomic landscape of these cryotolerant species grown at 12°C and 28°C, which we compared with the proteome of S. cerevisiae (poorly adapted at low temperature). Our results showed that the main differences among the proteomic profiling of the three Saccharomyces strains grown at 12°C and 28°C lay in translation, glycolysis and amino acid metabolism. Our data corroborate previous transcriptomic results, which suggest that S. kudriavzevii is better adapted to grow at low temperature as a result of enhanced more efficient translation. Fitter amino acid biosynthetic pathways can also be mechanisms that better explain biomass yield in cryotolerant strains. Yet even at low temperature, S. cerevisiae is the most fermentative competitive species. A higher concentration of glycolytic and alcoholic fermentation enzymes in the S. cerevisiae strain might explain such greater fermentation activity. BIOLOGICAL SIGNIFICANCE Temperature is one of the main relevant environmental variables that microorganisms have to cope with and it is also a key factor in some industrial processes that involve microorganisms. However, we are still far from understanding the molecular and physiological mechanisms of adaptation at low temperatures. The results obtained in this study provided a global atlas of the proteome changes triggered by temperature in three different species of the genus Saccharomyces with different degree of cryotolerance. These results would facilitate a better understanding of mechanisms for how yeast could adapt at the low temperature of growth.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980 Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980 Paterna, Valencia, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980 Paterna, Valencia, Spain.
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Taymaz-Nikerel H, Cankorur-Cetinkaya A, Kirdar B. Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations. Front Bioeng Biotechnol 2016; 4:17. [PMID: 26925399 PMCID: PMC4757645 DOI: 10.3389/fbioe.2016.00017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/04/2016] [Indexed: 12/22/2022] Open
Abstract
Cells respond to environmental and/or genetic perturbations in order to survive and proliferate. Characterization of the changes after various stimuli at different -omics levels is crucial to comprehend the adaptation of cells to the changing conditions. Genome-wide quantification and analysis of transcript levels, the genes affected by perturbations, extends our understanding of cellular metabolism by pointing out the mechanisms that play role in sensing the stress caused by those perturbations and related signaling pathways, and in this way guides us to achieve endeavors, such as rational engineering of cells or interpretation of disease mechanisms. Saccharomyces cerevisiae as a model system has been studied in response to different perturbations and corresponding transcriptional profiles were followed either statically or/and dynamically, short and long term. This review focuses on response of yeast cells to diverse stress inducing perturbations, including nutritional changes, ionic stress, salt stress, oxidative stress, osmotic shock, and to genetic interventions such as deletion and overexpression of genes. It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions.
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Affiliation(s)
| | | | - Betul Kirdar
- Department of Chemical Engineering, Bogazici University , Istanbul , Turkey
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Bertrand E, Vandenberghe LPS, Soccol CR, Sigoillot JC, Faulds C. First Generation Bioethanol. GREEN FUELS TECHNOLOGY 2016. [DOI: 10.1007/978-3-319-30205-8_8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Gamero A, Belloch C, Querol A. Genomic and transcriptomic analysis of aroma synthesis in two hybrids between Saccharomyces cerevisiae and S. kudriavzevii in winemaking conditions. Microb Cell Fact 2015; 14:128. [PMID: 26336982 PMCID: PMC4558966 DOI: 10.1186/s12934-015-0314-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/10/2015] [Indexed: 11/12/2022] Open
Abstract
Background Aroma is one of the most important attributes defining wine quality in which yeasts play a crucial role, synthesizing aromatic compounds or releasing odourless conjugates. A present-day trend in winemaking consists of lowering fermentation temperature to achieve higher aroma production and retention. S.cerevisiae × S.kudriavzevii hybrids seem to have inherited beneficial traits from their parental species, like fermenting efficiently at low temperature or producing higher amounts of certain aromatic compounds. In this study, allelic composition and gene expression of the genes related to aroma synthesis in two genetically and phenotypically different S.cerevisiae × S.kudriavzevii hybrids, Lalvin W27 and VIN7, were compared and related to aroma production in microvinifications at 12 and 28 °C. In addition, the contribution of the allele coming from each parental to the overall expression was explored by RT-PCR. Results The results indicated large differences in allele composition, gene expression and the contribution of each parental to the overall expression at the fermentation temperatures tested. Results obtained by RT-PCR showed that in ARO1 and ATF2 genes the S.kudriavzevii allele was more expressed than that of S.cerevisiae particularly at 12 °C. Conclusions This study revealed high differences regarding allele composition and gene expression in two S.cerevisiae × S.kudriavzevii hybrids, which may have led to different aroma profiles in winemaking conditions. The contribution of the alleles coming from each parental to the overall expression has proved to differently influence aroma synthesis. Besides, the quantitative contribution to the overall gene expression of the alleles coming from one parental strain or the other was clearly determined by the fermentation temperature for some genes.
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Affiliation(s)
- Amparo Gamero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Avda/Agustín Escardino Benlloch, 7, 46980, Paterna, Valencia, Spain.
| | - Carmela Belloch
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Avda/Agustín Escardino Benlloch, 7, 46980, Paterna, Valencia, Spain.
| | - Amparo Querol
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Avda/Agustín Escardino Benlloch, 7, 46980, Paterna, Valencia, Spain.
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Barbosa C, Mendes-Faia A, Lage P, Mira NP, Mendes-Ferreira A. Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii. Microb Cell Fact 2015; 14:124. [PMID: 26314747 PMCID: PMC4552253 DOI: 10.1186/s12934-015-0318-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/14/2015] [Indexed: 02/01/2023] Open
Abstract
Background The introduction of yeast starter cultures consisting in a blend of Saccharomyces cerevisiae and non-Saccharomyces yeast strains is emerging for production of wines with improved complexity of flavor. The rational use of this approach is, however, dependent on knowing the impact that co-inoculation has in the physiology of S. cerevisiae. In this work the transcriptome of S.cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniasporaguilliermondii, this being the first time that this relevant yeast–yeast interaction is examined at a genomic scale. Results Co-inoculation with H. guilliermondii reduced the overall genome-wide transcriptional response of S. cerevisiae throughout the fermentation, which was attributable to a lower fermentative activity of S. cerevisiae while in the mixed-fermentation. Approximately 350 genes S. cerevisiae genes were found to be differently expressed (FDR < 0.05) in response to the presence of H. guilliermondii in the fermentation medium. Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. The differences in the aromatic profiles of wines obtained in the single and in the mixed-fermentations correlated with the differential expression of S. cerevisiae genes encoding enzymes required for formation of aroma compounds. Conclusions By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. The availability of nutrients, in particular, of nitrogen and vitamins, stands out as a factor that may determine population dynamics, fermentative activity and by-product formation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0318-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catarina Barbosa
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal.
| | - Arlete Mendes-Faia
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI-Biosystems and Integrative Sciences Institute, Campo Grande, Lisbon, Portugal.
| | - Patrícia Lage
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal.
| | - Nuno P Mira
- iBB-Institute for Bioengineering and Biosciences, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal. .,Department of Bioengineering, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Ana Mendes-Ferreira
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI-Biosystems and Integrative Sciences Institute, Campo Grande, Lisbon, Portugal.
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Ballester-Tomás L, Randez-Gil F, Pérez-Torrado R, Prieto JA. Redox engineering by ectopic expression of glutamate dehydrogenase genes links NADPH availability and NADH oxidation with cold growth in Saccharomyces cerevisiae. Microb Cell Fact 2015; 14:100. [PMID: 26156706 PMCID: PMC4496827 DOI: 10.1186/s12934-015-0289-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/23/2015] [Indexed: 01/21/2023] Open
Abstract
Background Cold stress reduces microbial growth and metabolism being relevant in industrial processes like wine making and brewing. Knowledge on the cold transcriptional response of Saccharomyces cerevisiae suggests the need of a proper redox balance. Nevertheless, there are no direct evidence of the links between NAD(P) levels and cold growth and how engineering of enzymatic reactions requiring NAD(P) may be used to modify the performance of industrial strains at low temperature. Results Recombinant strains of S. cerevisiae modified for increased NADPH- and NADH-dependent Gdh1 and Gdh2 activity were tested for growth at low temperature. A high-copy number of the GDH2-encoded glutamate dehydrogenase gene stimulated growth at 15°C, while overexpression of GDH1 had detrimental effects, a difference likely caused by cofactor preferences. Indeed, neither the Trp− character of the tested strains, which could affect the synthesis of NAD(P), nor changes in oxidative stress susceptibility by overexpression of GDH1 and GDH2 account for the observed phenotypes. However, increased or reduced NADPH availability by knock-out or overexpression of GRE3, the NADPH-dependent aldose reductase gene, eliminated or exacerbated the cold-growth defect observed in YEpGDH1 cells. We also demonstrated that decreased capacity of glycerol production impairs growth at 15 but not at 30°C and that 15°C-grown baker’s yeast cells display higher fermentative capacity than those cultivated at 30°C. Thus, increasing NADH oxidation by overexpression of GDH2 would help to avoid perturbations in the redox metabolism induced by a higher fermentative/oxidative balance at low temperature. Finally, it is shown that overexpression of GDH2 increases notably the cold growth in the wine yeast strain QA23 in both standard growth medium and synthetic grape must. Conclusions Redox constraints limit the growth of S. cerevisiae at temperatures below the optimal. An adequate supply of NAD(P) precursors as well as a proper level of reducing equivalents in the form of NADPH are required for cold growth. However, a major limitation is the increased need of oxidation of NADH to NAD+ at low temperature. In this scenario, our results identify the ammonium assimilation pathway as a target for the genetic improvement of cold growth in industrial strains. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0289-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lidia Ballester-Tomás
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Roberto Pérez-Torrado
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Jose Antonio Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
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Zakhartsev M, Yang X, Reuss M, Pörtner HO. Metabolic efficiency in yeast Saccharomyces cerevisiae in relation to temperature dependent growth and biomass yield. J Therm Biol 2015; 52:117-29. [PMID: 26267506 DOI: 10.1016/j.jtherbio.2015.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 11/16/2022]
Abstract
Canonized view on temperature effects on growth rate of microorganisms is based on assumption of protein denaturation, which is not confirmed experimentally so far. We develop an alternative concept, which is based on view that limits of thermal tolerance are based on imbalance of cellular energy allocation. Therefore, we investigated growth suppression of yeast Saccharomyces cerevisiae in the supraoptimal temperature range (30-40°C), i.e. above optimal temperature (Topt). The maximal specific growth rate (μmax) of biomass, its concentration and yield on glucose (Yx/glc) were measured across the whole thermal window (5-40°C) of the yeast in batch anaerobic growth on glucose. Specific rate of glucose consumption, specific rate of glucose consumption for maintenance (mglc), true biomass yield on glucose (Yx/glc(true)), fractional conservation of substrate carbon in product and ATP yield on glucose (Yatp/glc) were estimated from the experimental data. There was a negative linear relationship between ATP, ADP and AMP concentrations and specific growth rate at any growth conditions, whilst the energy charge was always high (~0.83). There were two temperature regions where mglc differed 12-fold, which points to the existence of a 'low' (within 5-31°C) and a 'high' (within 33-40°C) metabolic mode regarding maintenance requirements. The rise from the low to high mode occurred at 31-32°C in step-wise manner and it was accompanied with onset of suppression of μmax. High mglc at supraoptimal temperatures indicates a significant reduction of scope for growth, due to high maintenance cost. Analysis of temperature dependencies of product formation efficiency and Yatp/glc revealed that the efficiency of energy metabolism approaches its lower limit at 26-31°C. This limit is reflected in the predetermined combination of Yx/glc(true), elemental biomass composition and degree of reduction of the growth substrate. Approaching the limit implies a reduction of the safety margin of metabolic efficiency. We hypothesize that a temperature increase above Topt (e.g. >31°C) triggers both an increment in mglc and suppression of μmax, which together contribute to an upshift of Yatp/glc from the lower limit and thus compensate for the loss of the safety margin. This trade-off allows adding 10 more degrees to Topt and extends the thermal window up to 40°C, sustaining survival and reproduction in supraoptimal temperatures. Deeper understanding of the limits of thermal tolerance can be practically exploited in biotechnological applications.
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Affiliation(s)
- Maksim Zakhartsev
- Alfred Wegener Institute for Marine and Polar Research (AWI), Bremerhaven, Germany; Institute of Biochemical Engineering (IBVT), University of Stuttgart, Stuttgart, Germany; Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
| | - Xuelian Yang
- Institute of Biochemical Engineering (IBVT), University of Stuttgart, Stuttgart, Germany; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing, China
| | - Matthias Reuss
- Institute of Biochemical Engineering (IBVT), University of Stuttgart, Stuttgart, Germany
| | - Hans Otto Pörtner
- Alfred Wegener Institute for Marine and Polar Research (AWI), Bremerhaven, Germany
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Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability. PLoS One 2015; 10:e0122709. [PMID: 25884705 PMCID: PMC4401569 DOI: 10.1371/journal.pone.0122709] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12 h, 24 h and 96 h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape-musts and the development of strategies to optimize yeast performance in industrial fermentations.
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Transcriptional response of Saccharomyces cerevisiae to low temperature during wine fermentation. Antonie van Leeuwenhoek 2015; 107:1029-48. [DOI: 10.1007/s10482-015-0395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/22/2015] [Indexed: 01/31/2023]
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Marchal A, Marullo P, Durand C, Moine V, Dubourdieu D. Fermentative conditions modulating sweetness in dry wines: genetics and environmental factors influencing the expression level of the Saccharomyces cerevisiae HSP12 gene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:304-311. [PMID: 25524156 DOI: 10.1021/jf504408t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Yeast lees influence the organoleptic properties of wines by increasing their sweet taste. This effect is in part due to the protein Hsp12p, which is regulated by different stress response pathways in Saccharomyces cerevisiae. This work investigated the genetics and environmental factors influencing the expression level of the HSP12 gene in an enological context. RT-qPCR confirmed that the HSP12 expression level is regulated by temperature change and ethanol content during the alcoholic fermentation but not by the sugar content. Moreover, this gene shows an important variation according to the yeast strain used. For the first time yeast strain is demonstrated to play an important role in the perception of sweetness in red wine due to post-fermentation lees autolysis. Interestingly, a correlation between the expression level of HSP12 and the sweetness perception was found using yeast strains of different origins. All of the findings provide new insights on the contribution of yeast to wine taste.
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Zepeda AB, Figueroa CA, Abdalla DSP, Maranhão AQ, Ulloa PH, Pessoa A, Farías JG. Biomarkers to evaluate the effects of temperature and methanol on recombinant Pichia pastoris. Braz J Microbiol 2014; 45:475-83. [PMID: 25242930 PMCID: PMC4166271 DOI: 10.1590/s1517-83822014000200014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/09/2013] [Indexed: 02/06/2023] Open
Abstract
Pichia pastoris is methylotrophic yeast used as an efficient expression system for heterologous protein production. In order to evaluate the effects of temperature (10 and 30 °C) and methanol (1 and 3% (v/v)) on genetically-modified Pichia pastoris, different biomarkers were evaluated: Heat stress (HSF-1 and Hsp70), oxidative stress (OGG1 and TBARS) and antioxidant (GLR). Three yeast cultures were performed: 3X = 3% methanol-10 °C, 4X = 3% methanol-30 °C, and 5X = 1% methanol-10°C. The expression level of HIF-1α, HSF-1, HSP-70 and HSP-90 biomarkers were measured by Western blot and in situ detection was performed by immunocytochemistry. Ours results show that at 3% methanol −30 °C there is an increase of mitochondrial OGG1 (mtOGG1), Glutathione Reductase (GLR) and TBARS. In addition, there was a cytosolic expression of HSF-1 and HSP-70, which indicates a deprotection against nucleolar fragmentation (apoptosis). On the other hand, at 3% methanol −10 °C and 1% and at methanol −10 °C conditions there was nuclear expression of OGG1, lower levels of TBARS and lower expression of GLR, cytosolic expression of HSF-1 and nuclear expression HSP-70. In conclusion, our results suggest that 3% methanol-30 °C is a condition that induces a strong oxidative stress and risk factors of apoptosis in modified-genetically P. pastoris.
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Affiliation(s)
- Andrea B Zepeda
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile. ; Departamento de Tecnologia Bioquímico-Farmacêutica Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carolina A Figueroa
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile. ; Departamento de Tecnologia Bioquímico-Farmacêutica Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Dulcineia S P Abdalla
- Departamento de Análises Clínicas e Toxicológicas Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Andrea Q Maranhão
- Departamento de Biología Celular Instituto de Ciências Biológicas Universidade de Brasilia BrasíliaDF Brazil Departamento de Biología Celular, Instituto de Ciências Biológicas, Universidade de Brasilia, Brasília, DF, Brazil
| | - Patricio H Ulloa
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
| | - Adalberto Pessoa
- Departamento de Tecnologia Bioquímico-Farmacêutica Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jorge G Farías
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
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Use of chemostat cultures mimicking different phases of wine fermentations as a tool for quantitative physiological analysis. Microb Cell Fact 2014; 13:85. [PMID: 24928139 PMCID: PMC4070652 DOI: 10.1186/1475-2859-13-85] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 06/05/2014] [Indexed: 11/25/2022] Open
Abstract
Background Saccharomyces cerevisiae is the most relevant yeast species conducting the alcoholic fermentation that takes place during winemaking. Although the physiology of this model organism has been extensively studied, systematic quantitative physiology studies of this yeast under winemaking conditions are still scarce, thus limiting the understanding of fermentative metabolism of wine yeast strains and the systematic description, modelling and prediction of fermentation processes. In this study, we implemented and validated the use of chemostat cultures as a tool to simulate different stages of a standard wine fermentation, thereby allowing to implement metabolic flux analyses describing the sequence of metabolic states of S. cerevisae along the wine fermentation. Results Chemostat cultures mimicking the different stages of standard wine fermentations of S. cerevisiae EC1118 were performed using a synthetic must and strict anaerobic conditions. The simulated stages corresponded to the onset of the exponential growth phase, late exponential growth phase and cells just entering stationary phase, at dilution rates of 0.27, 0.04, 0.007 h−1, respectively. Notably, measured substrate uptake and product formation rates at each steady state condition were generally within the range of corresponding conversion rates estimated during the different batch fermentation stages. Moreover, chemostat data were further used for metabolic flux analysis, where biomass composition data for each condition was considered in the stoichiometric model. Metabolic flux distributions were coherent with previous analyses based on batch cultivations data and the pseudo-steady state assumption. Conclusions Steady state conditions obtained in chemostat cultures reflect the environmental conditions and physiological states of S. cerevisiae corresponding to the different growth stages of a typical batch wine fermentation, thereby showing the potential of this experimental approach to systematically study the effect of environmental relevant factors such as temperature, sugar concentration, C/N ratio or (micro) oxygenation on the fermentative metabolism of wine yeast strains.
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Tronchoni J, Medina V, Guillamón JM, Querol A, Pérez-Torrado R. Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations. BMC Genomics 2014; 15:432. [PMID: 24898014 PMCID: PMC4058008 DOI: 10.1186/1471-2164-15-432] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 05/27/2014] [Indexed: 11/24/2022] Open
Abstract
Background Comparative transcriptomics and functional studies of different Saccharomyces species have opened up the possibility of studying and understanding new yeast abilities. This is the case of yeast adaptation to stress, in particular the cold stress response, which is especially relevant for the food industry. Since the species Saccharomyces kudriavzevii is adapted to grow at low temperatures, it has been suggested that it contains physiological adaptations that allow it to rapidly and efficiently acclimatise after cold shock. Results In this work, we aimed to provide new insights into the molecular basis determining this better cold adaptation of S. kudriavzevii strains. To this end, we have compared S. cerevisiae and S. kudriavzevii transcriptome after yeast adapted to cold shock. The results showed that both yeast mainly activated the genes related to translation machinery by comparing 12°C with 28°C, but the S. kudriavzevii response was stronger, showing an increased expression of dozens of genes involved in protein synthesis. This suggested enhanced translation efficiency at low temperatures, which was confirmed when we observed increased resistance to translation inhibitor paromomycin. Finally, 35S-methionine incorporation assays confirmed the increased S. kudriavzevii translation rate after cold shock. Conclusions This work confirms that S. kudriavzevii is able to grow at low temperatures, an interesting ability for different industrial applications. We propose that this adaptation is based on its enhanced ability to initiate a quick, efficient translation of crucial genes in cold adaptation among others, a mechanism that has been suggested for other microorganisms. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-432) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Roberto Pérez-Torrado
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Burjassot, P,O, Box 73E-46100 Valencia, Spain.
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Gamero A, Belloch C, Ibáñez C, Querol A. Molecular analysis of the genes involved in aroma synthesis in the species S. cerevisiae, S. kudriavzevii and S. bayanus var. uvarum in winemaking conditions. PLoS One 2014; 9:e97626. [PMID: 24854353 PMCID: PMC4031168 DOI: 10.1371/journal.pone.0097626] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 04/23/2014] [Indexed: 11/19/2022] Open
Abstract
The Saccharomyces genus is the main yeast involved in wine fermentations to play a crucial role in the production and release of aromatic compounds. Despite the several studies done into the genome-wide expression analysis using DNA microarray technology in wine S. cerevisiae strains, this is the first to investigate other species of the Saccharomyces genus. This research work investigates the expression of the genes involved in flavor compound production in three different Saccharomyces species (S. cerevisiae, S. bayanus var. uvarum and S. kudriavzevii) under low (12°C) and moderate fermentation temperatures (28°C). The global genes analysis showed that 30% of genes appeared to be differently expressed in the three cryophilic strains if compared to the reference strain (mesophilic S. cerevisiae), suggesting a very close cold adaptation response. Remarkable differences in the gene expression level were observed when comparing the three species, S. cerevisiae, S. bayanus var. uvarum and S. kudriavzevii, which will result in different aroma profiles. Knowledge of these differences in the transcriptome can be a tool to help modulate aroma to create wines with the desired aromatic traits.
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Affiliation(s)
- Amparo Gamero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Carmela Belloch
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Clara Ibáñez
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
- * E-mail:
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42
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Petruzzi L, Sinigaglia M, Corbo MR, Campaniello D, Speranza B, Bevilacqua A. Decontamination of ochratoxin A by yeasts: possible approaches and factors leading to toxin removal in wine. Appl Microbiol Biotechnol 2014; 98:6555-67. [DOI: 10.1007/s00253-014-5814-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 10/25/2022]
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Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles. Appl Environ Microbiol 2014; 80:4433-49. [PMID: 24814792 DOI: 10.1128/aem.00785-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose and extracellular metabolites as well as CO2 production rates showed regular, reproducible circadian rhythms. DTC also led to waves of transcriptional activation and repression, which involved one-sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to respond primarily to changes in the glucose concentration. Elimination of known glucose-responsive genes revealed an overrepresentation of previously identified temperature-responsive genes as well as genes involved in the cell cycle and de novo purine biosynthesis. In-depth analysis demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that the 24-h DTC was sufficiently slow to allow S. cerevisiae chemostat cultures to acclimate their transcriptome and physiology at the DTC temperature maximum and to approach acclimation at the DTC temperature minimum. Furthermore, this comparison and literature data on growth rate-dependent cell cycle phase distribution indicated that cell cycle synchronization was most likely an effect of imposed fluctuations of the relative growth rate (μ/μmax) rather than a direct effect of temperature.
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López-Malo M, García-Rios E, Chiva R, Guillamon JM, Martí-Raga M. Effect of deletion and overexpression of tryptophan metabolism genes on growth and fermentation capacity at low temperature in wine yeast. Biotechnol Prog 2014; 30:776-83. [DOI: 10.1002/btpr.1915] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/01/2014] [Indexed: 11/11/2022]
Affiliation(s)
- María López-Malo
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
- Dept. de Bioquímica i Biotecnologia, Biotecnologia Enològica, Facultat d'Enologia; Universitat Rovira i Virgili; Marcel·li Domingo s/n, 43007 Tarragona Spain
| | - Estefani García-Rios
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
| | - Rosana Chiva
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
| | - José Manuel Guillamon
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
| | - María Martí-Raga
- Dept. de Bioquímica i Biotecnologia, Biotecnologia Enològica, Facultat d'Enologia; Universitat Rovira i Virgili; Marcel·li Domingo s/n, 43007 Tarragona Spain
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Orellana M, Aceituno FF, Slater AW, Almonacid LI, Melo F, Agosin E. Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon-sufficient, nitrogen-limited fermentative conditions. FEMS Yeast Res 2014; 14:412-24. [PMID: 24387769 DOI: 10.1111/1567-1364.12135] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/09/2013] [Accepted: 12/29/2013] [Indexed: 11/27/2022] Open
Abstract
During alcoholic fermentation, Saccharomyces cerevisiae is exposed to continuously changing environmental conditions, such as decreasing sugar and increasing ethanol concentrations. Oxygen, a critical nutrient to avoid stuck and sluggish fermentations, is only discretely available throughout the process after pump-over operation. In this work, we studied the physiological response of the wine yeast S. cerevisiae strain EC1118 to a sudden increase in dissolved oxygen, simulating pump-over operation. With this aim, an impulse of dissolved oxygen was added to carbon-sufficient, nitrogen-limited anaerobic continuous cultures. Results showed that genes related to mitochondrial respiration, ergosterol biosynthesis, and oxidative stress, among other metabolic pathways, were induced after the oxygen impulse. On the other hand, mannoprotein coding genes were repressed. The changes in the expression of these genes are coordinated responses that share common elements at the level of transcriptional regulation. Beneficial and detrimental effects of these physiological processes on wine quality highlight the dual role of oxygen in 'making or breaking wines'. These findings will facilitate the development of oxygen addition strategies to optimize yeast performance in industrial fermentations.
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Affiliation(s)
- Marcelo Orellana
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
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46
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Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2013; 3:1979-95. [PMID: 24062529 PMCID: PMC3815060 DOI: 10.1534/g3.113.006601] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lipids play a central role in cellular function as constituents of membranes, as signaling molecules, and as storage materials. Although much is known about the role of lipids in regulating specific steps of metabolism, comprehensive studies integrating genome-wide expression data, metabolite levels, and lipid levels are currently lacking. Here, we map condition-dependent regulation controlling lipid metabolism in Saccharomyces cerevisiae by measuring 5636 mRNAs, 50 metabolites, 97 lipids, and 57 (13)C-reaction fluxes in yeast using a three-factor full-factorial design. Correlation analysis across eight environmental conditions revealed 2279 gene expression level-metabolite/lipid relationships that characterize the extent of transcriptional regulation in lipid metabolism relative to major metabolic hubs within the cell. To query this network, we developed integrative methods for correlation of multi-omics datasets that elucidate global regulatory signatures. Our data highlight many characterized regulators of lipid metabolism and reveal that sterols are regulated more at the transcriptional level than are amino acids. Beyond providing insights into the systems-level organization of lipid metabolism, we anticipate that our dataset and approach can join an emerging number of studies to be widely used for interrogating cellular systems through the combination of mathematical modeling and experimental biology.
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47
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Petruzzi L, Bevilacqua A, Baiano A, Beneduce L, Corbo MR, Sinigaglia M. In vitro removal of ochratoxin A by two strains of Saccharomyces cerevisiae and their performances under fermentative and stressing conditions. J Appl Microbiol 2013; 116:60-70. [PMID: 24112596 DOI: 10.1111/jam.12350] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/28/2013] [Accepted: 09/13/2013] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this research was to study the effect of time, temperature, sugar content and addition of diammonium phosphate (DAP) on ochratoxin A (OTA) removal by two strains of Saccharomyces cerevisiae using a completely randomized design. METHODS AND RESULTS The strains were grown in a medium containing OTA (2 μg l(-1)), two sugar levels (200 and 250 g l(-1)), with or without DAP (300 mg l(-1)), and incubated at 25-30°C. The yeasts were able to decrease the toxin amount by c. 70%, with the highest removing effect observed after 3 days at 30°C in the presence of 250 g l(-1) of sugars and with DAP; after 10 days, the toxin was partially released into the medium. The strains produced high ethanol and glycerol contents, showed high tolerance to single/combined stress conditions and possessed β-d-glucosidase, pectinase and xylanase activities. CONCLUSIONS Ochratoxin A removal was affected by time, temperature, sugar and addition of DAP. Moreover, the phenomenon was reversible. SIGNIFICANCE AND IMPACT OF THE STUDY Ochratoxin A removal could be an interesting trait for the selection of promising strains; however, the strains removing efficiently the toxin could release it back; thus, the selection of the starter should take into account both the removal and the binding ability of OTA.
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Affiliation(s)
- L Petruzzi
- Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, Foggia, Italy
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48
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Quirós M, Martínez-Moreno R, Albiol J, Morales P, Vázquez-Lima F, Barreiro-Vázquez A, Ferrer P, Gonzalez R. Metabolic flux analysis during the exponential growth phase of Saccharomyces cerevisiae in wine fermentations. PLoS One 2013; 8:e71909. [PMID: 23967264 PMCID: PMC3742454 DOI: 10.1371/journal.pone.0071909] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/04/2013] [Indexed: 12/27/2022] Open
Abstract
As a consequence of the increase in global average temperature, grapes with the adequate phenolic and aromatic maturity tend to be overripe by the time of harvest, resulting in increased sugar concentrations and imbalanced C/N ratios in fermenting musts. This fact sets obvious additional hurdles in the challenge of obtaining wines with reduced alcohols levels, a new trend in consumer demands. It would therefore be interesting to understand Saccharomyces cerevisiae physiology during the fermentation of must with these altered characteristics. The present study aims to determine the distribution of metabolic fluxes during the yeast exponential growth phase, when both carbon and nitrogen sources are in excess, using continuous cultures. Two different sugar concentrations were studied under two different winemaking temperature conditions. Although consumption and production rates for key metabolites were severely affected by the different experimental conditions studied, the general distribution of fluxes in central carbon metabolism was basically conserved in all cases. It was also observed that temperature and sugar concentration exerted a higher effect on the pentose phosphate pathway and glycerol formation than on glycolysis and ethanol production. Additionally, nitrogen uptake, both quantitatively and qualitatively, was strongly influenced by environmental conditions. This work provides the most complete stoichiometric model used for Metabolic Flux Analysis of S. cerevisiae in wine fermentations employed so far, including the synthesis and release of relevant aroma compounds and could be used in the design of optimal nitrogen supplementation of wine fermentations.
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Affiliation(s)
- Manuel Quirós
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja), Logroño, Spain.
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49
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Kim IS, Kim YS, Kim H, Jin I, Yoon HS. Saccharomyces cerevisiae KNU5377 stress response during high-temperature ethanol fermentation. Mol Cells 2013; 35:210-8. [PMID: 23512334 PMCID: PMC3887908 DOI: 10.1007/s10059-013-2258-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 02/03/2023] Open
Abstract
Fuel ethanol production is far more costly to produce than fossil fuels. There are a number of approaches to cost-effective fuel ethanol production from biomass. We characterized stress response of thermotolerant Saccharomyces cerevisiae KNU5377 during glucose-based batch fermentation at high temperature (40°C). S. cerevisiae KNU5377 (KNU5377) transcription factors (Hsf1, Msn2/4, and Yap1), metabolic enzymes (hexokinase, glyceraldehyde-3-phosphate dehydrogenase, glucose-6-phosphate dehydrogenase, isocitrate dehydrogenase, and alcohol dehydrogenase), antioxidant enzymes (thioredoxin 3, thioredoxin reductase, and porin), and molecular chaperones and its cofactors (Hsp104, Hsp82, Hsp60, Hsp42, Hsp30, Hsp26, Cpr1, Sti1, and Zpr1) are upregulated during fermentation, in comparison to S. cerevisiae S288C (S288C). Expression of glyceraldehyde-3-phosphate dehydrogenase increased significantly in KNU5377 cells. In addition, cellular hydroperoxide and protein oxidation, particularly lipid peroxidation of triosephosphate isomerase, was lower in KNU5377 than in S288C. Thus, KNU5377 activates various cell rescue proteins through transcription activators, improving tolerance and increasing alcohol yield by rapidly responding to fermentation stress through redox homeostasis and proteostasis.
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Affiliation(s)
- Il-Sup Kim
- Advanced Bio-resource Research Center, Kyungpook National University, Daegu 702-701,
Korea
| | - Young-Saeng Kim
- Department of Biology, Kyungpook National University, Daegu 702-701,
Korea
| | - Hyun Kim
- Department of Microbiology, Kyungpook National University, Daegu 702-701,
Korea
| | - Ingnyol Jin
- Department of Microbiology, Kyungpook National University, Daegu 702-701,
Korea
| | - Ho-Sung Yoon
- Advanced Bio-resource Research Center, Kyungpook National University, Daegu 702-701,
Korea
- Department of Biology, Kyungpook National University, Daegu 702-701,
Korea
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50
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Kim IS, Kim HY, Kim YS, Choi HG, Kang SH, Yoon HS. Expression of dehydrin gene from Arctic Cerastium arcticum increases abiotic stress tolerance and enhances the fermentation capacity of a genetically engineered Saccharomyces cerevisiae laboratory strain. Appl Microbiol Biotechnol 2013; 97:8997-9009. [PMID: 23377791 DOI: 10.1007/s00253-013-4729-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/13/2013] [Accepted: 01/15/2013] [Indexed: 11/25/2022]
Abstract
We investigated Arctic plants to determine if they have a specific mechanism enabling them to adapt to extreme environments because they are subject to such conditions throughout their life cycles. Among the cell defense systems of the Arctic mouse-ear chickweed Cerastium arcticum, we identified a stress-responsive dehydrin gene CaDHN that belongs to the SK5 subclass and contains conserved regions with one S segment at the N-terminus and five K segments from the N-terminus to the C-terminus. To investigate the molecular properties of CaDHN, the yeast Saccharomyces was transformed with CaDHN. CaDHN-expressing transgenic yeast (TG) cells recovered more rapidly from challenge with exogenous stimuli, including oxidants (hydrogen peroxide, menadione, and tert-butyl hydroperoxide), high salinity, freezing and thawing, and metal (Zn(2+)), than wild-type (WT) cells. TG cells were sensitive to copper, cobalt, and sodium dodecyl sulfate. In addition, the cell survival of TG cells was higher than that of WT cells when cells at the mid-log and stationary stages were exposed to increased ethanol concentrations. There was a significant difference in cultures that have an ethanol content >16 %. During glucose-based batch fermentation at generally used (30 °C) and low (18 °C) temperatures, TG cells produced a higher alcohol concentration through improved cell survival. Specifically, the final alcohol concentrations were 13.3 and 13.2 % in TG cells during fermentation at 30 and 18 °C, respectively, whereas they were 10.2 and 9.4 %, respectively, in WT cells under the same fermentation conditions. An in vitro assay revealed that purified CaDHN acted as a reactive oxygen species scavenger by neutralizing H2O2 and a chaperone by preventing high temperature-mediated catalase inactivation. Taken together, our results show that CaDHN expression in transgenic yeast confers tolerance to various abiotic stresses by improving redox homeostasis and enhances fermentation capacity, especially at low temperatures (18 °C).
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Affiliation(s)
- Il-Sup Kim
- Advanced Bio-resource R&D Center, Department of Biology, College of Natural Sciences, Kyungpook National University, #1370 Sankyuk-dong, Buk-gu, Daegu, 702-701, Republic of Korea
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