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Crandall JG, Fisher KJ, Sato TK, Hittinger CT. Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLoS Biol 2023; 21:e3001909. [PMID: 37943740 PMCID: PMC10635434 DOI: 10.1371/journal.pbio.3001909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.
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Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kaitlin J. Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Kato T, Takahashi T. Studies on the Genetic Characteristics of the Brewing Yeasts Saccharomyces: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2134972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Taku Kato
- Brewing Science Laboratories, Asahi Quality and Innovations Ltd, Moriya, Japan
| | - Tomoko Takahashi
- Core Technology Laboratories, Asahi Quality and Innovations Ltd, Moriya, Japan
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3
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Improving the Utilization of Isomaltose and Panose by Lager Yeast Saccharomyces pastorianus. FERMENTATION 2021. [DOI: 10.3390/fermentation7030107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Approximately 25% of all carbohydrates in industrial worts are poorly, if at all, fermented by brewing yeast. This includes dextrins, β-glucans, arabinose, xylose, disaccharides such as isomaltose, nigerose, kojibiose, and trisaccharides such as panose and isopanose. As the efficient utilization of carbohydrates during the wort’s fermentation impacts the alcohol yield and the organoleptic traits of the product, developing brewing strains with enhanced abilities to ferment subsets of these sugars is highly desirable. In this study, we developed Saccharomyces pastorianus laboratory yeast strains with a superior capacity to grow on isomaltose and panose. First, we designed a plasmid toolbox for the stable integration of genes into lager strains. Next, we used the toolbox to elevate the levels of the α-glucoside transporter Agt1 and the major isomaltase Ima1. This was achieved by integrating synthetic AGT1 and IMA1 genes under the control of strong constitutive promoters into defined genomic sites. As a result, strains carrying both genes showed a superior capacity to grow on panose and isomaltose, indicating that Ima1 and Agt1 act in synergy to consume these sugars. Our study suggests that non-GMO strategies aiming to develop strains with improved isomaltose and panose utilization could include identifying strains that overexpress AGT1 and IMA1.
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Industrially Applicable De Novo Lager Yeast Hybrids with a Unique Genomic Architecture: Creation and Characterization. Appl Environ Microbiol 2021; 87:AEM.02434-20. [PMID: 33188002 PMCID: PMC7848916 DOI: 10.1128/aem.02434-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/07/2020] [Indexed: 12/30/2022] Open
Abstract
All lager beer is produced using two related lager yeast types: group I and group II, which are highly similar, resulting in a lack of strain diversity for lager beer production. To date, approaches for generating new lager yeasts have generated strains possessing undesirable brewing characteristics which render them commercially inviable. Lager beer is produced by Saccharomyces pastorianus, which is a natural allopolyploid hybrid between Saccharomyces cerevisiae and Saccharomyces eubayanus. Lager strains are classified into two major groups based largely on genomic composition: group I and group II. Group I strains are allotriploid, whereas group II strains are allotetraploid. A lack of phenotypic diversity in commercial lager strains has led to substantial interest in the reconstitution of de novo allotetraploid lager strains by hybridization of S. cerevisiae and S. eubayanus strains. Such strategies rely on the hybridization of wild S. eubayanus isolates, which carry unacceptable traits for commercial lager beer such as phenolic off flavors and incomplete utilization of carbohydrates. Using an alternative breeding strategy, we have created de novo lager hybrids containing the domesticated S. eubayanus subgenome from an industrial S. pastorianus strain by hybridizing diploid meiotic segregants of this strain to a variety of S. cerevisiae ale strains. Five de novo hybrids were isolated which had fermentation characteristics similar to those of prototypical commercial lager strains but with unique phenotypic variation due to the contributions of the S. cerevisiae parents. Genomic analysis of these de novo lager hybrids identified novel allotetraploid genomes carrying three copies of the S. cerevisiae genome and one copy of the S. eubayanus genome. Most importantly, these hybrids do not possess the negative traits which result from breeding wild S. eubayanus. The de novo lager strains produced using industrial S. pastorianus in this study are immediately suitable for industrial lager beer production. IMPORTANCE All lager beer is produced using two related lager yeast types: group I and group II, which are highly similar, resulting in a lack of strain diversity for lager beer production. To date, approaches for generating new lager yeasts have generated strains possessing undesirable brewing characteristics which render them commercially inviable. We have used an alternative approach that circumvents this issue and created new lager strains that are directly suitable for lager beer production. These novel lager strains also possess a unique genomic architecture, which may lead to a better understanding of industrial yeast hybrids. We propose that strains created using our approach be classified as a third group of lager strains (group III). We anticipate that these novel lager strains will be of great industrial relevance and that this technique will be applicable to the creation of additional novel lager strains that will help broaden the diversity in commercial lager beer strains.
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5
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Brouwers N, Brickwedde A, Gorter de Vries AR, van den Broek M, Weening SM, van den Eijnden L, Diderich JA, Bai FY, Pronk JT, Daran JMG. Himalayan Saccharomyces eubayanus Genome Sequences Reveal Genetic Markers Explaining Heterotic Maltotriose Consumption by Saccharomyces pastorianus Hybrids. Appl Environ Microbiol 2019; 85:e01516-19. [PMID: 31519660 PMCID: PMC6821976 DOI: 10.1128/aem.01516-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
Saccharomyces pastorianus strains are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus that have been domesticated for centuries in lager beer brewing environments. As sequences and structures of S. pastorianus genomes are being resolved, molecular mechanisms and evolutionary origins of several industrially relevant phenotypes remain unknown. This study investigates how maltotriose metabolism, a key feature in brewing, may have arisen in early S. eubayanus × S. cerevisiae hybrids. To address this question, we generated a nearly complete genome assembly of Himalayan S. eubayanus strains of the Holarctic subclade. This group of strains has been proposed to be the S. eubayanus subgenome origin of current S. pastorianus strains. The Himalayan S. eubayanus genomes harbored several copies of an S. eubayanusAGT1 (SeAGT1) α-oligoglucoside transporter gene with high sequence identity to genes encountered in S. pastorianus Although Himalayan S. eubayanus strains cannot grow on maltose and maltotriose, their maltose-hydrolase and SeMALT1 and SeAGT1 maltose transporter genes complemented the corresponding null mutants of S. cerevisiae Expression, in Himalayan S. eubayanus of a functional S. cerevisiae maltose metabolism regulator gene (MALx3) enabled growth on oligoglucosides. The hypothesis that the maltotriose-positive phenotype in S. pastorianus is a result of heterosis was experimentally tested by constructing an S. cerevisiae × S. eubayanus laboratory hybrid with a complement of maltose metabolism genes that resembles that of current S. pastorianus strains. The ability of this hybrid to consume maltotriose in brewer's wort demonstrated regulatory cross talk between subgenomes and thereby validated this hypothesis. These results support experimentally the new postulated hypothesis on the evolutionary origin of an essential phenotype of lager brewing strains and valuable knowledge for industrial exploitation of laboratory-made S. pastorianus-like hybrids.IMPORTANCES. pastorianus, an S. cerevisiae × S. eubayanus hybrid, is used for production of lager beer, the most produced alcoholic beverage worldwide. It emerged by spontaneous hybridization and colonized early lager brewing processes. Despite accumulation and analysis of genome sequencing data of S. pastorianus parental genomes, the genetic blueprint of industrially relevant phenotypes remains unresolved. Assimilation of maltotriose, an abundant sugar in wort, has been postulated to be inherited from the S. cerevisiae parent. Here, we demonstrate that although Asian S. eubayanus isolates harbor a functional maltotriose transporter SeAGT1 gene, they are unable to grow on α-oligoglucosides, but expression of S. cerevisiae regulator MAL13 (ScMAL13) was sufficient to restore growth on trisaccharides. We hypothesized that the S. pastorianus maltotriose phenotype results from regulatory interaction between S. cerevisiae maltose transcription activator and the promoter of SeAGT1 We experimentally confirmed the heterotic nature of the phenotype, and thus these results provide experimental evidence of the evolutionary origin of an essential phenotype of lager brewing strains.
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Affiliation(s)
- Nick Brouwers
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Anja Brickwedde
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Susan M Weening
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Jasper A Diderich
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Eliodório KP, Cunha GCDGE, Müller C, Lucaroni AC, Giudici R, Walker GM, Alves SL, Basso TO. Advances in yeast alcoholic fermentations for the production of bioethanol, beer and wine. ADVANCES IN APPLIED MICROBIOLOGY 2019; 109:61-119. [PMID: 31677647 DOI: 10.1016/bs.aambs.2019.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Yeasts have a long-standing relationship with humankind that has widened in recent years to encompass production of diverse foods, beverages, fuels and medicines. Here, key advances in the field of yeast fermentation applied to alcohol production, which represents the predominant product of industrial biotechnology, will be presented. More specifically, we have selected industries focused in producing bioethanol, beer and wine. In these bioprocesses, yeasts from the genus Saccharomyces are still the main players, with Saccharomyces cerevisiae recognized as the preeminent industrial ethanologen. However, the growing demand for new products has opened the door to diverse yeasts, including non-Saccharomyces strains. Furthermore, the development of synthetic media that successfully simulate industrial fermentation medium will be discussed along with a general overview of yeast fermentation modeling.
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Affiliation(s)
| | | | - Caroline Müller
- Laboratory of Biochemistry and Genetics, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | - Ana Carolina Lucaroni
- Laboratory of Biochemistry and Genetics, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | - Reinaldo Giudici
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil
| | | | - Sérgio Luiz Alves
- Laboratory of Biochemistry and Genetics, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | - Thiago Olitta Basso
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil.
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7
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Bellut K, Michel M, Hutzler M, Zarnkow M, Jacob F, De Schutter DP, Daenen L, Lynch KM, Zannini E, Arendt EK. Investigation into the Potential ofLachancea fermentatiStrain KBI 12.1 for Low Alcohol Beer Brewing. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2019. [DOI: 10.1080/03610470.2019.1629227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Konstantin Bellut
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Maximilian Michel
- Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - Mathias Hutzler
- Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - Martin Zarnkow
- Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - Fritz Jacob
- Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | | | | | - Kieran M. Lynch
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Emanuele Zannini
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Elke K. Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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8
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Brouwers N, Gorter de Vries AR, van den Broek M, Weening SM, Elink Schuurman TD, Kuijpers NGA, Pronk JT, Daran JMG. In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation. PLoS Genet 2019; 15:e1007853. [PMID: 30946741 PMCID: PMC6448828 DOI: 10.1371/journal.pgen.1007853] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/26/2018] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces eubayanus is the non-S. cerevisiae parent of the lager-brewing hybrid S. pastorianus. In contrast to most S. cerevisiae and Frohberg-type S. pastorianus strains, S. eubayanus cannot utilize the α-tri-glucoside maltotriose, a major carbohydrate in brewer’s wort. In Saccharomyces yeasts, utilization of maltotriose is encoded by the subtelomeric MAL gene family, and requires transporters for maltotriose uptake. While S. eubayanus strain CBS 12357T harbors four SeMALT genes which enable uptake of the α-di-glucoside maltose, it lacks maltotriose transporter genes. In S. cerevisiae, sequence identity indicates that maltotriose and maltose transporters likely evolved from a shared ancestral gene. To study the evolvability of maltotriose utilization in S. eubayanus CBS 12357T, maltotriose-assimilating mutants obtained after UV mutagenesis were subjected to laboratory evolution in carbon-limited chemostat cultures on maltotriose-enriched wort. An evolved strain showed improved maltose and maltotriose fermentation in 7 L fermenter experiments on industrial wort. Whole-genome sequencing revealed a novel mosaic SeMALT413 gene, resulting from repeated gene introgressions by non-reciprocal translocation of at least three SeMALT genes. The predicted tertiary structure of SeMalT413 was comparable to the original SeMalT transporters, but overexpression of SeMALT413 sufficed to enable growth on maltotriose, indicating gene neofunctionalization had occurred. The mosaic structure of SeMALT413 resembles the structure of S. pastorianus maltotriose-transporter gene SpMTY1, which has high sequences identity to alternatingly S. cerevisiae MALx1, S. paradoxus MALx1 and S. eubayanus SeMALT3. Evolution of the maltotriose transporter landscape in hybrid S. pastorianus lager-brewing strains is therefore likely to have involved mechanisms similar to those observed in the present study. Fermentation of the wort sugar maltotriose is critical for the flavor profile obtained during beer brewing. The recently discovered yeast Saccharomyces eubayanus is gaining popularity as an alternative to S. pastorianus and S. cerevisiae for brewing, however it is unable to utilize maltotriose. Here, a combination of non-GMO mutagenesis and laboratory evolution of the S. eubayanus type strain CBS 12357T was used to enable maltotriose fermentation and improve brewing performance. The improved strain expressed a novel transporter gene, SeMALT413, which was formed by recombination between three different SeMALT maltose-transporter genes. Overexpression of SeMALT413 in CBS 12357T confirmed its neofunctionalization as a maltotriose transporter. As the S. pastorianus maltotriose transporter SpMty1 has a mosaic structure similar to SeMalT413, maltotriose utilization likely involved similar recombination events during the domestication of current lager brewing strains. Based on a posteriori sequence analysis, the emergence of gene functions has been attributed to gene neofunctionalization in a broad range of organisms. The real-time observation of neofunctionalization during laboratory evolution constitutes an important validation of the relevance and importance of this mechanism for Darwinian evolution.
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Affiliation(s)
- Nick Brouwers
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Arthur R. Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Susan M. Weening
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | | | - Niels G. A. Kuijpers
- HEINEKEN Supply Chain B.V., Global Innovation and Research, Zoeterwoude, Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jean-Marc G. Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
- * E-mail:
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9
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Baker EP, Hittinger CT. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. PLoS Genet 2019; 15:e1007786. [PMID: 30946740 PMCID: PMC6448821 DOI: 10.1371/journal.pgen.1007786] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/25/2018] [Indexed: 11/23/2022] Open
Abstract
At the molecular level, the evolution of new traits can be broadly divided between changes in gene expression and changes in protein-coding sequence. For proteins, the evolution of novel functions is generally thought to proceed through sequential point mutations or recombination of whole functional units. In Saccharomyces, the uptake of the sugar maltotriose into the cell is the primary limiting factor in its utilization, but maltotriose transporters are relatively rare, except in brewing strains. No known wild strains of Saccharomyces eubayanus, the cold-tolerant parent of hybrid lager-brewing yeasts (Saccharomyces cerevisiae x S. eubayanus), are able to consume maltotriose, which limits their ability to fully ferment malt extract. In one strain of S. eubayanus, we found a gene closely related to a known maltotriose transporter and were able to confer maltotriose consumption by overexpressing this gene or by passaging the strain on maltose. Even so, most wild strains of S. eubayanus lack native maltotriose transporters. To determine how this rare trait could evolve in naive genetic backgrounds, we performed an adaptive evolution experiment for maltotriose consumption, which yielded a single strain of S. eubayanus able to grow on maltotriose. We mapped the causative locus to a gene encoding a novel chimeric transporter that was formed by an ectopic recombination event between two genes encoding transporters that are unable to import maltotriose. In contrast to classic models of the evolution of novel protein functions, the recombination breakpoints occurred within a single functional domain. Thus, the ability of the new protein to carry maltotriose was likely acquired through epistatic interactions between independently evolved substitutions. By acquiring multiple mutations at once, the transporter rapidly gained a novel function, while bypassing potentially deleterious intermediate steps. This study provides an illuminating example of how recombination between paralogs can establish novel interactions among substitutions to create adaptive functions. Hybrids of the yeasts Saccharomyces cerevisiae and Saccharomyces eubayanus (lager-brewing yeasts) dominate the modern brewing industry. S. cerevisiae, also known as baker’s yeast, is well-known for its role in industry and scientific research. Less well recognized is S. eubayanus, which was only discovered as a pure species in 2011. While most lager-brewing yeasts rapidly and completely utilize the important brewing sugar maltotriose, no strain of S. eubayanus isolated to date is known to do so. Despite being unable to consume maltotriose, we identified one strain of S. eubayanus carrying a gene for a functional maltotriose transporter, although most strains lack this gene. During an adaptive evolution experiment, a strain of S. eubayanus without native maltotriose transporters evolved the ability to grow on maltotriose. Maltotriose consumption in the evolved strain resulted from a chimeric transporter that arose by shuffling genes encoding parent proteins that were unable to transport maltotriose. Traditionally, functional chimeric proteins are thought to evolve by shuffling discrete functional domains or modules, but the breakpoints in the chimera studied here occurred within the single functional module of the protein. These results support the less well-recognized role of shuffling duplicate gene sequences to generate novel proteins with adaptive functions.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Microbiology Doctoral Training Program, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Microbiology Doctoral Training Program, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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10
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Trichez D, Knychala MM, Figueiredo CM, Alves SL, da Silva MA, Miletti LC, de Araujo PS, Stambuk BU. Key amino acid residues of the AGT1 permease required for maltotriose consumption and fermentation by Saccharomyces cerevisiae. J Appl Microbiol 2018; 126:580-594. [PMID: 30466168 DOI: 10.1111/jam.14161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/22/2018] [Accepted: 11/10/2018] [Indexed: 12/24/2022]
Abstract
AIMS The AGT1 gene encodes for a general α-glucoside-H+ symporter required for efficient maltotriose fermentation by Saccharomyces cerevisiae. In the present study, we analysed the involvement of four charged amino acid residues present in this transporter that are required for maltotriose consumption and fermentation by yeast cells. METHODS AND RESULTS By using a knowledge-driven approach based on charge, conservation, location, three-dimensional (3D) structural modelling and molecular docking analysis, we identified four amino acid residues (Glu-120, Asp-123, Glu-167 and Arg-504) in the AGT1 permease that could mediate substrate binding and translocation. Mutant permeases were generated by site-directed mutagenesis of these charged residues, and expressed in a yeast strain lacking this permease (agt1∆). While mutating the Arg-504 or Glu-120 residues into alanine totally abolished (R504A mutant) or greatly reduced (E120A mutant) maltotriose consumption by yeast cells, as well as impaired the active transport of several other α-glucosides, in the case of the Asp-123 and Glu-167 amino acids, it was necessary to mutate both residues (D123G/E167A mutant) in order to impair maltotriose consumption and fermentation. CONCLUSIONS Based on the results obtained with mutant proteins, molecular docking and the localization of amino acid residues, we propose a transport mechanism for the AGT1 permease. SIGNIFICANCE AND IMPACT OF THE STUDY Our results present new insights into the structural basis for active α-glucoside-H+ symport activity by yeast transporters, providing the molecular bases for improving the catalytic properties of this type of sugar transporters.
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Affiliation(s)
- D Trichez
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - M M Knychala
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - C M Figueiredo
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - S L Alves
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - M A da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - L C Miletti
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - P S de Araujo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - B U Stambuk
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
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11
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Eizaguirre JI, Peris D, Rodríguez ME, Lopes CA, De Los Ríos P, Hittinger CT, Libkind D. Phylogeography of the wild Lager-brewing ancestor (Saccharomyces eubayanus) in Patagonia. Environ Microbiol 2018; 20:3732-3743. [PMID: 30105823 DOI: 10.1111/1462-2920.14375] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/06/2018] [Indexed: 11/28/2022]
Abstract
Saccharomyces eubayanus is the close relative of the Lager-brewing yeast and was firstly found in North Patagonia associated with Nothofagus trees. In recent years additional strains were found in North America, Asia and New Zealand, and genomic analyses showed the existence of two main populations of this yeast, both of them present in Patagonia. Here, we performed the most comprehensive study of S. eubayanus in Patagonia natural environments (400 samples) and confirmed that this region has the highest isolation success rate for this species described worldwide (more than 10-fold). The genetic characterization of 200 isolates (COX2, DCR1, intFR) revealed five geographically structured subpopulations. We hypothesized that marine ingressions and glaciations, which shaped the Patagonian landscape, contributed on population differentiation. The first large screening of fermentation performance of 60 wild S. eubayanus strains indicated which subpopulations would be more suitable for beer production.
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Affiliation(s)
- Juan I Eizaguirre
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), Spanish National Research Council (CSIC), Valencia, Spain
| | - María E Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Christian A Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
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12
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Brickwedde A, Brouwers N, van den Broek M, Gallego Murillo JS, Fraiture JL, Pronk JT, Daran JMG. Structural, Physiological and Regulatory Analysis of Maltose Transporter Genes in Saccharomyces eubayanus CBS 12357 T. Front Microbiol 2018; 9:1786. [PMID: 30147677 PMCID: PMC6097016 DOI: 10.3389/fmicb.2018.01786] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 07/17/2018] [Indexed: 11/13/2022] Open
Abstract
Saccharomyces pastorianus lager brewing yeasts are domesticated hybrids of Saccharomyces cerevisiae and cold-tolerant Saccharomyces eubayanus. To understand the contribution of both parental genomes to maltose metabolism in brewing wort, this study focuses on maltose transport in the S. eubayanus type strain CBS 12357T/FM1318. To obtain complete sequences of the MAL loci of this strain, a near-complete genome assembly was generated using the Oxford Nanopore Technology MinION sequencing platform. Except for CHRXII, all sixteen chromosomes were assembled as single contigs. Four loci harboring putative maltose transporter genes (SeMALT1-4), located in subtelomeric regions of CHRII, CHRV, CHRXIII, and CHRXVI, were completely resolved. The near-identical loci on CHRV and CHRXVI strongly resembled canonical S. cerevisiae MAL loci, while those on CHRII and CHRXIII showed different structures suggestive of gene loss. Overexpression of SeMALT1-4 in a maltose-transport-deficient S. cerevisiae strain restored growth on maltose, but not on maltotriose, indicating maltose-specific transport functionality of all four transporters. Simultaneous CRISPR-Cas9-assisted deletion of only SeMALT2 and SeMALT4, which shared 99.7% sequence identity, eliminated growth of S. eubayanus CBS 12357T on maltose. Transcriptome analysis of S. eubayanus CBS 12357T established that SeMALT1 and SeMALT3, are poorly expressed in maltose-grown cultures, while SeMALT2 and SeMALT4 were expressed at much higher levels than SeMALT1 and SeMALT3, indicating that only SeMALT2/4 are responsible for maltose consumption in CBS 12357T. These results represent a first genomic and physiological characterization of maltose transport in S. eubayanus CBS 12357T and provides a valuable resource for further industrial exploitation of this yeast.
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Affiliation(s)
- Anja Brickwedde
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Nick Brouwers
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | | | - Julie L Fraiture
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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13
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Nguyen HV, Boekhout T. Characterization of Saccharomyces uvarum (Beijerinck, 1898) and related hybrids: assessment of molecular markers that predict the parent and hybrid genomes and a proposal to name yeast hybrids. FEMS Yeast Res 2018; 17:3061370. [PMID: 28334169 DOI: 10.1093/femsyr/fox014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/01/2017] [Indexed: 11/15/2022] Open
Abstract
The use of the nuclear DNA reassociation technique has led taxonomists to consider Saccharomyces uvarum a synonym of S. bayanus. The latter, however, is not a species but a hybrid harbouring S. eubayanus (Seu) and S. uvarum (Su) subgenomes with a minor DNA contribution from S. cerevisiae (Sc). To recognize genetically pure lines of S. uvarum and putative interspecies hybrids among so-called S. bayanus strains present in public culture collections, we propose the use of four markers that were defined from the S. bayanus CBS 380T composite genome, namely SeuNTS2 (rDNA), ScMAL31, MTY1 and SuMEL1. Saccharomyces carlsbergensis CBS 1513 was found to be similar to S. bayanus except that it carries the SeuMEL1 allele. Different marker combinations revealed that among 33 strains examined only a few were similar to CBS 380T, but many pure S. uvarum lines and putative Su/Seu-related hybrids occurred. Our results demonstrated that these hybrids were erroneously considered authentic S. bayanus and therefore the varietal state 'Saccharomyces bayanus var. uvarum comb. nov. Naumov' is not valid. Our markers constitute a tool to get insights into the genomic makeup of Saccharomyces interspecies hybrids. We also make a proposal to name those hybrids that may also be applicable to other fungal hybrids.
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Affiliation(s)
- Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Teun Boekhout
- CBS-KNAW Fungal Biodiversity Centre, PO Box 85167, 3508 AD Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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14
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Vidgren V, Gibson B. Trans-regulation and localization of orthologous maltose transporters in the interspecies lager yeast hybrid. FEMS Yeast Res 2018; 18:5040228. [PMID: 29931058 PMCID: PMC6142294 DOI: 10.1093/femsyr/foy065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/15/2018] [Indexed: 11/12/2022] Open
Abstract
In the interspecies lager yeast hybrid there are MAL loci involved in maltose and maltotriose utilization derived from each parent (Saccharomyces cerevisiae and Saccharomyces eubayanus). We show that trans-regulation across hybrid subgenomes occurs for MAL genes. However, gene expression is less efficient with non-native activators (trans-activation) compared to native activators (cis-activation). MAL genes were induced by maltose and repressed by glucose irrespective of host. Despite the strong expression of S. cerevisiae-type genes in the S. eubayanus host, a very low amount of transporter protein was actually observed in cells. This suggests that proper formation and configuration of the S. cerevisiae transporters is not efficient in S. eubayanus. The S. eubayanus-type Malx1 transporter was present in the plasma membrane in high amounts in all hosts (S. cerevisiae, S. eubayanus and Saccharomyces pastorianus) at all times. However, the S. cerevisiae-type transporters appeared sequentially in the plasma membrane; scMalx1 was localized in the plasma membrane during early to late linear growth and subsequently withdrawn to intracellular compartments. In contrast, the scAgt1 transporter was found in the plasma membrane mainly in the stationary phase of growth. Different localization patterns may explain why certain transporter orthologues in natural S. pastorianus strains were lost to mutation.
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Affiliation(s)
- Virve Vidgren
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Finland
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Finland
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15
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Inhibition of Saccharomyces cerevisiae growth by simultaneous uptake of glucose and maltose. J Biosci Bioeng 2018; 125:52-58. [DOI: 10.1016/j.jbiosc.2017.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 11/18/2022]
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16
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Brickwedde A, van den Broek M, Geertman JMA, Magalhães F, Kuijpers NGA, Gibson B, Pronk JT, Daran JMG. Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast. Front Microbiol 2017; 8:1690. [PMID: 28943864 PMCID: PMC5596070 DOI: 10.3389/fmicb.2017.01690] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/21/2017] [Indexed: 01/01/2023] Open
Abstract
The lager brewing yeast Saccharomyces pastorianus, an interspecies hybrid of S. eubayanus and S. cerevisiae, ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion ("attenuation") of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains.
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Affiliation(s)
- Anja Brickwedde
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | | | | | | | - Niels G A Kuijpers
- HEINEKEN Supply Chain, Global Innovation and ResearchZoeterwoude, Netherlands
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd.Espoo, Finland
| | - Jack T Pronk
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
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17
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Gibson B, Geertman JMA, Hittinger CT, Krogerus K, Libkind D, Louis EJ, Magalhães F, Sampaio JP. New yeasts—new brews: modern approaches to brewing yeast design and development. FEMS Yeast Res 2017; 17:3861261. [DOI: 10.1093/femsyr/fox038] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/01/2017] [Indexed: 02/07/2023] Open
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18
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Chaturvedi N, Yadav BS, Pandey PN, Tripathi V. The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor. J Mol Graph Model 2017; 74:315-325. [PMID: 28475968 DOI: 10.1016/j.jmgm.2017.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
Dectin-1 is a recently discovered pattern-recognition receptor that plays an important role in antifungal innate immunity, which acts a specific receptor for β-glucan (BG). The present study, aimed at clarifying effect of BG and a new analog, maltotriose (MT) on Dectin-1 receptor. We implemented molecular docking of MT on Dectin-1 along with model-independent all-atom-molecular dynamics simulations. Simulations were carried out at three levels of complexity: (1) Apo-Dectin-1; (2) BG:Dectin-1; (3) MT:Dectin-1. All three system complexes were undergone stability check before showing a comparative analysis. A characteristic feature, noted for the MT:Dectin-1, is a shifting of loops (loop1 and loop2) orientation towards atoms of MT, a broad interaction suggested a robust and tight binding on comparison with BG:Dectin-1. Free energy estimation corroborated the observation, which furthermore, made a close agreement by revealing contribution of energy components of interacting residues. In addition, cluster analysis of complexes exhibit a smooth continuous transition to a new confirmation, represented by a series of clusters each having a longer lifetime. Principal component analysis revealed a broken pipe at binding site of BG:Dectin-1 during movement of atoms whereas in MT:Dectin-1 exhibited wide band and high amplitude motion of atoms in trajectory, was due to loop orientation toward MT. Observation was further shown by measuring distances and hydrogen binding calculation. Simulations of the BG:Dectin-1 and MT:Dectin-1 complex revealed first time the influence of BG and MT ligands. This study might extend the knowledge of the BG and MT interaction on Dectin-1 and proposed further potential bioassay of MT.
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Affiliation(s)
- Navaneet Chaturvedi
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Brijesh Singh Yadav
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | | | - Vijay Tripathi
- Institute of Soil, Water, Environmental Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
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19
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Krogerus K, Arvas M, De Chiara M, Magalhães F, Mattinen L, Oja M, Vidgren V, Yue JX, Liti G, Gibson B. Ploidy influences the functional attributes of de novo lager yeast hybrids. Appl Microbiol Biotechnol 2016; 100:7203-22. [PMID: 27183995 PMCID: PMC4947488 DOI: 10.1007/s00253-016-7588-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/03/2016] [Accepted: 04/24/2016] [Indexed: 12/25/2022]
Abstract
The genomes of hybrid organisms, such as lager yeast (Saccharomyces cerevisiae × Saccharomyces eubayanus), contain orthologous genes, the functionality and effect of which may differ depending on their origin and copy number. How the parental subgenomes in lager yeast contribute to important phenotypic traits such as fermentation performance, aroma production, and stress tolerance remains poorly understood. Here, three de novo lager yeast hybrids with different ploidy levels (allodiploid, allotriploid, and allotetraploid) were generated through hybridization techniques without genetic modification. The hybrids were characterized in fermentations of both high gravity wort (15 °P) and very high gravity wort (25 °P), which were monitored for aroma compound and sugar concentrations. The hybrid strains with higher DNA content performed better during fermentation and produced higher concentrations of flavor-active esters in both worts. The hybrid strains also outperformed both the parent strains. Genome sequencing revealed that several genes related to the formation of flavor-active esters (ATF1, ATF2¸ EHT1, EEB1, and BAT1) were present in higher copy numbers in the higher ploidy hybrid strains. A direct relationship between gene copy number and transcript level was also observed. The measured ester concentrations and transcript levels also suggest that the functionality of the S. cerevisiae- and S. eubayanus-derived gene products differs. The results contribute to our understanding of the complex molecular mechanisms that determine phenotypes in lager yeast hybrids and are expected to facilitate targeted strain development through interspecific hybridization.
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Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland.
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, FI-00076, Espoo, Finland.
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Matteo De Chiara
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Frederico Magalhães
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, FI-00076, Espoo, Finland
| | - Laura Mattinen
- ValiRx Finland Oy, Kiviharjuntie 8, FI-90220, Oulu, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Jia-Xing Yue
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
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20
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Magalhães F, Vidgren V, Ruohonen L, Gibson B. Maltose and maltotriose utilisation by group I strains of the hybrid lager yeast Saccharomyces pastorianus. FEMS Yeast Res 2016; 16:fow053. [PMID: 27364826 PMCID: PMC5815069 DOI: 10.1093/femsyr/fow053] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/12/2016] [Accepted: 06/26/2016] [Indexed: 11/13/2022] Open
Abstract
Brewer's wort is a challenging environment for yeast as it contains predominantly α-glucoside sugars. There exist two subgroups of the lager yeast Saccharomyces pastorianus which differ in sugar utilisation. We performed wort fermentations and compared representative strains from both groups with respect to their ability to transport and ferment maltose and maltotriose. Additionally, we mapped the transporters MALx1, AGT1, MPHx and MTT1 by Southern blotting. Contrary to previous observations, group I comprises a diverse set of strains, with varying ability to transport and ferment maltotriose. Of the eight group I strains, three efficiently utilised maltotriose, a property enabled by the presence of transmembrane transporters SeAGT1 and MTT1 A58, a variant of the group I type strain (CBS1513) performed particularly well, taking up maltotriose at a higher rate than maltose and retaining significant transport activity at temperatures as low as 0°C. Analysis of transporter distribution in this strain revealed an increased copy number of the MTT1 gene, which encodes the only permease known with higher affinity for maltotriose than maltose and low temperature dependence for transport. We propose that much of the variation in lager yeast fermentation behaviour is determined by the presence or absence of specific transmembrane transporters.
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Affiliation(s)
- Frederico Magalhães
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, PO Box 16100, FI-00076 Aalto, Espoo, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, PO Box 1000, FI-02044 VTT, Espoo, Finland
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21
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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22
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Baker E, Wang B, Bellora N, Peris D, Hulfachor AB, Koshalek JA, Adams M, Libkind D, Hittinger CT. The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. Mol Biol Evol 2015; 32:2818-31. [PMID: 26269586 PMCID: PMC4651232 DOI: 10.1093/molbev/msv168] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae (S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts have experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. Our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions.
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Affiliation(s)
- EmilyClare Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
| | - Bing Wang
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
| | - Nicolas Bellora
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Bariloche, Argentina
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
| | | | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
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23
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Spitaels F, Wieme AD, Janssens M, Aerts M, Van Landschoot A, De Vuyst L, Vandamme P. The microbial diversity of an industrially produced lambic beer shares members of a traditionally produced one and reveals a core microbiota for lambic beer fermentation. Food Microbiol 2015; 49:23-32. [DOI: 10.1016/j.fm.2015.01.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 01/27/2015] [Indexed: 11/28/2022]
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24
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Hebly M, Brickwedde A, Bolat I, Driessen MRM, de Hulster EAF, van den Broek M, Pronk JT, Geertman JM, Daran JM, Daran-Lapujade P. S. cerevisiae × S. eubayanus interspecific hybrid, the best of both worlds and beyond. FEMS Yeast Res 2015; 15:fov005. [PMID: 25743788 DOI: 10.1093/femsyr/fov005] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2015] [Indexed: 12/16/2022] Open
Abstract
Saccharomyces pastorianus lager-brewing yeasts have descended from natural hybrids of S. cerevisiae and S. eubayanus. Their alloploidy has undoubtedly contributed to successful domestication and industrial exploitation. To understand the early events that have led to the predominance of S. pastorianus as lager-brewing yeast, an interspecific hybrid between S. cerevisiae and S. eubayanus was experimentally constructed. Alloploidy substantially improved the performance of the S. cerevisiae × S. eubayanus hybrid as compared to either parent regarding two cardinal features of brewing yeasts: tolerance to low temperature and oligosaccharide utilization. The hybrid's S. eubayanus subgenome conferred better growth rates and biomass yields at low temperature, both on glucose and on maltose. Conversely, the ability of the hybrid to consume maltotriose, which was absent in the S. eubayanus CBS12357 type strain, was inherited from its S. cerevisiae parent. The S. cerevisiae × S. eubayanus hybrid even outperformed its parents, a phenomenon known as transgression, suggesting that fast growth at low temperature and oligosaccharide utilization may have been key selective advantages of the natural hybrids in brewing environments. To enable sequence comparisons of the parental and hybrid strains, the genome of S. eubayanus CBS12357 type strain (Patagonian isolate) was resequenced, resulting in an improved publicly available sequence assembly.
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Affiliation(s)
- Marit Hebly
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Netherlands Consortium for Systems Biology, 1098 XH Amsterdam, the Netherlands
| | - Anja Brickwedde
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Irina Bolat
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Maureen R M Driessen
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Netherlands Consortium for Systems Biology, 1098 XH Amsterdam, the Netherlands Platform Green Synthetic Biology, 2628 BC Delft, the Netherlands
| | - Jan-Maarten Geertman
- Heineken Global Supply Chain, Technology & Policies, 2382 PH Zoeterwoude, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Platform Green Synthetic Biology, 2628 BC Delft, the Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands Netherlands Consortium for Systems Biology, 1098 XH Amsterdam, the Netherlands
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25
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Gibson B, Liti G. Saccharomyces pastorianus: genomic insights inspiring innovation for industry. Yeast 2014; 32:17-27. [DOI: 10.1002/yea.3033] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 06/17/2014] [Accepted: 07/18/2014] [Indexed: 12/24/2022] Open
Affiliation(s)
- Brian Gibson
- VTT Technical Research Centre of Finland; Tietotie 2, PO Box 1000 FI-02044 VTT Espoo Finland
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081; Université de Nice Sophia Antipolis; 06107 Nice Cedex 2 France
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26
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Deželak M, Gebremariam MM, Cadež N, Zupan J, Raspor P, Zarnkow M, Becker T, Košir IJ. The influence of serial repitching of Saccharomyces pastorianus on its karyotype and protein profile during the fermentation of gluten-free buckwheat and quinoa wort. Int J Food Microbiol 2014; 185:93-102. [PMID: 24935690 DOI: 10.1016/j.ijfoodmicro.2014.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 05/22/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
Abstract
Gluten-free beer-like beverages from malted buckwheat and quinoa are somehow close to their commercial production, but rather high expenses are expected due to the relatively high price of grain, some technological adaptations of process and the need for external enzyme supplementation during mashing. One of the common and efficient cost reduction measures in the industrial scale is serial repitching of the yeast biomass, which has not been studied for the buckwheat and quinoa wort fermentation before. In that manner we have monitored possible changes in yeast's proteins and chromosomal DNA during eleven serial repitchings of the yeast Saccharomyces pastorianus strain TUM 34/70 for fermentation of the barley, buckwheat and quinoa wort. Karyotypes showed changes in regard to the raw materials used and many responsible candidate proteins are suggested which could cause these differences. Different relative expressions of some protein bands were also linked to the proteins involved in yeast stress response and proteins involved in fermentation performance. Results suggest that serial repitching of the strain TUM 34/70 seems suitable for the production of gluten-free beer-like beverages from buckwheat and quinoa.
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Affiliation(s)
- Matjaž Deželak
- Slovenian Institute of Hop Research and Brewing, Department of Agrochemistry and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia.
| | - Mekonnen M Gebremariam
- Technische Universität München, Center of Life and Food Sciences Weihenstephan, Chair of Brewing and Beverage Technology, Weihenstephaner Steig 20, D-85350 Freising, Germany.
| | - Neža Cadež
- University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Biotechnology, Microbiology and Food Safety, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Jure Zupan
- University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Biotechnology, Microbiology and Food Safety, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Peter Raspor
- University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Biotechnology, Microbiology and Food Safety, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Martin Zarnkow
- Technische Universität München, Center of Life and Food Sciences Weihenstephan, Chair of Brewing and Beverage Technology, Weihenstephaner Steig 20, D-85350 Freising, Germany.
| | - Thomas Becker
- Technische Universität München, Center of Life and Food Sciences Weihenstephan, Chair of Brewing and Beverage Technology, Weihenstephaner Steig 20, D-85350 Freising, Germany.
| | - Iztok Jože Košir
- Slovenian Institute of Hop Research and Brewing, Department of Agrochemistry and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia.
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27
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Lin X, Zhang CY, Bai XW, Song HY, Xiao DG. Effects of MIG1, TUP1 and SSN6 deletion on maltose metabolism and leavening ability of baker's yeast in lean dough. Microb Cell Fact 2014; 13:93. [PMID: 24993311 PMCID: PMC4094228 DOI: 10.1186/s12934-014-0093-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/18/2014] [Indexed: 11/17/2022] Open
Abstract
Background Glucose repression is a global regulatory system in baker’s yeast. Maltose metabolism in baker’s yeast strains is negatively influenced by glucose, thereby affecting metabolite productivity (leavening ability in lean dough). Even if the general repression system constituted by MIG1, TUP1 and SSN6 factors has already been reported, the functions of these three genes in maltose metabolism remain unclear. In this work, we explored the effects of MIG1 and/or TUP1 and/or SSN6 deletion on the alleviation of glucose-repression to promote maltose metabolism and leavening ability of baker’s yeast. Results Results strongly suggest that the deletion of MIG1 and/or TUP1 and/or SSN6 can exert various effects on glucose repression for maltose metabolism. The deletion of TUP1 was negative for glucose derepression to facilitate the maltose metabolism. By contrast, the deletion of MIG1 and/or SSN6, rather than other double-gene or triple-gene mutations could partly relieve glucose repression, thereby promoting maltose metabolism and the leavening ability of baker’s yeast in lean dough. Conclusions The mutants of industrial baker’s yeast with enhanced maltose metabolism and leavening ability in lean dough were developed by genetic engineering. These baker’s yeast strains had excellent potential industrial applications.
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Affiliation(s)
| | - Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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28
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Vidgren V, Viljanen K, Mattinen L, Rautio J, Londesborough J. Three Agt1 transporters from brewer's yeasts exhibit different temperature dependencies for maltose transport over the range of brewery temperatures (0-20 °C). FEMS Yeast Res 2014; 14:601-13. [DOI: 10.1111/1567-1364.12147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Virve Vidgren
- VTT Technical Research Centre of Finland; VTT Finland
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29
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Stewart GG, Hill AE, Russell I. 125thAnniversary Review: Developments in brewing and distilling yeast strains. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/jib.104] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Graham G. Stewart
- 13 Heol Nant Castan, Rhiwbina Cardiff CF14 6RP UK
- ICBD; Heriot-Watt University; Riccarton Edinburgh EH14 4AS UK
| | - Annie E. Hill
- ICBD; Heriot-Watt University; Riccarton Edinburgh EH14 4AS UK
| | - Inge Russell
- ICBD; Heriot-Watt University; Riccarton Edinburgh EH14 4AS UK
- Alltech Inc.; Nicholasville KY 40356 USA
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30
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Fischer S, Procopio S, Becker T. Self-cloning brewing yeast: a new dimension in beverage production. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-2092-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Bolat I, Romagnoli G, Zhu F, Pronk JT, Daran JM. Functional analysis and transcriptional regulation of two orthologs of ARO10, encoding broad-substrate-specificity 2-oxo-acid decarboxylases, in the brewing yeast Saccharomyces pastorianus CBS1483. FEMS Yeast Res 2013; 13:505-17. [PMID: 23692465 DOI: 10.1111/1567-1364.12051] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 05/16/2013] [Accepted: 05/16/2013] [Indexed: 01/26/2023] Open
Abstract
The hybrid genomes of Saccharomyces pastorianus consist of subgenomes similar to those of S. cerevisiae and S. eubayanus, and impact of the genome structure on flavour production and its regulation is poorly understood. This study focuses on ARO10, a 2-oxo-acid decarboxylase involved in production of higher alcohols. In S. pastorianus CBS1483, four ARO10 copies were identified, three resembled S. cerevisiae ARO10 and one S. eubayanus ARO10. Substrate specificities of lager strain (Lg)ScAro10 and LgSeubAro10 were compared by individually expressing them in a pdc1Δ-pdc5Δ-pdc6Δ-aro10Δ-thi3Δ S. cerevisiae strain. Both isoenzymes catalysed decarboxylation of the 2-oxo-acids derived from branched-chain, sulphur-containing amino acids and preferably phenylpyruvate. Expression of both alleles was induced by phenylalanine, however in contrast to the S. cerevisiae strain, the two genes were not induced by leucine. Additionally, LgSeubARO10 showed higher basal expression levels during growth with ammonia. ARO80, which encodes ARO10 transcriptional activator, is located on CHRIV and counts three Sc-like and one Seub-like copies. Deletion of LgSeubARO80 did not affect LgSeubARO10 phenylalanine induction, revealing 'trans' regulation across the subgenomes. ARO10 transcript levels showed a poor correlation with decarboxylase activities. These results provide insights into flavour formation in S. pastorianus and illustrate the complexity of functional characterization in aneuploid strains.
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Affiliation(s)
- Irina Bolat
- Industrial Microbiology Section, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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32
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Gibson BR, Londesborough J, Rautio J, Mattinen L, Vidgren V. Transcription ofα-glucoside transport and metabolism genes in the hybrid brewing yeastSaccharomyces pastorianuswith respect to gene provenance and fermentation temperature. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/jib.66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- B. R. Gibson
- VTT, Technical Research Centre of Finland; Tietotie 2, PO Box 1000; FI-02044 VTT; Espoo; Finland
| | - J. Londesborough
- VTT, Technical Research Centre of Finland; Tietotie 2, PO Box 1000; FI-02044 VTT; Espoo; Finland
| | - J. Rautio
- Plexpress Oy; Viikinkaari 6; 00790; Helsinki; Finland
| | - L. Mattinen
- Plexpress Oy; Viikinkaari 6; 00790; Helsinki; Finland
| | - V. Vidgren
- VTT, Technical Research Centre of Finland; Tietotie 2, PO Box 1000; FI-02044 VTT; Espoo; Finland
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