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Kessi-Pérez EI, Molinet J, Martínez C. Disentangling the genetic bases of Saccharomyces cerevisiae nitrogen consumption and adaptation to low nitrogen environments in wine fermentation. Biol Res 2020; 53:2. [PMID: 31918759 PMCID: PMC6950849 DOI: 10.1186/s40659-019-0270-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/31/2019] [Indexed: 12/16/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been considered for more than 20 years as a premier model organism for biological sciences, also being the main microorganism used in wide industrial applications, like alcoholic fermentation in the winemaking process. Grape juice is a challenging environment for S. cerevisiae, with nitrogen deficiencies impairing fermentation rate and yeast biomass production, causing stuck or sluggish fermentations, thus generating sizeable economic losses for wine industry. In the present review, we summarize some recent efforts in the search of causative genes that account for yeast adaptation to low nitrogen environments, specially focused in wine fermentation conditions. We start presenting a brief perspective of yeast nitrogen utilization under wine fermentative conditions, highlighting yeast preference for some nitrogen sources above others. Then, we give an outlook of S. cerevisiae genetic diversity studies, paying special attention to efforts in genome sequencing for population structure determination and presenting QTL mapping as a powerful tool for phenotype-genotype correlations. Finally, we do a recapitulation of S. cerevisiae natural diversity related to low nitrogen adaptation, specially showing how different studies have left in evidence the central role of the TORC1 signalling pathway in nitrogen utilization and positioned wild S. cerevisiae strains as a reservoir of beneficial alleles with potential industrial applications (e.g. improvement of industrial yeasts for wine production). More studies focused in disentangling the genetic bases of S. cerevisiae adaptation in wine fermentation will be key to determine the domestication effects over low nitrogen adaptation, as well as to definitely proof that wild S. cerevisiae strains have potential genetic determinants for better adaptation to low nitrogen conditions.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Jennifer Molinet
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudio Martínez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.
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Dahabieh MS, Thevelein JM, Gibson B. Multimodal Microorganism Development: Integrating Top-Down Biological Engineering with Bottom-Up Rational Design. Trends Biotechnol 2019; 38:241-253. [PMID: 31653446 DOI: 10.1016/j.tibtech.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Biological engineering has unprecedented potential to solve society's most pressing challenges. Engineering approaches must consider complex technical, economic, and social factors. This requires methods that confer gene/pathway-level functionality and organism-level robustness in rapid and cost-effective ways. This article compares foundational engineering approaches - bottom-up, gene-targeted engineering, and top-down, whole-genome engineering - and identifies significant complementarity between them. Cases drawn from engineering Saccharomyces cerevisiae exemplify the synergy of a combined approach. Indeed, multimodal engineering streamlines strain development by leveraging the complementarity of whole-genome and gene-targeted engineering to overcome the gap in design knowledge that restricts rational design. As biological engineers target more complex systems, this dual-track approach is poised to become an increasingly important tool to realize the promise of synthetic biology.
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Affiliation(s)
- Matthew S Dahabieh
- Renaissance BioScience, 410-2389 Health Sciences Mall, Vancouver, BC V6T1Z3, Canada
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, VTT, PO Box 1000, FI-02044 Espoo, Finland.
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Jakobson CM, She R, Jarosz DF. Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae. Nat Commun 2019; 10:1222. [PMID: 30874558 PMCID: PMC6420628 DOI: 10.1038/s41467-019-09166-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 02/21/2019] [Indexed: 02/06/2023] Open
Abstract
Quantitative genetics aims to map genotype to phenotype, often with the goal of understanding how organisms evolved. However, it remains unclear whether the genetic variants identified are exemplary of evolution. Here we analyzed progeny of two wild Saccharomyces cerevisiae isolates to identify 195 loci underlying complex metabolic traits, resolving 107 to single polymorphisms with diverse molecular mechanisms. More than 20% of causal variants exhibited patterns of emergence inconsistent with neutrality. Moreover, contrary to drift-centric expectation, variation in diverse wild yeast isolates broadly exhibited this property: over 30% of shared natural variants exhibited phylogenetic signatures suggesting that they are not neutral. This pattern is likely attributable to both homoplasy and balancing selection on ancestral polymorphism. Variants that emerged repeatedly were more likely to have done so in isolates from the same ecological niche. Our results underscore the power of super-resolution mapping of ecologically relevant traits in understanding adaptation and evolution.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Richard She
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Liti G, Warringer J, Blomberg A. Isolation and Laboratory Domestication of Natural Yeast Strains. Cold Spring Harb Protoc 2017; 2017:pdb.prot089052. [PMID: 28765292 DOI: 10.1101/pdb.prot089052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The process from yeast isolation to their use in laboratory experiments is lengthy. Historically, Saccharomyces strains were easily obtained by sampling alcoholic fermentation processes or other substrates associated with human activity in which Saccharomyces was heavily enriched. In contrast, wild Saccharomyces yeasts are found in complex microbial communities and small population sizes, making isolation challenging. We have overcome this problem by enriching yeast on media favoring the growth of Saccharomyces over other microorganisms. The isolation process is usually followed by molecular characterization that allows the strain identification. Finally, yeast isolated from domestic or wild environments need to be genetically manipulated before they can be used in laboratory experiments.
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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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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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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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