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Fred Sherman an Introduction to the Genetics and Molecular Fred Sherman An Introduction to the Genetics and Molecular Biology of the Yeast Saccharomyces cerevisiae. (2001) http://dbb.urmc.rochester.edu/labs/sherman_f/yeast/index.html Table of Contents • 1 Yeast as a Model Eukaryote • 11 Manipulating the Genome In • 2 Information on Yeast Vitro with Plasmids • 3 Yeast Strains 11.1 Cloning by Complementation • 4 Growth and Life Cycles 11.2 Mutagenesis In Vitro • 5 The Yeast Genome 11.3 Two-step Gene Replacement • 6 Genetic Nomenclature 11.4 Gene Disruption and One-step 6.1 Chromosomal Genes Gene Replacement 6.2 Mitochondrial Gene 11.5 Plasmid Shuffle 6.3 Non-Mendelian Determinants 11.6 Recovering mutant alleles • 7 Genetic Analyses • 12 Interactions of Genes 7.1 Overviews with Examples 12.1 Heterozygosity and Dominant- 7.2 Tetrad Analysis negative Mutations 7.3 Non-Mendelian Inheritance 12.2 Intragenic Complementation • 8 Transformation 12.3 Nonallelic Non- 8.1 Yeast Vector and DNA complementation Fragments 12.4 Suppressors 8.2 Synthetic Oligonucleotides 12.5 Synthetic Enhancement and 8.3 Mitochondrial Transformation Epistatic Relationships • 9 Yeast Vectors • 13 Genomic Analysis 9.1 YIp Vectors • 14 Analyses with Yeast Systems 9.2 YEp Vectors 14.1 Two-hybrid Systems 9.3 YCp Vectors 14.2 Yeast Artificial Chromosomes • 10 Genes Important for Genetic (YACs) Studies 14.3 Expression of Heterologous 10.1 URA3 and LYS2 Protein in Yeast 10.2 ADE1 and ADE2 • Key Words 10.3 GAL1 Promoter • Bibliography 10.4 lacZ and Other Reporters 1 1 Yeast is a Model Eukaryote mutations can be conveniently isolated and manifested in haploid strains, and This chapter deals only with the yeast S. complementation tests can be carried out in cerevisiae, and related interbreeding diploid strains. The development of DNA species. The fission yeast transformation has made yeast particularly Schizosaccharomyces pombe, which is accessible to gene cloning and genetic only distantly related to S. cerevisiae, has engineering techniques. Structural genes equally important features, but is not as corresponding to virtually any genetic trait well characterized. The general principles can be identified by complementation from of the numerous classical and modern plasmid libraries. Plasmids can be approaches for investigating S. cerevisiae introduced into yeast cells either as are described, and the explanation of terms replicating molecules or by integration into and nomenclature used in current yeast the genome. In contrast to most other studies are emphasized . This article should organisms, integrative recombination of be particularly useful to the uninitiated transforming DNA in yeast proceeds who are exposed for the first time to exclusively via homologous experimental studies of yeast. Detailed recombination. Exogenous DNA with at protocols are described in the primary least partial homologous segments can literature and in a number of reviews in the therefore be directed at will to specific books listed in the Bibliography. The locations in the genome. Also, homologous original citations for the material covered recombination, coupled with yeasts’ high in this chapter also can be found in these levels of gene conversion, has led to the comprehensive reviews. development of techniques for the direct replacement of genetically engineered Although yeasts have greater genetic DNA sequences into their normal complexity than bacteria, containing 3.5 chromosome locations. Thus, normal wild- times more DNA than Escherichia coli type genes, even those having no cells, they share many of the technical previously known mutations, can be advantages that permitted rapid progress in conveniently replaced with altered and the molecular genetics of prokaryotes and disrupted alleles. The phenotypes arising their viruses. Some of the properties that after disruption of yeast genes has make yeast particularly suitable for contributed significantly toward biological studies include rapid growth, understanding of the function of certain dispersed cells, the ease of replica plating proteins in vivo. Many investigators have and mutant isolation, a well-defined been shocked to find viable mutants with genetic system, and most important, a little of no detrimental phenotypes after highly versatile DNA transformation disrupting genes that were previously system. Unlike many other assumed to be essential. Also unique to microorganisms, S. cerevisiae is viable yeast, transformation can be carried out with numerous markers. Being directly with synthetic oligonucleotides, nonpathogenic, yeast can be handled with permitting the convenient productions of little precautions. Large quantities of numerous altered forms of proteins. These normal bakers’ yeast are commercially techniques have been extensively exploited available and can provide a cheap source in the analysis of gene regulation, for biochemical studies. structure-function relationships of proteins, chromosome structure, and other general Unlike most other microorganisms, strains questions in cell biology. The overriding of S. cerevisiae have both a stable haploid virtues of yeast are illustrated by the fact and diploid state. Thus, recessive that mammalian genes are being 2 introduced into yeast for systematic Jones et al., 1992; Pringle et al.,1997; analyses of the functions of the Wheals et al., 1995), including protocols corresponding gene products. applicable to yeasts (Fields & Johnson, 1993) and introductory material (Walker, In addition, yeast has proved to be valuable 1998). A more comprehensive listing of for studies of other organisms, including earlier reviews can be found in Sherman the use of the two-hybrid screening system (1991). Interesting and amusing accounts for the general detection of protein-protein of developments in the field are covered in interactions, the use of YACs for cloning The Early Days of Yeast Genetics (Hall & large fragments of DNA, and expression Linder, 1992). The journal Yeast publishes systems for the laboratory and commercial original research articles, reviews, short preparation of heterologous proteins. Many communications, sequencing reports, and of these techniques are described herein. selective lists of current articles on all aspects of Saccharomyces and other yeast During the last two decades, an ever- genera. increasing number of molecular biologists have taken up yeast as their primary Current and frequently-updated research system, resulting in a virtually information and databases on yeast can be autocatalytic stimulus for continuing conveniently retrieved on the Internet investigations of all aspects of molecular through World Wide Web, including the and cell biology. Most significantly, a "Saccharomyces Genomic Information knowledge of the DNA sequence of the Resource" (http://genome- complete genome, which was completed in www.stanford.edu/Saccharomyces/) and 1996, has altered the way molecular and linked files containing DNA sequences, cell biologist approach and carry out their lists of genes, home pages of yeast studies (see Dujon, 1996; Goffeau et al., workers, and other useful information 1996). In addition, plans are under way to concerning yeast. From the MIPS page systematically investigate the possible (http://www.mips.biochem.mpg.de/) you functions of all yeast genes by examining can access the annotated sequence the phenotypes of strains having disrupted information of the genome of genes. Saccharomyces cerevisiae and view the chromosomes graphically or as text, and 2 Information on Yeast more. The YPD page (http://www.proteome.com/YPDhome.htm A general introduction to a few selected l) contains a protein database with topics on yeast can be found in the book emphasis on the physical and functional chapters "Yeast as the E. coli of Eucaryotic properties of the yeast proteins. Cells" and "Recombinant DNA at Work" (Watson et al., 1987). Comprehensive and 3 Yeast Strains excellent reviews of the genetics and molecular biology of S. cerevisiae are Although genetic analyses and contained in three volumes entitled transformation can be performed with a "Molecular Biology of the Yeast number of taxonomically distinct varieties Saccharomyces" (Broach et al., 1991; of yeast, extensive studies have been Jones et al., 1992; Pringle et al., 1997). An limited primarily to the many freely important source for methods used in interbreeding species of the budding yeast genetics and molecular biology of yeast is Saccharomyces and to the fission yeast contained in the book edited by Guthrie Schizosaccharomyces pombe. Although and Fink (1991). Overviews of numerous "Saccharomyces cerevisiae" is commonly subjects are also covered in other sources used to designate many of the laboratory (Broach et al., 1991; Brown & Tuite, 1998; stocks of Saccharomyces used throughout 3 the world, it should be pointed out that laboratory strains produce high frequencies most of these strains originated from the of ρ - mutants. Another strain, D273–10B, interbred stocks of Winge, Lindegren, and has been extensively used as a typical others who employed fermentation normal yeast, especially for mitochondrial markers not only from S. cerevisiae but studies. One should examine the specific also from S. bayanus, S. carlsbergensis, S. characters of interest before initiating a chevalieri, S. chodati, S. diastaticus, etc. study with any strain. Also, there can be a Nevertheless, it is still recommended that high degree of inviability of the meiotic the interbreeding laboratory stocks of progeny from crosses among these Saccharomyces be denoted as S. "normal"
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