Yeast

Description

Finally, a stand-alone, all-inclusive textbook on yeast biology.
Based on the feedback resulting from his highly successful monograph, Horst Feldmann has totally rewritten he contents to produce a comprehensive, student-friendly textbook on the topic. The scope has been widened, with almost double the content so as to include all aspects of yeast biology, from genetics via cell biology right up to biotechnology applications. The cell and molecular biology sections have been vastly expanded, while information on other yeast species has been added, with contributions from additional authors. Naturally, the illustrations are in full color throughout, and the book is backed by a complimentary website.
The resulting textbook caters to the needs of an increasing number of students in biomedical research, cell and molecular biology, microbiology and biotechnology who end up using yeast as an important tool or model organism.

Yeast: Molecular and Cell Biology 2
- Contents 8
- Preface 20
- Authors 22
- 1 Introduction 24
  - 1.1 Historical Aspects 24
  - 1.2 Yeast as a Eukaryotic Model System 24
  - Further Reading 26
- 2 Yeast Cell Architecture and Functions 28
  - 2.1 General Morphology 28
  - 2.2 Cell Envelope 29
    - 2.2.1 Cell Wall 30
    - 2.2.2 Plasma Membrane 31
  - 2.3 Cytoplasm and Cytoskeleton 31
    - 2.3.1 Yeast Cytoplasm 31

Yeast: Molecular and Cell Biology 2
- Contents 8
- Preface 20
- Authors 22
- 1 Introduction 24
  - 1.1 Historical Aspects 24
  - 1.2 Yeast as a Eukaryotic Model System 24
  - Further Reading 26
- 2 Yeast Cell Architecture and Functions 28
  - 2.1 General Morphology 28
  - 2.2 Cell Envelope 29
    - 2.2.1 Cell Wall 30
    - 2.2.2 Plasma Membrane 31
  - 2.3 Cytoplasm and Cytoskeleton 31
    - 2.3.1 Yeast Cytoplasm 31
    - 2.3.2 Yeast Cytoskeleton 32
      - 2.3.2.2 Actin Structures 32
      - 2.3.2.1 Microtubules 32
      - 2.3.2.3 Motor Proteins 34
        
        2.3.2.3.1 Myosins 35
        
        2.3.2.3.2 Kinesins 36
        
        2.3.2.3.3 Dynein 36
      - 2.3.2.4 Other Cytoskeletal Factors 36
        
        2.3.2.4.1 Proteins Interacting with the Cytoskeleton 36
        
        2.3.2.4.2 Transport of Organellar Components 36
      - 2.4 Yeast Nucleus 37
        
        2.4.1 Overview 37
        
        2.4.2 Nuclear Pore 37
        
        2.4.2.1 Historical Developments 37
        
        2.4.2.2 Current View of the Nuclear Pore 38
        
        2.4.2.3 Yeast Nucleolus 40
        
        2.4.3 Yeast Chromosomes 40
      - 2.5 Organellar Compartments 40
        
        2.5.1 ER and the Golgi Apparatus 41
        
        2.5.2 Transport Vesicles 41
        
        2.5.3 Vacuolar System 43
        
        2.5.3.1 Yeast Vacuole 43
        
        2.5.3.2 Vacuolar Degradation 44
        
        2.5.5 Mitochondria 44
        
        2.5.5.1 Mitochondrial Structure 44
        
        2.5.4 Endocytosis and Exocytosis 44
        
        2.5.6 Peroxisomes 45
      - Further Reading 46
    - 3 Yeast Metabolism 48
      - 3.1 Metabolic Pathways and Energy 48
      - 3.2 Catabolism of Hexose Carbon Sources 48
        
        3.2.1 Principal Pathways 48
        
        3.2.2 Respiration Versus Fermentation 49
        
        3.2.3 Catabolism of Other Sugars – Galactose 50
        
        3.2.4 Metabolism of Non-Hexose Carbon Sources 51
      - 3.3 Gluconeogenesis and Carbohydrate Biosynthesis 53
        
        3.3.2 Storage Carbohydrates 53
        
        3.3.2.1 Glycogen 53
        
        3.3.2.2 Trehalose 54
        
        3.3.1 Gluconeogenesis 53
        
        3.3.3 Unusual Carbohydrates 54
        
        3.3.3.1 Unusual Hexoses and Amino Sugars 54
        
        3.3.3.2 Inositol and its Derivatives 55
        
        3.3.3.3 N- and O-Linked Glycosylation 56
        
        3.3.4 Structural Carbohydrates 57
      - 3.4 Fatty Acid and Lipid Metabolism 58
        
        3.4.1 Fatty Acids 58
        
        3.4.2 Lipids 58
        
        3.4.3 Glycolipids 59
        
        3.4.3.1 Phosphatidylinositol and Derivatives 59
        
        3.4.3.2 Sphingolipids 61
        
        3.4.3.3 Glycosylphosphatidylinositol (GPI) 62
        
        3.4.4 Isoprenoid Biosynthesis 63
      - 3.5 Nitrogen Metabolism 65
        
        3.5.1 Catabolic Pathways 65
        
        3.5.2 Amino Acid Biosynthesis Pathways 67
        
        3.5.2.1 Glutamate Family 67
        
        3.5.2.2 Aspartate Family 67
        
        3.5.2.3 Branched Amino Acids 68
        
        3.5.2.6 Alanine 69
        
        3.5.2.4 Lysine 69
        
        3.5.2.7 Aromatic Amino Acids 69
        
        3.5.2.5 Serine, Cysteine, and Glycine 69
        
        3.5.2.9 Amino Acid Methylation 70
        
        3.5.2.8 Histidine 70
        
        3.6 Nucleotide Metabolism 71
        
        3.6.1 Pyrimidine Derivatives 71
        
        3.6.2 Purine Derivatives 71
        
        3.6.4 Nucleotide Modification 73
        
        3.6.3 Deoxyribonucleotides 73
        
        3.7 Phosphorus and Sulfur Metabolism 74
        
        3.7.1 Phosphate 74
        
        3.7.2 Sulfur 75
        
        3.7.2.1 Fixation and Reduction of Sulfate 75
        
        3.7.2.2 Cycle of Activated Methyl Groups 76
        
        3.8 Vitamins and Cofactors 76
        
        3.8.2 Thiamine 76
        
        3.8.1 Biotin 76
        
        3.8.5 Riboflavin Derivatives 77
        
        3.8.3 Pyridoxine 77
        
        3.8.4 NAD 77
        
        3.8.7 Folate 78
        
        3.8.8 Tetrapyrroles 78
        
        3.8.6 Pantothenic Acid and Coenzyme A 78
        
        3.8.9 Ubiquinone (Coenzyme Q) 79
        
        3.9 Transition Metals 80
        
        Further Reading 81
        
        4 Yeast Molecular Techniques 82
        
        4.1 Handling of Yeast Cells 82
        
        4.1.2 Isolation of Particular Cell Types and Components 82
        
        4.1.1 Growth of Yeast Cells 82
        
        4.2 Genetic Engineering and Reverse Genetics 82
        
        4.2.1 Molecular Revolution 82
        
        4.2.2 Transformation of Yeast Cells 84
        
        4.2.2.1 Yeast Shuttle Vectors 84
        
        4.2.2.2 Yeast Expression Vectors 85
        
        4.2.2.3 Secretion of Heterologous Proteins from Yeast 86
        
        4.2.2.4 Fluorescent Proteins Fused to Yeast Proteins 86
        
        4.2.3 Yeast Cosmid Vectors 87
        
        4.2.4 Yeast Artificial Chromosomes 88
        
        4.3 More Genetic Tools from Yeast Cells 88
        
        4.3.1 Yeast Two-Hybrid System 88
        
        4.3.2 Yeast Three-Hybrid System 89
        
        4.3.3 Yeast One-Hybrid (Matchmaker) System 90
        
        4.4 Techniques in Yeast Genome Analyses 90
        
        4.4.1 Microarrays 90
        
        4.4.1.1 DNA-Based Approaches 90
        
        4.4.1.2 Proteome Analyses 91
        
        4.4.3 Mass Spectrometry 93
        
        4.4.2 Affinity Purification 93
        
        Further Reading 95
        
        5 Yeast Genetic Structures and Functions 96
        
        5.1 Yeast Chromosome Structure and Function 96
        
        5.1.1 Yeast Chromatin 96
        
        5.1.1.1 Organization of Chromatin Structure 96
        
        5.1.1.2 Modification of Chromatin Structure 96
        
        5.1.1.2.1 Modification of Histones 96
        
        5.1.1.2.2 Remodeling Chromatin Structure Overview 104
        
        5.1.2 Centromeres 108
        
        5.1.3 Replication Origins and Replication 108
        
        5.1.3.1 Initiation of Replication 108
        
        5.1.3.2 Replication Machinery 111
        
        5.1.3.2.1 DNA Polymerases 111
        
        5.1.3.2.2 Replication and Replication Factors 112
        
        5.1.3.2.3 Postreplication Repair and DNA Damage Tolerance 112
        
        5.1.3.3 Replication and Chromatin 113
        
        5.1.3.3.1 Chromatin Reorganization 113
        
        5.1.3.3.2 Silencing and Boundaries 114
        
        5.1.3.4 DNA Damage Checkpoints 116
        
        5.1.3.4.1 Checkpoints During Replication 116
        
        5.1.3.4.2 DSB Repair 117
        
        5.1.4 Telomeres 119
        
        5.1.5 Transposons in Yeast 121
        
        5.1.5.1 Classes of Transposable Elements 121
        
        5.1.5.2 Retrotransposons in S. cerevisiae 121
        
        5.1.5.2.1 Ty Elements and their Genomes 121
        
        5.1.5.2.2 Behavior of Ty Elements 122
        
        5.1.5.2.3 Expression of Ty Elements 123
        
        5.1.5.3 Ty Replication 124
        
        5.1.5.4 Interactions between Ty Elements and their Host 125
        
        5.2 Yeast tRNAs, Genes, and Processing 126
        
        5.2.1 Yeast tRNAs 126
        
        5.2.1.1 Yeast Led the Way to tRNA Structure 126
        
        5.2.1.2 Yeast tRNA Precursors and Processing 128
        
        5.2.2 Current Status of Yeast tRNA Research 129
        
        5.2.2.2 tRNA Processing and Maturation 129
        
        5.2.2.1 Yeast tRNAs and their Genes 129
        
        5.2.2.3 Participation of tRNAs in an Interaction Network 132
        
        5.2.2.3.1 Aminoacylation of tRNAs 132
        
        5.2.2.3.2 Rules, Codon Recognition, and Specific tRNA Modification 134
        
        5.2.2.3.3 Recognition of tRNAs in the Protein Biosynthetic Network 134
        
        5.3 Yeast Ribosomes: Components, Genes, and Maturation 136
        
        5.3.1 Historical Overview 136
        
        5.3.2 Ribosomal Components 136
        
        5.3.2.1 Ribosomal RNAs 136
        
        5.3.2.2 Ribosomal Proteins 137
        
        5.3.3 Components and Pathways of Yeast Ribosome Maturation 137
        
        5.4 Messenger RNAs 139
        
        5.4.1 First Approaches to the Structure of Yeast mRNAs 139
        
        5.4.2 Introns and Processing of pre-mRNA 140
        
        5.4.3 Provenance of Introns 144
        
        5.5 Extrachromosomal Elements 144
        
        5.5.1 Two Micron DNA 144
        
        5.5.2 Killer Plasmids 144
        
        5.5.3 Yeast Prions 144
        
        5.6 Yeast Mitochondrial Genome 146
        
        Further Reading 148
        
        6 Gene Families Involved in Cellular Dynamics 150
        
        6.1 ATP- and GTP-Binding Proteins 150
        
        6.1.1 ATPases 150
        
        6.1.1.1 P-Type ATPases 150
        
        6.1.1.2 V-Type ATPases 150
        
        6.1.1.3 Chaperones, Cochaperones, and Heat-Shock Proteins 151
        
        6.1.1.3.1 HSP70 Family 151
        
        6.1.1.3.2 HSP40 Family 152
        
        6.1.1.3.3 HSP90 Family 152
        
        6.1.1.3.6 HSP26 and HSP42 155
        
        6.1.1.3.4 HSP60 Family 155
        
        6.1.1.3.5 HSP104 155
        
        6.1.1.3.9 HSP30 156
        
        6.1.1.3.7 HSP150 156
        
        6.1.1.3.10 HSP10 156
        
        6.1.1.3.8 HSP31/32/33 156
        
        6.1.1.3.11 Others 156
        
        6.1.1.4 Other ATP-Binding Factors 156
        
        6.1.2 Small GTPases and Their Associates 156
        
        6.1.2.1 RAS Family 157
        
        6.1.2.4 ARF Family 157
        
        6.1.2.2 RAB Family 157
        
        6.1.2.3 RHO/RAC Family 157
        
        6.1.2.5 Ran GTPAse 159
        
        6.1.3 G-Proteins 159
        
        6.1.3.1 Mating Pheromone G-Protein 159
        
        6.1.3.3 RGS Family 160
        
        6.1.3.4 G-Like Proteins 160
        
        6.1.3.2 Gpr1-Associated G-Protein 160
        
        6.2 Regulatory ATPases: AAA and AAA+ Proteins 161
        
        6.2.1 ATP-Dependent Proteases 161
        
        6.2.6 Dynein 162
        
        6.2.4 Peroxisomal AAA Proteins 162
        
        6.2.2 Membrane Fusion Proteins 162
        
        6.2.5 Katanin and Vps4p 162
        
        6.2.3 Cdc48 162
        
        6.2.9 Other AAA+ Yeast Proteins 163
        
        6.2.7 DNA Replication Proteins 163
        
        6.2.8 RuvB-Like Proteins 163
        
        6.3 Protein Modification by Proteins and Programmed Protein Degradation 164
        
        6.3.1 Ubiquitin–Proteasome System (UPS) 164
        
        6.3.1.1 Initial Discoveries 164
        
        6.3.1.2 Ubiquitin and Factors in the Ubiquitin-Mediated Pathway 164
        
        6.3.1.3 E3 Ubiquitin Ligases 165
        
        6.3.1.3.1 HECT-Type Ligases 165
        
        6.3.1.3.2 RING Finger-Type Ligases 166
        
        6.3.1.3.3 Functions of Selected E3 Ligases 167
        
        6.3.1.4 Ubiquitin-Specific Proteases 170
        
        6.3.2 Yeast Proteasomes 170
        
        6.3.2.1 Initial Discoveries 170
        
        6.3.2.3 Regulation of Yeast Proteasome Activity 171
        
        6.3.2.2 Structure of the Proteasome 171
        
        6.3.3 More Functions for Ubiquitin 173
        
        6.3.4 Ubiquitin-Like Proteins (ULPs) and Cognate Factors 174
        
        6.3.4.1 SUMO 174
        
        6.3.4.2 Rub1 175
        
        6.3.4.3 Ubiquitin Domain Proteins 175
        
        6.3.4.4 Substrate Delivery to the Proteasome 176
        
        6.4 Yeast Protein Kinases and Phosphatases 176
        
        6.4.1 Protein Kinases in Yeast 176
        
        6.4.1.1 PKA as a Prototype Kinase 176
        
        6.4.1.2 Yeast Possesses a Multitude of Kinases 176
        
        6.4.2 Protein Phosphatases in Yeast 181
        
        6.5 Yeast Helicase Families 182
        
        6.5.1 RNA Helicases in Yeast 189
        
        6.5.1.1 Structures and Motifs 189
        
        6.5.1.2 Functions of RNA Helicases in Yeast 190
        
        6.5.2 DNA Helicases in Yeast 191
        
        6.5.2.1 Structures and Motifs 191
        
        6.5.2.2 Functions of DNA Helicases 191
        
        6.5.2.2.1 ASTRA Complex 193
        
        6.5.2.2.2 RAD Epistasis Group 193
        
        6.5.2.2.3 Monomeric DNA Helicases 193
        
        Further Reading 196
        
        7 Yeast Growth and the Yeast Cell Cycle 198
        
        7.1 Modes of Propagation 198
        
        7.1.1 Vegetative Reproduction 198
        
        7.1.1.1 Budding 198
        
        7.1.1.2 Septins and Bud Neck Filaments 201
        
        7.1.1.3 Spindle Pole Bodies and their Dynamics 202
        
        7.1.3 Filamentous Growth 204
        
        7.1.2 Sexual Reproduction 204
        
        7.1.4 Yeast Aging and Cell Death 206
        
        7.1.4.1 Yeast Lifespan 206
        
        7.1.4.2 Yeast Apoptosis 207
        
        7.1.4.2.1 External Triggers of Yeast Apoptosis 207
        
        7.1.4.2.2 Endogenous Triggers of Yeast Apoptosis 208
        
        7.1.4.2.3 Regulation of Yeast Apoptosis 208
        
        7.2 Cell Cycle 209
        
        7.2.1 Dynamics and Regulation of the Cell Cycle 209
        
        7.2.1.1 Some Historical Notes 209
        
        7.2.1.2 Periodic Events in the First Phases of the Cell Cycle 211
        
        7.2.1.2.1 CDK and Cyclins 212
        
        7.2.1.2.2 Regulation of the CDK/Cyclin System 213
        
        7.2.2 Dynamics and Regulation of Mitosis 216
        
        7.2.2.1 Sister Chromatids: Cohesion 216
        
        7.2.2.2 Spindle Assembly Checkpoint 219
        
        7.2.2.3 Chromosome Segregation 221
        
        7.2.2.4 Regulation of Mitotic Exit 222
        
        7.3 Meiosis 223
        
        7.3.1 Chromosome Treatment During Meiosis 223
        
        7.3.2 Regulation of Meiosis 224
        
        7.3.2.1 Early, Middle, and Late Meiotic Events 224
        
        7.3.2.2 Sporulation 225
        
        7.3.3 Checkpoints in Meiosis 225
        
        Further Reading 227
        
        8 Yeast Transport 230
        
        8.1 Intracellular Protein Sorting and Transport 230
        
        8.1.1 “Signal Hypothesis” 230
        
        8.1.2 Central Role of the ER 230
        
        8.1.3 Intracellular Protein Traficking and Sorting 231
        
        8.1.3.1 Some History 231
        
        8.1.3.2 Membrane Fusions 233
        
        8.1.3.2.1 SNAREs and All That 233
        
        8.1.3.2.2 Small GTPases and Transport Protein Particles 234
        
        8.1.3.3 ER-Associated Protein Degradation 237
        
        8.1.3.4 Golgi Network 238
        
        8.1.3.5 Vacuolar Network 239
        
        8.1.3.5.1 Autophagy 239
        
        8.1.3.5.2 Cytoplasm-to-Vacuole Targeting (CVT) Pathway 240
        
        8.1.3.5.3 Nomenclature in Autophagy and Cvt 241
        
        8.1.3.6 Endocytosis and the Multivesicular Body (MVB) Sorting Pathway 241
        
        8.1.3.6.1 Endocytosis by Vesicles Budding from the Membrane 241

Molecular and Cell Biology

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