A model organism in genetics, genomics and systems biology

[Pages:31]The yeast Saccharomyces cerevisiae

A model organism in genetics, genomics and

systems biology

Statement

"....the reason that yeast could serve as a model for all eukaryotic biology derives from the facility with which the relation between gene structure and protein function can be established." (Botstein and Fink, Science 1988).

"...yeast has graduated from a position as the premier model for eukaryotic cell biology to become the pioneer organism ... of the entirely new fields of study called "functional genomics" and "systems biology." These new fields look beyond the functions of individual genes and proteins, focusing on how these interact and work together to determine the properties of living cells and organisms." (Botstein and Fink, Genetics 2011).

Content

Yeast is a eukaryotic organism The yeast genome, definitions and gene ontology Foundations for model organism: tools for genetic tractability Defining function: functional genomics and networks The concepts of yeast strains and variability SGD: The Saccharomyces Genome Database

The yeast Saccharomyces cerevisiae: habitate, importance and use

Yeast lives primarily on fruits, flowers and other sugar containing substrates Free-living organism: yeast copes with a wide range of environmental conditions:

Temperatures from freezing to about 55?C are tolerated Yeasts proliferate from 12?C to 40?C Growth is possible from pH 2.8-8.0 Almost complete drying is tolerated (dry yeast) Yeast can still grow and ferment at sugar concentrations of 3M (high osmotic pressure) Yeast can tolerate up to 20% alcohol Saccharomyces cerevisiae is the main organism in wine production besides other yeasts; reason is the enormous fermentation capacity, low pH and high ethanol tolerance. Saccharomyces cerevisiae (carlsbergensis) is the beer yeast because it ferments sugar to alcohol even in the presence of oxygen, lager yeast ferments at 8?C. Saccharomyces cerevisiae is the yeast used in baking because it produces carbon dioxide from sugar very rapidly. Saccharomyces cerevisiae is used to produce commercially important proteins because it can be genetically engineered, it is regarded as safe and fermentation technology is highly advanced. Saccharomyces cerevisiae is the most important eukaryotic cellular model system because it can be studied by powerful genetics. Pioneers of genomics, functional genomics, systems and synthetic biology employ S. cerevisiae.

Saccharomyces cerevisiae is a eukaryote

Belongs to fungi, ascomycetes Unicellular organism with ability to produce pseudohyphae S. cerevisiae divides by budding (hence: budding yeast) while

Schizosaccharomyces pombe divides by fission (hence: fission yeast). Budding results in two cells of unequal size, a mother (old cell) and a daughter (new cell). Yeast life is not indefinite; yeast cells age and mothers die after about 30-40 divisions. Cell has a eukaryotic structure with different organelles:

Cell wall consisting of glucans, mannans and proteins Periplasmic space with hydrolytic enzymes Plasma membrane consisting of a phospholipid

bilayer and many different proteins Nucleus with nucleolus Vacuole as storage and hydrolytic organelle Secretory pathway with endoplasmic reticulum, Golgi

apparatus and secretory vesicles Peroxisomes for oxidative degradation Mitochondria for respiration

A yeast cells is about 4-7?m large The "eyes" at the bottom are bud scars

Life cycle of yeasts: yeast has a sex life

Yeast cells can proliferate both as haploids (1n, one copy of each chromosome) and as diploids (2n, two copies of each chromosome).

Haploid cells have one of two mating types: a or alpha (). Two haploid cells can mate to form a zygote from which a

diploid cell buds off. Under nitrogen starvation diploid cells undergo meiosis and

sporulation to form an ascus with four haploid spores. Those germinate to form haploid cells. Hence, the properties of the meiotic products can be studied

directly.

Yeast: a unicellular organisms with different cell types!

Thus, although yeast is unicellular, we can distinguish different cell types with different genetic programmes:

Haploid MATa versus MAT (can respond to pheromone, can mate; cannot do meiosis)

Haploid versus Diploid (MATa/alpha) (cannot respond to pheromone or mate, can sporulate)

Spores (survival structures)

Mothers and daughters (age n+1, can switch mating type, ago 0)

Yeast sex!

Central to sexual communication is the pheromone response signal transduction pathway.

All modules of that pathway consist of components conserved from yeast to human.

The pathway consists of a specific pheromone receptor, that binds a- or -factor; it belongs to the class of seven transmembrane G-protein coupled receptors, like many human hormone receptors.

Binding of pheromone stimulates reorientation of the cell towards the source of the pheromone (the mating partners).

Binding of pheromone also stimulates a signalling cascade, a so-called MAP (Mitogen Activated Protein) kinase pathway, similar to many pathways in human (animals and plants).

This signalling pathway causes cell cycle arrest to prepare cells for mating (cells must be synchronised in the G1 phase of the cell cycle to fuse to a diploid cell).

The pathway controls expression of genes important for mating.

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