Yeast: Molecular and Cell Biology Book

Table of Contents (2nd edition)
1 Introduction
1.1 Historical Aspects
1.2 Yeast as a Eukaryotic Model System
2 Yeast Cell Architecture and Functions
2.1 General Morphology
2.2 The Yeast Envelope
2.3 The Yeast Cytoplasm and Cytoskeleton
2.4 The Yeast Nucleus
2.4.1 Overview
2.4.2 The Nuclear Pore
2.5 Yeast Cell Organellar Structures
3 Yeast Metabolism
3.1 Metabolic Pathways and Energy
3.2 Catabolism of Hexose Carbon Sources
3.2.1 Principal Pathways
3.2.2 Respiration versus Fermentation
3.2.3 Catabolism of Other Sugars ? Galactose
3.2.4 Metabolism of Non-Hexose Carbon Sources
3.3 Gluconeogenesis and Carbohydrate Synthesis
3.3.1 Gluconeogenesis
3.3.2 Storage Carbohydrates
3.3.2.1 Glycogen
3.3.2.2 Trehalose
3.3.3 Unusual Carbohydrates
3.3.3.1 Unsual Hexoses and Aminosugars
3.3.3.2 Inositol and its Derivatives
3.3.3.3 N- and O-linked Glycosylation
3.3.4 Structural Carbohydrates
3.4 Fatty Acid and Lipid Metabolism
3.4.1 Fatty Acids
3.4.2 Lipids
3.4.3 Glycolipids
3.4.3.1 Phosphatidylinositol and Derivatives
3.4.3.2 Sphingolipids
3.4.3.3 Glycosylphosphatidylinositol (GPI)
3.4.4 Isoprenoid Biosynthesis
3.5 Nitrogen Metabolism
3.5.1 Catabolic Pathways
3.5.2 Amino Acid Biosynthesis
3.5.2.1 Glutamate Family
3.5.2.2 Aspartate Family
3.5.2.3 Branched Amino Acids
3.5.2.4 Lysine
3.5.2.5 Serine, Cysteine, Glycine
3.5.2.6 Alanine
3.5.2.7 Aromatic Amino Acids
3.5.2.8 Histidine
3.5.3 Protein Biosynthesis
3.5.3.1 Aminoacylation
3.5.3.2 The Recognition Problem
3.6 Nucleotide Metabolism
3.6.1 Pyrimidine Derivatives
3.6.2 Purine Derivatives
3.6.3 Deoxyribonucleotides
3.6.4 Nucleotide Modification
3.7 Phosphorus and Sulphur Metabolism
3.7.1 Inorganic Phosphate
3.7.2. Sulfur Requirement
3.7.2.1 Fixation and Reduction of Sulfate
3.7.2.2 Cycle of Activated Methylgroups
3.8 Vitamins and Cofactors
3.8.1 Biotin
3.8.2 Thiamine
3.8.3 Pyridoxine
3.8.4 Nicotinamide Adenine Dinucleotides (NAD)
3.8.5 Riboflavin Derivatives
3.8.6 Pantothenic Acid and Coenzyme A
3.8.7 Folate
3.8.8 Tetrapyrroles
3.8.9 Ubiquinone (Coenzyme Q)
3.9 Transition Metals
4 Yeast Molecular Techniques
4.1 Isolation of Particular Cell Types and Components
4.2 Genetic Engineering and Reverse Genetics
4.2.1 The Molecular Revolution
4.2.2 Transformation of Yeast Cells
4.2.2.1 Yeast Shuttle Vectors
4.2.2.2 Yeast Expression Vectors
4.2.2.3 Secretion of Heterologous Proteins from Yeast
4.2.2.4 GFP Fusion Proteins
4.2.3 Cosmid Vectors
4.2.4 Yeast Artificial Chromosomes (YACs)
4.3 More Genetic Tools from Yeast
4.3.1 The Two-Hybrid System
4.3.2 The One-Hybrid System
5 Yeast Genetic Structures and Functions
5.1 Yeast Chromosome Structure and Function
5.1.1 Yeast Chromatin
5.1.1.1 Organization of Chromatin Structure
5.1.1.2 Modification of Chromatin Structure
5.1.2 Centromeres
5.1.3 Replication Origins and Replication
5.1.3.1 Initiation of Replication
5.1.3.2 Elongation and Chromatin Remodeling
5.1.3.3 DNA Damage Checkpoints
5.1.4 Telomeres
5.1.5 Retrotransposons in Yeast
5.1.5.1 Types and Structure
5.1.5.2 Ty Replication
5.1.5.3 Interactions between Ty Elements and Their Host
5.2 Molecular Structures of Yeast tRNAs and their Genes
5.2.1 tRNAs
5.2.2 tRNA Precursors and Processing
5.3 Molecular Structures of Ribosomal Components and Their Genes Processing: Processosome
5.4 Messenger RNAs
5.4.1 Structure of Yeast mRNAs
5.4.2 Introns and Processing of Pre-mRNA
5.5 Extrachromosomal Elements
5.5.1 2? DNA
5.5.2 Killer Plasmids
5.5.3 Yeast Prions
5.6 The Yeast Mitochondrial Genome
6 Gene Families Involved in Yeast Cellular Dynamics
6.1 ATP- and GTP-binding Proteins
6.1.1 ATPases
6.1.1.1 P-type ATPases
6.1.1.2 V-type ATPases
6.1.1.3 Chaperones, Co-chaperones and Heat-Shock Proteins HSP70 Family HSP40 Family HSP90 Family HSP60 Family HSP104
6.1.1.4 Other ATP-binding Factors
6.1.2 Small GTPases and their Associates
6.1.2.1 Ras Family
6.1.2.2 Rab Family
6.1.2.3. Rho/Rac Family
6.1.2.4 Arf Family
6.1.3 G-Proteins
6.2 Regulatory ATPases ? AAA+ Proteins
6.2.1 ATP-dependent Proteases
6.2.2 Membrane Fusion Proteins
6.2.3 Cdc48p
6.2.4 Peroxisomal AAA Proteins
6.2.5 Katanin and Vps4p
6.2.6 Dynein
6.2.7 DNA Replication Proteins
6.2.8 RuvB-like Proteins
6.3 Protein Modification by Proteins and Programmed Protein Degradation
6.3.1 The Ubiquitin-Proteasome System (UPS)
6.3.1.1 Initial Discoveries
6.3.1.2 Ubiquitin and Factors in the Ubiquitin-mediated Pathway
6.3.1.3 E3 Ubiquitin LIgases HECT Type Ligases RING Finger Type Ligases Regulation of E3 Ligases
6.3.2 Yeast Proteasomes
6.3.2.1 Initial Discoveries
6.3.2.2 Proteasomal Structure
6.3.2.2 Regulation of Yeast Proteasome Activity
6.3.3 More Functions for Ubiquitin
6.3.4 Ubiquitin-like Proteins (ULPs) and Cognate Factors
6.3.4.1 SUMO
6.3.4.2 Rub1
6.3.4.3 Ubiquitin-domain Proteins (UDPs)
6.4 Yeast Protein Kinases and Phosphatases
6.4.1 Families of Protein Kinases
6.4.2 Protein Phosphatases
6.5 Helicases
6.5.1 RNA Helicases
6.5.2 DNA Helicases
6.6 RAD Proteins
7 Yeast Propagation and the Yeast Cell Cycle
7.1 Modes of Propagation
7.1.1 Vegetative Reproduction
7.1.1.1 Budding
7.1.1.2 Septins and Bud-neck Filaments
7.1.1.3 Spindle Pole Bodies
7.1.1.4 Spindle Dynamics
7.1.2 Sexual Reproduction
7.1.3 Filamentous Growth
7.1.4 Yeast Cell Death
7.2 The Cell Cycle
7.2.1 Dynamics and Regulation of the Cell Cycle
7.2.2 Sister Chromatids ? Cohesion and Separation
7.2.3 The Spindle Checkpoint (SCP)
7.2.4 Chromosome Segragation during Meiosis
8 Yeast Transport
8.1 Intracellular Protein Sorting and Transport
8.1.1 The ?Signal Hypothesis?
8.1.2 Central Role of the Endoplasmic Reticulum
8.1.3 Intracellular Protein Trafficking and Sorting
8.1.3.1 Some History
8.1.3.2 Membrane Fusions
8.1.3.3 ER-associated Protein Degradation (ERAD)
8.1.3.4 The Vacuolar Network
8.1.3.5 Endocytosis and the Multivesicular Body Sorting Pathway
8.1.3.6 Exocytosis
8.2 Nuclear Traffic
8.2.1 Nuclear Transport
8.2.2 Nuclear mRNA Quality Control
8.2.3 Nuclear Export of mRNA
8.2.4 Nuclear Dynamics of tRNA
8.3 Membrane Transporters in Yeast
8.3.1 Transport of Cations
8.3.2 Channels and ATPases
8.3.2.1 Channels
8.3.2.2 ATP-dependent Permeases
8.3.3 Ca++ Signaling and Transport Pathways in Yeast
8.3.3.1 Ca++ Transport
8.3.3.2 Ca++-mediated Control
8.3.3.3 Ca++ and Cell Death
8.3.4 Transition Metal Transport
8.3.4.1 Iron
8.3.4.2 Copper
8.3.4.3 Zinc
8.3.4.4 Manganese
8.3.5 Anion Transport
8.3.5.1 Phosphate Transport
8.3.5.2 Transport of Other Anions
8.3.6 Nutrient and Ammonium Transport
8.3.6.1 Carbohydrate Transport
8.3.6.2 Amino Acid Transport
8.3.6.3 Transport of Nucleotide Constituents/Nucleotide Sugars
8.3.6.4 Transport of Cofactors and Vitamins
8.3.6.5 Ammonium Transport
8.3.7 Mitochondrial Transport
8.3.7.1 Transport of Substrates
8.3.7.2 Electron Transport Chain
8.3.7.3 Proton Transport ? ATP Synthase
9 Yeast Gene Expression
9.1 Transcriptional Regulation and Transcription Factors
9.2 Polymerases and Cofactors
9.2.1 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 TBP
9.2.4.2 TFIIA
9.2.4.3 TFIIB
9.2.4.4 TFIIE and TFIIF
9.2.4.5 TFIIH
9.2.4.6 Transcription Activators
9.2.4.7 TFIID
9.2.4.8 SRB/Mediator
9.2.4.9 SAGA
9.2.4.10 Transcriptional Repressors
9.3 Transcriptional Initiation, Elongation and Regulation
9.3.1 Chromatin Remodelling
9.3.2 Regulator Complexes
9.4 DNA Repair Connected to Transcription
9.4.1 Nucleotide Excision Repair
9.4.2 Mismatch Repair
9.4.3 Thymidine Dimer Excision
9.5 Coupling Transcription to mRNA Processing
9.5.1 Polyadenylation
9.5.2 Generation of Functional mRNA
9.5.2.1 General Principles
9.5.2.2 Control of mRNA Decay
9.5.2.2.1 Exosome-mediated Pathways
9.5.2.2.2 Nonsense-mediated mRNA Decay
9.6 The Yeast Translation Apparatus
9.6.1 Initiation
9.6.2 Elongation and Termination
9.7 Protein Splicing ? Yeast Inteins
10 Molecular Signalling Cascades and Gene Regulation
10.1 Ras/cAMP Pathway
10.2 MAP Kinase Pathways
10.2.1 Mating Type Pathway
10.2.2 Filamentation/
Invasion Pathway
10.2.3 Control of Cell Integrity
10.2.4 High Osmolarity Growth (HOG) Pathway
10.2.5 Spore Wall Assembly Pathway
10.3 General Control by Gene Repression
10.3.1 Ssn6-Tup1 Repression
10.3.3 Activation and Repression by Rap1
10.4 Gene Regulation by Nutrients
10.4.1 The TOR System
10.4.2 Regulation of Glucose Metabolism
10.4.3 Regulation of Galactose Metabolism
10.4.4 General Amino Acid Control
10.4.5 Regulation of Arginine Metabolism
10.5 Stress Responses in Yeast
10.5.1 Temperature Stress and Heat-shock Proteins
10.5.2 Oxidative and Chemical Stresses
10.5.2.1 AP-1 Transcription Factors in Yeast
10.5.2.2 The STRE-dependent System
10.5.2.3 Pleiotropic Drug Resistance -
ABC Transporters
10.5.3 The Unfolded Protein Response
11 Function and Biogenesis of Mitochondria and Peroxisomes
11.1 Mitochondria
11.1.1 Genetic Biochemistry of Yeast Mitochondria
11.1.2 Mitochondrial Functions Critical to Cell Viability
11.1.2.1 Superoxide Dismutase (SOD)
11.1.2.2 Iron Homeostasis
11.1.3 Biogenesis of Mitochondria -
Protein Transport
11.1.3.1 The 'Presequence Pathway? and the 'MIA Pathway?
11.1.3.2 The 'Membrane Sorting Pathway?- Switch between TIM22 and TIM23
11.1.3.3 The '?-barrel Pathway?
11.1.3.4 The Endogenous Membrane Insertion Machinery
11.1.4 Mitochondrial Quality Control and Remodelling
11.2 Peroxisomes
12 Yeast Genome, Proteome, Transcriptome, Metabolome, and Regulatory Networks
12.1 The Yeast Genome Sequencing Project
12.2 Characteristics of the Yeast Genome
12.2.1 Comparison of Genetic and Physical Maps
12.2.2 Gene Organization
12.2.2.1 Protein Encoding Genes
12.2.2.2 Pseudogenes and Introns
12.2.3 Genetic Redundancy ? Gene Duplications
12.2.3.1 Duplicated Genes in Subtelomeric Regions
12.2.3.2 Duplicated Genes Internal to Chromosomes
12.2.3.3 Duplicated Genes in Clusters
12.2.4 Gene Typification and Gene Families
12.2.5 tRNA Multiplicity and Codon Capacity in Yeast
12.2.5.1 Correlation of tRNA Abundance to Gene Copy Number
12.2.5.2 tRNA Gene Redundancy and Codon Selection in Yeast
12.2.6 Functional Analysis of Yeast Genes
12.3 Functional Genomics
12.3.1 Yeast Transriptome
12.3.1.1 Genomic Profiling
12.3.1.2 Protein-DNA Interactions
12.3.2 Yeast Proteome
12.3.2.1 Protein Analysis
12.3.2.2 Proteome Chips
12.3.2.3 Protein-protein Interactions and Protein Complexes
12.3.3 Yeast Metabolome
12.3.4 Genetic Interaction Networks: Regulatory Networks and Oscillations
13 Disease Genes in Yeast
13.1 General Aspects
13.2 Trinucleotide Repeats and Neurodegenerative Diseases
13.3 Ageing and Age-related Diseases
13.4 Mitochondrial Diseases
14 Yeast Biotechnology
14.1 Fermentation and Metabolic Engineering
14.1.1 Typical Fermentation Procedures
14.1.2 Food and Chemical Industries ? Metabolic Engineering
14.2 Biopharmaceuticals from Health-Care Industries
14.3 Biomedical Research
14.4 Environmental Technologies -
Cell-surface Display
[15] Hemiascomycetous Yeasts
(suggested)
15.1 Selected Model Genomes
15.2 Genolevures Projects: Sequenced Genomes
15.3 Ecology, Adaptation of Metabolic Behavior
15.4 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 Species
16.2 Gene Duplication Mechanisms
16.2.1 Expansion of Tandem Gene Arrays
16.2.2 Segmental Duplications
16.2.3 Whole-Genome Duplications
16.2.4 Single Gene Duplications
16.3 Other Mechanisms of Genome Evolution Epilogue: The Future of Yeast Research