Fungi : experimental models in biology

PART I The Unique Features of Fungi Chapter 1 The Hyphal Mode of Life.............................................................3 1.1 Features of Hyphae...................................................................................3 1.1.1 Spread and Longevity .................................................................3 1.1.2 Indeterminate Growth ................................................................4 1.1.3 Apical Extension and Synchronized Growth.............................6 1.1.4 Spitzenkörper...............................................................................6 1.1.5 Tip-High Calcium ........................................................................8 1.1.6 Large Surface Area......................................................................9 1.1.7 Cytoskeleton...............................................................................10 1.1.8 Protein Secretion .......................................................................10 1.1.9 Nutrient Uptake ........................................................................12 1.2 Cell Wall...................................................................................................13 1.2.1 Composition and Structure.......................................................13 1.2.2 Hydrophobins.............................................................................14 1.3 Mycelium Formation ...............................................................................14 1.3.1 Septation ....................................................................................14 1.3.2 Branching ...................................................................................15 1.3.3 Hyphal Fusion ...........................................................................16 1.3.4 Multihyphal Structures.............................................................16 1.4 Concluding Remarks...............................................................................17 References...........................................................................................................17 Chapter 2 The Multinuclear Condition......................................................19 2.1 Nuclear Number and Hyphal Growth...................................................19 2.2 Chromosome Numbers............................................................................20 2.3 Nuclear Division Cycle ...........................................................................21 xii Contents 2.3.1 Temperature-Sensitive Mutants...............................................22 2.3.2 Kinetics of Nuclear Division Cycle...........................................23 2.4 Asynchronous Nuclear Divisions ...........................................................23 2.5 Nuclear Migration...................................................................................24 2.6 Positioning of Nuclei and Gene Regulation ..........................................25 2.7 Heterokaryosis.........................................................................................26 2.7.1 Sheltering of Lethal Mutation..................................................27 2.7.2 Nuclear Selection.......................................................................28 2.7.3 Nuclear Competence..................................................................29 2.8 Parasexual Recombination .....................................................................30 2.9 Concluding Remarks...............................................................................31 References...........................................................................................................31 PART II Interactions of Fungi with Other Organisms Chapter 3 Fungi as Symbiotic Partners.....................................................35 3.1 Mycorrhiza ...............................................................................................35 3.1.1 Types of Mycorrhiza ..................................................................36 3.1.2 Techniques of Studying Mycorrhizal Symbiosis......................36 3.1.3 Diffusible Host and Fungal Factors .........................................39 3.1.4 Differentially Expressed Plant Genes......................................40 3.1.5 Multiple Genomes......................................................................41 3.2 Lichen.......................................................................................................42 3.2.1 Mycobiont and Photobiont ........................................................44 3.2.2 Lichen Synthesis........................................................................44 3.2.3 Transfer of Carbohydrate in Lichen Symbiosis ......................45 3.3 Some Unanswered Questions.................................................................45 References...........................................................................................................45 Chapter 4 Fungi as Plant Pathogens .........................................................47 4.1 Early Ideas on Plant Diseases ...............................................................47 4.2 Some Striking Fungal Diseases .............................................................49 4.2.1 Diseases of Crop Plants ............................................................49 4.2.2 Fungal Diseases of Trees ..........................................................50 4.3 Classes of Plant Pathogenic Fungi ........................................................51 4.3.1 Necrotrophic and Biotrophic Fungi..........................................51 4.4 General Features of Pathogenesis .........................................................51 4.4.1 Adhesion of Spores ....................................................................53 4.4.2 Directional Growth ....................................................................53 4.4.3 Infection Structures...................................................................54 4.4.4 Production of Cutinase..............................................................57 4.4.5 Production of Toxins..................................................................57 4.4.6 Detoxification of Saponins ........................................................58 4.5 Concluding Remarks...............................................................................60 References...........................................................................................................60 Contents xiii PART III Model Fungi in Research Chapter 5 Neurospora : A Gateway to Biology ...........................................65 5.1 Habitat, Life Style and Life Cycle .........................................................65 5.2 Meiotic Events.........................................................................................70 5.3 Gene Maps...............................................................................................73 5.4 One Gene-One Enzyme Hypothesis.......................................................76 5.5 Molecular Revolution ..............................................................................78 5.6 Revelations from Genome Sequence......................................................78 5.7 Concluding Remarks...............................................................................79 References...........................................................................................................80 Chapter 6 Yeast: A Unicellular Paradigm for Complex Biological Processes ...................................................................81 6.1 Introduction .............................................................................................81 6.2 Molecular Mechanisms of DNA Replication and Cell Division.....................................................................................82 6.2.1 cdc Genes ...................................................................................85 6.3 Bud Growth and Polarity .......................................................................85 6.4 Mating and Signal Transduction Cascade ............................................89 6.5 Protein Targeting ....................................................................................91 6.6 Mitochondrial Biogenesis........................................................................92 6.7 Functional Genomics ..............................................................................94 6.7.1 Number of Yeast Genes.............................................................96 6.7.2 Expression Pattern of Genes Using DNA Microarrays ..........98 6.7.3 Mapping Transcription Network..............................................98 6.8 Proteomics and System Biology Modeling ..........................................100 6.9 Concluding Remarks.............................................................................103 References.........................................................................................................103 Chapter 7 Aspergillus nidulans : A Model for Study of Form and Asexual Reproduction.......................................................107 7.1 Conidiophore Morphogenesis ...............................................................108 7.1.1 Developmental Competence....................................................109 7.2 Microcycle Conidiation..........................................................................109 7.3 Conidiation Genes .................................................................................109 7.4 Conidiation Trigger ...............................................................................111 7.5 Regulatory Pathway..............................................................................112 7.6 Summary................................................................................................114 References.........................................................................................................114 Chapter 8 Ustilago maydis : Mechanisms in Sexual Reproduction.............................................................................117 8.1 Heterothallism vs. Homothallism ........................................................117 8.2 Cell-Cell Recognition.............................................................................118 8.2.1 Mating Types ...........................................................................118 xiv Contents 8.3 Extracellular Recognition .....................................................................121 8.3.1 The a Locus..............................................................................121 8.3.2 Pheromone and Receptor ........................................................122 8.4 Intracellular Recognition......................................................................124 8.4.1 The b Locus..............................................................................124 8.5 Overview ................................................................................................126 References.........................................................................................................126 PART IV Gene Manipulation in Fungi Chapter 9 Transformation of Fungi and Discovery of Gene-Silencing Phenomena.................................................129 9.1 Transformation Procedure....................................................................129 9.2 Homologous vs. Ectopic Integration of Transgene .............................131 9.3 Purification of Transformant................................................................132 9.4 Gene-Silencing Phenomena..................................................................132 9.4.1 Silencing by Mutation (RIP)...................................................132 9.4.2 Meiotic Silencing by Unpaired DNA (MSUD).......................134 9.4.3 Silencing by DNA Methylation (MIP)....................................135 9.4.4 Quelling ....................................................................................136 9.4.5 Internuclear Gene Silencing ...................................................140 9.5 Concluding Remarks.............................................................................141 References.........................................................................................................141 PART V Adaptations Chapter 10 Thermophilic Fungi: Eukaryotic Life at High Temperature ...............................................................145 10.1 Discovery................................................................................................146 10.1.1 Self-Heating of Stored Agricultural Products .......................146 10.1.2 Guayule Rets............................................................................148 10.1.3 Composts ..................................................................................148 10.2 Distribution in Soil ...............................................................................148 10.3 Physiology ..............................................................................................151 10.3.1 Cultivation ...............................................................................151 10.3.2 Metabolic Rate .........................................................................152 10.3.3 Efficiency of Growth ................................................................153 10.3.4 Carbon Sources in Environment ............................................153 10.3.5 Transport of Nutrients............................................................153 10.3.6 Protein Turnover .....................................................................154 10.4 Secretory Enzymes................................................................................154 10.4.1 Proteases ..................................................................................155 10.4.2 Lipases......................................................................................155 10.4.3 Amylases ..................................................................................155 Contents xv 10.4.4 Cellulases .................................................................................156 10.4.5 Xylanases .................................................................................156 10.4.6 Cell-Associated Enzymes ........................................................156 10.5 Concluding Remarks.............................................................................159 References.........................................................................................................160 Chapter 11 Photoresponses and Circadian Rhythm .................................163 11.1 Types of Photoresponses in Fungi .......................................................163 11.1.1 Pigmentation............................................................................163 11.1.2 Growth Rhythms .....................................................................163 11.1.3 Reproduction ............................................................................164 11.1.4 Spore Liberation ......................................................................165 11.1.5 Phototropism............................................................................166 11.1.6 Morphogenesis .........................................................................169 11.2 Circadian Rhythm in Neurospora ........................................................170 11.2.1 A Clock Gene ...........................................................................171 11.2.2 Regulatory Genes ....................................................................171 11.2.3 Clock-Controlled Genes...........................................................173 11.3 Entrainment ..........................................................................................173 11.4 Summary................................................................................................174 References.........................................................................................................175 Chapter 12 Decomposition of Biomass.......................................................177 12.1 Decay of Wood and Litter .....................................................................177 12.1.1 White-Rot and Brown-Rot Fungi ...........................................179 12.1.2 Litter Decomposers..................................................................179 12.2 Biochemistry of Degradation of Cell Wall Polymers ..........................180 12.2.1 Lignin Degradation .................................................................180 12.2.2 Cellulose Degradation .............................................................182 12.2.3 Hemicellulose Degradation .....................................................187 12.3 Concluding Remarks.............................................................................187 References.........................................................................................................188 PART VI Populations Chapter 13 Species, Their Diversity and Populations ..............................191 13.1 Value of Diversity..................................................................................191 13.1.1 Applied Research .....................................................................191 13.1.2 Basic Research.........................................................................193 13.2 Number of Fungal Species ...................................................................194 13.3 Species Recognition...............................................................................195 13.3.1 MSR, BSR and PSR.................................................................195 13.4 Discovery of Intraspecies Variability ...................................................196 13.4.1 Physiological Races..................................................................196 13.4.2 Vegetative Compatibility.........................................................197 xvi Contents 13.5 Generation of Variation ........................................................................197 13.5.1 Mutation and Heterokaryosis.................................................197 13.5.2 Transposable Elements ...........................................................198 13.6 Detection of Genetic Variation in Populations ...................................198 13.6.1 Isozymes ...................................................................................198 13.6.2 RFLP.........................................................................................199 13.6.3 RAPD........................................................................................199 13.6.4 Ribosomal DNA .......................................................................201 13.6.5 Mitochondrial DNA and Mitochondrial Plasmids.................202 13.6.6 DNA Sequence .........................................................................202 13.6.7 Karyotype Polymorphism........................................................203 13.6.8 Spore Killer Elements .............................................................203 13.7 Speciation...............................................................................................203 13.8 Concluding Remarks.............................................................................204 References.........................................................................................................205 Chapter 14 Senescence ................................................................................207 14.1 Discovery of Senescing Strains ............................................................207 14.2 Distinguishing Nucleus and Mitochondria Based Senescence..................................................................................208 14.2.1 Genetic Cross ...........................................................................208 14.2.2 Heterokaryon Test ...................................................................208 14.3 Senescence in Podospora anserina .......................................................209 14.3.1 Deletion and Rearrangements in Mitochondrial DNA.............................................................209 14.3.2 Nuclear Gene Control of Mitochondrial DNA Deletions .........................................................................212 14.4 Plasmid-Based Senescence in Neurospora ..........................................212 14.4.1 Mitochondrial Plasmids ..........................................................212 14.5 Nuclear Gene Mutants .........................................................................215 14.5.1 natural death ...........................................................................215 14.5.2 senescent ...................................................................................215 14.6 Aerobic Respiration, Aging and Senescence........................................218 14.7 Concluding Remarks.............................................................................220 References.........................................................................................................221 Appendix Naming, Defining, and Broadly Classifying Fungi................223 Naming of Fungi..............................................................................................223 Definition of a Fungus.....................................................................................223 Classification ....................................................................................................224 A Broad Classification of Fungi......................................................................224 Kingdom Eumyccta ...............................................................................224 Phylum Chytridiomycotina...................................................................225 Phylum Zygomycotina...........................................................................225 Phylum Glomeromycotina ....................................................................225 Phylum Ascomycotina...........................................................................228 Phylum Basidiomycotina ......................................................................229 Phylum Deuteromycotina (Fungi Anamorphici).................................229 Kingdom Straminipila (Stramenopila)...........................................................233 General References..........................................................................................233 Index ................................................................................................................235