101
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Quispe X, Tapia SM, Villarroel C, Oporto C, Abarca V, García V, Martínez C, Cubillos FA. Genetic basis of mycotoxin susceptibility differences between budding yeast isolates. Sci Rep 2017; 7:9173. [PMID: 28835621 PMCID: PMC5569051 DOI: 10.1038/s41598-017-09471-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/25/2017] [Indexed: 01/29/2023] Open
Abstract
Micophenolic acid (MPA) is an immunosuppressant mycotoxin which impairs yeast cell growth to variable degrees depending on the genetic background. Such variation could have emerged from several phenomena, including MPA gene resistance mutations and variations in copy number and localisation of resistance genes. To test this, we evaluated MPA susceptibility in four S. cerevisiae isolates and genetically dissected variation through the identification of Quantitative Trait Loci. Via linkage analysis we identified six QTLs, majority of which were located within subtelomeres and co-localised with IMD2, an inosine monophosphate dehydrogenase previously identified underlying MPA drug resistance in yeast cells. From chromosome end disruption and bioinformatics analysis, it was found that the subtelomere localisation of IMD2 within chromosome ends is variable depending on the strain, demonstrating the influence of IMD2 on the natural variation in yeast MPA susceptibility. Furthermore, GxE gene expression analysis of strains exhibiting opposite phenotypes indicated that ribosome biogenesis, RNA transport, and purine biosynthesis were impaired in strains most susceptible to MPA toxicity. Our results demonstrate that natural variation can be exploited to better understand the molecular mechanisms underlying mycotoxin susceptibility in eukaryote cells and demonstrate the role of subtelomeric regions in mediating interactions with the environment.
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Affiliation(s)
- Xtopher Quispe
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Sebastián M Tapia
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Carlos Villarroel
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Christian Oporto
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Valentina Abarca
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Verónica García
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile. .,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile. .,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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102
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Warringer J, Liti G, Blomberg A. Yeast Reciprocal Hemizygosity to Confirm the Causality of a Quantitative Trait Loci-Associated Gene. Cold Spring Harb Protoc 2017; 2017:pdb.prot089078. [PMID: 28765294 DOI: 10.1101/pdb.prot089078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pinpointing causal alleles within a quantitative trait loci region is a key challenge when dissecting the genetic basis of natural variation. In yeast, homing in on culprit genes is often achieved using engineered reciprocal hemizygotes as outlined here. Based on prior information on gene-trait associations, candidate genes are identified. In haploid versions of both founder strains, a candidate gene is then deleted. Gene knockouts are independently mated to a wild-type version of the other strain, such that two diploid hybrid strains are obtained. These strains are identical with regard to the nuclear genome, except for that they are hemizygotic at the locus of interest and contain different alleles of the candidate gene. If correctly measured, a trait difference between these reciprocal hemizygotes can confidently be ascribed to allelic variation at the target locus.
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Affiliation(s)
- Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden; .,Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), 1432 Ås, Norway
| | - Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, 06107 Nice, France
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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103
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Liti G, Warringer J, Blomberg A. Budding Yeast Strains and Genotype-Phenotype Mapping. Cold Spring Harb Protoc 2017; 2017:pdb.top077735. [PMID: 28765302 DOI: 10.1101/pdb.top077735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A small number of well-studied laboratory strains of Saccharomyces cerevisiae, mostly derived from S288C, are used in yeast research. Although powerful, studies for understanding S288C do not always capture the phenotypic essence or the genetic complexity of S. cerevisiae biology. This is particularly problematic for multilocus phenotypes identified in laboratory strains because these loci have never been jointly exposed to natural selection and the corresponding phenotypes do not represent optimization for any particular purpose or environment. Isolation and sequencing of new natural yeast strains also reveal that the total sequence diversity of the S. cerevisiae global population is poorly sampled in common laboratory strains. Here we discuss methodologies required for using the natural genetic variation in yeast to complete a genotype-phenotype map.
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Affiliation(s)
- Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, 06107 Nice, France
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), 1432 Ås, Norway
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden;
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104
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Marsit S, Leducq JB, Durand É, Marchant A, Filteau M, Landry CR. Evolutionary biology through the lens of budding yeast comparative genomics. Nat Rev Genet 2017; 18:581-598. [DOI: 10.1038/nrg.2017.49] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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105
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Origone A, del Mónaco S, Ávila J, González Flores M, Rodríguez M, Lopes C. Tolerance to winemaking stress conditions of Patagonian strains ofSaccharomyces eubayanusandSaccharomyces uvarum. J Appl Microbiol 2017; 123:450-463. [DOI: 10.1111/jam.13495] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/21/2017] [Accepted: 05/09/2017] [Indexed: 01/08/2023]
Affiliation(s)
- A.C. Origone
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos; Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue); Neuquén Argentina
| | - S.M. del Mónaco
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos; Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue); Neuquén Argentina
- Facultad de Ciencias Médicas; Universidad Nacional del Comahue; Cipolletti Río Negro Argentina
| | - J.R. Ávila
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos; Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue); Neuquén Argentina
| | - M. González Flores
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos; Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue); Neuquén Argentina
| | - M.E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos; Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue); Neuquén Argentina
- Facultad de Ciencias Médicas; Universidad Nacional del Comahue; Cipolletti Río Negro Argentina
| | - C.A. Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos; Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina - Universidad Nacional del Comahue); Neuquén Argentina
- Facultad de Ciencias Agrarias; Universidad Nacional del Comahue; Cinco Saltos Río Negro Argentina
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106
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Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses. G3-GENES GENOMES GENETICS 2017; 7:1693-1705. [PMID: 28592651 PMCID: PMC5473750 DOI: 10.1534/g3.117.042127] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.
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107
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Abstract
ABSTRACT
In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.
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108
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Ortiz-Merino RA, Kuanyshev N, Braun-Galleani S, Byrne KP, Porro D, Branduardi P, Wolfe KH. Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch. PLoS Biol 2017; 15:e2002128. [PMID: 28510588 PMCID: PMC5433688 DOI: 10.1371/journal.pbio.2002128] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/13/2017] [Indexed: 11/30/2022] Open
Abstract
Many interspecies hybrids have been discovered in yeasts, but most of these hybrids are asexual and can replicate only mitotically. Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility, restoring their ability to perform meiosis and sporulate. Here, we show that this process occurred naturally during the evolution of Zygosaccharomyces parabailii, an interspecies hybrid that was formed by mating between 2 parents that differed by 7% in genome sequence and by many interchromosomal rearrangements. Surprisingly, Z. parabailii has a full sexual cycle and is genetically haploid. It goes through mating-type switching and autodiploidization, followed by immediate sporulation. We identified the key evolutionary event that enabled Z. parabailii to regain fertility, which was breakage of 1 of the 2 homeologous copies of the mating-type (MAT) locus in the hybrid, resulting in a chromosomal rearrangement and irreparable damage to 1 MAT locus. This rearrangement was caused by HO endonuclease, which normally functions in mating-type switching. With 1 copy of MAT inactivated, the interspecies hybrid now behaves as a haploid. Our results provide the first demonstration that MAT locus damage is a naturally occurring evolutionary mechanism for whole-genome duplication and restoration of fertility to interspecies hybrids. The events that occurred in Z. parabailii strongly resemble those postulated to have caused ancient whole-genome duplication in an ancestor of Saccharomyces cerevisiae. It has recently been proposed that the whole-genome duplication (WGD) event that occurred during evolution of an ancestor of the yeast S. cerevisiae was the result of a hybridization between 2 parental yeast species that were significantly divergent in DNA sequence, followed by a doubling of the genome content to restore the hybrid’s ability to make viable spores. However, the molecular details of how genome doubling could occur in a hybrid were unclear because most known interspecies hybrid yeasts have no sexual cycle. We show here that Z. parabailii provides an almost exact precedent for the steps proposed to have occurred during the S. cerevisiae WGD. Two divergent haploid parental species, each with 8 chromosomes, mated to form a hybrid that was initially sterile but regained fertility when 1 copy of its mating-type locus became damaged by the mating-type switching apparatus. As a result of this damage, the Z. parabailii life cycle now consists of a 16-chromosome haploid phase and a transient 32-chromosome diploid phase. Each pair of homeologous genes behaves as 2 independent Mendelian loci during meiosis.
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Affiliation(s)
- Raúl A. Ortiz-Merino
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Nurzhan Kuanyshev
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | | | - Kevin P. Byrne
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Kenneth H. Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
- * E-mail:
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109
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Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy. PLoS Genet 2017; 13:e1006768. [PMID: 28493864 PMCID: PMC5444853 DOI: 10.1371/journal.pgen.1006768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/25/2017] [Accepted: 04/19/2017] [Indexed: 11/19/2022] Open
Abstract
The functional basis of genetic robustness, the ability of organisms to suppress the effects of mutations, remains incompletely understood. We exposed a set of 15 strains of Saccharomyces cerevisiae form diverse environments to increasing doses of the chemical mutagen EMS. The number of the resulting random mutations was similar for all tested strains. However, there were differences in immediate mortality after the mutagenic treatment and in defective growth of survivors. An analysis of gene expression revealed that immediate mortality was lowest in strains with lowest expression of transmembrane proteins, which are rich in thiol groups and thus vulnerable to EMS. A signal of genuine genetic robustness was detected for the other trait, the ability to grow well despite bearing non-lethal mutations. Increased tolerance of such mutations correlated with high expression of genes responsible for the oxidative energy metabolism, suggesting that the negative effect of mutations can be buffered if enough energy is available. We confirmed this finding in three additional tests of the ability to grow on (i) fermentable or non-fermentable sources of carbon, (ii) under chemical inhibition of the electron transport chain and (iii) during overexpression of its key component, cytochrome c. Our results add the capacity to generate energy as a general mechanism of genetic robustness. The ability to suppress phenotypic effects of mutations is termed genetic robustness. Its functional basis and evolutionary origin remain insufficiently understood despite decades of research. In fact, it is still largely untested whether genetic robustness is a trait of substantial, within-species variation. We used a model organism, Saccharomyces cerevisiae, to study both phenotypic signs and functional underpinnings of genetic robustness. We introduced random mutations into a set of well-characterized yeast strain. There was considerable variation in the growth rate among clones recovered after mutagenesis, which is an indication of genetic robustness. Using available data on gene expression for our strains, we found that genetic robustness was strongest among strains with enhanced expression of genes related to the energy metabolism. We reasoned that, regardless of the specific mutations, the capacity to generate metabolic energy may be a general underlying mechanism for buffering the effects of random mutations across the genome. We confirmed this hypothesis in further experiments in which we showed that genetic robustness decreases when the energy metabolism is compromised and increases when it is boosted.
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110
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Steenwyk J, Rokas A. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. G3 (BETHESDA, MD.) 2017; 7:1475-1485. [PMID: 28292787 PMCID: PMC5427499 DOI: 10.1534/g3.117.040105] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023]
Abstract
Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S. cerevisiae wine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ∼4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as the SNO gene family whose members are expressed before or during the diauxic shift, showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains, and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.
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Affiliation(s)
- Jacob Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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111
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Guillamón JM, Barrio E. Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection. Front Microbiol 2017; 8:806. [PMID: 28522998 PMCID: PMC5415627 DOI: 10.3389/fmicb.2017.00806] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.
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Affiliation(s)
- José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain.,Departamento de Genética, Universidad de ValenciaValencia, Spain
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112
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Lee KB, Wang J, Palme J, Escalante-Chong R, Hua B, Springer M. Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes. PLoS Genet 2017; 13:e1006766. [PMID: 28542190 PMCID: PMC5464677 DOI: 10.1371/journal.pgen.1006766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 06/08/2017] [Accepted: 04/19/2017] [Indexed: 01/26/2023] Open
Abstract
In nature, microbes often need to "decide" which of several available nutrients to utilize, a choice that depends on a cell's inherent preference and external nutrient levels. While natural environments can have mixtures of different nutrients, phenotypic variation in microbes' decisions of which nutrient to utilize is poorly studied. Here, we quantified differences in the concentration of glucose and galactose required to induce galactose-responsive (GAL) genes across 36 wild S. cerevisiae strains. Using bulk segregant analysis, we found that a locus containing the galactose sensor GAL3 was associated with differences in GAL signaling in eight different crosses. Using allele replacements, we confirmed that GAL3 is the major driver of GAL induction variation, and that GAL3 allelic variation alone can explain as much as 90% of the variation in GAL induction in a cross. The GAL3 variants we found modulate the diauxic lag, a selectable trait. These results suggest that ecological constraints on the galactose pathway may have led to variation in a single protein, allowing cells to quantitatively tune their response to nutrient changes in the environment.
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Affiliation(s)
- Kayla B. Lee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jue Wang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Systems Biology Graduate Program, Harvard University, Cambridge, Massachusetts, United States of America
- Ginkgo Bioworks, Boston, Massachusetts, United States of America
| | - Julius Palme
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technische Universität, München, Freising, Germany
| | | | - Bo Hua
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Systems Biology Graduate Program, Harvard University, Cambridge, Massachusetts, United States of America
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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113
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Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet 2017; 49:913-924. [PMID: 28416820 PMCID: PMC5446901 DOI: 10.1038/ng.3847] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/22/2017] [Indexed: 12/13/2022]
Abstract
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.
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Affiliation(s)
- Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Jing Li
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Johan Hallin
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Karl Persson
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | | | | | | | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | - Marco Cosentino Lagomarsino
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris-Seine, UPMC University Paris 06, Sorbonne Universités, CNRS, Paris, France
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris-Seine, UPMC University Paris 06, Sorbonne Universités, CNRS, Paris, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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114
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Almeida P, Barbosa R, Bensasson D, Gonçalves P, Sampaio JP. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites. Mol Ecol 2017; 26:2167-2182. [PMID: 28231394 DOI: 10.1111/mec.14071] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
Abstract
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives.
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Affiliation(s)
- Pedro Almeida
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Raquel Barbosa
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Douda Bensasson
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Paula Gonçalves
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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115
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Maxwell CS, Magwene PM. The quick and the dead: microbial demography at the yeast thermal limit. Mol Ecol 2017; 26:1631-1640. [DOI: 10.1111/mec.13955] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/25/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Colin S. Maxwell
- Department of Biology Duke University Box 90338 Durham NC 27708 USA
| | - Paul M. Magwene
- Department of Biology Duke University Box 90338 Durham NC 27708 USA
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116
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Eldarov MA, Kishkovskaia SA, Tanaschuk TN, Mardanov AV. Genomics and biochemistry of Saccharomyces cerevisiae wine yeast strains. BIOCHEMISTRY (MOSCOW) 2017; 81:1650-1668. [DOI: 10.1134/s0006297916130046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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117
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Gallone B, Steensels J, Prahl T, Soriaga L, Saels V, Herrera-Malaver B, Merlevede A, Roncoroni M, Voordeckers K, Miraglia L, Teiling C, Steffy B, Taylor M, Schwartz A, Richardson T, White C, Baele G, Maere S, Verstrepen KJ. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell 2016; 166:1397-1410.e16. [PMID: 27610566 PMCID: PMC5018251 DOI: 10.1016/j.cell.2016.08.020] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/08/2016] [Accepted: 08/08/2016] [Indexed: 12/04/2022]
Abstract
Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today’s industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PaperClip
We sequenced and phenotyped 157 S. cerevisiae yeasts Present-day industrial yeasts originate from only a few domesticated ancestors Beer yeasts show strong genetic and phenotypic hallmarks of domestication Domestication of industrial yeasts predates microbe discovery
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Affiliation(s)
- Brigida Gallone
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Troels Prahl
- White Labs, 9495 Candida Street, San Diego, CA 92126, USA
| | - Leah Soriaga
- Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Veerle Saels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Adriaan Merlevede
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Miguel Roncoroni
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Loren Miraglia
- Encinitas Brewing Science, 141 Rodney Avenue, Encinitas, CA 92024, USA
| | | | - Brian Steffy
- Illumina, 5200 Illumina Way, San Diego, CA 92122, USA
| | - Maryann Taylor
- Biological & Popular Culture (BioPop), 2205 Faraday Avenue, Suite E, Carlsbad, CA 92008, USA
| | - Ariel Schwartz
- Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Toby Richardson
- Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
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118
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Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G. Powerful decomposition of complex traits in a diploid model. Nat Commun 2016; 7:13311. [PMID: 27804950 PMCID: PMC5097135 DOI: 10.1038/ncomms13311] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/21/2016] [Indexed: 01/20/2023] Open
Abstract
Explaining trait differences between individuals is a core and challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We sequence and systematically pair the recombinant gametes of two intercrossed natural genomes into an array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of this approach by partitioning fitness traits of 6,642 Saccharomyces cerevisiae POLs across many environments, achieving near complete trait heritability and precisely estimating additive (73%), dominance (10%), second (7%) and third (1.7%) order epistasis components. We map quantitative trait loci (QTLs) and find nonadditive QTLs to outnumber (3:1) additive loci, dominant contributions to heterosis to outnumber overdominant, and extensive pleiotropy. The POL framework offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.
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Affiliation(s)
- Johan Hallin
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Kaspar Märtens
- Institute of Computer Science, University of Tartu, 50090 Tartu, Estonia
| | - Alexander I. Young
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Martin Zackrisson
- Department of Chemistry and Molecular Biology, Gothenburg University, 405 30 Gothenburg, Sweden
| | - Francisco Salinas
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Leopold Parts
- Institute of Computer Science, University of Tartu, 50090 Tartu, Estonia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, 405 30 Gothenburg, Sweden
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Gianni Liti
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
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119
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Jouhten P, Ponomarova O, Gonzalez R, Patil KR. Saccharomyces cerevisiae metabolism in ecological context. FEMS Yeast Res 2016; 16:fow080. [PMID: 27634775 PMCID: PMC5050001 DOI: 10.1093/femsyr/fow080] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/16/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype-environment-phenotype relationships.
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Affiliation(s)
- Paula Jouhten
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, DE 69117, Germany
| | - Olga Ponomarova
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, DE 69117, Germany
| | - Ramon Gonzalez
- Department of Microbiologia, Instituto de Fermentaciones Industriales (CSIC), C. Juan de la Cierva 3, Madrid, ES 28006, Spain
| | - Kiran R Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, DE 69117, Germany
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120
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Abstract
Genetic variation among individuals within a population provides the raw material for phenotypic diversity upon which natural selection operates. Some given variants can act on multiple standing genomic variations simultaneously and release previously inaccessible phenotypes, leading to increased adaptive potential upon challenging environments. Previously, we identified such a variant related to a tRNA nonsense suppressor in yeast. When introduced into other genetic backgrounds, the suppressor led to an increased population phenotypic variance on various culture conditions, conferring background and environment specific selective advantages. Nonetheless, most isolates are intolerant to the suppressor on rich media due to a severe fitness cost. Here, we found that the tolerance to suppressor is related to a surprising level of fitness outburst, showing a trade-off effect to accommodate the cost of carrying the suppressor. To dissect the genetic basis of such trade-offs, we crossed strains with contrasting tolerance levels on rich media, and analyzed the fitness distribution patterns in the offspring. Combining quantitative tetrad analysis and bulk segregant analysis, we identified two genes, namely MKT1 and RGA1, involved in suppressor tolerance. We showed that alleles from the tolerant parent for both genes conferred a significant gain of fitness, which increased the suppressor tolerance. Our results present a detailed dissection of suppressor tolerance in yeast and provide insights into the molecular basis of trade-offs between fitness and evolutionary potential.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, Strasbourg, France
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121
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Sardi M, Rovinskiy N, Zhang Y, Gasch AP. Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance. Appl Environ Microbiol 2016; 82:5838-49. [PMID: 27451446 PMCID: PMC5038035 DOI: 10.1128/aem.01603-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because the mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variations in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene overexpression in different Saccharomyces cerevisiae (yeast) strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six different S. cerevisiae strains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to identify common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene overexpression in three different strains, we revealed the breadth of the background-specific effects of gene fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms. IMPORTANCE Recent studies on natural variation within Saccharomyces cerevisiae have uncovered substantial phenotypic diversity. Here, we took advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated the physiological states of cells when exposed to this stress. We also explored the strain-specific effects of gene overexpression to further identify strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nikolay Rovinskiy
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
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122
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Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. eLife 2016; 5. [PMID: 27614020 PMCID: PMC5067116 DOI: 10.7554/elife.18981] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/05/2016] [Indexed: 12/25/2022] Open
Abstract
Evolutionary changes in transcription networks are an important source of diversity across species, yet the quantitative consequences of network evolution have rarely been studied. Here we consider the transcriptional 'rewiring' of the three GAL genes that encode the enzymes needed for cells to convert galactose to glucose. In Saccharomyces cerevisiae, the transcriptional regulator Gal4 binds and activates these genes. In the human pathogen Candida albicans (which last shared a common ancestor with S. cerevisiae some 300 million years ago), we show that different regulators, Rtg1 and Rtg3, activate the three GAL genes. Using single-cell dynamics and RNA-sequencing, we demonstrate that although the overall logic of regulation is the same in both species-the GAL genes are induced by galactose-there are major differences in both the quantitative response of these genes to galactose and in the position of these genes in the overall transcription network structure of the two species.
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Affiliation(s)
- Chiraj K Dalal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Ignacio A Zuleta
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Kaitlin F Mitchell
- Department of Medicine, University of Wisconsin, Madison, United States.,Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, United States
| | - David R Andes
- Department of Medicine, University of Wisconsin, Madison, United States.,Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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123
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Abstract
The capacity to map traits over large cohorts of individuals—phenomics—lags far behind the explosive development in genomics. For microbes, the estimation of growth is the key phenotype because of its link to fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved growth phenotypes at an unprecedented scale. Advancements were achieved through the introduction of transmissive scanning hardware and software technology, frequent acquisition of exact colony population size measurements, extraction of population growth rates from growth curves, and removal of spatial bias by reference-surface normalization. Our prototype arrangement automatically records and analyzes close to 100,000 growth curves in parallel. We demonstrate the power of the approach by extending and nuancing the known salt-defense biology in baker’s yeast. The introduced framework represents a major advance in microbial phenomics by providing high-quality data for extensive cohorts of individuals and generating well-populated and standardized phenomics databases
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124
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Venkataram S, Dunn B, Li Y, Agarwala A, Chang J, Ebel ER, Geiler-Samerotte K, Hérissant L, Blundell JR, Levy SF, Fisher DS, Sherlock G, Petrov DA. Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast. Cell 2016; 166:1585-1596.e22. [PMID: 27594428 PMCID: PMC5070919 DOI: 10.1016/j.cell.2016.08.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/07/2016] [Accepted: 07/29/2016] [Indexed: 01/11/2023]
Abstract
Adaptive evolution plays a large role in generating the phenotypic diversity observed in nature, yet current methods are impractical for characterizing the molecular basis and fitness effects of large numbers of individual adaptive mutations. Here, we used a DNA barcoding approach to generate the genotype-to-fitness map for adaptation-driving mutations from a Saccharomyces cerevisiae population experimentally evolved by serial transfer under limiting glucose. We isolated and measured the fitness of thousands of independent adaptive clones and sequenced the genomes of hundreds of clones. We found only two major classes of adaptive mutations: self-diploidization and mutations in the nutrient-responsive Ras/PKA and TOR/Sch9 pathways. Our large sample size and precision of measurement allowed us to determine that there are significant differences in fitness between mutations in different genes, between different paralogs, and even between different classes of mutations within the same gene.
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Affiliation(s)
| | - Barbara Dunn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yuping Li
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Atish Agarwala
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Jessica Chang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emily R Ebel
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Lucas Hérissant
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jamie R Blundell
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA; Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Daniel S Fisher
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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125
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Tamari Z, Yona AH, Pilpel Y, Barkai N. Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source. BMC Genomics 2016; 17:674. [PMID: 27552923 PMCID: PMC5477773 DOI: 10.1186/s12864-016-3010-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/11/2016] [Indexed: 11/10/2022] Open
Abstract
Background Cells constantly adapt to changes in their environment. When environment shifts between conditions that were previously encountered during the course of evolution, evolutionary-programmed responses are possible. Cells, however, may also encounter a new environment to which a novel response is required. To characterize the first steps in adaptation to a novel condition, we studied budding yeast growth on xylulose, a sugar that is very rarely found in the wild. Results We previously reported that growth on xylulose induces the expression of amino acid biosynthesis genes in multiple natural yeast isolates. This induction occurs despite the presence of amino acids in the growth medium and is a unique response to xylulose, not triggered by naturally available carbon sources. Propagating these strains for ~300 generations on xylulose significantly improved their growth rate. Notably, the most significant change in gene expression was the loss of amino acid biosynthesis gene induction. Furthermore, the reduction in amino-acid biosynthesis gene expression on xylulose was tightly correlated with the improvement in growth rate, suggesting that internal depletion of amino-acids presented a major bottleneck limiting growth in xylulose. Conclusions We discuss the possible implications of our results for explaining how cells maintain the balance between supply and demand of amino acids during growth in evolutionary ‘familiar’ vs. ‘novel’ conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3010-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zvi Tamari
- Department of molecular genetics, Weizmann institute of science, Rehovot, 76100, Israel.
| | - Avihu H Yona
- Department of molecular genetics, Weizmann institute of science, Rehovot, 76100, Israel
| | - Yitzhak Pilpel
- Department of molecular genetics, Weizmann institute of science, Rehovot, 76100, Israel
| | - Naama Barkai
- Department of molecular genetics, Weizmann institute of science, Rehovot, 76100, Israel
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126
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Shiers N, Zwiernik P, Aston JAD, Smith JQ. The correlation space of Gaussian latent tree models and model selection without fitting. Biometrika 2016. [DOI: 10.1093/biomet/asw032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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127
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Heterologous expression of cellulase genes in natural Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 2016; 100:8241-54. [PMID: 27470141 DOI: 10.1007/s00253-016-7735-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/29/2016] [Accepted: 07/08/2016] [Indexed: 12/17/2022]
Abstract
Enzyme cost is a major impediment to second-generation (2G) cellulosic ethanol production. One strategy to reduce enzyme cost is to engineer enzyme production capacity in a fermentative microorganism to enable consolidated bio-processing (CBP). Ideally, a strain with a high secretory phenotype, high fermentative capacity as well as an innate robustness to bioethanol-specific stressors, including tolerance to products formed during pre-treatment and fermentation of lignocellulosic substrates should be used. Saccharomyces cerevisiae is a robust fermentative yeast but has limitations as a potential CBP host, such as low heterologous protein secretion titers. In this study, we evaluated natural S. cerevisiae isolate strains for superior secretion activity and other industrially relevant characteristics needed during the process of lignocellulosic ethanol production. Individual cellulases namely Saccharomycopsis fibuligera Cel3A (β-glucosidase), Talaromyces emersonii Cel7A (cellobiohydrolase), and Trichoderma reesei Cel5A (endoglucanase) were utilized as reporter proteins. Natural strain YI13 was identified to have a high secretory phenotype, demonstrating a 3.7- and 3.5-fold higher Cel7A and Cel5A activity, respectively, compared to the reference strain S288c. YI13 also demonstrated other industrially relevant characteristics such as growth vigor, high ethanol titer, multi-tolerance to high temperatures (37 and 40 °C), ethanol (10 % w/v), and towards various concentrations of a cocktail of inhibitory compounds commonly found in lignocellulose hydrolysates. This study accentuates the value of natural S. cerevisiae isolate strains to serve as potential robust and highly productive chassis organisms for CBP strain development.
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128
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Sigwalt A, Caradec C, Brion C, Hou J, de Montigny J, Jung P, Fischer G, Llorente B, Friedrich A, Schacherer J. Dissection of quantitative traits by bulk segregant mapping in a protoploid yeast species. FEMS Yeast Res 2016; 16:fow056. [PMID: 27371856 DOI: 10.1093/femsyr/fow056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Since more than a decade ago, Saccharomyces cerevisiae has been used as a model to dissect complex traits, revealing the genetic basis of a large number of traits in fine detail. However, to have a more global view of the genetic architecture of traits across species, the examination of the molecular basis of phenotypes within non-conventional species would undoubtedly be valuable. In this respect, the Saccharomycotina yeasts represent ideal and potential non-model organisms. Here we sought to assess the feasibility of genetic mapping by bulk segregant analysis in the protoploid Lachancea kluyveri (formerly S. kluyveri) yeast species, a distantly related species to S. cerevisiae For this purpose, we designed a fluorescent mating-type marker, compatible with any mating-competent strains representative of this species, to rapidly create a large population of haploid segregants (>10(5) cells). Quantitative trait loci can be mapped by selecting and sequencing an enriched pool of progeny with extreme phenotypic values. As a test bed, we applied this strategy and mapped the causal loci underlying halotolerance phenotypes in L. kluyveri Overall, this study demonstrates that bulk segregant mapping is a powerful way for investigating the genetic basis of natural variations in non-model yeast organisms and more precisely in L. kluyveri.
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Affiliation(s)
- Anastasie Sigwalt
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Claudia Caradec
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Christian Brion
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Jacky de Montigny
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Paul Jung
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Gilles Fischer
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France
| | - Bertrand Llorente
- CRCM, CNRS - UMR7258, Inserm - U1068, Institut Paoli-Calmettes, Aix-Marseille Université, UM105, F-13009 Marseille, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
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129
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New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic fermentative profile and allow strain selection for winemaking. Food Chem 2016; 211:509-20. [PMID: 27283661 DOI: 10.1016/j.foodchem.2016.05.080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/10/2016] [Accepted: 05/12/2016] [Indexed: 11/23/2022]
Abstract
During must fermentation by Saccharomyces cerevisiae strains thousands of volatile aroma compounds are formed. The objective of the present work was to adapt computational approaches to analyze pheno-metabolomic diversity of a S. cerevisiae strain collection with different origins. Phenotypic and genetic characterization together with individual must fermentations were performed, and metabolites relevant to aromatic profiles were determined. Experimental results were projected onto a common coordinates system, revealing 17 statistical-relevant multi-dimensional modules, combining sets of most-correlated features of noteworthy biological importance. The present method allowed, as a breakthrough, to combine genetic, phenotypic and metabolomic data, which has not been possible so far due to difficulties in comparing different types of data. Therefore, the proposed computational approach revealed as successful to shed light into the holistic characterization of S. cerevisiae pheno-metabolome in must fermentative conditions. This will allow the identification of combined relevant features with application in selection of good winemaking strains.
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130
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Alcid EA, Tsukiyama T. Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi. Nat Struct Mol Biol 2016; 23:450-5. [PMID: 27018804 PMCID: PMC4856548 DOI: 10.1038/nsmb.3192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 02/16/2016] [Indexed: 01/25/2023]
Abstract
Antisense long noncoding RNAs (ASlncRNAs) have been implicated in regulating gene expression in response to physiological cues. However, little is known about the evolutionary dynamics of ASlncRNA and what underlies the evolution of their expression. Here, using budding yeast Saccharomyces spp. and Naumovozyma castellii as models, we show that ASlncRNA repertoires have expanded since the loss of RNA interference (RNAi), in terms of their expression levels, their lengths and their degree of overlap with coding genes. Furthermore, we show that RNAi is inhibitory to ASlncRNA transcriptomes and that increased expression of ASlncRNAs in the presence of RNAi is deleterious to N. castellii, which has retained RNAi. Together, our results suggest that the loss of RNAi had substantial effects on the genome-wide increase in expression of ASlncRNAs during the evolution of budding yeasts.
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Affiliation(s)
- Eric A Alcid
- Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Toshio Tsukiyama
- Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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131
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Li C, Qian W, Maclean CJ, Zhang J. The fitness landscape of a tRNA gene. Science 2016; 352:837-40. [PMID: 27080104 DOI: 10.1126/science.aae0568] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/23/2016] [Indexed: 12/14/2022]
Abstract
Fitness landscapes describe the genotype-fitness relationship and represent major determinants of evolutionary trajectories. However, the vast genotype space, coupled with the difficulty of measuring fitness, has hindered the empirical determination of fitness landscapes. Combining precise gene replacement and next-generation sequencing, we quantified Darwinian fitness under a high-temperature challenge for more than 65,000 yeast strains, each carrying a unique variant of the single-copy tRNA(CCU)(Arg) gene at its native genomic location. Approximately 1% of single point mutations in the gene were beneficial and 42% were deleterious. Almost half of all mutation pairs exhibited statistically significant epistasis, which had a strong negative bias, except when the mutations occurred at Watson-Crick paired sites. Fitness was broadly correlated with the predicted fraction of correctly folded transfer RNA (tRNA) molecules, thereby revealing a biophysical basis of the fitness landscape.
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Affiliation(s)
- Chuan Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenfeng Qian
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Calum J Maclean
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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132
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Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species. G3-GENES GENOMES GENETICS 2016; 6:1063-71. [PMID: 26888866 PMCID: PMC4825641 DOI: 10.1534/g3.115.026682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
It is now clear that the exploration of the genetic and phenotypic diversity of nonmodel species greatly improves our knowledge in biology. In this context, we recently launched a population genomic analysis of the protoploid yeast Lachancea kluyveri (formerly Saccharomyces kluyveri), highlighting a broad genetic diversity (π = 17 × 10−3) compared to the yeast model organism, S. cerevisiae (π = 4 × 10−3). Here, we sought to generate a comprehensive view of the phenotypic diversity in this species. In total, 27 natural L. kluyveri isolates were subjected to trait profiling using the following independent approaches: (i) analyzing growth in 55 growth conditions and (ii) investigating 501 morphological changes at the cellular level. Despite higher genetic diversity, the fitness variance observed in L. kluyveri is lower than that in S. cerevisiae. However, morphological features show an opposite trend. In addition, there is no correlation between the origins (ecological or geographical) of the isolate and the phenotypic patterns, demonstrating that trait variation follows neither population history nor source environment in L. kluyveri. Finally, pairwise comparisons between growth rate correlation and genetic diversity show a clear decrease in phenotypic variability linked to genome variation increase, whereas no such a trend was identified for morphological changes. Overall, this study reveals for the first time the phenotypic diversity of a distantly related species to S. cerevisiae. Given its genetic properties, L. kluyveri might be useful in further linkage mapping analyses of complex traits, and could ultimately provide a better insight into the evolution of the genotype–phenotype relationship across yeast species.
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133
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Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2016; 6:957-71. [PMID: 26869621 PMCID: PMC4825664 DOI: 10.1534/g3.115.025692] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Humans have been consuming wines for more than 7000 yr . For most of this time, fermentations were presumably performed by strains of Saccharomyces cerevisiae that naturally found their way into the fermenting must . In contrast, most commercial wines are now produced by inoculation with pure yeast monocultures, ensuring consistent, reliable and reproducible fermentations, and there are now hundreds of these yeast starter cultures commercially available. In order to thoroughly investigate the genetic diversity that has been captured by over 50 yr of commercial wine yeast development and domestication, whole genome sequencing has been performed on 212 strains of S. cerevisiae, including 119 commercial wine and brewing starter strains, and wine isolates from across seven decades. Comparative genomic analysis indicates that, despite their large numbers, commercial strains, and wine strains in general, are extremely similar genetically, possessing all of the hallmarks of a population bottle-neck, and high levels of inbreeding. In addition, many commercial strains from multiple suppliers are nearly genetically identical, suggesting that the limits of effective genetic variation within this genetically narrow group may be approaching saturation.
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134
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Nidelet T, Brial P, Camarasa C, Dequin S. Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments. Microb Cell Fact 2016; 15:58. [PMID: 27044358 PMCID: PMC4820951 DOI: 10.1186/s12934-016-0456-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background S. cerevisiae has attracted considerable interest in recent years as a model for ecology and evolutionary biology, revealing a substantial genetic and phenotypic diversity. However, there is a lack of knowledge on the diversity of metabolic networks within this species. Results To identify the metabolic and evolutionary constraints that shape metabolic fluxes in S. cerevisiae, we used a dedicated constraint-based model to predict the central carbon metabolism flux distribution of 43 strains from different ecological origins, grown in wine fermentation conditions. In analyzing these distributions, we observed a highly contrasted situation in flux variability, with quasi-constancy of the glycolysis and ethanol synthesis yield yet high flexibility of other fluxes, such as the pentose phosphate pathway and acetaldehyde production. Furthermore, these fluxes with large variability showed multimodal distributions that could be linked to strain origin, indicating a convergence between genetic origin and flux phenotype. Conclusions Flux variability is pathway-dependent and, for some flux, a strain origin effect can be found. These data highlight the constraints shaping the yeast operative central carbon network and provide clues for the design of strategies for strain improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0456-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thibault Nidelet
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
| | - Pascale Brial
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - Carole Camarasa
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
| | - Sylvie Dequin
- SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France
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135
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Kessi-Pérez EI, Araos S, García V, Salinas F, Abarca V, Larrondo LF, Martínez C, Cubillos FA. RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Res 2016; 16:fow021. [PMID: 26945894 DOI: 10.1093/femsyr/fow021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/23/2022] Open
Abstract
Different natural yeast populations have faced dissimilar selective pressures due to the heterogeneous fermentation substrates available around the world; this increases the genetic and phenotypic diversity in Saccharomyces cerevisiae In this context, we expect prominent differences between isolates when exposed to a particular condition, such as wine or sake musts. To better comprehend the mechanisms underlying niche adaptation between two S. cerevisiae isolates obtained from wine and sake fermentation processes, we evaluated fermentative and fungicide resistance phenotypes and identify the molecular origin of such adaptive variation. Multiple regions were associated with fermentation rate under different nitrogen conditions and fungicide resistance, with a single QTL co-localizing in all traits. Analysis around this region identified RIM15 as the causative locus driving fungicide sensitivity, together with efficient nitrogen utilization and glycerol production in the wine strain. A null RIM15 variant confers a greater fermentation rate through the utilization of available glucose instead of its storage. However, this variant has a detrimental effect on fungicide resistance since complex sugars are not synthesized and transported into the membrane. Together, our results reveal the antagonist pleiotropic nature of a RIM15 null variant, positively affecting a series of fermentation related phenotypes, but apparently detrimental in the wild.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Sebastián Araos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Verónica García
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Francisco Salinas
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 8331150, Chile
| | - Valentina Abarca
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 8331150, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 8331150, Chile
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136
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Dashko S, Liu P, Volk H, Butinar L, Piškur J, Fay JC. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations. Front Microbiol 2016; 7:215. [PMID: 26941733 PMCID: PMC4764737 DOI: 10.3389/fmicb.2016.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/09/2016] [Indexed: 11/23/2022] Open
Abstract
Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance.
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Affiliation(s)
- Sofia Dashko
- Wine Research Center, University of Nova GoricaVipava, Slovenia; Department of Biology, Lund UniversityLund, Sweden
| | - Ping Liu
- Department of Genetics and Center for Genome Sciences and System Biology, Washington University St. Louis, MO, USA
| | - Helena Volk
- Wine Research Center, University of Nova Gorica Vipava, Slovenia
| | - Lorena Butinar
- Wine Research Center, University of Nova Gorica Vipava, Slovenia
| | - Jure Piškur
- Wine Research Center, University of Nova GoricaVipava, Slovenia; Department of Biology, Lund UniversityLund, Sweden
| | - Justin C Fay
- Department of Genetics and Center for Genome Sciences and System Biology, Washington University St. Louis, MO, USA
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137
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Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Sci Rep 2016; 6:21849. [PMID: 26898953 PMCID: PMC4761897 DOI: 10.1038/srep21849] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/01/2016] [Indexed: 01/27/2023] Open
Abstract
Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype.
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138
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Polygenic evolution of a sugar specialization trade-off in yeast. Nature 2016; 530:336-9. [PMID: 26863195 DOI: 10.1038/nature16938] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 12/18/2015] [Indexed: 11/08/2022]
Abstract
The evolution of novel traits can involve many mutations scattered throughout the genome. Detecting and validating such a suite of alleles, particularly if they arose long ago, remains a key challenge in evolutionary genetics. Here we dissect an evolutionary trade-off of unprecedented genetic complexity between long-diverged species. When cultured in 1% glucose medium supplemented with galactose, Saccharomyces cerevisiae, but not S. bayanus or other Saccharomyces species, delayed commitment to galactose metabolism until glucose was exhausted. Promoters of seven galactose (GAL) metabolic genes from S. cerevisiae, when introduced together into S. bayanus, largely recapitulated the delay phenotype in 1% glucose-galactose medium, and most had partial effects when tested in isolation. Variation in GAL coding regions also contributed to the delay when tested individually in 1% glucose-galactose medium. When combined, S. cerevisiae GAL coding regions gave rise to profound growth defects in the S. bayanus background. In medium containing 2.5% glucose supplemented with galactose, wild-type S. cerevisiae repressed GAL gene expression and had a robust growth advantage relative to S. bayanus; transgenesis of S. cerevisiae GAL promoter alleles or GAL coding regions was sufficient for partial reconstruction of these phenotypes. S. cerevisiae GAL genes thus encode a regulatory program of slow induction and avid repression, and a fitness detriment during the glucose-galactose transition but a benefit when glucose is in excess. Together, these results make clear that genetic mapping of complex phenotypes is within reach, even in deeply diverged species.
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139
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Meersman E, Steensels J, Struyf N, Paulus T, Saels V, Mathawan M, Allegaert L, Vrancken G, Verstrepen KJ. Tuning Chocolate Flavor through Development of Thermotolerant Saccharomyces cerevisiae Starter Cultures with Increased Acetate Ester Production. Appl Environ Microbiol 2016; 82:732-46. [PMID: 26590272 PMCID: PMC4711123 DOI: 10.1128/aem.02556-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/09/2015] [Indexed: 11/20/2022] Open
Abstract
Microbial starter cultures have extensively been used to enhance the consistency and efficiency of industrial fermentations. Despite the advantages of such controlled fermentations, the fermentation involved in the production of chocolate is still a spontaneous process that relies on the natural microbiota at cocoa farms. However, recent studies indicate that certain thermotolerant Saccharomyces cerevisiae cultures can be used as starter cultures for cocoa pulp fermentation. In this study, we investigate the potential of specifically developed starter cultures to modulate chocolate aroma. Specifically, we developed several new S. cerevisiae hybrids that combine thermotolerance and efficient cocoa pulp fermentation with a high production of volatile flavor-active esters. In addition, we investigated the potential of two strains of two non-Saccharomyces species that produce very large amounts of fruity esters (Pichia kluyveri and Cyberlindnera fabianii) to modulate chocolate aroma. Gas chromatography-mass spectrometry (GC-MS) analysis of the cocoa liquor revealed an increased concentration of various flavor-active esters and a decrease in spoilage-related off-flavors in batches inoculated with S. cerevisiae starter cultures and, to a lesser extent, in batches inoculated with P. kluyveri and Cyb. fabianii. Additionally, GC-MS analysis of chocolate samples revealed that while most short-chain esters evaporated during conching, longer and more-fat-soluble ethyl and acetate esters, such as ethyl octanoate, phenylethyl acetate, ethyl phenylacetate, ethyl decanoate, and ethyl dodecanoate, remained almost unaffected. Sensory analysis by an expert panel confirmed significant differences in the aromas of chocolates produced with different starter cultures. Together, these results show that the selection of different yeast cultures opens novel avenues for modulating chocolate flavor.
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Affiliation(s)
- Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Nore Struyf
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Tinneke Paulus
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Veerle Saels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | | | | | | | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
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140
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Snoek T, Verstrepen KJ, Voordeckers K. How do yeast cells become tolerant to high ethanol concentrations? Curr Genet 2016; 62:475-80. [PMID: 26758993 DOI: 10.1007/s00294-015-0561-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/28/2015] [Indexed: 12/24/2022]
Abstract
The brewer's yeast Saccharomyces cerevisiae displays a much higher ethanol tolerance compared to most other organisms, and it is therefore commonly used for the industrial production of bioethanol and alcoholic beverages. However, the genetic determinants underlying this yeast's exceptional ethanol tolerance have proven difficult to elucidate. In this perspective, we discuss how different types of experiments have contributed to our understanding of the toxic effects of ethanol and the mechanisms and complex genetics underlying ethanol tolerance. In a second part, we summarize the different routes and challenges involved in obtaining superior industrial yeasts with improved ethanol tolerance.
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Affiliation(s)
- Tim Snoek
- VIB Laboratory for Systems Biology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.,The Novo Nordisk Foundation Center for Biosustainability, Copenhagen, Denmark
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Karin Voordeckers
- VIB Laboratory for Systems Biology, Gaston Geenslaan 1, 3001, Leuven, Belgium. .,CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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141
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Replenishment and mobilization of intracellular nitrogen pools decouples wine yeast nitrogen uptake from growth. Appl Microbiol Biotechnol 2016; 100:3255-65. [DOI: 10.1007/s00253-015-7273-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/14/2015] [Accepted: 12/19/2015] [Indexed: 11/30/2022]
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142
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Masneuf-Pomarede I, Bely M, Marullo P, Albertin W. The Genetics of Non-conventional Wine Yeasts: Current Knowledge and Future Challenges. Front Microbiol 2016; 6:1563. [PMID: 26793188 PMCID: PMC4707289 DOI: 10.3389/fmicb.2015.01563] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/23/2015] [Indexed: 11/13/2022] Open
Abstract
Saccharomyces cerevisiae is by far the most widely used yeast in oenology. However, during the last decade, several other yeasts species has been purposed for winemaking as they could positively impact wine quality. Some of these non-conventional yeasts (Torulaspora delbrueckii, Metschnikowia pulcherrima, Pichia kluyveri, Lachancea thermotolerans, etc.) are now proposed as starters culture for winemakers in mixed fermentation with S. cerevisiae, and several others are the subject of various studies (Hanseniaspora uvarum, Starmerella bacillaris, etc.). Along with their biotechnological use, the knowledge of these non-conventional yeasts greatly increased these last 10 years. The aim of this review is to describe the last updates and the current state-of-art of the genetics of non-conventional yeasts (including S. uvarum, T. delbrueckii, S. bacillaris, etc.). We describe how genomics and genetics tools provide new data into the population structure and biodiversity of non-conventional yeasts in winemaking environments. Future challenges will lie on the development of selection programs and/or genetic improvement of these non-conventional species. We discuss how genetics, genomics and the advances in next-generation sequencing will help the wine industry to develop the biotechnological use of non-conventional yeasts to improve the quality and differentiation of wines.
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Affiliation(s)
- Isabelle Masneuf-Pomarede
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
- Bordeaux Sciences AgroGradignan, France
| | - Marina Bely
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
| | - Philippe Marullo
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
- BiolaffortBordeaux, France
| | - Warren Albertin
- ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 Institut National de la Recherche Agronomique, Bordeaux INP, University BordeauxVillenave d'Ornon, France
- ENSCBP, Bordeaux INPPessac, France
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143
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Freel KC, Friedrich A, Sarilar V, Devillers H, Neuvéglise C, Schacherer J. Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis. Genome Biol Evol 2016; 8:733-41. [PMID: 26733577 PMCID: PMC4823976 DOI: 10.1093/gbe/evv262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10−3 which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10−3). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Véronique Sarilar
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Hugo Devillers
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
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144
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Gorter FA, Aarts MMG, Zwaan BJ, de Visser JAGM. Dynamics of Adaptation in Experimental Yeast Populations Exposed to Gradual and Abrupt Change in Heavy Metal Concentration. Am Nat 2016; 187:110-9. [DOI: 10.1086/684104] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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145
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Naranjo S, Smith JD, Artieri CG, Zhang M, Zhou Y, Palmer ME, Fraser HB. Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation. PLoS Genet 2015; 11:e1005751. [PMID: 26713447 PMCID: PMC4694769 DOI: 10.1371/journal.pgen.1005751] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/30/2015] [Indexed: 12/23/2022] Open
Abstract
Although single genes underlying several evolutionary adaptations have been identified, the genetic basis of complex, polygenic adaptations has been far more challenging to pinpoint. Here we report that the budding yeast Saccharomyces paradoxus has recently evolved resistance to citrinin, a naturally occurring mycotoxin. Applying a genome-wide test for selection on cis-regulation, we identified five genes involved in the citrinin response that are constitutively up-regulated in S. paradoxus. Four of these genes are necessary for resistance, and are also sufficient to increase the resistance of a sensitive strain when over-expressed. Moreover, cis-regulatory divergence in the promoters of these genes contributes to resistance, while exacting a cost in the absence of citrinin. Our results demonstrate how the subtle effects of individual regulatory elements can be combined, via natural selection, into a complex adaptation. Our approach can be applied to dissect the genetic basis of polygenic adaptations in a wide range of species.
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Affiliation(s)
- Santiago Naranjo
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Justin D. Smith
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Stanford Genome Technology Center, Stanford University, Stanford, California, United States of America
| | - Carlo G. Artieri
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Mian Zhang
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Yiqi Zhou
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Michael E. Palmer
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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146
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Clowers KJ, Will JL, Gasch AP. A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Mol Ecol 2015; 24:5886-98. [PMID: 26518477 PMCID: PMC4824287 DOI: 10.1111/mec.13439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 12/24/2022]
Abstract
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of S. cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak × vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases, the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.
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Affiliation(s)
- Katie J Clowers
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Jessica L Will
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
- Great Lakes Bioenergy Research Center, 1552 University Ave., Madison, WI, 53704, USA
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147
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Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM. The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res 2015; 44:D698-702. [PMID: 26578556 PMCID: PMC4702884 DOI: 10.1093/nar/gkv1250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/02/2015] [Indexed: 11/18/2022] Open
Abstract
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer.
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Affiliation(s)
- Travis K Sheppard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Giltae Song
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rama Balakrishnan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gail Binkley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria C Costanzo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyla S Dalusag
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sage T Hellerstedt
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert S Nash
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelley M Paskov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marek S Skrzypek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuai Weng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Edith D Wong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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148
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Abstract
The Saccharomyces sensu stricto group encompasses species ranging from the industrially ubiquitous yeast Saccharomyces cerevisiae to those that are confined to geographically limited environmental niches. The wealth of genomic data that are now available for the Saccharomyces genus is providing unprecedented insights into the genomic processes that can drive speciation and evolution, both in the natural environment and in response to human-driven selective forces during the historical "domestication" of these yeasts for baking, brewing, and winemaking.
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149
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Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat Rev Genet 2015; 16:567-82. [PMID: 26347030 DOI: 10.1038/nrg3937] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.
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150
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Zheng YL, Wang SA. Stress Tolerance Variations in Saccharomyces cerevisiae Strains from Diverse Ecological Sources and Geographical Locations. PLoS One 2015; 10:e0133889. [PMID: 26244846 PMCID: PMC4526645 DOI: 10.1371/journal.pone.0133889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/03/2015] [Indexed: 11/17/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a platform organism for bioethanol production from various feedstocks and robust strains are desirable for efficient fermentation because yeast cells inevitably encounter stressors during the process. Recently, diverse S. cerevisiae lineages were identified, which provided novel resources for understanding stress tolerance variations and related shaping factors in the yeast. This study characterized the tolerance of diverse S. cerevisiae strains to the stressors of high ethanol concentrations, temperature shocks, and osmotic stress. The results showed that the isolates from human-associated environments overall presented a higher level of stress tolerance compared with those from forests spared anthropogenic influences. Statistical analyses indicated that the variations of stress tolerance were significantly correlated with both ecological sources and geographical locations of the strains. This study provides guidelines for selection of robust S. cerevisiae strains for bioethanol production from nature.
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Affiliation(s)
- Yan-Lin Zheng
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Shi-An Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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