Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.

High concentrations of ammonium at physiological concentrations of potassium are toxic for the standard laboratory strain of Saccharomyces cerevisiae In the original description of this metabolic phenotype, we focused on the standard laboratory strains of Saccharomyces In this study, we screened a large collection of S. cerevisiae natural isolates and identified one strain that is resistant to high concentrations of ammonium. This strain, K12, was isolated in sake breweries. When the K12 strain was crossed to the standard laboratory strain (FY4), the resulting tetrads displayed 2:2 segregation of the resistance phenotype, suggesting a single gene trait. Using a bulk segregant analysis strategy, we mapped this trait to a 150-kb region on chromosome X containing the TRK1 gene. This gene encodes a transporter required for high-affinity potassium transport in S. cerevisiae Data from reciprocal hemizygosity experiments with TRK1 deletion strains in K12 and BY backgrounds, as well as analysis of the deletion of this gene in the K12 strain, demonstrate that the K12 allele of TRK1 is responsible for ammonium toxicity resistance. Furthermore, we determined the minimal amount of potassium required for both the K12 and laboratory strain needed for growth. These results demonstrate that the gene encoded by the K12 allele of TRK1 has a greater affinity for potassium than the standard allele of TRK1 found in Saccharomyces strains. We hypothesize that this greater-affinity allele of the potassium transporter reduces the flux of ammonium into the yeast cells under conditions of ammonium toxicity. These findings further refine our understanding of ammonium toxicity in yeast and provide an example of using natural variation to understand cellular processes

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

International audienceReconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements , and protein divergence into a single evolutionary framework

Analyse de la variabilité intraspécifique chez les levures : résistance à l'ammonium et aux composés azolés

In all species, mutations and chromosomal rearrangements are drivers of genomes evolution. These processes generate the genetic diversity at the origin of the phenotypic variations observed between the individuals of the same species. This variation is essential for their adaptation to a new environment. The yeasts are isolated from various ecological and geographical niches and show an important phenotypic variation. According to these characteristics, they are excellent modelorganisms to determine the genetic origins of the observed phenotypic variation. In this context, the study focused on the variation of resistance to ammonium and azole antifungals within two yeast species: Saccharomyces cerevisiae and Lachancea kluyveri. The analyses of the genetic origin of the resistance to these compounds show that this genetic variation could occur at several levels: coding sequence for resistance to ammonium and regulatory sequence for resistance to antifungal agents. In addition, evolving experiments have showed that the adaptation to a new environment was done by gene dosage, through the acquisition of extrachromosomes in both species studied.Dans toutes les espèces, les mutations et les réarrangements chromosomiques constituent des moteurs de l’évolution des génomes. Ils génèrent une diversité génétique à l’origine de la variation phénotypique observée entre les individus d’une même espèce. Cette variation est particulièrement importante chez les levures. Elles constituent donc d’excellents modèles pour déterminer les origines génétiques de la variation intra-spécifique. C’est dans ce contexte que ce travail s’est focalisé sur l’étude de la variation de résistance à l’ammonium et aux antifongiques azolés chez deux espèces de levures : Saccharomyces cerevisiae et Lachancea kluyveri. L’analyse des origines génétiques de la résistance à ces composés à mis en évidence que les variations génétiques pouvaient avoir lieu à plusieurs niveaux : séquence codante pour la résistance à l’ammonium et séquence régulatrice pour la résistance aux antifongiques. De plus, la réalisation d’expériences d’évolution adaptative a permis de mettre en évidence que l’adaptation à un nouvel environnement se faisait par dosage génique via l’acquisition d’un chromosome supplémentaire chez les espèces étudiées

Analysis of the intraspecific variability in the yeasts : ammonium and azoles antifungals resistance

Dans toutes les espèces, les mutations et les réarrangements chromosomiques constituent des moteurs de l’évolution des génomes. Ils génèrent une diversité génétique à l’origine de la variation phénotypique observée entre les individus d’une même espèce. Cette variation est particulièrement importante chez les levures. Elles constituent donc d’excellents modèles pour déterminer les origines génétiques de la variation intra-spécifique. C’est dans ce contexte que ce travail s’est focalisé sur l’étude de la variation de résistance à l’ammonium et aux antifongiques azolés chez deux espèces de levures : Saccharomyces cerevisiae et Lachancea kluyveri. L’analyse des origines génétiques de la résistance à ces composés à mis en évidence que les variations génétiques pouvaient avoir lieu à plusieurs niveaux : séquence codante pour la résistance à l’ammonium et séquence régulatrice pour la résistance aux antifongiques. De plus, la réalisation d’expériences d’évolution adaptative a permis de mettre en évidence que l’adaptation à un nouvel environnement se faisait par dosage génique via l’acquisition d’un chromosome supplémentaire chez les espèces étudiées.In all species, mutations and chromosomal rearrangements are drivers of genomes evolution. These processes generate the genetic diversity at the origin of the phenotypic variations observed between the individuals of the same species. This variation is essential for their adaptation to a new environment. The yeasts are isolated from various ecological and geographical niches and show an important phenotypic variation. According to these characteristics, they are excellent modelorganisms to determine the genetic origins of the observed phenotypic variation. In this context, the study focused on the variation of resistance to ammonium and azole antifungals within two yeast species: Saccharomyces cerevisiae and Lachancea kluyveri. The analyses of the genetic origin of the resistance to these compounds show that this genetic variation could occur at several levels: coding sequence for resistance to ammonium and regulatory sequence for resistance to antifungal agents. In addition, evolving experiments have showed that the adaptation to a new environment was done by gene dosage, through the acquisition of extrachromosomes in both species studied

Analysis of the intraspecific variability in the yeasts : ammonium and azoles antifungals resistance

Dans toutes les espèces, les mutations et les réarrangements chromosomiques constituent des moteurs de l’évolution des génomes. Ils génèrent une diversité génétique à l’origine de la variation phénotypique observée entre les individus d’une même espèce. Cette variation est particulièrement importante chez les levures. Elles constituent donc d’excellents modèles pour déterminer les origines génétiques de la variation intra-spécifique. C’est dans ce contexte que ce travail s’est focalisé sur l’étude de la variation de résistance à l’ammonium et aux antifongiques azolés chez deux espèces de levures : Saccharomyces cerevisiae et Lachancea kluyveri. L’analyse des origines génétiques de la résistance à ces composés à mis en évidence que les variations génétiques pouvaient avoir lieu à plusieurs niveaux : séquence codante pour la résistance à l’ammonium et séquence régulatrice pour la résistance aux antifongiques. De plus, la réalisation d’expériences d’évolution adaptative a permis de mettre en évidence que l’adaptation à un nouvel environnement se faisait par dosage génique via l’acquisition d’un chromosome supplémentaire chez les espèces étudiées.In all species, mutations and chromosomal rearrangements are drivers of genomes evolution. These processes generate the genetic diversity at the origin of the phenotypic variations observed between the individuals of the same species. This variation is essential for their adaptation to a new environment. The yeasts are isolated from various ecological and geographical niches and show an important phenotypic variation. According to these characteristics, they are excellent modelorganisms to determine the genetic origins of the observed phenotypic variation. In this context, the study focused on the variation of resistance to ammonium and azole antifungals within two yeast species: Saccharomyces cerevisiae and Lachancea kluyveri. The analyses of the genetic origin of the resistance to these compounds show that this genetic variation could occur at several levels: coding sequence for resistance to ammonium and regulatory sequence for resistance to antifungal agents. In addition, evolving experiments have showed that the adaptation to a new environment was done by gene dosage, through the acquisition of extrachromosomes in both species studied

Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case

High concentrations of ammonium at physiological concentrations of potassium are toxic for the standard laboratory strain of Saccharomyces cerevisiae. In the original description of this metabolic phenotype, we focused on the standard laboratory strains of Saccharomyces. In this study, we screened a large collection of S. cerevisiae natural isolates and identified one strain that is resistant to high concentrations of ammonium. This strain, K12, was isolated in sake breweries. When the K12 strain was crossed to the standard laboratory strain (FY4), the resulting tetrads displayed 2:2 segregation of the resistance phenotype, suggesting a single gene trait. Using a bulk segregant analysis strategy, we mapped this trait to a 150-kb region on chromosome X containing the TRK1 gene. This gene encodes a transporter required for high-affinity potassium transport in S. cerevisiae. Data from reciprocal hemizygosity experiments with TRK1 deletion strains in K12 and BY backgrounds, as well as analysis of the deletion of this gene in the K12 strain, demonstrate that the K12 allele of TRK1 is responsible for ammonium toxicity resistance. Furthermore, we determined the minimal amount of potassium required for both the K12 and laboratory strain needed for growth. These results demonstrate that the gene encoded by the K12 allele of TRK1 has a greater affinity for potassium than the standard allele of TRK1 found in Saccharomyces strains. We hypothesize that this greater-affinity allele of the potassium transporter reduces the flux of ammonium into the yeast cells under conditions of ammonium toxicity. These findings further refine our understanding of ammonium toxicity in yeast and provide an example of using natural variation to understand cellular processes