The first stand-alone textbook on yeast biology. Based on his successful monograph, Horst Feldmann has devised this easy-to-read, full-color textbook, finally satisfying the needs of the increasing number of students using yeast as an important tool or model organism. Table of Contents (2nd edition)1 Introduction1.1 Historical Aspects1.2 Yeast as a Eukaryotic Model System2 Yeast Cell Architecture and Functions2.1 General Morphology2.2 The Yeast Envelope2.3 The Yeast Cytoplasm and Cytoskeleton2.4 The Yeast Nucleus2.4.1 Overview2.4.2 The Nuclear Pore2.5 Yeast Cell Organellar Structures3 Yeast Metabolism3.1 Metabolic Pathways and Energy3.2 Catabolism of Hexose Carbon Sources3.2.1 Principal Pathways3.2.2 Respiration versus Fermentation3.2.3 Catabolism of Other Sugars ? Galactose3.2.4 Metabolism of Non-Hexose Carbon Sources3.3 Gluconeogenesis and Carbohydrate Synthesis3.3.1 Gluconeogenesis3.3.2 Storage Carbohydrates3.3.2.1 Glycogen3.3.2.2 Trehalose3.3.3 Unusual Carbohydrates3.3.3.1 Unsual Hexoses and Aminosugars3.3.3.2 Inositol and its Derivatives3.3.3.3 N- and O-linked Glycosylation3.3.4 Structural Carbohydrates3.4 Fatty Acid and Lipid Metabolism3.4.1 Fatty Acids3.4.2 Lipids3.4.3 Glycolipids3.4.3.1 Phosphatidylinositol and Derivatives3.4.3.2 Sphingolipids3.4.3.3 Glycosylphosphatidylinositol (GPI)3.4.4 Isoprenoid Biosynthesis3.5 Nitrogen Metabolism3.5.1 Catabolic Pathways3.5.2 Amino Acid Biosynthesis3.5.2.1 Glutamate Family3.5.2.2 Aspartate Family3.5.2.3 Branched Amino Acids3.5.2.4 Lysine3.5.2.5 Serine, Cysteine, Glycine3.5.2.6 Alanine3.5.2.7 Aromatic Amino Acids3.5.2.8 Histidine3.5.3 Protein Biosynthesis3.5.3.1 Aminoacylation3.5.3.2 The Recognition Problem3.6 Nucleotide Metabolism3.6.1 Pyrimidine Derivatives3.6.2 Purine Derivatives3.6.3 Deoxyribonucleotides3.6.4 Nucleotide Modification3.7 Phosphorus and Sulphur Metabolism3.7.1 Inorganic Phosphate3.7.2. Sulfur Requirement3.7.2.1 Fixation and Reduction of Sulfate3.7.2.2 Cycle of Activated Methylgroups3.8 Vitamins and Cofactors3.8.1 Biotin3.8.2 Thiamine3.8.3 Pyridoxine3.8.4 Nicotinamide Adenine Dinucleotides (NAD)3.8.5 Riboflavin Derivatives3.8.6 Pantothenic Acid and Coenzyme A3.8.7 Folate3.8.8 Tetrapyrroles3.8.9 Ubiquinone (Coenzyme Q)3.9 Transition Metals4 Yeast Molecular Techniques4.1 Isolation of Particular Cell Types and Components4.2 Genetic Engineering and Reverse Genetics4.2.1 The Molecular Revolution4.2.2 Transformation of Yeast Cells4.2.2.1 Yeast Shuttle Vectors4.2.2.2 Yeast Expression Vectors4.2.2.3 Secretion of Heterologous Proteins from Yeast4.2.2.4 GFP Fusion Proteins4.2.3 Cosmid Vectors4.2.4 Yeast Artificial Chromosomes (YACs)4.3 More Genetic Tools from Yeast4.3.1 The Two-Hybrid System4.3.2 The One-Hybrid System5 Yeast Genetic Structures and Functions5.1 Yeast Chromosome Structure and Function5.1.1 Yeast Chromatin5.1.1.1 Organization of Chromatin Structure5.1.1.2 Modification of Chromatin Structure5.1.2 Centromeres5.1.3 Replication Origins and Replication5.1.3.1 Initiation of Replication5.1.3.2 Elongation and Chromatin Remodeling5.1.3.3 DNA Damage Checkpoints5.1.4 Telomeres5.1.5 Retrotransposons in Yeast5.1.5.1 Types and Structure5.1.5.2 Ty Replication5.1.5.3 Interactions between Ty Elements and Their Host5.2 Molecular Structures of Yeast tRNAs and their Genes5.2.1 tRNAs5.2.2 tRNA Precursors and Processing5.3 Molecular Structures of Ribosomal Components and Their GenesProcessing: Processosome5.4 Messenger RNAs5.4.1 Structure of Yeast mRNAs5.4.2 Introns and Processing of Pre-mRNA5.5 Extrachromosomal Elements5.5.1 2? DNA5.5.2 Killer Plasmids5.5.3 Yeast Prions5.6 The Yeast Mitochondrial Genome6 Gene Families Involved in Yeast Cellular Dynamics6.1 ATP- and GTP-binding Proteins6.1.1 ATPases6.1.1.1 P-type ATPases6.1.1.2 V-type ATPases6.1.1.3 Chaperones, Co-chaperones and Heat-Shock ProteinsHSP70 FamilyHSP40 FamilyHSP90 FamilyHSP60 FamilyHSP1046.1.1.4 Other ATP-binding Factors6.1.2 Small GTPases and their Associates6.1.2.1 Ras Family6.1.2.2 Rab Family6.1.2.3. Rho/Rac Family6.1.2.4 Arf Family6.1.3 G-Proteins6.2 Regulatory ATPases ? AAA+ Proteins6.2.1 ATP-dependent Proteases6.2.2 Membrane Fusion Proteins6.2.3 Cdc48p6.2.4 Peroxisomal AAA Proteins6.2.5 Katanin and Vps4p6.2.6 Dynein6.2.7 DNA Replication Proteins6.2.8 RuvB-like Proteins6.3 Protein Modification by Proteins and Programmed Protein Degradation6.3.1 The Ubiquitin-Proteasome System (UPS)6.3.1.1 Initial Discoveries6.3.1.2 Ubiquitin and Factors in the Ubiquitin-mediated Pathway6.3.1.3 E3 Ubiquitin LIgasesHECT Type LigasesRING Finger Type LigasesRegulation of E3 Ligases6.3.2 Yeast Proteasomes6.3.2.1 Initial Discoveries6.3.2.2 Proteasomal Structure6.3.2.2 Regulation of Yeast Proteasome Activity6.3.3 More Functions for Ubiquitin6.3.4 Ubiquitin-like Proteins (ULPs) and Cognate Factors6.3.4.1 SUMO6.3.4.2 Rub16.3.4.3 Ubiquitin-domain Proteins (UDPs)6.4 Yeast Protein Kinases and Phosphatases6.4.1 Families of Protein Kinases6.4.2 Protein Phosphatases6.5 Helicases6.5.1 RNA Helicases6.5.2 DNA Helicases6.6 RAD Proteins7 Yeast Propagation and the Yeast Cell Cycle7.1 Modes of Propagation7.1.1 Vegetative Reproduction7.1.1.1 Budding7.1.1.2 Septins and Bud-neck Filaments7.1.1.3 Spindle Pole Bodies7.1.1.4 Spindle Dynamics7.1.2 Sexual Reproduction7.1.3 Filamentous Growth7.1.4 Yeast Cell Death7.2 The Cell Cycle7.2.1 Dynamics and Regulation of the Cell Cycle7.2.2 Sister Chromatids ? Cohesion and Separation7.2.3 The Spindle Checkpoint (SCP)7.2.4 Chromosome Segragation during Meiosis8 Yeast Transport8.1 Intracellular Protein Sorting and Transport8.1.1 The ?Signal Hypothesis?8.1.2 Central Role of the Endoplasmic Reticulum8.1.3 Intracellular Protein Trafficking and Sorting8.1.3.1 Some History8.1.3.2 Membrane Fusions8.1.3.3 ER-associated Protein Degradation (ERAD)8.1.3.4 The Vacuolar Network8.1.3.5 Endocytosis and the Multivesicular Body Sorting Pathway8.1.3.6 Exocytosis8.2 Nuclear Traffic8.2.1 Nuclear Transport8.2.2 Nuclear mRNA Quality Control8.2.3 Nuclear Export of mRNA8.2.4 Nuclear Dynamics of tRNA8.3 Membrane Transporters in Yeast8.3.1 Transport of Cations8.3.2 Channels and ATPases8.3.2.1 Channels8.3.2.2 ATP-dependent Permeases8.3.3 Ca++ Signaling and Transport Pathways in Yeast8.3.3.1 Ca++ Transport8.3.3.2 Ca++-mediated Control8.3.3.3 Ca++ and Cell Death8.3.4 Transition Metal Transport8.3.4.1 Iron8.3.4.2 Copper8.3.4.3 Zinc8.3.4.4 Manganese8.3.5 Anion Transport8.3.5.1 Phosphate Transport8.3.5.2 Transport of Other Anions8.3.6 Nutrient and Ammonium Transport8.3.6.1 Carbohydrate Transport8.3.6.2 Amino Acid Transport8.3.6.3 Transport of Nucleotide Constituents/Nucleotide Sugars8.3.6.4 Transport of Cofactors and Vitamins8.3.6.5 Ammonium Transport8.3.7 Mitochondrial Transport8.3.7.1 Transport of Substrates8.3.7.2 Electron Transport Chain8.3.7.3 Proton Transport ? ATP Synthase9 Yeast Gene Expression9.1 Transcriptional Regulation and Transcription Factors9.2 Polymerases and Cofactors9.2.1 RNA Polymerase I (Pol I)9.2.2 RNA Polymerase III (Pol III)9.2.3 RNA Polymerase II (Pol II)9.2.4 General Transcription Factors (GTFs)9.2.4.1 TBP9.2.4.2 TFIIA9.2.4.3 TFIIB9.2.4.4 TFIIE and TFIIF9.2.4.5 TFIIH9.2.4.6 Transcription Activators9.2.4.7 TFIID9.2.4.8 SRB/Mediator9.2.4.9 SAGA9.2.4.10 Transcriptional Repressors9.3 Transcriptional Initiation, Elongation and Regulation9.3.1 Chromatin Remodelling9.3.2 Regulator Complexes9.4 DNA Repair Connected to Transcription9.4.1 Nucleotide Excision Repair9.4.2 Mismatch Repair9.4.3 Thymidine Dimer Excision9.5 Coupling Transcription to mRNA Processing9.5.1 Polyadenylation9.5.2 Generation of Functional mRNA9.5.2.1 General Principles9.5.2.2 Control of mRNA Decay9.5.2.2.1 Exosome-mediated Pathways9.5.2.2.2 Nonsense-mediated mRNA Decay9.6 The Yeast Translation Apparatus9.6.1 Initiation9.6.2 Elongation and Termination9.7 Protein Splicing ? Yeast Inteins10 Molecular Signalling Cascades and Gene Regulation10.1 Ras/cAMP Pathway10.2 MAP Kinase Pathways10.2.1 Mating Type Pathway10.2.2 Filamentation/Invasion Pathway10.2.3 Control of Cell Integrity10.2.4 High Osmolarity Growth (HOG) Pathway10.2.5 Spore Wall Assembly Pathway10.3 General Control by Gene Repression10.3.1 Ssn6-Tup1 Repression10.3.3 Activation and Repression by Rap110.4 Gene Regulation by Nutrients10.4.1 The TOR System10.4.2 Regulation of Glucose Metabolism10.4.3 Regulation of Galactose Metabolism10.4.4 General Amino Acid Control10.4.5 Regulation of Arginine Metabolism10.5 Stress Responses in Yeast10.5.1 Temperature Stress and Heat-shock Proteins10.5.2 Oxidative and Chemical Stresses10.5.2.1 AP-1 Transcription Factors in Yeast10.5.2.2 The STRE-dependent System10.5.2.3 Pleiotropic Drug Resistance -ABC Transporters10.5.3 The Unfolded Protein Response11 Function and Biogenesis of Mitochondria and Peroxisomes11.1 Mitochondria11.1.1 Genetic Biochemistry of Yeast Mitochondria11.1.2 Mitochondrial Functions Critical to Cell Viability11.1.2.1 Superoxide Dismutase (SOD)11.1.2.2 Iron Homeostasis11.1.3 Biogenesis of Mitochondria -Protein Transport11.1.3.1 The `Presequence Pathway? and the `MIA Pathway?11.1.3.2 The `Membrane Sorting Pathway?- Switch between TIM22 and TIM2311.1.3.3 The `?-barrel Pathway?11.1.3.4 The Endogenous Membrane Insertion Machinery11.1.4 Mitochondrial Quality Control and Remodelling11.2 Peroxisomes12 Yeast Genome, Proteome, Transcriptome, Metabolome, and Regulatory Networks12.1 The Yeast Genome Sequencing Project12.2 Characteristics of the Yeast Genome12.2.1 Comparison of Genetic and Physical Maps12.2.2 Gene Organization12.2.2.1 Protein Encoding Genes12.2.2.2 Pseudogenes and Introns12.2.3 Genetic Redundancy ? Gene Duplications12.2.3.1 Duplicated Genes in Subtelomeric Regions12.2.3.2 Duplicated Genes Internal to Chromosomes12.2.3.3 Duplicated Genes in Clusters12.2.4 Gene Typification and Gene Families12.2.5 tRNA Multiplicity and Codon Capacity in Yeast12.2.5.1 Correlation of tRNA Abundance to Gene Copy Number12.2.5.2 tRNA Gene Redundancy and Codon Selection in Yeast12.2.6 Functional Analysis of Yeast Genes12.3 Functional Genomics12.3.1 Yeast Transriptome12.3.1.1 Genomic Profiling12.3.1.2 Protein-DNA Interactions12.3.2 Yeast Proteome12.3.2.1 Protein Analysis12.3.2.2 Proteome Chips12.3.2.3 Protein-protein Interactions and Protein Complexes12.3.3 Yeast Metabolome12.3.4 Genetic Interaction Networks: Regulatory Networks and Oscillations13 Disease Genes in Yeast13.1 General Aspects13.2 Trinucleotide Repeats and Neurodegenerative Diseases13.3 Ageing and Age-related Diseases13.4 Mitochondrial Diseases14 Yeast Biotechnology14.1 Fermentation and Metabolic Engineering14.1.1 Typical Fermentation Procedures14.1.2 Food and Chemical Industries ? Metabolic Engineering14.2 Biopharmaceuticals from Health-Care Industries14.3 Biomedical Research14.4 Environmental Technologies -Cell-surface Display[15] Hemiascomycetous Yeasts(suggested)15.1 Selected Model Genomes15.2 Genolevures Projects: Sequenced Genomes15.3 Ecology, Adaptation of Metabolic Behavior15.4 Differences in Architectual Features and Genetic Outfit(Genes/Introns/snRNAs/Codon usage/Modes of Propagation)15.5 Differences in Molecular Mechanisms(Replication, Transcription, DNA-repair, Specific Regulatory Pathways)15.6 Application in Biotechnology[16] Yeast Evolutionary Genomics(suggested)16.1 Yeast Populations and Species16.2 Gene Duplication Mechanisms16.2.1 Expansion of Tandem Gene Arrays16.2.2 Segmental Duplications16.2.3 Whole-Genome Duplications16.2.4 Single Gene Duplications16.3 Other Mechanisms of Genome EvolutionEpilogue: The Future of Yeast Research