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Stovicek V, Lengeler KB, Wendt T, Rasmussen M, Katz M, Förster J. Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast. N Biotechnol 2024; 82:92-106. [PMID: 38788897 DOI: 10.1016/j.nbt.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.
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Affiliation(s)
- Vratislav Stovicek
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Klaus B Lengeler
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; Traitomic A/S, J.C. Jacobsens Gade 1, DK-1799 Copenhagen V, Denmark
| | - Magnus Rasmussen
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Jochen Förster
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; DTU Biosustain, The Novo Nordisk Foundation Center for Biosustainability, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
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2
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Ward CM, Onetto CA, Van Den Heuvel S, Cuijvers KM, Hale LJ, Borneman AR. Recombination, admixture and genome instability shape the genomic landscape of Saccharomyces cerevisiae derived from spontaneous grape ferments. PLoS Genet 2024; 20:e1011223. [PMID: 38517929 PMCID: PMC10990190 DOI: 10.1371/journal.pgen.1011223] [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: 09/28/2023] [Revised: 04/03/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024] Open
Abstract
Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing natural populations in many countries. Despite this, Oceania is thought to lack native populations of S. cerevisiae, only being introduced after colonisation. Here we investigate the genomic landscape of 411 S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that exhibited high levels of genome instability. Assigning genomic windows to putative ancestral origin revealed that few closely related starter lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with European derived beer yeast along with three independent admixture events from potentially endemic Oceanic lineages that was associated with genome instability. Finally, we investigated Australian ecological niches for basal isolates, identifying phylogenetically distinct S. cerevisiae of non-European, non-domesticated origin associated with admixture loci. Our results illustrate the effect commercial use of microbes may have on local microorganism genetic diversity and demonstrates the presence of non-domesticated, potentially endemic lineages of S. cerevisiae in Australian niches that are actively admixing.
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Affiliation(s)
- Chris M. Ward
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
| | - Cristobal A. Onetto
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Laura J. Hale
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
| | - Anthony R. Borneman
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
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3
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Kerruish DWM, Cormican P, Kenny EM, Kearns J, Colgan E, Boulton CA, Stelma SNE. The origins of the Guinness stout yeast. Commun Biol 2024; 7:68. [PMID: 38216745 PMCID: PMC10786833 DOI: 10.1038/s42003-023-05587-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/14/2023] [Indexed: 01/14/2024] Open
Abstract
Beer is made via the fermentation of an aqueous extract predominantly composed of malted barley flavoured with hops. The transforming microorganism is typically a single strain of Saccharomyces cerevisiae, and for the majority of major beer brands the yeast strain is a unique component. The present yeast used to make Guinness stout brewed in Dublin, Ireland, can be traced back to 1903, but its origins are unknown. To that end, we used Illumina and Nanopore sequencing to generate whole-genome sequencing data for a total of 22 S. cerevisiae yeast strains: 16 from the Guinness collection and 6 other historical Irish brewing. The origins of the Guinness yeast were determined with a SNP-based analysis, demonstrating that the Guinness strains occupy a distinct group separate from other historical Irish brewing yeasts. Assessment of chromosome number, copy number variation and phenotypic evaluation of key brewing attributes established Guinness yeast-specific SNPs but no specific chromosomal amplifications. Our analysis also demonstrated the effects of yeast storage on phylogeny. Altogether, our results suggest that the Guinness yeast used today is related to the first deposited Guinness yeast; the 1903 Watling Laboratory Guinness yeast.
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Affiliation(s)
| | | | | | - Jessica Kearns
- Diageo Ireland, St James's Gate, The Liberties, Dublin, Ireland
| | - Eibhlin Colgan
- Diageo Ireland, St James's Gate, The Liberties, Dublin, Ireland
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4
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Chen J, Garfinkel DJ, Bergman CM. Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572574. [PMID: 38187645 PMCID: PMC10769310 DOI: 10.1101/2023.12.20.572574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely-related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two S. mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of S. paradoxus, S. cerevisiae, S. eubayanus, S. kudriavzevii and the ancestor of the S. mikatae/S. jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally-transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.
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Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
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5
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Smukowski Heil C. Loss of Heterozygosity and Its Importance in Evolution. J Mol Evol 2023; 91:369-377. [PMID: 36752826 PMCID: PMC10276065 DOI: 10.1007/s00239-022-10088-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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6
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Natalino M, Fumasoni M. Experimental approaches to study evolutionary cell biology using yeasts. Yeast 2023; 40:123-133. [PMID: 36896914 DOI: 10.1002/yea.3848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/16/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
The past century has witnessed tremendous advances in understanding how cells function. Nevertheless, how cellular processes have evolved is still poorly understood. Many studies have highlighted surprising molecular diversity in how cells from diverse species execute the same processes, and advances in comparative genomics are likely to reveal much more molecular diversity than was believed possible until recently. Extant cells remain therefore the product of an evolutionary history that we vastly ignore. Evolutionary cell biology has emerged as a discipline aiming to address this knowledge gap by combining evolutionary, molecular, and cellular biology thinking. Recent studies have shown how even essential molecular processes, such as DNA replication, can undergo fast adaptive evolution under certain laboratory conditions. These developments open new lines of research where the evolution of cellular processes can be investigated experimentally. Yeasts naturally find themselves at the forefront of this research line. Not only do they allow the observation of fast evolutionary adaptation, but they also provide numerous genomic, synthetic, and cellular biology tools already developed by a large community. Here we propose that yeasts can serve as an "evolutionary cell lab" to test hypotheses, principles, and ideas in evolutionary cell biology. We discuss various experimental approaches available for this purpose, and how biology at large can benefit from them.
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7
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Peris D, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 2023; 14:690. [PMID: 36755033 PMCID: PMC9908912 DOI: 10.1038/s41467-023-36139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
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Grants
- R01 GM080669 NIGMS NIH HHS
- T32 GM007133 NIGMS NIH HHS
- We thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing Illumina and Sanger sequencing facilities and services; Maria Sardi, Audrey Gasch, and Ursula Bond for providing strains; Sean McIlwain for providing guidance for genome ultra-scaffolding; Yury V. Bukhman for discussing applications of the Growth Curve Analysis Tool (GCAT); Mick McGee for HPLC analysis; Raúl Ortíz-Merino for assistance during YGAP annotations; Jessica Leigh for assistance with PopART; Cecile Ané for suggestions about BUCKy utilization and phylogenetic network analyses; Samina Naseeb and Daniela Delneri for sharing preliminary multi-locus Saccharomyces jurei data; and Branden Timm, Brian Kyle, and Dan Metzger for computational assistance. Some computations were performed on Tirant III of the Spanish Supercomputing Network (‘‘Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin-Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. DP is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. QKL was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB-1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. CRL holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by a NSERC Discovery Grant.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain.
| | - Emily J Ubbelohde
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Meihua Christina Kuang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Kominek
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin A Koshalek
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Katie Hyma
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Guillaume Charron
- Canada Natural Resources, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Carla Gonçalves
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Qi-Ming Wang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Russel L Wrobel
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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8
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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9
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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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10
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Díaz-Muñoz C, Verce M, De Vuyst L, Weckx S. Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population. iScience 2022; 25:105309. [PMID: 36304120 PMCID: PMC9593892 DOI: 10.1016/j.isci.2022.105309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/22/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022] Open
Abstract
Various yeast strains have been proposed as candidate starter cultures for cocoa fermentation, especially strains of Saccharomyces cerevisiae. In the current study, the genome of the cocoa strain S. cerevisiae IMDO 050523 was unraveled based on a combination of long- and short-read sequencing. It consisted of 16 nuclear chromosomes and a mitochondrial chromosome, which were organized in 20 contigs, with only two small gaps. A phylogenomic analysis of this genome together with another 105 S cerevisiae genomes, among which 20 from cocoa strains showed a geographical distribution of the latter, including S. cerevisiae IMDO 050523. Its genome clustered together with that of a West African fermented food population, indicating a wider adaptation to West African food niches than cocoa. Furthermore, S. cerevisiae IMDO 050523 contained genetic signatures involved in sucrose hydrolysis, pectin degradation, osmotolerance, and conserved amino acid changes in key ester-producing enzymes that could point toward specific niche adaptations.
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Affiliation(s)
- Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium,Corresponding author
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11
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Bozdag GO, Ono J. Evolution and molecular bases of reproductive isolation. Curr Opin Genet Dev 2022; 76:101952. [PMID: 35849861 PMCID: PMC10210581 DOI: 10.1016/j.gde.2022.101952] [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: 04/14/2022] [Revised: 05/31/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
Abstract
The most challenging problem in speciation research is disentangling the relative strength and order in which different reproductive barriers evolve. Here, we review recent developments in the study of reproductive isolation in yeasts. With over a thousand genome-sequenced isolates readily available for testing the viability, sterility, and fitness of both intraspecies and interspecies hybrid crosses, Saccharomyces yeasts are an ideal model to study such fundamental questions. Our survey demonstrates that, while chromosomal-level mutations are widespread at the intraspecific level, anti-recombination-driven chromosome missegregation is the primary reproductive barrier between species. Finally, despite their strength, all of these postzygotic barriers can be resolved through the asexual life history of hybrids.
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Affiliation(s)
- G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA. https://twitter.com/ozan_g_b
| | - Jasmine Ono
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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12
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Mullis MN, Ghione C, Lough-Stevens M, Goldstein I, Matsui T, Levy SF, Dean MD, Ehrenreich IM. Complex genetics cause and constrain fungal persistence in different parts of the mammalian body. Genetics 2022; 222:6698696. [PMID: 36103708 PMCID: PMC9630980 DOI: 10.1093/genetics/iyac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/26/2022] [Indexed: 12/05/2022] Open
Abstract
Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae. Employing chromosomally encoded DNA barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain vs the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in nonbrain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.
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Affiliation(s)
- Martin N Mullis
- University of Southern California Molecular and Computational Biology Section, Department of Biological Sciences, , Los Angeles, CA 90089, USA
| | - Caleb Ghione
- University of Southern California Molecular and Computational Biology Section, Department of Biological Sciences, , Los Angeles, CA 90089, USA
| | - Michael Lough-Stevens
- University of Southern California Molecular and Computational Biology Section, Department of Biological Sciences, , Los Angeles, CA 90089, USA
| | - Ilan Goldstein
- University of Southern California Molecular and Computational Biology Section, Department of Biological Sciences, , Los Angeles, CA 90089, USA
| | - Takeshi Matsui
- Stanford University Joint Initiative for Metrology in Biology, , CA 94305, USA
- SLAC National Accelerator Laboratory , Menlo Park, CA, 94025, USA
- Stanford University Department of Genetics, , Stanford, CA 94305, USA
| | - Sasha F Levy
- Stanford University Joint Initiative for Metrology in Biology, , CA 94305, USA
- SLAC National Accelerator Laboratory , Menlo Park, CA, 94025, USA
- Stanford University Department of Genetics, , Stanford, CA 94305, USA
| | - Matthew D Dean
- University of Southern California Molecular and Computational Biology Section, Department of Biological Sciences, , Los Angeles, CA 90089, USA
| | - Ian M Ehrenreich
- University of Southern California Molecular and Computational Biology Section, Department of Biological Sciences, , Los Angeles, CA 90089, USA
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13
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Saada OA, Friedrich A, Schacherer J. Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms. Genomics 2022; 114:110369. [PMID: 35483655 DOI: 10.1016/j.ygeno.2022.110369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/09/2022] [Accepted: 04/11/2022] [Indexed: 01/14/2023]
Abstract
Phasing, and in particular polyploid phasing, have been challenging problems held back by the limited read length of high-throughput short read sequencing methods which can't overcome the distance between heterozygous sites and labor high cost of alternative methods such as the physical separation of chromosomes for example. Recently developed single molecule long-read sequencing methods provide much longer reads which overcome this previous limitation. Here we review the alignment-based methods of polyploid phasing that rely on four main strategies: population inference methods, which leverage the genetic information of several individuals to phase a sample; objective function minimization methods, which minimize a function such as the Minimum Error Correction (MEC); graph partitioning methods, which represent the read data as a graph and split it into k haplotype subgraphs; cluster building methods, which iteratively grow clusters of similar reads into a final set of clusters that represent the haplotypes. We discuss the advantages and limitations of these methods and the metrics used to assess their performance, proposing that accuracy and contiguity are the most meaningful metrics. Finally, we propose the field of alignment-based polyploid phasing would greatly benefit from the use of a well-designed benchmarking dataset with appropriate evaluation metrics. We consider that there are still significant improvements which can be achieved to obtain more accurate and contiguous polyploid phasing results which reflect the complexity of polyploid genome architectures.
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Affiliation(s)
- Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France; Institut Universitaire de France (IUF), Paris, France.
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14
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Silva M, Pontes A, Franco-Duarte R, Soares P, Sampaio JP, Sousa MJ, Brito PH. A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast. Mol Ecol 2022; 32:2396-2412. [PMID: 35298044 DOI: 10.1111/mec.16428] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content, or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix - Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread-production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.
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Affiliation(s)
- Margarida Silva
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Pontes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Maria João Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Patrícia H Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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15
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Saada OA, Tsouris A, Large C, Friedrich A, Dunham MJ, Schacherer J. Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts. Curr Biol 2022; 32:1350-1361.e3. [PMID: 35180385 DOI: 10.1016/j.cub.2022.01.068] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/02/2021] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
Abstract
Yeasts, and in particular Saccharomyces cerevisiae, have been used for brewing beer for thousands of years. Population genomic surveys highlighted that beer yeasts are polyphyletic, with the emergence of different domesticated subpopulations characterized by high genetic diversity and ploidy level. However, the different origins of these subpopulations are still unclear as reconstruction of polyploid genomes is required. To gain better insight into the differential evolutionary trajectories, we sequenced the genomes of 35 Saccharomyces cerevisiae isolates coming from different beer-brewing clades, using a long-read sequencing strategy. By phasing the genomes and using a windowed approach, we identified three main beer subpopulations based on allelic content (European dominant, Asian dominant, and African beer). They were derived from different admixtures between populations and are characterized by distinctive genomic patterns. By comparing the fully phased genes, the most diverse in our dataset are enriched for functions relevant to the brewing environment such as carbon metabolism, oxidoreduction, and cell wall organization activity. Finally, independent domestication, evolution, and adaptation events across subpopulations were also highlighted by investigating specific genes previously linked to the brewing process. Altogether, our analysis based on phased polyploid genomes has led to new insight into the contrasting evolutionary history of beer isolates.
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Affiliation(s)
- Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Chris Large
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France; Institut Universitaire de France (IUF), Paris, France.
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16
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17
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Abstract
Consumer demands for new sensory experiences have driven the research of unconventional yeasts in beer. While much research exists on the use of various common Saccharomyces cerevisiae strains as well as non-Saccharomyces yeasts, there exists a gap in knowledge regarding other non-cerevisiae Saccharomyces species in the fermentation of beer, in addition to S. pastorianus. Here, five distinct species of Saccharomyces from the UC Davis Phaff Yeast Culture Collection, as well as one interspecies hybrid from Fermentis, were chosen to ferment 40 L pilot-scale beers. S. kudriavzevii, S. mikatae, S. paradoxus, S. bayanus, and S. uvarum yeasts were used to ferment wort in duplicate pairs, with one fermenter in each pair receiving 10 g/L dry-hop during fermentation. Analytical measurements were made each day of fermentation and compared to controls of SafAle™ US-05 and SafLager™ W 34/70 for commercial brewing parameters of interest. Finished beers were also analyzed for aroma, taste, and mouthfeel to determine the flavor of each yeast as it pertains to brewing potential. All beers exhibited spicy characteristics, likely from the presence of phenols; dry-hopping increased fruit notes while also increasing perceived bitterness and astringency. All of the species in this study displayed great brewing potential, and might be an ideal addition to beer depending on a brewery’s desire to experiment with flavor and willingness to bring a new yeast into their production environment.
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18
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Zhang J, Plowman JE, Tian B, Clerens S, On SLW. The influence of growth conditions on MALDI-TOF MS spectra of winemaking yeast: implications for industry applications. J Microbiol Methods 2021; 188:106280. [PMID: 34274408 DOI: 10.1016/j.mimet.2021.106280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Previous studies have shown MALDI-TOF MS to be a powerful tool in wine yeast identification and potential prediction of application. However, it is also established that substrate composition influences protein expression, but the degree to which this may affect MALDI-TOF spectra (and analytical results thereof) has not been fully explored. To further inform assay optimisation, the influence on MALDI-TOF spectra was determined using eight Saccharomyces strains of diverse origins cultivated on grape juices from Pinot Noir and Chardonnay varieties, synthetic grape juice, and laboratory-grade artificial culture media (YPD broth and agar). Our results demonstrated significant influences of culture media on strain MALDI-TOF spectra. Yeast culture on YPD agar is recommended for taxonomic studies, with YPD broth culture of S. cerevisiae offering improved intra-subspecific differentiation Furthermore, our data supported a correlation between MALDI spectra and the potential industrial application of individual yeast strains.
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Affiliation(s)
- Junwen Zhang
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85054, Lincoln, New Zealand
| | | | - Bin Tian
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85054, Lincoln, New Zealand
| | - Stefan Clerens
- AgResearch Ltd, Lincoln Research Centre, Lincoln, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85054, Lincoln, New Zealand.
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19
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Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
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Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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20
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Rácz HV, Mukhtar F, Imre A, Rádai Z, Gombert AK, Rátonyi T, Nagy J, Pócsi I, Pfliegler WP. How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes. Yeast 2021; 38:453-470. [PMID: 33844327 DOI: 10.1002/yea.3562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.
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Affiliation(s)
- Hanna Viktória Rácz
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary.,Doctoral School of Nutrition and Food Sciences, University of Debrecen, Debrecen, Hungary
| | - Fezan Mukhtar
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Alexandra Imre
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Rádai
- MTA-ÖK Lendület Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | | | - Tamás Rátonyi
- Institute of Land Use, Technology and Regional Development, University of Debrecen, Debrecen, Hungary
| | - János Nagy
- Institute of Land Use, Technology and Regional Development, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Walter P Pfliegler
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
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21
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Abou Saada O, Tsouris A, Eberlein C, Friedrich A, Schacherer J. nPhase: an accurate and contiguous phasing method for polyploids. Genome Biol 2021; 22:126. [PMID: 33926549 PMCID: PMC8082856 DOI: 10.1186/s13059-021-02342-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/08/2021] [Indexed: 01/06/2023] Open
Abstract
While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.
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Affiliation(s)
- Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR, 7156, Strasbourg, France
| | - Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR, 7156, Strasbourg, France
| | - Chris Eberlein
- Université de Strasbourg, CNRS, GMGM UMR, 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR, 7156, Strasbourg, France.
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156, Strasbourg, France. .,Institut Universitaire de France (IUF), Paris, France.
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22
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Boulton C. Provocation: all yeast cells are born equal, but some grow to be more equal than others. JOURNAL OF THE INSTITUTE OF BREWING 2021. [DOI: 10.1002/jib.647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Scopel EFC, Hose J, Bensasson D, Gasch AP. Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages. Genetics 2021; 217:iyab015. [PMID: 33734361 PMCID: PMC8049548 DOI: 10.1093/genetics/iyab015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/21/2021] [Indexed: 01/06/2023] Open
Abstract
Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual's genetic makeup influences its tolerance of karyotypic imbalance. Here we investigated within-species variation in aneuploidy prevalence and tolerance, using Saccharomyces cerevisiae as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The relationships between lineages with high aneuploidy frequencies suggest that increased aneuploidy prevalence emerged multiple times in S. cerevisiae evolution. Separate from aneuploidy prevalence, analyzing growth phenotypes revealed that some genetic backgrounds-such as the European Wine lineage-show fitness costs in aneuploids compared to euploids, whereas other clades with high aneuploidy frequencies show little evidence of major deleterious effects. Our analysis confirms that chromosome gain can produce phenotypic benefits, which could influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.
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Affiliation(s)
- Eduardo F C Scopel
- Institute of Bioinformatics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - James Hose
- Laboratory of Genetics and Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Douda Bensasson
- Institute of Bioinformatics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Audrey P Gasch
- Laboratory of Genetics and Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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24
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Gómez-Muñoz C, García-Ortega LF, Montalvo-Arredondo J, Pérez-Ortega E, Damas-Buenrostro LC, Riego-Ruiz L. Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. G3-GENES GENOMES GENETICS 2021; 11:6188626. [PMID: 33768233 PMCID: PMC8495930 DOI: 10.1093/g3journal/jkab088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022]
Abstract
Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations between them. To improve the assembly of a previously sequenced lager yeast hybrid Saccharomyces sp. 790 and elucidate its genome structure, we proposed the use of alternative experimental evidence. We determined the phylogenetic position of Saccharomyces sp. 790 and established it as S. pastorianus 790. Then, we obtained from this yeast a bacterial artificial chromosome (BAC) genomic library with its BAC-end sequences (BESs). To analyze these data, we developed a pipeline (applicable to other assemblies) that classifies BES pairs alignments according to their orientation. For the case of S. pastorianus 790, paired-end BESs alignments validated parts of the assembly and unpaired-end ones suggested contig joins or misassemblies. Importantly, the BACs library was preserved and used for verification experiments. Unpaired-end alignments were used to upgrade the previous assembly and provided an improved detection of translocations. With this, we proposed a genome structure of S. pastorianus 790, which was similar to that of other lager yeasts; however, when we estimated chromosome copy number and experimentally measured its genome size, we discovered that one key difference is the outstanding S. pastorianus 790 ploidy level (allopentaploid). Altogether, our results show the value of combining bioinformatic analyses with experimental data such as long-insert clone information to improve a short-read assembly of a hybrid genome.
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Affiliation(s)
- Cintia Gómez-Muñoz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216
| | - Luis Fernando García-Ortega
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216.,Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico, 36824
| | - Javier Montalvo-Arredondo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216.,Dirección General Académica, Universidad Autónoma Agraria Antonio Narro, Saltillo, Mexico, 25315
| | | | | | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216
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25
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Olofsson JK, Curran EV, Nyirenda F, Bianconi ME, Dunning LT, Milenkovic V, Sotelo G, Hidalgo O, Powell RF, Lundgren MR, Leitch IJ, Nosil P, Osborne CP, Christin PA. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Mol Ecol 2021; 30:2116-2130. [PMID: 33682242 DOI: 10.1111/mec.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
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Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Matheus E Bianconi
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | | | - Marjorie R Lundgren
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | - Patrik Nosil
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
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26
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Bigey F, Segond D, Friedrich A, Guezenec S, Bourgais A, Huyghe L, Agier N, Nidelet T, Sicard D. Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes. Curr Biol 2021; 31:722-732.e5. [DOI: 10.1016/j.cub.2020.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/07/2020] [Accepted: 11/05/2020] [Indexed: 10/22/2022]
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27
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Fischer G, Liti G, Llorente B. The budding yeast life cycle: More complex than anticipated? Yeast 2020; 38:5-11. [PMID: 33197073 DOI: 10.1002/yea.3533] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 11/07/2022] Open
Abstract
The budding yeast, Saccharomyces cerevisiae, has served as a model for nearly a century to understand the principles of the eukaryotic life cycle. The canonical life cycle of S. cerevisiae comprises a regular alternation between haploid and diploid phases. Haploid gametes generated by sporulation are expected to quickly restore the diploid phase mainly through inbreeding via intratetrad mating or haploselfing, thereby promoting genome homozygotization. However, recent large population genomics data unveiled that heterozygosity and polyploidy are unexpectedly common. This raises the interesting paradox of a haplo-diplobiontic species being well-adapted to inbreeding and able to maintain high levels of heterozygosity and polyploidy, thereby suggesting an unanticipated complexity of the yeast life cycle. Here, we propose that unprogrammed mating type switching, heterothallism, reduced spore formation and viability, cell-cell fusion and dioecy could play key and uncharted contributions to generate and maintain heterozygosity through polyploidization.
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Affiliation(s)
- Gilles Fischer
- CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Sorbonne Université, Paris, France
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
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Novel Non-Cerevisiae Saccharomyces Yeast Species Used in Beer and Alcoholic Beverage Fermentations. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6040116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A great deal of research in the alcoholic beverage industry was done on non-Saccharomyces yeast strains in recent years. The increase in research interest could be attributed to the changing of consumer tastes and the search for new beer sensory experiences, as well as the rise in popularity of mixed-fermentation beers. The search for unique flavors and aromas, such as the higher alcohols and esters, polyfunctional thiols, lactones and furanones, and terpenoids that produce fruity and floral notes led to the use of non-cerevisiae Saccharomyces species in the fermentation process. Additionally, a desire to invoke new technologies and techniques for making alcoholic beverages also led to the use of new and novel yeast species. Among them, one of the most widely used non-cerevisiae strains is S. pastorianus, which was used in the production of lager beer for centuries. The goal of this review is to focus on some of the more distinct species, such as those species of Saccharomyces sensu stricto yeasts: S. kudriavzevii, S. paradoxus, S. mikatae, S. uvarum, and S. bayanus. In addition, this review discusses other Saccharomyces spp. that were used in alcoholic fermentation. Most importantly, the factors professional brewers might consider when selecting a strain of yeast for fermentation, are reviewed herein. The factors include the metabolism and fermentation potential of carbon sources, attenuation, flavor profile of fermented beverage, flocculation, optimal temperature range of fermentation, and commercial availability of each species. While there is a great deal of research regarding the use of some of these species on a laboratory scale wine fermentation, much work remains for their commercial use and efficacy for the production of beer.
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Davydenko S, Meledina T, Mittenberg A, Shabelnikov S, Vonsky M, Morozov A. Proteomics Answers Which Yeast Genes Are Specific for Baking, Brewing, and Ethanol Production. Bioengineering (Basel) 2020; 7:E147. [PMID: 33217975 PMCID: PMC7711625 DOI: 10.3390/bioengineering7040147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/29/2022] Open
Abstract
Yeast strains are convenient models for studying domestication processes. The ability of yeast to ferment carbon sources from various substrates and to produce ethanol and carbon dioxide is the core of brewing, winemaking, and ethanol production technologies. The present study reveals the differences among yeast strains used in various industries. To understand this, we performed a proteomic study of industrial Saccharomyces cerevisiae strains followed by a comparative analysis of available yeast genetic data. Individual protein expression levels in domesticated strains from different industries indicated modulation resulting from response to technological environments. The innovative nature of this research was the discovery of genes overexpressed in yeast strains adapted to brewing, baking, and ethanol production, typical genes for specific domestication were found. We discovered a gene set typical for brewer's yeast strains. Baker's yeast had a specific gene adapted to osmotic stress. Toxic stress was typical for yeast used for ethanol production. The data obtained can be applied for targeted improvement of industrial strains.
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Affiliation(s)
- Svetlana Davydenko
- Innovation & Research Department, Baltika Breweries—Part of the Carlsberg Group, 6-th Verkhnij ln. 3, 194292 St. Petersburg, Russia;
| | - Tatiana Meledina
- Faculty of Biotechnologies (BioTech), ITMO University, Lomonosova st. 9, 191002 St. Petersburg, Russia;
| | - Alexey Mittenberg
- Proteomics and Mass Spectrometry Group, Cell Technologies Center, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av. 4, 194064 St. Petersburg, Russia; (A.M.); (S.S.)
| | - Sergey Shabelnikov
- Proteomics and Mass Spectrometry Group, Cell Technologies Center, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av. 4, 194064 St. Petersburg, Russia; (A.M.); (S.S.)
| | - Maksim Vonsky
- Department of State Standards and Reference Materials in the Area of Bioanalytical and Medical Measurements, D.I. Mendeleyev Institute for Metrology VNIIM, Moskovsky pr. 19, 190005 St. Petersburg, Russia;
| | - Artyom Morozov
- Faculty of Biotechnologies (BioTech), ITMO University, Lomonosova st. 9, 191002 St. Petersburg, Russia;
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30
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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: 28] [Impact Index Per Article: 7.0] [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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Molinet J, Cubillos FA. Wild Yeast for the Future: Exploring the Use of Wild Strains for Wine and Beer Fermentation. Front Genet 2020; 11:589350. [PMID: 33240332 PMCID: PMC7667258 DOI: 10.3389/fgene.2020.589350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/28/2020] [Indexed: 01/05/2023] Open
Abstract
The continuous usage of single Saccharomyces cerevisiae strains as starter cultures in fermentation led to the domestication and propagation of highly specialized strains in fermentation, resulting in the standardization of wines and beers. In this way, hundreds of commercial strains have been developed to satisfy producers’ and consumers’ demands, including beverages with high/low ethanol content, nutrient deprivation tolerance, diverse aromatic profiles, and fast fermentations. However, studies in the last 20 years have demonstrated that the genetic and phenotypic diversity in commercial S. cerevisiae strains is low. This lack of diversity limits alternative wines and beers, stressing the need to explore new genetic resources to differentiate each fermentation product. In this sense, wild strains harbor a higher than thought genetic and phenotypic diversity, representing a feasible option to generate new fermentative beverages. Numerous recent studies have identified alleles in wild strains that could favor phenotypes of interest, such as nitrogen consumption, tolerance to cold or high temperatures, and the production of metabolites, such as glycerol and aroma compounds. Here, we review the recent literature on the use of commercial and wild S. cerevisiae strains in wine and beer fermentation, providing molecular evidence of the advantages of using wild strains for the generation of improved genetic stocks for the industry according to the product style.
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Affiliation(s)
- Jennifer Molinet
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
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Abstract
The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evolution of diverse Saccharomyces species and hybrids, which occupy a variety of wild and domesticated habitats. In this article, we introduce readers to the mechanisms isolating Saccharomyces species, the circumstances in which reproductive isolation mechanisms are effective and ineffective, and the evolutionary consequences of partial reproductive isolation. We discuss both the evolutionary history of the genus Saccharomyces and the human history of taxonomists and biologists struggling with species concepts in this fascinating genus.
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Affiliation(s)
- Jasmine Ono
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Duncan Greig
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Primrose J Boynton
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
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33
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The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions. G3-GENES GENOMES GENETICS 2020; 10:3087-3097. [PMID: 32605927 PMCID: PMC7466965 DOI: 10.1534/g3.120.401149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genome sequences of archeological Saccharomyces cerevisiae isolates can reveal insights about the history of human baking, brewing and winemaking activities. A yeast strain called Jean-Talon was recently isolated from the vaults of the Intendant’s Palace of Nouvelle France on a historical site in Québec City. This site was occupied by breweries from the end of the 17th century until the middle of the 20th century when poisoning caused by cobalt added to the beer led to a shutdown of brewing activities. We sequenced the genome of the Jean-Talon strain and reanalyzed the genomes of hundreds of strains to determine how it relates to other domesticated and wild strains. The Jean-Talon strain is most closely related to industrial beer strains from the beer and bakery genetic groups from the United Kingdom and Belgium. It has numerous aneuploidies and Copy Number Variants (CNVs), including the main gene conferring cobalt resistance in yeast. The Jean-Talon strain has indeed higher tolerance to cobalt compared to other yeast strains, consistent with adaptation to the most recent brewing activities on the site. We conclude from this that the Jean-Talon strain most likely derives from recent brewing activities and not from the original breweries of Nouvelle France on the site.
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34
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Giannakou K, Cotterrell M, Delneri D. Genomic Adaptation of Saccharomyces Species to Industrial Environments. Front Genet 2020; 11:916. [PMID: 33193572 PMCID: PMC7481385 DOI: 10.3389/fgene.2020.00916] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023] Open
Abstract
The budding yeast has been extensively studied for its physiological performance in fermentative environments and, due to its remarkable plasticity, is used in numerous industrial applications like in brewing, baking and wine fermentations. Furthermore, thanks to its small and relatively simple eukaryotic genome, the molecular mechanisms behind its evolution and domestication are more easily explored. Considerable work has been directed into examining the industrial adaptation processes that shaped the genotypes of species and hybrids belonging to the Saccharomyces group, specifically in relation to beverage fermentation performances. A variety of genetic mechanisms are responsible for the yeast response to stress conditions, such as genome duplication, chromosomal re-arrangements, hybridization and horizontal gene transfer, and these genetic alterations are also contributing to the diversity in the Saccharomyces industrial strains. Here, we review the recent genetic and evolutionary studies exploring domestication and biodiversity of yeast strains.
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Affiliation(s)
- Konstantina Giannakou
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Cloudwater Brew Co., Manchester, United Kingdom
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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35
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Koonthongkaew J, Toyokawa Y, Ohashi M, Large CRL, Dunham MJ, Takagi H. Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast. Appl Microbiol Biotechnol 2020. [PMID: 32776205 DOI: 10.1101/2020.06.26.166157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.
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Affiliation(s)
- Jirasin Koonthongkaew
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Yoichi Toyokawa
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Masataka Ohashi
- Nara Prefecture Institute of Industrial Development, 129-1 Kashiwagi-cho, Nara, Nara, 630-8031, Japan
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Hiroshi Takagi
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan.
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36
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Pontes A, Hutzler M, Brito PH, Sampaio JP. Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae-Phylogeny, Phenotypes, Ecology and Domestication. Microorganisms 2020; 8:E903. [PMID: 32549402 PMCID: PMC7356373 DOI: 10.3390/microorganisms8060903] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/02/2022] Open
Abstract
Saccharomyces cerevisiae-the most emblematic and industrially relevant yeast-has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and biologists not informed on taxonomic matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisiae, with emphasis on the most relevant technological groups, but absent in wild lineages. We analyzed the phylogeny of a representative and well-balanced dataset of S. cerevisiae genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction, among wild populations, of those associated with low- or high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus giving more resolution to the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases, we could trace their origin to wild reservoirs, while in other cases gene inactivation associated with domestication was also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (A.P.); (P.H.B.)
| | - Mathias Hutzler
- Research Center Weihenstephan for Brewing and Food Quality, TU München, D-85354 Freising, Germany;
| | - Patrícia H. Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (A.P.); (P.H.B.)
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (A.P.); (P.H.B.)
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37
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The Yeast Atlas of Appalachia: Species and Phenotypic Diversity of Herbicide Resistance in Wild Yeast. DIVERSITY 2020. [DOI: 10.3390/d12040139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glyphosate and copper-based herbicides/fungicides affect non-target organisms, and these incidental exposures can impact microbial populations. In this study, glyphosate resistance was found in the historical collection of S. cerevisiae, which was collected over the last century, but only in yeast isolated after the introduction of glyphosate. Although herbicide application was not recorded, the highest glyphosate-resistant S. cerevisiae were isolated from agricultural sites. In an effort to assess glyphosate resistance and impact on non-target microorganisms, different yeast species were harvested from 15 areas with known herbicidal histories, including an organic farm, conventional farm, remediated coal mine, suburban locations, state park, and a national forest. Yeast representing 23 genera were isolated from 237 samples of plant, soil, spontaneous fermentation, nut, flower, fruit, feces, and tree material samples. Saccharomyces, Candida, Metschnikowia, Kluyveromyces, Hanseniaspora, and Pichia were other genera commonly found across our sampled environments. Managed areas had less species diversity, and at the brewery only Saccharomyces and Pichia were isolated. A conventional farm growing RoundUp Ready™ corn had the lowest phylogenetic diversity and the highest glyphosate resistance. The mine was sprayed with multiple herbicides including a commercial formulation of glyphosate; however, the S. cerevisiae did not have elevated glyphosate resistance. In contrast to the conventional farm, the mine was exposed to glyphosate only one year prior to sample isolation. Glyphosate resistance is an example of the anthropogenic selection of nontarget organisms.
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Morard M, Benavent-Gil Y, Ortiz-Tovar G, Pérez-Través L, Querol A, Toft C, Barrio E. Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity. Microb Genom 2020; 6:e000333. [PMID: 32065577 PMCID: PMC7200066 DOI: 10.1099/mgen.0.000333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/15/2020] [Indexed: 01/03/2023] Open
Abstract
Interspecific hybridization has played an important role in the evolution of eukaryotic organisms by favouring genetic interchange between divergent lineages to generate new phenotypic diversity involved in the adaptation to new environments. This way, hybridization between Saccharomyces species, involving the fusion between their metabolic capabilities, is a recurrent adaptive strategy in industrial environments. In the present study, whole-genome sequences of natural hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii were obtained to unveil the mechanisms involved in the origin and evolution of hybrids, as well as the ecological and geographic contexts in which spontaneous hybridization and hybrid persistence take place. Although Saccharomyces species can mate using different mechanisms, we concluded that rare-mating is the most commonly used, but other mechanisms were also observed in specific hybrids. The preponderance of rare-mating was confirmed by performing artificial hybridization experiments. The mechanism used to mate determines the genomic structure of the hybrid and its final evolutionary outcome. The evolution and adaptability of the hybrids are triggered by genomic instability, resulting in a wide diversity of genomic rearrangements. Some of these rearrangements could be adaptive under the stressful conditions of the industrial environment.
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Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Yaiza Benavent-Gil
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Guadalupe Ortiz-Tovar
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Centro de Estudios Vitivinícolas de Baja California, México, CETYS Universidad, Ensenada, Baja California, Mexico
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Institute for Integrative and Systems Biology, Universitat de València and CSIC, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
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Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination. PLoS Genet 2020; 16:e1008632. [PMID: 32084126 PMCID: PMC7055915 DOI: 10.1371/journal.pgen.1008632] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/04/2020] [Accepted: 01/27/2020] [Indexed: 01/04/2023] Open
Abstract
Transposable elements constitute a large fraction of most eukaryotic genomes. Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation. Mobility of the Ty1 retrotransposon in Saccharomyces yeasts is regulated by copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1 gag capsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains of S. cerevisiae and S. paradoxus to investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a tester element with a gag sequence from the canonical Ty1 subfamily in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1' subfamily that have a divergent gag sequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing a canonical gag sequence. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1' is the ancestral subfamily present in wild strains of S. cerevisiae, and that canonical Ty1 in S. cerevisiae is a derived subfamily that acquired gag from S. paradoxus by horizontal transfer and recombination. Our results provide evidence that variation in the ability of S. cerevisiae and S. paradoxus strains to repress canonical Ty1 transposition via CNC is regulated by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.
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40
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Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens. Genes (Basel) 2020; 11:genes11010101. [PMID: 31963231 PMCID: PMC7017293 DOI: 10.3390/genes11010101] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/02/2020] [Accepted: 01/14/2020] [Indexed: 01/13/2023] Open
Abstract
Hybridization is increasingly recognized as an important force impacting adaptation and evolution in many lineages of fungi. During hybridization, divergent genomes and alleles are brought together into the same cell, potentiating adaptation by increasing genomic plasticity. Here, we review hybridization in fungi by focusing on two fungal pathogens of animals. Hybridization is common between the basidiomycete yeast species Cryptococcus neoformans × Cryptococcus deneoformans, and hybrid genotypes are frequently found in both environmental and clinical settings. The two species show 10-15% nucleotide divergence at the genome level, and their hybrids are highly heterozygous. Though largely sterile and unable to mate, these hybrids can propagate asexually and generate diverse genotypes by nondisjunction, aberrant meiosis, mitotic recombination, and gene conversion. Under stress conditions, the rate of such genetic changes can increase, leading to rapid adaptation. Conversely, in hybrids formed between lineages of the chytridiomycete frog pathogen Batrachochytrium dendrobatidis (Bd), the parental genotypes are considerably less diverged (0.2% divergent). Bd hybrids are formed from crosses between lineages that rarely undergo sex. A common theme in both species is that hybrids show genome plasticity via aneuploidy or loss of heterozygosity and leverage these mechanisms as a rapid way to generate genotypic/phenotypic diversity. Some hybrids show greater fitness and survival in both virulence and virulence-associated phenotypes than parental lineages under certain conditions. These studies showcase how experimentation in model species such as Cryptococcus can be a powerful tool in elucidating the genotypic and phenotypic consequences of hybridization.
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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Dahabieh MS, Thevelein JM, Gibson B. Multimodal Microorganism Development: Integrating Top-Down Biological Engineering with Bottom-Up Rational Design. Trends Biotechnol 2019; 38:241-253. [PMID: 31653446 DOI: 10.1016/j.tibtech.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Biological engineering has unprecedented potential to solve society's most pressing challenges. Engineering approaches must consider complex technical, economic, and social factors. This requires methods that confer gene/pathway-level functionality and organism-level robustness in rapid and cost-effective ways. This article compares foundational engineering approaches - bottom-up, gene-targeted engineering, and top-down, whole-genome engineering - and identifies significant complementarity between them. Cases drawn from engineering Saccharomyces cerevisiae exemplify the synergy of a combined approach. Indeed, multimodal engineering streamlines strain development by leveraging the complementarity of whole-genome and gene-targeted engineering to overcome the gap in design knowledge that restricts rational design. As biological engineers target more complex systems, this dual-track approach is poised to become an increasingly important tool to realize the promise of synthetic biology.
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Affiliation(s)
- Matthew S Dahabieh
- Renaissance BioScience, 410-2389 Health Sciences Mall, Vancouver, BC V6T1Z3, Canada
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, VTT, PO Box 1000, FI-02044 Espoo, Finland.
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Thesseling FA, Bircham PW, Mertens S, Voordeckers K, Verstrepen KJ. A Hands-On Guide to Brewing and Analyzing Beer in the Laboratory. ACTA ACUST UNITED AC 2019; 54:e91. [PMID: 31518063 PMCID: PMC9286407 DOI: 10.1002/cpmc.91] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Beer would not exist without microbes. During fermentation, yeast cells convert cereal‐derived sugars into ethanol and CO2. Yeast also produces a wide array of aroma compounds that influence beer taste and aroma. The complex interaction between all these aroma compounds results in each beer having its own distinctive palette. This article contains all protocols needed to brew beer in a standard lab environment and focuses on the use of yeast in beer brewing. More specifically, it provides protocols for yeast propagation, brewing calculations and, of course, beer brewing. At the end, we have also included protocols for analyses that can be performed on the resulting brew, with a focus on yeast‐derived aroma compounds. © 2019 The Authors.
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Affiliation(s)
- Florian A Thesseling
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Peter W Bircham
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Stijn Mertens
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Karin Voordeckers
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Kevin J Verstrepen
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
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Steensels J, Gallone B, Voordeckers K, Verstrepen KJ. Domestication of Industrial Microbes. Curr Biol 2019; 29:R381-R393. [DOI: 10.1016/j.cub.2019.04.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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