Schizosaccharomyces pombe – жасуша бөлінуін зерттеу моделі

Species of yeast

Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length. Its genome, which is approximately 14.1 million base pairs, is estimated to contain 4,970 protein coding genes and at least 450 non coding RNAs. These cells maintain their shape by growing exclusively through the cell tips and divide by medial fission to produce two daughter cells of equal size, which makes them a powerful tool in cell cycle research. Fission yeast was isolated in 1893 by Paul Lindner from East African millet beer. The species name pombe is the Swahili word for beer. It was first developed as an experimental model in the 1950s: by Urs Leupold for studying genetics, and by Murdoch Mitchison for studying the cell cycle. Paul Nurse, a fission yeast researcher, successfully merged the independent schools of fission yeast genetics and cell cycle research. Together with Lee Hartwell and Tim Hunt, Nurse won the 2001 Nobel Prize in Physiology or Medicine for work on cell cycle regulation. The sequence of the S. pombe genome was published in 2002, by a consortium led by the Sanger Institute, becoming the sixth model eukaryotic organism whose genome has been fully sequenced. S. pombe researchers are supported by the PomBase MOD (model organism database). This has fully unlocked the power of this organism, with many genes orthologous to human genes identified 70% to date, including many genes involved in human disease. In 2006, sub cellular localization of almost all the proteins in S. pombe was published using green fluorescent protein as a molecular tag. Schizosaccharomyces pombe has also become an important organism in studying the cellular responses to DNA damage and the process of DNA replication. Approximately 160 natural strains of S. pombe have been isolated. These have been collected from a variety of locations including Europe, North and South America, and Asia. The majority of these strains have been collected from cultivated fruits such as apples and grapes, or from the various alcoholic beverages, such as Brazilian Cachaça. S. pombe is also known to be present in fermented tea, kombucha. It is not clear at present whether S. pombe is the major fermenter or a contaminant in such brews. The natural ecology of Schizosaccharomyces yeasts is not well studied.

Schizosaccharomyces pombe was first discovered in 1893 when a group working in a Brewery Association Laboratory in Germany was looking at sediment found in millet beer imported from East Africa that gave it an acidic taste. The term schizo, meaning "split" or "fission", had previously been used to describe other Schizosaccharomycetes. The addition of the word pombe was due to its isolation from East African beer, as pombe means "beer" in Swahili. The standard S. pombe strains were isolated by Urs Leupold in 1946 and 1947 from a culture that he obtained from the yeast collection in Delft, The Netherlands. It was deposited there by A. Osterwalder under the name S. pombe var. liquefaciens, after he isolated it in 1924 from French wine (most probably rancid) at the Federal Experimental Station of Vini and Horticulture in Wädenswil, Switzerland. The culture used by Urs Leupold contained (besides others) cells with the mating types h90 (strain 968), h (strain 972), and h+ (strain 975). Subsequent to this, there have been two large efforts to isolate S. pombe from fruit, nectar, or fermentations: one by Florenzano et al. in the vineyards of western Sicily, and the other by Gomes et al. (2002) in four regions of southeast Brazil.

The fission yeast S. pombe belongs to the division Ascomycota, which represents the largest and most diverse group of fungi. Free living ascomycetes are commonly found in tree exudates, on plant roots and in surrounding soil, on ripe and rotting fruits, and in association with insect vectors that transport them between substrates. Many of these associations are symbiotic or saprophytic, although numerous ascomycetes (and their basidiomycete cousins) represent important plant pathogens that target myriad plant species, including commercial crops. Among the ascomycetous yeast genera, the fission yeast Schizosaccharomyces is unique because of the deposition of α (1,3) glucan or pseudonigeran in the cell wall in addition to the better known β glucans and the virtual lack of chitin. Species of this genus also differ in mannan composition, which shows terminal d galactose sugars in the side chains of their mannans. S. pombe undergo aerobic fermentation in the presence of excess sugar. S. pombe can degrade L malic acid, one of the dominant organic acids in wine, which makes them diverse among other Saccharomyces strains.

The yeast species Schizosaccharomyces pombe and Saccharomyces cerevisiae are both extensively studied; these two species diverged approximately 300 to 600 million years before present, and are significant tools in molecular and cellular biology. Some of the technical discriminants between these two species are:

S. cerevisiae has approximately 5,600 open reading frames; S. pombe has approximately 5,070 open reading frames. Despite similar gene numbers, S. cerevisiae has only about 250 introns, while S. pombe has nearly 5,000. S. cerevisiae has 16 chromosomes, S. pombe has 3. S. cerevisiae is often diploid while S. pombe is usually haploid. S. pombe has a shelterin like telomere complex while S. cerevisiae does not. S. cerevisiae is in the G1 phase of the cell cycle for an extended period (as a consequence, G1 S transition is tightly controlled), while S. pombe remains in the G2 phase of the cell cycle for an extended period (as a consequence, G2 M transition is under tight control). Both species share genes with higher eukaryotes that they do not share with each other. S. pombe has RNAi machinery genes like those in vertebrates, while this is missing from S. cerevisiae. S. cerevisiae also has greatly simplified heterochromatin compared to S. pombe. Conversely, S. cerevisiae has well developed peroxisomes, while S. pombe does not. S. cerevisiae has small point centromere of 125 bp, and sequence defined replication origins of about the same size. On the converse, S. pombe has large, repetitive centromeres (40–100 kb) more similar to mammalian centromeres, and degenerate replication origins of at least 1kb.

S. pombe gene products (proteins and RNAs) participate in many cellular processes common across all life. The fission yeast GO slim provides a categorical high level overview of the biological role of all S. pombe gene products.

The general features of cytokinesis are shown here. The site of cell division is determined before anaphase. The anaphase spindle (in green on the figure) is then positioned so that the segregated chromosomes are on opposite sides of the predetermined cleavage plane.

In fission yeast, where growth governs progression through G2/M, a wee1 mutation causes entry into mitosis at an abnormally small size, resulting in a shorter G2. G1 is lengthened, suggesting that progression through Start (beginning of cell cycle) is responsive to growth when the G2/M control is lost. Furthermore, cells in poor nutrient conditions grow slowly and therefore take longer to double in size and divide. Low nutrient levels also reset the growth threshold so that cell progresses through the cell cycle at a smaller size. Upon exposure to stressful conditions [heat (40 °C) or the oxidizing agent hydrogen peroxide] S. pombe cells undergo aging as measured by increased cell division time and increased probability of cell death. Finally, wee1 mutant fission yeast cells are smaller than wild type cells, but take just as long to go through the cell cycle. This is possible because small yeast cells grow slower, that is, their added total mass per unit time is smaller than that of normal cells. A spatial gradient is thought to coordinate cell size and mitotic entry in fission yeast. The Pom1 protein kinase (green) is localized to the cell cortex, with the highest concentration at the cell tips. The cell cycle regulators Cdr2, Cdr1 and Wee1 are present in cortical nodes in the middle of the cell (blue and red dots). a, In small cells, the Pom1 gradient reaches most of the cortical nodes (blue dots). Pom1 inhibits Cdr2, preventing Cdr2 and Cdr1 from inhibiting Wee1, and allowing Wee1 to phosphorylate Cdk1, thus inactivating cyclin dependent kinase (CDK) activity and preventing entry into mitosis. b, In long cells, the Pom1 gradient does not reach the cortical nodes (red dots), and therefore Cdr2 and Cdr1 remain active in the nodes. Cdr2 and Cdr1 inhibit Wee1, preventing phosphorylation of Cdk1 and thereby leading to activation of CDK and mitotic entry. (This simplified diagram omits several other regulators of CDK activity.)

Fission yeast switches mating type by a replication coupled recombination event, which takes place during S phase of the cell cycle. Fission yeast uses intrinsic asymmetry of the DNA replication process to switch the mating type; it was the first system where the direction of replication was shown to be required for the change of the cell type. Studies of the mating type switching system lead to a discovery and characterization of a site specific replication termination site RTS1, a site specific replication pause site MPS1, and a novel type of chromosomal imprint, marking one of the sister chromatids at the mating type locus mat1. In addition, work on the silenced donor region has led to great advances in understanding formation and maintenance of heterochromatin.

Schizosaccharomyces pombe is a facultative sexual microorganism that can undergo mating when nutrients are limiting. Exposure of S. pombe to hydrogen peroxide, an agent that causes oxidative stress leading to oxidative DNA damage, strongly induces mating and formation of meiotic spores. This finding suggests that meiosis, and particularly meiotic recombination, may be an adaptation for repairing DNA damage. This recombination requires uracil DNA glycosylase, an enzyme that removes uracil from the DNA backbone and initiates base excision repair. On the basis of this finding, it was proposed that base excision repair of either a uracil base, an abasic site, or a single strand nick is sufficient to initiate recombination in S. pombe.

Fission yeast has become a notable model system to study basic principles of a cell that can be used to understand more complex organisms like mammals and in particular humans. This single cell eukaryote is nonpathogenic and easily grown and manipulated in the lab. Many of the genes responsible for cell division and cellular organization in fission yeast cell are also found in the human's genome. Cell cycle regulation and division are crucial for growth and development of any cell. Fission yeast's conserved genes has been heavily studied and the reason for many recent biomedical developments. Fission yeast is also a practical model system to observe cell division because fission yeast's are cylindrically shaped single celled eukaryotes that divide and reproduce by medial fission.

Schizosaccharomyces pombe is often used to study cell division and growth because of conserved genomic regions also seen in humans including: heterochromatin proteins, large origins of replication, large centromeres, conserved cellular checkpoints, telomere function, gene splicing, and many other cellular processes. S. pombes genome was fully sequenced in 2002, the sixth eukaryotic genome to be sequenced as part of the Genome Project. An estimated 4,979 genes were discovered within three chromosomes containing about 14Mb of DNA. This DNA is contained within 3 different chromosomes in the nucleus with gaps in the centromeric (40kb) and telomeric (260kb) regions. PomBase reports over 69% of protein coding genes have human orthologs and over 500 of these are associated with human disease This makes S. pombe a great system to use to study human genes and disease pathways, especially cell cycle and DNA checkpoint systems. The genome of S. pombe contains meiotic drivers and drive suppressors called wtf genes.

Biodiversity and evolutionary study of fission yeast was carried out on 161 strains of Schizosaccharomyces pombe collected from 20 countries. Modeling of the evolutionary rate showed that all strains derived from a common ancestor that has lived since ~2,300 years ago. The study also identified a set of 57 strains of fission yeast that each differed by ≥1,900 SNPs, Since most strains of fission yeast were isolated from brewed beverages, there is no ecological or historical context to this dispersal.

DNA replication in yeast has been increasingly studied by many researchers. Further understanding of DNA replication, gene expression, and conserved mechanisms in yeast can provide researchers with information on how these systems operate in mammalian cells in general and human cells in particular. Other stages, such as cellular growth and aging, are also observed in yeast in order to understand these mechanisms in more complex systems. S. pombe stationary phase cells undergo chronological aging due to production of reactive oxygen species that cause DNA damages. Most such damages can ordinarily be repaired by DNA base excision repair and nucleotide excision repair. Defects in these repair processes lead to reduced survival. Cytokinesis is one of the components of cell division that is often observed in fission yeast. Well conserved components of cytokinesis are observed in fission yeast and allow us to look at various genomic scenarios and pinpoint mutations. Cytokinesis is a permanent step and very crucial to the wellbeing of the cell. Contractile ring formation in particular is heavily studied by researchers using S. pombe as a model system. The contractile ring is highly conserved in both fission yeast and human cytokinesis. These checkpoints ensure any mutagens are eliminated. This is done often by relay signals that stimulate ubiquitination of the targets and delay cytokinesis. Researchers using fission yeast as a model system also look at organelle dynamics and responses and the possible correlations between yeast cells and mammalian cells. Mitochondria diseases, and various organelle systems such as the Golgi apparatus and endoplasmic reticulum, can be further understood, by observing fission yeast's chromosome dynamics and protein expression levels and regulation.

RecA and RecA like proteins are required for recombinational repair of DNA double strand breaks. Five RecA like proteins have been described in S. pombe that are linked to meiotic recombination, and all five RecA homologs appear to be required for normal levels of meiotic recombination.