Budding Yeast Saccharomyces Cerevisiae as a Model Genetic Organism

Abstract

Budding yeast has served as an experimental organism for genetic research for over 50 years. The yeast shares a common cell division cycle and cellular architecture with other eukaryotes, and as a microorganism, it is easily propagated and manipulated in the laboratory. An intense focus on the central dogma, the cell cycle and sexual reproduction unleashed new fields including gene silencing, homologous recombination and differential gene expression, among others. The ease of genetic analysis allowed researchers to study processes to a degree not seen for other model organisms. As was often the case, new techniques were developed in yeast that are now broadly used. Budding yeast was the first eukaryote to be sequenced, which, in turn, led to genome‐wide analyses to map gene networks common to all life. Research on yeast has also informed us on the molecular basis of human diseases from birth defects to neurodegenerative disorders.

Key Concepts

  • Budding yeast is nonpathogenic, easy to grow and amenable to genetic analysis.
  • Core cellular functions and cell architecture are highly conserved with other eukaryotes.
  • Genes from other species can be expressed in yeast and function in place of the homologous yeast gene.
  • Sexual reproduction allows for genetic recombination and recovery of haploid yeasts expressing recessive phenotypes.
  • Homologous recombination is used to facilitate genome engineering.
  • Many tools used in molecular biology were developed in yeast (e.g. yeast two‐hybrid assay).
  • Budding yeast was the first eukaryote to have its entire genome sequenced.
  • A vast amount of yeast information has been catalogued in the Saccharomyces Genome Database (SGD) and is readily accessible to anyone.
  • The yeast knockout collection has been used for genome‐wide studies of gene function.

Keywords: Saccharomyces cerevisiae; budding yeast; homologous recombination; mating type; gene knockout; tetrad analysis; synthetic lethality; autonomously replicating sequence (ARS); yeast artificial chromosome (YAC); Saccharomyces Genome Database (SGD)

Figure 1. The life cycle of Saccharomyces cerevisiae. Cells can be grown vegetatively as haploids or diploid. Sporulation is a cellular pathway that is induced by limited nutrients. The output of sporulation is four haploid spores (tetrad) that is encased in an ascus coat.
Figure 2. Schematic of genome engineering strategies using homologous recombination. YFG is ‘Your Favorite Gene’ and URA3 is used as a selectable marker. (a) Two‐step allele replacement to replace the wild‐type allele of YFG1 with a mutated allele. For the first step, a strain with the wild‐type YFG1 allele is transformed with a plasmid bearing the mutated Y*G1 allele and the URA3 selectable marker. Transformed cells that have integrated the plasmid DNA (deoxyribonucleic acid) sequences into the chromosome by homologous recombination can be selected by growth on media lacking uracil. For the second step, a recombination event between homologous regions will loop out the duplicated sequences and depending on the placement of the recombination event, the mutation will remain in the chromosome. Although this excision event is rare, the relevant strain can be isolated through negative selection against the presence of URA3 by plating on media containing 5‐FOA (5‐fluorouracil‐6‐carboxylic acid monohydrate; 5‐fluororotic acid). Cells containing URA3 will die as the Ura3 enzyme will convert 5‐FOA to a product that is toxic to the cell. (b) Allele replacement using a linear DNA fragment with a selectable marker flanked by regions of homology that target integration in place of the wild‐type allele. Note that a region of YFG1 is missing in this fragment. (c) Gene conversion to copy information from the chromosome to a plasmid. Before transformation, a plasmid is cut with restriction enzymes to create a gap in the YFG1 sequence. This gap is filled with the wild‐type sequences in the chromosome by homologous recombination. Note that this plasmid has both CEN and ARS sequences so that it can be stably propagated in the cell.
Figure 3. Spore clones of dissected tetrads from a wild‐type strain on nutrient‐rich media containing yeast extract, peptone and dextrose (YPD) and grown for 2 days at 30 °C. Each colony arose from a single spore of a tetrad. The middle line of cells represents the pool of cells that was used to find tetrads for microdissection.
Figure 4. Meiotic segregation in the budding yeast. (a) Cross between two mutants, yfg1 × yfg2. The white and black boxes represent the mutant alleles of yfg1 and yfg2, respectively. The black circle represents the centromere. (b) Schematic of chromosomes after DNA replication and the pairing of homologous chromosomes. (c) Schematic of three possible chromosome configurations after recombination and synapsis. CO stands for crossover. (d) Tetrad classes resulting from a given crossover event are represented with the genotype indicated in the spore. Not shown: two‐strand double crossovers result in PD (parental ditype); three‐strand double crossovers result in TT (tetratype).
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References

Brar GA and Weissman JS (2015) Ribosome profiling reveals the what, when, where and how of protein synthesis. Nature Reviews. Molecular Cell Biology 16: 651–664.

Costanzo M, VanderSluis B, Koch EN, et al. (2016) A global genetic interaction network maps a wiring diagram of cellular function. Science 353. pii: aaf1420.

Cramer P, Bushnell DA, Fu J, et al. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288: 640–649.

Dekker J, Rippe K, Dekker M and Kleckner N (2002) Capturing chromosome conformation. Science 295: 1306–1311.

Duan Z, Andronescu M, Schutz K, et al. (2012) A genome‐wide 3C‐method for characterizing the three‐dimensional architectures of genomes. Methods 58: 277–288.

Fields S and Song O (1989) A novel genetic system to detect protein‐protein interactions. Nature 340: 245–246.

Gallone B, Steensels J, Prahl T, et al. (2016) Domestication and divergence of Saccharomyces cerevisiae Beer Yeasts. Cell 166: 1397.

Giaever G and Nislow C (2014) The yeast deletion collection: a decade of functional genomics. Genetics 197: 451–465.

Gottschling DE, Aparicio OM, Billington BL and Zakian VA (1990) Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63: 751–762.

Greig D and Leu JY (2009) Natural history of budding yeast. Current Biology 19: R886–R890.

Haber JE (2012) Mating‐type genes and MAT switching in Saccharomyces cerevisiae. Genetics 191: 33–64.

Hartwell LH, Culotti J and Reid B (1970) Genetic control of the cell‐division cycle in yeast. I. Detection of mutants. Proceedings of the National Academy of Sciences of the United States of America 66: 352–359.

Heinicke S, Livstone MS, Lu C, et al. (2007) The Princeton Protein Orthology Database (P‐POD): a comparative genomics analysis tool for biologists. PLoS One 2: e766.

Heitman J, Movva NR and Hall MN (1991) Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253: 905–909.

Heitman J, Koller A, Kunz J, et al. (1993) The immunosuppressant FK506 inhibits amino acid import in Saccharomyces cerevisiae. Molecular and Cellular Biology 13: 5010–5019.

Huh WK, Falvo JV, Gerke LC, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686–691.

Keeney S, Giroux CN and Kleckner N (1997) Meiosis‐specific DNA double‐strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88: 375–384.

Ma J and Ptashne M (1987) Deletion analysis of GAL4 defines two transcriptional activating segments. Cell 48: 847–853.

Maxmen A (2017) Synthetic yeast chromosomes help probe mysteries of evolution. Nature 543: 298–299.

Murray NE and Gann A (2007) What has phage lambda ever done for us? Current Biology 17: R305–R312.

Nagalakshmi U, Wang Z, Waern K, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344–1349.

Nizhnikov AA, Antonets KS, Inge‐Vechtomov SG and Derkatch IL (2014) Modulation of efficiency of translation termination in Saccharomyces cerevisiae Turning nonsense into sense. Prion 8: 247–260.

Novick P, Field C and Schekman R (1980) Identification of 23 complementation groups required for post‐translational events in the yeast secretory pathway. Cell 21: 205–215.

Outeiro TF and Lindquist S (2003) Yeast cells provide insight into alpha‐synuclein biology and pathobiology. Science 302: 1772–1775.

Poloumienko A, Dershowitz A, De J and Newlon CS (2001) Completion of replication map of Saccharomyces cerevisiae chromosome III. Molecular Biology of the Cell 12: 3317–3327.

Rine J and Herskowitz I (1987) Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116: 9–22.

Shampay J, Szostak JW and Blackburn EH (1984) DNA sequences of telomeres maintained in yeast. Nature 310: 154–157.

Siliciano PG, Brow DA, Roiha H and Guthrie C (1987) An essential snRNA from S. cerevisiae has properties predicted for U4, including interaction with a U6‐like snRNA. Cell 50: 585–592.

Spellman PT, Sherlock G, Zhang MQ, et al. (1998) Comprehensive identification of cell cycle‐regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9: 3273–3297.

Stearns T and Botstein D (1988) Unlinked noncomplementation: isolation of new conditional‐lethal mutations in each of the tubulin genes of Saccharomyces cerevisiae. Genetics 119: 249–260.

Szostak JW, Orr‐Weaver TL, Rothstein RJ and Stahl FW (1983) The double‐strand‐break repair model for recombination. Cell 33: 25–35.

Tsukada M and Ohsumi Y (1993) Isolation and characterization of autophagy‐defective mutants of Saccharomyces cerevisiae. FEBS Letters 333: 169–174.

Tuite MF, Dobson MJ, Roberts NA, et al. (1982) Regulated high efficiency expression of human interferon‐alpha in Saccharomyces cerevisiae. EMBO Journal 1: 603–608.

Vijayraghavan U, Parker R, Tamm J, et al. (1986) Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO Journal 5: 1683–1695.

Further Reading

Cherry JM, Ball C, Dolinski K, et al. (2017) Saccharomyces Genome Database. http://genome‐www.stanford.edu/Saccharomyces/

Botstein D (1993) A phage geneticist turns to yeast. In: Hall MN and Linder P (eds) The Early Days of Yeast Genetics. Cold Spring Harbor: Princeton.edu.

Botstein D and Fink G (2011) Yeast: an experimental organism for 21st century biology. Genetics 189 (3): 695–704.

Duina AA, Miller ME and Keeney JB (2014) Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system. Genetics 197 (1): 33–48.

Rine J (2014) The future of a model organism model. Molecular Biology of the Cell 25: 549.

Michels CA (2002) Genetic Techniques for Biological Research: A Case Study Approach. West Sussix: Wiley.

Sherman F (1998) An Introduction to the Genetics and Molecular Biology of the Yeast Saccharomyces cerevisiae. http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html

The official website of the Nobel Prize: Nobelprize.org

Usaj M, Tan Y, Wang W, et al. (2017) TheCellMap.org: a web‐accessible database for visualizing and mining the global yeast genetic interaction network. G3 (Bathesda, Md.) 7 (5): 1539–1549.

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Burgess, Sean M, and Powers, Ted(Nov 2017) Budding Yeast Saccharomyces Cerevisiae as a Model Genetic Organism. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000821.pub2]