1
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Henriques D, Minebois R, dos Santos D, Barrio E, Querol A, Balsa-Canto E. A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii. Microbiol Spectr 2023; 11:e0351922. [PMID: 37227304 PMCID: PMC10269563 DOI: 10.1128/spectrum.03519-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
Saccharomyces kudriavzevii is a cold-tolerant species identified as a good alternative for industrial winemaking. Although S. kudriavzevii has never been found in winemaking, its co-occurrence with Saccharomyces cerevisiae in Mediterranean oaks is well documented. This sympatric association is believed to be possible due to the different growth temperatures of the two yeast species. However, the mechanisms behind the cold tolerance of S. kudriavzevii are not well understood. In this work, we propose the use of a dynamic genome-scale model to compare the metabolic routes used by S. kudriavzevii at two temperatures, 25°C and 12°C, to decipher pathways relevant to cold tolerance. The model successfully recovered the dynamics of biomass and external metabolites and allowed us to link the observed phenotype with exact intracellular pathways. The model predicted fluxes that are consistent with previous findings, but it also led to novel results which we further confirmed with intracellular metabolomics and transcriptomic data. The proposed model (along with the corresponding code) provides a comprehensive picture of the mechanisms of cold tolerance that occur within S. kudriavzevii. The proposed strategy offers a systematic approach to explore microbial diversity from extracellular fermentation data at low temperatures. IMPORTANCE Nonconventional yeasts promise to provide new metabolic pathways for producing industrially relevant compounds and tolerating specific stressors such as cold temperatures. The mechanisms behind the cold tolerance of S. kudriavzevii or its sympatric relationship with S. cerevisiae in Mediterranean oaks are not well understood. This study proposes a dynamic genome-scale model to investigate metabolic pathways relevant to cold tolerance. The predictions of the model would indicate the ability of S. kudriavzevii to produce assimilable nitrogen sources from extracellular proteins present in its natural niche. These predictions were further confirmed with metabolomics and transcriptomic data. This finding suggests that not only the different growth temperature preferences but also this proteolytic activity may contribute to the sympatric association with S. cerevisiae. Further exploration of these natural adaptations could lead to novel engineering targets for the biotechnological industry.
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Affiliation(s)
- David Henriques
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
| | - Romain Minebois
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | | | - Eladio Barrio
- Genomics Department, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | - Eva Balsa-Canto
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
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2
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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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3
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Louet C, Blot C, Shelest E, Guerillot P, Zannini F, Pétrowski J, Frey P, Duplessis S. Annotation survey and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit. Fungal Genet Biol 2022; 161:103698. [PMID: 35483517 DOI: 10.1016/j.fgb.2022.103698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster -two of the most represented TF families in fungi- indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.
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Affiliation(s)
| | - Carla Blot
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Ekaterina Shelest
- School of biological Sciences, University of Portsmouth, King Henry 1 Street, PO1 D2Y, Portsmouth, United Kingdom
| | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
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4
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Tian Z, Du Y, Yang F, Zhao J, Liu S, Zhang D, Long CA. Chromosome Genome Sequencing and Comparative Transcriptome-Based Analyses of Kloeckera apiculata 34-9 Unveil the Potential Biocontrol Mechanisms Against Citrus Green Mold. Front Microbiol 2021; 12:752529. [PMID: 34858366 PMCID: PMC8631199 DOI: 10.3389/fmicb.2021.752529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/15/2021] [Indexed: 12/02/2022] Open
Abstract
Biological control is an environmentally friendly, safe, and replaceable strategy for disease management. Genome sequences of a certain biocontrol agent could lay a solid foundation for the research of molecular biology, and the more refined the reference genome, the more information it provides. In the present study, a higher resolution genome of Kloeckera apiculata 34-9 was assembled using high-throughput chromosome conformation capture (Hi-C) technology. A total of 8.07 M sequences of K. apiculata 34-9 genome was anchored onto 7 pesudochromosomes, which accounting for about 99.51% of the whole assembled sequences, and 4,014 protein-coding genes were annotated. Meanwhile, the detailed gene expression changes of K. apiculata 34-9 were obtained under low temperature and co-incubation with Penicillium digitatum treatments, respectively. Totally 254 differentially expressed genes (DEGs) were detected with low temperature treatment, of which 184 and 70 genes were upregulated and downregulated, respectively. Some candidate genes were significantly enriched in ribosome biosynthesis in eukaryotes and ABC transporters. The expression of gene Kap003732 and Kap001595 remained upregulated and downregulated through the entire time-points, respectively, indicating that they might be core genes for positive and negative response to low temperature stress. When co-incubation with P. digitatum, a total of 2,364 DEGs were found, and there were 1,247 upregulated and 1,117 downregulated genes, respectively. Biosynthesis of lysine and arginine, and phenylalanine metabolism were the highest enrichment of the cluster and KEGG analyses of the co-DEGs, the results showed that they might be involved in the positive regulation of K. apiculata 34-9 response to P. digitatum. The completeness of K. apiculata 34-9 genome and the transcriptome data presented here are essential for providing a high-quality genomic resource and it might serve as valuable molecular properties for further studies on yeast genome, expression pattern of biocontrol system, and postharvest citrus storage and preservation.
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Affiliation(s)
- Zhonghuan Tian
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
| | - Yujie Du
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
| | - Fan Yang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
| | - Juan Zhao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
| | - Shuqi Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
| | - Deyao Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
| | - Chao-An Long
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, China.,National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, China
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5
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Pinheiro T, Lip KYF, García-Ríos E, Querol A, Teixeira J, van Gulik W, Guillamón JM, Domingues L. Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions. Sci Rep 2020; 10:22329. [PMID: 33339840 PMCID: PMC7749138 DOI: 10.1038/s41598-020-77846-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/20/2020] [Indexed: 12/28/2022] Open
Abstract
Elucidation of temperature tolerance mechanisms in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- and supra-optimal temperatures under chemostat conditions. We employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains in all conditions was performed by sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS), allowing the quantification of 997 proteins, data available via ProteomeXchange (PXD016567). Our analysis demonstrated that temperature responses differ between the strains; however, we also found some common responsive proteins, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome. The proteomic data evidenced that the cold response involves strong repression of translation-related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation while, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects the yeast proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.
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Affiliation(s)
- Tânia Pinheiro
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Ka Ying Florence Lip
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Estéfani García-Ríos
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - José Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - José Manuel Guillamón
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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6
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Minebois R, Pérez‐Torrado R, Querol A. Metabolome segregation of four strains of
Saccharomyces cerevisiae
,
Saccharomyces uvarum
and
Saccharomyces kudriavzevii
conducted under low temperature oenological conditions. Environ Microbiol 2020; 22:3700-3721. [DOI: 10.1111/1462-2920.15135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Romain Minebois
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA‐CSIC Paterna E‐46980 Spain
| | - Roberto Pérez‐Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA‐CSIC Paterna E‐46980 Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA‐CSIC Paterna E‐46980 Spain
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7
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Lairón-Peris M, Pérez-Través L, Muñiz-Calvo S, Guillamón JM, Heras JM, Barrio E, Querol A. Differential Contribution of the Parental Genomes to a S. cerevisiae × S. uvarum Hybrid, Inferred by Phenomic, Genomic, and Transcriptomic Analyses, at Different Industrial Stress Conditions. Front Bioeng Biotechnol 2020; 8:129. [PMID: 32195231 PMCID: PMC7062649 DOI: 10.3389/fbioe.2020.00129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/10/2020] [Indexed: 01/09/2023] Open
Abstract
In European regions of cold climate, S. uvarum can replace S. cerevisiae in wine fermentations performed at low temperatures. S. uvarum is a cryotolerant yeast that produces more glycerol, less acetic acid and exhibits a better aroma profile. However, this species exhibits a poor ethanol tolerance compared with S. cerevisiae. In the present study, we obtained by rare mating (non-GMO strategy), and a subsequent sporulation, an interspecific S. cerevisiae × S. uvarum spore-derivative hybrid that improves or maintains a combination of parental traits of interest for the wine industry, such as good fermentation performance, increased ethanol tolerance, and high glycerol and aroma productions. Genomic sequencing analysis showed that the artificial spore-derivative hybrid is an allotriploid, which is very common among natural hybrids. Its genome contains one genome copy from the S. uvarum parental genome and two heterozygous copies of the S. cerevisiae parental genome, with the exception of a monosomic S. cerevisiae chromosome III, where the sex-determining MAT locus is located. This genome constitution supports that the original hybrid from which the spore was obtained likely originated by a rare-mating event between a mating-competent S. cerevisiae diploid cell and either a diploid or a haploid S. uvarum cell of the opposite mating type. Moreover, a comparative transcriptomic analysis reveals that each spore-derivative hybrid subgenome is regulating different processes during the fermentation, in which each parental species has demonstrated to be more efficient. Therefore, interactions between the two subgenomes in the spore-derivative hybrid improve those differential species-specific adaptations to the wine fermentation environments, already present in the parental species.
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Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Laura Pérez-Través
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Sara Muñiz-Calvo
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | | | - Eladio Barrio
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
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8
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DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species. Microorganisms 2020; 8:microorganisms8020296. [PMID: 32093408 PMCID: PMC7074839 DOI: 10.3390/microorganisms8020296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species.
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9
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Wang X, Tang D, Wang W. Adaptation strategies of
Pseudomonas protegens
SN15‐2 to hyperosmotic growth environment. J Appl Microbiol 2020; 128:1720-1734. [DOI: 10.1111/jam.14582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- X. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - D. Tang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - W. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
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10
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Gong M, Li Z, Wan J, Chen M, Wang H, Shang J, Zhou S, Tan Q, Wang Y, Bao D. Chilling stress reduced protein translation by the ubiquitination of ribosomal proteins in Volvariella volvacea. J Proteomics 2020; 215:103668. [PMID: 31982547 DOI: 10.1016/j.jprot.2020.103668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 01/08/2023]
Abstract
In Volvariella volvacea, an important edible mushroom species, cryogenic autolysis is a typical part of abnormal metabolism; however, the underlying mechanisms remain unclear. Ubiquitylome analysis revealed that chilling stress (CS) affected protein translation and degradation by ubiquitination. Comparative proteomics analysis showed that CS downregulated protein expression in V. volvacea V23 instead of VH3 (improved chilling stress resistance strain). The integrative ubiquitylome, proteomics, and transcriptome analyses indicated that CS reduced protein translation by the ubiquitination of ribosomal proteins. An activity assay of the 20S proteasome showed that CS decreased the degradation efficiency of the ubiquitin-proteasome system. UBEV2, one type of ubiquitin-conjugating enzyme E2 (UBE2) in V. volvacea, was upregulated after cold stress treatment using western blot analysis. GST pull-down experiments of UBEV2 provided evidence that CS affected protein translation by the ubiquitination of ribosomal proteins. Co-IP experiments confirmed that UBEV2 bound to the ubiquitinated SSB2, a ribosome-associated molecular chaperone. An anti-freezing experiment demonstrated that the UBE2 inhibitor could improve the cold stress resistance of V. volvacea. Our observations revealed that CS triggered ubiquitination-mediated autolysis associated with a decrease in protein translation and highlighted the mechanistic role of UBEV2 in facilitating cryogenic autolysis in V. volvacea. SIGNIFICANCE: Volvariella volvacea, the edible straw mushroom, is a highly nutritious food source widely cultivated on a commercial scale in tropical and subtropical regions. The challenges associated with the cryogenic autolysis preservation of V. volvacea have limited its marketability. This issue of cryogenic autolysis is both an interesting scientific problem to solve and a practical economic matter. Integrative ubiquitylome, proteomics, and transcriptome analyses, together with GST pulldown and Co-IP experiments, indicated that chilling stress reduced protein translation by the ubiquitination of ribosomal proteins in V. volvacea. This study significantly contributes to our understanding of ubiquitination-mediated autolysis associated with a decrease in protein translation in V. volvacea. Our data highlight the mechanistic role of UBEV2 in facilitating the cryogenic autolysis of V. volvacea. We provided a new idea for the preservation of V. volvacea by inhibiting UBEV2 to increase its marketability.
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Affiliation(s)
- Ming Gong
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhengpeng Li
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jianing Wan
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Mingjie Chen
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Hong Wang
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Junjun Shang
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Sichi Zhou
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Ying Wang
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
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11
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Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Gonçalves P, Sampaio JP, Libkind D, Hittinger CT. Fermentation innovation through complex hybridization of wild and domesticated yeasts. Nat Ecol Evol 2019; 3:1576-1586. [PMID: 31636426 DOI: 10.1038/s41559-019-0998-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022]
Abstract
The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries.
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Affiliation(s)
- Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Food Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - EmilyClare P Baker
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ursula Bond
- Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA. .,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. .,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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12
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Stress tolerance phenotype of industrial yeast: industrial cases, cellular changes, and improvement strategies. Appl Microbiol Biotechnol 2019; 103:6449-6462. [DOI: 10.1007/s00253-019-09993-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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13
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Macías LG, Morard M, Toft C, Barrio E. Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation. Front Genet 2019; 10:187. [PMID: 30930934 PMCID: PMC6425871 DOI: 10.3389/fgene.2019.00187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/21/2019] [Indexed: 12/02/2022] Open
Abstract
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis behind these phenotypic differences of biotechnological interest by using a species-based comparative genomics approach. In this work, we sequenced, assembled and annotated two new genomes of S. kudriavzevii. We used a combination of different statistical methods to identify functional divergence, signatures of positive selection and acceleration of substitution rates at specific amino acid sites of proteins in S. kudriavzevii when compared to S. cerevisiae, and vice versa. We provide a list of candidate genes in which positive selection could be acting during the evolution of both S. cerevisiae and S. kudriavzevii clades. Some of them could be related to certain important differences in metabolism previously reported by other authors such us DAL3 and ARO4, involved in nitrogen assimilation and amino acid biosynthesis. In addition, three of those genes (FBA1, ZIP1, and RQC2) showed accelerated evolutionary rates in Sk branch. Finally, genes of the riboflavin biosynthesis were also among those genes with a significant higher rate of nucleotide substitution and those proteins have amino acid positions contributing to functional divergence.
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Affiliation(s)
- Laura G Macías
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Miguel Morard
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
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14
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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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15
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Lopandic K. Saccharomyces interspecies hybrids as model organisms for studying yeast adaptation to stressful environments. Yeast 2018; 35:21-38. [PMID: 29131388 DOI: 10.1002/yea.3294] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/02/2017] [Accepted: 10/25/2017] [Indexed: 01/05/2023] Open
Abstract
The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes. Such fusing usually results in a wide variety of alterations at the genetic and chromosomal levels. The observed changes have suggested a high genome plasticity and a significant role of interspecies hybridization in the adaptation of yeasts to environmental stresses and industrial processes. There is a high probability that harsh wine and beer fermentation environments, from which the majority of interspecies hybrids have been isolated so far, influence their selection and stabilization as well as their genomic and phenotypic heterogeneity. The lessons we have learned about geno- and phenotype plasticity and the diversity of natural and commercial yeast hybrids have already had a strong impact on the development of artificial hybrids that can be successfully used in the fermentation-based food and beverage industry. The creation of artificial hybrids through the crossing of strains with desired attributes is a possibility to obtain a vast variety of new, but not genetically modified yeasts with a range of improved and beneficial traits. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Ksenija Lopandic
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11/3, A-1190, Vienna, Austria
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16
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Querol A, Pérez-Torrado R, Alonso-Del-Real J, Minebois R, Stribny J, Oliveira BM, Barrio E. New Trends in the Uses of Yeasts in Oenology. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 85:177-210. [PMID: 29860974 DOI: 10.1016/bs.afnr.2018.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The most important factor in winemaking is the quality of the final product and the new trends in oenology are dictated by wine consumers and producers. Traditionally the red wine is the most consumed and more popular; however, in the last times, the wine companies try to attract other groups of populations, especially young people and women that prefer sweet, whites or rosé wines, very fruity and with low alcohol content. Besides the new trends in consumer preferences, there are also increased concerns on the effects of alcohol consumption on health and the effects of global climate change on grape ripening and wine composition producing wines with high alcohol content. Although S. cerevisiae is the most frequent species in wines, and the subject of most studies, S. uvarum and hybrids between Saccharomyces species such as S. cerevisiae×S. kudriavzevii and S. cerevisiae×S. uvarum are also involved in wine fermentations and can be preponderant in certain wine regions. New yeast starters of non-cerevisiae strains (S. uvarum) or hybrids (S. cerevisiae×S. uvarum and S. cerevisiae×S. kudriavzevii) can contribute to solve some problems of the wineries. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts, while fulfilling the requirements of the commercial yeasts, such as a good fermentative performance and aromatic profiles that are of great interest for the wine industry. In this review, we will analyze different applications of nonconventional yeasts to solve the current winemaking demands.
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Affiliation(s)
- Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain.
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Romain Minebois
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Jiri Stribny
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Bruno M Oliveira
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
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17
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Ortiz-Tovar G, Pérez-Torrado R, Adam AC, Barrio E, Querol A. A comparison of the performance of natural hybrids Saccharomyces cerevisiae × Saccharomyces kudriavzevii at low temperatures reveals the crucial role of their S. kudriavzevii genomic contribution. Int J Food Microbiol 2018; 274:12-19. [PMID: 29574243 DOI: 10.1016/j.ijfoodmicro.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/17/2022]
Abstract
Fermentation performance at low temperature is a common approach to obtain wines with better aroma, and is critical in industrial applications. Natural hybrids S. cerevisiae × S. kudriavzevii, isolated from fermentations in cold-climate European countries, have provided an understanding of the mechanisms of adaptation to grow at low temperature. In this work, we studied the performance of 23 S. cerevisiae × S. kudriavzevii hybrids at low temperature (8, 12 and 24 °C) to characterize their phenotypes. Kinetic parameters and spot tests revealed a different ability to grow at low temperature. Interestingly, the genome content of the S. kudriavzevii in hybrids was moderately correlated with a shorter lag phase, and the genetic origin of hybrids influenced their performance at low temperature (8 °C). The parental expression of cold marker genes (NSR1, GUT2 and GPD1) showed that the relative expression of the S. kudriavzevii alleles was higher than the expression of the S. cerevisiae alleles in hybrids with a better growth at low-temperatures. These results suggest that the genomic contribution of S. kudriavzevii to hybrids is important for improving the fitness of these strains at low temperature.
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Affiliation(s)
- Guadalupe Ortiz-Tovar
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Ana Cris Adam
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, E-46980 Paterna, Spain.
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18
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Pérez-Torrado R, Barrio E, Querol A. Alternative yeasts for winemaking: Saccharomyces non-cerevisiae and its hybrids. Crit Rev Food Sci Nutr 2017; 58:1780-1790. [DOI: 10.1080/10408398.2017.1285751] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
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19
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Tronchoni J, García-Ríos E, Guillamón JM, Querol A, Pérez-Torrado R. Transcriptomic analysis of Saccharomyces cerevisiae x Saccharomyceskudriavzevii hybrids during low temperature winemaking. F1000Res 2017; 6:679. [PMID: 29067162 PMCID: PMC5635440 DOI: 10.12688/f1000research.11550.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Although Saccharomyces cerevisiae is the most frequently isolated species in wine fermentation, and the most studied species, other species and interspecific hybrids have greatly attracted the interest of researchers in this field in the last few years, given their potential to solve new winemaking industry challenges. S. cerevisiae x S. kudriavzevii hybrids exhibit good fermentative capabilities at low temperatures, and produce wines with smaller alcohol quantities and larger glycerol quantities, which can be very useful to solve challenges in the winemaking industry such as the necessity to enhance the aroma profile. METHODS In this study, we performed a transcriptomic study of S. cerevisiae x S. kudriavzevii hybrids in low temperature winemaking conditions. RESULTS The results revealed that the hybrids have acquired both fermentative abilities and cold adaptation abilities, attributed to S. cerevisiae and S. kudriavzevii parental species, respectively, showcasing their industrially relevant characteristics. For several key genes, we also studied the contribution to gene expression of each of the alleles of S. cerevisiae and S. kudriavzevii in the S. cerevisiae x S. kudriavzevii hybrids. From the results, it is not clear how important the differential expression of the specific parental alleles is to the phenotype of the hybrids. CONCLUSIONS This study shows that the fermentative abilities of S. cerevisiae x S. kudriavzevii hybrids at low temperatures do not seem to result from differential expression of specific parental alleles of the key genes involved in this phenotype.
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Affiliation(s)
- Jordi Tronchoni
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain.,Instituto de Ciencias de la Vid y del Vino (ICVV), Gobierno de La Rioja-CSIC-Universidad de La Rioja, Logroño, La Rioja, Spain
| | - Estéfani García-Ríos
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
| | - Jose Manuel Guillamón
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
| | - Roberto Pérez-Torrado
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain
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20
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Hypoxia and iron requirements are the main drivers in transcriptional adaptation of Kluyveromyces lactis during wine aerobic fermentation. Int J Food Microbiol 2017; 246:40-49. [DOI: 10.1016/j.ijfoodmicro.2017.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 01/06/2023]
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21
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Pathway swapping: Toward modular engineering of essential cellular processes. Proc Natl Acad Sci U S A 2016; 113:15060-15065. [PMID: 27956602 DOI: 10.1073/pnas.1606701113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent developments in synthetic biology enable one-step implementation of entire metabolic pathways in industrial microorganisms. A similarly radical remodelling of central metabolism could greatly accelerate fundamental and applied research, but is impeded by the mosaic organization of microbial genomes. To eliminate this limitation, we propose and explore the concept of "pathway swapping," using yeast glycolysis as the experimental model. Construction of a "single-locus glycolysis" Saccharomyces cerevisiae platform enabled quick and easy replacement of this yeast's entire complement of 26 glycolytic isoenzymes by any alternative, functional glycolytic pathway configuration. The potential of this approach was demonstrated by the construction and characterization of S. cerevisiae strains whose growth depended on two nonnative glycolytic pathways: a complete glycolysis from the related yeast Saccharomyces kudriavzevii and a mosaic glycolysis consisting of yeast and human enzymes. This work demonstrates the feasibility and potential of modular, combinatorial approaches to engineering and analysis of core cellular processes.
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22
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Salvadó Z, Ramos-Alonso L, Tronchoni J, Penacho V, García-Ríos E, Morales P, Gonzalez R, Guillamón JM. Genome-wide identification of genes involved in growth and fermentation activity at low temperature in Saccharomyces cerevisiae. Int J Food Microbiol 2016; 236:38-46. [PMID: 27442849 DOI: 10.1016/j.ijfoodmicro.2016.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/23/2016] [Accepted: 07/09/2016] [Indexed: 01/17/2023]
Abstract
Fermentation at low temperatures is one of the most popular current winemaking practices because of its reported positive impact on the aromatic profile of wines. However, low temperature is an additional hurdle to develop Saccharomyces cerevisiae wine yeasts, which are already stressed by high osmotic pressure, low pH and poor availability of nitrogen sources in grape must. Understanding the mechanisms of adaptation of S. cerevisiae to fermentation at low temperature would help to design strategies for process management, and to select and improve wine yeast strains specifically adapted to this winemaking practice. The problem has been addressed by several approaches in recent years, including transcriptomic and other high-throughput strategies. In this work we used a genome-wide screening of S. cerevisiae diploid mutant strain collections to identify genes that potentially contribute to adaptation to low temperature fermentation conditions. Candidate genes, impaired for growth at low temperatures (12°C and 18°C), but not at a permissive temperature (28°C), were deleted in an industrial homozygous genetic background, wine yeast strain FX10, in both heterozygosis and homozygosis. Some candidate genes were required for growth at low temperatures only in the laboratory yeast genetic background, but not in FX10 (namely the genes involved in aromatic amino acid biosynthesis). Other genes related to ribosome biosynthesis (SNU66 and PAP2) were required for low-temperature fermentation of synthetic must (SM) in the industrial genetic background. This result coincides with our previous findings about translation efficiency with the fitness of different wine yeast strains at low temperature.
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Affiliation(s)
- Zoel Salvadó
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain; Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Lucía Ramos-Alonso
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Vanessa Penacho
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Estéfani García-Ríos
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de la Rioja, Gobierno de La Rioja), Madre de Dios 51, 26006 Logroño, La Rioja, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain.
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23
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García-Ríos E, Querol A, Guillamón JM. iTRAQ-based proteome profiling of Saccharomyces cerevisiae and cryotolerant species Saccharomyces uvarum and Saccharomyces kudriavzevii during low-temperature wine fermentation. J Proteomics 2016; 146:70-9. [PMID: 27343759 DOI: 10.1016/j.jprot.2016.06.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED Temperature is one of the most important parameters to affect the duration and rate of alcoholic fermentation and final wine quality. Some species of the Saccharomyces genus have shown better adaptation at low temperature than Saccharomyces cerevisiae, which was the case of cryotolerant yeasts Saccharomyces uvarum and Saccharomyces kudriavzevii. In an attempt to detect inter-specific metabolic differences, we characterized the proteomic landscape of these cryotolerant species grown at 12°C and 28°C, which we compared with the proteome of S. cerevisiae (poorly adapted at low temperature). Our results showed that the main differences among the proteomic profiling of the three Saccharomyces strains grown at 12°C and 28°C lay in translation, glycolysis and amino acid metabolism. Our data corroborate previous transcriptomic results, which suggest that S. kudriavzevii is better adapted to grow at low temperature as a result of enhanced more efficient translation. Fitter amino acid biosynthetic pathways can also be mechanisms that better explain biomass yield in cryotolerant strains. Yet even at low temperature, S. cerevisiae is the most fermentative competitive species. A higher concentration of glycolytic and alcoholic fermentation enzymes in the S. cerevisiae strain might explain such greater fermentation activity. BIOLOGICAL SIGNIFICANCE Temperature is one of the main relevant environmental variables that microorganisms have to cope with and it is also a key factor in some industrial processes that involve microorganisms. However, we are still far from understanding the molecular and physiological mechanisms of adaptation at low temperatures. The results obtained in this study provided a global atlas of the proteome changes triggered by temperature in three different species of the genus Saccharomyces with different degree of cryotolerance. These results would facilitate a better understanding of mechanisms for how yeast could adapt at the low temperature of growth.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980 Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980 Paterna, Valencia, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980 Paterna, Valencia, Spain.
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24
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Lopandic K, Pfliegler WP, Tiefenbrunner W, Gangl H, Sipiczki M, Sterflinger K. Genotypic and phenotypic evolution of yeast interspecies hybrids during high-sugar fermentation. Appl Microbiol Biotechnol 2016; 100:6331-6343. [PMID: 27075738 DOI: 10.1007/s00253-016-7481-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/09/2016] [Accepted: 03/13/2016] [Indexed: 01/22/2023]
Abstract
The yeasts of the Saccharomyces genus exhibit a low pre-zygotic barrier and readily form interspecies hybrids. Following the hybridization event, the parental genomes undergo gross chromosomal rearrangements and genome modifications that may markedly influence the metabolic activity of descendants. In the present study, two artificially constructed hybrid yeasts (Saccharomyces cerevisiae x Saccharomyces uvarum and S. cerevisiae x Saccharomyces kudriavzevii) were used in order to evaluate the influence of high-sugar wine fermentation on the evolution of their genotypic and phenotypic properties. It was demonstrated that the extent of genomic modifications differs among the hybrids and their progeny, but that stress should not always be a generator of large genomic disturbances. The major genome changes were observed after meiosis in the F1 segregants in the form of the loss of different non-S. cerevisiae chromosomes. Under fermentation condition, each spore clone from a tetrad developed a mixed population characterized by different genotypic and phenotypic properties. The S. cerevisiae x S. uvarum spore clones revealed large modifications at the sequence level of the S. cerevisiae sub-genome, and some of the clones lost a few additional S. cerevisiae and S. uvarum chromosomes. The S. cerevisiae x S. kudriavzevii segregants were subjected to consecutive loss of the S. kudriavzevii markers and chromosomes. Both the hybrid types showed increased ethanol and glycerol production as well as better sugar consumption than their parental strains. The hybrid segregants responded differently to stress and a correlation was found between the observed genotypes and fermentation performances.
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Affiliation(s)
- Ksenija Lopandic
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 11, A-1190, Vienna, Austria.
| | - Walter P Pfliegler
- Department of Biotechnology and Microbiology, University of Debrecen & Postdoctoral Fellowship Programme of the Hungarian Academy of Sciences (MTA), Egyetem tér 1, Debrecen, H-4032, Hungary
| | | | - Helmut Gangl
- Bundesamt für Weinbau, Gölbeszeile 1, A-7000, Eisenstadt, Austria
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Katja Sterflinger
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 11, A-1190, Vienna, Austria
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Pérez-Torrado R, Oliveira BM, Zemančíková J, Sychrová H, Querol A. Alternative Glycerol Balance Strategies among Saccharomyces Species in Response to Winemaking Stress. Front Microbiol 2016; 7:435. [PMID: 27064588 PMCID: PMC4814467 DOI: 10.3389/fmicb.2016.00435] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/17/2016] [Indexed: 01/15/2023] Open
Abstract
Production and balance of glycerol is essential for the survival of yeast cells in certain stressful conditions as hyperosmotic or cold shock that occur during industrial processes as winemaking. These stress responses are well-known in S. cerevisiae, however, little is known in other phylogenetically close related Saccharomyces species associated with natural or fermentation environments such as S. uvarum, S. paradoxus or S. kudriavzevii. In this work we have investigated the expression of four genes (GPD1, GPD2, STL1, and FPS1) crucial in the glycerol pool balance in the four species with a biotechnological potential (S. cerevisiae; S. paradoxus; S. uvarum; and S. kudriavzevii), and the ability of strains to grow under osmotic and cold stresses. The results show different pattern and level of expression among the different species, especially for STL1. We also studied the function of Stl1 glycerol symporter in the survival to osmotic changes and cell growth capacity in winemaking environments. These experiments also revealed a different functionality of the glycerol transporters among the different species studied. All these data point to different strategies to handle glycerol accumulation in response to winemaking stresses as hyperosmotic or cold-hyperosmotic stress in the different species, with variable emphasis in the production, influx, or efflux of glycerol.
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Affiliation(s)
- Roberto Pérez-Torrado
- Food Biotechnology Department, Systems Biology in Yeast of Biotechnological Interest, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC Valencia, Spain
| | - Bruno M Oliveira
- Food Biotechnology Department, Systems Biology in Yeast of Biotechnological Interest, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC Valencia, Spain
| | - Jana Zemančíková
- Department of Membrane Transport, Institute of Physiology CAS, Prague, Czech Republic
| | - Hana Sychrová
- Department of Membrane Transport, Institute of Physiology CAS, Prague, Czech Republic
| | - Amparo Querol
- Food Biotechnology Department, Systems Biology in Yeast of Biotechnological Interest, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC Valencia, Spain
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26
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Szopinska A, Christ E, Planchon S, König H, Evers D, Renaut J. Stuck at work? Quantitative proteomics of environmental wine yeast strains reveals the natural mechanism of overcoming stuck fermentation. Proteomics 2016; 16:593-608. [DOI: 10.1002/pmic.201500225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 11/30/2015] [Accepted: 12/30/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Aleksandra Szopinska
- Department ‘Environmental Research and Innovation’; Luxembourg Institute of Science and Technology; Belvaux Grand-duchy of Luxembourg
| | - Eva Christ
- Institute of Microbiology and Wine Research; Johannes Gutenberg University Mainz; Mainz Germany
| | - Sebastien Planchon
- Department ‘Environmental Research and Innovation’; Luxembourg Institute of Science and Technology; Belvaux Grand-duchy of Luxembourg
| | - Helmut König
- Institute of Microbiology and Wine Research; Johannes Gutenberg University Mainz; Mainz Germany
| | - Daniele Evers
- Department ‘Environmental Research and Innovation’; Luxembourg Institute of Science and Technology; Belvaux Grand-duchy of Luxembourg
| | - Jenny Renaut
- Department ‘Environmental Research and Innovation’; Luxembourg Institute of Science and Technology; Belvaux Grand-duchy of Luxembourg
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27
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Stribny J, Gamero A, Pérez-Torrado R, Querol A. Saccharomyces kudriavzevii and Saccharomyces uvarum differ from Saccharomyces cerevisiae during the production of aroma-active higher alcohols and acetate esters using their amino acidic precursors. Int J Food Microbiol 2015; 205:41-6. [DOI: 10.1016/j.ijfoodmicro.2015.04.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/14/2015] [Accepted: 04/03/2015] [Indexed: 01/23/2023]
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28
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Sui Y, Wisniewski M, Droby S, Liu J. Responses of yeast biocontrol agents to environmental stress. Appl Environ Microbiol 2015; 81:2968-75. [PMID: 25710368 PMCID: PMC4393439 DOI: 10.1128/aem.04203-14] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological control of postharvest diseases, utilizing wild species and strains of antagonistic yeast species, is a research topic that has received considerable attention in the literature over the past 30 years. In principle, it represents a promising alternative to chemical fungicides for the management of postharvest decay of fruits, vegetables, and grains. A yeast-based biocontrol system is composed of a tritrophic interaction between a host (commodity), a pathogen, and a yeast species, all of which are affected by environmental factors such as temperature, pH, and UV light as well as osmotic and oxidative stresses. Additionally, during the production process, biocontrol agents encounter various severe abiotic stresses that also impact their viability. Therefore, understanding the ecological fitness of the potential yeast biocontrol agents and developing strategies to enhance their stress tolerance are essential to their efficacy and commercial application. The current review provides an overview of the responses of antagonistic yeast species to various environmental stresses, the methods that can be used to improve stress tolerance and efficacy, and the related mechanisms associated with improved stress tolerance.
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Affiliation(s)
- Yuan Sui
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Michael Wisniewski
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Kearneysville, West Virginia, USA
| | - Samir Droby
- Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Jia Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
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29
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Transcriptional response of Saccharomyces cerevisiae to low temperature during wine fermentation. Antonie van Leeuwenhoek 2015; 107:1029-48. [DOI: 10.1007/s10482-015-0395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/22/2015] [Indexed: 01/31/2023]
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30
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García-Ríos E, López-Malo M, Guillamón JM. Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations. BMC Genomics 2014; 15:1059. [PMID: 25471357 PMCID: PMC4265444 DOI: 10.1186/1471-2164-15-1059] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/26/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The wine industry needs better-adapted yeasts to grow at low temperature because it is interested in fermenting at low temperature to improve wine aroma. Elucidating the response to cold in Saccharomyces cerevisiae is of paramount importance for the selection or genetic improvement of wine strains. RESULTS We followed a global approach by comparing transcriptomic, proteomic and genomic changes in two commercial wine strains, which showed clear differences in their growth and fermentation capacity at low temperature. These strains were selected according to the maximum growth rate in a synthetic grape must during miniaturized batch cultures at different temperatures. The fitness differences of the selected strains were corroborated by directly competing during fermentations at optimum and low temperatures. The up-regulation of the genes of the sulfur assimilation pathway and glutathione biosynthesis suggested a crucial role in better performance at low temperature. The presence of some metabolites of these pathways, such as S-Adenosilmethionine (SAM) and glutathione, counteracted the differences in growth rate at low temperature in both strains. Generally, the proteomic and genomic changes observed in both strains also supported the importance of these metabolic pathways in adaptation at low temperature. CONCLUSIONS This work reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature. We propose that a greater activation of this metabolic route enhances the synthesis of key metabolites, such as glutathione, whose protective effects can contribute to improve the fermentation process.
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Affiliation(s)
- Estéfani García-Ríos
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
| | - María López-Malo
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
- />Biotecnologia Enològica. Departament de Bioquímica i Biotecnologia, Facultat de Enologia, Universitat Rovira i Virgili, Marcel•li Domingo s/n, 43007 Tarragona, Spain
| | - José Manuel Guillamón
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
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31
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Sardu A, Treu L, Campanaro S. Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software. BMC Genomics 2014; 15:1045. [PMID: 25441755 PMCID: PMC4302112 DOI: 10.1186/1471-2164-15-1045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/20/2014] [Indexed: 11/17/2022] Open
Abstract
Background RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains. Results In order to fill this gap, an innovative software called ORA (Overlapped Reads Assembler) was developed. This software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. It can also determine the size and the position of the untranslated regions (UTR) and of polycistronic transcripts. As a case study, we analyzed the transcriptional landscape of six S. cerevisiae strains in two different key steps of the fermentation process. This comparative analysis revealed differences in the UTR regions of transcripts. By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional role. Conclusions By comparing the results obtained using ORA with previous studies and with the transcriptome structure determined with other software, it was proven that ORA has a remarkable reliability. The results obtained from the training set made it possible to detect the presence of transcripts with variable UTRs between S. cerevisiae strains. Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1045) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Stefano Campanaro
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
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