Polymorphism within the nuclear and 2 micron genomes of Saccharomyces cerevisiae

Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element

Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.

Tools for the study of genome rearrangements in laboratory and industrial yeast strains

In order to investigate the extent of genome rearrangements in laboratory and industrial yeast strains, a set of plasmids, containing ca. 300 bp fragments from highly conserved genes from S. cerevisiae, has been constructed. We chose three unique PCR products, each from a single gene, per chromosome: one from close to the centromere, and one from each chromosome end. Using these plasmids as probes to hybridize a Southern blot from a pulsed-field gel electrophoresis separation of the 16 yeast chromosomes, it is possible to identify large chromosomal rearrangements such as reciprocal translocations.

Analysis of production brewing strains of yeast by DNA fingerprinting

Production brewing strains of the yeast Saccharomyces cerevisiae were analysed by DNA fingerprinting, using a Southern blotting and hybridization procedure and employing the Ty1-15 transposon as a probe. The ability to differentiate readily between strains was very dependent on the restriction enzyme used to digest the DNA prior to Southern blotting and hybridization; the enzymes EcoRI, PstI and SalI were found to be particularly useful in this respect. The method was applicable to the differentiation of both ale and lager yeasts, and was sufficiently sensitive to distinguish between very closely related strains. DNA fingerprinting by this approach confirmed, for example, that a flocculent strain isolated during a production-scale fermentation with a lager yeast was genotypically different from the parent.

Evaluation of molecular typing techniques to assign genetic diversity among Saccharomyces cerevisiae strains

Discrimination of strains within the species Saccharomyces cerevisiae was demonstrated by the use of four different techniques to type 15 strains isolated from spoiled wine and beer. Random amplified polymorphic DNA with specific oligonucleotides and PCR fingerprinting with the microsatellite oligonucleotide primers (GAC)5 and (GTG)5 enabled discrimination between the strains tested. Additionally, restriction enzyme analysis, with TaqI and MseI, of PCR-amplified fragments from the complete internal transcribed spacer and nontranscribed spacer, both present in the rRNA-encoding gene cluster, proved to be suitable for generating intraspecies-specific patterns. Random amplified polymorphic DNA with primers 24 and OPA-11 and PCR fingerprinting with primer (GTG)5 appeared to generate the highest degree of diversity. However, the results indicated that there was no single PCR-mediated typing technique enabling discrimination on the strain level. Discrimination of each individual strain was nevertheless possible by combining the results obtained with all typing techniques.

Physiological and molecular characterization of flor yeasts: polymorphism of flor yeast populations

Yeast strains which form velum on the surface of Sherry wine during the aging process have been isolated and characterized. According to their metabolic and molecular features most of the yeasts that were isolated belong to different races of Saccharomyces cerevisiae (beticus, cheresiensis, montuliensis and rouxii). Due to the conditions under which these yeasts were isolated, all strains have in common the capacity to develop a film as an adaptive mechanism which allows them to grow and survive in 15.5% vol. ethanol. All strains were prototrophs for amino acids and most vitamins but they gave different responses to the killer factor. However, whereas their physiological features were similar, they showed a great heterogeneity with regards to the nuclear and mitochondrial genome (mtDNA): DNA content per cell was quite variable (1.3 to 2n), electrophoretic karyotypes of nuclear genomes indicated a main pattern with some variations, and polymorphism shown by the mtDNA was very high. Under extreme conditions such as Sherry wine with 15.5% vol. ethanol, no fermentable sugar and an exclusively oxidative metabolism, cells hardly grow and the maintenance of a live population depends on survival and respiration, which in turn depend on the mtDNA. At the same time these environmental conditions are mutagenic for the mtDNA, causing an increase in variation. Thus, the polymorphism observed might reflect the enormous variability induced by the ethanol followed by the selection of those mtDNA sequences which make the mitochondria metabolically active under these conditions.

Transpogenes: the transposition-like integration of short sequence DNA into the yeast 2 micron plasmid creates the STB locus and plasmid-size polymorphism

The type-2 2 mu plasmid of industrial yeast strains exhibits extensive size polymorphism in the STB (plasmid stability) locus and IR (inverted repeat)-right region. Comparative DNA sequence analyses of STB alleles identified a 38-bp sequence flanked by a 25-bp direct repeat as the underlying structural motif. Variable unequal recombination within the direct repeat accounted for the observed polymorphism of STB alleles. IR-right polymorphism was observed to result from tandem duplication of a 22-bp sequence flanked by a 9-bp direct repeat. The flanking direct repeats marked both loci as originating from the transposition-like integration of short DNA fragments. We call these structures transpogenes and note that these are hybrid structures of host and foreign DNA which can evolve into functional loci.

Chromosomal rearrangements during vegetative growth of a wild strain of Saccharomyces cerevisiae

Electrophoretic karyotypes of two strains of Saccharomyces cerevisiae, a haploid laboratory strain and a wild strain known to be at least diploid, have been checked during vegetative growth. The karyotype of the haploid strain was very stable; however, the diploid strain underwent frequent modifications. In most cases the number of bands was reduced, but occasionally we observed one band splitting into two. In one case, chromosomal rearrangements took place between differently sized copies of chromosomes I and VI. We concluded that the chromosome length polymorphism observed among wild strains of S. cerevisiae could be explained partly by chromosomal structure reorganization occurring during mitosis.

Genetic diversity of the yeast Candida utilis

The electrophoretic karyotypes and some mtDNA restriction fragment patterns of 13 strains of Candida utilis and one strain of Hansenula jadinii were compared. PFGE separations revealed remarkable chromosome length polymorphisms between two groups of strains suggesting that perhaps they do not belong to the same species. However, all strains had the same or similar EcoRI, HindIII and BamHI mtDNA restriction patterns. The mtDNA genomes had an average size range of 55 kb. These results support the supposition that C. utilis is a yeast with a highly variable electrophoretic karyotype as already known for another imperfect yeast species, Candida albicans.

Analysis of the chromosomal DNA polymorphism of wine strains of Saccharomyces cerevisiae

Wine yeast strains are characterized by a high chromosomal DNA polymorphism. This can be explained partly by a size difference of different variants of specific chromosomes. This difference can reach up to 45% of the size of the chromosome in question. Two strains, SB1 and Eg8, have a very complex chromosomal pattern and show one band hybridizing with probes from two different chromosomes derived from a reference strain. This is an indication of the presence of "hybrid" chromosomes in these wine strains. The most astonishing result concerns chromosome VIII, frequently present in wine strains in two variant forms. The first normal form has a size of about 580 kb while the second is around 1000 kb. These two forms segregate at meiosis and recombine with a normal chromosome VIII from a laboratory strain. Wine yeasts are thus very different from haploid laboratory strains.