Molecular Genetics of Schizosaccharomyces pombe
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As a result of the enormous amount of information that has been collected with E. coli over the past half century (e.g. genome sequence, mutant phenotypes, metabolic and regulatory networks, etc.), we now have detailed knowledge about gene regulation, protein activity, several hundred enzyme reactions, metabolic pathways, macromolecular machines, and regulatory interactions for this model organism. However, understanding how all these processes interact to form a living cell will require further characterization, quantification, data integration, and mathematical modeling, systems biology. No organism can rival E. coli with respect to the amount of available basic information and experimental tractability for the technologies needed for this undertaking. A focused, systematic effort to understand the E. coli cell will accelerate the development of new post-genomic technologies, including both experimental and computational tools. It will also lead to new technologies that will be applicable to other organisms, from microbes to plants, animals, and humans. E. coli is not only the best studied free-living model organism, but is also an extensively used microbe for industrial applications, especially for the production of small molecules of interest. It is an excellent representative of Gram-negative commensal bacteria. E. coli may represent a perfect model organism for systems biology that is aimed at elucidating both its free-living and commensal life-styles, which should open the door to whole-cell modeling and simulation.
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Post-genomics may be defined in different ways depending on how one views the challenges after the discovery of the genome. A traditional view is to follow the concept of the central dogma in molecular biology, namely from genome to transcriptome to proteome. Projects are ongoing to analyse gene expression profiles both at the mRNA and protein levels, and to catalogue protein 3D structure families, which will no doubt help the understanding of the information in the genome. However, once complete, such experimentally determined catalogues of genes, RNAs and proteins only tell us about the building blocks of life. They do not tell us much about how life operates as a system, such as higher order functional behaviours of the cell or the organism. Thus, an alternative view of post-genomics is to go up from the molecular level to the cellular level and eventually to still higher levels, i.e., the biological systems. Bioinformatics provides basic concepts as well as practical methods to integrate this view with the traditional view and to analyse complex interactions among building blocks and with dynamic environments.
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The yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have become popular and successful model systems for understanding eukaryotic biology at the cellular and molecular levels. The reasons for this success are experimental tractability, especially in applying classical and molecular genetic methods to associate genes with proteins and functions within the cell.
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How cells maintain specific levels of each protein and whether that control is evolutionarily conserved are key questions. Here, we report proteome-wide steady-state protein turnover rate measurements for the evolutionarily distant but ecologically similar yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe. We find that the half-life of most proteins is much longer than currently thought and determined to a large degree by protein synthesis and dilution due to cell division. However, we detect a significant subset of proteins (∼15%) in both yeasts that are turned over rapidly. In addition, the relative abundances of orthologous proteins between the two yeasts are highly conserved across the 400 million years of evolution. In contrast, their respective turnover rates differ considerably. Our data provide a high-confidence resource for studying protein degradation in common yeast model systems.
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The yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe: models for cell biology research.
Yeast species provide excellent models for fundamental biological research. In this review, I will describe characteristics of the two most common laboratory systems: the fission yeast Schizosaccharomyces pombe, and the budding yeast Saccharomyces cerevisiae. They have substantial similarities that make them powerful as research tools, and also striking biological differences that make them complementary experimental models. Each provides unique tools for understanding environmental effects on cellular systems.
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