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Life cycle of Saccharomyces yeasts; genomes, ploidy, aneuploidy, and interspecific hybrids

Budding yeasts, which are members of the fungal genus Saccharomyces (Latin: ‘sugar fungus'), are minuscule single-celled organisms, yet they are ultimately responsible for producing almost all of the alcoholic beverages consumed in the world, including beer, wine, sake, and distilled spirits. In the case of beer brewing, Saccharomyces yeasts are the primary biological agents that transform wort into beer, by metabolizing sugars present in the wort (mostly maltose, glucose, and maltotriose) and converting them into ethanol and carbon dioxide; these organisms are thus literally ‘sugar (-eating) fungi'. Yeasts, as are all fungi, are eukaryotic organisms, with their genomes organized into linear chromosomes contained within a nucleus. Yeasts also contain cytoplasmically located mitochondria, which have their own separate genome, but this chapter will not discuss mitochondria and their genomes in further detail. For Saccharomyces

yeasts, the typical strains found in nature have a diploid genome containing two copies of each of 16 different chromosomes (16 pairs of chromosomes, hence 32 chromosomes total in the diploid genome). Haploid cells (containing just one copy of each of the chromosomes) can exist briefly within the sexual mating cycle, derived by sporulation of the diploid cell, or can exist indefinitely as free- living cells if they are unable to mate successfully, for example due to mutations in the mating system.

As illustrated in Fig. 5.1, the life cycle of typical Saccharomyces yeasts includes both asexual and sexual phases, with both diploid and, under some conditions, haploid cells able to undergo mitosis (i.e. to divide asexually, also called ‘clonally') in an

unlimited manner when there are sufficient nutrients. However, when nutrients, especially nitrogen, become limiting, a diploid cell - but not a haploid - is able to progress through meiosis and produce 4 haploid spores (two spores each of two different, or ‘opposite', mating types, called ‘a' and ‘a'), which are resistant to desiccation and other environmental stresses (see Herskowitz, 1988, for a review of the yeast life cycle). Upon resumption of nutrient availability and beneficial environmental conditions, the haploid spores can germinate (become metabolically active) and then divide and continue to grow asexually, or - when and if they come into contact with a haploid cell of the opposite mating type - they can undergo cell fusion and mating

Life cycle of S

Figure 5.1 Life cycle of S. cerevisiae. Yeast cells can exist in both a haploid and diploid state. Haploid cells, shown on the left side of the figure, are either mating type ‘a’ or mating type ‘a’; haploids are capable of fusing to and mating with a cell of the opposite mating type (centre-left of figure; see also Fig. 5.3A), resulting in a diploid cell that now contains the genetic material (chromosomes) from both parental haploids. The resulting diploid cell is heterozygous for the mating-type locus, and thus is called ‘a/a’, a situation that makes them incapable of mating. In nutrient-rich conditions, HO-deficient haploid cells (see main text), and all diploid cells, can proliferate by asexually (i.e. clonally) ‘budding off’ new daughter cells by mitotic division, as indicated by the circular arrowed cycles. When exposed to certain nutrient-poor conditions, diploids can undergo sporulation (meiosis followed by spore formation; right side), resulting in the conversion of a diploid cell into four haploid spores: two spores possessing mating type ‘a’ and two possessing mating type ‘a’. The spores can germinate into haploid cells when conditions improve (top and bottom arrows leading back to haploid cycles). The ‘sexual phase’ of yeast reproduction encompasses both the mating and fusion of the opposite-mating-type haploid cells that results in a diploid cell containing the genetic material of the 2 parents in a single nucleus, as well as the subsequent meiotic division of the diploid cell, which results in recombination, or genetic exchange, between the two parental sets of chromosomes, and yields 4 haploid cells whose chromosomes are recombinant, i.e. containing portions of each parental DNA (note; meiotic recombination is not indicated in this figure).

(conjugation) with that other cell to form a new diploid cell (see Merlini et al., 2013, for review). Normal (‘wild-type') haploid cells contain an enzyme, HO endonuclease, that causes a ‘mother' cell (i.e. a cell that has given rise to a newly budded ‘daughter' cell formed after mitotic, i.e. asexual, cell division) to switch its mating type to the opposite of that of the daughter cell (Cosma, 2004; Haber, 2012). This allows the mother and daughter haploid cells, which are in close proximity and of opposite mating types, to mate and regenerate the diploid genome very quickly after sporulation. This behaviour has been postulated as not merely acting to restore diploidy, per se, but instead to quickly restore to cells that are germinating in uncertain or variable environments the ability to make stress- resistant spores if nutrient levels fall again (Knop, 2006; Hanson et al., 2014). After mating, the resulting diploid cells are a/a - in this state they do not express either mating type and therefore do not mate with other cells, and the HO gene (which encodes HO endonuclease) is turned off. However, haploid cells with a disabling mutation in the HO gene, such as laboratory strains with a natural HO gene mutation, or any strain that has been genetically modified to introduce an HO gene mutation, will produce daughter cells that do not switch their mating type; these types of yeast strains can exist indefinitely as free-living, mitotically dividing, mating-competent haploids of a particular mating type. Note that if these cells do encounter a cell of the opposite mating type, they are able to mate with it and form a diploid cell. However, since virtually all brewing-related yeast strains do not have HO gene mutations and cannot exist as free-living, mating-competent haploids, this chapter will not discuss any types of yeast breeding and/or genetic manipulations that require such cells.

 
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