Genotypic characterization of strains of commercial wine yeasts by tetrad analysis

Metabolic engineering of a stable haploid strain derived from lignocellulosic inhibitor tolerant Saccharomyces cerevisiae natural isolate YB-2625

BACKGROUND

Significant genetic diversity exists across Saccharomyces strains. Natural isolates and domesticated brewery and industrial strains are typically more robust than laboratory strains when challenged with inhibitory lignocellulosic hydrolysates. These strains also contain genes that are not present in lab strains and likely contribute to their superior inhibitor tolerance. However, many of these strains have poor sporulation efficiencies and low spore viability making subsequent gene analysis, further metabolic engineering, and genomic analyses of the strains challenging. This work aimed to develop an inhibitor tolerant haploid with stable mating type from S. cerevisiae YB-2625, which was originally isolated from bagasse.

RESULTS

Haploid spores isolated from four tetrads from strain YB-2625 were tested for tolerance to furfural and HMF. Due to natural mutations present in the HO-endonuclease, all haploid strains maintained a stable mating type. One of the haploids, YRH1946, did not flocculate and showed enhanced tolerance to furfural and HMF. The tolerant haploid strain was further engineered for xylose fermentation by integration of the genes for xylose metabolism at two separate genomic locations (ho∆ and pho13∆). In fermentations supplemented with inhibitors from acid hydrolyzed corn stover, the engineered haploid strain derived from YB-2625 was able to ferment all of the glucose and 19% of the xylose, whereas the engineered lab strains performed poorly in fermentations.

CONCLUSIONS

Understanding the molecular mechanisms of inhibitor tolerance will aid in developing strains with improved growth and fermentation performance using biomass-derived sugars. The inhibitor tolerant, xylose fermenting, haploid strain described in this work has potential to serve as a platform strain for identifying pathways required for inhibitor tolerance, and for metabolic engineering to produce fuels and chemicals from undiluted lignocellulosic hydrolysates.

Interspecies Hybridisation and Genome Chimerisation in Saccharomyces: Combining of Gene Pools of Species and Its Biotechnological Perspectives

Over the last one and a half decade, interspecies hybridisation has gained continuously increasing attention as a breeding technique suitable for transferring of genetic information between Saccharomyces species and mixing of their gene pools without genetic engineering. The hybrids frequently show positive transgressive phenotypes. Segregation of the hybrid genome results in mosaic (chimeric) strains that can outperform both the parents and the hybrids or exhibit novel positive phenotypic properties. Mitotic segregation can take place during the vegetative propagation of the sterile allodiploid hybrid cells. Meiotic segregation becomes possible after genome duplication (tetraploidisation) if it is followed by break-down of sterility. The allotetraploid cells are seemingly fertile because they form viable spores. But because of the autodiploidisation of the meiosis, sterile allodiploid spores are produced and thus the hybrid genome does not segregate (the second sterility barrier). However, malsegregation of MAT-carrying chromosomes in one of the subgenomes during allotetraploid meiosis (loss of MAT heterozygosity) results in fertile alloaneuploid spores. The breakdown of (the second) sterility barrier is followed by the loss of additional chromosomes in rapid succession and recombination between the subgenomes. The process (genome autoreduction in meiosis or GARMe) chimerises the genome and generates strains with chimeric (mosaic) genomes composed of various combinations of the genes of the parental strains. Since one of the subgenomes is preferentially reduced, the outcome is usually a strain having an (almost) complete genome from one parent and only a few genes or mosaics from the genome of the other parent. The fertility of the spores produced during GARMe provides possibilities also for introgressive backcrossing with one or the other parental strain, but genome chimerisation and gene transfer through series of backcrosses always with the same parent is likely to be less efficient than through meiotic or mitotic genome autoreduction. Hybridisation and the evolution of the hybrid genome (resizing and chimerisation) have been exploited in the improvement of industrial strains and applied to the breeding of new strains for specific purposes. Lists of successful projects are shown and certain major trends are discussed.

New Lager Brewery Strains Obtained by Crossing Techniques Using Cachaça (Brazilian Spirit) Yeasts

The development of hybrids has been an effective approach to generate novel yeast strains with optimal technological profile for use in beer production. This study describes the generation of a new yeast strain for lager beer production by direct mating between two Saccharomyces cerevisiae strains isolated from cachaça distilleries: one that was strongly flocculent, and the other with higher production of acetate esters. The first step in this procedure was to analyze the sporulation ability and reproductive cycle of strains belonging to a specific collection of yeasts isolated from cachaça fermentation vats. Most strains showed high rates of sporulation, spore viability, and homothallic behavior. In order to obtain new yeast strains with desirable properties useful for lager beer production, we compare haploid-to-haploid and diploid-to-diploid mating procedures. Moreover, an assessment of parental phenotype traits showed that the segregant diploid C2-1d generated from a diploid-to-diploid mating experiment showed good fermentation performance at low temperature, high flocculation capacity, and desirable production of acetate esters that was significantly better than that of one type lager strain. Therefore, strain C2-1d might be an important candidate for the production of lager beer, with distinct fruit traces and originating using a non-genetically modified organism (GMO) approach.IMPORTANCE Recent work has suggested the utilization of hybridization techniques for the generation of novel non-genetically modified brewing yeast strains with combined properties not commonly found in a unique yeast strain. We have observed remarkable traits, especially low temperature tolerance, maltotriose utilization, flocculation ability, and production of volatile aroma compounds, among a collection of Saccharomyces cerevisiae strains isolated from cachaça distilleries, which allow their utilization in the production of beer. The significance of our research is in the use of breeding/hybridization techniques to generate yeast strains that would be appropriate for producing new lager beers by exploring the capacity of cachaça yeast strains to flocculate and to ferment maltose at low temperature, with the concomitant production of flavoring compounds.

Diversity and adaptive evolution of Saccharomyces wine yeast: a review

Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains.

This review summarizes current knowledge and recent advances on the diversity and evolutionary history of Saccharomyces cerevisiae wine yeasts, focusing on the domestication fingerprints identified in these strains.

Fast method for identifying inter- and intra-species Saccharomyces hybrids in extensive genetic improvement programs based on yeast breeding

AIMS

The present work proposes a two-step molecular strategy to select inter- and intra-species Saccharomyces hybrids obtained by spore-to-spore mating, one of the most used methods for generating improved hybrids from homothallic wine yeasts.

METHODS AND RESULTS

As low spore viability and haplo-selfing are the main causes of failed mating, at first, we used colony screening PCR (csPCR) of discriminative gene markers to select hybrids directly on dissection plate and discard homozygous diploid colonies arisen from one auto-diploidized progenitor. Then, pre-selected candidates were submitted to recursive streaking and conventional PCR in order to discriminate between the hybrids with stable genomic background and the false-positive admixtures of progenitor cells both undergone haplo-selfing. csPCRs of internal transcribed spacer (ITS) 1 or 2, and the subsequent digestion with diagnostic endonucleases HaeIII and RsaI, respectively, were efficient to select six new Saccharomyces cerevisiae × Saccharomyces uvarum hybrids from 64 crosses. Intragenic minisatellite regions in PIR3, HSP150, and DAN4 genes showed high inter-strain size variation detectable by cost-effective agarose gel electrophoresis and were successful to validate six new intra-species S. cerevisiae hybrids from 34 crosses.

CONCLUSIONS

Both protocols reduce significantly the number of massive DNA extractions, prevent misinterpretations caused by one or both progenitors undergone haplo-selfing, and can be easily implemented in yeast labs without any specific instrumentation.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides a method for the marker-assisted selection of several inter- and intra-species yeast hybrids in a cost-effective, rapid and reproducible manner.

Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia

Mudai is a traditional fermented beverage, made from the seeds of the Araucaria araucana tree by Mapuche communities. The main goal of the present study was to identify and characterize the yeast microbiota responsible of Mudai fermentation as well as from A. araucana seeds and bark from different locations in Northern Patagonia. Only Hanseniaspora uvarum and a commercial bakery strain of Saccharomyces cerevisiae were isolated from Mudai and all Saccharomyces isolates recovered from A. araucana seed and bark samples belonged to the cryotolerant species Saccharomyces eubayanus and Saccharomyces uvarum. These two species were already reported in Nothofagus trees from Patagonia; however, this is the first time that they were isolated from A. araucana, which extends their ecological distribution. The presence of these species in A. araucana seeds and bark samples, led us to postulate a potential role for them as the original yeasts responsible for the elaboration of Mudai before the introduction of commercial S. cerevisiae cultures. The molecular and genetic characterization of the S. uvarum and S. eubayanus isolates and their comparison with European S. uvarum strains and S. eubayanus hybrids (S. bayanus and S. pastorianus), allowed their ecology and evolution us to be examined.

Starvation-associated genome restructuring can lead to reproductive isolation in yeast

Knowledge of the mechanisms that lead to reproductive isolation is essential for understanding population structure and speciation. While several models have been advanced to explain post-mating reproductive isolation, experimental data supporting most are indirect. Laboratory investigations of this phenomenon are typically carried out under benign conditions, which result in low rates of genetic change unlikely to initiate reproductive isolation. Previously, we described an experimental system using the yeast Saccharomyces cerevisiae where starvation served as a proxy to any stress that decreases reproduction and/or survivorship. We showed that novel lineages with restructured genomes quickly emerged in starved populations, and that these survivors were more fit than their ancestors when re-starved. Here we show that certain yeast lineages that survive starvation have become reproductively isolated from their ancestor. We further demonstrate that reproductive isolation arises from genomic rearrangements, whose frequency in starving yeast is several orders of magnitude greater than an unstarved control. By contrast, the frequency of point mutations is less than 2-fold greater. In a particular case, we observe that a starved lineage becomes reproductively isolated as a direct result of the stress-related accumulation of a single chromosome. We recapitulate this result by demonstrating that introducing an extra copy of one or several chromosomes into naïve, i.e. unstarved, yeast significantly diminishes their fertility. This type of reproductive barrier, whether arising spontaneously or via genetic manipulation, can be removed by making a lineage euploid for the altered chromosomes. Our model provides direct genetic evidence that reproductive isolation can arise frequently in stressed populations via genome restructuring without the precondition of geographic isolation.

Development and characterization of hybrids from native wine yeasts

For commercial purposes, the winemaking industry is constantly searching for new yeast strains. Historically, this has been achieved by collecting wild strains and selecting the best for industrial use through an enological evaluation. Furthermore, the increasing consumer demands have forced the industry to incorporate new strategies such as genetic engineering to obtain improved strains. In response to the lack of public acceptance of this methodology, alternative strategies based on breeding have gained acceptance in recent years. Through the use of conjugation of individual spores without the support of genetic engineering methods we generated intraspecific hybrids from wild strains with outstanding enological characteristics and interdelta fingerprinting was used to confirm the hybrid condition. A detailed enological characterization of the hybrids in synthetic and natural must indicates that physiological parameters such as sporulation, residual sugar, ethanol yield and total nitrogen uptake are within the levels determined for the parental strains, however, other parameters such as growth rate, lag phase and ethanol production show statistical differences with some parental or commercial strains. These findings allow us to propose these hybrids as new wine-making strains.

Genetics of yeast impacting wine quality

The availability of the sequence of the Saccharomyces genome in combination with the development of chemical analytical technologies with dynamic ranges sensitive enough to detect volatile aromatic compounds has generated a renewed interest in defining the role of yeast in the generation of wine aroma and flavor. Genetic differences among wine strains are well documented and aroma profiles also appear to vary, implying that specific allelic alterations may exist and impact the production of compounds associated with flavor. Partial or complete sequencing data on several wine strains are available and reveal underlying genetic differences across strains in key genes implicated in flavor formation. This review discusses the current understanding of the roles of Saccharomyces in wine flavor with an emphasis on positive contributions to flavor and highlights the discoveries of the underlying enzymatic and metabolic mechanisms responsible for the yeast contribution to wine quality.

Transcriptional regulation and the diversification of metabolism in wine yeast strains

Transcription factors and their binding sites have been proposed as primary targets of evolutionary adaptation because changes to single transcription factors can lead to far-reaching changes in gene expression patterns. Nevertheless, there is very little concrete evidence for such evolutionary changes. Industrial wine yeast strains, of the species Saccharomyces cerevisiae, are a geno- and phenotypically diverse group of organisms that have adapted to the ecological niches of industrial winemaking environments and have been selected to produce specific styles of wine. Variation in transcriptional regulation among wine yeast strains may be responsible for many of the observed differences and specific adaptations to different fermentative conditions in the context of commercial winemaking. We analyzed gene expression profiles of wine yeast strains to assess the impact of transcription factor expression on metabolic networks. The data provide new insights into the molecular basis of variations in gene expression in industrial strains and their consequent effects on metabolic networks important to wine fermentation. We show that the metabolic phenotype of a strain can be shifted in a relatively predictable manner by changing expression levels of individual transcription factors, opening opportunities to modify transcription networks to achieve desirable outcomes.

Strategies to select yeast starters cultures for production of flavor compounds in cachaça fermentations

In this work, we have used classical genetics techniques to find improved starter strains to produce cachaça with superior sensorial quality. Our strategy included the selection of yeast strains resistant to 5,5',5″-trifluor-D: ,L: -leucine (TLF) and cerulenin, since these strains produce higher levels of higher alcohols and esters than parental strains. However, no clear relationship was observed when levels of flavoring compounds were compared with the levels expression of the genes (BAT1, BAT2, ATF2, EEB1 genes) involved with the biosynthesis of flavoring compounds. Furthermore, we determined the stability of phenotypes considered as the best indicators of the quality of the cachaça for a parental strain and its segregants. By applying the principal component analysis, a cluster of segregants, showing a high number of characteristics similar to the parental strain, was recognized. One segregant, that was resistant to TLF and cerulenin, also showed growth stability after six consecutive replications on plates containing high concentrations of sugar and ethanol. "Cachaça" produced at laboratory scale using a parental strain and this segregant showed a higher level of flavoring compounds. Both strains predominated in an open fermentative process through seven cycles, as was shown by mitochondrial restriction fragment length polymorphisms analysis. Based on the physical chemical composition of the obtained products, the results demonstrate the usefulness of the developed strategies for the selection of yeast strains to be used as starters in "cachaça" production.

Industrial yeast strain engineered to ferment ethanol from lignocellulosic biomass

In this study an industrial Saccharomyces cerevisiae yeast strain capable of fermenting ethanol from pretreated lignocellulosic material was engineered. Genes encoding cellulases (endoglucanase, exoglucanase and β-glucosidase) were integrated into the chromosomal ribosomal DNA and delta regions of a derivative of the K1-V1116 wine yeast strain. The engineered cellulolytic yeast produces ethanol in one step through simultaneous saccharification and fermentation of pretreated biomass without the addition of exogenously produced enzymes. When ethanol fermentation was performed with 10% dry weight of pretreated corn stover, the recombinant strain fermented 63% of the cellulose in 96 h and the ethanol titer reached 2.6% v/v. These results demonstrate that cellulolytic S. cerevisiae strains can be used as a platform for developing an economical advanced biofuel process.

The genomes of fermentative Saccharomyces

Many different yeast species can take part in spontaneous fermentations, but the species of the genus Saccharomyces, including Saccharomyces cerevisiae in particular, play a leading role in the production of fermented beverages and food. In recent years, the development of whole-genome scanning techniques, such as DNA chip-based analysis and high-throughput sequencing methods, has considerably increased our knowledge of fermentative Saccharomyces genomes, shedding new light on the evolutionary history of domesticated strains and the molecular mechanisms involved in their adaptation to fermentative niches. Genetic exchange frequently occurs between fermentative Saccharomyces and is an important mechanism for generating diversity and for adaptation to specific ecological niches. We review and discuss here recent advances in the genomics of Saccharomyces species and related hybrids involved in major fermentation processes.

Physiological and genetic stability of hybrids of industrial wine yeasts Saccharomyces sensu stricto complex

AIMS

The aim of this study was to examine the physiological and genetic stability of hybrids of industrial wine yeasts Saccharomyces sensu stricto complex subjected to acidic stress during fermentation.

METHODS AND RESULTS

Laboratory-constructed yeast hybrids, one intraspecific Saccharomyces cerevisiae × S. cerevisiae and three interspecific S. cerevisiae × Saccharomyces bayanus, were subcultured in aerobic or anaerobic conditions in media with or without l-malic acid. Changes in the biochemical profiles, karyotypes and mitochondrial DNA profiles of the segregates were assessed after 50-190 generations. All yeast segregates showed a tendency to increase the range of the tested compounds utilized as sole carbon sources. Interspecific hybrids were alloaneuploid and their genomes tended to undergo extensive rearrangement especially during fermentation. The karyotypes of segregates lost up to four and appearance up to five bands were recorded. The changes in their mtDNA patterns were even broader reaching 12 missing and six additional bands. These hybrids acquired the ability to sporulate and significantly changed their biochemical profiles. The alloaneuploid intraspecific S. cerevisiae hybrid was characterized by high genetic stability despite the phenotypic changes. L-malic acid was not found to affect the extent of genomic changes of the hybrids, which suggests that their demalication ability is combined with resistance to acidic stress.

CONCLUSIONS

The results reveal the plasticity and extent of changes of chromosomal and mitochondrial DNA of interspecific hybrids of industrial wine yeast especially under anaerobiosis. They imply that karyotyping and restriction analysis of mitochondrial DNA make it possible to quickly assess the genetic stability of genetically modified industrial wine yeasts but may not be applied as the only method for their identification and discrimination.

SIGNIFICANCE AND IMPACT OF THE STUDY

Laboratory-constructed interspecific hybrids of industrial strains may provide a model for studying the adaptive evolution of wine yeasts under fermentative stress.

Genome-wide survey of post-meiotic segregation during yeast recombination

Background

When mismatches in heteroduplex DNA formed during meiotic recombination are left unrepaired, post-meiotic segregation of the two mismatched alleles occurs during the ensuing round of mitosis. This gives rise to somatic mosaicism in multicellular organisms and leads to unexpected allelic combinations among progeny. Despite its implications for inheritance, post-meiotic segregation has been studied at only a few loci.

Results

By genotyping tens of thousands of genetic markers in yeast segregants and their clonal progeny, we analyzed post-meiotic segregation at a genome-wide scale. We show that post-meiotic segregation occurs in close to 10% of recombination events. Although the overall number of markers affected in a single meiosis is small, the rate of post-meiotic segregation is more than five orders of magnitude larger than the base substitution mutation rate. Post-meiotic segregation took place with equal relative frequency in crossovers and non-crossovers, and usually at the edges of gene conversion tracts. Furthermore, post-meiotic segregation tended to occur in markers that are isolated from other heterozygosities and preferentially at polymorphism types that are relatively uncommon in the yeast species.

Conclusions

Overall, our survey reveals the genome-wide characteristics of post-meiotic segregation. The results show that post-meiotic segregation is widespread in meiotic recombination and could be a significant determinant of allelic inheritance and allele frequencies at the population level.

Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species

Partial or whole-genome duplications have played a major role in the evolution of new species. We have investigated the variation of ploidy level in a panel of domesticated strains of Saccharomyces cerevisiae coming from different geographical origins. Segregation studies and crosses with tester strains of different ploidy levels showed that part of the strains were well-balanced autotetraploids displaying tetrasomic inheritance. The presence of up to four different alleles for various loci is consistent with a polyploidization mechanism relying on the fusion of two nonreduced meiospores coming from two S. cerevisiae strains. Autotetraploidy was also in accordance with karyotype and flow cytometry analyses. Interestingly, most bakery strains were tetraploids, suggesting a link between ploidy level and human use. The null or drastically reduced fertility of the hybrids between tetraploid and diploid strains indicated that domesticated S. cerevisiae strains are composed of two groups isolated by post-zygotic reproductive barriers.

Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots

Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential) genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG) clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i) the evolution of non-random distributions of meiotic crossovers, (ii) the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii) the evolution of EG enrichment in pericentromeric regions and (iv) the associated absence of meiotic crossovers (cold centromeres). Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new aspect of the evolution of genome architectures that complements insights about molecular constraints, such as the interference of pericentromeric crossovers with chromosome segregation.

Microsatellite analysis of genetic diversity among clinical and nonclinical Saccharomyces cerevisiae isolates suggests heterozygote advantage in clinical environments

The genetic structure of a global sample of 170 clinical and nonclinical Saccharomyces cerevisiae isolates was analysed using 12 microsatellite markers. High levels of genetic diversity were revealed both among the clinical and among the nonclinical S. cerevisiae isolates without significant differentiation between these two groups of isolates, rendering a single origin of pathogenic isolates unlikely. This suggests that S. cerevisiae is a true opportunistic pathogen, with a diversity of unrelated genetic backgrounds able to cause infections in humans, and that the ability of S. cerevisiae isolates to cause infections is likely due to a combination of their phenotypic plasticity and the immune system status of the exposed individuals. As was previously reported for bread, beer and wine strains and for environmental S. cerevisiae isolates, the microsatellite genotypes indicated ploidy level variation, from possibly haploid up to tetraploid, among clinical S. cerevisiae isolates. However, rather than haploid, sporulation proficiency and spore viability data indicated that most S. cerevisiae isolates that were mono-allelic at all examined microsatellite loci were likely homothallic and self-diploidized. Interestingly, the proportion of heterozygous clinical isolates was found to be significantly higher than the proportion of heterozygous nonclinical isolates, suggesting a selective advantage of heterozygous S. cerevisiae yeasts in clinical environments.

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates

Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to characterize phenotypic diversity within and between populations. We explored the phenotypic variation in stress sensitivity and genomic expression in a large panel of Saccharomyces strains collected from diverse environments. We measured the sensitivity of 52 strains to 14 environmental conditions, compared genomic expression in 18 strains, and identified gene copy-number variations in six of these isolates. Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression. Analysis of these datasets reveals relationships between strains from similar niches, suggests common and unique features of yeast habitats, and implicates genes whose variable expression is linked to stress resistance. Using a simple metric to suggest cases of selection, we found that strains collected from oak exudates are phenotypically more similar than expected based on their genetic diversity, while sake and vineyard isolates display more diverse phenotypes than expected under a neutral model. We also show that the laboratory strain S288c is phenotypically distinct from all of the other strains studied here, in terms of stress sensitivity, gene expression, Ty copy number, mitochondrial content, and gene-dosage control. These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics.

Much attention has been given to the ways in which organisms evolve new phenotypes and the influence of the environment on this process. A major focus of study is defining the genetic basis for phenotypes important for organismal fitness. As a first step toward this goal, we surveyed phenotypic variation in diverse yeast strains collected from different environments by characterizing variations in stress resistance and genomic expression. We uncovered many phenotypic differences across yeast strains, both in stress tolerance and gene expression. The similarities and differences of the strains analyzed uncovered phenotypes shared by strains that live in similar environments, suggesting common features of yeast niches as well as mechanisms that different strains use to thrive in those conditions. We provide evidence that some characteristics of strains isolated from oak tree soil have been selected for, perhaps because of the shared selective pressures imposed by their environment. One theme emerging from our studies is that the laboratory strain of yeast, long used as a model for yeast physiology and basic biology, is aberrant compared to all other strains. This result raises caution about making general conclusions about yeast biology based on a single strain with a specific genetic makeup.

Improvement of Saccharomyces yeast strains used in brewing, wine making and baking

Yeast was the first microorganism domesticated by mankind. Indeed, the production of bread and alcoholic beverages such as beer and wine dates from antiquity, even though the fact that the origin of alcoholic fermentation is a microorganism was not known until the nineteenth century. The use of starter cultures in yeast industries became a common practice after methods for the isolation of pure yeast strains were developed. Moreover, effort has been undertaken to improve these strains, first by classical genetic methods and later by genetic engineering. In general, yeast strain development has aimed at improving the velocity and efficiency of the respective production process and the quality of the final products. This review highlights the achievements in genetic engineering of Saccharomyces yeast strains applied in food and beverage industry.

New perspectives in safety and quality enhancement of wine through selection of yeasts based on the parietal adsorption activity

The present article aims to review research papers that focus on the parietal adsorption activity of wine yeast and on its contribution to the enhancement of wine safety and quality. There is a great diversity among yeasts for their parietal adsorption activity: the outermost layer of the cell wall has a chemical composition that notably varies from yeast to yeast. Parietal mannoproteins can contain phosphate, pyruvate, or glucuronic acid, which impart negative charges, modifying the electrostatic and ionic interactions with wine components. The following could give a good reason to propose a specific selection of wine yeasts based on their parietal adsorption activity to improve wine safety and quality: (a) ochratoxin A content of wines is greatly reduced by expressly selected yeasts, sequestering the toxin during winemaking; (b) yeast influences concentration and composition of phenolic compounds in wine, above all by adsorbing them on cell wall; (c) among grape pigments, anthocyanins, in particular, may be adsorbed by yeast cell wall; and (d) yeast can also interact with wine colour producing anthocyanin-beta-d-glucosidase, pyruvic acid, and acetaldehyde or releasing mannoproteins and different polysaccharides. Genomic strategies could also be used to obtain a further enhancement of the adsorption/non-adsorption activity of wine yeasts. Based on winemaking requirements and on parietal adsorption activity, a specific selection of yeasts might be performed: (a) to protect wine colour during red winemaking, (b) to remove residual wine colour during white winemaking, (c) to selectively remove ochratoxin A, and (d) to protect phenolic compounds responsible for antioxidant activity.

Wine colour adsorption phenotype: an inheritable quantitative trait loci of yeasts

AIMS

In this work, a population of 88 descendants derived from three wine strains of Saccharomyces cerevisiae was tested for the enological trait 'wine colour adsorption' (WCA) to evaluate its inheritability.

METHODS AND RESULTS

The WCA phenotype was tested on plate agar medium specifically formulated for the purpose. After 10 days of anaerobic incubation at 28 degrees C, a computer-assisted assessment of WCA aptitude of the yeasts was carried out. The biomass colour -- ranging from white to dark brown -- reflects the adsorption of grape pigments: white and dark brown biomass colour corresponds to low and high adsorption, respectively. In order to confirm biomass colour results, microvinification trials using red must were performed, and the obtained wines were analysed.

CONCLUSIONS

The analysis of the progeny demonstrated that the enological trait WCA is inheritable and polygenic.

SIGNIFICANCE AND IMPACT OF THE STUDY

A way to describe the polygenic effect of the WCA trait has been found, also showing that this trait is inheritable. The impact of the work revolves more around the large-scale screening method, which could then assist in breeding wine yeast, and can also be used as a scientific tool to investigate WCA trait.

Functional genomics of wine yeast Saccharomyces cerevisiae

The application of genomic technologies to the analysis of wine strains of Saccharomyces cerevisiae has greatly enhanced our understanding of both native and laboratory strains of this important model eukaryote. Not only are differences in transcript, protein, and metabolite profiles being uncovered, but the heritable basis of these differences is also being elucidated. Although some challenges remain in the application of functional genomic technologies to commercial and native strains of S. cerevisiae, recent improvements, particularly in data analysis, have greatly extended the utility of these tools. Comparative analysis of laboratory and wine isolates is refining our understanding of the mechanisms of genome evolution. Genomic analysis of Saccharomyces in native environments is providing evidence of gene function to previously uncharacterized open reading frames and delineating the physiological parameters of ecological niche specialization and stress adaptation. The wealth of information being generated will soon be utilized to construct commercial stains with more desirable phenotypes, traits that will be designed to be genetically stable under commercial production conditions.

Evolution of thehemiascomycete yeasts: on life styles and the importance of inbreeding

The term 'breeding system' is used to describe the morphological and behavioural aspects of the sexual life cycle of a species. The yeast breeding system provides three alternatives that enable hapoids to return to the diploid state that is necessary for meiosis: mating of unrelated haploids (amphimixis), mating between spores from the same tetrad (intratetrad mating, automixis) and mother daughter mating upon mating type switching (haplo-selfing). The frequency of specific mating events affects the level of heterozygosity present in individuals and the genetic diversity of populations. This review discusses the reproductive strategies of yeasts, in particular S. cerevisiae (Bakers' or budding yeast). Emphasis is put on intratetrad mating, its implication for diversity, and how the particular genome structure could have evolved to ensure the preservation of a high degree of heterozygosity in conjunction with frequent intratetrad matings. I also discuss how the ability of yeast to control the number of spores that are formed accounts for high intratetrad mating rates and for enhanced transmission of genomic variation. I extend the discussion to natural genetic variation and propose that a high level of plasticity is inherent in the yeast breeding system, which may allow variation of the breeding behaviour in accordance with the needs imposed by the environment.

A homozygous diploid subset of commercial wine yeast strains

Genetic analysis was performed on 45 commercial yeasts which are used in winemaking because of their superior fermentation properties. Genome sizes were estimated by propidium iodide fluorescence and flow cytometry. Forty strains had genome sizes consistent with their being diploid, while five had a range of aneuploid genome sizes that ranged from 1.2 to 1.8 times larger. The diploid strains are all Saccharomyces cerevisiae, based on genetic analysis of microsatellite and minisatellite markers and on DNA sequence analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA of four strains. Four of the five aneuploid strains appeared to be interspecific hybrids between Saccharomyces kudriavzevii and Saccharomyces cerevisiae, with the fifth a hybrid between two S. cerevisiae strains. An identification fingerprint was constructed for the commercial yeast strains using 17 molecular markers. These included six published trinucleotide microsatellites, seven new dinucleotide microsatellites, and four published minisatellite markers. The markers provided unambiguous identification of the majority of strains; however, several had identical or similar patterns, and likely represent the same strain or mutants derived from it. The combined use of all 17 polymorphic loci allowed us to identify a set of eleven commercial wine yeast strains that appear to be genetically homozygous. These strains are presumed to have undergone inbreeding to maintain their homozygosity, a process referred to previously as 'genome renewal'.

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system

Spindle pole bodies (SPBs) provide a structural basis for genome inheritance and spore formation during meiosis in yeast. Upon carbon source limitation during sporulation, the number of haploid spores formed per cell is reduced. We show that precise spore number control (SNC) fulfills two functions. SNC maximizes the production of spores (1-4) that are formed by a single cell. This is regulated by the concentration of three structural meiotic SPB components, which is dependent on available amounts of carbon source. Using experiments and computer simulation, we show that the molecular mechanism relies on a self-organizing system, which is able to generate particular patterns (different numbers of spores) in dependency on one single stimulus (gradually increasing amounts of SPB constituents). We also show that SNC enhances intratetrad mating, whereby maximal amounts of germinated spores are able to return to a diploid lifestyle without intermediary mitotic division. This is beneficial for the immediate fitness of the population of postmeiotic cells.

Peculiarities of strains adapted to Sardinian sherry-like wine ageing conditions

Saccharomyces cerevisiae flor yeasts, which are subjected to stressful conditions during wine ageing, exhibit a number of characteristics which distinguish them from non-flor S. cerevisiae wine strains. In the present work, 22 flor and 14 non-flor S. cerevisiae wine strains are compared, in order to elucidate other possible peculiarities of these yeasts. The results obtained demonstrate that in contrast to the homothallic nature of the non-flor strains, 77% of the flor strains exhibit two variants of a semi-homothallic life cycle. Moreover, the flor-forming ability is shown to be inversely correlated to spore viability and the utilisation of maltose and galactose.

Gradual genome stabilisation by progressive reduction of the Saccharomyces uvarum genome in an interspecific hybrid with Saccharomyces cerevisiae

Considerable amounts of molecular and genetic data indicate that interspecific hybridisation may not be rare among natural strains of Saccharomyces sensu stricto. Although a post-zygotic barrier operating during meiosis usually prevents the production of viable spores, stable hybrids can arise which can even evolve into distinct species. This study was aimed to analyse the genome of a fertile Saccharomyces cerevisiae x S. uvarum hybrid and monitor its changes over four filial generations of viable spores. The molecular genetic analysis demonstrated that the two species did not contribute equally to the formation and stabilisation of the hybrid genome. S. cerevisiae provided the mitochondrial DNA and the more stable part of the nuclear genome. The S. uvarum part of the hybrid nuclear genome became progressively smaller by loosing complete chromosomes and genetic markers in the course of successive meiotic divisions. Certain S. uvarum chromosomes were eliminated and/or underwent rearrangements in interactions with S. cerevisiae chromosomes. Numerous S. uvarum chromosomes acquired S. cerevisiae telomere sequences. The gradual elimination of large parts of the S. uvarum genome was associated with a progressive increase of sporulation efficiency. We hypothesise that this sort of genomic alterations may contribute to speciation in Saccharomyces sensu stricto.

Hypervariable noncoding sequences in Saccharomyces cerevisiae

Compared to protein-coding sequences, the evolution of noncoding sequences and the selective constraints placed on these sequences is not well characterized. To compare the evolution of coding and noncoding sequences, we have conducted a survey for DNA polymorphism at five randomly chosen loci among a diverse collection of 81 strains of Saccharomyces cerevisiae. Average rates of both polymorphism and divergence are 40% lower at noncoding sites and 90% lower at nonsynonymous sites in comparison to synonymous sites. Although noncoding and coding sequences show substantial variability in ratios of polymorphism to divergence, two of the loci, MLS1 and PDR10, show a higher rate of polymorphism at noncoding compared to synonymous sites. The high rate of polymorphism is not accompanied by a high rate of divergence and is limited to a few small regions. These hypervariable regions include sites with three segregating bases at a single site and adjacent polymorphic sites. We show that this clustering of polymorphic sites is significantly greater than one would expect on the basis of the spacing between polymorphic fourfold degenerate sites. Although hypervariable noncoding sequences could result from selection on regulatory mutations, they could also result from transient mutational hotspots.

Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres

The recent release of sequences of several unexplored yeast species that cover an evolutionary range comparable to the entire phylum of chordates offers us a unique opportunity to investigate how genes involved in adaptation have been shaped by evolution. We have examined how three different sets of genes, all related to adaptative processes at the genomic level, have evolved in hemiascomycetes: (1) the mating-type genes that govern sexuality, (2) the silencing genes that are connected to regulation of mating-type cassettes and to telomere position effect, and (3) the gene families found repeated in subtelomeric regions. We report new combinations of mating-type genes and cassettes in hemiascomycetous species; we show that silencing proteins diverge rapidly. We have also found that in all species studied, subtelomeric gene families exist and are specific to each species.

Inheritable nature of enological quantitative traits is demonstrated by meiotic segregation of industrial wine yeast strains

Wine yeast strains exhibit a wide variability in their technological properties. The large number of allelic variants and the high degree of heterozygosity explain this genetic variability found among the yeast flora. Furthermore, most enological traits are controlled by polygenic systems presenting complex interactions between the alleles. Taking this into account, we hypothesized that the meiotic segregation of such alleles from a given strain might generate a progeny population with very different technological properties. In this work, a population of 50 progeny clones derived from four industrial wine strains of Saccharomyces cerevisiae was characterized for three major enological traits: ethanol tolerance, volatile-acidity production and hydrogen sulphide production. For this purpose, reliable laboratory fermentation tests were developed in accordance with enological practice. A wide variability in the values of the various parameters was found among spore clones obtained after sporulation. Many clones presenting better aptitudes than the parental strains were obtained. Moreover, analysis of the progeny demonstrated that: (1) traits are in part inheritable; (2) traits are clearly polygenic; (3) broad relations of dominance/recessivity can be established. All these findings constitute an initial step for establishing breeding strategies for wine yeast improvement.

Steric-hyperlayer sedimentation field flow fractionation and flow cytometry analysis applied to the study of Saccharomyces cerevisiae

Sedimentation field flow fractionation separation associated with flow cytometry has been used for the characterization of several commercial Saccharomyces cerevisiae yeasts used for wine production. A new type of channel 80 microm thick and new operating conditions, such as sample introduction when field and flow are established and a channel inlet connected to the accumulation wall, were used. Good repeatability (5% RSD) and reduced analysis time (2-10 min) were obtained. The avoidance of the stop-flow relaxation process in conjunction with the use of a channel of reduced thickness has demonstrated that an effective "steric-hyperlayer" mode driving to a major focusing effect of the species in the channel thickness is involved in the elution of the yeast cells. Flow cytometry analyses were performed, and the forward scattering and side scattering yeast characteristics correlation maps were obtained. Field flow fractionation and flow cytometry information obtained indicated that the fractogram profiles of the yeast cell depended not only on the size, but also on the shape and density.

Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids

Crossings between strains of Saccharomyces cerevisiae and Saccharomyces bayanus were carried out. Genetic, molecular and electrophoretic karyotyping data indicated that interspecific hybrids were obtained. The hybrid cells segregated "grande" and "petite" colonies, and the latter ranged between 20 and 50%; unlike "grande" colonies, "petite" colonies did not sporulate and did not ferment maltose. In the hybrids, the extent of sporulation varied between 10 and 20%; only very rare asci (around 10(-4)) held viable ascospores. Clones from the viable ascospores sporulated and produced asci with viable ascospores able to give mating with spores from both hybrid derivatives and parental species. Fertile asci could derive from allotetraploid cells generated by endomitotic events in allodiploid cells, a mechanism that enables overcoming the species barrier between S. cerevisiae and S. bayanus.

Genetic analysis of the karyotype instability in natural wine yeast strains

Yeast strains isolated from the wild may show high rates of changes in their karyotypes during vegetative growth. We analysed over 500 karyotypes from mitotic and meiotic derivatives of strain DC5, which has a chromosome rearrangement rate of 8.2 x 10(-3) changes/generation. About 70% of the meiotic derivatives of DC5 had low rearrangement rates, with an average of 5.8 x 10(-4) changes/generation, suggesting that karyotype instability behaved as a dominant phenotype. Diploid derivatives with low karyotype variability in mitosis also had low rates of chromosomal rearrangement during meiosis, suggesting that the two phenotypes may be linked. DC5 and some of its meiotic derivatives (both with high and low karyotype variability) had chromosome XII hypervariable bands. Their distribution among the meiotic products indicates that they are not indicators for genetic instability. To our knowledge, data in this paper are the first to indicate that karyotypically unstable yeast strains may give stable progeny at high rates. Understanding of the relevant mechanism(s) may allow the design of genetic strategies to stabilize karyotypes from natural and/or industrial wine yeasts with unacceptable karyotype rearrangement rates.

Evolution and variation of the yeast (Saccharomyces) genome

In this review we describe the role of the yeast Saccharomyces in the development of human societies including the use of this organism in the making of wine, bread, beer, and distilled beverages. We also discuss the tremendous diversity of yeast found in natural (i.e., noninoculated) wine fermentations and the scientific uses of yeast over the past 60 years. In conclusion, we present ideas on the model of "genome renewal" and the use of this model to explain the mode by which yeast has evolved and how diversity can be generated.