Eukaryotes Saccharomyces cerevisiae

Fig. 3.3 Representative biotransformations serve as a basis for the development of a biosimulation-based approach. Model substrates for studying drug metabolism in the model eukaryote Saccharomyces cerevisiae ethyl acetoacetate (1), ethyl 4-chloro-acetoacetate (2) and ethyl 4,4,4-trifluoro-acetoacetate (3).

Figure 29.1 RNA polymerase structures. The three-dimensional structures of RNA polymerases from a prokaryote Thermus aquaticus) and a eukaryote (Saccharomyces cerevisiae).

Our group at Indiana University has been participating in these efforts since 1963, using, as do many others in the field, the versatile, unicellular eukaryote, Saccharomyces cerevisiae (Baker s yeast)—an ascomycete—as our object of study. Throughout, our interests have been centered as much on the limits of the autonomy of its mitochondrial organelles in their own biosynthesis as on the process itself " on what mitochondria cannot do by and for themselves on what and how they depend on the rest of the cell and how this mutual interdependence is brought about and regulated. 

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

Fig. 2.2 Landmark events in the cell cycle of Saccharomyces cerevisiae. Gl, S, G2 and M are the classical phases of the eukaryotic cell cycle.

Eukaryotic organisms Fungi Saccharomyces cerevisiae D7 Gene conversion Kochetal. 1988 ... 

It was tempting to base the study of membrane transport in eukaryotic cells on similar simple principles. For this purpose, as well as for molecular biology as a whole, the yeast Saccharomyces cerevisiae appeared to be the best suited organism. From early times on, this yeast has occupied a privileged place for mankind. Due to... 

From a genetical point of view, Saccharomyces cerevisiae is an ideal organism which may be considered the Escherichia coli of eukaryotic cells [4,5]. This is true in particular for the study of metabolic regulation and for that of membrane transport [6]. Finally, the astonishing resemblance between many yeast proteins and certain mammalian-cell proteins has seriously broadened the scope of interest. Although a few reports have appeared on amino acid transport in some other yeasts, most investigations in this field have used strains of Saccharomyces cerevisiae. 

In this chapter, we shall focus on the molecular aspects of amino acid transport and its regulation in Saccharomyces cerevisiae. Kinetic, biochemical and genetic aspects of the amino acid transport systems of eukaryotic microorganisms have been reviewed earlier [7,8]. 

In Saccharomyces cerevisiae, as in most eukaryotic cells, the plasma membrane is not freely permeable to nitrogenous compounds such as amino acids. Therefore, the first step in their utilization is their catalyzed transport across the plasma membrane. Most of the transported amino acids are accumulated inside the yeast cells against a concentration gradient. When amino acids are to be used as a general source of nitrogen, this concentration is crucial because most enzymes which catalyze the first step of catabolic pathways have a low affinity for their substrates. 

Despite the limited information available, rather clear predictions can be made about the probable structure, location, and energy coupling of the amino acid transporters of Saccharomyces cerevisiae, by comparing them with better known systems in both prokaryotes and eukaryotes. 

Interesting as it is, the study of transporters for amino acids and other nitrogenous nutrients in Saccharomyces cerevisiae is a tricky field. Many difficulties must be circumvented to avoid trivial errors. These practical problems are linked with several features of eukaryotic uptake systems, the first being the multiplicity of permeases which transport a given substrate. In relation to this, a major point is to make certain that one is not studying more than one uptake system at a time, and this can hardly be done without genetics. Once individual uptake systems have been identified and separated with the help of genetics, a second difficulty arises, which... 

The budding yeast Saccharomyces cerevisiae is an extremely attractive eukaryotic model system for the study of genes involved in iron metabolism. This is because of its short generation time, the ease with which relatively large amounts of... 

Purification of FLAG-Tagged Eukaryotic Initiation Factor 2B Complexes, Subcomplexes, and Fragments from Saccharomyces cerevisiae... 

There are numerous protocols for polysomal gradients preparations that differ mainly at the step for harvesting the cells, and the gradient composition and separation times. The protocol presented later was optimized for isolation of polysomal mRNA from the yeast Saccharomyces cerevisiae, yet many steps will be similar to other eukaryotes and the procedure can easily be modified for other organisms. We will use this protocol as a template on which we will indicate and highlight points that are critical for the microarray analysis. Generally, the RNA isolated by this protocol can be used for analysis by DNA microarray, Northern blot, or RT-PCR. 

GFP has also been proposed as a successor to the Ames and SOS chromotest. Billinton et al. [8] obtained a reporter system, employed as genotoxicity biosensor, that uses eukaryotic cells (the baker yeast Saccharomyces cerevisiae) instead of bacteria. The strain produces green fluorescent protein, codon optimized for yeast, when DNA damage has occurred. It was demonstrated that the reporter does not falsely respond to chemicals that delay mitosis, and responds appropriately to the genetic regulation of DNA repair. 

Weeks et al. 1979) or DNA damage (Nakamura et al. 1987) following hexachloroethane treatment. Similar results were reported for eukaryotic cells. Hexachloroethane did not cause gene mutation in cells harvested from the stationary growth phase (Bronzetti et al. 1989) or DNA damage in yeast (Saccharomyces cerevisiae) (Simmon and Kauhanen 1978), chromosomal aberrations in fungi (Aspergillus nidulans) (Crebelli et al. 

Fig. 6. Distribution of the most common folds in selected bacterial, archaeal, and eukaryotic proteomes. The vertical axis shows the fraction of all predicted folds in the respective proteome. Fold name abbreviations FAD/NAD, FAD/NAD(P)-binding Rossman-like domains TIM, TIM-barrel domains SAM-MTR, S-adenosylmethionine-dependent methyltransferases PK, serine-threonine protein kinases PP-Loop, ATP pyrophosphatases. mge, Mycoplasma genitalium rpr, Rickettsiaprowazekii hh x, Borrelia burgdorferi ctr, Chlamydia trachomatis hpy, Helicobacter pylori tma, Thermotoga maritima ssp, Synechocystis sp. mtu, Mycobacterium tuberculosis eco, Escherichia coli mja, Methanococcus jannaschii pho, Pyrococcus horikoshii see, Saccharomyces cerevisiae, cel, Caenorhabditis elegans.

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