Saccharomyces cerevisiae

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A Microbial Biorealm page on the genus Saccharomyces cerevisiae

Saccharomyces cerevisiae.
Numbered ticks are 11 µM apart.
Photograph by Bob Blaylock.

Contents

Classification

Higher order taxa

Domain: Eukarya
Kingdom: Fungi
Subkingdom: Dikarya
Phylum: Ascomycota
Subphylum: Saccharomycotina
Class: Saccharomycetes
Order: Saccharomycetales
Family: Saccharomycetaceae
Genus: Saccharomyces
Species: Cerevisiae

Species

Taxonomy of Saccharomyces cerevisiae

Major Strains of Saccharomyces cerevisiae

1. Wild-type Strains

Saccharomyces boulardii: Formerly used as a probiotic used to treat diarrhea caused by bacteria. Clinical tests have demonstrated that this and a species of S. cerevisiae were genetically identical. (1)

Saccharomyces uvaruium: Used in fermenting lager-type beer. Due to a recent reclassification, this species is now considered to be another wild-type strain. (2)

2. Laboratory Strains

While S. cerevisiae contains many different strains used in research, below are some of the strains most commonly used in laboratories. The choice of which strain to use depends on what part of the organism is being studied.

S288c: This strain was isolated in the 1950's by Robert K. Mortimer through genetic crosses. It was used as a parental strain when isolating mutants (3). S288c was the strain used when the genome of S. cerevisiae was fully sequenced in 1996. However, its low rate of sporulation and the lack of protein growth in the absence of nitrogen prompted scientists to pick alternative strains for their research. (4)

A634A: Used in cell cycle studies. It is also closely related to S288c due to a cross with S288c and another unknown strain. (4)

BY4716: Since this is nearly identical to S288c, it is often used as a reference or control stain. (4)

CEN.PK: In Europe, this is used as a secondary reference strain alongside S288c when studying the yeast genome. Additionally, it can grow well on several different carbon sources as well as under anaerobic conditions. It is used when studying rates of growth and product formation.(5)

∑1278b: What distinguishes this strain is that it contains genes unique for nitrogen metabolism. (6). It is best studied when nitrogen is limited; cells become elongated and undergo a unique budding pattern where cells remain physically attached to each other. This is known as pseudohyphal growth. (4)

SK1: Because this strain produces lots of spores, it is used in meiotic studies. (7)

W303: Closely related to S288c due to a cross between S288c and an unknown strain, (4), it is used in genetic and biochemical analysis. (7).

Description and significance

Saccharomyces cerevisiae is an eukaryotic microbe. More specifically, it is a globular-shaped, yellow-green yeast belonging to the Fungi kingdom, which includes multicellular organisms such as mushrooms and molds. Natural strains of the yeast have been found on the surfaces of plants, the gastrointestinal tracts and body surfaces of insects and warm-blooded animals, soils from all regions of the world and even in aquatic environments (8). Most often it is found in areas where fermentation can occur, such as the on the surface of fruit, storage cellars and on the equipment used during the fermentation process (9)

S. cerevisiae is famously known for its role in food production. It is the critical component in the fermentation process that converts sugar into alcohol, an ingredient shared in beer, wine and distilled beverages. It is also used in the baking process as a leavening agent; yeast releasing gas into their environment results in the spongy-like texture of breads and cakes. Because of its role in fermentation, humans have known about and used Saccharomyces cerevisiae for a long time. Archaeologists have found evidence of a fermented beverage in a pot in China as early as 7000BC (10), and molecular evidence of yeast being used in fermentation was found in a wine jar dating back to 3150BC (11).

Isolation of the species did not occur until 1938, when Emil Mrak isolated it from rotten figs found in Merced, California. (3). Taking advantage of its unique reproductive cycle, Robert Mortimer performed genetic crosses that used the isolated fig strain and other yeast strains obtained through other researchers. As a result, he created a new strain called S288c (3), which was then used as a parental strain in order to isolate most of the mutant strains currently used in research (3). Furthermore, this strain was then used to sequence the S. cerevisiae genome (9).

S. cerevisiae is also considered to be a "model organism" by scientists. Its big advantage is that it is both a unicellular and eukaryotic organism. As a eukaryote, a majority of the yeast genes and proteins have human homologs (12), and a greater understanding of the yeast genome would also help scientists understand the human genome. Another advantage is its fast growth grate. On a normal yeast medium, it takes 90 minutes for the yeast population to double. (13), and colonies are usually visible 2-3 days after placing them on fresh medium. Since the complete genome sequence is now available, mutants unique to eukaryotic organisms can now be expressed in an eukaryote as opposed to studying a similar gene in prokaryotes.

Genome structure

On April 24, 1996, the complete yeast genome sequence was available to the public. The genome contains 12,068 kilobases contained in sixteen linear chromosomes. (12). Unlike prokaryotes, DNA is concentrated in the nucleus, and are grouped into chromosomes during DNA replication. 70% the genome contains of open reading frames (ORF's), DNA sequences that would code for a protein, and the average ORF length is about 1450 bp long (14). Relative to more complex eukaryotes like nematodes (6kb) and humans (30kb), the yeast genome is more compact(12). In the genome, 5,885 genes code for proteins, 275 code for tRNA, 40 code for snRNA's, and 140 genes on chromosome 12 code for ribosomal RNA. 4% of the genome is comprised of introns, which are pieces of mRNA cut by snRNA-protein complexes prior to translation(12). Out of all the genes that code for proteins, 11% of the protenome is devoted to metabolism, 3% to energy production and storage, 3% to DNA replication, 7% to transcription and 6% to translation. Nearly 430 proteins are involved in intracellular trafficking, and 250 proteins have structural roles.

Protein-coding genes have been documented in the genome, but so far a few of those genes have been identified. Furthermore, the genome also shows signs of two or more copies of a gene in different locations. The genes that code for citrate synthase, an enzyme that converts acetyl CoA and oxaloacetate to citrate, is located in three different chromosomes. Chromosome 3 encodes the enzyme in the peroxidase, chromosome 12 encodes the enzyme in the mitochondria and another copy of the gene is located in chromosome 16. (12). One reason for the redundancy in the genome could be that multiple copies of a yeast gene are required in order for it to survive in its natural habitat (12).

Using the completed genome, scientists have reconstructed the metabolic network of S. cerevisiae. 708 ORF's were identified to take part in metabolism, with the possibility to conduct 1035 metabolic reactions. (15). More than 85% of these reactions involved transport in and out of the cytoplasmic or mitochondrial membrane, and the other reactions were mainly involved in the metabolism of amino acids, nucleotides and vitamins. (15). Additionally, ORF's involved in metabolism have been classified based on the pathway they are most involved with. Most ORF's take part in the electron transport chain and chemiosmosis, the final steps of aerobic respiration, followed by the breakdown of bigger carbohydrates. (15).

The mitochondrial DNA sequence has been attempted, but it is incomplete and contains many errors. The mitochondrial genome is about 85,000 base pairs long and contains seven hypothetical ORF's. Further experiments will determine if any of the seven ORF's are expressed in the mitochondria. In addition to the ORF's, the genome contains genes for three subunits of complex IV used in the electron transport chain, and three subunits of ATP synthase. (16).

S. cerevisiae strain A364A also contains a 2um circle plasmid. It is 6,318 base pairs long and constitutes 3% of the yeast genome. (17). Although the sequence contains coding regions for three proteins, the exact identity or function of the proteins is unknown. Like nuclear chromosomes, the plasmid is comprised of chromatin and histones, and can condense itself during mitosis. Unlike bacterial plasmids, which replicate independently of the bacterial chromosome, it replicates only once during the S phase of the cell cycle, and is regulated by the same genes that regulate nuclear DNA replication (17). While there is no evidence that it can integrate into chromosomal DNA, the yeast plasmid is capable of acting as vector in yeast transformation. (17). Foreign DNA extracted from eukaryotes could now be inserted directly into an eukaryote.

Cell structure and metabolism

Saccharomyces cerevisiae can exist in two different forms: haploid or diploid. It is usually found in the diploid form. (11). The diploid form is ellipsoid-shaped with a diameter of 5-6um, while the haploid form is more spherical with a diameter of 4um. (13). In exponential phase, haploid cells reproduce more than diploid cells. Haploid and diploid cells can reproduce asexually in a process called budding, where the daughter cell protrudes off a parent cell. The buds of haploid cells are adjacent to each other, while the buds of diploid cells are located in opposite poles. (13). Additionally, diploid cells can exhibit pseudohyphal growth if it is growing on a poor carbon source, exposed to heat or high osmolarity. Activated by cAMP, newly developed cells remain attached to the parent cell through a septum. (18).

In addition to budding, diploid cells can undergo a meiotic process called sporulation to produce four haploid spores. Haploid spores can be one of two mating type, a or α. These spores can also undergo budding to produce more haploid cells. a and α cells can also mate and fuse together, producing a diploid cell. S. cerevisiae strains are further distinguished by differences in the haploid stage. In heterothallic strains, the spores resulting from sporulation cannot undergo budding, and their mating type cannot be changed. . However, in homothallic strains, the presence of a HO gene allows the spores to change mating type as they grow (11). Sporulation can be induced if the yeast is exposed to either a poor carbon or nitrogen source or lack of a nitrogen source. Spores also have a higher tolerance to conditions such as high temperature. (11).

As a eukaryote, S. cerevisiae contains membrane-bound organelles. Its chromosomes are located in the nucleus, and it uses mitochondria to conduct cellular respiration. Like all other fungi, the cell's shape is based on its cell wall. The cell wall protects the cell from its environment as well as from any changes in osmotic pressure. The inner cell wall has a high concentration of β-glucans, while the outer cell wall has a high concentration of mannoprotein. Chitin is usually located in the septum. (19).

S cerevisiae can live in both aerobic as well as anaerobic conditions. In the presence of oxygen, yeast can undergo aerobic respiration, where glucose is broken to CO2 and ATP is produced by protons falling down their gradient to an ATPase. When oxygen is lacking, yeast only get their energy from glycolysis and the sugar is instead converted into ethanol, a less efficient process than aerobic respiration. The main source of carbon and energy is glucose, and when glucose concentrations are high enough, gene expression of enzumes used in respiration are repressed and fermentation takes over respiration (2). However, yeast can also use other sugars as a carbon source. Sucrose can be converted into glucose and fructose by using an enzyme called invertase, and maltose can be converted into two molecules of glucose by using the enzyme mannase (2).

Ecology

It has been difficult to observe and collect Saccharomyces cerevisiae outside areas of human contact, so not much research has been done on its interactions in natural environments. Because it is rarely associated with any other environments other than areas that are close to sites of fermentation, people have wondered whether the yeast could ever be found in the wild. (19). So far, most interactions with its environment have been limited to fermentation. In 1871, Louis Pasteur discovered that grapes had to be crushed in order for fermentation to occur (9). The grape itself has been an ideal habitat for yeast due to its high sugar concentration and low pH, precluding the growth of rival species. (8). Despite this, not many intact grapes contain S. cerevisiae at any one time. In an estimate, only one intact grape berry has the yeast on its surface. (3).

While intact grapes have little to no yeast present on the skin, damaged grapes are more likely to contain the yeast as well as other organisms. Berries were damaged due to the weather, mold infections or birds feeding on the grapes. Additionally, insects may also appear more often if the berry is already damaged. (3) These insects would harbor the yeast in their bodies and deposit them unknowingly while feeding, and the yeast would divide upon exposure to the grape. While it is known that insects harbor microorganisms inside their bodies, it is unknown how yeast is introduced into the insect. (3).

Pathology

Saccharoyces cerevisiae is not normally considered to be a pathogen. In healthy people, disease resulting from S. cerevisiae colonizing in a particular area are very rare, but have been reported. While yeast that normally colonize in the GI tract are not the direct cause of any disease, hypersensitivity to antibodies produced against could prove an irritant for people with Crohn's disease, an autoimmune disorder. (20). 1% of all vaginal yeast infections occur due to S. cerevisiae in the vagina, but symptoms associated with it are identical to the symptoms caused due to another organism more commonly associated with yeast infections, Candida albicans. (21). The only people susceptible to serious problems are immunosuppressed individuals, followed by those who have taken S. cerevisiae as an probiotic for diarrhea. For these individuals, the prevailing condition is fungemia (1). Caused by the presence of yeasts in the blood, its symptoms have been described as "flu-like".

Application to Biotechnology

1. Ethanol Production

One of the oldest applications of Saccharomyces cerevisiae in biotechnology is its role the creation of alcoholic beverages. In a process called fermentation, yeast feeds off sugars from their substrate and convert it to ethanol, giving these beverages their alcoholic content. Depending on the beverage, yeast is incorporated into the creation process in several ways.

Winemakers select their yeast based on several factors: type of grape, local climate, geographical area and the desired taste of the final product. (2). Yeast is then produced in the winery, then added to the crushed grapes when it is time for fermentation. Champagne is an exception where natural yeast strains are used, since yeast goes directly into the bottle instead of a huge vat. (2). More gas is trapped in the bottle, creating sparkling wine.

In brewing beer, two different types of yeasts are produced in the fermentation process, depending on the type of beer created. Top-fermenting yeasts, also known as ale yeasts, form foam on top of the wort, the liquid containing the sugars used to be converted into ethanol. The yeast stays at the top of the tank, and begins to ferment at warm temperatures. This process is used in the creation of ales, porters, stouts and wheat beers. (2). Bottom-fermenting yeasts, also known as lagers yeast, ferment at cooler temperatures, and the yeast settle at the bottom of the tank. (2). They are used in the production of most commercial beers sold in America.

Another process is used to create the beverages collectively known as spirits, such as vodka and tequilla. Yeast used in the fermentation of these beverages are isolated from beet or sugar cane. Selection criteria for these yeasts include high ethanol production, have high tolerance to ethanol concentration, and must be able to ferment various substrates specific to the beverage.(2).

2. Food Production

S. cerevisiae also acts as a leavening agent. During preparation, dried yeast cells are added with the rest of the ingredients. While baking, yeast reacts with its environment and releases gas. This gas is trapped, forming holes as it bakes. This contributes to the spongy-like texture of breads and cakes seen after baking. While dried yeast cells include a leavening agent, unleavened yeast could also be used to add flavor to the bread. (2).

Yeast used to brew beer is still useful after the fermentation process. After fermentation is finished, the leftover yeast is dried and can be sold in liquid, tablet or powdered form. It is an excellent source of B vitamins, various minerals and proteins, and can be taken as a nutritional supplement (2). Yeast still contains these nutrients even after being broken down by its own enzymes, and the resulting yeast extract can be used as a flavor enhancer (2). One of the components of the famous food paste Vegemite contains yeast extract. Finally, S. cerevisiae has also been shown to survive living in the gastrointestinal tract while eliminating the potentially pathogenic bacteria residing. Since it does not colonize the GI tract permanently, it is used as a probiotic.

Current Research

Lantana camara used as substrate for fuel ethanol production

Research is being conducted to find economically viable methods to produce ethanol, a possible alternate fuel source to petroleum since it can be made from renewable resources. Currently, starch-containing plants are used for ethanol production, but starch production is limited. Cellulose, another complex sugar, is preferred over starch because it is the more abundant sugar in plants, but cellulose is harder to break down than starch. Since the breakdown of cellulose would be more costly than the breakdown down starch, an abundant source of cellulose would be needed to offset the cost of its breakdown. Lantana camara, a hard-to-eradicate weed, would be used as the cellulose source. L. camara was first pre-treated with the enzyme cellulase as well as various strong acids and bases to break up the cellulose. A heat tolerant strain of Saccharomyces cerevisiae found from India would be used to conduct fermentation. 97.4 grams of sugar would be used to make 42 grams of ethanol, giving an ethanol yield of 0·431 per gram with a fermentation efficiency of 84.36% Despite the presence of fermentation inhibitors, the by-product of cellulose breakdown, the high carbohydrate content of the weed and the efficiency of the yeast proved that it could be viable to produce ethanol from a more abundant resource. (22)

Increased glycolytic flux due to whole-genome duplication

Whole-genome duplication occurs when a cell replicates its DNA normally, but does not distribute its DNA equally during mitosis. While one copy is only needed for the organism to function, the excess genes are promptly deleted through mutations and gene loss. However, the genes coding for the enzymes involved in glycolysis have managed to survive in duplicate. This suggests that natural selection may have played a role in picking out yeast strains based on rapid growth on medium such as glucose. Surviving duplicate copies of the glycolytic enzymes would not only lead to increase glycolytic flux, but would eventually have the yeast prefer fermentation over aerobic respiration. This is possible since one unique aspect of S. cerevisiae is that even in oxygen, it would continue to convert sugar to ethanol despite being the more inefficient pathway in a glucose-rich environment (23).

Effects of Aneuploidy on Cellular Physiology and Cell Division in Haploid Yeast

Haploid cells of S. cerevisiae containing an extra copy of one or more chromosomes mated with another haploid cell with a normal amount of chromosomes, producing a diploid possessing three or more copies of the inherited chromosomes. To create yeast cells with additional chromosomes, researchers looked for haploid cells lacking the KAR1 gene, preventing nuclear fusion. Occasionally, chromosome transfer would still occur, and the union of this particular mating was then selected for. When compared with diploid yeast cells with the normal number of chromosomes, the aneuploid cells expressed unique traits. Doubling time was slightly increased in the aneuploids due to a delay in the G1 stage of the cell cycle. Aneuploid cells would also show increased glucose uptake mostly because as a result of extra chromosomes, certain genes located on the duplicated chromosome are overexpressed. In the presence of protein synthesis inhibitor chemicals such as cycloheximide, aneuploids were more likely to produce unfolded proteins. Since tumors in humans posses similar characteristics to yeast cells, studying phenotype expression in aneuploid yeast cells could provide a stepping stone to studying phenotypes in tumor cells (24).

References

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[2]. Bekatorou, A., Psarianos, C., and Koutinas, A.A. "Production of Food Grade Yeasts". Food Technology Biotechnology. 2006. Volume 44. p. 407–415

[3]. Mortimer, R.K., and Johnston, John R. "Genealogy of Principal Strains of the Yeast Genetic Stock Center". Genetics. 1986. Volume 113. p. 35-43

[4]. Schacherer, J., Ruderfer, D.M, Gresham, D., Dolinski, K., Botstein, D., and Kruglyak, L."Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains." PLoS ONE. 2007. 2(3): e322.

[5]. van Dijken, J.P., Bauerb, J., Brambillac, J., Dubocd, P., Francoise, J.M., Gancedof, C., Giusepping, M.L.F., Heijnenh, J.J., Hoarei, M., Langej, H.C., Maddenk, E.A., Niederbergerb, P., Nielsend, J., Parroue, J.L., Petitf, T., Porroc, D., Reussj, M., van Rielg, N., Rizzij, M., Steensmaa, H.Y., Verripsg, C.T., Vindeløvd, J., and Pronka, J.T. "An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains". Enzyme and Microbial Technology. 2000. Volume 26. p. 706-714.

[6]. Nomura, M., Nakamori, S., and Takagi, H. "Characterization of Novel Acetyltransferases Found in Budding and Fission Yeasts That Detoxify a Proline Analogue, Azetidine-2-Carboxylic Acid". J. Biochem. 2003. Volume 133. p. 67-74.

[7]. Williams, R.M., Primig, M., Washburn, B.K., Winzeler, E.A., Bellis, M., Sarrauste de Menthière, C., Davis, R.W., and Esposito, R.E. "The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast" The National Academy of Sciences. 2002. Volume 99. p. 13431–13436.

[8]. Martini, A. "Origin and Domestication of the Wine Yeast Saccharomyces cerevisiae". Journal of Wine Research. 1993. Volume 4. p. 165-176

[9]. Mortimer, R.K. "Evolution and Variation of the Yeast (Saccharomyces) Genome". Genome. 2000. Volume 10. p. 403-409

[10]. Legras, J., Merdinoglu, D., Cornuet, J. and Karst, F. "Bread, Beer and Wine: Saccharomyces cerevisiae diversity reflects human history". Molecular Ecology. 2007. Volume 16. p. 2091-2102.

[11]. Landry, C.R., Townsend, J.P., Hartl, D.L. and Cavalieri, D. "Ecological and evolutionary genomics of Saccharomyces cerevisiae". Molecular Ecology. 2006. Volume 15. p. 575–591.

[12]. Goffeau A., Barrel, B. G., Bussey, H., Davis, R.W., Dujon B., Feldmann H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H. and Oliver, S.G. "Life with 6000 genes." Science. 1996. Volume 274. p. 546 - 567

[13]. Sherman, F. "Getting Started with Yeast". Methods Enzymology. 2002. Volume 350. p. 3-41

[14].Dujon, B. "The yeast genome project: what did we learn?". Trends in Genetics. 1996. Volume 12. p. 263-270

[15]. Förster, J., Famili, I., Fu, P., Palsson, B.O. and Nielsen, J. "Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network". Genome. 2003. Volume 13. p. 244-253

[16]. Foury, F., Roganti, T., Lecrenier, N., and Purnelle, B. "The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae". Federation of European Biochemical Societies. 1998. Volume 440. p. 325-331

[17]. Hartley, J.L., and Donelson, J.E. "Nucleotide sequence of the yeast plasmid". Nature. 1980. Volume 286. 860-864

[18]. Zaragoza, O., and Gancedo, J.M. "Pseudohyphal growth is induced in Saccharomyces cerevisiae by a combination of stress and cAMP signalling". Antonie van Leeuwenhoek. 2000. Volume 78. 187-194

[19]. Cabib, E., Silverman, S.J., Shaw, A., Das Gupta, S., Park, H., Mullins, J.T., Mol, P.C., and Bowers, B. "Carbohydrates as structural constituents of yeast cell wall and septum. Pure and Applied Chemistry. 1991. Volume 63, p. 483-489.

[20]. Main, J., McKenzie, H., Yeaman, G.R., Kerr, M.A., Robson, D., Pennington, C.R., and Parratt, D. "Antibody to Saccharomyces cerevisiae (bakers' yeast) in Crohn's disease.". British Medical Journal. 1988. Volume 297. p. 1105-1106.

[21]. McCullough, M.J., Clemons, K.V., Farina C., McCusker, J.H., and Stevens, D.A. "Epidemiological Investigation of Vaginal Saccharomyces cerevisiae Isolates by a Genotypic Method". Journal of Clinical Microbiology. 1998. Volume 36. p. 557-562

[22]. Pasha, C., Nagavalli, M., and Venkateswar Rao, L. "Lantana camara for fuel ethanol production using thermotolerant yeast". Letters in Applied Microbiology. 2007. Volume 44. p. 666-672.

[23]. Conant, G.C. and Wolfe, K.H. "Increased glycolytic flux as an outcome of whole-genome duplication in yeast". Molecular Systems Biology. 2007.

[24]. Torres, E.M., Sokolsky, T., Tucker, C.M., Chan, L.Y., Boselli, M., Dunham, M.J., and Amon, A. "Effects of Aneuploidy on Cellular Physiology and Cell Division in Haploid Yeast". Science. Volume 317. p. 916 - 924.

Edited by Isabella Ballesta, student of Rachel Larsen

Edited by KLB

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