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Lusakunwiwat P, Thananusak R, Nopgason R, Laoteng K, Vongsangnak W. Holistic transcriptional responses of Cordyceps militaris to different culture temperatures. Gene 2024; 923:148574. [PMID: 38768876 DOI: 10.1016/j.gene.2024.148574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Cordyceps militaris is a medicinal entomopathogenic fungus containing valuable biometabolites for pharmaceutical applications. Its genetic inheritance and environmental factors play a crucial role in the production of biomass enriched with cordycepin. While temperature is a crucial controlled parameter for fungal cultivation, its impacts on growth and metabolite biosynthesis remains poorly characterized. This study aimed to investigate the metabolic responses and cordycepin production of C. militaris strain TBRC6039 under various temperature conditions through transcriptome analysis. Among 9599 expressed genes, 576 genes were significantly differentially expressed at culture temperatures of 15 and 25 °C. The changes in the transcriptional responses induced by these temperatures were found in several metabolisms involved in nutrient assimilation and energy source, including amino acids metabolism (e.g., glycine, serine and threonine metabolism) and lipid metabolism (e.g., biosynthesis of unsaturated fatty acids and steroid biosynthesis). At the lower temperature (15 °C), the biosynthetic pathways of lipids, specifically ergosterol and squalene, were the target for maintaining membrane function by transcriptional upregulation. Our study revealed the responsive mechanisms of C. militaris in acclimatization to temperature conditions that provide an insight on physiological manipulation for the production of metabolites by C. militaris.
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Affiliation(s)
| | - Roypim Thananusak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Rujirek Nopgason
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
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2
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Planells-Cárcel A, Kazakova J, Pérez C, Gonzalez-Ramirez M, Garcia-Parrilla MC, Guillamón JM. A consortium of different Saccharomyces species enhances the content of bioactive tryptophan-derived compounds in wine fermentations. Int J Food Microbiol 2024; 416:110681. [PMID: 38490108 DOI: 10.1016/j.ijfoodmicro.2024.110681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
In recent years, the presence of molecules derived from aromatic amino acids in wines has been increasingly demonstrated to have a significant influence on wine quality and stability. In addition, interactions between different yeast species have been observed to influence these final properties. In this study, a screening of 81 yeast strains from different environments was carried out to establish a consortium that would promote the improvement of indolic compound levels in wine. Two strains, Saccharomyces uvarum and Saccharomyces eubayanus, with robust fermentative capacity were selected to be combined with a Saccharomyces cerevisiae strain with a predisposition towards the production of indolic compounds. Fermentation dynamics were studied in pure cultures, co-inoculations and sequential inoculations, analysing strain interactions and end-of-fermentation characteristics. Fermentations showing significant interactions were further analyzed for the resulting indolic compounds and aroma profile, with the aim of observing potential interactions and synergies resulting from the combination of different strains in the final wine. Sequential inoculation of S. cerevisiae after S. uvarum or S. eubayanus was observed to increase indolic compound levels, particularly serotonin and 3-indoleacetic acid. This study is the first to demonstrate how the formation of microbial consortia can serve as a useful strategy to enhance compounds with interesting properties in wine, paving the way for future studies and combinations.
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Affiliation(s)
- Andrés Planells-Cárcel
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
| | - Julia Kazakova
- Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González 2, 41012 Sevilla, Spain
| | - Cristina Pérez
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
| | - Marina Gonzalez-Ramirez
- Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González 2, 41012 Sevilla, Spain
| | - M Carmen Garcia-Parrilla
- Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González 2, 41012 Sevilla, Spain
| | - José M Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain.
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3
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Contreras‐Ruiz A, Minebois R, Alonso‐del‐Real J, Barrio E, Querol A. Differences in metabolism among Saccharomyces species and their hybrids during wine fermentation. Microb Biotechnol 2024; 17:e14476. [PMID: 38801338 PMCID: PMC11129674 DOI: 10.1111/1751-7915.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
This study aimed to investigate how parental genomes contribute to yeast hybrid metabolism using a metabolomic approach. Previous studies have explored central carbon and nitrogen metabolism in Saccharomyces species during wine fermentation, but this study analyses the metabolomes of Saccharomyces hybrids for the first time. We evaluated the oenological performance and intra- and extracellular metabolomes, and we compared the strains according to nutrient consumption and production of the main fermentative by-products. Surprisingly, no common pattern was observed for hybrid genome influence; each strain behaved differently during wine fermentation. However, this study suggests that the genome of the S. cerevisiae species may play a more relevant role in fermentative metabolism. Variations in biomass/nitrogen ratios were also noted, potentially linked to S. kudriavzevii and S. uvarum genome contributions. These results open up possibilities for further research using different "omics" approaches to comprehend better metabolic regulation in hybrid strains with genomes from different species.
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Affiliation(s)
- Alba Contreras‐Ruiz
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Romain Minebois
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Javier Alonso‐del‐Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
- Departament de GenèticaUniversitat de ValènciaValènciaSpain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
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4
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Crequer E, Ropars J, Jany J, Caron T, Coton M, Snirc A, Vernadet J, Branca A, Giraud T, Coton E. A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche. Evol Appl 2023; 16:1438-1457. [PMID: 37622099 PMCID: PMC10445096 DOI: 10.1111/eva.13578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 08/26/2023] Open
Abstract
Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue-cheese-making fungus Penicillium roqueforti. The two cheese populations show footprints of domestication, but the adaptation of the two non-cheese populations to their ecological niches (i.e., silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small-scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. The Termignon population indeed displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non-Roquefort population, and intermediate phenotypes between cheese and non-cheese populations. Phenotypically, the non-Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g., dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits for cheese-making in the cheese populations and enhanced ability to metabolise sugars in the lumber/spoiled food population, support the inference of domestication in cheese fungi and more generally of adaptation to anthropized environments.
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Affiliation(s)
- Ewen Crequer
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Luc Jany
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Thibault Caron
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Monika Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Alodie Snirc
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Philippe Vernadet
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Antoine Branca
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Tatiana Giraud
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Emmanuel Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
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5
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Yang C, Dong A, Deng L, Wang F, Liu J. Deciphering the change pattern of lipid metabolism in Saccharomyces cerevisiae responding to low temperature. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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6
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García-Ríos E, Guillamón JM. Genomic Adaptations of Saccharomyces Genus to Wine Niche. Microorganisms 2022; 10:microorganisms10091811. [PMID: 36144411 PMCID: PMC9500811 DOI: 10.3390/microorganisms10091811] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.
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Affiliation(s)
- Estéfani García-Ríos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
- Department of Science, Universidad Internacional de Valencia-VIU, Pintor Sorolla 21, 46002 Valencia, Spain
- Correspondence:
| | - José Manuel Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
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7
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Li C, Xu Y, Li Z, Cheng P, Yu G. Transcriptomic and metabolomic analysis reveals the potential mechanisms underlying the improvement of β-carotene and torulene production in Rhodosporidiobolus colostri under low temperature treatment. Food Res Int 2022; 156:111158. [DOI: 10.1016/j.foodres.2022.111158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
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8
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Genome-wide effect of non-optimal temperatures under anaerobic conditions on gene expression in Saccharomyces cerevisiae. Genomics 2022; 114:110386. [PMID: 35569731 DOI: 10.1016/j.ygeno.2022.110386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/28/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Understanding of thermal adaptation mechanisms in yeast is crucial to develop better-adapted strains to industrial processes, providing more economical and sustainable products. We have analyzed the transcriptomic responses of three Saccharomyces cerevisiae strains, a commercial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and a commercial bioethanol strain, Ethanol Red, grown at non-optimal temperatures under anaerobic chemostat conditions. Transcriptomic analysis of the three strains revealed a huge complexity of cellular mechanisms and responses. Overall, cold exerted a stronger transcriptional response in the three strains comparing with heat conditions, with a higher number of down-regulating genes than of up-regulating genes regardless the strain analyzed. The comparison of the transcriptome at both sub- and supra-optimal temperatures showed the presence of common genes up- or down-regulated in both conditions, but also the presence of common genes up- or down-regulated in the three studied strains. More specifically, we have identified and validated three up-regulated genes at sub-optimal temperature in the three strains, OPI3, EFM6 and YOL014W. Finally, the comparison of the transcriptomic data with a previous proteomic study with the same strains revealed a good correlation between gene activity and protein abundance, mainly at low temperature. Our work provides a global insight into the specific mechanisms involved in temperature adaptation regarding both transcriptome and proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.
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9
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Isolation and identification of aroma-producing non-Saccharomyces yeast strains and the enological characteristic comparison in wine making. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Guo R, He M, Zhang X, Ji X, Wei Y, Zhang QL, Zhang Q. Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature. Front Microbiol 2021; 12:727105. [PMID: 34603256 PMCID: PMC8481953 DOI: 10.3389/fmicb.2021.727105] [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: 06/18/2021] [Accepted: 08/26/2021] [Indexed: 12/20/2022] Open
Abstract
Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.
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Affiliation(s)
- Rui Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Meixia He
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiaoqing Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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Temperatures Outside the Optimal Range for Helicobacter pylori Increase Its Harboring within Candida Yeast Cells. BIOLOGY 2021; 10:biology10090915. [PMID: 34571792 PMCID: PMC8472035 DOI: 10.3390/biology10090915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/23/2022]
Abstract
Simple Summary Helicobacter pylori is associated with the development of diverse gastric pathologies. This bacterium has been shown to invade yeast to protect itself from environmental factors such as changes in pH, the presence of antibiotics or variations in nutrients that affect their viability. However, intra-yeast H. pylori has been reported from other sources, including food, or when the storage temperature is outside the optimal growth range for H. pylori, which is 30–37 °C. It is necessary to continue investigating the environmental factors that participate in the entry of the bacteria into yeast. In this work, it was evaluated whether temperature changes promote the entry of H. pylori into Candida and whether this endosymbiosis favors bacterial viability. It was observed that H. pylori significantly increased its invasiveness to yeast when these two microorganisms were co-cultured under 40 °C. The results support that H. pylori invades yeasts to protect itself from stressful environments, favoring its viability in these environments. In addition, it can be suggested that this microorganism would use yeast as a transmission vehicle, thereby contributing to its dissemination in the population. However, the latter still needs to be confirmed. Abstract Helicobacter pylori is capable of entering into yeast, but the factors driving this endosymbiosis remain unknown. This work aimed to determine if temperatures outside the optimal range for H. pylori increase its harboring within Candida. H. pylori strains were co-cultured with Candida strains in Brucella broth supplemented with 5% fetal bovine serum and incubated at 4, 25, 37 or 40 °C. After co-culturing, yeasts containing bacteria-like bodies (Y-BLBs) were observed by optical microscopy, and the bacterium were identified as H. pylori by FISH. The H. pylori 16S rRNA gene was amplified from the total DNA of Y-BLBs. The viability of intra-yeast H. pylori cells was confirmed using a viability assay. All H. pylori strains were capable of entering into all Candida strains assayed. The higher percentages of Y-BLBs are obtained at 40 °C with any of the Candida strains. H pylori also increased its harboring within yeast in co-cultures incubated at 25 °C when compared to those incubated at 37 °C. In conclusion, although H. pylori grew significantly at 40 °C, this temperature increased its harboring within Candida. The endosymbiosis between both microorganisms is strain-dependent and permits bacterial cells to remain viable under the stressing environmental conditions assayed.
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Aguiar‐Cervera JE, Delneri D, Severn O. A high‐throughput screening method for the discovery of
Saccharomyces
and non‐
Saccharomyces
yeasts with potential in the brewing industry. ENGINEERING BIOLOGY 2021; 5:72-80. [PMID: 36968259 PMCID: PMC9996697 DOI: 10.1049/enb2.12013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/03/2021] [Accepted: 08/19/2021] [Indexed: 12/28/2022] Open
Abstract
Both Saccharomyces and non-Saccharomyces yeast strains are of great importance for the fermentation industry, especially with the flourishing of craft breweries, which are driving current innovations. Non-conventional yeasts can produce novel beverages with attractive characteristics such as flavour, texture, and reduced alcohol content; however, they have been poorly explored. A new method for screening the fitness of conventional and non-conventional yeast libraries utilising robotic platforms and solidified media representing industrial conditions is proposed. As proof of concept, a library formed of 6 conventional and 17 non-conventional yeast strains was distributed in 96, 384 and 1536 arrays onto a YPD agar medium. Following this, the library was replicated in different conditions mimicking beer and cider fermentation conditions. The colony size was monitored over time, and fitness values measured in maximum pixels/h and maximum biomass were calculated. Significant differences in growth were observed in between the different strains and conditions. As examples, Candida milleri Y-7245 displayed good performance in wort conditions, and Kazachstania yakushimaensis Y-48837 stood out for its performance in apple juice. The method is proposed to be used as a pre-screening step when studying vast yeast libraries. This would enable interested parties to discover potential hits for further study at a low initial cost. Furthermore, this method can be used in other applications where the desired screening media can be solidified.
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Affiliation(s)
- Jose E. Aguiar‐Cervera
- Singer Instruments Co. Ltd Somerset UK
- Faculty of Biology Medicine and Health Manchester Institute of Biotechnology The University of Manchester Manchester UK
| | - Daniela Delneri
- Faculty of Biology Medicine and Health Manchester Institute of Biotechnology The University of Manchester Manchester UK
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13
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Lu S, Zheng F, Wen L, He Y, Wang D, Wu M, Wang B. Yeast engineering technologies and their applications to the food industry. FOOD BIOTECHNOL 2021. [DOI: 10.1080/08905436.2021.1942037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Siyan Lu
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Fei Zheng
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Liankui Wen
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Yang He
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Donghui Wang
- SBU of Agriculture, Sinochem Group Co., Ltd., Beijing, China
| | - Manyu Wu
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Bixiang Wang
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
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14
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Gonzalez R, Morales P. Truth in wine yeast. Microb Biotechnol 2021; 15:1339-1356. [PMID: 34173338 PMCID: PMC9049622 DOI: 10.1111/1751-7915.13848] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022] Open
Abstract
Evolutionary history and early association with anthropogenic environments have made Saccharomyces cerevisiae the quintessential wine yeast. This species typically dominates any spontaneous wine fermentation and, until recently, virtually all commercially available wine starters belonged to this species. The Crabtree effect, and the ability to grow under fully anaerobic conditions, contribute decisively to their dominance in this environment. But not all strains of Saccharomyces cerevisiae are equally suitable as starter cultures. In this article, we review the physiological and genetic characteristics of S. cerevisiae wine strains, as well as the biotic and abiotic factors that have shaped them through evolution. Limited genetic diversity of this group of yeasts could be a constraint to solving the new challenges of oenology. However, research in this field has for many years been providing tools to increase this diversity, from genetic engineering and classical genetic tools to the inclusion of other yeast species in the catalogues of wine yeasts. On occasion, these less conventional species may contribute to the generation of interspecific hybrids with S. cerevisiae. Thus, our knowledge about wine strains of S. cerevisiae and other wine yeasts is constantly expanding. Over the last decades, wine yeast research has been a pillar for the modernisation of oenology, and we can be confident that yeast biotechnology will keep contributing to solving any challenges, such as climate change, that we may face in the future.
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Affiliation(s)
- Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera de Burgos, km 6, Logroño, La Rioja, 26071, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera de Burgos, km 6, Logroño, La Rioja, 26071, Spain
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15
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Li R, Deed RC. Reciprocal hemizygosity analysis reveals that the Saccharomyces cerevisiae CGI121 gene affects lag time duration in synthetic grape must. G3-GENES GENOMES GENETICS 2021; 11:6157830. [PMID: 33681985 PMCID: PMC8759811 DOI: 10.1093/g3journal/jkab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/23/2021] [Indexed: 11/19/2022]
Abstract
It is standard practice to ferment white wines at low temperatures (10–18°C). However, low temperatures increase fermentation duration and risk of problem ferments, leading to significant costs. The lag duration at fermentation initiation is heavily impacted by temperature; therefore, identification of Saccharomyces cerevisiae genes influencing fermentation kinetics is of interest for winemaking. We selected 28 S. cerevisiae BY4743 single deletants, from a prior list of open reading frames (ORFs) mapped to quantitative trait loci (QTLs) on Chr. VII and XIII, influencing the duration of fermentative lag time. Five BY4743 deletants, Δapt1, Δcgi121, Δclb6, Δrps17a, and Δvma21, differed significantly in their fermentative lag duration compared to BY4743 in synthetic grape must (SGM) at 15 °C, over 72 h. Fermentation at 12.5°C for 528 h confirmed the longer lag times of BY4743 Δcgi121, Δrps17a, and Δvma21. These three candidates ORFs were deleted in S. cerevisiae RM11-1a and S288C to perform single reciprocal hemizygosity analysis (RHA). RHA hybrids and single deletants of RM11-1a and S288C were fermented at 12.5°C in SGM and lag time measurements confirmed that the S288C allele of CGI121 on Chr. XIII, encoding a component of the EKC/KEOPS complex, increased fermentative lag phase duration. Nucleotide sequences of RM11-1a and S288C CGI121 alleles differed by only one synonymous nucleotide, suggesting that intron splicing, codon bias, or positional effects might be responsible for the impact on lag phase duration. This research demonstrates a new role of CGI121 and highlights the applicability of QTL analysis for investigating complex phenotypic traits in yeast.
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Affiliation(s)
- Runze Li
- School of Chemical Sciences and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Rebecca C Deed
- School of Chemical Sciences and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
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16
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Yeast Fermentation at Low Temperatures: Adaptation to Changing Environmental Conditions and Formation of Volatile Compounds. Molecules 2021; 26:molecules26041035. [PMID: 33669237 PMCID: PMC7919833 DOI: 10.3390/molecules26041035] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
Yeast plays a key role in the production of fermented foods and beverages, such as bread, wine, and other alcoholic beverages. They are able to produce and release from the fermentation environment large numbers of volatile organic compounds (VOCs). This is the reason for the great interest in the possibility of adapting these microorganisms to fermentation at reduced temperatures. By doing this, it would be possible to obtain better sensory profiles of the final products. It can reduce the addition of artificial flavors and enhancements to food products and influence other important factors of fermented food production. Here, we reviewed the genetic and physiological mechanisms by which yeasts adapt to low temperatures. Next, we discussed the importance of VOCs for the food industry, their biosynthesis, and the most common volatiles in fermented foods and described the beneficial impact of decreased temperature as a factor that contributes to improving the composition of the sensory profiles of fermented foods.
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17
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Feng L, Wang J, Ye D, Song Y, Qin Y, Liu Y. Yeast population dynamics during spontaneous fermentation of icewine and selection of indigenous Saccharomyces cerevisiae strains for the winemaking in Qilian, China. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5385-5394. [PMID: 32535908 DOI: 10.1002/jsfa.10588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/08/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Icewine produced in China is becoming popular, but there is only limited knowledge available on the yeast population that occurs during fermentation and also on the selection of indigenous Saccharomyces cerevisiae strains for its production. In this work, we first investigated yeast species and the evolution of yeast population in spontaneous fermentations of icewine produced in the Qilian region of China and then analyzed the biodiversity and important enological properties of S. cerevisiae isolates. RESULTS Seven species of five genera including S. cerevisiae, S. uvarum, Torulaspora delbrueckii, Hanseniaspora uvarum, Lachancea thermotolerans, Metschnikowia aff. fructicola and H. osmophila were identified by the colony morphology on Wallerstein Laboratory Nutrient medium and sequence analysis of the 26S rRNA gene D1/D2 domain. Saccharomyces cerevisiae, H. uvarum and L. thermotolerans were the dominant species, representing almost 87% of the total yeast isolates. Microvinification with seven preselected S. cerevisiae strains were performed on Vidal. All selected strains could complete fermentations, and the enochemical parameters were within the acceptable ranges of the wine industry. W5B3 produced higher amounts of ethyl hexanoate and ethyl octanoate than other strains. R3A10 was a low volatile acid producer and the corresponding icewine presented the highest values on some odorants including β-damascenone, 1-octen-3-ol, ethyl 2-methylbutyrate, and isoamyl alcohol. Vidal icewines fermented with R3A10, R3A16 and W5B3 were well accepted by the judges because of superior sensory quality. CONCLUSION Three indigenous strains (R3A10, R3A16 and W5B3) could be used as starters and could potentially improve the regional character of the icewine in Qilian. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Li Feng
- Jiyang College of Zhejiang A&F University, Zhuji, China
- College of Enology, Northwest A&F University, Yangling, China
| | - Jiaming Wang
- Labstat International ULC, Chemistry, Kitchener, Ontario, Canada
| | - Dongqing Ye
- College of Enology, Northwest A&F University, Yangling, China
| | - Yuyang Song
- College of Enology, Northwest A&F University, Yangling, China
| | - Yi Qin
- College of Enology, Northwest A&F University, Yangling, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, Yangling, China
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18
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Next Generation Winemakers: Genetic Engineering in Saccharomyces cerevisiae for Trendy Challenges. Bioengineering (Basel) 2020; 7:bioengineering7040128. [PMID: 33066502 PMCID: PMC7712467 DOI: 10.3390/bioengineering7040128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
The most famous yeast of all, Saccharomyces cerevisiae, has been used by humankind for at least 8000 years, to produce bread, beer and wine, even without knowing about its existence. Only in the last century we have been fully aware of the amazing power of this yeast not only for ancient uses but also for biotechnology purposes. In the last decades, wine culture has become and more demanding all over the world. By applying as powerful a biotechnological tool as genetic engineering in S. cerevisiae, new horizons appear to develop fresh, improved, or modified wine characteristics, properties, flavors, fragrances or production processes, to fulfill an increasingly sophisticated market that moves around 31.4 billion € per year.
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19
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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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20
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Uncovering mechanisms of greengage wine fermentation against acidic stress via genomic, transcriptomic, and metabolic analyses of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:7619-7629. [DOI: 10.1007/s00253-020-10772-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023]
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21
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de Witt RN, Kroukamp H, Van Zyl WH, Paulsen IT, Volschenk H. QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance. FEMS Yeast Res 2020; 19:5528620. [PMID: 31276593 DOI: 10.1093/femsyr/foz047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Decoding the genetic basis of lignocellulosic inhibitor tolerance in Saccharomyces cerevisiae is crucial for rational engineering of bioethanol strains with enhanced robustness. The genetic diversity of natural strains present an invaluable resource for the exploration of complex traits of industrial importance from a pan-genomic perspective to complement the limited range of specialised, tolerant industrial strains. Natural S. cerevisiae isolates have lately garnered interest as a promising toolbox for engineering novel, genetically encoded tolerance phenotypes into commercial strains. To this end, we investigated the genetic basis for lignocellulosic inhibitor tolerance of natural S. cerevisiae isolates. A total of 12 quantitative trait loci underpinning tolerance were identified by next-generation sequencing linked bulk-segregant analysis of superior interbred pools. Our findings corroborate the current perspective of lignocellulosic inhibitor tolerance as a multigenic, complex trait. Apart from a core set of genetic variants required for inhibitor tolerance, an additional genetic background-specific response was observed. Functional analyses of the identified genetic loci revealed the uncharacterised ORF, YGL176C and the bud-site selection XRN1/BUD13 as potentially beneficial alleles contributing to tolerance to a complex lignocellulosic inhibitor mixture. We present evidence for the consideration of both regulatory and coding sequence variants for strain improvement.
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Affiliation(s)
- R N de Witt
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
| | - H Kroukamp
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde, NSW 2109, Australia
| | - W H Van Zyl
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
| | - I T Paulsen
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde, NSW 2109, Australia
| | - H Volschenk
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
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22
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Lip KYF, García-Ríos E, Costa CE, Guillamón JM, Domingues L, Teixeira J, van Gulik WM. Selection and subsequent physiological characterization of industrial Saccharomyces cerevisiae strains during continuous growth at sub- and- supra optimal temperatures. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00462. [PMID: 32477898 PMCID: PMC7251540 DOI: 10.1016/j.btre.2020.e00462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 11/04/2022]
Abstract
A phenotypic screening of 12 industrial yeast strains and the well-studied laboratory strain CEN.PK113-7D at cultivation temperatures between 12 °C and 40 °C revealed significant differences in maximum growth rates and temperature tolerance. From those 12, two strains, one performing best at 12 °C and the other at 40 °C, plus the laboratory strain, were selected for further physiological characterization in well-controlled bioreactors. The strains were grown in anaerobic chemostats, at a fixed specific growth rate of 0.03 h-1 and sequential batch cultures at 12 °C, 30 °C, and 39 °C. We observed significant differences in biomass and ethanol yields on glucose, biomass protein and storage carbohydrate contents, and biomass yields on ATP between strains and cultivation temperatures. Increased temperature tolerance coincided with higher energetic efficiency of cell growth, indicating that temperature intolerance is a result of energy wasting processes, such as increased turnover of cellular components (e.g. proteins) due to temperature induced damage.
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Affiliation(s)
- Ka Ying Florence Lip
- Department of Biotechnology, Delft University of Technology, Delft 2629HZ, the Netherlands
| | - Estéfani García-Ríos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Carlos E. Costa
- Centre of Biological Engineering, University of Minho, Braga 4710-057, Portugal
| | - José Manuel Guillamón
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lucília Domingues
- Centre of Biological Engineering, University of Minho, Braga 4710-057, Portugal
| | - José Teixeira
- Centre of Biological Engineering, University of Minho, Braga 4710-057, Portugal
| | - Walter M. van Gulik
- Department of Biotechnology, Delft University of Technology, Delft 2629HZ, the Netherlands
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23
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Microbial community composition and its role in volatile compound formation during the spontaneous fermentation of ice wine made from Vidal grapes. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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24
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Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
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25
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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26
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Correlating Genotype and Phenotype in the Asexual Yeast Candida orthopsilosis Implicates ZCF29 in Sensitivity to Caffeine. G3-GENES GENOMES GENETICS 2019; 9:3035-3043. [PMID: 31352406 PMCID: PMC6723125 DOI: 10.1534/g3.119.400348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Candida orthopsilosis is diploid asexual yeast that causes human disease. Most C. orthopsilosis isolates arose from at least four separate hybridizations between related, but not identical, parents. Here, we used population genomics data to correlate genotypic and phenotypic variation in 28 C. orthopsilosis isolates. We used cosine similarity scores to identify 65 variants with potential high-impact (deleterious effects) that correlated with specific phenotypes. Of these, 19 were Single Nucleotide Polymorphisms (SNPs) that changed stop or start codons, or splice sites. One variant resulted in a premature stop codon in both alleles of the gene ZCF29 in C. orthopsilosis isolate 185, which correlated with sensitivity to nystatin and caffeine. We used CRISPR-Cas9 editing to introduce this polymorphism into two resistant C. orthopsilosis isolates. Introducing the stop codon resulted in sensitivity to caffeine and to ketoconazole, but not to nystatin. Our analysis shows that it is possible to associate genomic variants with phenotype in asexual Candida species, but that only a small amount of genomic variation can be easily explored.
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27
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Marullo P, Durrens P, Peltier E, Bernard M, Mansour C, Dubourdieu D. Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study. BMC Genomics 2019; 20:680. [PMID: 31462217 PMCID: PMC6714461 DOI: 10.1186/s12864-019-5959-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. Among them, high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes. RESULTS In this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genes VHS1 and OYE2 characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (> 240 g/L of sugar) carried out at high temperatures (> 28 °C). Phenotypes impacted were mostly related to the late stage of alcoholic fermentation during the stationary growth phase of yeast. CONCLUSIONS Our findings illustrate the complex genetic determinism of stuck fermentation and open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.
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Affiliation(s)
- Philippe Marullo
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140, Bordeaux INP, Villenave d'Ornon, France. .,Biolaffort, 33100, Bordeaux, France.
| | - Pascal Durrens
- CNRS UMR 5800, University of Bordeaux, 33405, Talence, France.,Inria Bordeaux Sud-Ouest, Joint team Pleiade Inria/INRA/CNRS, 33405, Talence, France
| | - Emilien Peltier
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, 33100, Bordeaux, France
| | - Margaux Bernard
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, 33100, Bordeaux, France
| | | | - Denis Dubourdieu
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140, Bordeaux INP, Villenave d'Ornon, France
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28
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Peltier E, Friedrich A, Schacherer J, Marullo P. Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains. Front Genet 2019; 10:683. [PMID: 31396264 PMCID: PMC6664092 DOI: 10.3389/fgene.2019.00683] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/01/2019] [Indexed: 11/13/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is certainly the prime industrial microorganism and is related to many biotechnological applications including food fermentations, biofuel production, green chemistry, and drug production. A noteworthy characteristic of this species is the existence of subgroups well adapted to specific processes with some individuals showing optimal technological traits. In the last 20 years, many studies have established a link between quantitative traits and single-nucleotide polymorphisms found in hundreds of genes. These natural variations constitute a pool of QTNs (quantitative trait nucleotides) that modulate yeast traits of economic interest for industry. By selecting a subset of genes functionally validated, a total of 284 QTNs were inventoried. Their distribution across pan and core genome and their frequency within the 1,011 Saccharomyces cerevisiae genomes were analyzed. We found that 150 of the 284 QTNs have a frequency lower than 5%, meaning that these variants would be undetectable by genome-wide association studies (GWAS). This analysis also suggests that most of the functional variants are private to a subpopulation, possibly due to their adaptive role to specific industrial environment. In this review, we provide a literature survey of their phenotypic impact and discuss the opportunities and the limits of their use for industrial strain selection.
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Affiliation(s)
- Emilien Peltier
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
| | - Anne Friedrich
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Philippe Marullo
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
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29
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Somani A, Box WG, Smart KA, Powell CD. Physiological and transcriptomic response of Saccharomyces pastorianus to cold storage. FEMS Yeast Res 2019; 19:5420514. [PMID: 31073596 DOI: 10.1093/femsyr/foz025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/22/2019] [Indexed: 11/13/2022] Open
Abstract
Removal of yeast biomass at the end of fermentation, followed by a period of storage before re-inoculation into a subsequent fermentation, is common in the brewing industry. Storage is typically conducted at cold temperatures to preserve yeast quality, a practice which has unfavourable cost and environmental implications. To determine the potential for alleviating these effects, the transcriptomic and physiological response of Saccharomyces pastorianus strain W34/70 to standard (4°C) and elevated (10°C) storage temperatures was explored. Higher temperatures resulted in increased expression of genes associated with the production and mobilisation of intracellular glycogen, trehalose, glycerol and fatty acids, although these observations were limited to early stages of storage. Intracellular trehalose and glycerol concentrations were higher at 4°C than at 10°C, as a consequence of the cellular response to cold stress. However, significant changes in glycogen degradation or cellular fatty acid composition did not occur between the two sets of populations, ensuring that cell viability remained consistent. It is anticipated that this data may lead to changes in standard practice for handling yeast cultures, without compromising yeast quality. This work has significance not only for the brewing industry, but also for food and biofuel sectors requiring short-term storage of liquid yeast.
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Affiliation(s)
- Abhishek Somani
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom.,Institute of Biological, Environmental and Rural Sciences, Gogerddan Campus, University of Aberystwyth, Aberystwyth, Ceredigion, SY23 3EB, United Kingdom
| | - Wendy G Box
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Katherine A Smart
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom.,Department of Chemical Engineering and Biotechnology, University of Cambridge, Phillipa Fawcet Drive, Cambridge, Cambridgeshire, CB3 0AS, United Kingdom
| | - Chris D Powell
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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30
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García-Ríos E, Nuévalos M, Barrio E, Puig S, Guillamón JM. A new chromosomal rearrangement improves the adaptation of wine yeasts to sulfite. Environ Microbiol 2019; 21:1771-1781. [PMID: 30859719 DOI: 10.1111/1462-2920.14586] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 11/27/2022]
Abstract
Sulfite-generating compounds are widely used during winemaking as preservatives because of its antimicrobial and antioxidant properties. Thus, wine yeast strains have developed different genetic strategies to increase its sulfite resistance. The most efficient sulfite detoxification mechanism in Saccharomyces cerevisiae uses a plasma membrane protein called Ssu1 to efflux sulfite. In wine yeast strains, two chromosomal translocations (VIIItXVI and XVtXVI) involving the SSU1 promoter region have been shown to upregulate SSU1 expression and, as a result, increase sulfite tolerance. In this study, we have identified a novel chromosomal rearrangement that triggers wine yeast sulfite adaptation. An inversion in chromosome XVI (inv-XVI) probably due to sequence microhomology, which involves SSU1 and GCR1 regulatory regions, increases the expression of SSU1 and the sulfite resistance of a commercial wine yeast strain. A detailed dissection of this chimeric SSU1 promoter indicates that both the removed SSU1 promoter sequence and the relocated GCR1 sequence contribute to SSU1 upregulation and sulfite tolerance. However, no relevant function has been attributed to the SSU1-promoter-binding transcription factor Fzf1. These results unveil a new genomic event that confers an evolutive advantage to wine yeast strains.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Marcos Nuévalos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain.,Departament de Genètica, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
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31
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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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32
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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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33
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Feng L, Jia H, Qin Y, Song Y, Tao S, Liu Y. Rapid Identification of Major QTL S Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae. Front Microbiol 2018; 9:2110. [PMID: 30254614 PMCID: PMC6141824 DOI: 10.3389/fmicb.2018.02110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022] Open
Abstract
Temperatures had a strong effect on many life history traits, including growth, development and reproduction. At near-freezing temperatures (0–4°C), yeast cells could trigger series of biochemical reactions to respond and adapt to the stress, protect them against sever cold and freeze injury. Different Saccharomyces cerevisiae strains vary greatly in their ability to grow at near-freezing temperatures. However, the molecular mechanisms that allow yeast cells to sustain this response are not yet fully understood and the genetic basis of tolerance and sensitivity to near-freeze stress remains unclear. Uncovering the genetic determinants of this trait is, therefore, of is of significant interest. In order to investigate the genetic basis that underlies near-freezing temperature tolerance in S. cerevisiae, we mapped the major quantitative trait loci (QTLs) using bulk segregant analysis (BSA) in the F2 segregant population of two Chinese indigenous S. cerevisiae strains with divergent tolerance capability at 4°C. By genome-wide comparison of single-nucleotide polymorphism (SNP) profiles between two bulks of segregants with high and low tolerance to near-freezing temperature, a hot region located on chromosome IV was identified tightly associated with the near-freezing temperature tolerance. The Reciprocal hemizygosity analysis (RHA) and gene deletion was used to validate the genes involved in the trait, showed that the gene NAT1 plays a role in the near-freezing temperature tolerance. This study improved our understanding of the genetic basis of the variability of near-freezing temperature tolerance in yeasts. The superior allele identified could be used to genetically improve the near-freezing stress adaptation of industrial yeast strains.
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Affiliation(s)
- Li Feng
- College of Enology, Northwest A&F University, Yangling, China
| | - He Jia
- College of Enology, Northwest A&F University, Yangling, China
| | - Yi Qin
- College of Enology, Northwest A&F University, Yangling, China
| | - Yuyang Song
- College of Enology, Northwest A&F University, Yangling, China
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, Yangling, China
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34
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Gao YT, Zhang YS, Wen X, Song XW, Meng D, Li BJ, Wang MY, Tao YQ, Zhao H, Guan WQ, Du G. The glycerol and ethanol production kinetics in low-temperature wine fermentation usingSaccharomyces cerevisiaeyeast strains. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Ting Gao
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Yu-Shu Zhang
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Xiang Wen
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Xiao-Wan Song
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Dan Meng
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Bing-Juan Li
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Mei-Yan Wang
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Yong-Qing Tao
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Hui Zhao
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Wen-Qiang Guan
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Gang Du
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
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35
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Tapia SM, Cuevas M, Abarca V, Delgado V, Rojas V, García V, Brice C, Martínez C, Salinas F, Larrondo LF, Cubillos FA. GPD1 and ADH3 Natural Variants Underlie Glycerol Yield Differences in Wine Fermentation. Front Microbiol 2018; 9:1460. [PMID: 30018610 PMCID: PMC6037841 DOI: 10.3389/fmicb.2018.01460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
Glycerol is one of the most important by-products of alcohol fermentation, and depending on its concentration it can contribute to wine flavor intensity and aroma volatility. Here, we evaluated the potential of utilizing the natural genetic variation of non-coding regions in budding yeast to identify allelic variants that could modulate glycerol phenotype during wine fermentation. For this we utilized four Saccharomyces cerevisiae strains (WE - Wine/European, SA – Sake, NA – North American, and WA – West African), which were previously profiled for genome-wide Allele Specific Expression (ASE) levels. The glycerol yields under Synthetic Wine Must (SWM) fermentations differed significantly between strains; WA produced the highest glycerol yields while SA produced the lowest yields. Subsequently, from our ASE database, we identified two candidate genes involved in alcoholic fermentation pathways, ADH3 and GPD1, exhibiting significant expression differences between strains. A reciprocal hemizygosity assay demonstrated that hemizygotes expressing GPD1WA, GPD1SA, ADH3WA and ADH3SA alleles had significantly greater glycerol yields compared to GPD1WE and ADH3WE. We further analyzed the gene expression profiles for each GPD1 variant under SWM, demonstrating that the expression of GPD1WE occurred earlier and was greater compared to the other alleles. This result indicates that the level, timing, and condition of expression differ between regulatory regions in the various genetic backgrounds. Furthermore, promoter allele swapping demonstrated that these allele expression patterns were transposable across genetic backgrounds; however, glycerol yields did not differ between wild type and modified strains, suggesting a strong trans effect on GPD1 gene expression. In this line, Gpd1 protein levels in parental strains, particularly Gpd1pWE, did not necessarily correlate with gene expression differences, but rather with glycerol yield where low Gpd1pWE levels were detected. This suggests that GPD1WE is influenced by recessive negative post-transcriptional regulation which is absent in the other genetic backgrounds. This dissection of regulatory mechanisms in GPD1 allelic variants demonstrates the potential to exploit natural alleles to improve glycerol production in wine fermentation and highlights the difficulties of trait improvement due to alternative trans-regulation and gene-gene interactions in the different genetic background.
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Affiliation(s)
- Sebastián M Tapia
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile
| | - Mara Cuevas
- Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile
| | - Valentina Abarca
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile
| | - Verónica Delgado
- Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Vicente Rojas
- Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Verónica García
- Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago, Chile
| | - Claire Brice
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile
| | - Luis F Larrondo
- Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile
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36
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Eder M, Sanchez I, Brice C, Camarasa C, Legras JL, Dequin S. QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation. BMC Genomics 2018; 19:166. [PMID: 29490607 PMCID: PMC5831830 DOI: 10.1186/s12864-018-4562-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/20/2018] [Indexed: 01/07/2023] Open
Abstract
Background The volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermented beverages, such as wine. Although the metabolic pathways and genes behind yeast fermentative aroma formation are well described, little is known about the genetic mechanisms underlying variations between strains in the production of these aroma compounds. To increase our knowledge about the links between genetic variation and volatile production, we performed quantitative trait locus (QTL) mapping using 130 F2-meiotic segregants from two S. cerevisiae wine strains. The segregants were individually genotyped by next-generation sequencing and separately phenotyped during wine fermentation. Results Using different QTL mapping strategies, we were able to identify 65 QTLs in the genome, including 55 that influence the formation of 30 volatile secondary metabolites, 14 with an effect on sugar consumption and central carbon metabolite production, and 7 influencing fermentation parameters. For ethyl lactate, ethyl octanoate and propanol formation, we discovered 2 interacting QTLs each. Within 9 of the detected regions, we validated the contribution of 13 genes in the observed phenotypic variation by reciprocal hemizygosity analysis. These genes are involved in nitrogen uptake and metabolism (AGP1, ALP1, ILV6, LEU9), central carbon metabolism (HXT3, MAE1), fatty acid synthesis (FAS1) and regulation (AGP2, IXR1, NRG1, RGS2, RGT1, SIR2) and explain variations in the production of characteristic sensorial esters (e.g., 2-phenylethyl acetate, 2-metyhlpropyl acetate and ethyl hexanoate), higher alcohols and fatty acids. Conclusions The detection of QTLs and their interactions emphasizes the complexity of yeast fermentative aroma formation. The validation of underlying allelic variants increases knowledge about genetic variation impacting metabolic pathways that lead to the synthesis of sensorial important compounds. As a result, this work lays the foundation for tailoring S. cerevisiae strains with optimized volatile metabolite production for fermented beverages and other biotechnological applications. Electronic supplementary material The online version of this article (10.1186/s12864-018-4562-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Eder
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Isabelle Sanchez
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France.,MISTEA, INRA, SupAgro, F-34060, Montpellier, France
| | - Claire Brice
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Carole Camarasa
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Jean-Luc Legras
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Sylvie Dequin
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France.
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37
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Gallone B, Mertens S, Gordon JL, Maere S, Verstrepen KJ, Steensels J. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts. Curr Opin Biotechnol 2018; 49:148-155. [DOI: 10.1016/j.copbio.2017.08.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/20/2017] [Accepted: 08/14/2017] [Indexed: 11/27/2022]
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38
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Wine yeast phenomics: A standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions. PLoS One 2018; 13:e0190094. [PMID: 29351285 PMCID: PMC5774694 DOI: 10.1371/journal.pone.0190094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/07/2017] [Indexed: 11/19/2022] Open
Abstract
This work describes the set up of a small scale fermentation methodology for measuring quantitative traits of hundreds of samples in an enological context. By using standardized screw cap vessels, the alcoholic fermentation kinetics of Saccharomyces cerevisiae strains were measured by following their weight loss over the time. This dispositive was coupled with robotized enzymatic assays for measuring metabolites of enological interest in natural grape juices. Despite the small volume used, kinetic parameters and fermentation end products measured are similar with those observed in larger scale vats. The vessel used also offers the possibility to assay 32 volatiles compounds using a headspace solid-phase micro-extraction coupled to gas chromatography and mass spectrometry. The vessel shaking applied strongly impacted most of the phenotypes investigated due to oxygen transfer occuring in the first hours of the alcoholic fermentation. The impact of grape must and micro-oxygenation was investigated illustrating some relevant genetic x environmental interactions. By phenotyping a wide panel of commercial wine starters in five grape juices, broad phenotypic correlations between kinetics and metabolic end products were evidentiated. Moreover, a multivariate analysis illustrates that some grape musts are more able than others to discriminate commercial strains since some are less robust to environmental changes.
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39
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Quispe X, Tapia SM, Villarroel C, Oporto C, Abarca V, García V, Martínez C, Cubillos FA. Genetic basis of mycotoxin susceptibility differences between budding yeast isolates. Sci Rep 2017; 7:9173. [PMID: 28835621 PMCID: PMC5569051 DOI: 10.1038/s41598-017-09471-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/25/2017] [Indexed: 01/29/2023] Open
Abstract
Micophenolic acid (MPA) is an immunosuppressant mycotoxin which impairs yeast cell growth to variable degrees depending on the genetic background. Such variation could have emerged from several phenomena, including MPA gene resistance mutations and variations in copy number and localisation of resistance genes. To test this, we evaluated MPA susceptibility in four S. cerevisiae isolates and genetically dissected variation through the identification of Quantitative Trait Loci. Via linkage analysis we identified six QTLs, majority of which were located within subtelomeres and co-localised with IMD2, an inosine monophosphate dehydrogenase previously identified underlying MPA drug resistance in yeast cells. From chromosome end disruption and bioinformatics analysis, it was found that the subtelomere localisation of IMD2 within chromosome ends is variable depending on the strain, demonstrating the influence of IMD2 on the natural variation in yeast MPA susceptibility. Furthermore, GxE gene expression analysis of strains exhibiting opposite phenotypes indicated that ribosome biogenesis, RNA transport, and purine biosynthesis were impaired in strains most susceptible to MPA toxicity. Our results demonstrate that natural variation can be exploited to better understand the molecular mechanisms underlying mycotoxin susceptibility in eukaryote cells and demonstrate the role of subtelomeric regions in mediating interactions with the environment.
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Affiliation(s)
- Xtopher Quispe
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Sebastián M Tapia
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Carlos Villarroel
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Christian Oporto
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Valentina Abarca
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Verónica García
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile. .,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile. .,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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