Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system

Abstract

The budding yeast Saccharomyces cerevisiae is a powerful model organism for studying fundamental aspects of eukaryotic cell biology. This Primer article presents a brief historical perspective on the emergence of this organism as a premier experimental system over the course of the past century. An overview of the central features of the S. cerevisiae genome, including the nature of its genetic elements and general organization, is also provided. Some of the most common experimental tools and resources available to yeast geneticists are presented in a way designed to engage and challenge undergraduate and graduate students eager to learn more about the experimental amenability of budding yeast. Finally, a discussion of several major discoveries derived from yeast studies highlights the far-reaching impact that the yeast system has had and will continue to have on our understanding of a variety of cellular processes relevant to all eukaryotes, including humans.

Keywords: Saccharomyces cerevisiae; education; primer; yeast.

Figure 1

Budding yeast cells. (A) Confocal fluorescence microscopy of haploid yeast expressing Spc42-GFP (green: spindle pole body marker) and Histone H2-mCherry (red: nuclear marker). The yeast strain was constructed by Shawnecca Burke, an undergraduate in M.E.M.’s research laboratory by crossing strains kindly provided by Jan Skotheim (Stanford University) and Mark Winey (University of Colorado at Boulder) (photo by Mary Miller). (B) Epifluorescence microscopy of diploid yeast cells expressing Spt16-GFP, a nuclear protein. The yeast strain was generated by students in A.A.D.’s Spring 2005 Advanced Cell Biology class (photo by Andrea Duina). (C) Electron microscopy of dividing yeast cells (photo by Christine Walls). Note that buds are visible emerging from some of the cells in each of the panels. Unbudded cells are ∼5 μm in diameter.

Figure 2

A simplified life cycle diagram of laboratory budding yeast. Haploid yeast cells can be one of two mating types: MATa (a cell) or MATα (α cell). These cells can undergo mitotic cell division through budding, producing daughter cells. In laboratory strains, the mating type of haploid cells is stable due to the absence of a functional HO endonuclease. The two cell types release pheromones, initiating the formation of schmoos and subsequent mating, resulting ultimately in a stable diploid MATa/MATα (a/α cell). Diploid cells also divide mitotically by budding to produce genetically identical daughter cells. Under nitrogen-poor conditions, diploids are induced to undergo meiosis, forming four haploid spores, which can germinate into two MATa cells and two MATα cells.

Figure 3

Cartoon representation of the S. cerevisiae chromosome III and simplified view of the change that it undergoes following a mating-type switching event. In a haploid MATa cell, the MAT locus on chromosome III houses the MATa allele (top). During a mating-type switching event, the genetic information at HMLα is used to replace the MATa allele at the MAT locus with the MATα allele. The resulting chromosome III (bottom) expresses MATα information, which causes the cell to become phenotypically MATα. A similar mating-type switching mechanism operates during the switch of MATα cells into MATa cells. The genetic elements shown in the diagram (HMLα, CEN, MATa, MATα, and HMRa) and their relative positions across the chromosome are depicted roughly to scale (note that chromosome III is 316,620 bp in length). The asterisks next to MATa and MATα highlight the fact that these alleles are actively expressed, as opposed to the alleles present at the HMLα and HMRa loci that are transcriptionally silent.

Figure 4

One-step gene replacement and analysis of meiotic products through tetrad analysis. (A) Deletion of KIR1. Step 1: A KIR1 homozygous diploid cell (KIR1/KIR1: only the cell nucleus is shown here) is transformed with a linear DNA molecule (usually generated by PCR) containing a selectable marker gene flanked by regions identical in sequence to those that flank the endogenous KIR1 gene (red regions in the center panel). Step 2: Following homologous recombination between the introduced DNA fragment and one of the two KIR1 genes, the transformed cell is heterozygous for the KIR1 gene and its genotype is KIR1/kir1∆. (B) Generation of spores, tetrad manipulation, and tetrad analysis. The KIR1/kir1∆ cell from A is then triggered to undergo meiosis through nitrogen starvation to produce a tetrad—a set of four spores encased in an ascus sac. Step 1: The ascus membrane is partially digested and, through the use of a light microscope equipped with a micromanipulator, the four spores are released and placed in a row onto permissive solid growth medium and allowed to germinate; note that no cells are visible to the naked eye immediately after this manipulation on the growth medium (the dark rectangle is a photograph of a section of a growth plate as it would look after the tetrad dissection). Step 2: Following ∼3 days of incubation at 30°, the germinated spores give rise to visible colonies on the growth medium (the photograph shows actual yeast colonies derived from germinated spores). Step 3: The colonies are then replica-plated to solid growth medium containing Kill-It and allowed to incubate at 30° for 2 days. The 2:2 growth pattern of the colonies on the drug plate (two alive and two unable to grow) is consistent with classic Mendelian segregation of a heterozygous trait and can be used to infer the genotypes of the cells in each colony (and, by extension, of the original spores) as indicated to the right of the photograph. (Given the hypothetical nature of the experiment, it should be noted that the actual genotypes of the cells photographed in this figure are not as indicated in the figure and that the medium in the last photograph does not contain Kill-It.)

Figure 5

The yeast two-hybrid system. (A) (Top) Representation of the yeast Gal4 transcription activator with the DNA-binding and transcription activation domains colored in different shades of blue, as indicated. (Bottom) Representations of two hypothetical hybrid proteins. The bait consists of a fusion of the Gal4 DNA-binding domain and protein X (orange), and the prey consists of the Gal4 activation domain fused to protein Y (green). (B) (Left) Hypothetical scenario in which proteins X and Y do not interact with each other. In this case, the bait protein is recruited to the regulatory region of a reporter gene (lacZ) but is unable to activate transcription without an activation domain. Yeast colonies derived from such cells remain white when grown in the presence of X-gal, a substrate for the lacZ product. (Right) Hypothetical scenario in which proteins X and Y physically interact with each other. The bait, bound to the regulatory region of the reporter gene, recruits the prey through an interaction between proteins X and Y, which in turn activates lacZ transcription through its activation domain. Colonies derived from these cells will turn blue when grown in the presence of X-gal. Thus, interaction between proteins X and Y can easily be tested by monitoring yeast colony color. Note that interactions between bait and prey proteins may not necessarily be direct but may be mediated by bridging proteins. Since proteins X and Y can be derived from any source, interactions between proteins from any species may be assessed using this system.