Yeast. Molecular and Cell Biology

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.

Table of Contents

1. Introduction
1. Historical Aspects
2. Yeast as a Eukaryotic Model System
2. Yeast Cell Architecture and Functions
1. General Morphology
2. The Yeast Envelope
3. The Yeast Cytoplasm and Cytoskeleton
4. The Yeast Nucleus
1. Overview
2. The Nuclear Pore
5. Yeast Cell Organellar Structures
3. Yeast Metabolism
1. Metabolic Pathways and Energy
2. Catabolism of Hexose Carbon Sources
1. Principal Pathways
2. Respiration versus Fermentation
3. Catabolism of Other Sugars ? Galactose
4. Metabolism of Non-Hexose Carbon Sources
3. Gluconeogenesis and Carbohydrate Synthesis
1. Gluconeogenesis
2. Storage Carbohydrates
1. Glycogen
2. Trehalose
3. Unusual Carbohydrates
1. Unsual Hexoses and Aminosugars
2. Inositol and its Derivatives
3. N- and O-linked Glycosylation
4. Structural Carbohydrates
4. Fatty Acid and Lipid Metabolism
1. Fatty Acids
2. Lipids
3. Glycolipids
1. Phosphatidylinositol and Derivatives
2. Sphingolipids
3. Glycosylphosphatidylinositol (GPI)
4. Isoprenoid Biosynthesis
5. Nitrogen Metabolism
1. Catabolic Pathways
2. Amino Acid Biosynthesis
1. Glutamate Family
2. Aspartate Family
3. Branched Amino Acids
4. Lysine
5. Serine, Cysteine, Glycine
6. Alanine
7. Aromatic Amino Acids
8. Histidine
3. Protein Biosynthesis
1. Aminoacylation
2. The Recognition Problem
6. Nucleotide Metabolism
1. Pyrimidine Derivatives
2. Purine Derivatives
3. Deoxyribonucleotides
4. Nucleotide Modification
7. Phosphorus and Sulphur Metabolism
1. Inorganic Phosphate
2. Sulfur Requirement
1. Fixation and Reduction of Sulfate
2. Cycle of Activated Methylgroups
8. Vitamins and Cofactors
1. Biotin
2. Thiamine
3. Pyridoxine
4. Nicotinamide Adenine Dinucleotides (NAD)
5. Riboflavin Derivatives
6. Pantothenic Acid and Coenzyme A
7. Folate
8. Tetrapyrroles
9. Ubiquinone (Coenzyme Q)
9. Transition Metals
4. Yeast Molecular Techniques
1. Isolation of Particular Cell Types and Components
2. Genetic Engineering and Reverse Genetics
1. The Molecular Revolution
2. Transformation of Yeast Cells
1. Yeast Shuttle Vectors
2. Yeast Expression Vectors
3. Secretion of Heterologous Proteins from Yeast
4. GFP Fusion Proteins
3. Cosmid Vectors
4. Yeast Artificial Chromosomes (YACs)
3. More Genetic Tools from Yeast
1. The Two-Hybrid System
2. The One-Hybrid System
5. Yeast Genetic Structures and Functions
1. Yeast Chromosome Structure and Function
1. Yeast Chromatin
1. Organization of Chromatin Structure
2. Modification of Chromatin Structure
2. Centromeres
3. Replication Origins and Replication
1. Initiation of Replication
2. Elongation and Chromatin Remodeling
3. DNA Damage Checkpoints
4. Telomeres
5. Retrotransposons in Yeast
1. Types and Structure
2. Ty Replication
3. Interactions between Ty Elements and Their Host
2. Molecular Structures of Yeast tRNAs and their Genes
1. tRNAs
2. tRNA Precursors and Processing
3. Molecular Structures of Ribosomal Components and Their Genes
4. Processing: Processosome
5. Messenger RNAs
1. Structure of Yeast mRNAs
2. Introns and Processing of Pre-mRNA
6. Extrachromosomal Elements
1. 2? DNA
2. Killer Plasmids
3. Yeast Prions
7. The Yeast Mitochondrial Genome
6. Gene Families Involved in Yeast Cellular Dynamics
1. ATP- and GTP-binding Proteins
1. ATPases
1. P-type ATPases
2. V-type ATPases
3. Chaperones, Co-chaperones and Heat-Shock Proteins
1. HSP70 Family
2. HSP40 Family
3. HSP90 Family
4. HSP60 Family
5. HSP104
4. Other ATP-binding Factors
2. Small GTPases and their Associates
1. Ras Family
2. Rab Family
3. Rho/Rac Family
4. Arf Family
3. G-Proteins
2. Regulatory ATPases ? AAA+ Proteins
1. ATP-dependent Proteases
2. Membrane Fusion Proteins
3. Cdc48p
4. Peroxisomal AAA Proteins
5. Katanin and Vps4p
6. Dynein
7. DNA Replication Proteins
8. RuvB-like Proteins
3. Protein Modification by Proteins and Programmed Protein Degradation
1. The Ubiquitin-Proteasome System (UPS)
1. Initial Discoveries
2. Ubiquitin and Factors in the Ubiquitin-mediated Pathway
3. E3 Ubiquitin LIgases
1. HECT Type Ligases
2. RING Finger Type Ligases
3. Regulation of E3 Ligases
2. Yeast Proteasomes
1. Initial Discoveries
2. Proteasomal Structure
3. Regulation of Yeast Proteasome Activity
3. More Functions for Ubiquitin
4. Ubiquitin-like Proteins (ULPs) and Cognate Factors
1. SUMO
2. Rub1
3. Ubiquitin-domain Proteins (UDPs)
4. Yeast Protein Kinases and Phosphatases
1. Families of Protein Kinases
2. Protein Phosphatases
5. Helicases
1. RNA Helicases
2. DNA Helicases
6. RAD Proteins
7. Yeast Propagation and the Yeast Cell Cycle
1. Modes of Propagation
1. Vegetative Reproduction
1. Budding
2. Septins and Bud-neck Filaments
3. Spindle Pole Bodies
4. Spindle Dynamics
2. Sexual Reproduction
3. Filamentous Growth
4. Yeast Cell Death
2. The Cell Cycle
1. Dynamics and Regulation of the Cell Cycle
2. Sister Chromatids ? Cohesion and Separation
3. The Spindle Checkpoint (SCP)
4. Chromosome Segragation during Meiosis
8. Yeast Transport
1. Intracellular Protein Sorting and Transport
1. The ?Signal Hypothesis?
2. Central Role of the Endoplasmic Reticulum
3. Intracellular Protein Trafficking and Sorting
1. Some History
2. Membrane Fusions
3. ER-associated Protein Degradation (ERAD)
4. The Vacuolar Network
5. Endocytosis and the Multivesicular Body Sorting Pathway
6. Exocytosis
2. Nuclear Traffic
1. Nuclear Transport
2. Nuclear mRNA Quality Control
3. Nuclear Export of mRNA
4. Nuclear Dynamics of tRNA
3. Membrane Transporters in Yeast
1. Transport of Cations
2. Channels and ATPases
1. Channels
2. ATP-dependent Permeases
3. Ca++ Signaling and Transport Pathways in Yeast
1. Ca++ Transport
2. Ca++-mediated Control
3. Ca++ and Cell Death
4. Transition Metal Transport
1. Iron
2. Copper
3. Zinc
4. Manganese
5. Anion Transport
1. Phosphate Transport
2. Transport of Other Anions
6. Nutrient and Ammonium Transport
1. Carbohydrate Transport
2. Amino Acid Transport
3. Transport of Nucleotide Constituents/Nucleotide Sugars
4. Transport of Cofactors and Vitamins
5. Ammonium Transport
7. Mitochondrial Transport
1. Transport of Substrates
2. Electron Transport Chain
3. Proton Transport ? ATP Synthase
9. Yeast Gene Expression
1. Transcriptional Regulation and Transcription Factors
2. Polymerases and Cofactors
1. RNA Polymerase I (Pol I)
2. RNA Polymerase III (Pol III)
3. RNA Polymerase II (Pol II)
4. General Transcription Factors (GTFs)
1. TBP
2. TFIIA
3. TFIIB
4. TFIIE and TFIIF
5. TFIIH
6. Transcription Activators
7. TFIID
8. SRB/Mediator
9. SAGA
10. Transcriptional Repressors
3. Transcriptional Initiation, Elongation and Regulation
1. Chromatin Remodelling
2. Regulator Complexes
4. DNA Repair Connected to Transcription
1. Nucleotide Excision Repair
2. Mismatch Repair
3. Thymidine Dimer Excision
5. Coupling Transcription to mRNA Processing
1. Polyadenylation
2. Generation of Functional mRNA
1. General Principles
2. Control of mRNA Decay
1. Exosome-mediated Pathways
2. Nonsense-mediated mRNA Decay
6. The Yeast Translation Apparatus
1. Initiation
2. Elongation and Termination
7. Protein Splicing ? Yeast Inteins
10. Molecular Signalling Cascades and Gene Regulation
1. Ras/cAMP Pathway
2. MAP Kinase Pathways
1. Mating Type Pathway
2. Filamentation/ Invasion Pathway
3. Control of Cell Integrity
4. High Osmolarity Growth (HOG) Pathway
5. Spore Wall Assembly Pathway
3. General Control by Gene Repression
1. Ssn6-Tup1 Repression
2. Activation and Repression by Rap1
4. Gene Regulation by Nutrients
1. The TOR System
2. Regulation of Glucose Metabolism
3. Regulation of Galactose Metabolism
4. General Amino Acid Control
5. Regulation of Arginine Metabolism
5. Stress Responses in Yeast
1. Temperature Stress and Heat-shock Proteins
2. Oxidative and Chemical Stresses
1. AP-1 Transcription Factors in Yeast
2. The STRE-dependent System
3. Pleiotropic Drug Resistance - ABC Transporters
4. The Unfolded Protein Response
11. Function and Biogenesis of Mitochondria and Peroxisomes
1. Mitochondria
1. Genetic Biochemistry of Yeast Mitochondria
2. Mitochondrial Functions Critical to Cell Viability
1. Superoxide Dismutase (SOD)
2. Iron Homeostasis
3. Biogenesis of Mitochondria - Protein Transport
1. The `Presequence Pathway? and the `MIA Pathway?
2. The `Membrane Sorting Pathway?- Switch between TIM22 and TIM23
3. The `?-barrel Pathway?
4. The Endogenous Membrane Insertion Machinery
4. Mitochondrial Quality Control and Remodelling
2. Peroxisomes
12. Yeast Genome, Proteome, Transcriptome, Metabolome, and Regulatory Networks
1. The Yeast Genome Sequencing Project
2. Characteristics of the Yeast Genome
1. Comparison of Genetic and Physical Maps
2. Gene Organization
1. Protein Encoding Genes
2. Pseudogenes and Introns
3. Genetic Redundancy ? Gene Duplications
1. Duplicated Genes in Subtelomeric Regions
2. Duplicated Genes Internal to Chromosomes
3. Duplicated Genes in Clusters
4. Gene Typification and Gene Families
5. tRNA Multiplicity and Codon Capacity in Yeast
1. Correlation of tRNA Abundance to Gene Copy Number
2. tRNA Gene Redundancy and Codon Selection in Yeast
6. Functional Analysis of Yeast Genes
3. Functional Genomics
1. Yeast Transriptome
1. Genomic Profiling
2. Protein-DNA Interactions
2. Yeast Proteome
1. Protein Analysis
2. Proteome Chips
3. Protein-protein Interactions and Protein Complexes
3. Yeast Metabolome
4. Genetic Interaction Networks: Regulatory Networks and Oscillations
13. Disease Genes in Yeast
1. General Aspects
2. Trinucleotide Repeats and Neurodegenerative Diseases
3. Ageing and Age-related Diseases
4. Mitochondrial Diseases
14. Yeast Biotechnology
1. Fermentation and Metabolic Engineering
1. Typical Fermentation Procedures
2. Food and Chemical Industries ? Metabolic Engineering
2. Biopharmaceuticals from Health-Care Industries
3. Biomedical Research
4. Environmental Technologies - Cell-surface Display
15. Hemiascomycetous Yeasts (suggested)
1. Selected Model Genomes
2. Genolevures Projects: Sequenced Genomes
3. Ecology, Adaptation of Metabolic Behavior
4. Differences in Architectual Features and Genetic Outfit (Genes/Introns/snRNAs/Codon usage/Modes of Propagation)
5. Differences in Molecular Mechanisms (Replication, Transcription, DNA-repair, Specific Regulatory Pathways)
6. Application in Biotechnology
16. Yeast Evolutionary Genomics (suggested)
1. Yeast Populations and Species
2. Gene Duplication Mechanisms
1. Expansion of Tandem Gene Arrays
2. Segmental Duplications
3. Whole-Genome Duplications
4. Single Gene Duplications
3. Other Mechanisms of Genome Evolution
17. Epilogue: The Future of Yeast Research

Author Information

Horst Feldmann studied Organic Chemistry in Cologne and did his PhD in this discipline. From 1962 to 1967 he worked at the Institute of Genetics in Cologne. In 1974 he became Professor of Physiological Chemistry at the Medical Faculty in Munich. His pioneering research included sequencing yeast tRNA. He extensively studied tRNA and protein biogenesis, yeast retrotransposons and mitochondrial genome and was a co-ordinator in the EU project "Sequencing and Analysis of the Yeast Genome". From 1971 until 2007 he was one of the organizers of the International "Spetses Summer Schools on Molecular and Cell Biology". Horst Feldmann was a member of the Board of FEBS and served as chairman of the Advanced Courses Committee, Secretary of the Prize "Biochemical Analysis" and the Head of SFB "Mechanisms and Factors in Gene Regulation". He has also served as member of a number of different committees, namely the DFG, IUBMB, DISNAT (German-Israeli cooperation). He is also an Honorary Member of Hellenic Society for Biochemistry and Biophysics. In 1996 he received the FEBS Diplome d'Honneur.