1
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Fukuda N. Apparent diameter and cell density of yeast strains with different ploidy. Sci Rep 2023; 13:1513. [PMID: 36707648 PMCID: PMC9883461 DOI: 10.1038/s41598-023-28800-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Optical density at 600 nm (OD600) measurements are routinely and quickly taken to estimate cell density in cultivation and to track cell growth. The yeast Saccharomyces cerevisiae is one of the microorganisms most used in industry, and the OD600 values are frequently adopted as the indicator of yeast cell density, according to the Beer-Lambert law. Because the OD600 value is based on turbidity measurement, the Beer-Lambert law can be applied only for microbial cultivation with low cell densities. The proportionality constants strongly depend on several parameters such as cell size. Typically, yeast strains are categorized into haploids and diploids. It is well known that cell size of diploid yeasts is larger than haploid cells. Additionally, polyploid (especially triploid and tetraploid) yeast cells are also employed in several human-activities such as bread-making and lager-brewing. As a matter of fact, there is almost no attention paid to the difference in the proportionality constants depending on the yeast ploidy. This study presents information for cell size of haploid, diploid, triploid, and tetraploid yeasts with isogenic background, and describes their proportionality constants (k) corresponding to the molar extinction coefficient (ε) in the Beer-Lambert law. Importantly, it was found that the constants are inversely proportional to apparent cell diameters estimated by flow cytometric analysis. Although each cell property highly depends on genetic and environmental factors, a set of results obtained from yeast strains with different ploidy in the current study would serve as a major reference source for researchers and technical experts.
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Affiliation(s)
- Nobuo Fukuda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka, 563-8577, Japan.
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2
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Barbitoff YA, Matveenko AG, Matiiv AB, Maksiutenko EM, Moskalenko SE, Drozdova PB, Polev DE, Beliavskaia AY, Danilov LG, Predeus AV, Zhouravleva GA. Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. G3-GENES GENOMES GENETICS 2021; 11:6129118. [PMID: 33677552 PMCID: PMC8759820 DOI: 10.1093/g3journal/jkab029] [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: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023]
Abstract
Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.
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Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Anton B Matiiv
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg 199034, Russia
| | | | | | - Alexandra Y Beliavskaia
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Alexander V Predeus
- Bioinformatics Institute, St. Petersburg 197342, Russia.,University of Liverpool, Liverpool, UK, L7 3EA
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
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3
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Varela C, Bartel C, Nandorfy DE, Borneman A, Schmidt S, Curtin C. Identification of flocculant wine yeast strains with improved filtration-related phenotypes through application of high-throughput sedimentation rate assays. Sci Rep 2020; 10:2738. [PMID: 32066762 PMCID: PMC7026045 DOI: 10.1038/s41598-020-59579-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/30/2020] [Indexed: 11/24/2022] Open
Abstract
In most yeast-driven biotechnological applications, biomass is separated from the aqueous phase after fermentation or production has finished. During winemaking, yeasts are removed after fermentation by racking, filtration, or centrifugation, which add costs to the overall process and may reduce product yield. Theoretically, clarification and filtration can be aided through use of yeast strains that form flocs due to cell-cell binding, a process known as flocculation. However, because early flocculation can cause stuck/sluggish fermentations, this phenotype is not common amongst commercially available wine yeasts. In this study we sought to identify wine strains that exhibit late-fermentation flocculant behaviour using two complementary approaches; a high-throughput sedimentation rate assay of individual strains and a competitive sedimentation assay using a barcoded yeast collection. Amongst 103 wine strains, several exhibited strong sedimentation at the end of the wine fermentation process under various environmental conditions. Two of these strains, AWRI1688 and AWRI1759, were further characterised during red winemaking trials. Shiraz wines produced with both strains displayed improved filtration-related properties. AWRI1759 produced wines with greater filterability, whereas AWRI1688 enabled the recovery of larger wine volumes after racking. Thus, this study demonstrates the effective use of sedimentation screening assays to identify wine yeasts with practical winemaking applications.
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Affiliation(s)
- Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia. .,Department of Wine & Food Science, University of Adelaide, Glen Osmond, SA 5064, Adelaide, Australia.
| | - Caroline Bartel
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | | | - Anthony Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Simon Schmidt
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Chris Curtin
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia.,College of Agricultural Sciences, Oregon State University, Wiegand Hall, 3051 SW Campus Way, Corvallis, OR, 97331, USA
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4
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Kuzdzal‐Fick JJ, Chen L, Balázsi G. Disadvantages and benefits of evolved unicellularity versus multicellularity in budding yeast. Ecol Evol 2019; 9:8509-8523. [PMID: 31410258 PMCID: PMC6686284 DOI: 10.1002/ece3.5322] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
Multicellular organisms appeared on Earth through several independent major evolutionary transitions. Are such transitions reversible? Addressing this fundamental question entails understanding the benefits and costs of multicellularity versus unicellularity. For example, some wild yeast strains form multicellular clumps, which might be beneficial in stressful conditions, but this has been untested. Here, we show that unicellular yeast evolve from clump-forming ancestors by propagating samples from suspension after larger clumps have settled. Unicellular yeast strains differed from their clumping ancestors mainly by mutations in the AMN1 (Antagonist of Mitotic exit Network) gene. Ancestral yeast clumps were more resistant to freeze/thaw, hydrogen peroxide, and ethanol stressors than their unicellular counterparts, but they grew slower without stress. These findings suggest disadvantages and benefits to multicellularity and unicellularity that may have impacted the emergence of multicellular life forms.
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Affiliation(s)
- Jennie J. Kuzdzal‐Fick
- Department of Systems BiologyThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexas
| | - Lin Chen
- Department of Systems BiologyThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Gábor Balázsi
- Department of Systems BiologyThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Louis and Beatrice Laufer Center for Physical & Quantitative BiologyStony Brook UniversityStony BrookNew York
- Department of Biomedical EngineeringStony Brook UniversityStony BrookNew York
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5
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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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6
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Vergara-Álvarez I, Quiroz-Figueroa F, Tamayo-Ordóñez MC, Oliva-Hernández AA, Larralde-Corona CP, Narváez-Zapata JA. Flocculation and Expression of FLO Genes of a Saccharomyces cerevisiae Mezcal Strain with High Stress Tolerance. Food Technol Biotechnol 2019; 57:544-553. [PMID: 32123516 PMCID: PMC7029389 DOI: 10.17113/ftb.57.04.19.6063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mezcal is a distillate produced by spontaneous fermentation of the must obtained from stalks of Agave spp. plants that are cooked and pressed. Agave must contains a high amount of fructose and phenolic compounds, and fermentation usually occurs under stressful (and uncontrolled) environmental conditions. Yeasts capable of growing under such conditions usually display advantageous biological and industrial traits for stress tolerance such as flocculation. In this study, seven Saccharomyces cerevisiae strains isolated from mezcal must were exposed to temperatures ranging between 10 and 40 °C, and to different sugar sources (fructose or glucose). Yeasts grown in fructose increased their stress tolerance, determined by colony count in a microdrop assay, under low temperature (10 °C) compared to the growth at 40 °C on solid cultures. The most stress-tolerant mezcal strain (Sc3Y8) and a commercial wine (Fermichamp) strain, used as control, were grown under fermentation conditions and exposed to long-term temperature stress to determine their performance and their potential for flocculation. Compared to glucose, fermentation on fructose increased the metabolite accumulation at the end of culture, particularly at 40 °C, with 2.3, 1.3 and 3.4 times more glycerol (8.6 g/L), ethanol (43.6 g/L) and acetic acid (7.3 g/L), respectively. Using confocal microscopy analysis, we detected morphological changes such as aggregation and wall recognition at the level of budding scars in yeast, particularly in the Sc3Y8 strain when it was exposed to 40 °C. The analysis confirmed that this mezcal strain was positive for flocculation in the presence of Ca2+ ions. Analysis of FLO1, FLO5 and FLO11 gene expression implicated in flocculation in both Saccharomyces strains showed a strong transcriptional induction, mainly of the FLO5 gene in the mezcal Sc3Y8 strain.
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Affiliation(s)
- Israel Vergara-Álvarez
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico.,Aix-Marseille University, LCB (UMR7283), CNRS, Marseille, France
| | - Francisco Quiroz-Figueroa
- National Polytechnic Institute (Instituto Politécnico Nacional), CIIDIR-IPN Unidad Sinaloa, Blvd. Juan de Dios Bátiz Paredes no. 250, Col. San Joachin, C.P. 81101 Guasave (Sinaloa), Mexico
| | - María Concepción Tamayo-Ordóñez
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico.,Genetic Engineering Laboratory, Department of Biotechnology, Faculty of Chemical Sciences, Autonomous University of Coahuila, Saltillo Unit, Mexico
| | - Amanda Alejandra Oliva-Hernández
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico
| | - Claudia Patricia Larralde-Corona
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico
| | - José Alberto Narváez-Zapata
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico
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7
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Fang O, Hu X, Wang L, Jiang N, Yang J, Li B, Luo Z. Amn1 governs post-mitotic cell separation in Saccharomyces cerevisiae. PLoS Genet 2018; 14:e1007691. [PMID: 30273335 PMCID: PMC6181423 DOI: 10.1371/journal.pgen.1007691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 10/11/2018] [Accepted: 09/12/2018] [Indexed: 11/18/2022] Open
Abstract
Post-mitotic cell separation is one of the most prominent events in the life cycle of eukaryotic cells, but the molecular underpinning of this fundamental biological process is far from being concluded and fully characterized. We use budding yeast Saccharomyces cerevisiae as a model and demonstrate AMN1 as a major gene underlying post-mitotic cell separation in a natural yeast strain, YL1C. Specifically, we define a novel 11-residue domain by which Amn1 binds to Ace2. Moreover, we demonstrate that Amn1 induces proteolysis of Ace2 through the ubiquitin proteasome system and in turn, down-regulates Ace2’s downstream target genes involved in hydrolysis of the primary septum, thus leading to inhibition of cell separation and clumping of haploid yeast cells. Using ChIP assays and site-specific mutation experiments, we show that Ste12 and the a1-α12 heterodimer are two direct regulators of AMN1. Specifically, a1-α2, a diploid-specific heterodimer, prevents Ste12 from inactivating AMN1 through binding to its promoter. This demonstrates how the Amn1-governed cell separation is highly cell type dependent. Finally, we show that AMN1368D from YL1C is a dominant allele in most strains of S. cerevisiae and evolutionarily conserved in both genic structure and phenotypic effect in two closely related yeast species, K. lactis and C. glabrata. Separation of mother and daughter cells after mitosis in eukaryotes enacts various functional and/or developmental needs and has significant medical and industrial implications. How this cellular behaviour is regulated is far from being concluded. We report here a novel Amn1 mediated post-mitotic cell separation in a budding yeast strain, YL1C and demonstrate that the post-mitotic cell separation can be regulated through a ubiquitin-conjugated protein degradation of Ace2 by Amn1. The Amn1-governed switch of cell separation is evolutionarily conserved and highly cell type dependent. These findings provide insights into the molecular mechanism of how post-mitotic cell separation is regulated in budding yeast, and data for translating into medical and industrial applications.
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Affiliation(s)
- Ou Fang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
- School of Biosciences, the University of Birmingham, Birmingham, United Kingdom
- Department of Evolution and Ecology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaohua Hu
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lin Wang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Jiang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jixuan Yang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Li
- Department of Evolution and Ecology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zewei Luo
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
- School of Biosciences, the University of Birmingham, Birmingham, United Kingdom
- * E-mail: ,
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8
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García-Ríos E, Morard M, Parts L, Liti G, Guillamón JM. The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae. BMC Genomics 2017; 18:159. [PMID: 28196526 PMCID: PMC5310122 DOI: 10.1186/s12864-017-3572-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/09/2017] [Indexed: 12/25/2022] Open
Abstract
Background Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci. Results In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature. We detected four genomic regions involved in the adaptation at low temperature, three of them located in the subtelomeric regions (chromosomes XIII, XV and XVI) and one in the chromosome XIV. The QTL analysis revealed that subtelomeric regions play a key role in defining individual variation, which emphasizes the importance of these regions’ adaptive nature. Conclusions The reciprocal hemizygosity analysis (RHA), run to validate the genes involved in low-temperature fermentation, showed that genetic variation in mitochondrial proteins, maintenance of correct asymmetry and distribution of phospholipid in the plasma membrane are key determinants of low-temperature adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3572-2) contains supplementary material, which is available to authorized users.
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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
| | - Miguel Morard
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980-Paterna, Valencia, Spain.,Departament de Genètica, Facultat de Ciències Biològiques, Universitat de València, Dr. Moliner, 50, E-46100 Burjassot, València, Spain
| | - Leopold Parts
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Wellcome Trust Sanger Institute, Hinxton, CB101SA, UK
| | - Gianni Liti
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - José M 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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9
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Drozdova PB, Tarasov OV, Matveenko AG, Radchenko EA, Sopova JV, Polev DE, Inge-Vechtomov SG, Dobrynin PV. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PLoS One 2016; 11:e0154722. [PMID: 27152522 PMCID: PMC4859572 DOI: 10.1371/journal.pone.0154722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/18/2016] [Indexed: 01/09/2023] Open
Abstract
The Peterhof genetic collection of Saccharomyces cerevisiae strains (PGC) is a large laboratory stock that has accumulated several thousands of strains for over than half a century. It originated independently of other common laboratory stocks from a distillery lineage (race XII). Several PGC strains have been extensively used in certain fields of yeast research but their genomes have not been thoroughly explored yet. Here we employed whole genome sequencing to characterize five selected PGC strains including one of the closest to the progenitor, 15V-P4, and several strains that have been used to study translation termination and prions in yeast (25-25-2V-P3982, 1B-D1606, 74-D694, and 6P-33G-D373). The genetic distance between the PGC progenitor and S288C is comparable to that between two geographically isolated populations. The PGC seems to be closer to two bakery strains than to S288C-related laboratory stocks or European wine strains. In genomes of the PGC strains, we found several loci which are absent from the S288C genome; 15V-P4 harbors a rare combination of the gene cluster characteristic for wine strains and the RTM1 cluster. We closely examined known and previously uncharacterized gene variants of particular strains and were able to establish the molecular basis for known phenotypes including phenylalanine auxotrophy, clumping behavior and galactose utilization. Finally, we made sequencing data and results of the analysis available for the yeast community. Our data widen the knowledge about genetic variation between Saccharomyces cerevisiae strains and can form the basis for planning future work in PGC-related strains and with PGC-derived alleles.
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Affiliation(s)
- Polina B. Drozdova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | - Oleg V. Tarasov
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Scientific Center of RAS, St. Petersburg, Russia
| | - Andrew G. Matveenko
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Elina A. Radchenko
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | - Julia V. Sopova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, St. Petersburg, Russia
| | - Dmitrii E. Polev
- Research Resource Center for Molecular and Cell Technologies, Research Park, Saint-Petersburg State University, St. Petersburg, Russia
| | - Sergey G. Inge-Vechtomov
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Pavel V. Dobrynin
- Bioinformatics Institute, St. Petersburg, Russia
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
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10
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Tofalo R, Perpetuini G, Di Gianvito P, Arfelli G, Schirone M, Corsetti A, Suzzi G. Characterization of specialized flocculent yeasts to improve sparkling wine fermentation. J Appl Microbiol 2016; 120:1574-84. [DOI: 10.1111/jam.13113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 02/10/2016] [Accepted: 02/19/2016] [Indexed: 11/29/2022]
Affiliation(s)
- R. Tofalo
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Perpetuini
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - P. Di Gianvito
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Arfelli
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - M. Schirone
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - A. Corsetti
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Suzzi
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
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11
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Regulatory Rewiring in a Cross Causes Extensive Genetic Heterogeneity. Genetics 2015; 201:769-77. [PMID: 26232408 DOI: 10.1534/genetics.115.180661] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/28/2015] [Indexed: 11/18/2022] Open
Abstract
Genetic heterogeneity occurs when individuals express similar phenotypes as a result of different underlying mechanisms. Although such heterogeneity is known to be a potential source of unexplained heritability in genetic mapping studies, its prevalence and molecular basis are not fully understood. Here we show that substantial genetic heterogeneity underlies a model phenotype--the ability to grow invasively--in a cross of two Saccharomyces cerevisiae strains. The heterogeneous basis of this trait across genotypes and environments makes it difficult to detect causal loci with standard genetic mapping techniques. However, using selective genotyping in the original cross, as well as in targeted backcrosses, we detected four loci that contribute to differences in the ability to grow invasively. Identification of causal genes at these loci suggests that they act by changing the underlying regulatory architecture of invasion. We verified this point by deleting many of the known transcriptional activators of invasion, as well as the gene encoding the cell surface protein Flo11 from five relevant segregants and showing that these individuals differ in the genes they require for invasion. Our work illustrates the extensive genetic heterogeneity that can underlie a trait and suggests that regulatory rewiring is a basic mechanism that gives rise to this heterogeneity.
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Liu J, Martin-Yken H, Bigey F, Dequin S, François JM, Capp JP. Natural yeast promoter variants reveal epistasis in the generation of transcriptional-mediated noise and its potential benefit in stressful conditions. Genome Biol Evol 2015; 7:969-84. [PMID: 25762217 PMCID: PMC4419794 DOI: 10.1093/gbe/evv047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The increase in phenotypic variability through gene expression noise is proposed to be an evolutionary strategy in selective environments. Differences in promoter-mediated noise between Saccharomyces cerevisiae strains could have been selected for thanks to the benefit conferred by gene expression heterogeneity in the stressful conditions, for instance, those experienced by industrial strains. Here, we used a genome-wide approach to identify promoters conferring high noise levels in the industrial wine strain EC1118. Many promoters of genes related to environmental factors were identified, some of them containing genetic variations compared with their counterpart in the laboratory strain S288c. Each variant of eight promoters has been fused to yeast-Enhanced Green Fluorescent Protein and integrated in the genome of both strains. Some industrial variants conferred higher expression associated, as expected, with lower noise, but other variants either increased or decreased expression without modifying variability, so that they might exhibit different levels of transcriptional-mediated noise at equal mean. At different induction conditions giving similar expression for both variants of the CUP1 promoter, we indeed observed higher noise with the industrial variant. Nevertheless, this difference was only observed in the industrial strain, revealing epistasis in the generation of promoter-mediated noise. Moreover, the increased expression variability conferred by this natural yeast promoter variant provided a clear benefit in the face of an environmental stress. Thus, modulation of gene expression noise by a combination of promoter modifications and trans-influences might be a possible adaptation mechanism in yeast.
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Affiliation(s)
- Jian Liu
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Hélène Martin-Yken
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Frédéric Bigey
- INRA, UMR 1083 Sciences Pour l'Œnologie, Montpellier, France
| | - Sylvie Dequin
- INRA, UMR 1083 Sciences Pour l'Œnologie, Montpellier, France
| | - Jean-Marie François
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Jean-Pascal Capp
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
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Singh R, Sinha H. Tiled ChrI RHS collection: a pilot high-throughput screening tool for identification of allelic variants. Yeast 2014; 32:335-43. [PMID: 25407353 DOI: 10.1002/yea.3059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/13/2014] [Accepted: 11/13/2014] [Indexed: 11/08/2022] Open
Abstract
Reciprocal hemizygosity analysis is a genetic technique that allows phenotypic determination of the allelic effects of a gene in a genetically uniform background. Expanding this single gene technique to generate a genome-wide collection is termed as reciprocal hemizygosity scanning (RHS). The RHS collection should circumvent the need for linkage mapping and provide the power to identify all possible allelic variants for a given phenotype. However, the published RHS collections based on the existing genome-wide haploid deletion library reported a high rate of false positives. In this study, we report de novo construction of a RHS collection that is not based on the yeast deletion library. This collection has been constructed for the shortest yeast chromosome, ChrI. Using this ChrI RHS collection, we identified 13 allelic variants for the previously mapped loci and novel allelic variants for the growth differences in different environments. A few of these novel variants, which were fine mapped to a gene level, identified novel genetic variation for the previously studied environmental conditions. The availability of a genome-wide RHS collection would thus help us uncover a comprehensive list of allelic variants and better our understanding of the molecular pathways modulating a quantitative trait.
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Affiliation(s)
- Rohini Singh
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Alvarez F, Correa LFDM, Araújo TM, Mota BEF, da Conceição LEFR, Castro IDM, Brandão RL. Variable flocculation profiles of yeast strains isolated from cachaça distilleries. Int J Food Microbiol 2014; 190:97-104. [PMID: 25209588 DOI: 10.1016/j.ijfoodmicro.2014.08.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 08/04/2014] [Accepted: 08/09/2014] [Indexed: 10/24/2022]
Abstract
In cachaça production, the use of yeast cells as starters with predictable flocculation behavior facilitates the cell recovery at the end of each fermentation cycle. Therefore, the aim of this work was to explain the behavior of cachaça yeast strains in fermentation vats containing sugarcane through the determination of biochemical and molecular parameters associated with flocculation phenotypes. By analyzing thirteen cachaça yeast strains isolated from different distilleries, our results demonstrated that neither classic biochemical measurements (e.g., percentage of flocculation, EDTA sensitivity, cell surface hydrophobicity, and sugar residues on the cell wall) nor modern molecular approaches, such as polymerase chain reaction (PCR) and real-time PCR (q-PCR), were sufficient to distinctly classify the cachaça yeast strains according to their flocculation behavior. It seems that flocculation is indeed a strain-specific phenomenon that is difficult to explain and/or categorize by the available methodologies.
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Affiliation(s)
- Florencia Alvarez
- Cerlev - Projetos e Inovação na Biotecnologia da Fermentação Ltda, Rua Amaro Lanari 59, Saramenha, 35.400-000 Ouro Preto, MG, Brazil
| | - Lygia Fátima da Mata Correa
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | - Thalita Macedo Araújo
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | - Bruno Eduardo Fernandes Mota
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | | | - Ieso de Miranda Castro
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil.
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Tofalo R, Perpetuini G, Di Gianvito P, Schirone M, Corsetti A, Suzzi G. Genetic diversity of FLO1 and FLO5 genes in wine flocculent Saccharomyces cerevisiae strains. Int J Food Microbiol 2014; 191:45-52. [PMID: 25218464 DOI: 10.1016/j.ijfoodmicro.2014.08.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/23/2014] [Indexed: 11/16/2022]
Abstract
Twenty-eight flocculent wine strains were tested for adhesion and flocculation phenotypic variability. Moreover, the expression patterns of the main genes involved in flocculation (FLO1, FLO5 and FLO8) were studied both in synthetic medium and in presence of ethanol stress. Molecular identification and typing were achieved by PCR-RFLP of the 5.8S ITS rRNA region and microsatellite PCR fingerprinting, respectively. All isolates belong to Saccharomyces cerevisiae species. The analysis of microsatellites highlighted the intraspecific genetic diversity of flocculent wine S. cerevisiae strains allowing obtaining strain-specific profiles. Moreover, strains were characterized on the basis of adhesive properties. A wide biodiversity was observed even if none of the tested strains were able to form biofilms (or 'mats'), or to adhere to polystyrene. Moreover, genetic diversity of FLO1 and FLO5 flocculating genes was determined by PCR. Genetic diversity was detected for both genes, but a relationship with the flocculation degree was not found. So, the expression patterns of FLO1, FLO5 and FLO8 genes was investigated in a synthetic medium and a relationship between the expression of FLO5 gene and the flocculation capacity was established. To study the expression of FLO1, FLO5 and FLO8 genes in floc formation and ethanol stress resistance qRT-PCR was carried out and also in this case strains with flocculent capacity showed higher levels of FLO5 gene expression. This study confirmed the diversity of flocculation phenotype and genotype in wine yeasts. Moreover, the importance of FLO5 gene in development of high flocculent characteristic of wine yeasts was highlighted. The obtained collection of S. cerevisiae flocculent wine strains could be useful to study the relationship between the genetic variation and flocculation phenotype in wine yeasts.
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Affiliation(s)
- Rosanna Tofalo
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via C.R. Lerici 1, 64023 Mosciano S. Angelo, Italy
| | - Giorgia Perpetuini
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via C.R. Lerici 1, 64023 Mosciano S. Angelo, Italy
| | - Paola Di Gianvito
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via C.R. Lerici 1, 64023 Mosciano S. Angelo, Italy
| | - Maria Schirone
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via C.R. Lerici 1, 64023 Mosciano S. Angelo, Italy
| | - Aldo Corsetti
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via C.R. Lerici 1, 64023 Mosciano S. Angelo, Italy
| | - Giovanna Suzzi
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via C.R. Lerici 1, 64023 Mosciano S. Angelo, Italy.
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Abstract
Dissecting the molecular basis of quantitative traits is a significant challenge and is essential for understanding complex diseases. Even in model organisms, precisely determining causative genes and their interactions has remained elusive, due in part to difficulty in narrowing intervals to single genes and in detecting epistasis or linked quantitative trait loci. These difficulties are exacerbated by limitations in experimental design, such as low numbers of analyzed individuals or of polymorphisms between parental genomes. We address these challenges by applying three independent high-throughput approaches for QTL mapping to map the genetic variants underlying 11 phenotypes in two genetically distant Saccharomyces cerevisiae strains, namely (1) individual analysis of >700 meiotic segregants, (2) bulk segregant analysis, and (3) reciprocal hemizygosity scanning, a new genome-wide method that we developed. We reveal differences in the performance of each approach and, by combining them, identify eight polymorphic genes that affect eight different phenotypes: colony shape, flocculation, growth on two nonfermentable carbon sources, and resistance to two drugs, salt, and high temperature. Our results demonstrate the power of individual segregant analysis to dissect QTL and address the underestimated contribution of interactions between variants. We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies.
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