Ploidy-Regulated Variation in Biofilm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae

Modern industrial winemaking is based on the use of starter cultures of specialized wine strains of Saccharomyces cerevisiae yeast. Commercial wine strains have a number of advantages over natural isolates, and it is their use that guarantees the stability and reproducibility of industrial winemaking technologies. For the highly competitive wine market with new demands for improved wine quality, it has become increasingly critical to develop new wine strains and winemaking technologies. Novel opportunities for precise wine strain engineering based on detailed knowledge of the molecular nature of a particular trait or phenotype have recently emerged due to the rapid progress in genomic and “postgenomic” studies with wine yeast strains. The review summarizes the current achievements of the metabolic engineering of wine yeast, the results of recent studies and the prospects for the application of genomic editing technologies for improving wine S. cerevisiae strains.

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Novel approach in developing Saccharomyces cerevisiae hybrid bioethanol producers by mating of natural isolates having desirable traits

Journal of Biotechnology ◽

10.1016/j.jbiotec.2018.06.294 ◽

2018 ◽

Vol 280 ◽

pp. S89

Author(s):

Bojan Zunar ◽

Anamarija Stafa ◽

Antonio Zandona ◽

Marina Svetec Miklenic ◽

Bozidar Santek ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Novel Approach ◽

Natural Isolates

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Microbial Synergy via an Ethanol-Triggered Pathway

Molecular and Cellular Biology ◽

10.1128/mcb.24.9.3874-3884.2004 ◽

2004 ◽

Vol 24 (9) ◽

pp. 3874-3884 ◽

Cited By ~ 81

Author(s):

Michael G. Smith ◽

Shelley G. Des Etages ◽

Michael Snyder

Keyword(s):

Saccharomyces Cerevisiae ◽

Caenorhabditis Elegans ◽

Dimethyl Sulfoxide ◽

Cell Physiology ◽

Low Doses ◽

Microbial Interaction ◽

Signaling Molecule ◽

Bacterial Physiology ◽

Diffusible Factor ◽

Natural Isolates

ABSTRACT We have discovered a microbial interaction between yeast, bacteria, and nematodes. Upon coculturing, Saccharomyces cerevisiae stimulated the growth of several species of Acinetobacter, including, A. baumannii, A. haemolyticus, A. johnsonii, and A. radioresistens, as well as several natural isolates of Acinetobacter. This enhanced growth was due to a diffusible factor that was shown to be ethanol by chemical assays and evaluation of strains lacking ADH1, ADH3, and ADH5, as all three genes are involved in ethanol production by yeast. This effect is specific to ethanol: methanol, butanol, and dimethyl sulfoxide were unable to stimulate growth to any appreciable level. Low doses of ethanol not only stimulated growth to a higher cell density but also served as a signaling molecule: in the presence of ethanol, Acinetobacter species were able to withstand the toxic effects of salt, indicating that ethanol alters cell physiology. Furthermore, ethanol-fed A. baumannii displayed increased pathogenicity when confronted with a predator, Caenorhabditis elegans. Our results are consistent with the concept that ethanol can serve as a signaling molecule which can affect bacterial physiology and survival.

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Improvement of natural isolates of Saccharomyces cerevisiae strains for synthesis of a chiral building block using classic genetics

Applied Microbiology and Biotechnology ◽

10.1007/s00253-008-1344-2 ◽

2008 ◽

Vol 78 (4) ◽

pp. 659-667 ◽

Cited By ~ 3

Author(s):

Netta Nir ◽

Moran Bahalul ◽

Roi Feingersch ◽

Tal Katz-Ezov ◽

Yechezkel Kashi ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Building Block ◽

Chiral Building Block ◽

Natural Isolates

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Mitochondrial-Nuclear Epistasis Contributes to Phenotypic Variation and Coadaptation in Natural Isolates of Saccharomyces cerevisiae

Genetics ◽

10.1534/genetics.114.168575 ◽

2014 ◽

Vol 198 (3) ◽

pp. 1251-1265 ◽

Cited By ~ 47

Author(s):

Swati Paliwal ◽

Anthony C. Fiumera ◽

Heather L. Fiumera

Keyword(s):

Saccharomyces Cerevisiae ◽

Phenotypic Variation ◽

Natural Isolates

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Tetrad analysis without tetrad dissection: Meiotic recombination and genomic diversity in the yeast Komagataella phaffii (Pichia pastoris)

10.1101/704627 ◽

2019 ◽

Author(s):

Stephanie Braun-Galleani ◽

Julie A. Dias ◽

Aisling Y. Coughlan ◽

Adam P. Ryan ◽

Kevin P. Byrne ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Diversity ◽

Pichia Pastoris ◽

Meiotic Recombination ◽

Genomic Diversity ◽

Tetrad Analysis ◽

Komagataella Phaffii ◽

Rich Media ◽

Natural Isolates ◽

Almost All

AbstractKomagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were formerly called Pichia pastoris. However, almost all laboratory work on K. phaffii has been done on strains derived from a single natural isolate, CBS7435. There is little information about the genetic properties of K. phaffii or its sequence diversity. Genetic analysis is difficult because, although K. phaffii makes asci with four spores, the spores are small and tend to clump together, making the asci hard to dissect. Here, we sequenced the genomes of all the known isolates of this species, and find that K. phaffii has only been isolated from nature four times. We analyzed the meiotic recombination landscape in a cross between auxotrophically marked strains derived from two isolates that differ at 44,000 single nucleotide polymorphism sites. We conducted tetrad analysis by making use of the property that haploids of this species do not mate in rich media, which enabled us to isolate and sequence the four types of haploid cell that are present in the colony that forms when a tetratype ascus germinates. We found that approximately 25 crossovers occur per meiosis, which is 3.5 times fewer than in Saccharomyces cerevisiae. Recombination is suppressed, and genetic diversity among natural isolates is low, in a region around centromeres that is much larger than the centromeres themselves. Our method of tetrad analysis without tetrad dissection will be applicable to other species whose spores do not mate spontaneously after germination.Author summaryTo better understand the basic genetics of the budding yeast Komagataella phaffii, which has many applications in biotechnology, we investigated its genetic diversity and its meiotic recombination landscape. We made a genetic cross between strains derived from two natural isolates, and developed a method for characterizing the genomes of the four spores resulting from meiosis, which were previously impossible to isolate. We found that K. phaffii has a lower recombination rate than Saccharomyces cerevisiae. It shows a large zone of suppressed recombination around its centromeres, which may be due to the structural differences between centromeres in K. phaffii and S. cerevisiae.

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Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

Genome Biology and Evolution ◽

10.1093/gbe/evu199 ◽

2014 ◽

Vol 6 (9) ◽

pp. 2557-2566 ◽

Cited By ~ 31

Author(s):

Dana J. Wohlbach ◽

Nikolay Rovinskiy ◽

Jeffrey A. Lewis ◽

Maria Sardi ◽

Wendy S. Schackwitz ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Comparative Genomics ◽

Bioenergy Production ◽

Natural Isolates

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Variation in filamentous growth and response to quorum-sensing compounds in environmental isolates of Saccharomyces cerevisiae

10.1101/548099 ◽

2019 ◽

Author(s):

B. Adam Lenhart ◽

Brianna Meeks ◽

Helen A. Murphy

Keyword(s):

Saccharomyces Cerevisiae ◽

Quorum Sensing ◽

Natural Populations ◽

Filamentous Growth ◽

West African ◽

Natural Genetic Variation ◽

Pseudohyphal Growth ◽

Natural Isolates ◽

Candidate Loci ◽

Computational Image Analysis

AbstractIn fungi, filamentous growth is a major developmental transition that occurs in response to environmental cues. In diploid Saccharomyces cerevisiae, it is known as pseudohyphal growth and presumed to be a foraging mechanism. Rather than normal unicellular growth, multicellular filaments composed of elongated, attached cells spread over and into surfaces. This morphogenetic switch can be induced through quorum sensing with the aromatic alcohols phenylethanol and tryptophol. Most research investigating pseudohyphal growth has been conducted in a single lab background, Σ1278b. To investigate the natural variation in this phenotype and its induction, we assayed the diverse 100-genomes collection of environmental S. cerevisiae isolates. Using computational image analysis, we quantified the production of pseudohyphae and observed a large amount of variation. Unlike ecological niche, population membership was associated with pseudohyphal growth, with the West African population having the most. Surprisingly, most strains showed little or no response to exogenous phenylethanol or tryptophol. We also investigated the amount of natural genetic variation in pseudohyphal growth using a mapping population derived from a single, highly-heterozygous clinical isolate that contained as much phenotypic variation as the environmental panel. A bulk-segregant analysis uncovered five major peaks with candidate loci that have been implicated in the Σ1278b background. Our results indicate that the filamentous growth response is a generalized, highly variable phenotype in natural populations, while response to quorum sensing molecules is surprisingly rare. These findings highlight the importance of coupling studies in tractable lab strains with natural isolates in order to understand the relevance and distribution of well-studied traits.

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Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host

10.1101/2021.03.01.433327 ◽

2021 ◽

Author(s):

Claudine Bleykasten-Grosshans ◽

Romeo Fabrizio ◽

Anne Friedrich ◽

Joseph Schacherer

Keyword(s):

Saccharomyces Cerevisiae ◽

Transposable Element ◽

Interspecific Hybridization ◽

Genetic Background ◽

Evolutionary History ◽

Large Set ◽

Transpositional Activity ◽

Wide Range ◽

Natural Isolates ◽

History Of

AbstractTransposable elements (TE) are an important source of genetic variation with a dynamic and content that greatly differ in a wide range of species. The origin of the intraspecific content variation is not always clear and little is known about the precise nature of it. Here, we surveyed the species-wide content of the Ty LTR-retrotransposons in a broad collection of 1,011 Saccharomyces cerevisiae natural isolates to understand what can stand behind the variation of the repertoire, i.e. the type and number of Ty elements. We have compiled an exhaustive catalog of all TE variants present in the S. cerevisiae species by identifying a large set of new variants. The characterization of the TE content in each isolate clearly highlighted that each subpopulation exhibits a unique and specific repertoire, retracing the evolutionary history of the species. Most interestingly, we have shown that ancient interspecific hybridization events had a major impact in the birth of new variants and therefore in the shaping of the TE repertoires. We also investigated the transpositional activity of these elements in a large set of natural isolates, and we found a broad variability related to the level of ploidy as well as the genetic background. Overall, our results pointed out that the evolution of the Ty content is deeply impacted by clade-specific events such as introgressions and therefore follows the population structure. In addition, our study lays the foundation for future investigations to better understand the transpositional regulation and more broadly the TE-host interactions.Authors summaryMobile DNA elements are widely distributed in the genomes of many eukaryotes, but their contents greatly vary between species, populations and even individuals. In fact, little is known about the origin of this variation of transposable element (TE) content across individuals of the same species. Here, we surveyed the Ty LTR-retrotransposon content in a broad collection of 1,011 Saccharomyces cerevisiae yeast natural isolates. We have defined an exhaustive and precise catalog of the TE variants present in the S. cerevisiae species. We found that the TE content follows the evolutionary history of the species because each subpopulation has a unique and specific content. Interestingly, our results highlighted that ancient interspecific hybridization events led to the appearance of new TE variants and therefore had a strong impact on the variation of the TE repertoires in this species. We also investigated the transpositional activity of these elements and found a wide variability related to the genetic background diversity. Altogether, our results have led to a better understanding of the variability of TE content at a species level.

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