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Muller G, de Godoy VR, Dário MG, Duval EH, Alves-Jr SL, Bücker A, Rosa CA, Dunn B, Sherlock G, Stambuk BU. Improved Sugarcane-Based Fermentation Processes by an Industrial Fuel-Ethanol Yeast Strain. J Fungi (Basel) 2023; 9:803. [PMID: 37623574 PMCID: PMC10456111 DOI: 10.3390/jof9080803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
In Brazil, sucrose-rich broths (cane juice and/or molasses) are used to produce billions of liters of both fuel ethanol and cachaça per year using selected Saccharomyces cerevisiae industrial strains. Considering the important role of feedstock (sugar) prices in the overall process economics, to improve sucrose fermentation the genetic characteristics of a group of eight fuel-ethanol and five cachaça industrial yeasts that tend to dominate the fermentors during the production season were determined by array comparative genomic hybridization. The widespread presence of genes encoding invertase at multiple telomeres has been shown to be a common feature of both baker's and distillers' yeast strains, and is postulated to be an adaptation to sucrose-rich broths. Our results show that only two strains (one fuel-ethanol and one cachaça yeast) have amplification of genes encoding invertase, with high specific activity. The other industrial yeast strains had a single locus (SUC2) in their genome, with different patterns of invertase activity. These results indicate that invertase activity probably does not limit sucrose fermentation during fuel-ethanol and cachaça production by these industrial strains. Using this knowledge, we changed the mode of sucrose metabolism of an industrial strain by avoiding extracellular invertase activity, overexpressing the intracellular invertase, and increasing its transport through the AGT1 permease. This approach allowed the direct consumption of the disaccharide by the cells, without releasing glucose or fructose into the medium, and a 11% higher ethanol production from sucrose by the modified industrial yeast, when compared to its parental strain.
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Affiliation(s)
- Gabriela Muller
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Victor R. de Godoy
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Marcelo G. Dário
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Eduarda H. Duval
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Sergio L. Alves-Jr
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Augusto Bücker
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Carlos A. Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil;
| | - Barbara Dunn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; (B.D.); (G.S.)
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; (B.D.); (G.S.)
| | - Boris U. Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
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2
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Isolation, Identification, Optimization of Baker’s Yeast from Natural Sources, Scale-Up Production Using Molasses as a Cheap Carbohydrate Source, and Evaluation for Bread Production. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
(1) Background: Bangladesh must has to spend a large amount of foreign currency to import commercial baker’s yeast every year. We could save money by finding a potential Saccharomyces cerevisiae from natural sources compatible with commercial baker’s yeast production. (2) Methods: Grapes, rice, pineapples were collected, processed, and inoculated on YMA plates and incubated at 30 °C for 48 h. Then 11 single morphologically well-formed colonies were isolated, purified, and identified, three as S. cerevisiae, three as S. rouxii, three as S. bisporus, and two as S. exigus based on standard cultural, morphological, and biochemical characteristics. Identified S. cerevisiae (designated as G2, P5 and R3) were then assessed for CO2 production as a measure of their baking potential during bread production and compared with two commercial strains (designated as C1 and C2). (3) Results: Isolate-G2 produced the maximum of 1830 mm3 of gas, whereas C1, C2, R3, and P5 produced 1520, 1680, 770, and 610 mm3 gas, respectively. No strain produced H2S which is associated with an off-flavor and unpleasant taste. These isolates showed maximum cell density at a pH range of 4–5.5 in 4–16% molasses broth at 30 °C after 4 days of incubation and maximum 4.75 × 109, 7.9 × 108, 1.472 × 1010, 2.08 × 1010 and 5.24 × 109 CFU mL−1 were produced by C1, C2, G2, P5 and R3, respectively. Isolate-G2 was found to have the most potential, whereas isolate-R3 and P5 have satisfactory potential. (4) Conclusions: G2 could be a good candidate for commercial trials.
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Madden AA, Lahue C, Gordy CL, Little JL, Nichols LM, Calvert MD, Dunn RR, Smukowski Heil C. Sugar-seeking insects as a source of diverse bread-making yeasts with enhanced attributes. Yeast 2021; 39:108-127. [PMID: 34687090 DOI: 10.1002/yea.3676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 11/10/2022] Open
Abstract
Insects represent a particularly interesting habitat in which to search for novel yeasts of value to industry. Insect-associated yeasts have the potential to have traits relevant to modern food and beverage production due to insect-yeast interactions, with such traits including diverse carbohydrate metabolisms, high sugar tolerance, and general stress tolerance. Here, we consider the potential value of insect-associated yeasts in the specific context of baking. We isolated 63 yeast strains from 13 species of hymenoptera from the United States, representing 37 yeast species from 14 genera. Screening for the ability to ferment maltose, a sugar important for bread production, resulted in the identification of 13 strains of Candida, Lachancea, and Pichia species. We assessed their ability to leaven dough. All strains produced baked loaves comparable to a commercial baking strain of Saccharomyces cerevisiae. The same 13 strains were also grown under various sugar and salt conditions relevant to osmotic challenges experienced in the manufacturing processes and the production of sweet dough. We show that many of these yeast strains, most notably strains of Lachancea species, grow at a similar or higher rate and population size as commercial baker's yeast. We additionally assessed the comparative phenotypes and genetics of insect-associated S. cerevisiae strains unable to ferment maltose and identified baking-relevant traits, including variations in the HOG1 signaling pathway and diverse carbohydrate metabolisms. Our results suggest that non-conventional yeasts have high potential for baking and, more generally, showcase the success of bioprospecting in insects for identifying yeasts relevant for industrial uses.
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Affiliation(s)
- Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.,The Microbe Institute, Everett, Massachusetts, USA
| | - Caitlin Lahue
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,University of North Carolina Chapel-Hill, Chapel Hill, North Carolina, USA
| | - Claire L Gordy
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Joy L Little
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Martha D Calvert
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.,Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
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4
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Ansari F, Alian Samakkhah S, Bahadori A, Jafari SM, Ziaee M, Khodayari MT, Pourjafar H. Health-promoting properties of Saccharomyces cerevisiae var. boulardii as a probiotic; characteristics, isolation, and applications in dairy products. Crit Rev Food Sci Nutr 2021; 63:457-485. [PMID: 34254862 DOI: 10.1080/10408398.2021.1949577] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Saccharomyces cerevisiae var. boulardii (S. boulardii) has been isolated from lychee (Litchi chinensis), mangosteen fruit, kombucha, and dairy products like kefir. Dairy products containing S. boulardii have been revealed to possess potential probiotic activities owing to their ability to produce organic acids, essential enzymes, vitamins, and other important metabolites such as vanillic acid, phenyl ethyl alcohol, and erythromycin. S. boulardii has a wide spectrum of anti-carcinogenic, antibacterial antiviral, and antioxidant activity, and is known to reduce serum cholesterol levels. However, this yeast has mainly been prescribed for prophylaxis treatment of gastrointestinal infectious diseases, and stimulating the immune system in a number of commercially available products. The present comprehensive review article reviews the properties of S. boulardii related to their use in fermented dairy foods as a probiotic microorganism or starter culture. Technical aspects regarding the integration of this yeast into the dairy foods matrix its health advantages, therapeutic functions, microencapsulation, and viability in harsh conditions, and safety aspects are highlighted.
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Affiliation(s)
- Fereshteh Ansari
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.,Research Center for Evidence-Based Medicine, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Iranian EBM Centre: A Joanna Briggs Institute Affiliated Group
| | - Shohre Alian Samakkhah
- Department of Food Hygiene and Quality Control, Faculty of Veterinary of Medicine, Amol University of Special Modern Technology, Amol, Iran
| | - Ali Bahadori
- Department of Medical Microbiology, Sarab Faculty of Medical Sciences, Sarab, Iran
| | - Seyedeh Maedeh Jafari
- Department of Comparative Bioscience, Faculty of Veterinary Medicine, Tehran University, Tehran, Iran
| | - Mojtaba Ziaee
- Medicinal Plants Research Center, Maragheh University of Medical Sciences, Maragheh, Iran
| | | | - Hadi Pourjafar
- Alborz University of Medical Sciences, Dietary Supplements and Probiotic Research Center, Karaj, Iran.,Department of Food Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
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5
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Lahue C, Madden AA, Dunn RR, Smukowski Heil C. History and Domestication of Saccharomyces cerevisiae in Bread Baking. Front Genet 2020; 11:584718. [PMID: 33262788 PMCID: PMC7686800 DOI: 10.3389/fgene.2020.584718] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.
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Affiliation(s)
- Caitlin Lahue
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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6
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Korhola M, Naumova ES, Partti E, Aittamaa M, Turakainen H, Naumov GI. Exploiting heterozygosity in industrial yeasts to create new and improved baker's yeasts. Yeast 2019; 36:571-587. [PMID: 31243797 DOI: 10.1002/yea.3428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023] Open
Abstract
The main aim of the work was to utilize heterozygosity of industrial yeast strains to construct new baker's yeast strains. Commercial baker's yeast strain ALKO 743, its more ethanol tolerant descendant ALKO 554 selected initially for growth over 300 generations in increasing ethanol concentrations in a glucose medium, and ALKO 3460 from an old domestic sour dough starter were used as starting strains. Isolated meiotic segregants of the strains were characterized genetically for sporulation ability and mating type, and the ploidy was determined physically. Heterozygosity of the segregant strains was estimated by a variety of molecular characterizations and fermentation and growth assays. The results showed wide heterozygosity and that the segregants were clustered into subgroups. This clustering was used for choosing distantly or closely related partners for strain construction crosses. Intrastrain hybrids made with segregants of ALKO 743 showed 16-24% hybrid vigour or heterosis. Interstrain hybrids with segregants of ALKO 743 and ALKO 3460 showed a wide variety of characteristics but also clear heterosis of 27-31% effects as assayed by lean and sugar dough raising. Distiller's yeast ALKO 554 turned out to be a diploid genetic segregant and not just a more ethanol tolerant mutant of the tetraploid parent strain ALKO 743.
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Affiliation(s)
- Matti Korhola
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Edvard Partti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Marja Aittamaa
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Hilkka Turakainen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Gennadi I Naumov
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
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7
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Gilchrist C, Stelkens R. Aneuploidy in yeast: Segregation error or adaptation mechanism? Yeast 2019; 36:525-539. [PMID: 31199875 PMCID: PMC6772139 DOI: 10.1002/yea.3427] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 01/24/2023] Open
Abstract
Aneuploidy is the loss or gain of chromosomes within a genome. It is often detrimental and has been associated with cell death and genetic disorders. However, aneuploidy can also be beneficial and provide a quick solution through changes in gene dosage when cells face environmental stress. Here, we review the prevalence of aneuploidy in Saccharomyces, Candida, and Cryptococcus yeasts (and their hybrid offspring) and analyse associations with chromosome size and specific stressors. We discuss how aneuploidy, a segregation error, may in fact provide a natural route for the diversification of microbes and enable important evolutionary innovations given the right ecological circumstances, such as the colonisation of new environments or the transition from commensal to pathogenic lifestyle. We also draw attention to a largely unstudied cross link between hybridisation and aneuploidy. Hybrid meiosis, involving two divergent genomes, can lead to drastically increased rates of aneuploidy in the offspring due to antirecombination and chromosomal missegregation. Because hybridisation and aneuploidy have both been shown to increase with environmental stress, we believe it important and timely to start exploring the evolutionary significance of their co-occurrence.
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Affiliation(s)
- Ciaran Gilchrist
- Division of Population Genetics, Department of ZoologyStockholm UniversityStockholmSweden
| | - Rike Stelkens
- Division of Population Genetics, Department of ZoologyStockholm UniversityStockholmSweden
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8
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Naumova ES, Sadykova AZ, Martynenko NN, Naumov GI. Hybrid Selection of Saccharomyces cerevisiae Yeasts for Thermotolerance and Fermentation Activity. Microbiology (Reading) 2018. [DOI: 10.1134/s002626171802008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Adamczyk J, Deregowska A, Potocki L, Kuna E, Kaplan J, Pabian S, Kwiatkowska A, Lewinska A, Wnuk M. Relationships between rDNA, Nop1 and Sir complex in biotechnologically relevant distillery yeasts. Arch Microbiol 2016; 198:715-23. [PMID: 27329282 PMCID: PMC4969353 DOI: 10.1007/s00203-016-1258-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/26/2016] [Accepted: 06/09/2016] [Indexed: 11/30/2022]
Abstract
Distillery yeasts are poorly characterized physiological group among the Saccharomyces sensu stricto complex. As industrial yeasts are under constant environmental stress during fermentation processes and the nucleolus is a stress sensor, in the present study, nucleolus-related parameters were evaluated in 22 commercially available distillery yeast strains. Distillery yeasts were found to be a heterogeneous group with a variable content and length of rDNA and degree of nucleolus fragmentation. The levels of rDNA were negatively correlated with Nop1 (r = -0.59, p = 0.0038). Moreover, the protein levels of Sir transcriptional silencing complex and longevity regulators, namely Sir1, Sir2, Sir3 and Fob1, were studied and negative correlations between Sir2 and Nop1 (r = -0.45, p = 0.0332), and between Sir2 and Fob1 (r = -0.49, p = 0.0211) were revealed. In general, S. paradoxus group of distillery yeasts with higher rDNA pools and Sir2 level than S. bayanus group was found to be more tolerant to fermentation-associated stress stimuli, namely mild cold/heat stresses and KCl treatment. We postulate that rDNA state may be considered as a novel factor that may modulate a biotechnological process.
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Affiliation(s)
- Jagoda Adamczyk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Anna Deregowska
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Leszek Potocki
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Ewelina Kuna
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Jakub Kaplan
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Sylwia Pabian
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | | | - Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland.
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10
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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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11
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Deregowska A, Skoneczny M, Adamczyk J, Kwiatkowska A, Rawska E, Skoneczna A, Lewinska A, Wnuk M. Genome-wide array-CGH analysis reveals YRF1 gene copy number variation that modulates genetic stability in distillery yeasts. Oncotarget 2015; 6:30650-63. [PMID: 26384347 PMCID: PMC4741559 DOI: 10.18632/oncotarget.5594] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022] Open
Abstract
Industrial yeasts, economically important microorganisms, are widely used in diverse biotechnological processes including brewing, winemaking and distilling. In contrast to a well-established genome of brewer's and wine yeast strains, the comprehensive evaluation of genomic features of distillery strains is lacking. In the present study, twenty two distillery yeast strains were subjected to electrophoretic karyotyping and array-based comparative genomic hybridization (array-CGH). The strains analyzed were assigned to the Saccharomyces sensu stricto complex and grouped into four species categories: S. bayanus, S. paradoxus, S. cerevisiae and S. kudriavzevii. The genomic diversity was mainly revealed within subtelomeric regions and the losses and/or gains of fragments of chromosomes I, III, VI and IX were the most frequently observed. Statistically significant differences in the gene copy number were documented in six functional gene categories: 1) telomere maintenance via recombination, DNA helicase activity or DNA binding, 2) maltose metabolism process, glucose transmembrane transporter activity; 3) asparagine catabolism, cellular response to nitrogen starvation, localized in cell wall-bounded periplasmic space, 4) siderophore transport, 5) response to copper ion, cadmium ion binding and 6) L-iditol 2- dehydrogenase activity. The losses of YRF1 genes (Y' element ATP-dependent helicase) were accompanied by decreased level of Y' sequences and an increase in DNA double and single strand breaks, and oxidative DNA damage in the S. paradoxus group compared to the S. bayanus group. We postulate that naturally occurring diversity in the YRF1 gene copy number may promote genetic stability in the S. bayanus group of distillery yeast strains.
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Affiliation(s)
- Anna Deregowska
- Department of Genetics, University of Rzeszow, Rzeszow, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jagoda Adamczyk
- Department of Genetics, University of Rzeszow, Rzeszow, Poland
| | | | - Ewa Rawska
- Department of Genetics, University of Rzeszow, Rzeszow, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Poland
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Rzeszow, Poland
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Naumov GI, Naumova ES. Invertase overproduction may provide for inulin fermentation by selection strains of Saccharomyces cerevisiae. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715020095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Naumova ES, Sadykova AZ, Martynenko NN, Naumov GI. Molecular polymorphism of β-fructosidase SUC genes in the Saccharomyces yeasts. Mol Biol 2014. [DOI: 10.1134/s0026893314040086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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